Informatics Infrastructure for the Materials Genome Initiative

NASA Astrophysics Data System (ADS)

Dima, Alden; Bhaskarla, Sunil; Becker, Chandler; Brady, Mary; Campbell, Carelyn; Dessauw, Philippe; Hanisch, Robert; Kattner, Ursula; Kroenlein, Kenneth; Newrock, Marcus; Peskin, Adele; Plante, Raymond; Li, Sheng-Yen; Rigodiat, Pierre-François; Amaral, Guillaume Sousa; Trautt, Zachary; Schmitt, Xavier; Warren, James; Youssef, Sharief

2016-08-01

A materials data infrastructure that enables the sharing and transformation of a wide range of materials data is an essential part of achieving the goals of the Materials Genome Initiative. We describe two high-level requirements of such an infrastructure as well as an emerging open-source implementation consisting of the Materials Data Curation System and the National Institute of Standards and Technology Materials Resource Registry.

Overcoming Intermediary Bias Through the Use of Social Media Intelligence

DTIC Science & Technology

2015-05-23

PMESII-PT Politics, Military, Economy, Social, Information, Infrastructure, Physical Environment and Time. OSINT Open Source Intelligence...Intelligence (SOCMINT) is a sub-set of open source intelligence ( OSINT ). OSINT has existed for an extended period of time, but it is a relatively new...author determined that there are two 1 Walter R, Draeger, "Take Advantage of OSINT ," Military

The EDRN knowledge environment: an open source, scalable informatics platform for biological sciences research

NASA Astrophysics Data System (ADS)

Crichton, Daniel; Mahabal, Ashish; Anton, Kristen; Cinquini, Luca; Colbert, Maureen; Djorgovski, S. George; Kincaid, Heather; Kelly, Sean; Liu, David

2017-05-01

We describe here the Early Detection Research Network (EDRN) for Cancer's knowledge environment. It is an open source platform built by NASA's Jet Propulsion Laboratory with contributions from the California Institute of Technology, and Giesel School of Medicine at Dartmouth. It uses tools like Apache OODT, Plone, and Solr, and borrows heavily from JPL's Planetary Data System's ontological infrastructure. It has accumulated data on hundreds of thousands of biospecemens and serves over 1300 registered users across the National Cancer Institute (NCI). The scalable computing infrastructure is built such that we are being able to reach out to other agencies, provide homogeneous access, and provide seamless analytics support and bioinformatics tools through community engagement.

Web accessibility and open source software.

PubMed

Obrenović, Zeljko

2009-07-01

A Web browser provides a uniform user interface to different types of information. Making this interface universally accessible and more interactive is a long-term goal still far from being achieved. Universally accessible browsers require novel interaction modalities and additional functionalities, for which existing browsers tend to provide only partial solutions. Although functionality for Web accessibility can be found as open source and free software components, their reuse and integration is complex because they were developed in diverse implementation environments, following standards and conventions incompatible with the Web. To address these problems, we have started several activities that aim at exploiting the potential of open-source software for Web accessibility. The first of these activities is the development of Adaptable Multi-Interface COmmunicator (AMICO):WEB, an infrastructure that facilitates efficient reuse and integration of open source software components into the Web environment. The main contribution of AMICO:WEB is in enabling the syntactic and semantic interoperability between Web extension mechanisms and a variety of integration mechanisms used by open source and free software components. Its design is based on our experiences in solving practical problems where we have used open source components to improve accessibility of rich media Web applications. The second of our activities involves improving education, where we have used our platform to teach students how to build advanced accessibility solutions from diverse open-source software. We are also partially involved in the recently started Eclipse projects called Accessibility Tools Framework (ACTF), the aim of which is development of extensible infrastructure, upon which developers can build a variety of utilities that help to evaluate and enhance the accessibility of applications and content for people with disabilities. In this article we briefly report on these activities.

Scaling Agile Infrastructure to People

NASA Astrophysics Data System (ADS)

Jones, B.; McCance, G.; Traylen, S.; Barrientos Arias, N.

2015-12-01

When CERN migrated its infrastructure away from homegrown fabric management tools to emerging industry-standard open-source solutions, the immediate technical challenges and motivation were clear. The move to a multi-site Cloud Computing model meant that the tool chains that were growing around this ecosystem would be a good choice, the challenge was to leverage them. The use of open-source tools brings challenges other than merely how to deploy them. Homegrown software, for all the deficiencies identified at the outset of the project, has the benefit of growing with the organization. This paper will examine what challenges there were in adapting open-source tools to the needs of the organization, particularly in the areas of multi-group development and security. Additionally, the increase in scale of the plant required changes to how Change Management was organized and managed. Continuous Integration techniques are used in order to manage the rate of change across multiple groups, and the tools and workflow for this will be examined.

Developing an Open Source, Reusable Platform for Distributed Collaborative Information Management in the Early Detection Research Network

NASA Technical Reports Server (NTRS)

Hart, Andrew F.; Verma, Rishi; Mattmann, Chris A.; Crichton, Daniel J.; Kelly, Sean; Kincaid, Heather; Hughes, Steven; Ramirez, Paul; Goodale, Cameron; Anton, Kristen;

Application of Open Source Software by the Lunar Mapping and Modeling Project

NASA Astrophysics Data System (ADS)

Ramirez, P.; Goodale, C. E.; Bui, B.; Chang, G.; Kim, R. M.; Law, E.; Malhotra, S.; Rodriguez, L.; Sadaqathullah, S.; Mattmann, C. A.; Crichton, D. J.

2011-12-01

The Lunar Mapping and Modeling Project (LMMP), led by the Marshall Space Flight center (MSFC), is responsible for the development of an information system to support lunar exploration, decision analysis, and release of lunar data to the public. The data available through the lunar portal is predominantly derived from present lunar missions (e.g., the Lunar Reconnaissance Orbiter (LRO)) and from historical missions (e.g., Apollo). This project has created a gold source of data, models, and tools for lunar explorers to exercise and incorporate into their activities. At Jet Propulsion Laboratory (JPL), we focused on engineering and building the infrastructure to support cataloging, archiving, accessing, and delivery of lunar data. We decided to use a RESTful service-oriented architecture to enable us to abstract from the underlying technology choices and focus on interfaces to be used internally and externally. This decision allowed us to leverage several open source software components and integrate them by either writing a thin REST service layer or relying on the API they provided; the approach chosen was dependent on the targeted consumer of a given interface. We will discuss our varying experience using open source products; namely Apache OODT, Oracle Berkley DB XML, Apache Solr, and Oracle OpenSSO (now named OpenAM). Apache OODT, developed at NASA's Jet Propulsion Laboratory and recently migrated over to Apache, provided the means for ingestion and cataloguing of products within the infrastructure. Its usage was based upon team experience with the project and past benefit received on other projects internal and external to JPL. Berkeley DB XML, distributed by Oracle for both commercial and open source use, was the storage technology chosen for our metadata. This decision was in part based on our use Federal Geographic Data Committee (FGDC) Metadata, which is expressed in XML, and the desire to keep it in its native form and exploit other technologies built on top of XML. Apache Solr, an open source search engine, was used to drive our search interface and as way to store references to metadata and data exposed via REST endpoints. As was the case with Apache OODT there was team experience with this component that helped drive this choice. Lastly, OpenSSO, an open source single sign on service, was used to secure and provide access constraints to our REST based services. For this product there was little past experience but given our service based approach seemed to be a natural fit. Given our exposure to open source we will discuss the tradeoffs and benefits received by the choices made. Moreover, we will dive into the context of how the software packages were used and the impact of their design and extensibility had on the construction of the infrastructure. Finally, we will compare our encounter across open source solutions and attributes that can vary the impression one will get. This comprehensive account of our endeavor should aid others in their assessment and use of open source.

The TENCompetence Infrastructure: A Learning Network Implementation

NASA Astrophysics Data System (ADS)

Vogten, Hubert; Martens, Harrie; Lemmers, Ruud

The TENCompetence project developed a first release of a Learning Network infrastructure to support individuals, groups and organisations in professional competence development. This infrastructure Learning Network infrastructure was released as open source to the community thereby allowing users and organisations to use and contribute to this development as they see fit. The infrastructure consists of client applications providing the user experience and server components that provide the services to these clients. These services implement the domain model (Koper 2006) by provisioning the entities of the domain model (see also Sect. 18.4) and henceforth will be referenced as domain entity services.

Open Source Software Projects Needing Security Investments

DTIC Science & Technology

2015-06-19

modtls, BouncyCastle, gpg, otr, axolotl. 7. Static analyzers: Clang, Frama-C. 8. Nginx. 9. OpenVPN . It was noted that the funding model may be similar...to OpenSSL, where consulting funds the company. It was also noted that OpenVPN needs to correctly use OpenSSL in order to be secure, so focusing on...Dovecot 4. Other high-impact network services: OpenSSH, OpenVPN , BIND, ISC DHCP, University of Delaware NTPD 5. Core infrastructure data parsers

Dynamic VM Provisioning for TORQUE in a Cloud Environment

NASA Astrophysics Data System (ADS)

Zhang, S.; Boland, L.; Coddington, P.; Sevior, M.

2014-06-01

Cloud computing, also known as an Infrastructure-as-a-Service (IaaS), is attracting more interest from the commercial and educational sectors as a way to provide cost-effective computational infrastructure. It is an ideal platform for researchers who must share common resources but need to be able to scale up to massive computational requirements for specific periods of time. This paper presents the tools and techniques developed to allow the open source TORQUE distributed resource manager and Maui cluster scheduler to dynamically integrate OpenStack cloud resources into existing high throughput computing clusters.

Open source information on the U.S. infrastructure

NASA Astrophysics Data System (ADS)

Freiwald, David A.

1995-05-01

Terrorism is expected to increase on a global scale, with the US also becoming more of a target. Since there has not been a war in the lower 48 states of the continental US since about the turn of the century, the US has been quite open and lax about publishing information on our infrastructure, namely details on locations of power lines, gas and oil pipelines, etc.-- information not publically available in Europe. Examples are given, along with comments on the potential implications. Finally, brief remarks are given on some ways to address the situation.

ggCyto: Next Generation Open-Source Visualization Software for Cytometry.

PubMed

Van, Phu; Jiang, Wenxin; Gottardo, Raphael; Finak, Greg

2018-06-01

Open source software for computational cytometry has gained in popularity over the past few years. Efforts such as FlowCAP, the Lyoplate and Euroflow projects have highlighted the importance of efforts to standardize both experimental and computational aspects of cytometry data analysis. The R/BioConductor platform hosts the largest collection of open source cytometry software covering all aspects of data analysis and providing infrastructure to represent and analyze cytometry data with all relevant experimental, gating, and cell population annotations enabling fully reproducible data analysis. Data visualization frameworks to support this infrastructure have lagged behind. ggCyto is a new open-source BioConductor software package for cytometry data visualization built on ggplot2 that enables ggplot-like functionality with the core BioConductor flow cytometry data structures. Amongst its features are the ability to transform data and axes on-the-fly using cytometry-specific transformations, plot faceting by experimental meta-data variables, and partial matching of channel, marker and cell populations names to the contents of the BioConductor cytometry data structures. We demonstrate the salient features of the package using publicly available cytometry data with complete reproducible examples in a supplementary material vignette. https://bioconductor.org/packages/devel/bioc/html/ggcyto.html. gfinak@fredhutch.org. Supplementary data are available at Bioinformatics online and at http://rglab.org/ggcyto/.

Curriculum-Guided Crowd Sourcing of Assessments in a Developing Country

ERIC Educational Resources Information Center

Zualkernan, Imran A.; Raza, Anjana; Karim, Asad

2012-01-01

Success of Wikipedia has opened a number of possibilities for crowd sourcing learning resources. However, not all crowd sourcing initiatives are successful. For developing countries, adoption factors like lack of infrastructure and poor teacher training can have an impact on success of such systems. This paper presents an exploratory study to…

Building integrated business environments: analysing open-source ESB

NASA Astrophysics Data System (ADS)

Martínez-Carreras, M. A.; García Jimenez, F. J.; Gómez Skarmeta, A. F.

2015-05-01

Integration and interoperability are two concepts that have gained significant prominence in the business field, providing tools which enable enterprise application integration (EAI). In this sense, enterprise service bus (ESB) has played a crucial role as the underpinning technology for creating integrated environments in which companies may connect all their legacy-applications. However, the potential of these technologies remains unknown and some important features are not used to develop suitable business environments. The aim of this paper is to describe and detail the elements for building the next generation of integrated business environments (IBE) and to analyse the features of ESBs as the core of this infrastructure. For this purpose, we evaluate how well-known open-source ESB products fulfil these needs. Moreover, we introduce a scenario in which the collaborative system 'Alfresco' is integrated in the business infrastructure. Finally, we provide a comparison of the different open-source ESBs available for IBE requirements. According to this study, Fuse ESB provides the best results, considering features such as support for a wide variety of standards and specifications, documentation and implementation, security, advanced business trends, ease of integration and performance.

Reflections on the role of open source in health information system interoperability.

PubMed

Sfakianakis, S; Chronaki, C E; Chiarugi, F; Conforti, F; Katehakis, D G

2007-01-01

This paper reflects on the role of open source in health information system interoperability. Open source is a driving force in computer science research and the development of information systems. It facilitates the sharing of information and ideas, enables evolutionary development and open collaborative testing of code, and broadens the adoption of interoperability standards. In health care, information systems have been developed largely ad hoc following proprietary specifications and customized design. However, the wide deployment of integrated services such as Electronic Health Records (EHRs) over regional health information networks (RHINs) relies on interoperability of the underlying information systems and medical devices. This reflection is built on the experiences of the PICNIC project that developed shared software infrastructure components in open source for RHINs and the OpenECG network that offers open source components to lower the implementation cost of interoperability standards such as SCP-ECG, in electrocardiography. Open source components implementing standards and a community providing feedback from real-world use are key enablers of health care information system interoperability. Investing in open source is investing in interoperability and a vital aspect of a long term strategy towards comprehensive health services and clinical research.

Online molecular image repository and analysis system: A multicenter collaborative open-source infrastructure for molecular imaging research and application.

PubMed

Rahman, Mahabubur; Watabe, Hiroshi

2018-05-01

Molecular imaging serves as an important tool for researchers and clinicians to visualize and investigate complex biochemical phenomena using specialized instruments; these instruments are either used individually or in combination with targeted imaging agents to obtain images related to specific diseases with high sensitivity, specificity, and signal-to-noise ratios. However, molecular imaging, which is a multidisciplinary research field, faces several challenges, including the integration of imaging informatics with bioinformatics and medical informatics, requirement of reliable and robust image analysis algorithms, effective quality control of imaging facilities, and those related to individualized disease mapping, data sharing, software architecture, and knowledge management. As a cost-effective and open-source approach to address these challenges related to molecular imaging, we develop a flexible, transparent, and secure infrastructure, named MIRA, which stands for Molecular Imaging Repository and Analysis, primarily using the Python programming language, and a MySQL relational database system deployed on a Linux server. MIRA is designed with a centralized image archiving infrastructure and information database so that a multicenter collaborative informatics platform can be built. The capability of dealing with metadata, image file format normalization, and storing and viewing different types of documents and multimedia files make MIRA considerably flexible. With features like logging, auditing, commenting, sharing, and searching, MIRA is useful as an Electronic Laboratory Notebook for effective knowledge management. In addition, the centralized approach for MIRA facilitates on-the-fly access to all its features remotely through any web browser. Furthermore, the open-source approach provides the opportunity for sustainable continued development. MIRA offers an infrastructure that can be used as cross-boundary collaborative MI research platform for the rapid achievement in cancer diagnosis and therapeutics. Copyright © 2018 Elsevier Ltd. All rights reserved.

PACS for Bhutan: a cost effective open source architecture for emerging countries.

PubMed

Ratib, Osman; Roduit, Nicolas; Nidup, Dechen; De Geer, Gerard; Rosset, Antoine; Geissbuhler, Antoine

2016-10-01

This paper reports the design and implementation of an innovative and cost-effective imaging management infrastructure suitable for radiology centres in emerging countries. It was implemented in the main referring hospital of Bhutan equipped with a CT, an MRI, digital radiology, and a suite of several ultrasound units. They lacked the necessary informatics infrastructure for image archiving and interpretation and needed a system for distribution of images to clinical wards. The solution developed for this project combines several open source software platforms in a robust and versatile archiving and communication system connected to analysis workstations equipped with a FDA-certified version of the highly popular Open-Source software. The whole system was implemented on standard off-the-shelf hardware. The system was installed in three days, and training of the radiologists as well as the technical and IT staff was provided onsite to ensure full ownership of the system by the local team. Radiologists were rapidly capable of reading and interpreting studies on the diagnostic workstations, which had a significant benefit on their workflow and ability to perform diagnostic tasks more efficiently. Furthermore, images were also made available to several clinical units on standard desktop computers through a web-based viewer. • Open source imaging informatics platforms can provide cost-effective alternatives for PACS • Robust and cost-effective open architecture can provide adequate solutions for emerging countries • Imaging informatics is often lacking in hospitals equipped with digital modalities.

A GeoNode-Based Multiscale Platform For Management, Visualization And Integration Of DInSAR Data With Different Geospatial Information Sources

NASA Astrophysics Data System (ADS)

Buonanno, Sabatino; Fusco, Adele; Zeni, Giovanni; Manunta, Michele; Lanari, Riccardo

2017-04-01

This work describes the implementation of an efficient system for managing, viewing, analyzing and updating remotely sensed data, with special reference to Differential Interferometric Synthetic Aperture Radar (DInSAR) data. The DInSAR products measure Earth surface deformation both in space and time, producing deformation maps and time series[1,2]. The use of these data in research or operational contexts requires tools that have to handle temporal and spatial variability with high efficiency. For this aim we present an implementation based on Spatial Data Infrastructure (SDI) for data integration, management and interchange, by using standard protocols[3]. SDI tools provide access to static datasets that operate only with spatial variability . In this paper we use the open source project GeoNode as framework to extend SDI infrastructure functionalities to ingest very efficiently DInSAR deformation maps and deformation time series. GeoNode allows to realize comprehensive and distributed infrastructure, following the standards of the Open Geospatial Consortium, Inc. - OGC, for remote sensing data management, analysis and integration [4,5]. In the current paper we explain the methodology used for manage the data complexity and data integration using the opens source project GeoNode. The solution presented in this work for the ingestion of DinSAR products is a very promising starting point for future developments of the OGC compliant implementation of a semi-automatic remote sensing data processing chain . [1] Berardino, P., Fornaro, G., Lanari, R., & Sansosti, E. (2002). A new Algorithm for Surface Deformation Monitoring based on Small Baseline Differential SAR Interferograms. IEEE Transactions on Geoscience and Remote Sensing, 40, 11, pp. 2375-2383. [2] Lanari R., F. Casu, M. Manzo, G. Zeni,, P. Berardino, M. Manunta and A. Pepe (2007), An overview of the Small Baseline Subset Algorithm: a DInSAR Technique for Surface Deformation Analysis, P. Appl. Geophys., 164, doi: 10.1007/s00024-007-0192-9. [3] Nebert, D.D. (ed). 2000. Developing Spatial data Infrastructures: The SDI Cookbook. [4] Geonode (www.geonode.org) [5] Kolodziej, k. (ed). 2004. OGC OpenGIS Web Map Server Cookbook. Open Geospatial Consortium, 1.0.2 edition.

caGrid 1.0: An Enterprise Grid Infrastructure for Biomedical Research

PubMed Central

Oster, Scott; Langella, Stephen; Hastings, Shannon; Ervin, David; Madduri, Ravi; Phillips, Joshua; Kurc, Tahsin; Siebenlist, Frank; Covitz, Peter; Shanbhag, Krishnakant; Foster, Ian; Saltz, Joel

2008-01-01

Objective To develop software infrastructure that will provide support for discovery, characterization, integrated access, and management of diverse and disparate collections of information sources, analysis methods, and applications in biomedical research. Design An enterprise Grid software infrastructure, called caGrid version 1.0 (caGrid 1.0), has been developed as the core Grid architecture of the NCI-sponsored cancer Biomedical Informatics Grid (caBIG™) program. It is designed to support a wide range of use cases in basic, translational, and clinical research, including 1) discovery, 2) integrated and large-scale data analysis, and 3) coordinated study. Measurements The caGrid is built as a Grid software infrastructure and leverages Grid computing technologies and the Web Services Resource Framework standards. It provides a set of core services, toolkits for the development and deployment of new community provided services, and application programming interfaces for building client applications. Results The caGrid 1.0 was released to the caBIG community in December 2006. It is built on open source components and caGrid source code is publicly and freely available under a liberal open source license. The core software, associated tools, and documentation can be downloaded from the following URL: https://cabig.nci.nih.gov/workspaces/Architecture/caGrid. Conclusions While caGrid 1.0 is designed to address use cases in cancer research, the requirements associated with discovery, analysis and integration of large scale data, and coordinated studies are common in other biomedical fields. In this respect, caGrid 1.0 is the realization of a framework that can benefit the entire biomedical community. PMID:18096909

caGrid 1.0: an enterprise Grid infrastructure for biomedical research.

PubMed

Oster, Scott; Langella, Stephen; Hastings, Shannon; Ervin, David; Madduri, Ravi; Phillips, Joshua; Kurc, Tahsin; Siebenlist, Frank; Covitz, Peter; Shanbhag, Krishnakant; Foster, Ian; Saltz, Joel

2008-01-01

To develop software infrastructure that will provide support for discovery, characterization, integrated access, and management of diverse and disparate collections of information sources, analysis methods, and applications in biomedical research. An enterprise Grid software infrastructure, called caGrid version 1.0 (caGrid 1.0), has been developed as the core Grid architecture of the NCI-sponsored cancer Biomedical Informatics Grid (caBIG) program. It is designed to support a wide range of use cases in basic, translational, and clinical research, including 1) discovery, 2) integrated and large-scale data analysis, and 3) coordinated study. The caGrid is built as a Grid software infrastructure and leverages Grid computing technologies and the Web Services Resource Framework standards. It provides a set of core services, toolkits for the development and deployment of new community provided services, and application programming interfaces for building client applications. The caGrid 1.0 was released to the caBIG community in December 2006. It is built on open source components and caGrid source code is publicly and freely available under a liberal open source license. The core software, associated tools, and documentation can be downloaded from the following URL: https://cabig.nci.nih.gov/workspaces/Architecture/caGrid. While caGrid 1.0 is designed to address use cases in cancer research, the requirements associated with discovery, analysis and integration of large scale data, and coordinated studies are common in other biomedical fields. In this respect, caGrid 1.0 is the realization of a framework that can benefit the entire biomedical community.

Increasing the impact of medical image computing using community-based open-access hackathons: The NA-MIC and 3D Slicer experience.

PubMed

Kapur, Tina; Pieper, Steve; Fedorov, Andriy; Fillion-Robin, J-C; Halle, Michael; O'Donnell, Lauren; Lasso, Andras; Ungi, Tamas; Pinter, Csaba; Finet, Julien; Pujol, Sonia; Jagadeesan, Jayender; Tokuda, Junichi; Norton, Isaiah; Estepar, Raul San Jose; Gering, David; Aerts, Hugo J W L; Jakab, Marianna; Hata, Nobuhiko; Ibanez, Luiz; Blezek, Daniel; Miller, Jim; Aylward, Stephen; Grimson, W Eric L; Fichtinger, Gabor; Wells, William M; Lorensen, William E; Schroeder, Will; Kikinis, Ron

2016-10-01

The National Alliance for Medical Image Computing (NA-MIC) was launched in 2004 with the goal of investigating and developing an open source software infrastructure for the extraction of information and knowledge from medical images using computational methods. Several leading research and engineering groups participated in this effort that was funded by the US National Institutes of Health through a variety of infrastructure grants. This effort transformed 3D Slicer from an internal, Boston-based, academic research software application into a professionally maintained, robust, open source platform with an international leadership and developer and user communities. Critical improvements to the widely used underlying open source libraries and tools-VTK, ITK, CMake, CDash, DCMTK-were an additional consequence of this effort. This project has contributed to close to a thousand peer-reviewed publications and a growing portfolio of US and international funded efforts expanding the use of these tools in new medical computing applications every year. In this editorial, we discuss what we believe are gaps in the way medical image computing is pursued today; how a well-executed research platform can enable discovery, innovation and reproducible science ("Open Science"); and how our quest to build such a software platform has evolved into a productive and rewarding social engineering exercise in building an open-access community with a shared vision. Copyright © 2016 Elsevier B.V. All rights reserved.

An IoT-Based Solution for Monitoring a Fleet of Educational Buildings Focusing on Energy Efficiency.

PubMed

Amaxilatis, Dimitrios; Akrivopoulos, Orestis; Mylonas, Georgios; Chatzigiannakis, Ioannis

2017-10-10

Raising awareness among young people and changing their behaviour and habits concerning energy usage is key to achieving sustained energy saving. Additionally, young people are very sensitive to environmental protection so raising awareness among children is much easier than with any other group of citizens. This work examines ways to create an innovative Information & Communication Technologies (ICT) ecosystem (including web-based, mobile, social and sensing elements) tailored specifically for school environments, taking into account both the users (faculty, staff, students, parents) and school buildings, thus motivating and supporting young citizens' behavioural change to achieve greater energy efficiency. A mixture of open-source IoT hardware and proprietary platforms on the infrastructure level, are currently being utilized for monitoring a fleet of 18 educational buildings across 3 countries, comprising over 700 IoT monitoring points. Hereon presented is the system's high-level architecture, as well as several aspects of its implementation, related to the application domain of educational building monitoring and energy efficiency. The system is developed based on open-source technologies and services in order to make it capable of providing open IT-infrastructure and support from different commercial hardware/sensor vendors as well as open-source solutions. The system presented can be used to develop and offer new app-based solutions that can be used either for educational purposes or for managing the energy efficiency of the building. The system is replicable and adaptable to settings that may be different than the scenarios envisioned here (e.g., targeting different climate zones), different IT infrastructures and can be easily extended to accommodate integration with other systems. The overall performance of the system is evaluated in real-world environment in terms of scalability, responsiveness and simplicity.

An IoT-Based Solution for Monitoring a Fleet of Educational Buildings Focusing on Energy Efficiency

PubMed Central

Akrivopoulos, Orestis

2017-01-01

Raising awareness among young people and changing their behaviour and habits concerning energy usage is key to achieving sustained energy saving. Additionally, young people are very sensitive to environmental protection so raising awareness among children is much easier than with any other group of citizens. This work examines ways to create an innovative Information & Communication Technologies (ICT) ecosystem (including web-based, mobile, social and sensing elements) tailored specifically for school environments, taking into account both the users (faculty, staff, students, parents) and school buildings, thus motivating and supporting young citizens’ behavioural change to achieve greater energy efficiency. A mixture of open-source IoT hardware and proprietary platforms on the infrastructure level, are currently being utilized for monitoring a fleet of 18 educational buildings across 3 countries, comprising over 700 IoT monitoring points. Hereon presented is the system’s high-level architecture, as well as several aspects of its implementation, related to the application domain of educational building monitoring and energy efficiency. The system is developed based on open-source technologies and services in order to make it capable of providing open IT-infrastructure and support from different commercial hardware/sensor vendors as well as open-source solutions. The system presented can be used to develop and offer new app-based solutions that can be used either for educational purposes or for managing the energy efficiency of the building. The system is replicable and adaptable to settings that may be different than the scenarios envisioned here (e.g., targeting different climate zones), different IT infrastructures and can be easily extended to accommodate integration with other systems. The overall performance of the system is evaluated in real-world environment in terms of scalability, responsiveness and simplicity. PMID:28994719

Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics

PubMed Central

Giacomoni, Franck; Le Corguillé, Gildas; Monsoor, Misharl; Landi, Marion; Pericard, Pierre; Pétéra, Mélanie; Duperier, Christophe; Tremblay-Franco, Marie; Martin, Jean-François; Jacob, Daniel; Goulitquer, Sophie; Thévenot, Etienne A.; Caron, Christophe

2015-01-01

Summary: The complex, rapidly evolving field of computational metabolomics calls for collaborative infrastructures where the large volume of new algorithms for data pre-processing, statistical analysis and annotation can be readily integrated whatever the language, evaluated on reference datasets and chained to build ad hoc workflows for users. We have developed Workflow4Metabolomics (W4M), the first fully open-source and collaborative online platform for computational metabolomics. W4M is a virtual research environment built upon the Galaxy web-based platform technology. It enables ergonomic integration, exchange and running of individual modules and workflows. Alternatively, the whole W4M framework and computational tools can be downloaded as a virtual machine for local installation. Availability and implementation: http://workflow4metabolomics.org homepage enables users to open a private account and access the infrastructure. W4M is developed and maintained by the French Bioinformatics Institute (IFB) and the French Metabolomics and Fluxomics Infrastructure (MetaboHUB). Contact: contact@workflow4metabolomics.org PMID:25527831

Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics.

PubMed

Giacomoni, Franck; Le Corguillé, Gildas; Monsoor, Misharl; Landi, Marion; Pericard, Pierre; Pétéra, Mélanie; Duperier, Christophe; Tremblay-Franco, Marie; Martin, Jean-François; Jacob, Daniel; Goulitquer, Sophie; Thévenot, Etienne A; Caron, Christophe

2015-05-01

The complex, rapidly evolving field of computational metabolomics calls for collaborative infrastructures where the large volume of new algorithms for data pre-processing, statistical analysis and annotation can be readily integrated whatever the language, evaluated on reference datasets and chained to build ad hoc workflows for users. We have developed Workflow4Metabolomics (W4M), the first fully open-source and collaborative online platform for computational metabolomics. W4M is a virtual research environment built upon the Galaxy web-based platform technology. It enables ergonomic integration, exchange and running of individual modules and workflows. Alternatively, the whole W4M framework and computational tools can be downloaded as a virtual machine for local installation. http://workflow4metabolomics.org homepage enables users to open a private account and access the infrastructure. W4M is developed and maintained by the French Bioinformatics Institute (IFB) and the French Metabolomics and Fluxomics Infrastructure (MetaboHUB). contact@workflow4metabolomics.org. © The Author 2014. Published by Oxford University Press.

GéoSAS: A modular and interoperable Open Source Spatial Data Infrastructure for research

NASA Astrophysics Data System (ADS)

Bera, R.; Squividant, H.; Le Henaff, G.; Pichelin, P.; Ruiz, L.; Launay, J.; Vanhouteghem, J.; Aurousseau, P.; Cudennec, C.

2015-05-01

To-date, the commonest way to deal with geographical information and processes still appears to consume local resources, i.e. locally stored data processed on a local desktop or server. The maturity and subsequent growing use of OGC standards to exchange data on the World Wide Web, enhanced in Europe by the INSPIRE Directive, is bound to change the way people (and among them research scientists, especially in environmental sciences) make use of, and manage, spatial data. A clever use of OGC standards can help scientists to better store, share and use data, in particular for modelling. We propose a framework for online processing by making an intensive use of OGC standards. We illustrate it using the Spatial Data Infrastructure (SDI) GéoSAS which is the SDI set up for researchers' needs in our department. It is based on the existing open source, modular and interoperable Spatial Data Architecture geOrchestra.

Air pollution abatement performances of green infrastructure in open road and built-up street canyon environments - A review

NASA Astrophysics Data System (ADS)

Abhijith, K. V.; Kumar, Prashant; Gallagher, John; McNabola, Aonghus; Baldauf, Richard; Pilla, Francesco; Broderick, Brian; Di Sabatino, Silvana; Pulvirenti, Beatrice

2017-08-01

Intensifying the proportion of urban green infrastructure has been considered as one of the remedies for air pollution levels in cities, yet the impact of numerous vegetation types deployed in different built environments has to be fully synthesised and quantified. This review examined published literature on neighbourhood air quality modifications by green interventions. Studies were evaluated that discussed personal exposure to local sources of air pollution under the presence of vegetation in open road and built-up street canyon environments. Further, we critically evaluated the available literature to provide a better understanding of the interactions between vegetation and surrounding built-up environments and ascertain means of reducing local air pollution exposure using green infrastructure. The net effects of vegetation in each built-up environment are also summarised and possible recommendations for the future design of green infrastructure are proposed. In a street canyon environment, high-level vegetation canopies (trees) led to a deterioration in air quality, while low-level green infrastructure (hedges) improved air quality conditions. For open road conditions, wide, low porosity and tall vegetation leads to downwind pollutant reductions while gaps and high porosity vegetation could lead to no improvement or even deteriorated air quality. The review considers that generic recommendations can be provided for vegetation barriers in open road conditions. Green walls and roofs on building envelopes can also be used as effective air pollution abatement measures. The critical evaluation of the fundamental concepts and the amalgamation of key technical features of past studies by this review could assist urban planners to design and implement green infrastructures in the built environment.

Virtual Labs (Science Gateways) as platforms for Free and Open Source Science

NASA Astrophysics Data System (ADS)

Lescinsky, David; Car, Nicholas; Fraser, Ryan; Friedrich, Carsten; Kemp, Carina; Squire, Geoffrey

2016-04-01

The Free and Open Source Software (FOSS) movement promotes community engagement in software development, as well as provides access to a range of sophisticated technologies that would be prohibitively expensive if obtained commercially. However, as geoinformatics and eResearch tools and services become more dispersed, it becomes more complicated to identify and interface between the many required components. Virtual Laboratories (VLs, also known as Science Gateways) simplify the management and coordination of these components by providing a platform linking many, if not all, of the steps in particular scientific processes. These enable scientists to focus on their science, rather than the underlying supporting technologies. We describe a modular, open source, VL infrastructure that can be reconfigured to create VLs for a wide range of disciplines. Development of this infrastructure has been led by CSIRO in collaboration with Geoscience Australia and the National Computational Infrastructure (NCI) with support from the National eResearch Collaboration Tools and Resources (NeCTAR) and the Australian National Data Service (ANDS). Initially, the infrastructure was developed to support the Virtual Geophysical Laboratory (VGL), and has subsequently been repurposed to create the Virtual Hazards Impact and Risk Laboratory (VHIRL) and the reconfigured Australian National Virtual Geophysics Laboratory (ANVGL). During each step of development, new capabilities and services have been added and/or enhanced. We plan on continuing to follow this model using a shared, community code base. The VL platform facilitates transparent and reproducible science by providing access to both the data and methodologies used during scientific investigations. This is further enhanced by the ability to set up and run investigations using computational resources accessed through the VL. Data is accessed using registries pointing to catalogues within public data repositories (notably including the NCI National Environmental Research Data Interoperability Platform), or by uploading data directly from user supplied addresses or files. Similarly, scientific software is accessed through registries pointing to software repositories (e.g., GitHub). Runs are configured by using or modifying default templates designed by subject matter experts. After the appropriate computational resources are identified by the user, Virtual Machines (VMs) are spun up and jobs are submitted to service providers (currently the NeCTAR public cloud or Amazon Web Services). Following completion of the jobs the results can be reviewed and downloaded if desired. By providing a unified platform for science, the VL infrastructure enables sophisticated provenance capture and management. The source of input data (including both collection and queries), user information, software information (version and configuration details) and output information are all captured and managed as a VL resource which can be linked to output data sets. This provenance resource provides a mechanism for publication and citation for Free and Open Source Science.

Enabling cross-disciplinary research by linking data to Open Access publications

NASA Astrophysics Data System (ADS)

Rettberg, N.

2012-04-01

OpenAIREplus focuses on the linking of research data to associated publications. The interlinking of research objects has implications for optimising the research process, allowing the sharing, enrichment and reuse of data, and ultimately serving to make open data an essential part of first class research. The growing call for more concrete data management and sharing plans, apparent at funder and national level, is complemented by the increasing support for a scientific infrastructure that supports the seamless access to a range of research materials. This paper will describe the recently launched OpenAIREplus and will detail how it plans to achieve its goals of developing an Open Access participatory infrastructure for scientific information. OpenAIREplus extends the current collaborative OpenAIRE project, which provides European researchers with a service network for the deposit of peer-reviewed FP7 grant-funded Open Access publications. This new project will focus on opening up the infrastructure to data sources from subject-specific communities to provide metadata about research data and publications, facilitating the linking between these objects. The ability to link within a publication out to a citable database, or other research data material, is fairly innovative and this project will enable users to search, browse, view, and create relationships between different information objects. In this regard, OpenAIREplus will build on prototypes of so-called "Enhanced Publications", originally conceived in the DRIVER-II project. OpenAIREplus recognizes the importance of representing the context of publications and datasets, thus linking to resources about the authors, their affiliation, location, project data and funding. The project will explore how links between text-based publications and research data are managed in different scientific fields. This complements a previous study in OpenAIRE on current disciplinary practices and future needs for infrastructural Open Access services, taking into account the variety within research approaches. Adopting Linked Data mechanisms on top of citation and content mining, it will approach the interchange of data between generic infrastructures such as OpenAIREplus and subject specific service providers. The paper will also touch on the other challenges envisaged in the project with regard to the culture of sharing data, as well as IPR, licensing and organisational issues.

Cyberinfrastructure for Airborne Sensor Webs

NASA Technical Reports Server (NTRS)

Freudinger, Lawrence C.

2009-01-01

Since 2004 the NASA Airborne Science Program has been prototyping and using infrastructure that enables researchers to interact with each other and with their instruments via network communications. This infrastructure uses satellite links and an evolving suite of applications and services that leverage open-source software. The use of these tools has increased near-real-time situational awareness during field operations, resulting in productivity improvements and the collection of better data. This paper describes the high-level system architecture and major components, with example highlights from the use of the infrastructure. The paper concludes with a discussion of ongoing efforts to transition to operational status.

ImTK: an open source multi-center information management toolkit

NASA Astrophysics Data System (ADS)

Alaoui, Adil; Ingeholm, Mary Lou; Padh, Shilpa; Dorobantu, Mihai; Desai, Mihir; Cleary, Kevin; Mun, Seong K.

2008-03-01

The Information Management Toolkit (ImTK) Consortium is an open source initiative to develop robust, freely available tools related to the information management needs of basic, clinical, and translational research. An open source framework and agile programming methodology can enable distributed software development while an open architecture will encourage interoperability across different environments. The ISIS Center has conceptualized a prototype data sharing network that simulates a multi-center environment based on a federated data access model. This model includes the development of software tools to enable efficient exchange, sharing, management, and analysis of multimedia medical information such as clinical information, images, and bioinformatics data from multiple data sources. The envisioned ImTK data environment will include an open architecture and data model implementation that complies with existing standards such as Digital Imaging and Communications (DICOM), Health Level 7 (HL7), and the technical framework and workflow defined by the Integrating the Healthcare Enterprise (IHE) Information Technology Infrastructure initiative, mainly the Cross Enterprise Document Sharing (XDS) specifications.

Executable research compendia in geoscience research infrastructures

NASA Astrophysics Data System (ADS)

Nüst, Daniel

2017-04-01

From generation through analysis and collaboration to communication, scientific research requires the right tools. Scientists create their own software using third party libraries and platforms. Cloud computing, Open Science, public data infrastructures, and Open Source enable scientists with unprecedented opportunites, nowadays often in a field "Computational X" (e.g. computational seismology) or X-informatics (e.g. geoinformatics) [0]. This increases complexity and generates more innovation, e.g. Environmental Research Infrastructures (environmental RIs [1]). Researchers in Computational X write their software relying on both source code (e.g. from https://github.com) and binary libraries (e.g. from package managers such as APT, https://wiki.debian.org/Apt, or CRAN, https://cran.r-project.org/). They download data from domain specific (cf. https://re3data.org) or generic (e.g. https://zenodo.org) data repositories, and deploy computations remotely (e.g. European Open Science Cloud). The results themselves are archived, given persistent identifiers, connected to other works (e.g. using https://orcid.org/), and listed in metadata catalogues. A single researcher, intentionally or not, interacts with all sub-systems of RIs: data acquisition, data access, data processing, data curation, and community support [3]. To preserve computational research [3] proposes the Executable Research Compendium (ERC), a container format closing the gap of dependency preservation by encapsulating the runtime environment. ERCs and RIs can be integrated for different uses: (i) Coherence: ERC services validate completeness, integrity and results (ii) Metadata: ERCs connect the different parts of a piece of research and faciliate discovery (iii) Exchange and Preservation: ERC as usable building blocks are the shared and archived entity (iv) Self-consistency: ERCs remove dependence on ephemeral sources (v) Execution: ERC services create and execute a packaged analysis but integrate with existing platforms for display and control These integrations are vital for capturing workflows in RIs and connect key stakeholders (scientists, publishers, librarians). They are demonstrated using developments by the DFG-funded project Opening Reproducible Research (http://o2r.info). Semi-automatic creation of ERCs based on research workflows is a core goal of the project. References [0] Tony Hey, Stewart Tansley, Kristin Tolle (eds), 2009. The Fourth Paradigm: Data-Intensive Scientific Discovery. Microsoft Research. [1] P. Martin et al., Open Information Linking for Environmental Research Infrastructures, 2015 IEEE 11th International Conference on e-Science, Munich, 2015, pp. 513-520. doi: 10.1109/eScience.2015.66 [2] Y. Chen et al., Analysis of Common Requirements for Environmental Science Research Infrastructures, The International Symposium on Grids and Clouds (ISGC) 2013, Taipei, 2013, http://pos.sissa.it/archive/conferences/179/032/ISGC [3] Opening Reproducible Research, Geophysical Research Abstracts Vol. 18, EGU2016-7396, 2016, http://meetingorganizer.copernicus.org/EGU2016/EGU2016-7396.pdf

S3DB core: a framework for RDF generation and management in bioinformatics infrastructures

PubMed Central

2010-01-01

Background Biomedical research is set to greatly benefit from the use of semantic web technologies in the design of computational infrastructure. However, beyond well defined research initiatives, substantial issues of data heterogeneity, source distribution, and privacy currently stand in the way towards the personalization of Medicine. Results A computational framework for bioinformatic infrastructure was designed to deal with the heterogeneous data sources and the sensitive mixture of public and private data that characterizes the biomedical domain. This framework consists of a logical model build with semantic web tools, coupled with a Markov process that propagates user operator states. An accompanying open source prototype was developed to meet a series of applications that range from collaborative multi-institution data acquisition efforts to data analysis applications that need to quickly traverse complex data structures. This report describes the two abstractions underlying the S3DB-based infrastructure, logical and numerical, and discusses its generality beyond the immediate confines of existing implementations. Conclusions The emergence of the "web as a computer" requires a formal model for the different functionalities involved in reading and writing to it. The S3DB core model proposed was found to address the design criteria of biomedical computational infrastructure, such as those supporting large scale multi-investigator research, clinical trials, and molecular epidemiology. PMID:20646315

Chemotion ELN: an Open Source electronic lab notebook for chemists in academia.

PubMed

Tremouilhac, Pierre; Nguyen, An; Huang, Yu-Chieh; Kotov, Serhii; Lütjohann, Dominic Sebastian; Hübsch, Florian; Jung, Nicole; Bräse, Stefan

2017-09-25

The development of an electronic lab notebook (ELN) for researchers working in the field of chemical sciences is presented. The web based application is available as an Open Source software that offers modern solutions for chemical researchers. The Chemotion ELN is equipped with the basic functionalities necessary for the acquisition and processing of chemical data, in particular the work with molecular structures and calculations based on molecular properties. The ELN supports planning, description, storage, and management for the routine work of organic chemists. It also provides tools for communicating and sharing the recorded research data among colleagues. Meeting the requirements of a state of the art research infrastructure, the ELN allows the search for molecules and reactions not only within the user's data but also in conventional external sources as provided by SciFinder and PubChem. The presented development makes allowance for the growing dependency of scientific activity on the availability of digital information by providing Open Source instruments to record and reuse research data. The current version of the ELN has been using for over half of a year in our chemistry research group, serves as a common infrastructure for chemistry research and enables chemistry researchers to build their own databases of digital information as a prerequisite for the detailed, systematic investigation and evaluation of chemical reactions and mechanisms.

The Earth System Grid Federation: An Open Infrastructure for Access to Distributed Geospatial Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ananthakrishnan, Rachana; Bell, Gavin; Cinquini, Luca

2013-01-01

The Earth System Grid Federation (ESGF) is a multi-agency, international collaboration that aims at developing the software infrastructure needed to facilitate and empower the study of climate change on a global scale. The ESGF s architecture employs a system of geographically distributed peer nodes, which are independently administered yet united by the adoption of common federation protocols and application programming interfaces (APIs). The cornerstones of its interoperability are the peer-to-peer messaging that is continuously exchanged among all nodes in the federation; a shared architecture and API for search and discovery; and a security infrastructure based on industry standards (OpenID, SSL,more » GSI and SAML). The ESGF software is developed collaboratively across institutional boundaries and made available to the community as open source. It has now been adopted by multiple Earth science projects and allows access to petabytes of geophysical data, including the entire model output used for the next international assessment report on climate change (IPCC-AR5) and a suite of satellite observations (obs4MIPs) and reanalysis data sets (ANA4MIPs).« less

The Earth System Grid Federation: An Open Infrastructure for Access to Distributed Geo-Spatial Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cinquini, Luca; Crichton, Daniel; Miller, Neill

2012-01-01

The Earth System Grid Federation (ESGF) is a multi-agency, international collaboration that aims at developing the software infrastructure needed to facilitate and empower the study of climate change on a global scale. The ESGF s architecture employs a system of geographically distributed peer nodes, which are independently administered yet united by the adoption of common federation protocols and application programming interfaces (APIs). The cornerstones of its interoperability are the peer-to-peer messaging that is continuously exchanged among all nodes in the federation; a shared architecture and API for search and discovery; and a security infrastructure based on industry standards (OpenID, SSL,more » GSI and SAML). The ESGF software is developed collaboratively across institutional boundaries and made available to the community as open source. It has now been adopted by multiple Earth science projects and allows access to petabytes of geophysical data, including the entire model output used for the next international assessment report on climate change (IPCC-AR5) and a suite of satellite observations (obs4MIPs) and reanalysis data sets (ANA4MIPs).« less

The Earth System Grid Federation : an Open Infrastructure for Access to Distributed Geospatial Data

NASA Technical Reports Server (NTRS)

Cinquini, Luca; Crichton, Daniel; Mattmann, Chris; Harney, John; Shipman, Galen; Wang, Feiyi; Ananthakrishnan, Rachana; Miller, Neill; Denvil, Sebastian; Morgan, Mark;

A Shared Infrastructure for Federated Search Across Distributed Scientific Metadata Catalogs

NASA Astrophysics Data System (ADS)

Reed, S. A.; Truslove, I.; Billingsley, B. W.; Grauch, A.; Harper, D.; Kovarik, J.; Lopez, L.; Liu, M.; Brandt, M.

2013-12-01

The vast amount of science metadata can be overwhelming and highly complex. Comprehensive analysis and sharing of metadata is difficult since institutions often publish to their own repositories. There are many disjoint standards used for publishing scientific data, making it difficult to discover and share information from different sources. Services that publish metadata catalogs often have different protocols, formats, and semantics. The research community is limited by the exclusivity of separate metadata catalogs and thus it is desirable to have federated search interfaces capable of unified search queries across multiple sources. Aggregation of metadata catalogs also enables users to critique metadata more rigorously. With these motivations in mind, the National Snow and Ice Data Center (NSIDC) and Advanced Cooperative Arctic Data and Information Service (ACADIS) implemented two search interfaces for the community. Both the NSIDC Search and ACADIS Arctic Data Explorer (ADE) use a common infrastructure which keeps maintenance costs low. The search clients are designed to make OpenSearch requests against Solr, an Open Source search platform. Solr applies indexes to specific fields of the metadata which in this instance optimizes queries containing keywords, spatial bounds and temporal ranges. NSIDC metadata is reused by both search interfaces but the ADE also brokers additional sources. Users can quickly find relevant metadata with minimal effort and ultimately lowers costs for research. This presentation will highlight the reuse of data and code between NSIDC and ACADIS, discuss challenges and milestones for each project, and will identify creation and use of Open Source libraries.

The Athabasca University eduSource Project: Building an Accessible Learning Object Repository

ERIC Educational Resources Information Center

Cleveland-Innes, Martha; McGreal, Rory; Anderson, Terry; Friesen, Norm; Ally, Mohamed; Tin, Tony; Graham, Rodger; Moisey, Susan; Petrinjak, Anita; Schafer, Steve

2005-01-01

Athabasca University--Canada's Open University (AU) made the commitment to put all of its courses online as part of its Strategic University Plan. In pursuit of this goal, AU participated in the eduSource project, a pan-Canadian effort to build the infrastructure for an interoperable network of learning object repositories. AU acted as a leader in…

Waggle: A Framework for Intelligent Attentive Sensing and Actuation

NASA Astrophysics Data System (ADS)

Sankaran, R.; Jacob, R. L.; Beckman, P. H.; Catlett, C. E.; Keahey, K.

2014-12-01

Advances in sensor-driven computation and computationally steered sensing will greatly enable future research in fields including environmental and atmospheric sciences. We will present "Waggle," an open-source hardware and software infrastructure developed with two goals: (1) reducing the separation and latency between sensing and computing and (2) improving the reliability and longevity of sensing-actuation platforms in challenging and costly deployments. Inspired by "deep-space probe" systems, the Waggle platform design includes features that can support longitudinal studies, deployments with varying communication links, and remote management capabilities. Waggle lowers the barrier for scientists to incorporate real-time data from their sensors into their computations and to manipulate the sensors or provide feedback through actuators. A standardized software and hardware design allows quick addition of new sensors/actuators and associated software in the nodes and enables them to be coupled with computational codes both insitu and on external compute infrastructure. The Waggle framework currently drives the deployment of two observational systems - a portable and self-sufficient weather platform for study of small-scale effects in Chicago's urban core and an open-ended distributed instrument in Chicago that aims to support several research pursuits across a broad range of disciplines including urban planning, microbiology and computer science. Built around open-source software, hardware, and Linux OS, the Waggle system comprises two components - the Waggle field-node and Waggle cloud-computing infrastructure. Waggle field-node affords a modular, scalable, fault-tolerant, secure, and extensible platform for hosting sensors and actuators in the field. It supports insitu computation and data storage, and integration with cloud-computing infrastructure. The Waggle cloud infrastructure is designed with the goal of scaling to several hundreds of thousands of Waggle nodes. It supports aggregating data from sensors hosted by the nodes, staging computation, relaying feedback to the nodes and serving data to end-users. We will discuss the Waggle design principles and their applicability to various observational research pursuits, and demonstrate its capabilities.

Agile Infrastructure Monitoring

NASA Astrophysics Data System (ADS)

Andrade, P.; Ascenso, J.; Fedorko, I.; Fiorini, B.; Paladin, M.; Pigueiras, L.; Santos, M.

2014-06-01

At the present time, data centres are facing a massive rise in virtualisation and cloud computing. The Agile Infrastructure (AI) project is working to deliver new solutions to ease the management of CERN data centres. Part of the solution consists in a new "shared monitoring architecture" which collects and manages monitoring data from all data centre resources. In this article, we present the building blocks of this new monitoring architecture, the different open source technologies selected for each architecture layer, and how we are building a community around this common effort.

Open-source mobile digital platform for clinical trial data collection in low-resource settings.

PubMed

van Dam, Joris; Omondi Onyango, Kevin; Midamba, Brian; Groosman, Nele; Hooper, Norman; Spector, Jonathan; Pillai, Goonaseelan Colin; Ogutu, Bernhards

2017-02-01

Governments, universities and pan-African research networks are building durable infrastructure and capabilities for biomedical research in Africa. This offers the opportunity to adopt from the outset innovative approaches and technologies that would be challenging to retrofit into fully established research infrastructures such as those regularly found in high-income countries. In this context we piloted the use of a novel mobile digital health platform, designed specifically for low-resource environments, to support high-quality data collection in a clinical research study. Our primary aim was to assess the feasibility of a using a mobile digital platform for clinical trial data collection in a low-resource setting. Secondarily, we sought to explore the potential benefits of such an approach. The investigative site was a research institute in Nairobi, Kenya. We integrated an open-source platform for mobile data collection commonly used in the developing world with an open-source, standard platform for electronic data capture in clinical trials. The integration was developed using common data standards (Clinical Data Interchange Standards Consortium (CDISC) Operational Data Model), maximising the potential to extend the approach to other platforms. The system was deployed in a pharmacokinetic study involving healthy human volunteers. The electronic data collection platform successfully supported conduct of the study. Multidisciplinary users reported high levels of satisfaction with the mobile application and highlighted substantial advantages when compared with traditional paper record systems. The new system also demonstrated a potential for expediting data quality review. This pilot study demonstrated the feasibility of using a mobile digital platform for clinical research data collection in low-resource settings. Sustainable scientific capabilities and infrastructure are essential to attract and support clinical research studies. Since many research structures in Africa are being developed anew, stakeholders should consider implementing innovative technologies and approaches.

Generalizable open source urban water portfolio simulation framework demonstrated using a multi-objective risk-based planning benchmark problem.

NASA Astrophysics Data System (ADS)

Trindade, B. C.; Reed, P. M.

2017-12-01

The growing access and reduced cost for computing power in recent years has promoted rapid development and application of multi-objective water supply portfolio planning. As this trend continues there is a pressing need for flexible risk-based simulation frameworks and improved algorithm benchmarking for emerging classes of water supply planning and management problems. This work contributes the Water Utilities Management and Planning (WUMP) model: a generalizable and open source simulation framework designed to capture how water utilities can minimize operational and financial risks by regionally coordinating planning and management choices, i.e. making more efficient and coordinated use of restrictions, water transfers and financial hedging combined with possible construction of new infrastructure. We introduce the WUMP simulation framework as part of a new multi-objective benchmark problem for planning and management of regionally integrated water utility companies. In this problem, a group of fictitious water utilities seek to balance the use of the mentioned reliability driven actions (e.g., restrictions, water transfers and infrastructure pathways) and their inherent financial risks. Several traits of this problem make it ideal for a benchmark problem, namely the presence of (1) strong non-linearities and discontinuities in the Pareto front caused by the step-wise nature of the decision making formulation and by the abrupt addition of storage through infrastructure construction, (2) noise due to the stochastic nature of the streamflows and water demands, and (3) non-separability resulting from the cooperative formulation of the problem, in which decisions made by stakeholder may substantially impact others. Both the open source WUMP simulation framework and its demonstration in a challenging benchmarking example hold value for promoting broader advances in urban water supply portfolio planning for regions confronting change.

Dissemination of metabolomics results: role of MetaboLights and COSMOS.

PubMed

Salek, Reza M; Haug, Kenneth; Steinbeck, Christoph

2013-05-17

With ever-increasing amounts of metabolomics data produced each year, there is an even greater need to disseminate data and knowledge produced in a standard and reproducible way. To assist with this a general purpose, open source metabolomics repository, MetaboLights, was launched in 2012. To promote a community standard, initially culminated as metabolomics standards initiative (MSI), COordination of Standards in MetabOlomicS (COSMOS) was introduced. COSMOS aims to link life science e-infrastructures within the worldwide metabolomics community as well as develop and maintain open source exchange formats for raw and processed data, ensuring better flow of metabolomics information.

Open Source Dataturbine (OSDT) Android Sensorpod in Environmental Observing Systems

NASA Astrophysics Data System (ADS)

Fountain, T. R.; Shin, P.; Tilak, S.; Trinh, T.; Smith, J.; Kram, S.

2014-12-01

The OSDT Android SensorPod is a custom-designed mobile computing platform for assembling wireless sensor networks for environmental monitoring applications. Funded by an award from the Gordon and Betty Moore Foundation, the OSDT SensorPod represents a significant technological advance in the application of mobile and cloud computing technologies to near-real-time applications in environmental science, natural resources management, and disaster response and recovery. It provides a modular architecture based on open standards and open-source software that allows system developers to align their projects with industry best practices and technology trends, while avoiding commercial vendor lock-in to expensive proprietary software and hardware systems. The integration of mobile and cloud-computing infrastructure represents a disruptive technology in the field of environmental science, since basic assumptions about technology requirements are now open to revision, e.g., the roles of special purpose data loggers and dedicated site infrastructure. The OSDT Android SensorPod was designed with these considerations in mind, and the resulting system exhibits the following characteristics - it is flexible, efficient and robust. The system was developed and tested in the three science applications: 1) a fresh water limnology deployment in Wisconsin, 2) a near coastal marine science deployment at the UCSD Scripps Pier, and 3) a terrestrial ecological deployment in the mountains of Taiwan. As part of a public education and outreach effort, a Facebook page with daily ocean pH measurements from the UCSD Scripps pier was developed. Wireless sensor networks and the virtualization of data and network services is the future of environmental science infrastructure. The OSDT Android SensorPod was designed and developed to harness these new technology developments for environmental monitoring applications.

BioContainers: an open-source and community-driven framework for software standardization.

PubMed

da Veiga Leprevost, Felipe; Grüning, Björn A; Alves Aflitos, Saulo; Röst, Hannes L; Uszkoreit, Julian; Barsnes, Harald; Vaudel, Marc; Moreno, Pablo; Gatto, Laurent; Weber, Jonas; Bai, Mingze; Jimenez, Rafael C; Sachsenberg, Timo; Pfeuffer, Julianus; Vera Alvarez, Roberto; Griss, Johannes; Nesvizhskii, Alexey I; Perez-Riverol, Yasset

2017-08-15

BioContainers (biocontainers.pro) is an open-source and community-driven framework which provides platform independent executable environments for bioinformatics software. BioContainers allows labs of all sizes to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful analysis pipelines. BioContainers is based on popular open-source projects Docker and rkt frameworks, that allow software to be installed and executed under an isolated and controlled environment. Also, it provides infrastructure and basic guidelines to create, manage and distribute bioinformatics containers with a special focus on omics technologies. These containers can be integrated into more comprehensive bioinformatics pipelines and different architectures (local desktop, cloud environments or HPC clusters). The software is freely available at github.com/BioContainers/. yperez@ebi.ac.uk. © The Author(s) 2017. Published by Oxford University Press.

BioContainers: an open-source and community-driven framework for software standardization

PubMed Central

da Veiga Leprevost, Felipe; Grüning, Björn A.; Alves Aflitos, Saulo; Röst, Hannes L.; Uszkoreit, Julian; Barsnes, Harald; Vaudel, Marc; Moreno, Pablo; Gatto, Laurent; Weber, Jonas; Bai, Mingze; Jimenez, Rafael C.; Sachsenberg, Timo; Pfeuffer, Julianus; Vera Alvarez, Roberto; Griss, Johannes; Nesvizhskii, Alexey I.; Perez-Riverol, Yasset

2017-01-01

Abstract Motivation BioContainers (biocontainers.pro) is an open-source and community-driven framework which provides platform independent executable environments for bioinformatics software. BioContainers allows labs of all sizes to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful analysis pipelines. BioContainers is based on popular open-source projects Docker and rkt frameworks, that allow software to be installed and executed under an isolated and controlled environment. Also, it provides infrastructure and basic guidelines to create, manage and distribute bioinformatics containers with a special focus on omics technologies. These containers can be integrated into more comprehensive bioinformatics pipelines and different architectures (local desktop, cloud environments or HPC clusters). Availability and Implementation The software is freely available at github.com/BioContainers/. Contact yperez@ebi.ac.uk PMID:28379341

Virtualization of open-source secure web services to support data exchange in a pediatric critical care research network

PubMed Central

Sward, Katherine A; Newth, Christopher JL; Khemani, Robinder G; Cryer, Martin E; Thelen, Julie L; Enriquez, Rene; Shaoyu, Su; Pollack, Murray M; Harrison, Rick E; Meert, Kathleen L; Berg, Robert A; Wessel, David L; Shanley, Thomas P; Dalton, Heidi; Carcillo, Joseph; Jenkins, Tammara L; Dean, J Michael

2015-01-01

Objectives To examine the feasibility of deploying a virtual web service for sharing data within a research network, and to evaluate the impact on data consistency and quality. Material and Methods Virtual machines (VMs) encapsulated an open-source, semantically and syntactically interoperable secure web service infrastructure along with a shadow database. The VMs were deployed to 8 Collaborative Pediatric Critical Care Research Network Clinical Centers. Results Virtual web services could be deployed in hours. The interoperability of the web services reduced format misalignment from 56% to 1% and demonstrated that 99% of the data consistently transferred using the data dictionary and 1% needed human curation. Conclusions Use of virtualized open-source secure web service technology could enable direct electronic abstraction of data from hospital databases for research purposes. PMID:25796596

Navigating the unfolding open data landscape in ecology and evolution.

PubMed

Culina, Antica; Baglioni, Miriam; Crowther, Tom W; Visser, Marcel E; Woutersen-Windhouwer, Saskia; Manghi, Paolo

2018-03-01

Open access to data is revolutionizing the sciences. To allow ecologists and evolutionary biologists to confidently find and use the existing data, we provide an overview of the landscape of online data infrastructures, and highlight the key points to consider when using open data. We introduce an online collaborative platform to keep a community-driven, updated list of the best sources that enable search for data in one interface. In doing so, our aim is to lower the barrier to accessing open data, and encourage its use by researchers hoping to increase the scope, reliability and value of their findings.

Use of Open Standards and Technologies at the Lunar Mapping and Modeling Project

NASA Astrophysics Data System (ADS)

Law, E.; Malhotra, S.; Bui, B.; Chang, G.; Goodale, C. E.; Ramirez, P.; Kim, R. M.; Sadaqathulla, S.; Rodriguez, L.

2011-12-01

The Lunar Mapping and Modeling Project (LMMP), led by the Marshall Space Flight center (MSFC), is tasked by NASA. The project is responsible for the development of an information system to support lunar exploration activities. It provides lunar explorers a set of tools and lunar map and model products that are predominantly derived from present lunar missions (e.g., the Lunar Reconnaissance Orbiter (LRO)) and from historical missions (e.g., Apollo). At Jet Propulsion Laboratory (JPL), we have built the LMMP interoperable geospatial information system's underlying infrastructure and a single point of entry - the LMMP Portal by employing a number of open standards and technologies. The Portal exposes a set of services to users to allow search, visualization, subset, and download of lunar data managed by the system. Users also have access to a set of tools that visualize, analyze and annotate the data. The infrastructure and Portal are based on web service oriented architecture. We designed the system to support solar system bodies in general including asteroids, earth and planets. We employed a combination of custom software, commercial and open-source components, off-the-shelf hardware and pay-by-use cloud computing services. The use of open standards and web service interfaces facilitate platform and application independent access to the services and data, offering for instances, iPad and Android mobile applications and large screen multi-touch with 3-D terrain viewing functions, for a rich browsing and analysis experience from a variety of platforms. The web services made use of open standards including: Representational State Transfer (REST); and Open Geospatial Consortium (OGC)'s Web Map Service (WMS), Web Coverage Service (WCS), Web Feature Service (WFS). Its data management services have been built on top of a set of open technologies including: Object Oriented Data Technology (OODT) - open source data catalog, archive, file management, data grid framework; openSSO - open source access management and federation platform; solr - open source enterprise search platform; redmine - open source project collaboration and management framework; GDAL - open source geospatial data abstraction library; and others. Its data products are compliant with Federal Geographic Data Committee (FGDC) metadata standard. This standardization allows users to access the data products via custom written applications or off-the-shelf applications such as GoogleEarth. We will demonstrate this ready-to-use system for data discovery and visualization by walking through the data services provided through the portal such as browse, search, and other tools. We will further demonstrate image viewing and layering of lunar map images from the Internet, via mobile devices such as Apple's iPad.

Smart Cities Intelligence System (SMACiSYS) Integrating Sensor Web with Spatial Data Infrastructures (sensdi)

NASA Astrophysics Data System (ADS)

Bhattacharya, D.; Painho, M.

2017-09-01

The paper endeavours to enhance the Sensor Web with crucial geospatial analysis capabilities through integration with Spatial Data Infrastructure. The objective is development of automated smart cities intelligence system (SMACiSYS) with sensor-web access (SENSDI) utilizing geomatics for sustainable societies. There has been a need to develop automated integrated system to categorize events and issue information that reaches users directly. At present, no web-enabled information system exists which can disseminate messages after events evaluation in real time. Research work formalizes a notion of an integrated, independent, generalized, and automated geo-event analysing system making use of geo-spatial data under popular usage platform. Integrating Sensor Web With Spatial Data Infrastructures (SENSDI) aims to extend SDIs with sensor web enablement, converging geospatial and built infrastructure, and implement test cases with sensor data and SDI. The other benefit, conversely, is the expansion of spatial data infrastructure to utilize sensor web, dynamically and in real time for smart applications that smarter cities demand nowadays. Hence, SENSDI augments existing smart cities platforms utilizing sensor web and spatial information achieved by coupling pairs of otherwise disjoint interfaces and APIs formulated by Open Geospatial Consortium (OGC) keeping entire platform open access and open source. SENSDI is based on Geonode, QGIS and Java, that bind most of the functionalities of Internet, sensor web and nowadays Internet of Things superseding Internet of Sensors as well. In a nutshell, the project delivers a generalized real-time accessible and analysable platform for sensing the environment and mapping the captured information for optimal decision-making and societal benefit.

Learning Analytics Platform, towards an Open Scalable Streaming Solution for Education

ERIC Educational Resources Information Center

Lewkow, Nicholas; Zimmerman, Neil; Riedesel, Mark; Essa, Alfred

2015-01-01

Next generation digital learning environments require delivering "just-in-time feedback" to learners and those who support them. Unlike traditional business intelligence environments, streaming data requires resilient infrastructure that can move data at scale from heterogeneous data sources, process the data quickly for use across…

Open Drug Discovery Teams: A Chemistry Mobile App for Collaboration.

PubMed

Ekins, Sean; Clark, Alex M; Williams, Antony J

2012-08-01

The Open Drug Discovery Teams (ODDT) project provides a mobile app primarily intended as a research topic aggregator of predominantly open science data collected from various sources on the internet. It exists to facilitate interdisciplinary teamwork and to relieve the user from data overload, delivering access to information that is highly relevant and focused on their topic areas of interest. Research topics include areas of chemistry and adjacent molecule-oriented biomedical sciences, with an emphasis on those which are most amenable to open research at present. These include rare and neglected diseases, and precompetitive and public-good initiatives such as green chemistry. The ODDT project uses a free mobile app as user entry point. The app has a magazine-like interface, and server-side infrastructure for hosting chemistry-related data as well as value added services. The project is open to participation from anyone and provides the ability for users to make annotations and assertions, thereby contributing to the collective value of the data to the engaged community. Much of the content is derived from public sources, but the platform is also amenable to commercial data input. The technology could also be readily used in-house by organizations as a research aggregator that could integrate internal and external science and discussion. The infrastructure for the app is currently based upon the Twitter API as a useful proof of concept for a real time source of publicly generated content. This could be extended further by accessing other APIs providing news and data feeds of relevance to a particular area of interest. As the project evolves, social networking features will be developed for organizing participants into teams, with various forms of communication and content management possible.

Open Drug Discovery Teams: A Chemistry Mobile App for Collaboration

PubMed Central

Ekins, Sean; Clark, Alex M; Williams, Antony J

2012-01-01

Abstract The Open Drug Discovery Teams (ODDT) project provides a mobile app primarily intended as a research topic aggregator of predominantly open science data collected from various sources on the internet. It exists to facilitate interdisciplinary teamwork and to relieve the user from data overload, delivering access to information that is highly relevant and focused on their topic areas of interest. Research topics include areas of chemistry and adjacent molecule-oriented biomedical sciences, with an emphasis on those which are most amenable to open research at present. These include rare and neglected diseases, and precompetitive and public-good initiatives such as green chemistry. The ODDT project uses a free mobile app as user entry point. The app has a magazine-like interface, and server-side infrastructure for hosting chemistry-related data as well as value added services. The project is open to participation from anyone and provides the ability for users to make annotations and assertions, thereby contributing to the collective value of the data to the engaged community. Much of the content is derived from public sources, but the platform is also amenable to commercial data input. The technology could also be readily used in-house by organizations as a research aggregator that could integrate internal and external science and discussion. The infrastructure for the app is currently based upon the Twitter API as a useful proof of concept for a real time source of publicly generated content. This could be extended further by accessing other APIs providing news and data feeds of relevance to a particular area of interest. As the project evolves, social networking features will be developed for organizing participants into teams, with various forms of communication and content management possible. PMID:23198003

Computational Infrastructure for Geodynamics (CIG)

NASA Astrophysics Data System (ADS)

Gurnis, M.; Kellogg, L. H.; Bloxham, J.; Hager, B. H.; Spiegelman, M.; Willett, S.; Wysession, M. E.; Aivazis, M.

2004-12-01

Solid earth geophysicists have a long tradition of writing scientific software to address a wide range of problems. In particular, computer simulations came into wide use in geophysics during the decade after the plate tectonic revolution. Solution schemes and numerical algorithms that developed in other areas of science, most notably engineering, fluid mechanics, and physics, were adapted with considerable success to geophysics. This software has largely been the product of individual efforts and although this approach has proven successful, its strength for solving problems of interest is now starting to show its limitations as we try to share codes and algorithms or when we want to recombine codes in novel ways to produce new science. With funding from the NSF, the US community has embarked on a Computational Infrastructure for Geodynamics (CIG) that will develop, support, and disseminate community-accessible software for the greater geodynamics community from model developers to end-users. The software is being developed for problems involving mantle and core dynamics, crustal and earthquake dynamics, magma migration, seismology, and other related topics. With a high level of community participation, CIG is leveraging state-of-the-art scientific computing into a suite of open-source tools and codes. The infrastructure that we are now starting to develop will consist of: (a) a coordinated effort to develop reusable, well-documented and open-source geodynamics software; (b) the basic building blocks - an infrastructure layer - of software by which state-of-the-art modeling codes can be quickly assembled; (c) extension of existing software frameworks to interlink multiple codes and data through a superstructure layer; (d) strategic partnerships with the larger world of computational science and geoinformatics; and (e) specialized training and workshops for both the geodynamics and broader Earth science communities. The CIG initiative has already started to leverage and develop long-term strategic partnerships with open source development efforts within the larger thrusts of scientific computing and geoinformatics. These strategic partnerships are essential as the frontier has moved into multi-scale and multi-physics problems in which many investigators now want to use simulation software for data interpretation, data assimilation, and hypothesis testing.

Open Data Infrastructures And The Future Of Science

NASA Astrophysics Data System (ADS)

Boulton, G. S.

2016-12-01

Open publication of the evidence (the data) supporting a scientific claim has been the bedrock on which the scientific advances of the modern era of science have been built. It is also of immense importance in confronting three challenges unleashed by the digital revolution. The first is the threat the digital data storm poses to the principle of "scientific self-correction", in which false concepts are weeded out because of a demonstrable failure in logic or in the replication of observations or experiments. Large and complex data volumes are difficult to make openly available in ways that make rigorous scrutiny possible. Secondly, linking and integrating data from different sources about the same phenomena have created profound new opportunities for understanding the Earth. If data are neither accessible nor useable, such opportunities cannot be seized. Thirdly, open access publication, open data and ubiquitous modern communications enhance the prospects for an era of "Open Science" in which science emerges from behind its laboratory doors to engage in co-production of knowledge with other stakeholders in addressing major contemporary challenges to human society, in particular the need for long term thinking about planetary sustainability. If the benefits of an open data regime are to be realised, only a small part of the challenge lies in providing "hard" infrastructure. The major challenges lie in the "soft" infrastructure of relationships between the components of national science systems, of analytic and software tools, of national and international standards and the normative principles adopted by scientists themselves. The principles that underlie these relationships, the responsibilities of key actors and the rules of the game needed to maximise national performance and facilitate international collaboration are set out in an International Accord on Open Data.

Building a Community Infrastructure for Scalable On-Line Performance Analysis Tools around Open|Speedshop

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miller, Barton

2014-06-30

Peta-scale computing environments pose significant challenges for both system and application developers and addressing them required more than simply scaling up existing tera-scale solutions. Performance analysis tools play an important role in gaining this understanding, but previous monolithic tools with fixed feature sets have not sufficed. Instead, this project worked on the design, implementation, and evaluation of a general, flexible tool infrastructure supporting the construction of performance tools as “pipelines” of high-quality tool building blocks. These tool building blocks provide common performance tool functionality, and are designed for scalability, lightweight data acquisition and analysis, and interoperability. For this project, wemore » built on Open|SpeedShop, a modular and extensible open source performance analysis tool set. The design and implementation of such a general and reusable infrastructure targeted for petascale systems required us to address several challenging research issues. All components needed to be designed for scale, a task made more difficult by the need to provide general modules. The infrastructure needed to support online data aggregation to cope with the large amounts of performance and debugging data. We needed to be able to map any combination of tool components to each target architecture. And we needed to design interoperable tool APIs and workflows that were concrete enough to support the required functionality, yet provide the necessary flexibility to address a wide range of tools. A major result of this project is the ability to use this scalable infrastructure to quickly create tools that match with a machine architecture and a performance problem that needs to be understood. Another benefit is the ability for application engineers to use the highly scalable, interoperable version of Open|SpeedShop, which are reassembled from the tool building blocks into a flexible, multi-user interface set of tools. This set of tools targeted at Office of Science Leadership Class computer systems and selected Office of Science application codes. We describe the contributions made by the team at the University of Wisconsin. The project built on the efforts in Open|SpeedShop funded by DOE/NNSA and the DOE/NNSA Tri-Lab community, extended Open|Speedshop to the Office of Science Leadership Class Computing Facilities, and addressed new challenges found on these cutting edge systems. Work done under this project at Wisconsin can be divided into two categories, new algorithms and techniques for debugging, and foundation infrastructure work on our Dyninst binary analysis and instrumentation toolkits and MRNet scalability infrastructure.« less

Dissemination of metabolomics results: role of MetaboLights and COSMOS

PubMed Central

2013-01-01

With ever-increasing amounts of metabolomics data produced each year, there is an even greater need to disseminate data and knowledge produced in a standard and reproducible way. To assist with this a general purpose, open source metabolomics repository, MetaboLights, was launched in 2012. To promote a community standard, initially culminated as metabolomics standards initiative (MSI), COordination of Standards in MetabOlomicS (COSMOS) was introduced. COSMOS aims to link life science e-infrastructures within the worldwide metabolomics community as well as develop and maintain open source exchange formats for raw and processed data, ensuring better flow of metabolomics information. PMID:23683662

Toward Global Real Time Hydrologic Modeling - An "Open" View From the Trenches

NASA Astrophysics Data System (ADS)

Nelson, J.

2015-12-01

Big Data has become a popular term to describe the exponential growth of data and related cyber infrastructure to process it so that better analysis can be performed and lead to improved decision-making. How are we doing in the hydrologic sciences? As part of a significant collaborative effort that brought together scientists from public, private, and academic organizations a new transformative hydrologic forecasting modeling infrastructure has been developed. How was it possible to go from deterministic hydrologic forecasts largely driven through manual interactions at 3600 stations to automated 15-day ensemble forecasts at 2.67 million stations? Earth observations of precipitation, temperature, moisture, and other atmospheric and land surface conditions form the foundation of global hydrologic forecasts, but this project demonstrates a critical component to harness these resources can be summed up in one word: OPEN. Whether it is open data sources, open software solutions with open standards, or just being open to collaborations and building teams across institutions, disciplines, and international boundaries, time and time again through my involvement in the development of a high-resolution real time global hydrologic forecasting model I have discovered that in every aspect the sum has always been greater than the parts. While much has been accomplished, much more remains to be done, but the most important lesson learned has been to the degree that we can remain open and work together, the greater our ability will be to use big data hydrologic modeling resources to solve the world's most vexing water related challenges. This presentation will demonstrate a transformational global real time hydrologic forecasting application based on downscaled ECMWF ensemble forecasts, RAPID routing, and Tethys Platform for cloud computing and visualization with discussions of the human and cyber infrastructure connections that make it successful and needs moving forward.

Using Citygml to Deploy Smart-City Services for Urban Ecosystems

NASA Astrophysics Data System (ADS)

Prandi, F.; De Amicis, R.; Piffer, S.; Soave, M.; Cadzow, S.; Gonzalez Boix, E.; D'Hont, E.

2013-05-01

The rapid technological evolution, which is characterizing all the disciplines involved within the wide concept of smart cities, becomes a key factor to trigger true user-driven innovation. In this context 3D city models will play an increasingly important role in our daily lives and become an essential part of the modern city information infrastructure (Spatial Data Infrastructure). The goal of this paper is to introduce the i-SCOPE (interoperable Smart City services through an Open Platform for urban Ecosystems) project methodology and implementations together with key technologies and open standards. Based on interoperable 3D CityGML UIMs, the aim of i-Scope is to deliver an open platform on top of which it possible to develop, within different domains, various "smart city" services. Moreover, in i-SCOPE different issues, transcending the mere technological domain, are being tackled, including aspects dealing with social and environmental issues. Indeed several tasks including citizen awareness, crowd source and voluntary based data collection as well as privacy issue concerning involved people should be considered.

Creating a Rackspace and NASA Nebula compatible cloud using the OpenStack project (Invited)

NASA Astrophysics Data System (ADS)

Clark, R.

2010-12-01

NASA and Rackspace have both provided technology to the OpenStack that allows anyone to create a private Infrastructure as a Service (IaaS) cloud using open source software and commodity hardware. OpenStack is designed and developed completely in the open and with an open governance process. NASA donated Nova, which powers the compute portion of NASA Nebula Cloud Computing Platform, and Rackspace donated Swift, which powers Rackspace Cloud Files. The project is now in continuous development by NASA, Rackspace, and hundreds of other participants. When you create a private cloud using Openstack, you will have the ability to easily interact with your private cloud, a government cloud, and an ecosystem of public cloud providers, using the same API.

Web Server Security on Open Source Environments

NASA Astrophysics Data System (ADS)

Gkoutzelis, Dimitrios X.; Sardis, Manolis S.

Administering critical resources has never been more difficult that it is today. In a changing world of software innovation where major changes occur on a daily basis, it is crucial for the webmasters and server administrators to shield their data against an unknown arsenal of attacks in the hands of their attackers. Up until now this kind of defense was a privilege of the few, out-budgeted and low cost solutions let the defender vulnerable to the uprising of innovating attacking methods. Luckily, the digital revolution of the past decade left its mark, changing the way we face security forever: open source infrastructure today covers all the prerequisites for a secure web environment in a way we could never imagine fifteen years ago. Online security of large corporations, military and government bodies is more and more handled by open source application thus driving the technological trend of the 21st century in adopting open solutions to E-Commerce and privacy issues. This paper describes substantial security precautions in facing privacy and authentication issues in a totally open source web environment. Our goal is to state and face the most known problems in data handling and consequently propose the most appealing techniques to face these challenges through an open solution.

Development of a cloud-based Bioinformatics Training Platform.

PubMed

Revote, Jerico; Watson-Haigh, Nathan S; Quenette, Steve; Bethwaite, Blair; McGrath, Annette; Shang, Catherine A

2017-05-01

The Bioinformatics Training Platform (BTP) has been developed to provide access to the computational infrastructure required to deliver sophisticated hands-on bioinformatics training courses. The BTP is a cloud-based solution that is in active use for delivering next-generation sequencing training to Australian researchers at geographically dispersed locations. The BTP was built to provide an easy, accessible, consistent and cost-effective approach to delivering workshops at host universities and organizations with a high demand for bioinformatics training but lacking the dedicated bioinformatics training suites required. To support broad uptake of the BTP, the platform has been made compatible with multiple cloud infrastructures. The BTP is an open-source and open-access resource. To date, 20 training workshops have been delivered to over 700 trainees at over 10 venues across Australia using the BTP. © The Author 2016. Published by Oxford University Press.

Development of a cloud-based Bioinformatics Training Platform

PubMed Central

Revote, Jerico; Watson-Haigh, Nathan S.; Quenette, Steve; Bethwaite, Blair; McGrath, Annette

2017-01-01

Abstract The Bioinformatics Training Platform (BTP) has been developed to provide access to the computational infrastructure required to deliver sophisticated hands-on bioinformatics training courses. The BTP is a cloud-based solution that is in active use for delivering next-generation sequencing training to Australian researchers at geographically dispersed locations. The BTP was built to provide an easy, accessible, consistent and cost-effective approach to delivering workshops at host universities and organizations with a high demand for bioinformatics training but lacking the dedicated bioinformatics training suites required. To support broad uptake of the BTP, the platform has been made compatible with multiple cloud infrastructures. The BTP is an open-source and open-access resource. To date, 20 training workshops have been delivered to over 700 trainees at over 10 venues across Australia using the BTP. PMID:27084333

Evaluation of Urban Drainage Infrastructure: New York City Case Study

NASA Astrophysics Data System (ADS)

Hamidi, A.; Grossberg, M.; Khanbilvardi, R.

2017-12-01

Flood response in an urban area is the product of interactions of spatially and temporally varying rainfall and infrastructures. In urban areas, however, the complex sub-surface networks of tunnels, waste and storm water drainage systems are often inaccessible, pose challenges for modeling and prediction of the drainage infrastructure performance. The increased availability of open data in cities is an emerging information asset for a better understanding of the dynamics of urban water drainage infrastructure. This includes crowd sourced data and community reporting. A well-known source of this type of data is the non-emergency hotline "311" which is available in many US cities, and may contain information pertaining to the performance of physical facilities, condition of the environment, or residents' experience, comfort and well-being. In this study, seven years of New York City 311 (NYC311) call during 2010-2016 is employed, as an alternative approach for identifying the areas of the city most prone to sewer back up flooding. These zones are compared with the hydrologic analysis of runoff flooding zones to provide a predictive model for the City. The proposed methodology is an example of urban system phenomenology using crowd sourced, open data. A novel algorithm for calculating the spatial distribution of flooding complaints across NYC's five boroughs is presented in this study. In this approach, the features that represent reporting bias are separated from those that relate to actual infrastructure system performance. The sewer backup results are assessed with the spatial distribution of runoff in NYC during 2010-2016. With advances in radar technologies, a high spatial-temporal resolution data set for precipitation is available for most of the United States that can be implemented in hydrologic analysis of dense urban environments. High resolution gridded Stage IV radar rainfall data along with the high resolution spatially distributed land cover data are employed to investigate the urban pluvial flooding. The monthly results of excess runoff are compared with the sewer backup in NYC to build a predictive model of flood zones according to the 311 phone calls.

A Messaging Infrastructure for WLCG

NASA Astrophysics Data System (ADS)

Casey, James; Cons, Lionel; Lapka, Wojciech; Paladin, Massimo; Skaburskas, Konstantin

2011-12-01

During the EGEE-III project operational tools such as SAM, Nagios, Gridview, the regional Dashboard and GGUS moved to a communication architecture based on ActiveMQ, an open-source enterprise messaging solution. LHC experiments, in particular ATLAS, developed prototypes of systems using the same messaging infrastructure, validating the system for their use-cases. In this paper we describe the WLCG messaging use cases and outline an improved messaging architecture based on the experience gained during the EGEE-III period. We show how this provides a solid basis for many applications, including the grid middleware, to improve their resilience and reliability.

Infrastructure for Multiphysics Software Integration in High Performance Computing-Aided Science and Engineering

DOE Office of Scientific and Technical Information (OSTI.GOV)

Campbell, Michael T.; Safdari, Masoud; Kress, Jessica E.

The project described in this report constructed and exercised an innovative multiphysics coupling toolkit called the Illinois Rocstar MultiPhysics Application Coupling Toolkit (IMPACT). IMPACT is an open source, flexible, natively parallel infrastructure for coupling multiple uniphysics simulation codes into multiphysics computational systems. IMPACT works with codes written in several high-performance-computing (HPC) programming languages, and is designed from the beginning for HPC multiphysics code development. It is designed to be minimally invasive to the individual physics codes being integrated, and has few requirements on those physics codes for integration. The goal of IMPACT is to provide the support needed to enablemore » coupling existing tools together in unique and innovative ways to produce powerful new multiphysics technologies without extensive modification and rewrite of the physics packages being integrated. There are three major outcomes from this project: 1) construction, testing, application, and open-source release of the IMPACT infrastructure, 2) production of example open-source multiphysics tools using IMPACT, and 3) identification and engagement of interested organizations in the tools and applications resulting from the project. This last outcome represents the incipient development of a user community and application echosystem being built using IMPACT. Multiphysics coupling standardization can only come from organizations working together to define needs and processes that span the space of necessary multiphysics outcomes, which Illinois Rocstar plans to continue driving toward. The IMPACT system, including source code, documentation, and test problems are all now available through the public gitHUB.org system to anyone interested in multiphysics code coupling. Many of the basic documents explaining use and architecture of IMPACT are also attached as appendices to this document. Online HTML documentation is available through the gitHUB site. There are over 100 unit tests provided that run through the Illinois Rocstar Application Development (IRAD) lightweight testing infrastructure that is also supplied along with IMPACT. The package as a whole provides an excellent base for developing high-quality multiphysics applications using modern software development practices. To facilitate understanding how to utilize IMPACT effectively, two multiphysics systems have been developed and are available open-source through gitHUB. The simpler of the two systems, named ElmerFoamFSI in the repository, is a multiphysics, fluid-structure-interaction (FSI) coupling of the solid mechanics package Elmer with a fluid dynamics module from OpenFOAM. This coupling illustrates how to combine software packages that are unrelated by either author or architecture and combine them into a robust, parallel multiphysics system. A more complex multiphysics tool is the Illinois Rocstar Rocstar Multiphysics code that was rebuilt during the project around IMPACT. Rocstar Multiphysics was already an HPC multiphysics tool, but now that it has been rearchitected around IMPACT, it can be readily expanded to capture new and different physics in the future. In fact, during this project, the Elmer and OpenFOAM tools were also coupled into Rocstar Multiphysics and demonstrated. The full Rocstar Multiphysics codebase is also available on gitHUB, and licensed for any organization to use as they wish. Finally, the new IMPACT product is already being used in several multiphysics code coupling projects for the Air Force, NASA and the Missile Defense Agency, and initial work on expansion of the IMPACT-enabled Rocstar Multiphysics has begun in support of a commercial company. These initiatives promise to expand the interest and reach of IMPACT and Rocstar Multiphysics, ultimately leading to the envisioned standardization and consortium of users that was one of the goals of this project.« less

OpenFDA: an innovative platform providing access to a wealth of FDA's publicly available data.

PubMed

Kass-Hout, Taha A; Xu, Zhiheng; Mohebbi, Matthew; Nelsen, Hans; Baker, Adam; Levine, Jonathan; Johanson, Elaine; Bright, Roselie A

2016-05-01

The objective of openFDA is to facilitate access and use of big important Food and Drug Administration public datasets by developers, researchers, and the public through harmonization of data across disparate FDA datasets provided via application programming interfaces (APIs). Using cutting-edge technologies deployed on FDA's new public cloud computing infrastructure, openFDA provides open data for easier, faster (over 300 requests per second per process), and better access to FDA datasets; open source code and documentation shared on GitHub for open community contributions of examples, apps and ideas; and infrastructure that can be adopted for other public health big data challenges. Since its launch on June 2, 2014, openFDA has developed four APIs for drug and device adverse events, recall information for all FDA-regulated products, and drug labeling. There have been more than 20 million API calls (more than half from outside the United States), 6000 registered users, 20,000 connected Internet Protocol addresses, and dozens of new software (mobile or web) apps developed. A case study demonstrates a use of openFDA data to understand an apparent association of a drug with an adverse event. With easier and faster access to these datasets, consumers worldwide can learn more about FDA-regulated products. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved.

OpenFDA: an innovative platform providing access to a wealth of FDA’s publicly available data

PubMed Central

Kass-Hout, Taha A; Mohebbi, Matthew; Nelsen, Hans; Baker, Adam; Levine, Jonathan; Johanson, Elaine; Bright, Roselie A

2016-01-01

Objective The objective of openFDA is to facilitate access and use of big important Food and Drug Administration public datasets by developers, researchers, and the public through harmonization of data across disparate FDA datasets provided via application programming interfaces (APIs). Materials and Methods Using cutting-edge technologies deployed on FDA’s new public cloud computing infrastructure, openFDA provides open data for easier, faster (over 300 requests per second per process), and better access to FDA datasets; open source code and documentation shared on GitHub for open community contributions of examples, apps and ideas; and infrastructure that can be adopted for other public health big data challenges. Results Since its launch on June 2, 2014, openFDA has developed four APIs for drug and device adverse events, recall information for all FDA-regulated products, and drug labeling. There have been more than 20 million API calls (more than half from outside the United States), 6000 registered users, 20,000 connected Internet Protocol addresses, and dozens of new software (mobile or web) apps developed. A case study demonstrates a use of openFDA data to understand an apparent association of a drug with an adverse event. Conclusion With easier and faster access to these datasets, consumers worldwide can learn more about FDA-regulated products. PMID:26644398

Application of crowd-sourced data to multi-scale evolutionary exposure and vulnerability models

NASA Astrophysics Data System (ADS)

Pittore, Massimiliano

2016-04-01

Seismic exposure, defined as the assets (population, buildings, infrastructure) exposed to earthquake hazard and susceptible to damage, is a critical -but often neglected- component of seismic risk assessment. This partly stems from the burden associated with the compilation of a useful and reliable model over wide spatial areas. While detailed engineering data have still to be collected in order to constrain exposure and vulnerability models, the availability of increasingly large crowd-sourced datasets (e. g. OpenStreetMap) opens up the exciting possibility to generate incrementally evolving models. Integrating crowd-sourced and authoritative data using statistical learning methodologies can reduce models uncertainties and also provide additional drive and motivation to volunteered geoinformation collection. A case study in Central Asia will be presented and discussed.

CosmoQuest: A Cyber-Infrastructure for Crowdsourcing Planetary Surface Mapping and More

NASA Astrophysics Data System (ADS)

Gay, P.; Lehan, C.; Moore, J.; Bracey, G.; Gugliucci, N.

2014-04-01

The design and implementation of programs to crowdsource science presents a unique set of challenges to system architects, programmers, and designers. The CosmoQuest Citizen Science Builder (CSB) is an open source platform designed to take advantage of crowd computing and open source platforms to solve crowdsourcing problems in Planetary Science. CSB combines a clean user interface with a powerful back end to allow the quick design and deployment of citizen science sites that meet the needs of both the random Joe Public, and the detail driven Albert Professional. In this talk, the software will be overviewed, and the results of usability testing and accuracy testing with both citizen and professional scientists will be discussed.

An informatics model for guiding assembly of telemicrobiology workstations for malaria collaborative diagnostics using commodity products and open-source software.

PubMed

Suhanic, West; Crandall, Ian; Pennefather, Peter

2009-07-17

Deficits in clinical microbiology infrastructure exacerbate global infectious disease burdens. This paper examines how commodity computation, communication, and measurement products combined with open-source analysis and communication applications can be incorporated into laboratory medicine microbiology protocols. Those commodity components are all now sourceable globally. An informatics model is presented for guiding the use of low-cost commodity components and free software in the assembly of clinically useful and usable telemicrobiology workstations. The model incorporates two general principles: 1) collaborative diagnostics, where free and open communication and networking applications are used to link distributed collaborators for reciprocal assistance in organizing and interpreting digital diagnostic data; and 2) commodity engineering, which leverages globally available consumer electronics and open-source informatics applications, to build generic open systems that measure needed information in ways substantially equivalent to more complex proprietary systems. Routine microscopic examination of Giemsa and fluorescently stained blood smears for diagnosing malaria is used as an example to validate the model. The model is used as a constraint-based guide for the design, assembly, and testing of a functioning, open, and commoditized telemicroscopy system that supports distributed acquisition, exploration, analysis, interpretation, and reporting of digital microscopy images of stained malarial blood smears while also supporting remote diagnostic tracking, quality assessment and diagnostic process development. The open telemicroscopy workstation design and use-process described here can address clinical microbiology infrastructure deficits in an economically sound and sustainable manner. It can boost capacity to deal with comprehensive measurement of disease and care outcomes in individuals and groups in a distributed and collaborative fashion. The workstation enables local control over the creation and use of diagnostic data, while allowing for remote collaborative support of diagnostic data interpretation and tracking. It can enable global pooling of malaria disease information and the development of open, participatory, and adaptable laboratory medicine practices. The informatic model highlights how the larger issue of access to generic commoditized measurement, information processing, and communication technology in both high- and low-income countries can enable diagnostic services that are much less expensive, but substantially equivalent to those currently in use in high-income countries.

ISTIMES Integrated System for Transport Infrastructures Surveillance and Monitoring by Electromagnetic Sensing

NASA Astrophysics Data System (ADS)

Argenti, M.; Giannini, V.; Averty, R.; Bigagli, L.; Dumoulin, J.

2012-04-01

The EC FP7 ISTIMES project has the goal of realizing an ICT-based system exploiting distributed and local sensors for non destructive electromagnetic monitoring in order to make critical transport infrastructures more reliable and safe. Higher situation awareness thanks to real time and detailed information and images of the controlled infrastructure status allows improving decision capabilities for emergency management stakeholders. Web-enabled sensors and a service-oriented approach are used as core of the architecture providing a sys-tem that adopts open standards (e.g. OGC SWE, OGC CSW etc.) and makes efforts to achieve full interoperability with other GMES and European Spatial Data Infrastructure initiatives as well as compliance with INSPIRE. The system exploits an open easily scalable network architecture to accommodate a wide range of sensors integrated with a set of tools for handling, analyzing and processing large data volumes from different organizations with different data models. Situation Awareness tools are also integrated in the system. Definition of sensor observations and services follows a metadata model based on the ISO 19115 Core set of metadata elements and the O&M model of OGC SWE. The ISTIMES infrastructure is based on an e-Infrastructure for geospatial data sharing, with a Data Cata-log that implements the discovery services for sensor data retrieval, acting as a broker through static connections based on standard SOS and WNS interfaces; a Decision Support component which helps decision makers providing support for data fusion and inference and generation of situation indexes; a Presentation component which implements system-users interaction services for information publication and rendering, by means of a WEB Portal using SOA design principles; A security framework using Shibboleth open source middleware based on the Security Assertion Markup Language supporting Single Sign On (SSO). ACKNOWLEDGEMENT - The research leading to these results has received funding from the European Community's Seventh Framework Programme (FP7/2007-2013) under Grant Agreement n° 225663

A data infrastructure for the assessment of health care performance: lessons from the BRIDGE-health project.

PubMed

Bernal-Delgado, Enrique; Estupiñán-Romero, Francisco

2018-01-01

The integration of different administrative data sources from a number of European countries has been shown useful in the assessment of unwarranted variations in health care performance. This essay describes the procedures used to set up a data infrastructure (e.g., data access and exchange, definition of the minimum common wealth of data required, and the development of the relational logic data model) and, the methods to produce trustworthy healthcare performance measurements (e.g., ontologies standardisation and quality assurance analysis). The paper ends providing some hints on how to use these lessons in an eventual European infrastructure on public health research and monitoring. Although the relational data infrastructure developed has been proven accurate, effective to compare health system performance across different countries, and efficient enough to deal with hundred of millions of episodes, the logic data model might not be responsive if the European infrastructure aims at including electronic health records and carrying out multi-cohort multi-intervention comparative effectiveness research. The deployment of a distributed infrastructure based on semantic interoperability, where individual data remain in-country and open-access scripts for data management and analysis travel around the hubs composing the infrastructure, might be a sensible way forward.

The Integration of CloudStack and OCCI/OpenNebula with DIRAC

NASA Astrophysics Data System (ADS)

Méndez Muñoz, Víctor; Fernández Albor, Víctor; Graciani Diaz, Ricardo; Casajús Ramo, Adriàn; Fernández Pena, Tomás; Merino Arévalo, Gonzalo; José Saborido Silva, Juan

2012-12-01

The increasing availability of Cloud resources is arising as a realistic alternative to the Grid as a paradigm for enabling scientific communities to access large distributed computing resources. The DIRAC framework for distributed computing is an easy way to efficiently access to resources from both systems. This paper explains the integration of DIRAC with two open-source Cloud Managers: OpenNebula (taking advantage of the OCCI standard) and CloudStack. These are computing tools to manage the complexity and heterogeneity of distributed data center infrastructures, allowing to create virtual clusters on demand, including public, private and hybrid clouds. This approach has required to develop an extension to the previous DIRAC Virtual Machine engine, which was developed for Amazon EC2, allowing the connection with these new cloud managers. In the OpenNebula case, the development has been based on the CernVM Virtual Software Appliance with appropriate contextualization, while in the case of CloudStack, the infrastructure has been kept more general, which permits other Virtual Machine sources and operating systems being used. In both cases, CernVM File System has been used to facilitate software distribution to the computing nodes. With the resulting infrastructure, the cloud resources are transparent to the users through a friendly interface, like the DIRAC Web Portal. The main purpose of this integration is to get a system that can manage cloud and grid resources at the same time. This particular feature pushes DIRAC to a new conceptual denomination as interware, integrating different middleware. Users from different communities do not need to care about the installation of the standard software that is available at the nodes, nor the operating system of the host machine which is transparent to the user. This paper presents an analysis of the overhead of the virtual layer, doing some tests to compare the proposed approach with the existing Grid solution. License Notice: Published under licence in Journal of Physics: Conference Series by IOP Publishing Ltd.

The Role of GIS and Data Librarians in Cyber-infrastructure Support and Governance

NASA Astrophysics Data System (ADS)

Branch, B. D.

2012-12-01

A governance road-map for cyber-infrastructure in the geosciences will include an intentional librarian core capable of technical skills that include GIS and open source support for data curation that involves all aspects of data life cycle management. Per Executive Order 12906 and other policy; spatial data, literacy, and curation are critical cyber-infrastructure needs in the near future. A formal earth science and space informatics librarian may be an outcome of such development. From e-science to e-research, STEM pipelines need librarians as critical data intermediaries in technical assistance and collaboration efforts with scientists' data and outreach needs. Future training concerns should advocate trans-disciplinary data science and policy skills that will be necessary for data management support and procurement.

SensorWeb Hub infrastructure for open access to scientific research data

NASA Astrophysics Data System (ADS)

de Filippis, Tiziana; Rocchi, Leandro; Rapisardi, Elena

2015-04-01

The sharing of research data is a new challenge for the scientific community that may benefit from a large amount of information to solve environmental issues and sustainability in agriculture and urban contexts. Prerequisites for this challenge is the development of an infrastructure that ensure access, management and preservation of data, technical support for a coordinated and harmonious management of data that, in the framework of Open Data Policies, should encourages the reuse and the collaboration. The neogeography and the citizen as sensors approach, highlight that new data sources need a new set of tools and practices so to collect, validate, categorize, and use / access these "crowdsourced" data, that integrate the data sets produced in the scientific field, thus "feeding" the overall available data for analysis and research. When the scientific community embraces the dimension of collaboration and sharing, access and re-use, in order to accept the open innovation approach, it should redesign and reshape the processes of data management: the challenges of technological and cultural innovation, enabled by web 2.0 technologies, bring to the scenario where the sharing of structured and interoperable data will constitute the unavoidable building block to set up a new paradigm of scientific research. In this perspective the Institute of Biometeorology, CNR, whose aim is contributing to sharing and development of research data, has developed the "SensorWebHub" (SWH) infrastructure to support the scientific activities carried out in several research projects at national and international level. It is designed to manage both mobile and fixed open source meteorological and environmental sensors, in order to integrate the existing agro-meteorological and urban monitoring networks. The proposed architecture uses open source tools to ensure sustainability in the development and deployment of web applications with geographic features and custom analysis, as requested by the different research projects. The SWH components are organized in typical client-server architecture and interact from the sensing process to the representation of the results to the end-users. The Web Application enables to view and analyse the data stored in the GeoDB. The interface is designed following Internet browsers specifications allowing the visualization of collected data in different formats (tabular, chart and geographic map). The services for the dissemination of geo-referenced information, adopt the OGC specifications. SWH is a bottom-up collaborative initiative to share real time research data and pave the way for a open innovation approach in the scientific research. Until now this framework has been used for several WebGIS applications and WebApp for environmental monitoring at different temporal and spatial scales.

Characterizing Crowd Participation and Productivity of Foldit Through Web Scraping

DTIC Science & Technology

2016-03-01

Berkeley Open Infrastructure for Network Computing CDF Cumulative Distribution Function CPU Central Processing Unit CSSG Crowdsourced Serious Game...computers at once can create a similar capacity. According to Anderson [6], principal investigator for the Berkeley Open Infrastructure for Network...extraterrestrial life. From this project, a software-based distributed computing platform called the Berkeley Open Infrastructure for Network Computing

A Platform for Innovation and Standards Evaluation: a Case Study from the OpenMRS Open-Source Radiology Information System.

PubMed

Gichoya, Judy W; Kohli, Marc; Ivange, Larry; Schmidt, Teri S; Purkayastha, Saptarshi

2018-05-10

Open-source development can provide a platform for innovation by seeking feedback from community members as well as providing tools and infrastructure to test new standards. Vendors of proprietary systems may delay adoption of new standards until there are sufficient incentives such as legal mandates or financial incentives to encourage/mandate adoption. Moreover, open-source systems in healthcare have been widely adopted in low- and middle-income countries and can be used to bridge gaps that exist in global health radiology. Since 2011, the authors, along with a community of open-source contributors, have worked on developing an open-source radiology information system (RIS) across two communities-OpenMRS and LibreHealth. The main purpose of the RIS is to implement core radiology workflows, on which others can build and test new radiology standards. This work has resulted in three major releases of the system, with current architectural changes driven by changing technology, development of new standards in health and imaging informatics, and changing user needs. At their core, both these communities are focused on building general-purpose EHR systems, but based on user contributions from the fringes, we have been able to create an innovative system that has been used by hospitals and clinics in four different countries. We provide an overview of the history of the LibreHealth RIS, the architecture of the system, overview of standards integration, describe challenges of developing an open-source product, and future directions. Our goal is to attract more participation and involvement to further develop the LibreHealth RIS into an Enterprise Imaging System that can be used in other clinical imaging including pathology and dermatology.

SAME4HPC: A Promising Approach in Building a Scalable and Mobile Environment for High-Performance Computing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Karthik, Rajasekar

2014-01-01

In this paper, an architecture for building Scalable And Mobile Environment For High-Performance Computing with spatial capabilities called SAME4HPC is described using cutting-edge technologies and standards such as Node.js, HTML5, ECMAScript 6, and PostgreSQL 9.4. Mobile devices are increasingly becoming powerful enough to run high-performance apps. At the same time, there exist a significant number of low-end and older devices that rely heavily on the server or the cloud infrastructure to do the heavy lifting. Our architecture aims to support both of these types of devices to provide high-performance and rich user experience. A cloud infrastructure consisting of OpenStack withmore » Ubuntu, GeoServer, and high-performance JavaScript frameworks are some of the key open-source and industry standard practices that has been adopted in this architecture.« less

Abstract - Cooperative Research and Development Agreement between Environmental Defense Fund and National Energy Technology Laboratory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rose, Kelly K.; Zavala-Zraiza, Daniel

Here, we summarize an effort to develop a global oil and gas infrastructure (GOGI) taxonomy and geodatabase, using a combination of big data computing, custom search and data integration algorithms, and expert driven spatio-temporal analytics to identify, access, and evaluate open oil and gas data resources and uncertainty trends worldwide. This approach leveraged custom National Energy Technology Laboratory (NETL) tools and capabilities in collaboration with Environmental Defense Fund (EDF) and Carbon Limits subject matter expertise, to identify over 380 datasets and integrate more than 4.8 million features into the GOGI database. In addition to acquisition of open oil and gasmore » infrastructure data, information was collected and analyzed to assess the spatial, temporal, and source quality of these resources, and estimate their completeness relative to the top 40 hydrocarbon producing and consuming countries.« less

SPARX, a new environment for Cryo-EM image processing.

PubMed

Hohn, Michael; Tang, Grant; Goodyear, Grant; Baldwin, P R; Huang, Zhong; Penczek, Pawel A; Yang, Chao; Glaeser, Robert M; Adams, Paul D; Ludtke, Steven J

2007-01-01

SPARX (single particle analysis for resolution extension) is a new image processing environment with a particular emphasis on transmission electron microscopy (TEM) structure determination. It includes a graphical user interface that provides a complete graphical programming environment with a novel data/process-flow infrastructure, an extensive library of Python scripts that perform specific TEM-related computational tasks, and a core library of fundamental C++ image processing functions. In addition, SPARX relies on the EMAN2 library and cctbx, the open-source computational crystallography library from PHENIX. The design of the system is such that future inclusion of other image processing libraries is a straightforward task. The SPARX infrastructure intelligently handles retention of intermediate values, even those inside programming structures such as loops and function calls. SPARX and all dependencies are free for academic use and available with complete source.

Virtualization of open-source secure web services to support data exchange in a pediatric critical care research network.

PubMed

Frey, Lewis J; Sward, Katherine A; Newth, Christopher J L; Khemani, Robinder G; Cryer, Martin E; Thelen, Julie L; Enriquez, Rene; Shaoyu, Su; Pollack, Murray M; Harrison, Rick E; Meert, Kathleen L; Berg, Robert A; Wessel, David L; Shanley, Thomas P; Dalton, Heidi; Carcillo, Joseph; Jenkins, Tammara L; Dean, J Michael

2015-11-01

To examine the feasibility of deploying a virtual web service for sharing data within a research network, and to evaluate the impact on data consistency and quality. Virtual machines (VMs) encapsulated an open-source, semantically and syntactically interoperable secure web service infrastructure along with a shadow database. The VMs were deployed to 8 Collaborative Pediatric Critical Care Research Network Clinical Centers. Virtual web services could be deployed in hours. The interoperability of the web services reduced format misalignment from 56% to 1% and demonstrated that 99% of the data consistently transferred using the data dictionary and 1% needed human curation. Use of virtualized open-source secure web service technology could enable direct electronic abstraction of data from hospital databases for research purposes. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Clarity: An Open Source Manager for Laboratory Automation

PubMed Central

Delaney, Nigel F.; Echenique, José Rojas; Marx, Christopher J.

2013-01-01

Software to manage automated laboratories interfaces with hardware instruments, gives users a way to specify experimental protocols, and schedules activities to avoid hardware conflicts. In addition to these basics, modern laboratories need software that can run multiple different protocols in parallel and that can be easily extended to interface with a constantly growing diversity of techniques and instruments. We present Clarity: a laboratory automation manager that is hardware agnostic, portable, extensible and open source. Clarity provides critical features including remote monitoring, robust error reporting by phone or email, and full state recovery in the event of a system crash. We discuss the basic organization of Clarity; demonstrate an example of its implementation for the automated analysis of bacterial growth; and describe how the program can be extended to manage new hardware. Clarity is mature; well documented; actively developed; written in C# for the Common Language Infrastructure; and is free and open source software. These advantages set Clarity apart from currently available laboratory automation programs. PMID:23032169

GRACKLE: a chemistry and cooling library for astrophysics

NASA Astrophysics Data System (ADS)

Smith, Britton D.; Bryan, Greg L.; Glover, Simon C. O.; Goldbaum, Nathan J.; Turk, Matthew J.; Regan, John; Wise, John H.; Schive, Hsi-Yu; Abel, Tom; Emerick, Andrew; O'Shea, Brian W.; Anninos, Peter; Hummels, Cameron B.; Khochfar, Sadegh

2017-04-01

We present the GRACKLE chemistry and cooling library for astrophysical simulations and models. GRACKLE provides a treatment of non-equilibrium primordial chemistry and cooling for H, D and He species, including H2 formation on dust grains; tabulated primordial and metal cooling; multiple ultraviolet background models; and support for radiation transfer and arbitrary heat sources. The library has an easily implementable interface for simulation codes written in C, C++ and FORTRAN as well as a PYTHON interface with added convenience functions for semi-analytical models. As an open-source project, GRACKLE provides a community resource for accessing and disseminating astrochemical data and numerical methods. We present the full details of the core functionality, the simulation and PYTHON interfaces, testing infrastructure, performance and range of applicability. GRACKLE is a fully open-source project and new contributions are welcome.

RAIN: A Bio-Inspired Communication and Data Storage Infrastructure.

PubMed

Monti, Matteo; Rasmussen, Steen

2017-01-01

We summarize the results and perspectives from a companion article, where we presented and evaluated an alternative architecture for data storage in distributed networks. We name the bio-inspired architecture RAIN, and it offers file storage service that, in contrast with current centralized cloud storage, has privacy by design, is open source, is more secure, is scalable, is more sustainable, has community ownership, is inexpensive, and is potentially faster, more efficient, and more reliable. We propose that a RAIN-style architecture could form the backbone of the Internet of Things that likely will integrate multiple current and future infrastructures ranging from online services and cryptocurrency to parts of government administration.

Modernized build and test infrastructure for control software at ESO: highly flexible building, testing, and automatic quality practices for telescope control software

NASA Astrophysics Data System (ADS)

Pellegrin, F.; Jeram, B.; Haucke, J.; Feyrin, S.

2016-07-01

The paper describes the introduction of a new automatized build and test infrastructure, based on the open-source software Jenkins1, into the ESO Very Large Telescope control software to replace the preexisting in-house solution. A brief introduction to software quality practices is given, a description of the previous solution, the limitations of it and new upcoming requirements. Modifications required to adapt the new system are described, how these were implemented to current software and the results obtained. An overview on how the new system may be used in future projects is also presented.

SLURM: Simple Linux Utility for Resource Management

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jette, M; Dunlap, C; Garlick, J

2002-07-08

Simple Linux Utility for Resource Management (SLURM) is an open source, fault-tolerant, and highly scalable cluster management and job scheduling system for Linux clusters of thousands of nodes. Components include machine status, partition management, job management, scheduling and stream copy modules. The design also includes a scalable, general-purpose communication infrastructure. This paper presents a overview of the SLURM architecture and functionality.

Linux Makes the Grade: An Open Source Solution That's Time Has Come

ERIC Educational Resources Information Center

Houston, Melissa

2007-01-01

In 2001, Indiana officials at the Department of Education were taking stock. The schools had an excellent network infrastructure and had installed significant numbers of computers for 1 million public school enrollees. Yet students were spending less than an hour a week on the computer. It was then that state officials knew each student needed a…

My care pathways - creating open innovation in healthcare.

PubMed

Lundberg, Nina; Koch, Sabine; Hägglund, Maria; Bolin, Peter; Davoody, Nadia; Eltes, Johan; Jarlman, Olof; Perlich, Anja; Vimarlund, Vivian; Winsnes, Casper

2013-01-01

In this paper we describe initial results from the Swedish innovation project "My Care Pathways" which envisions enabling citizens to track their own health by providing them with online access to their historical, current and prospective future events. We describe an information infrastructure and its base services as well as the use of this solution as an open source platform for open innovation in healthcare. This will facilitate the development of end-user e-services for citizens. We have technically enabled the information infrastructure in close collaboration with decision makers in three Swedish health care regions, and system vendors as well as with National eHealth projects. Close collaboration between heterogeneous actors made implementation in real practice possible. However, a number of challenges, mainly related to legal and business issues, persist when implementing our results. Future work should therefore target the development of business models for sustainable provision of end-user e-services in a public health care system such as the Swedish one. Also, a legal analysis of the development of third party provider (nonhealthcare based) personal health data e-services should be done.

Toward Knowledge Systems for Sustainability Science

NASA Astrophysics Data System (ADS)

Zaks, D. P.; Jahn, M.

2011-12-01

Managing ecosystems for the outcomes of agricultural productivity and resilience will require fundamentally different knowledge management systems. In the industrial paradigm of the 20th century, land was considered an open, unconstrained system managed for maximum yield. While dramatic increases in yield occurred in some crops and locations, unintended but often foreseeable consequences emerged. While productivity remains a key objective, we must develop analytic systems that can identify better management options for the full range of monetized and non-monetized inputs, outputs and outcomes that are captured in the following framing question: How much valued service (e.g. food, materials, energy) can we draw from a landscape while maintaining adequate levels of other valued or necessary services (e.g. biodiversity, water, climate regulation, cultural services) including the long-term productivity of the land? This question is placed within our contemporary framing of valued services, but structured to illuminate the shifts required to achieve long-term sufficiency and planetary resilience. This framing also highlights the need for fundamentally new knowledge systems including information management infrastructures, which effectively support decision-making on landscapes. The purpose of this initiative by authors from diverse fields across government and academic science is to call attention to the need for a vision and investment in sustainability science for landscape management. Substantially enhanced capabilities are needed to compare and integrate information from diverse sources, collected over time that link choices made to meet our needs from landscapes to both short and long term consequences. To further the goal of an information infrastructure for sustainability science, three distinct but interlocking domains are best distinguished: 1) a domain of data, information and knowledge assets; 2) a domain that houses relevant models and tools in a curated space; and 3) a domain that includes decision support tools and systems tailored toward frame particular trade-offs, which may focus on inputs or outputs and may range in scale from local to global. An information infrastructure for sustainability science is best built be built and maintained as a modular, open source, open standard, open access, open content platform. We have defined the scope of this challenge, managing choices within agroecosystems, recognizing that any decision on a landscape involves multidimensional tradeoffs. An effort to address this challenge will need a cohesive, coherent and targeted approach toward an integrated knowledge management infrastructure for sustainability science applied to land management is essential to move more rapidly toward sustainable, productive, and resilient landscapes.

Anti-social networking: crowdsourcing and the cyber defence of national critical infrastructures.

PubMed

Johnson, Chris W

2014-01-01

We identify four roles that social networking plays in the 'attribution problem', which obscures whether or not cyber-attacks were state-sponsored. First, social networks motivate individuals to participate in Distributed Denial of Service attacks by providing malware and identifying potential targets. Second, attackers use an individual's social network to focus attacks, through spear phishing. Recipients are more likely to open infected attachments when they come from a trusted source. Third, social networking infrastructures create disposable architectures to coordinate attacks through command and control servers. The ubiquitous nature of these architectures makes it difficult to determine who owns and operates the servers. Finally, governments recruit anti-social criminal networks to launch attacks on third-party infrastructures using botnets. The closing sections identify a roadmap to increase resilience against the 'dark side' of social networking.

Autonomous watersheds: Reducing flooding and stream erosion through real-time control

NASA Astrophysics Data System (ADS)

Kerkez, B.; Wong, B. P.

2017-12-01

We introduce an analytical toolchain, based on dynamical system theory and feedback control, to determine how many control points (valves, gates, pumps, etc.) are needed to transform urban watersheds from static to adaptive. Advances and distributed sensing and control stand to fundamentally change how we manage urban watersheds. In lieu of new and costly infrastructure, the real-time control of stormwater systems will reduce flooding, mitigate stream erosion, and improve the treatment of polluted runoff. We discuss the how open source technologies, in the form of wireless sensor nodes and remotely-controllable valves (open-storm.org), have been deployed to build "smart" stormwater systems in the Midwestern US. Unlike "static" infrastructure, which cannot readily adapt to changing inputs and land uses, these distributed control assets allow entire watersheds to be reconfigured on a storm-by-storm basis. Our results show how the control of even just a few valves within urban catchments (1-10km^2) allows for the real-time "shaping" of hydrographs, which reduces downstream erosion and flooding. We also introduce an equivalence framework that can be used by decision-makers to objectively compare investments into "smart" system to more traditional solutions, such as gray and green stormwater infrastructure.

2015 ESGF Progress Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Williams, D. N.

2015-06-22

The Earth System Grid Federation (ESGF) is a multi-agency, international collaboration whose purpose is to develop the software infrastructure needed to facilitate and empower the study of climate change on a global scale. ESGF’s architecture employs a system of geographically distributed peer nodes that are independently administered yet united by common federation protocols and application programming interfaces. The cornerstones of its interoperability are the peer-to-peer messaging, which is continuously exchanged among all nodes in the federation; a shared architecture for search and discovery; and a security infrastructure based on industry standards. ESGF integrates popular application engines available from the open-sourcemore » community with custom components (for data publishing, searching, user interface, security, and messaging) that were developed collaboratively by the team. The full ESGF infrastructure has now been adopted by multiple Earth science projects and allows access to petabytes of geophysical data, including the Coupled Model Intercomparison Project (CMIP)—output used by the Intergovernmental Panel on Climate Change assessment reports. ESGF is a successful example of integration of disparate open-source technologies into a cohesive functional system that serves the needs of the global climate science community.« less

Exploring social and infrastructural factors affecting open burning of municipal solid waste (MSW) in Indian cities: A comparative case study of three neighborhoods of Delhi.

PubMed

Ramaswami, Anu; Baidwan, Navneet Kaur; Nagpure, Ajay Singh

2016-11-01

Open municipal solid waste (MSW)-burning is a major source of particulate matter emissions in developing world cities. Despite a legal ban, MSW-burning is observed ubiquitously in Indian cities with little being known about the factors shaping it. This study seeks to uncover social and infrastructural factors that affect MSW-burning at the neighborhood level. We couple physical assessments of the infrastructure provision and the MSW-burning incidences in three different neighborhoods of varying socio-economic status in Delhi, with an accompanying study of the social actors (interviews of waste handlers and households) to explore the extent to which, and potential reasons why, MSW-burning occurs. The observed differences in MSW-burning incidences range from 130 km -2  day -1 in low-income to 30 km -2  day -1 in the high-income areas. However, two high-income areas neighborhoods with functional infrastructure service also showed statistical differences in MSW-burning incidences. Our interviews revealed that, while the waste handlers were aware of the health risks associated with MSW-burning, it was not a high priority in the context of the other difficulties they faced. The awareness of the legal ban on MSW-burning was low among both waste handlers and households. In addition to providing infrastructure for waste pickup, informal restrictions from residents and neighborhood associations can play a significant role in restricting MSW-burning at the neighborhood scale. A more efficient management of MSW requires a combined effort that involves interplay of both social and infrastructural systems. © The Author(s) 2016.

Photonics and terahertz tchnologies: part 1

NASA Astrophysics Data System (ADS)

Romaniuk, Ryszard S.

2011-10-01

This digest paper debates basic features of the terahertz band of frequencies. There are presented fundamental characteristics of the basic terahertz system consisting of a THz source, propagation media, transmission lines, THz signal processing, and detectors. Such a system finds research application, but also practical in two main areas: terahertz imaging - transmissive and reflective, and as a close range THz radar, but also as sensory systems mainly for molecular sensing. There were launched in this country a few THz research projects concerning the THz sources, detectors and their applications. Among these projects there is an infrastructural one called FOTEH, opened at the WUT. The details of this project are debated and the consequences of its realization in this country. The first part of the paper is an introduction debating THz band and comparing it with the photonics one. The second part presents the assumptions of the infrastructural FOTEH project on Photonics and Terahertz Technologies.

World Wind: NASA's Virtual Globe

NASA Astrophysics Data System (ADS)

Hogan, P.

2007-12-01

Virtual globes have set the standard for information exchange. Once you've experienced the visually rich and highly compelling nature of data delivered via virtual globes with their highly engaging context of 3D, it's hard to go back to a flat 2D world. Just as the sawbones of not-too-long-ago have given way to sophisticated surgical operating theater, today's medium for information exchange is just beginning to leap from the staid chalkboards and remote libraries to fingertip navigable 3D worlds. How we harness this technology to serve a world inundated with information will describe the quality of our future. Our instincts for discovery and entertainment urge us on. There's so much we could know if the world's knowledge was presented to us in its natural context. Virtual globes are almost magical in their ability to reveal natural wonders. Anyone flying along a chain of volcanoes, a mid-ocean ridge or deep ocean trench, while simultaneously seeing the different depths to the history of earthquakes in those areas, will be delighted to sense Earth's dynamic nature in a way that would otherwise take several paragraphs of "boring" text. The sophisticated concepts related to global climate change would be far more comprehensible when experienced via a virtual globe. There is a large universe of public and private geospatial data sets that virtual globes can bring to light. The benefit derived from access to this data within virtual globes represents a significant return on investment for government, industry, the general public, and especially in the realm of education. Data access remains a key issue. Just as the highway infrastructure allows unimpeded access from point A to point B, an open standards-based infrastructure for data access allows virtual globes to exchange data in the most efficient manner possible. This data can be either free or proprietary. The Open Geospatial Consortium is providing the leadership necessary for this open standards-based data access infrastructure. The open-source community plays a crucial role in advancing virtual globe technology. This world community identifies, tracks and resolves technical problems, suggests new features and source code modifications, and often provides high-resolution data sets and other types of user-generated content, all while extending the functionality of virtual globe technology. NASA World Wind is one example of open source virtual globe technology that provides the world with the ability to build any desired functionality and make any desired data accessible.

Social network of PESCA (Open Source Platform for eHealth).

PubMed

Sanchez, Carlos L; Romero-Cuevas, Miguel; Lopez, Diego M; Lorca, Julio; Alcazar, Francisco J; Ruiz, Sergio; Mercado, Carmen; Garcia-Fortea, Pedro

2008-01-01

Information and Communication Technologies (ICTs) are revolutionizing how healthcare systems deliver top-quality care to citizens. In this way, Open Source Software (OSS) has demonstrated to be an important strategy to spread ICTs use. Several human and technological barriers in adopting OSS for healthcare have been identified. Human barriers include user acceptance, limited support, technical skillfulness, awareness, resistance to change, etc., while Technological barriers embrace need for open standards, heterogeneous OSS developed without normalization and metrics, lack of initiatives to evaluate existing health OSS and need for quality control and functional validation. The goals of PESCA project are to create a platform of interoperable modules to evaluate, classify and validate good practices in health OSS. Furthermore, a normalization platform will provide interoperable solutions in the fields of healthcare services, health surveillance, health literature, and health education, knowledge and research. Within the platform, the first goal to achieve is the setup of the collaborative work infrastructure. The platform is being organized as a Social Network which works to evaluate five scopes of every existing open source tools for eHealth: Open Source Software, Quality, Pedagogical, Security and privacy and Internationalization/I18N. In the meantime, the knowledge collected from the networking will configure a Good Practice Repository on eHealth promoting the effective use of ICT on behalf of the citizen's health.

Model Based Verification of Cyber Range Event Environments

DTIC Science & Technology

2015-11-13

Commercial and Open Source Systems," in SOSP, Cascais, Portugal, 2011. [3] Sanjai Narain, Sharad Malik, and Ehab Al-Shaer, "Towards Eliminating...Configuration Errors in Cyber Infrastructure," in 4th IEEE Symposium on Configuration Analytics and Automation, Arlington, VA, 2011. [4] Sanjai Narain...Verlag, 2010. [5] Sanjai Narain, "Network Configuration Management via Model Finding," in 19th Large Installation System Administration Conference, San

Developing a WWW Resource Centre for Acquiring and Accessing Open Learning Materials on Research Methods (ReMOTE).

ERIC Educational Resources Information Center

Newton, Robert; Marcella, Rita; Middleton, Iain; McConnell, Michael

This paper reports on ReMOTE (Research Methods Online Teaching Environment), a Robert Gordon University (Scotland) project focusing on the development of a World Wide Web (WWW) site devoted to the teaching of research methods. The aim of ReMOTE is to provide an infrastructure that allows direct links to specialist sources in order to enable the…

Efficient Probabilistic Forecasting for High-Resolution Models through Clustered-State Data Assimilation

NASA Astrophysics Data System (ADS)

Hamidi, A.; Grossberg, M.; Khanbilvardi, R.

2016-12-01

Flood response in an urban area is the product of interactions of spatially and temporally varying rainfall and infrastructures. In urban areas, however, the complex sub-surface networks of tunnels, waste and storm water drainage systems are often inaccessible, pose challenges for modeling and prediction of the drainage infrastructure performance. The increased availability of open data in cities is an emerging information asset for a better understanding of the dynamics of urban water drainage infrastructure. This includes crowd sourced data and community reporting. A well-known source of this type of data is the non-emergency hotline "311" which is available in many US cities, and may contain information pertaining to the performance of physical facilities, condition of the environment, or residents' experience, comfort and well-being. In this study, seven years of New York City 311 (NYC311) call during 2010-2016 is employed, as an alternative approach for identifying the areas of the city most prone to sewer back up flooding. These zones are compared with the hydrologic analysis of runoff flooding zones to provide a predictive model for the City. The proposed methodology is an example of urban system phenomenology using crowd sourced, open data. A novel algorithm for calculating the spatial distribution of flooding complaints across NYC's five boroughs is presented in this study. In this approach, the features that represent reporting bias are separated from those that relate to actual infrastructure system performance. The sewer backup results are assessed with the spatial distribution of runoff in NYC during 2010-2016. With advances in radar technologies, a high spatial-temporal resolution data set for precipitation is available for most of the United States that can be implemented in hydrologic analysis of dense urban environments. High resolution gridded Stage IV radar rainfall data along with the high resolution spatially distributed land cover data are employed to investigate the urban pluvial flooding. The monthly results of excess runoff are compared with the sewer backup in NYC to build a predictive model of flood zones according to the 311 phone calls.

SLURM: Simple Linux Utility for Resource Management

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jette, M; Dunlap, C; Garlick, J

2002-04-24

Simple Linux Utility for Resource Management (SLURM) is an open source, fault-tolerant, and highly scalable cluster management and job scheduling system for Linux clusters of thousands of nodes. Components include machine status, partition management, job management, and scheduling modules. The design also includes a scalable, general-purpose communication infrastructure. Development will take place in four phases: Phase I results in a solid infrastructure; Phase II produces a functional but limited interactive job initiation capability without use of the interconnect/switch; Phase III provides switch support and documentation; Phase IV provides job status, fault-tolerance, and job queuing and control through Livermore's Distributed Productionmore » Control System (DPCS), a meta-batch and resource management system.« less

LLVM Infrastructure and Tools Project Summary

DOE Office of Scientific and Technical Information (OSTI.GOV)

McCormick, Patrick Sean

2017-11-06

This project works with the open source LLVM Compiler Infrastructure (http://llvm.org) to provide tools and capabilities that address needs and challenges faced by ECP community (applications, libraries, and other components of the software stack). Our focus is on providing a more productive development environment that enables (i) improved compilation times and code generation for parallelism, (ii) additional features/capabilities within the design and implementations of LLVM components for improved platform/performance portability and (iii) improved aspects related to composition of the underlying implementation details of the programming environment, capturing resource utilization, overheads, etc. -- including runtime systems that are often not easilymore » addressed by application and library developers.« less

Virtualized Networks and Virtualized Optical Line Terminal (vOLT)

NASA Astrophysics Data System (ADS)

Ma, Jonathan; Israel, Stephen

2017-03-01

The success of the Internet and the proliferation of the Internet of Things (IoT) devices is forcing telecommunications carriers to re-architecture a central office as a datacenter (CORD) so as to bring the datacenter economics and cloud agility to a central office (CO). The Open Network Operating System (ONOS) is the first open-source software-defined network (SDN) operating system which is capable of managing and controlling network, computing, and storage resources to support CORD infrastructure and network virtualization. The virtualized Optical Line Termination (vOLT) is one of the key components in such virtualized networks.

Do Open Source LMSs Support Personalization? A Comparative Evaluation

NASA Astrophysics Data System (ADS)

Kerkiri, Tania; Paleologou, Angela-Maria

A number of parameters that support the LMSs capabilities towards content personalization are presented and substantiated. These parameters constitute critical criteria for an exhaustive investigation of the personalization capabilities of the most popular open source LMSs. Results are comparatively shown and commented upon, thus highlighting a course of conduct for the implementation of new personalization methodologies for these LMSs, aligned at their existing infrastructure, to maintain support of the numerous educational institutions entrusting major part of their curricula to them. Meanwhile, new capabilities arise as drawn from a more efficient description of the existing resources -especially when organized into widely available repositories- that lead to qualitatively advanced learner-oriented courses which would ideally meet the challenge of combining personification of demand and personalization of thematic content at once.

Monitoring of the infrastructure and services used to handle and automatically produce Alignment and Calibration conditions at CMS

NASA Astrophysics Data System (ADS)

Sipos, Roland; Govi, Giacomo; Franzoni, Giovanni; Di Guida, Salvatore; Pfeiffer, Andreas

2017-10-01

The CMS experiment at CERN LHC has a dedicated infrastructure to handle the alignment and calibration data. This infrastructure is composed of several services, which take on various data management tasks required for the consumption of the non-event data (also called as condition data) in the experiment activities. The criticality of these tasks imposes tights requirements for the availability and the reliability of the services executing them. In this scope, a comprehensive monitoring and alarm generating system has been developed. The system has been implemented based on the Nagios open source industry standard for monitoring and alerting services, and monitors the database back-end, the hosting nodes and key heart-beat functionalities for all the services involved. This paper describes the design, implementation and operational experience with the monitoring system developed and deployed at CMS in 2016.

Scalable Collaborative Infrastructure for a Learning Healthcare System (SCILHS): Architecture

PubMed Central

Mandl, Kenneth D; Kohane, Isaac S; McFadden, Douglas; Weber, Griffin M; Natter, Marc; Mandel, Joshua; Schneeweiss, Sebastian; Weiler, Sarah; Klann, Jeffrey G; Bickel, Jonathan; Adams, William G; Ge, Yaorong; Zhou, Xiaobo; Perkins, James; Marsolo, Keith; Bernstam, Elmer; Showalter, John; Quarshie, Alexander; Ofili, Elizabeth; Hripcsak, George; Murphy, Shawn N

2014-01-01

We describe the architecture of the Patient Centered Outcomes Research Institute (PCORI) funded Scalable Collaborative Infrastructure for a Learning Healthcare System (SCILHS, http://www.SCILHS.org) clinical data research network, which leverages the $48 billion dollar federal investment in health information technology (IT) to enable a queryable semantic data model across 10 health systems covering more than 8 million patients, plugging universally into the point of care, generating evidence and discovery, and thereby enabling clinician and patient participation in research during the patient encounter. Central to the success of SCILHS is development of innovative ‘apps’ to improve PCOR research methods and capacitate point of care functions such as consent, enrollment, randomization, and outreach for patient-reported outcomes. SCILHS adapts and extends an existing national research network formed on an advanced IT infrastructure built with open source, free, modular components. PMID:24821734

Sustaining Open Source Communities through Hackathons - An Example from the ASPECT Community

NASA Astrophysics Data System (ADS)

Heister, T.; Hwang, L.; Bangerth, W.; Kellogg, L. H.

2016-12-01

The ecosystem surrounding a successful scientific open source software package combines both social and technical aspects. Much thought has been given to the technology side of writing sustainable software for large infrastructure projects and software libraries, but less about building the human capacity to perpetuate scientific software used in computational modeling. One effective format for building capacity is regular multi-day hackathons. Scientific hackathons bring together a group of science domain users and scientific software contributors to make progress on a specific software package. Innovation comes through the chance to work with established and new collaborations. Especially in the domain sciences with small communities, hackathons give geographically distributed scientists an opportunity to connect face-to-face. They foster lively discussions amongst scientists with different expertise, promote new collaborations, and increase transparency in both the technical and scientific aspects of code development. ASPECT is an open source, parallel, extensible finite element code to simulate thermal convection, that began development in 2011 under the Computational Infrastructure for Geodynamics. ASPECT hackathons for the past 3 years have grown the number of authors to >50, training new code maintainers in the process. Hackathons begin with leaders establishing project-specific conventions for development, demonstrating the workflow for code contributions, and reviewing relevant technical skills. Each hackathon expands the developer community. Over 20 scientists add >6,000 lines of code during the >1 week event. Participants grow comfortable contributing to the repository and over half continue to contribute afterwards. A high return rate of participants ensures continuity and stability of the group as well as mentoring for novice members. We hope to build other software communities on this model, but anticipate each to bring their own unique challenges.

Roadmap for cardiovascular circulation model

PubMed Central

Bradley, Christopher P.; Suresh, Vinod; Mithraratne, Kumar; Muller, Alexandre; Ho, Harvey; Ladd, David; Hellevik, Leif R.; Omholt, Stig W.; Chase, J. Geoffrey; Müller, Lucas O.; Watanabe, Sansuke M.; Blanco, Pablo J.; de Bono, Bernard; Hunter, Peter J.

2016-01-01

Abstract Computational models of many aspects of the mammalian cardiovascular circulation have been developed. Indeed, along with orthopaedics, this area of physiology is one that has attracted much interest from engineers, presumably because the equations governing blood flow in the vascular system are well understood and can be solved with well‐established numerical techniques. Unfortunately, there have been only a few attempts to create a comprehensive public domain resource for cardiovascular researchers. In this paper we propose a roadmap for developing an open source cardiovascular circulation model. The model should be registered to the musculo‐skeletal system. The computational infrastructure for the cardiovascular model should provide for near real‐time computation of blood flow and pressure in all parts of the body. The model should deal with vascular beds in all tissues, and the computational infrastructure for the model should provide links into CellML models of cell function and tissue function. In this work we review the literature associated with 1D blood flow modelling in the cardiovascular system, discuss model encoding standards, software and a model repository. We then describe the coordinate systems used to define the vascular geometry, derive the equations and discuss the implementation of these coupled equations in the open source computational software OpenCMISS. Finally, some preliminary results are presented and plans outlined for the next steps in the development of the model, the computational software and the graphical user interface for accessing the model. PMID:27506597

Roadmap for cardiovascular circulation model.

PubMed

Safaei, Soroush; Bradley, Christopher P; Suresh, Vinod; Mithraratne, Kumar; Muller, Alexandre; Ho, Harvey; Ladd, David; Hellevik, Leif R; Omholt, Stig W; Chase, J Geoffrey; Müller, Lucas O; Watanabe, Sansuke M; Blanco, Pablo J; de Bono, Bernard; Hunter, Peter J

2016-12-01

Computational models of many aspects of the mammalian cardiovascular circulation have been developed. Indeed, along with orthopaedics, this area of physiology is one that has attracted much interest from engineers, presumably because the equations governing blood flow in the vascular system are well understood and can be solved with well-established numerical techniques. Unfortunately, there have been only a few attempts to create a comprehensive public domain resource for cardiovascular researchers. In this paper we propose a roadmap for developing an open source cardiovascular circulation model. The model should be registered to the musculo-skeletal system. The computational infrastructure for the cardiovascular model should provide for near real-time computation of blood flow and pressure in all parts of the body. The model should deal with vascular beds in all tissues, and the computational infrastructure for the model should provide links into CellML models of cell function and tissue function. In this work we review the literature associated with 1D blood flow modelling in the cardiovascular system, discuss model encoding standards, software and a model repository. We then describe the coordinate systems used to define the vascular geometry, derive the equations and discuss the implementation of these coupled equations in the open source computational software OpenCMISS. Finally, some preliminary results are presented and plans outlined for the next steps in the development of the model, the computational software and the graphical user interface for accessing the model. © 2016 The Authors. The Journal of Physiology © 2016 The Physiological Society.

Scaling the CERN OpenStack cloud

NASA Astrophysics Data System (ADS)

Bell, T.; Bompastor, B.; Bukowiec, S.; Castro Leon, J.; Denis, M. K.; van Eldik, J.; Fermin Lobo, M.; Fernandez Alvarez, L.; Fernandez Rodriguez, D.; Marino, A.; Moreira, B.; Noel, B.; Oulevey, T.; Takase, W.; Wiebalck, A.; Zilli, S.

2015-12-01

CERN has been running a production OpenStack cloud since July 2013 to support physics computing and infrastructure services for the site. In the past year, CERN Cloud Infrastructure has seen a constant increase in nodes, virtual machines, users and projects. This paper will present what has been done in order to make the CERN cloud infrastructure scale out.

Design for Connecting Spatial Data Infrastructures with Sensor Web (sensdi)

NASA Astrophysics Data System (ADS)

Bhattacharya, D.; M., M.

2016-06-01

Integrating Sensor Web With Spatial Data Infrastructures (SENSDI) aims to extend SDIs with sensor web enablement, converging geospatial and built infrastructure, and implement test cases with sensor data and SDI. It is about research to harness the sensed environment by utilizing domain specific sensor data to create a generalized sensor webframework. The challenges being semantic enablement for Spatial Data Infrastructures, and connecting the interfaces of SDI with interfaces of Sensor Web. The proposed research plan is to Identify sensor data sources, Setup an open source SDI, Match the APIs and functions between Sensor Web and SDI, and Case studies like hazard applications, urban applications etc. We take up co-operative development of SDI best practices to enable a new realm of a location enabled and semantically enriched World Wide Web - the "Geospatial Web" or "Geosemantic Web" by setting up one to one correspondence between WMS, WFS, WCS, Metadata and 'Sensor Observation Service' (SOS); 'Sensor Planning Service' (SPS); 'Sensor Alert Service' (SAS); a service that facilitates asynchronous message interchange between users and services, and between two OGC-SWE services, called the 'Web Notification Service' (WNS). Hence in conclusion, it is of importance to geospatial studies to integrate SDI with Sensor Web. The integration can be done through merging the common OGC interfaces of SDI and Sensor Web. Multi-usability studies to validate integration has to be undertaken as future research.

Crowd-Sourced Help with Emergent Knowledge for Optimized Formal Verification (CHEKOFV)

DTIC Science & Technology

2016-03-01

up game Binary Fission, which was deployed during Phase Two of CHEKOFV. Xylem: The Code of Plants is a casual game for players using mobile ...there are the design and engineering challenges of building a game infrastructure that integrates verification technology with crowd participation...the backend processes that annotate the originating software. Allowing players to construct their own equations opened up the flexibility to receive

JNDMS Task Authorization 2 Report

DTIC Science & Technology

2013-10-01

uses Barnyard to store alarms from all DREnet Snort sensors in a MySQL database. Barnyard is an open source tool designed to work with Snort to take...Technology ITI Information Technology Infrastructure J2EE Java 2 Enterprise Edition JAR Java Archive. This is an archive file format defined by Java ...standards. JDBC Java Database Connectivity JDW JNDMS Data Warehouse JNDMS Joint Network and Defence Management System JNDMS Joint Network Defence and

Virtual Hubs for facilitating access to Open Data

NASA Astrophysics Data System (ADS)

Mazzetti, Paolo; Latre, Miguel Á.; Ernst, Julia; Brumana, Raffaella; Brauman, Stefan; Nativi, Stefano

2015-04-01

In October 2014 the ENERGIC-OD (European NEtwork for Redistributing Geospatial Information to user Communities - Open Data) project, funded by the European Union under the Competitiveness and Innovation framework Programme (CIP), has started. In response to the EU call, the general objective of the project is to "facilitate the use of open (freely available) geographic data from different sources for the creation of innovative applications and services through the creation of Virtual Hubs". In ENERGIC-OD, Virtual Hubs are conceived as information systems supporting the full life cycle of Open Data: publishing, discovery and access. They facilitate the use of Open Data by lowering and possibly removing the main barriers which hampers geo-information (GI) usage by end-users and application developers. Data and data services heterogeneity is recognized as one of the major barriers to Open Data (re-)use. It imposes end-users and developers to spend a lot of effort in accessing different infrastructures and harmonizing datasets. Such heterogeneity cannot be completely removed through the adoption of standard specifications for service interfaces, metadata and data models, since different infrastructures adopt different standards to answer to specific challenges and to address specific use-cases. Thus, beyond a certain extent, heterogeneity is irreducible especially in interdisciplinary contexts. ENERGIC-OD Virtual Hubs address heterogeneity adopting a mediation and brokering approach: specific components (brokers) are dedicated to harmonize service interfaces, metadata and data models, enabling seamless discovery and access to heterogeneous infrastructures and datasets. As an innovation project, ENERGIC-OD will integrate several existing technologies to implement Virtual Hubs as single points of access to geospatial datasets provided by new or existing platforms and infrastructures, including INSPIRE-compliant systems and Copernicus services. ENERGIC OD will deploy a set of five Virtual Hubs (VHs) at national level in France, Germany, Italy, Poland, Spain and an additional one at the European level. VHs will be provided according to the cloud Software-as-a-Services model. The main expected impact of VHs is the creation of new business opportunities opening up access to Research Data and Public Sector Information. Therefore, ENERGIC-OD addresses not only end-users, who will have the opportunity to access the VH through a geo-portal, but also application developers who will be able to access VH functionalities through simple Application Programming Interfaces (API). ENERGIC-OD Consortium will develop ten different applications on top of the deployed VHs. They aim to demonstrate how VHs facilitate the development of new and multidisciplinary applications based on the full exploitation of (open) GI, hence stimulating innovation and business activities.

BluePyOpt: Leveraging Open Source Software and Cloud Infrastructure to Optimise Model Parameters in Neuroscience.

PubMed

Van Geit, Werner; Gevaert, Michael; Chindemi, Giuseppe; Rössert, Christian; Courcol, Jean-Denis; Muller, Eilif B; Schürmann, Felix; Segev, Idan; Markram, Henry

2016-01-01

At many scales in neuroscience, appropriate mathematical models take the form of complex dynamical systems. Parameterizing such models to conform to the multitude of available experimental constraints is a global non-linear optimisation problem with a complex fitness landscape, requiring numerical techniques to find suitable approximate solutions. Stochastic optimisation approaches, such as evolutionary algorithms, have been shown to be effective, but often the setting up of such optimisations and the choice of a specific search algorithm and its parameters is non-trivial, requiring domain-specific expertise. Here we describe BluePyOpt, a Python package targeted at the broad neuroscience community to simplify this task. BluePyOpt is an extensible framework for data-driven model parameter optimisation that wraps and standardizes several existing open-source tools. It simplifies the task of creating and sharing these optimisations, and the associated techniques and knowledge. This is achieved by abstracting the optimisation and evaluation tasks into various reusable and flexible discrete elements according to established best-practices. Further, BluePyOpt provides methods for setting up both small- and large-scale optimisations on a variety of platforms, ranging from laptops to Linux clusters and cloud-based compute infrastructures. The versatility of the BluePyOpt framework is demonstrated by working through three representative neuroscience specific use cases.

Lowering the barriers to computational modeling of Earth's surface: coupling Jupyter Notebooks with Landlab, HydroShare, and CyberGIS for research and education.

NASA Astrophysics Data System (ADS)

Bandaragoda, C.; Castronova, A. M.; Phuong, J.; Istanbulluoglu, E.; Strauch, R. L.; Nudurupati, S. S.; Tarboton, D. G.; Wang, S. W.; Yin, D.; Barnhart, K. R.; Tucker, G. E.; Hutton, E.; Hobley, D. E. J.; Gasparini, N. M.; Adams, J. M.

2017-12-01

The ability to test hypotheses about hydrology, geomorphology and atmospheric processes is invaluable to research in the era of big data. Although community resources are available, there remain significant educational, logistical and time investment barriers to their use. Knowledge infrastructure is an emerging intellectual framework to understand how people are creating, sharing and distributing knowledge - which has been dramatically transformed by Internet technologies. In addition to the technical and social components in a cyberinfrastructure system, knowledge infrastructure considers educational, institutional, and open source governance components required to advance knowledge. We are designing an infrastructure environment that lowers common barriers to reproducing modeling experiments for earth surface investigation. Landlab is an open-source modeling toolkit for building, coupling, and exploring two-dimensional numerical models. HydroShare is an online collaborative environment for sharing hydrologic data and models. CyberGIS-Jupyter is an innovative cyberGIS framework for achieving data-intensive, reproducible, and scalable geospatial analytics using the Jupyter Notebook based on ROGER - the first cyberGIS supercomputer, so that models that can be elastically reproduced through cloud computing approaches. Our team of geomorphologists, hydrologists, and computer geoscientists has created a new infrastructure environment that combines these three pieces of software to enable knowledge discovery. Through this novel integration, any user can interactively execute and explore their shared data and model resources. Landlab on HydroShare with CyberGIS-Jupyter supports the modeling continuum from fully developed modelling applications, prototyping new science tools, hands on research demonstrations for training workshops, and classroom applications. Computational geospatial models based on big data and high performance computing can now be more efficiently developed, improved, scaled, and seamlessly reproduced among multidisciplinary users, thereby expanding the active learning curriculum and research opportunities for students in earth surface modeling and informatics.

The Federal Geospatial Platform a shared infrastructure for publishing, discovering and exploiting public data and spatial applications.

NASA Astrophysics Data System (ADS)

Dabolt, T. O.

2016-12-01

The proliferation of open data and data services continues to thrive and is creating new challenges on how researchers, policy analysts and other decision makes can quickly discover and use relevant data. While traditional metadata catalog approaches used by applications such as data.gov prove to be useful starting points for data search they can quickly frustrate end users who are seeking ways to quickly find and then use data in machine to machine environs. The Geospatial Platform is overcoming these obstacles and providing end users and applications developers a richer more productive user experience. The Geospatial Platform leverages a collection of open source and commercial technology hosted on Amazon Web Services providing an ecosystem of services delivering trusted, consistent data in open formats to all users as well as a shared infrastructure for federal partners to serve their spatial data assets. It supports a diverse array of communities of practice ranging on topics from the 16 National Geospatial Data Assets Themes, to homeland security and climate adaptation. Come learn how you can contribute your data and leverage others or check it out on your own at https://www.geoplatform.gov/

Open Data in Global Environmental Research: The Belmont Forum's Open Data Survey.

PubMed

Schmidt, Birgit; Gemeinholzer, Birgit; Treloar, Andrew

2016-01-01

This paper presents the findings of the Belmont Forum's survey on Open Data which targeted the global environmental research and data infrastructure community. It highlights users' perceptions of the term "open data", expectations of infrastructure functionalities, and barriers and enablers for the sharing of data. A wide range of good practice examples was pointed out by the respondents which demonstrates a substantial uptake of data sharing through e-infrastructures and a further need for enhancement and consolidation. Among all policy responses, funder policies seem to be the most important motivator. This supports the conclusion that stronger mandates will strengthen the case for data sharing.

Managing and Integrating Open Environmental Data - Technological Requirements and Challenges

NASA Astrophysics Data System (ADS)

Devaraju, Anusuriya; Kunkel, Ralf; Jirka, Simon

2014-05-01

Understanding environment conditions and trends requires information. This information is usually generated from sensor observations. Today, several infrastructures (e.g., GEOSS, EarthScope, NEON, NETLAKE, OOI, TERENO, WASCAL, and PEER-EurAqua) have been deployed to promote full and open exchange of environmental data. Standards for interfaces as well as data models/formats (OGC, CUAHSI, INSPIRE, SEE Grid, ISO) and open source tools have been developed to support seamless data exchange between various domains and organizations. In spite of this growing interest, it remains a challenge to manage and integrate open environmental data on the fly due to the distributed and heterogeneous nature of the data. Intuitive tools and standardized interfaces are vital to hide the technical complexity of underlying data management infrastructures. Meaningful descriptions of raw sensor data are necessary to achieve interoperability among different sources. As raw sensor data sets usually goes through several layers of summarization and aggregation, metadata and quality measures associated with these should be captured. Further processing of sensor data sets requires that they should be made compatible with existing environmental models. We need data policies and management plans on how to handle and publish open sensor data coming from different institutions. Clearly, a better management and usability of open environmental data is crucial, not only to gather large amounts of data, but also to cater various aspects such as data integration, privacy and trust, uncertainty, quality control, visualization, and data management policies. The proposed talk presents several key findings in terms of requirements, ongoing developments and technical challenges concerning these aspects from our recent work. This includes two workshops on open observation data and supporting tools, as well as the long-term environmental monitoring initiatives such as TERENO and TERENO-MED. Workshops Details: Spin the Sensor Web: Sensor Web Workshop 2013, Muenster, 21st-22nd November 2013 (http://52north.org/news/spin-the-sensor-web-sensor-web-workshop-2013) Special Session on Management of Open Environmental Observation Data - MOEOD 2014, Lisbon, 8th January 2014 (http://www.sensornets.org/MOEOD.aspx?y=2014) Monitoring Networks: TERENO : http://teodoor.icg.kfa-juelich.de/ TERENO-MED : http://www.tereno-med.net/

Open Clients for Distributed Databases

NASA Astrophysics Data System (ADS)

Chayes, D. N.; Arko, R. A.

2001-12-01

We are actively developing a collection of open source example clients that demonstrate use of our "back end" data management infrastructure. The data management system is reported elsewhere at this meeting (Arko and Chayes: A Scaleable Database Infrastructure). In addition to their primary goal of being examples for others to build upon, some of these clients may have limited utility in them selves. More information about the clients and the data infrastructure is available on line at http://data.ldeo.columbia.edu. The available examples to be demonstrated include several web-based clients including those developed for the Community Review System of the Digital Library for Earth System Education, a real-time watch standers log book, an offline interface to use log book entries, a simple client to search on multibeam metadata and others are Internet enabled and generally web-based front ends that support searches against one or more relational databases using industry standard SQL queries. In addition to the web based clients, simple SQL searches from within Excel and similar applications will be demonstrated. By defining, documenting and publishing a clear interface to the fully searchable databases, it becomes relatively easy to construct client interfaces that are optimized for specific applications in comparison to building a monolithic data and user interface system.

78 FR 60279 - Notice of Open Meeting of the Environmental Financial Advisory Board (EFAB)

Federal Register 2010, 2011, 2012, 2013, 2014

2013-10-01

... costs; increasing public and private investment; and building state, local, and tribal financial... Infrastructure Investment; and Green Infrastructure. The meeting is open to the public, however, seating is...

Removing a barrier to computer-based outbreak and disease surveillance--the RODS Open Source Project.

PubMed

Espino, Jeremy U; Wagner, M; Szczepaniak, C; Tsui, F C; Su, H; Olszewski, R; Liu, Z; Chapman, W; Zeng, X; Ma, L; Lu, Z; Dara, J

2004-09-24

Computer-based outbreak and disease surveillance requires high-quality software that is well-supported and affordable. Developing software in an open-source framework, which entails free distribution and use of software and continuous, community-based software development, can produce software with such characteristics, and can do so rapidly. The objective of the Real-Time Outbreak and Disease Surveillance (RODS) Open Source Project is to accelerate the deployment of computer-based outbreak and disease surveillance systems by writing software and catalyzing the formation of a community of users, developers, consultants, and scientists who support its use. The University of Pittsburgh seeded the Open Source Project by releasing the RODS software under the GNU General Public License. An infrastructure was created, consisting of a website, mailing lists for developers and users, designated software developers, and shared code-development tools. These resources are intended to encourage growth of the Open Source Project community. Progress is measured by assessing website usage, number of software downloads, number of inquiries, number of system deployments, and number of new features or modules added to the code base. During September--November 2003, users generated 5,370 page views of the project website, 59 software downloads, 20 inquiries, one new deployment, and addition of four features. Thus far, health departments and companies have been more interested in using the software as is than in customizing or developing new features. The RODS laboratory anticipates that after initial installation has been completed, health departments and companies will begin to customize the software and contribute their enhancements to the public code base.

A generic open-source software framework supporting scenario simulations in bioterrorist crises.

PubMed

Falenski, Alexander; Filter, Matthias; Thöns, Christian; Weiser, Armin A; Wigger, Jan-Frederik; Davis, Matthew; Douglas, Judith V; Edlund, Stefan; Hu, Kun; Kaufman, James H; Appel, Bernd; Käsbohrer, Annemarie

2013-09-01

Since the 2001 anthrax attack in the United States, awareness of threats originating from bioterrorism has grown. This led internationally to increased research efforts to improve knowledge of and approaches to protecting human and animal populations against the threat from such attacks. A collaborative effort in this context is the extension of the open-source Spatiotemporal Epidemiological Modeler (STEM) simulation and modeling software for agro- or bioterrorist crisis scenarios. STEM, originally designed to enable community-driven public health disease models and simulations, was extended with new features that enable integration of proprietary data as well as visualization of agent spread along supply and production chains. STEM now provides a fully developed open-source software infrastructure supporting critical modeling tasks such as ad hoc model generation, parameter estimation, simulation of scenario evolution, estimation of effects of mitigation or management measures, and documentation. This open-source software resource can be used free of charge. Additionally, STEM provides critical features like built-in worldwide data on administrative boundaries, transportation networks, or environmental conditions (eg, rainfall, temperature, elevation, vegetation). Users can easily combine their own confidential data with built-in public data to create customized models of desired resolution. STEM also supports collaborative and joint efforts in crisis situations by extended import and export functionalities. In this article we demonstrate specifically those new software features implemented to accomplish STEM application in agro- or bioterrorist crisis scenarios.

Open-Source Software in Computational Research: A Case Study

DOE PAGES

Syamlal, Madhava; O'Brien, Thomas J.; Benyahia, Sofiane; ...

2008-01-01

A case study of open-source (OS) development of the computational research software MFIX, used for multiphase computational fluid dynamics simulations, is presented here. The verification and validation steps required for constructing modern computational software and the advantages of OS development in those steps are discussed. The infrastructure used for enabling the OS development of MFIX is described. The impact of OS development on computational research and education in gas-solids flow, as well as the dissemination of information to other areas such as geophysical and volcanology research, is demonstrated. This study shows that the advantages of OS development were realized inmore » the case of MFIX: verification by many users, which enhances software quality; the use of software as a means for accumulating and exchanging information; the facilitation of peer review of the results of computational research.« less

The management challenge for household waste in emerging economies like Brazil: realistic source separation and activation of reverse logistics.

PubMed

Fehr, M

2014-09-01

Business opportunities in the household waste sector in emerging economies still evolve around the activities of bulk collection and tipping with an open material balance. This research, conducted in Brazil, pursued the objective of shifting opportunities from tipping to reverse logistics in order to close the balance. To do this, it illustrated how specific knowledge of sorted waste composition and reverse logistics operations can be used to determine realistic temporal and quantitative landfill diversion targets in an emerging economy context. Experimentation constructed and confirmed the recycling trilogy that consists of source separation, collection infrastructure and reverse logistics. The study on source separation demonstrated the vital difference between raw and sorted waste compositions. Raw waste contained 70% biodegradable and 30% inert matter. Source separation produced 47% biodegradable, 20% inert and 33% mixed material. The study on collection infrastructure developed the necessary receiving facilities. The study on reverse logistics identified private operators capable of collecting and processing all separated inert items. Recycling activities for biodegradable material were scarce and erratic. Only farmers would take the material as animal feed. No composting initiatives existed. The management challenge was identified as stimulating these activities in order to complete the trilogy and divert the 47% source-separated biodegradable discards from the landfills. © The Author(s) 2014.

Experience of public procurement of Open Compute servers

NASA Astrophysics Data System (ADS)

Bärring, Olof; Guerri, Marco; Bonfillou, Eric; Valsan, Liviu; Grigore, Alexandru; Dore, Vincent; Gentit, Alain; Clement, Benoît; Grossir, Anthony

2015-12-01

The Open Compute Project. OCP (http://www.opencompute.org/). was launched by Facebook in 2011 with the objective of building efficient computing infrastructures at the lowest possible cost. The technologies are released as open hardware. with the goal to develop servers and data centres following the model traditionally associated with open source software projects. In 2013 CERN acquired a few OCP servers in order to compare performance and power consumption with standard hardware. The conclusions were that there are sufficient savings to motivate an attempt to procure a large scale installation. One objective is to evaluate if the OCP market is sufficiently mature and broad enough to meet the constraints of a public procurement. This paper summarizes this procurement. which started in September 2014 and involved the Request for information (RFI) to qualify bidders and Request for Tender (RFT).

Soil Monitor: an open source web application for real-time soil sealing monitoring and assessment

NASA Astrophysics Data System (ADS)

Langella, Giuliano; Basile, Angelo; Giannecchini, Simone; Iamarino, Michela; Munafò, Michele; Terribile, Fabio

2016-04-01

Soil sealing is one of the most important causes of land degradation and desertification. In Europe, soil covered by impermeable materials has increased by about 80% from the Second World War till nowadays, while population has only grown by one third. There is an increasing concern at the high political levels about the need to attenuate imperviousness itself and its effects on soil functions. European Commission promulgated a roadmap (COM(2011) 571) by which the net land take would be zero by 2050. Furthermore, European Commission also published a report in 2011 providing best practices and guidelines for limiting soil sealing and imperviousness. In this scenario, we developed an open source and an open source based Soil Sealing Geospatial Cyber Infrastructure (SS-GCI) named as "Soil Monitor". This tool merges a webGIS with parallel geospatial computation in a fast and dynamic fashion in order to provide real-time assessments of soil sealing at high spatial resolution (20 meters and below) over the whole Italy. Common open source webGIS packages are used to implement both the data management and visualization infrastructures, such as GeoServer and MapStore. The high-speed geospatial computation is ensured by a GPU parallelism using the CUDA (Computing Unified Device Architecture) framework by NVIDIA®. This kind of parallelism required the writing - from scratch - all codes needed to fulfil the geospatial computation built behind the soil sealing toolbox. The combination of GPU computing with webGIS infrastructures is relatively novel and required particular attention at the Java-CUDA programming interface. As a result, Soil Monitor is smart because it can perform very high time-consuming calculations (querying for instance an Italian administrative region as area of interest) in less than one minute. The web application is embedded in a web browser and nothing must be installed before using it. Potentially everybody can use it, but the main targets are the stakeholders dealing with sealing, such as policy makers, land owners and asphalt/cement companies. As a matter of fact, Soil Monitor can be used to improve the spatial planning therefore limiting the progression of disordered soil sealing which causes both the direct loss of soils due to imperviousness but also the indirect loss caused by fragmentation of soils (which has different negative effects on the durability of soil functions, such as habitat corridors). Further, in a future version, Soil Monitor would estimate the best location for a new building or help compensating soil losses by actions in other areas to offset drawbacks at zero. The presented SS-GCI dealing with soil sealing - if opportunely scaled - would aid the implementation of best practices for limiting soil sealing or mitigating its effects on soil functions.

Open Data in Global Environmental Research: The Belmont Forum’s Open Data Survey

PubMed Central

Schmidt, Birgit; Gemeinholzer, Birgit; Treloar, Andrew

2016-01-01

This paper presents the findings of the Belmont Forum’s survey on Open Data which targeted the global environmental research and data infrastructure community. It highlights users’ perceptions of the term “open data”, expectations of infrastructure functionalities, and barriers and enablers for the sharing of data. A wide range of good practice examples was pointed out by the respondents which demonstrates a substantial uptake of data sharing through e-infrastructures and a further need for enhancement and consolidation. Among all policy responses, funder policies seem to be the most important motivator. This supports the conclusion that stronger mandates will strengthen the case for data sharing. PMID:26771577

Mapping, Awareness, and Virtualization Network Administrator Training Tool (MAVNATT) Architecture and Framework

DTIC Science & Technology

2015-06-01

unit may setup and teardown the entire tactical infrastructure multiple times per day. This tactical network administrator training is a critical...language and runs on Linux and Unix based systems. All provisioning is based around the Nagios Core application, a powerful backend solution for network...start up a large number of virtual machines quickly. CORE supports the simulation of fixed and mobile networks. CORE is open-source, written in Python

The AppScale Cloud Platform

PubMed Central

Krintz, Chandra

2013-01-01

AppScale is an open source distributed software system that implements a cloud platform as a service (PaaS). AppScale makes cloud applications easy to deploy and scale over disparate cloud fabrics, implementing a set of APIs and architecture that also makes apps portable across the services they employ. AppScale is API-compatible with Google App Engine (GAE) and thus executes GAE applications on-premise or over other cloud infrastructures, without modification. PMID:23828721

OpenCyto: An Open Source Infrastructure for Scalable, Robust, Reproducible, and Automated, End-to-End Flow Cytometry Data Analysis

PubMed Central

Finak, Greg; Frelinger, Jacob; Jiang, Wenxin; Newell, Evan W.; Ramey, John; Davis, Mark M.; Kalams, Spyros A.; De Rosa, Stephen C.; Gottardo, Raphael

2014-01-01

Flow cytometry is used increasingly in clinical research for cancer, immunology and vaccines. Technological advances in cytometry instrumentation are increasing the size and dimensionality of data sets, posing a challenge for traditional data management and analysis. Automated analysis methods, despite a general consensus of their importance to the future of the field, have been slow to gain widespread adoption. Here we present OpenCyto, a new BioConductor infrastructure and data analysis framework designed to lower the barrier of entry to automated flow data analysis algorithms by addressing key areas that we believe have held back wider adoption of automated approaches. OpenCyto supports end-to-end data analysis that is robust and reproducible while generating results that are easy to interpret. We have improved the existing, widely used core BioConductor flow cytometry infrastructure by allowing analysis to scale in a memory efficient manner to the large flow data sets that arise in clinical trials, and integrating domain-specific knowledge as part of the pipeline through the hierarchical relationships among cell populations. Pipelines are defined through a text-based csv file, limiting the need to write data-specific code, and are data agnostic to simplify repetitive analysis for core facilities. We demonstrate how to analyze two large cytometry data sets: an intracellular cytokine staining (ICS) data set from a published HIV vaccine trial focused on detecting rare, antigen-specific T-cell populations, where we identify a new subset of CD8 T-cells with a vaccine-regimen specific response that could not be identified through manual analysis, and a CyTOF T-cell phenotyping data set where a large staining panel and many cell populations are a challenge for traditional analysis. The substantial improvements to the core BioConductor flow cytometry packages give OpenCyto the potential for wide adoption. It can rapidly leverage new developments in computational cytometry and facilitate reproducible analysis in a unified environment. PMID:25167361

OpenCyto: an open source infrastructure for scalable, robust, reproducible, and automated, end-to-end flow cytometry data analysis.

PubMed

Finak, Greg; Frelinger, Jacob; Jiang, Wenxin; Newell, Evan W; Ramey, John; Davis, Mark M; Kalams, Spyros A; De Rosa, Stephen C; Gottardo, Raphael

2014-08-01

Flow cytometry is used increasingly in clinical research for cancer, immunology and vaccines. Technological advances in cytometry instrumentation are increasing the size and dimensionality of data sets, posing a challenge for traditional data management and analysis. Automated analysis methods, despite a general consensus of their importance to the future of the field, have been slow to gain widespread adoption. Here we present OpenCyto, a new BioConductor infrastructure and data analysis framework designed to lower the barrier of entry to automated flow data analysis algorithms by addressing key areas that we believe have held back wider adoption of automated approaches. OpenCyto supports end-to-end data analysis that is robust and reproducible while generating results that are easy to interpret. We have improved the existing, widely used core BioConductor flow cytometry infrastructure by allowing analysis to scale in a memory efficient manner to the large flow data sets that arise in clinical trials, and integrating domain-specific knowledge as part of the pipeline through the hierarchical relationships among cell populations. Pipelines are defined through a text-based csv file, limiting the need to write data-specific code, and are data agnostic to simplify repetitive analysis for core facilities. We demonstrate how to analyze two large cytometry data sets: an intracellular cytokine staining (ICS) data set from a published HIV vaccine trial focused on detecting rare, antigen-specific T-cell populations, where we identify a new subset of CD8 T-cells with a vaccine-regimen specific response that could not be identified through manual analysis, and a CyTOF T-cell phenotyping data set where a large staining panel and many cell populations are a challenge for traditional analysis. The substantial improvements to the core BioConductor flow cytometry packages give OpenCyto the potential for wide adoption. It can rapidly leverage new developments in computational cytometry and facilitate reproducible analysis in a unified environment.

78 FR 57644 - Critical Infrastructure Partnership Advisory Council (CIPAC)

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-19

... DEPARTMENT OF HOMELAND SECURITY [Docket No. DHS-2103-0050] Critical Infrastructure Partnership... management; Notice of an open Federal Advisory Committee Meeting. SUMMARY: The Critical Infrastructure... involving critical infrastructure security and resiliency. Off-topic questions or comments will not be...

C3-PRO: Connecting ResearchKit to the Health System Using i2b2 and FHIR.

PubMed

Pfiffner, Pascal B; Pinyol, Isaac; Natter, Marc D; Mandl, Kenneth D

2016-01-01

A renewed interest by consumer information technology giants in the healthcare domain is focused on transforming smartphones into personal health data storage devices. With the introduction of the open source ResearchKit, Apple provides a framework for researchers to inform and consent research subjects, and to readily collect personal health data and patient reported outcomes (PRO) from distributed populations. However, being research backend agnostic, ResearchKit does not provide data transmission facilities, leaving research apps disconnected from the health system. Personal health data and PROs are of the most value when presented in context along with health system data. Our aim was to build a toolchain that allows easy and secure integration of personal health and PRO data into an open source platform widely adopted across 140 academic medical centers. We present C3-PRO: the Consent, Contact, and Community framework for Patient Reported Outcomes. This open source toolchain connects, in a standards-compliant fashion, any ResearchKit app to the widely-used clinical research infrastructure Informatics for Integrating Biology and the Bedside (i2b2). C3-PRO leverages the emerging health data standard Fast Healthcare Interoperability Resources (FHIR).

Open source pipeline for ESPaDOnS reduction and analysis

NASA Astrophysics Data System (ADS)

Martioli, Eder; Teeple, Doug; Manset, Nadine; Devost, Daniel; Withington, Kanoa; Venne, Andre; Tannock, Megan

2012-09-01

OPERA is a Canada-France-Hawaii Telescope (CFHT) open source collaborative software project currently under development for an ESPaDOnS echelle spectro-polarimetric image reduction pipeline. OPERA is designed to be fully automated, performing calibrations and reduction, producing one-dimensional intensity and polarimetric spectra. The calibrations are performed on two-dimensional images. Spectra are extracted using an optimal extraction algorithm. While primarily designed for CFHT ESPaDOnS data, the pipeline is being written to be extensible to other echelle spectrographs. A primary design goal is to make use of fast, modern object-oriented technologies. Processing is controlled by a harness, which manages a set of processing modules, that make use of a collection of native OPERA software libraries and standard external software libraries. The harness and modules are completely parametrized by site configuration and instrument parameters. The software is open- ended, permitting users of OPERA to extend the pipeline capabilities. All these features have been designed to provide a portable infrastructure that facilitates collaborative development, code re-usability and extensibility. OPERA is free software with support for both GNU/Linux and MacOSX platforms. The pipeline is hosted on SourceForge under the name "opera-pipeline".

C3-PRO: Connecting ResearchKit to the Health System Using i2b2 and FHIR

PubMed Central

Pfiffner, Pascal B.; Pinyol, Isaac; Natter, Marc D.; Mandl, Kenneth D.

2016-01-01

A renewed interest by consumer information technology giants in the healthcare domain is focused on transforming smartphones into personal health data storage devices. With the introduction of the open source ResearchKit, Apple provides a framework for researchers to inform and consent research subjects, and to readily collect personal health data and patient reported outcomes (PRO) from distributed populations. However, being research backend agnostic, ResearchKit does not provide data transmission facilities, leaving research apps disconnected from the health system. Personal health data and PROs are of the most value when presented in context along with health system data. Our aim was to build a toolchain that allows easy and secure integration of personal health and PRO data into an open source platform widely adopted across 140 academic medical centers. We present C3-PRO: the Consent, Contact, and Community framework for Patient Reported Outcomes. This open source toolchain connects, in a standards-compliant fashion, any ResearchKit app to the widely-used clinical research infrastructure Informatics for Integrating Biology and the Bedside (i2b2). C3-PRO leverages the emerging health data standard Fast Healthcare Interoperability Resources (FHIR). PMID:27031856

Low-cost embedded systems for democratizing ocean sensor technology in the coastal zone

NASA Astrophysics Data System (ADS)

Glazer, B. T.; Lio, H. I.

2017-12-01

Environmental sciences suffer from undersampling. Enabling sustained and unattended data collection in the coastal zone typically involves expensive instrumentation and infrastructure deployed as cabled observatories or moorings with little flexibility in deployment location following initial installation. High costs of commercially-available or custom instruments have limited the number of sensor sites that can be targeted by academic researchers, and have also limited engagement with the public. We have developed a novel, low-cost, open-source sensor and software platform to enable wireless data transfer of biogeochemical sensors in the coastal zone. The platform is centered upon widely available, low-cost, single board computers and microcontrollers. We have used a blend of on-hand research-grade sensors and low-cost open-source electronics that can be assembled by tech-savvy non-engineers. Robust, open-source code that remains customizable for specific miniNode configurations can match a specific site's measurement needs, depending on the scientific research priorities. We have demonstrated prototype capabilities and versatility through lab testing and field deployments of multiple sensor nodes with multiple sensor inputs, all of which are streaming near-real-time data from Kaneohe Bay over wireless RF links to a shore-based base station.

Scalable Collaborative Infrastructure for a Learning Healthcare System (SCILHS): architecture.

PubMed

Mandl, Kenneth D; Kohane, Isaac S; McFadden, Douglas; Weber, Griffin M; Natter, Marc; Mandel, Joshua; Schneeweiss, Sebastian; Weiler, Sarah; Klann, Jeffrey G; Bickel, Jonathan; Adams, William G; Ge, Yaorong; Zhou, Xiaobo; Perkins, James; Marsolo, Keith; Bernstam, Elmer; Showalter, John; Quarshie, Alexander; Ofili, Elizabeth; Hripcsak, George; Murphy, Shawn N

2014-01-01

We describe the architecture of the Patient Centered Outcomes Research Institute (PCORI) funded Scalable Collaborative Infrastructure for a Learning Healthcare System (SCILHS, http://www.SCILHS.org) clinical data research network, which leverages the $48 billion dollar federal investment in health information technology (IT) to enable a queryable semantic data model across 10 health systems covering more than 8 million patients, plugging universally into the point of care, generating evidence and discovery, and thereby enabling clinician and patient participation in research during the patient encounter. Central to the success of SCILHS is development of innovative 'apps' to improve PCOR research methods and capacitate point of care functions such as consent, enrollment, randomization, and outreach for patient-reported outcomes. SCILHS adapts and extends an existing national research network formed on an advanced IT infrastructure built with open source, free, modular components. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Cloudweaver: Adaptive and Data-Driven Workload Manager for Generic Clouds

NASA Astrophysics Data System (ADS)

Li, Rui; Chen, Lei; Li, Wen-Syan

Cloud computing denotes the latest trend in application development for parallel computing on massive data volumes. It relies on clouds of servers to handle tasks that used to be managed by an individual server. With cloud computing, software vendors can provide business intelligence and data analytic services for internet scale data sets. Many open source projects, such as Hadoop, offer various software components that are essential for building a cloud infrastructure. Current Hadoop (and many others) requires users to configure cloud infrastructures via programs and APIs and such configuration is fixed during the runtime. In this chapter, we propose a workload manager (WLM), called CloudWeaver, which provides automated configuration of a cloud infrastructure for runtime execution. The workload management is data-driven and can adapt to dynamic nature of operator throughput during different execution phases. CloudWeaver works for a single job and a workload consisting of multiple jobs running concurrently, which aims at maximum throughput using a minimum set of processors.

Jali - Unstructured Mesh Infrastructure for Multi-Physics Applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Garimella, Rao V; Berndt, Markus; Coon, Ethan

2017-04-13

Jali is a parallel unstructured mesh infrastructure library designed for use by multi-physics simulations. It supports 2D and 3D arbitrary polyhedral meshes distributed over hundreds to thousands of nodes. Jali can read write Exodus II meshes along with fields and sets on the mesh and support for other formats is partially implemented or is (https://github.com/MeshToolkit/MSTK), an open source general purpose unstructured mesh infrastructure library from Los Alamos National Laboratory. While it has been made to work with other mesh frameworks such as MOAB and STKmesh in the past, support for maintaining the interface to these frameworks has been suspended formore » now. Jali supports distributed as well as on-node parallelism. Support of on-node parallelism is through direct use of the the mesh in multi-threaded constructs or through the use of "tiles" which are submeshes or sub-partitions of a partition destined for a compute node.« less

Big-BOE: Fusing Spanish Official Gazette with Big Data Technology.

PubMed

Basanta-Val, Pablo; Sánchez-Fernández, Luis

2018-06-01

The proliferation of new data sources, stemmed from the adoption of open-data schemes, in combination with an increasing computing capacity causes the inception of new type of analytics that process Internet of things with low-cost engines to speed up data processing using parallel computing. In this context, the article presents an initiative, called BIG-Boletín Oficial del Estado (BOE), designed to process the Spanish official government gazette (BOE) with state-of-the-art processing engines, to reduce computation time and to offer additional speed up for big data analysts. The goal of including a big data infrastructure is to be able to process different BOE documents in parallel with specific analytics, to search for several issues in different documents. The application infrastructure processing engine is described from an architectural perspective and from performance, showing evidence on how this type of infrastructure improves the performance of different types of simple analytics as several machines cooperate.

caCORE: a common infrastructure for cancer informatics.

PubMed

Covitz, Peter A; Hartel, Frank; Schaefer, Carl; De Coronado, Sherri; Fragoso, Gilberto; Sahni, Himanso; Gustafson, Scott; Buetow, Kenneth H

2003-12-12

Sites with substantive bioinformatics operations are challenged to build data processing and delivery infrastructure that provides reliable access and enables data integration. Locally generated data must be processed and stored such that relationships to external data sources can be presented. Consistency and comparability across data sets requires annotation with controlled vocabularies and, further, metadata standards for data representation. Programmatic access to the processed data should be supported to ensure the maximum possible value is extracted. Confronted with these challenges at the National Cancer Institute Center for Bioinformatics, we decided to develop a robust infrastructure for data management and integration that supports advanced biomedical applications. We have developed an interconnected set of software and services called caCORE. Enterprise Vocabulary Services (EVS) provide controlled vocabulary, dictionary and thesaurus services. The Cancer Data Standards Repository (caDSR) provides a metadata registry for common data elements. Cancer Bioinformatics Infrastructure Objects (caBIO) implements an object-oriented model of the biomedical domain and provides Java, Simple Object Access Protocol and HTTP-XML application programming interfaces. caCORE has been used to develop scientific applications that bring together data from distinct genomic and clinical science sources. caCORE downloads and web interfaces can be accessed from links on the caCORE web site (http://ncicb.nci.nih.gov/core). caBIO software is distributed under an open source license that permits unrestricted academic and commercial use. Vocabulary and metadata content in the EVS and caDSR, respectively, is similarly unrestricted, and is available through web applications and FTP downloads. http://ncicb.nci.nih.gov/core/publications contains links to the caBIO 1.0 class diagram and the caCORE 1.0 Technical Guide, which provide detailed information on the present caCORE architecture, data sources and APIs. Updated information appears on a regular basis on the caCORE web site (http://ncicb.nci.nih.gov/core).

Perspectives in understanding open access to research data - infrastructure and technology challenges

NASA Astrophysics Data System (ADS)

Bigagli, Lorenzo; Sondervan, Jeroen

2014-05-01

The Policy RECommendations for Open Access to Research Data in Europe (RECODE) project, started in February 2013 with a duration of two years, has the objective to identify a series of targeted and over-arching policy recommendations for Open Access to European research data, based on existing good practice and addressing such hindering factors as stakeholder fragmentation, technical and infrastructural issues, ethical and legal issues, and financial and institutional policies. In this work we focus on the technical and infrastructural aspect, where by "infrastructure" we mean the technological assets (hardware and software), the human resources, and all the policies, processes, procedures and training for managing and supporting its continuous operation and evolution. The context targeted by RECODE includes heterogeneous networks, initiatives, projects and communities that are fragmented by discipline, geography, stakeholder category (publishers, academics, repositories, etc.) as well as other boundaries. Many of these organizations are already addressing key technical and infrastructural barriers to Open Access to research data. Such barriers may include: lack of automatic mechanisms for policy enforcement, lack of metadata and data models supporting open access, obsolescence of infrastructures, scarce awareness about new technological solutions, lack of training and/or expertise on IT and semantics aspects. However, these organizations are often heterogeneous and fragmented by discipline, geography, stakeholder category (publishers, academics, repositories, etc.) as well as other boundaries, and often work in isolation, or with limited contact with one another. RECODE has addressed these challenges, and the possible solutions to mitigate them, engaging all the identified stakeholders in a number of ways, including an online questionnaire, case studies interviews, literature review, a workshop. The conclusions have been validated by the RECODE Advisory Board and will contribute to shape the RECODE policy guidelines for Open Access to Research Data. In the work, we report on the identified technological and infrastructural issues, classified according to the barriers of heterogeneity, sustainability, volume, quality, and security.

3rd Annual Earth System Grid Federation and 3rd Annual Earth System Grid Federation and Ultrascale Visualization Climate Data Analysis Tools Face-to-Face Meeting Report December 2013

DOE Office of Scientific and Technical Information (OSTI.GOV)

Williams, Dean N.

The climate and weather data science community gathered December 3–5, 2013, at Lawrence Livermore National Laboratory, in Livermore, California, for the third annual Earth System Grid Federation (ESGF) and Ultra-scale Visualization Climate Data Analysis Tools (UV-CDAT) Face-to-Face (F2F) Meeting, which was hosted by the Department of Energy, National Aeronautics and Space Administration, National Oceanic and Atmospheric Administration, the European Infrastructure for the European Network of Earth System Modelling, and the Australian Department of Education. Both ESGF and UV-CDAT are global collaborations designed to develop a new generation of open-source software infrastructure that provides distributed access and analysis to observed andmore » simulated data from the climate and weather communities. The tools and infrastructure developed under these international multi-agency collaborations are critical to understanding extreme weather conditions and long-term climate change, while the F2F meetings help to build a stronger climate and weather data science community and stronger federated software infrastructure. The 2013 F2F meeting determined requirements for existing and impending national and international community projects; enhancements needed for data distribution, analysis, and visualization infrastructure; and standards and resources needed for better collaborations.« less

OpenFlyData: an exemplar data web integrating gene expression data on the fruit fly Drosophila melanogaster.

PubMed

Miles, Alistair; Zhao, Jun; Klyne, Graham; White-Cooper, Helen; Shotton, David

2010-10-01

Integrating heterogeneous data across distributed sources is a major requirement for in silico bioinformatics supporting translational research. For example, genome-scale data on patterns of gene expression in the fruit fly Drosophila melanogaster are widely used in functional genomic studies in many organisms to inform candidate gene selection and validate experimental results. However, current data integration solutions tend to be heavy weight, and require significant initial and ongoing investment of effort. Development of a common Web-based data integration infrastructure (a.k.a. data web), using Semantic Web standards, promises to alleviate these difficulties, but little is known about the feasibility, costs, risks or practical means of migrating to such an infrastructure. We describe the development of OpenFlyData, a proof-of-concept system integrating gene expression data on D. melanogaster, combining Semantic Web standards with light-weight approaches to Web programming based on Web 2.0 design patterns. To support researchers designing and validating functional genomic studies, OpenFlyData includes user-facing search applications providing intuitive access to and comparison of gene expression data from FlyAtlas, the BDGP in situ database, and FlyTED, using data from FlyBase to expand and disambiguate gene names. OpenFlyData's services are also openly accessible, and are available for reuse by other bioinformaticians and application developers. Semi-automated methods and tools were developed to support labour- and knowledge-intensive tasks involved in deploying SPARQL services. These include methods for generating ontologies and relational-to-RDF mappings for relational databases, which we illustrate using the FlyBase Chado database schema; and methods for mapping gene identifiers between databases. The advantages of using Semantic Web standards for biomedical data integration are discussed, as are open issues. In particular, although the performance of open source SPARQL implementations is sufficient to query gene expression data directly from user-facing applications such as Web-based data fusions (a.k.a. mashups), we found open SPARQL endpoints to be vulnerable to denial-of-service-type problems, which must be mitigated to ensure reliability of services based on this standard. These results are relevant to data integration activities in translational bioinformatics. The gene expression search applications and SPARQL endpoints developed for OpenFlyData are deployed at http://openflydata.org. FlyUI, a library of JavaScript widgets providing re-usable user-interface components for Drosophila gene expression data, is available at http://flyui.googlecode.com. Software and ontologies to support transformation of data from FlyBase, FlyAtlas, BDGP and FlyTED to RDF are available at http://openflydata.googlecode.com. SPARQLite, an implementation of the SPARQL protocol, is available at http://sparqlite.googlecode.com. All software is provided under the GPL version 3 open source license.

Getting Open Source Right for Big Data Analytics: Software Sharing, Governance, Collaboration and Most of All, Fun!

NASA Astrophysics Data System (ADS)

Mattmann, C. A.

2013-12-01

A wave of open source big data analytic infrastructure is currently shaping government, private sector, and academia. Projects are consuming, adapting, and contributing back to various ecosystems of software e.g., the Apache Hadoop project and its ecosystem of related efforts including Hive, HBase, Pig, Oozie, Ambari, Knox, Tez and Yarn, to name a few; the Berkeley AMPLab stack which includes Spark, Shark, Mesos, Tachyon, BlinkDB, MLBase, and other emerging efforts; MapR and its related stack of technologies, offerings from commercial companies building products around these tools e.g., Hortonworks Data Platform (HDP), Cloudera's CDH project, etc. Though the technologies all offer different capabilities including low latency support/in-memory, versus record oriented file I/O, high availability, support for the Map Reduce programming paradigm or other dataflow/workflow constructs, there is a common thread that binds these products - they are all released under an open source license e.g., Apache2, MIT, BSD, GPL/LGPL, etc.; all thrive in various ecosystems, such as Apache, or Berkeley AMPLab; all are developed collaboratively, and all technologies provide plug in architecture models and methodologies for allowing others to contribute, and participate via various community models. This talk will cover the open source aspects and governance aspects of the aforementioned Big Data ecosystems and point out the differences, subtleties, and implications of those differences. The discussion will be by example, using several national deployments and Big Data initiatives stemming from the Administration including DARPA's XDATA program; NASA's CMAC program; NSF's EarthCube and geosciences BigData projects. Lessons learned from these efforts in terms of the open source aspects of these technologies will help guide the AGU community in their use, deployment and understanding.

BluePyOpt: Leveraging Open Source Software and Cloud Infrastructure to Optimise Model Parameters in Neuroscience

PubMed Central

Van Geit, Werner; Gevaert, Michael; Chindemi, Giuseppe; Rössert, Christian; Courcol, Jean-Denis; Muller, Eilif B.; Schürmann, Felix; Segev, Idan; Markram, Henry

2016-01-01

At many scales in neuroscience, appropriate mathematical models take the form of complex dynamical systems. Parameterizing such models to conform to the multitude of available experimental constraints is a global non-linear optimisation problem with a complex fitness landscape, requiring numerical techniques to find suitable approximate solutions. Stochastic optimisation approaches, such as evolutionary algorithms, have been shown to be effective, but often the setting up of such optimisations and the choice of a specific search algorithm and its parameters is non-trivial, requiring domain-specific expertise. Here we describe BluePyOpt, a Python package targeted at the broad neuroscience community to simplify this task. BluePyOpt is an extensible framework for data-driven model parameter optimisation that wraps and standardizes several existing open-source tools. It simplifies the task of creating and sharing these optimisations, and the associated techniques and knowledge. This is achieved by abstracting the optimisation and evaluation tasks into various reusable and flexible discrete elements according to established best-practices. Further, BluePyOpt provides methods for setting up both small- and large-scale optimisations on a variety of platforms, ranging from laptops to Linux clusters and cloud-based compute infrastructures. The versatility of the BluePyOpt framework is demonstrated by working through three representative neuroscience specific use cases. PMID:27375471

Authentic Astronomical Discovery in Planetariums: Bringing Data to Domes

NASA Astrophysics Data System (ADS)

Wyatt, Ryan Jason; Subbarao, Mark; Christensen, Lars; Emmons, Ben; Hurt, Robert

2018-01-01

Planetariums offer a unique opportunity to disseminate astronomical discoveries using data visualization at all levels of complexity: the technical infrastructure to display data and a sizeable cohort of enthusiastic educators to interpret results. “Data to Dome” is an initiative the International Planetarium Society to develop our community’s capacity to integrate data in fulldome planetarium systems—including via open source software platforms such as WorldWide Telescope and OpenSpace. We are cultivating a network of planetarium professionals who integrate data into their presentations and share their content with others. Furthermore, we propose to shorten the delay between discovery and dissemination in planetariums. Currently, the “latest science” is often presented days or weeks after discoveries are announced, and we can shorten this to hours or even minutes. The Data2Dome (D2D) initiative, led by the European Southern Observatory, proposes technical infrastructure and data standards that will streamline content flow from research institutions to planetariums, offering audiences a unique opportunity to access to the latest astronomical data in near real time.

ArrayNinja: An Open Source Platform for Unified Planning and Analysis of Microarray Experiments.

PubMed

Dickson, B M; Cornett, E M; Ramjan, Z; Rothbart, S B

2016-01-01

Microarray-based proteomic platforms have emerged as valuable tools for studying various aspects of protein function, particularly in the field of chromatin biochemistry. Microarray technology itself is largely unrestricted in regard to printable material and platform design, and efficient multidimensional optimization of assay parameters requires fluidity in the design and analysis of custom print layouts. This motivates the need for streamlined software infrastructure that facilitates the combined planning and analysis of custom microarray experiments. To this end, we have developed ArrayNinja as a portable, open source, and interactive application that unifies the planning and visualization of microarray experiments and provides maximum flexibility to end users. Array experiments can be planned, stored to a private database, and merged with the imaged results for a level of data interaction and centralization that is not currently attainable with available microarray informatics tools. © 2016 Elsevier Inc. All rights reserved.

A framework for integration of scientific applications into the OpenTopography workflow

NASA Astrophysics Data System (ADS)

Nandigam, V.; Crosby, C.; Baru, C.

2012-12-01

The NSF-funded OpenTopography facility provides online access to Earth science-oriented high-resolution LIDAR topography data, online processing tools, and derivative products. The underlying cyberinfrastructure employs a multi-tier service oriented architecture that is comprised of an infrastructure tier, a processing services tier, and an application tier. The infrastructure tier consists of storage, compute resources as well as supporting databases. The services tier consists of the set of processing routines each deployed as a Web service. The applications tier provides client interfaces to the system. (e.g. Portal). We propose a "pluggable" infrastructure design that will allow new scientific algorithms and processing routines developed and maintained by the community to be integrated into the OpenTopography system so that the wider earth science community can benefit from its availability. All core components in OpenTopography are available as Web services using a customized open-source Opal toolkit. The Opal toolkit provides mechanisms to manage and track job submissions, with the help of a back-end database. It allows monitoring of job and system status by providing charting tools. All core components in OpenTopography have been developed, maintained and wrapped as Web services using Opal by OpenTopography developers. However, as the scientific community develops new processing and analysis approaches this integration approach is not scalable efficiently. Most of the new scientific applications will have their own active development teams performing regular updates, maintenance and other improvements. It would be optimal to have the application co-located where its developers can continue to actively work on it while still making it accessible within the OpenTopography workflow for processing capabilities. We will utilize a software framework for remote integration of these scientific applications into the OpenTopography system. This will be accomplished by virtually extending the OpenTopography service over the various infrastructures running these scientific applications and processing routines. This involves packaging and distributing a customized instance of the Opal toolkit that will wrap the software application as an OPAL-based web service and integrate it into the OpenTopography framework. We plan to make this as automated as possible. A structured specification of service inputs and outputs along with metadata annotations encoded in XML can be utilized to automate the generation of user interfaces, with appropriate tools tips and user help features, and generation of other internal software. The OpenTopography Opal toolkit will also include the customizations that will enable security authentication, authorization and the ability to write application usage and job statistics back to the OpenTopography databases. This usage information could then be reported to the original service providers and used for auditing and performance improvements. This pluggable framework will enable the application developers to continue to work on enhancing their application while making the latest iteration available in a timely manner to the earth sciences community. This will also help us establish an overall framework that other scientific application providers will also be able to use going forward.

Exploiting IoT Technologies and Open Source Components for Smart Seismic Network Instrumentation

NASA Astrophysics Data System (ADS)

Germenis, N. G.; Koulamas, C. A.; Foundas, P. N.

2017-12-01

The data collection infrastructure of any seismic network poses a number of requirements and trade-offs related to accuracy, reliability, power autonomy and installation & operational costs. Having the right hardware design at the edge of this infrastructure, embedded software running inside the instruments is the heart of pre-processing and communication services implementation and their integration with the central storage and processing facilities of the seismic network. This work demonstrates the feasibility and benefits of exploiting software components from heterogeneous sources in order to realize a smart seismic data logger, achieving higher reliability, faster integration and less development and testing costs of critical functionality that is in turn responsible for the cost and power efficient operation of the device. The instrument's software builds on top of widely used open source components around the Linux kernel with real-time extensions, the core Debian Linux distribution, the earthworm and seiscomp tooling frameworks, as well as components from the Internet of Things (IoT) world, such as the CoAP and MQTT protocols for the signaling planes, besides the widely used de-facto standards of the application domain at the data plane, such as the SeedLink protocol. By using an innovative integration of features based on lower level GPL components of the seiscomp suite with higher level processing earthworm components, coupled with IoT protocol extensions to the latter, the instrument can implement smart functionality such as network controlled, event triggered data transmission in parallel with edge archiving and on demand, short term historical data retrieval.

VoIP attacks detection engine based on neural network

NASA Astrophysics Data System (ADS)

Safarik, Jakub; Slachta, Jiri

2015-05-01

The security is crucial for any system nowadays, especially communications. One of the most successful protocols in the field of communication over IP networks is Session Initiation Protocol. It is an open-source project used by different kinds of applications, both open-source and proprietary. High penetration and text-based principle made SIP number one target in IP telephony infrastructure, so security of SIP server is essential. To keep up with hackers and to detect potential malicious attacks, security administrator needs to monitor and evaluate SIP traffic in the network. But monitoring and following evaluation could easily overwhelm the security administrator in networks, typically in networks with a number of SIP servers, users and logically or geographically separated networks. The proposed solution lies in automatic attack detection systems. The article covers detection of VoIP attacks through a distributed network of nodes. Then the gathered data analyze aggregation server with artificial neural network. Artificial neural network means multilayer perceptron network trained with a set of collected attacks. Attack data could also be preprocessed and verified with a self-organizing map. The source data is detected by distributed network of detection nodes. Each node contains a honeypot application and traffic monitoring mechanism. Aggregation of data from each node creates an input for neural networks. The automatic classification on a centralized server with low false positive detection reduce the cost of attack detection resources. The detection system uses modular design for easy deployment in final infrastructure. The centralized server collects and process detected traffic. It also maintains all detection nodes.

AstroCloud, a Cyber-Infrastructure for Astronomy Research: Cloud Computing Environments

NASA Astrophysics Data System (ADS)

Li, C.; Wang, J.; Cui, C.; He, B.; Fan, D.; Yang, Y.; Chen, J.; Zhang, H.; Yu, C.; Xiao, J.; Wang, C.; Cao, Z.; Fan, Y.; Hong, Z.; Li, S.; Mi, L.; Wan, W.; Wang, J.; Yin, S.

2015-09-01

AstroCloud is a cyber-Infrastructure for Astronomy Research initiated by Chinese Virtual Observatory (China-VO) under funding support from NDRC (National Development and Reform commission) and CAS (Chinese Academy of Sciences). Based on CloudStack, an open source software, we set up the cloud computing environment for AstroCloud Project. It consists of five distributed nodes across the mainland of China. Users can use and analysis data in this cloud computing environment. Based on GlusterFS, we built a scalable cloud storage system. Each user has a private space, which can be shared among different virtual machines and desktop systems. With this environments, astronomer can access to astronomical data collected by different telescopes and data centers easily, and data producers can archive their datasets safely.

Geospatial-enabled Data Exploration and Computation through Data Infrastructure Building Blocks

NASA Astrophysics Data System (ADS)

Song, C. X.; Biehl, L. L.; Merwade, V.; Villoria, N.

2015-12-01

Geospatial data are present everywhere today with the proliferation of location-aware computing devices and sensors. This is especially true in the scientific community where large amounts of data are driving research and education activities in many domains. Collaboration over geospatial data, for example, in modeling, data analysis and visualization, must still overcome the barriers of specialized software and expertise among other challenges. The GABBs project aims at enabling broader access to geospatial data exploration and computation by developing spatial data infrastructure building blocks that leverage capabilities of end-to-end application service and virtualized computing framework in HUBzero. Funded by NSF Data Infrastructure Building Blocks (DIBBS) initiative, GABBs provides a geospatial data architecture that integrates spatial data management, mapping and visualization and will make it available as open source. The outcome of the project will enable users to rapidly create tools and share geospatial data and tools on the web for interactive exploration of data without requiring significant software development skills, GIS expertise or IT administrative privileges. This presentation will describe the development of geospatial data infrastructure building blocks and the scientific use cases that help drive the software development, as well as seek feedback from the user communities.

A scalable infrastructure for CMS data analysis based on OpenStack Cloud and Gluster file system

NASA Astrophysics Data System (ADS)

Toor, S.; Osmani, L.; Eerola, P.; Kraemer, O.; Lindén, T.; Tarkoma, S.; White, J.

2014-06-01

The challenge of providing a resilient and scalable computational and data management solution for massive scale research environments requires continuous exploration of new technologies and techniques. In this project the aim has been to design a scalable and resilient infrastructure for CERN HEP data analysis. The infrastructure is based on OpenStack components for structuring a private Cloud with the Gluster File System. We integrate the state-of-the-art Cloud technologies with the traditional Grid middleware infrastructure. Our test results show that the adopted approach provides a scalable and resilient solution for managing resources without compromising on performance and high availability.

An open-source software platform for data management, visualisation, model building and model sharing in water, energy and other resource modelling domains.

NASA Astrophysics Data System (ADS)

Knox, S.; Meier, P.; Mohammed, K.; Korteling, B.; Matrosov, E. S.; Hurford, A.; Huskova, I.; Harou, J. J.; Rosenberg, D. E.; Thilmant, A.; Medellin-Azuara, J.; Wicks, J.

2015-12-01

Capacity expansion on resource networks is essential to adapting to economic and population growth and pressures such as climate change. Engineered infrastructure systems such as water, energy, or transport networks require sophisticated and bespoke models to refine management and investment strategies. Successful modeling of such complex systems relies on good data management and advanced methods to visualize and share data.Engineered infrastructure systems are often represented as networks of nodes and links with operating rules describing their interactions. Infrastructure system management and planning can be abstracted to simulating or optimizing new operations and extensions of the network. By separating the data storage of abstract networks from manipulation and modeling we have created a system where infrastructure modeling across various domains is facilitated.We introduce Hydra Platform, a Free Open Source Software designed for analysts and modelers to store, manage and share network topology and data. Hydra Platform is a Python library with a web service layer for remote applications, called Apps, to connect. Apps serve various functions including network or results visualization, data export (e.g. into a proprietary format) or model execution. This Client-Server architecture allows users to manipulate and share centrally stored data. XML templates allow a standardised description of the data structure required for storing network data such that it is compatible with specific models.Hydra Platform represents networks in an abstract way and is therefore not bound to a single modeling domain. It is the Apps that create domain-specific functionality. Using Apps researchers from different domains can incorporate different models within the same network enabling cross-disciplinary modeling while minimizing errors and streamlining data sharing. Separating the Python library from the web layer allows developers to natively expand the software or build web-based apps in other languages for remote functionality. Partner CH2M is developing a commercial user-interface for Hydra Platform however custom interfaces and visualization tools can be built. Hydra Platform is available on GitHub while Apps will be shared on a central repository.

Defense Expenditures in Pakistan: A Source of Stimulus for or Competition With the Private Sector

DTIC Science & Technology

1994-01-01

private sector activity, particularly investment, is the only viable option open to the authorities. It follows that for policy purposes the most important issue involves restructuring government expenditures and their financing in a manner that would provide the maximum inducement to private sector capital formation, especially in manufacturing. Operationally, this means finding an optimal balance between the government’s three most important budgetary items: defense, public consumption and infrastructural development. More importantly because

General consumer communication tools for improved image management and communication in medicine.

PubMed

Rosset, Chantal; Rosset, Antoine; Ratib, Osman

2005-12-01

We elected to explore new technologies emerging on the general consumer market that can improve and facilitate image and data communication in medical and clinical environment. These new technologies developed for communication and storage of data can improve the user convenience and facilitate the communication and transport of images and related data beyond the usual limits and restrictions of a traditional picture archiving and communication systems (PACS) network. We specifically tested and implemented three new technologies provided on Apple computer platforms. (1) We adopted the iPod, a MP3 portable player with a hard disk storage, to easily and quickly move large number of DICOM images. (2) We adopted iChat, a videoconference and instant-messaging software, to transmit DICOM images in real time to a distant computer for conferencing teleradiology. (3) Finally, we developed a direct secure interface to use the iDisk service, a file-sharing service based on the WebDAV technology, to send and share DICOM files between distant computers. These three technologies were integrated in a new open-source image navigation and display software called OsiriX allowing for manipulation and communication of multimodality and multidimensional DICOM image data sets. This software is freely available as an open-source project at http://homepage.mac.com/rossetantoine/OsiriX. Our experience showed that the implementation of these technologies allowed us to significantly enhance the existing PACS with valuable new features without any additional investment or the need for complex extensions of our infrastructure. The added features such as teleradiology, secure and convenient image and data communication, and the use of external data storage services open the gate to a much broader extension of our imaging infrastructure to the outside world.

OpenCMISS: a multi-physics & multi-scale computational infrastructure for the VPH/Physiome project.

PubMed

Bradley, Chris; Bowery, Andy; Britten, Randall; Budelmann, Vincent; Camara, Oscar; Christie, Richard; Cookson, Andrew; Frangi, Alejandro F; Gamage, Thiranja Babarenda; Heidlauf, Thomas; Krittian, Sebastian; Ladd, David; Little, Caton; Mithraratne, Kumar; Nash, Martyn; Nickerson, David; Nielsen, Poul; Nordbø, Oyvind; Omholt, Stig; Pashaei, Ali; Paterson, David; Rajagopal, Vijayaraghavan; Reeve, Adam; Röhrle, Oliver; Safaei, Soroush; Sebastián, Rafael; Steghöfer, Martin; Wu, Tim; Yu, Ting; Zhang, Heye; Hunter, Peter

2011-10-01

The VPH/Physiome Project is developing the model encoding standards CellML (cellml.org) and FieldML (fieldml.org) as well as web-accessible model repositories based on these standards (models.physiome.org). Freely available open source computational modelling software is also being developed to solve the partial differential equations described by the models and to visualise results. The OpenCMISS code (opencmiss.org), described here, has been developed by the authors over the last six years to replace the CMISS code that has supported a number of organ system Physiome projects. OpenCMISS is designed to encompass multiple sets of physical equations and to link subcellular and tissue-level biophysical processes into organ-level processes. In the Heart Physiome project, for example, the large deformation mechanics of the myocardial wall need to be coupled to both ventricular flow and embedded coronary flow, and the reaction-diffusion equations that govern the propagation of electrical waves through myocardial tissue need to be coupled with equations that describe the ion channel currents that flow through the cardiac cell membranes. In this paper we discuss the design principles and distributed memory architecture behind the OpenCMISS code. We also discuss the design of the interfaces that link the sets of physical equations across common boundaries (such as fluid-structure coupling), or between spatial fields over the same domain (such as coupled electromechanics), and the concepts behind CellML and FieldML that are embodied in the OpenCMISS data structures. We show how all of these provide a flexible infrastructure for combining models developed across the VPH/Physiome community. Copyright © 2011 Elsevier Ltd. All rights reserved.

NOAA's Data Catalog and the Federal Open Data Policy

NASA Astrophysics Data System (ADS)

Wengren, M. J.; de la Beaujardiere, J.

2014-12-01

The 2013 Open Data Policy Presidential Directive requires Federal agencies to create and maintain a 'public data listing' that includes all agency data that is currently or will be made publicly-available in the future. The directive requires the use of machine-readable and open formats that make use of 'common core' and extensible metadata formats according to the best practices published in an online repository called 'Project Open Data', to use open licenses where possible, and to adhere to existing metadata and other technology standards to promote interoperability. In order to meet the requirements of the Open Data Policy, the National Oceanic and Atmospheric Administration (NOAA) has implemented an online data catalog that combines metadata from all subsidiary NOAA metadata catalogs into a single master inventory. The NOAA Data Catalog is available to the public for search and discovery, providing access to the NOAA master data inventory through multiple means, including web-based text search, OGC CS-W endpoint, as well as a native Application Programming Interface (API) for programmatic query. It generates on a daily basis the Project Open Data JavaScript Object Notation (JSON) file required for compliance with the Presidential directive. The Data Catalog is based on the open source Comprehensive Knowledge Archive Network (CKAN) software and runs on the Amazon Federal GeoCloud. This presentation will cover topics including mappings of existing metadata in standard formats (FGDC-CSDGM and ISO 19115 XML ) to the Project Open Data JSON metadata schema, representation of metadata elements within the catalog, and compatible metadata sources used to feed the catalog to include Web Accessible Folder (WAF), Catalog Services for the Web (CS-W), and Esri ArcGIS.com. It will also discuss related open source technologies that can be used together to build a spatial data infrastructure compliant with the Open Data Policy.

An open-source wireless sensor stack: from Arduino to SDI-12 to Water One Flow

NASA Astrophysics Data System (ADS)

Hicks, S.; Damiano, S. G.; Smith, K. M.; Olexy, J.; Horsburgh, J. S.; Mayorga, E.; Aufdenkampe, A. K.

2013-12-01

Implementing a large-scale streaming environmental sensor network has previously been limited by the high cost of the datalogging and data communication infrastructure. The Christina River Basin Critical Zone Observatory (CRB-CZO) is overcoming the obstacles to large near-real-time data collection networks by using Arduino, an open source electronics platform, in combination with XBee ZigBee wireless radio modules. These extremely low-cost and easy-to-use open source electronics are at the heart of the new DIY movement and have provided solutions to countless projects by over half a million users worldwide. However, their use in environmental sensing is in its infancy. At present a primary limitation to widespread deployment of open-source electronics for environmental sensing is the lack of a simple, open-source software stack to manage streaming data from heterogeneous sensor networks. Here we present a functioning prototype software stack that receives sensor data over a self-meshing ZigBee wireless network from over a hundred sensors, stores the data locally and serves it on demand as a CUAHSI Water One Flow (WOF) web service. We highlight a few new, innovative components, including: (1) a versatile open data logger design based the Arduino electronics platform and ZigBee radios; (2) a software library implementing SDI-12 communication protocol between any Arduino platform and SDI12-enabled sensors without the need for additional hardware (https://github.com/StroudCenter/Arduino-SDI-12); and (3) 'midStream', a light-weight set of Python code that receives streaming sensor data, appends it with metadata on the fly by querying a relational database structured on an early version of the Observations Data Model version 2.0 (ODM2), and uses the WOFpy library to serve the data as WaterML via SOAP and REST web services.

FOSS Tools for Research Infrastructures - A Success Story?

NASA Astrophysics Data System (ADS)

Stender, V.; Schroeder, M.; Wächter, J.

2015-12-01

Established initiatives and mandated organizations, e.g. the Initiative for Scientific Cyberinfrastructures (NSF, 2007) or the European Strategy Forum on Research Infrastructures (ESFRI, 2008), promote and foster the development of sustainable research infrastructures. The basic idea behind these infrastructures is the provision of services supporting scientists to search, visualize and access data, to collaborate and exchange information, as well as to publish data and other results. Especially the management of research data is gaining more and more importance. In geosciences these developments have to be merged with the enhanced data management approaches of Spatial Data Infrastructures (SDI). The Centre for GeoInformationTechnology (CeGIT) at the GFZ German Research Centre for Geosciences has the objective to establish concepts and standards of SDIs as an integral part of research infrastructure architectures. In different projects, solutions to manage research data for land- and water management or environmental monitoring have been developed based on a framework consisting of Free and Open Source Software (FOSS) components. The framework provides basic components supporting the import and storage of data, discovery and visualization as well as data documentation (metadata). In our contribution, we present our data management solutions developed in three projects, Central Asian Water (CAWa), Sustainable Management of River Oases (SuMaRiO) and Terrestrial Environmental Observatories (TERENO) where FOSS components build the backbone of the data management platform. The multiple use and validation of tools helped to establish a standardized architectural blueprint serving as a contribution to Research Infrastructures. We examine the question of whether FOSS tools are really a sustainable choice and whether the increased efforts of maintenance are justified. Finally it should help to answering the question if the use of FOSS for Research Infrastructures is a success story.

An Open and Scalable Learning Infrastructure for Food Safety

ERIC Educational Resources Information Center

Manouselis, Nikos; Thanopoulos, Charalampos; Vignare, Karen; Geith, Christine

2013-01-01

In the last several years, a variety of approaches and tools have been developed for giving access to open educational resources (OER) related to food safety, security, and food standards, as well to various targeted audiences (e.g., farmers, agronomists). The aim of this paper is to present a technology infrastructure currently in demonstration…

Challenges for Data Archival Centers in Evolving Environmental Sciences

NASA Astrophysics Data System (ADS)

Wei, Y.; Cook, R. B.; Gu, L.; Santhana Vannan, S. K.; Beaty, T.

2015-12-01

Environmental science has entered into a big data era as enormous data about the Earth environment are continuously collected through field and airborne missions, remote sensing observations, model simulations, sensor networks, etc. An open-access and open-management data infrastructure for data-intensive science is a major grand challenge in global environmental research (BERAC, 2010). Such an infrastructure, as exemplified in EOSDIS, GEOSS, and NSF EarthCube, will provide a complete lifecycle of environmental data and ensures that data will smoothly flow among different phases of collection, preservation, integration, and analysis. Data archival centers, as the data integration units closest to data providers, serve as the source power to compile and integrate heterogeneous environmental data into this global infrastructure. This presentation discusses the interoperability challenges and practices of geosciences from the aspect of data archival centers, based on the operational experiences of the NASA-sponsored Oak Ridge National Laboratory Distributed Active Archive Center (ORNL DAAC) and related environmental data management activities. Specifically, we will discuss the challenges to 1) encourage and help scientists to more actively share data with the broader scientific community, so that valuable environmental data, especially those dark data collected by individual scientists in small independent projects, can be shared and integrated into the infrastructure to tackle big science questions; 2) curate heterogeneous multi-disciplinary data, focusing on the key aspects of identification, format, metadata, data quality, and semantics to make them ready to be plugged into a global data infrastructure. We will highlight data curation practices at the ORNL DAAC for global campaigns such as BOREAS, LBA, SAFARI 2000; and 3) enhance the capabilities to more effectively and efficiently expose and deliver "big" environmental data to broad range of users and systems. Experiences and challenges with integrating large data sets via the ORNL DAAC's data discovery and delivery Web services will be discussed.

Developing a data life cycle for carbon and greenhouse gas measurements: challenges, experiences and visions

NASA Astrophysics Data System (ADS)

Kutsch, W. L.

2015-12-01

Environmental research infrastructures and big data integration networks require common data policies, standardized workflows and sophisticated e-infrastructure to optimise the data life cycle. This presentation summarizes the experiences in developing the data life cycle for the Integrated Carbon Observation System (ICOS), a European Research Infrastructure. It will also outline challenges that still exist and visions for future development. As many other environmental research infrastructures ICOS RI built on a large number of distributed observational or experimental sites. Data from these sites are transferred to Thematic Centres and quality checked, processed and integrated there. Dissemination will be managed by the ICOS Carbon Portal. This complex data life cycle has been defined in detail by developing protocols and assigning responsibilities. Since data will be shared under an open access policy there is a strong need for common data citation tracking systems that allow data providers to identify downstream usage of their data so as to prove their importance and show the impact to stakeholders and the public. More challenges arise from interoperating with other infrastructures or providing data for global integration projects as done e.g. in the framework of GEOSS or in global integration approaches such as fluxnet or SOCAt. Here, common metadata systems are the key solutions for data detection and harvesting. The metadata characterises data, services, users and ICT resources (including sensors and detectors). Risks may arise when data of high and low quality are mixed during this process or unexperienced data scientists without detailed knowledge on the data aquisition derive scientific theories through statistical analyses. The vision of fully open data availability is expressed in a recent GEO flagship initiative that will address important issues needed to build a connected and interoperable global network for carbon cycle and greenhouse gas observations and aims to meet the most urgent needs for integration between different information sources and methodologies, between different regional networks and from data providers to users.

Photonics and terahertz technologies: part 2

NASA Astrophysics Data System (ADS)

Romaniuk, Ryszard S.

2011-10-01

This digest paper debates basic features of the terahertz band of frequencies and compares it to the classical photonics. There are presented fundamental characteristics of the basic terahertz system consisting of a THz source, propagation media, transmission lines, THz signal processing, and detectors. Such a system finds research application, but also practical in two main areas: terahertz imaging - transmission and reflective, and as a close range THz radar, but also as sensory systems mainly for molecular sensing. There were launched in this country a few THz research projects concerning the THz sources, detectors and their applications. Among these projects there is an infrastructural one called FOTEH, opened at the WUT. The details of this project are debated and the consequences of its realization in this country. The first part of the paper is an introduction debating THz band and comparing it with the photonics one. The second part presents the assumptions of the infrastructural FOTEH project on Photonics and Terahertz Technologies. The project is expected to have impact on the development of photonics and relate fields in Poland.

2014 Earth System Grid Federation and Ultrascale Visualization Climate Data Analysis Tools Conference Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Williams, Dean N.

2015-01-27

The climate and weather data science community met December 9–11, 2014, in Livermore, California, for the fourth annual Earth System Grid Federation (ESGF) and Ultrascale Visualization Climate Data Analysis Tools (UV-CDAT) Face-to-Face (F2F) Conference, hosted by the Department of Energy, National Aeronautics and Space Administration, National Oceanic and Atmospheric Administration, the European Infrastructure for the European Network of Earth System Modelling, and the Australian Department of Education. Both ESGF and UVCDATremain global collaborations committed to developing a new generation of open-source software infrastructure that provides distributed access and analysis to simulated and observed data from the climate and weather communities.more » The tools and infrastructure created under these international multi-agency collaborations are critical to understanding extreme weather conditions and long-term climate change. In addition, the F2F conference fosters a stronger climate and weather data science community and facilitates a stronger federated software infrastructure. The 2014 F2F conference detailed the progress of ESGF, UV-CDAT, and other community efforts over the year and sets new priorities and requirements for existing and impending national and international community projects, such as the Coupled Model Intercomparison Project Phase Six. Specifically discussed at the conference were project capabilities and enhancements needs for data distribution, analysis, visualization, hardware and network infrastructure, standards, and resources.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Akyol, Bora A.; Allwardt, Craig H.; Beech, Zachary W.

VOLTTRON is a flexible, reliable, and scalable platform for distributed control and sensing. VOLTTRON serves in four primary roles: •A reference platform for researchers to quickly develop control applications for transactive energy. •A reference platform with flexible data store support for energy analytics applications either in academia or in commercial enterprise. •A platform from which commercial enterprise can develop products without license issues and easily integrate into their product line. •An accelerator to drive industry adoption of transactive energy and advanced building energy analytics. Pacific Northwest National Laboratory, with funding from the U.S. Department of Energy’s Building Technologies Office, developedmore » and maintains VOLTTRON as an open-source community project. VOLTTRON source code includes agent execution software; agents that perform critical services that enable and enhance VOLTTRON functionality; and numerous agents that utilize the platform to perform a specific function (fault detection, demand response, etc.). The platform supports energy, operational, and financial transactions between networked entities (equipment, organizations, buildings, grid, etc.) and enhance the control infrastructure of existing buildings through the use of open-source device communication, control protocols, and integrated analytics.« less

Open source software projects of the caBIG In Vivo Imaging Workspace Software special interest group.

PubMed

Prior, Fred W; Erickson, Bradley J; Tarbox, Lawrence

2007-11-01

The Cancer Bioinformatics Grid (caBIG) program was created by the National Cancer Institute to facilitate sharing of IT infrastructure, data, and applications among the National Cancer Institute-sponsored cancer research centers. The program was launched in February 2004 and now links more than 50 cancer centers. In April 2005, the In Vivo Imaging Workspace was added to promote the use of imaging in cancer clinical trials. At the inaugural meeting, four special interest groups (SIGs) were established. The Software SIG was charged with identifying projects that focus on open-source software for image visualization and analysis. To date, two projects have been defined by the Software SIG. The eXtensible Imaging Platform project has produced a rapid application development environment that researchers may use to create targeted workflows customized for specific research projects. The Algorithm Validation Tools project will provide a set of tools and data structures that will be used to capture measurement information and associated needed to allow a gold standard to be defined for the given database against which change analysis algorithms can be tested. Through these and future efforts, the caBIG In Vivo Imaging Workspace Software SIG endeavors to advance imaging informatics and provide new open-source software tools to advance cancer research.

Baobab Laboratory Information Management System: Development of an Open-Source Laboratory Information Management System for Biobanking

PubMed Central

Bendou, Hocine; Sizani, Lunga; Reid, Tim; Swanepoel, Carmen; Ademuyiwa, Toluwaleke; Merino-Martinez, Roxana; Meuller, Heimo; Abayomi, Akin

2017-01-01

A laboratory information management system (LIMS) is central to the informatics infrastructure that underlies biobanking activities. To date, a wide range of commercial and open-source LIMSs are available and the decision to opt for one LIMS over another is often influenced by the needs of the biobank clients and researchers, as well as available financial resources. The Baobab LIMS was developed by customizing the Bika LIMS software (www.bikalims.org) to meet the requirements of biobanking best practices. The need to implement biobank standard operation procedures as well as stimulate the use of standards for biobank data representation motivated the implementation of Baobab LIMS, an open-source LIMS for Biobanking. Baobab LIMS comprises modules for biospecimen kit assembly, shipping of biospecimen kits, storage management, analysis requests, reporting, and invoicing. The Baobab LIMS is based on the Plone web-content management framework. All the system requirements for Plone are applicable to Baobab LIMS, including the need for a server with at least 8 GB RAM and 120 GB hard disk space. Baobab LIMS is a server–client-based system, whereby the end user is able to access the system securely through the internet on a standard web browser, thereby eliminating the need for standalone installations on all machines. PMID:28375759

Baobab Laboratory Information Management System: Development of an Open-Source Laboratory Information Management System for Biobanking.

PubMed

Bendou, Hocine; Sizani, Lunga; Reid, Tim; Swanepoel, Carmen; Ademuyiwa, Toluwaleke; Merino-Martinez, Roxana; Meuller, Heimo; Abayomi, Akin; Christoffels, Alan

2017-04-01

A laboratory information management system (LIMS) is central to the informatics infrastructure that underlies biobanking activities. To date, a wide range of commercial and open-source LIMSs are available and the decision to opt for one LIMS over another is often influenced by the needs of the biobank clients and researchers, as well as available financial resources. The Baobab LIMS was developed by customizing the Bika LIMS software ( www.bikalims.org ) to meet the requirements of biobanking best practices. The need to implement biobank standard operation procedures as well as stimulate the use of standards for biobank data representation motivated the implementation of Baobab LIMS, an open-source LIMS for Biobanking. Baobab LIMS comprises modules for biospecimen kit assembly, shipping of biospecimen kits, storage management, analysis requests, reporting, and invoicing. The Baobab LIMS is based on the Plone web-content management framework. All the system requirements for Plone are applicable to Baobab LIMS, including the need for a server with at least 8 GB RAM and 120 GB hard disk space. Baobab LIMS is a server-client-based system, whereby the end user is able to access the system securely through the internet on a standard web browser, thereby eliminating the need for standalone installations on all machines.

Vehicle infrastructure integration (VII) based road-condition warning system for highway collision prevention.

DOT National Transportation Integrated Search

2009-05-01

As a major ITS initiative, the Vehicle Infrastructure Integration (VII) program is to revolutionize : transportation by creating an enabling communication infrastructure that will open up a wide range of : safety applications. The road-condition warn...

The Semi-opened Infrastructure Model (SopIM): A Frame to Set Up an Organizational Learning Process

NASA Astrophysics Data System (ADS)

Grundstein, Michel

In this paper, we introduce the "Semi-opened Infrastructure Model (SopIM)" implemented to deploy Artificial Intelligence and Knowledge-based Systems within a large industrial company. This model illustrates what could be two of the operating elements of the Model for General Knowledge Management within the Enterprise (MGKME) that are essential to set up the organizational learning process that leads people to appropriate and use concepts, methods and tools of an innovative technology: the "Ad hoc Infrastructures" element, and the "Organizational Learning Processes" element.

Beyond imperviousness: A statistical approach to identifying functional differences between development morphologies on variable source area-type response in urbanized watersheds

NASA Astrophysics Data System (ADS)

Lim, T. C.

2016-12-01

Empirical evidence has shown linkages between urbanization, hydrological regime change, and degradation of water quality and aquatic habitat. Percent imperviousness, has long been suggested as the dominant source of these negative changes. However, recent research identifying alternative pathways of runoff production at the watershed scale have called into question percent impervious surface area's primacy in urban runoff production compared to other aspects of urbanization including change in vegetative cover, imported water and water leakages, and the presence of drainage infrastructure. In this research I show how a robust statistical methodology can detect evidence of variable source area (VSA)-type hydrologic response associated with incremental hydraulic connectivity in watersheds. I then use logistic regression to explore how evidence of VSA-type response relates to the physical and meterological characteristics of the watershed. I find that impervious surface area is highly correlated with development, but does not add significant explanatory power beyond percent developed in predicting VSA-type response. Other aspects of development morphology, including percent developed open space and type of drainage infrastructure also do not add to the explanatory power of undeveloped land in predicting VSA-type response. Within only developed areas, the effect of developed open space was found to be more similar to that of total impervious area than to undeveloped land. These findings were consistent when tested across a national cross-section of urbanized watersheds, a higher resolution dataset of Baltimore Metropolitan Area watersheds, and a subsample of watersheds confirmed not to be served by combined sewer systems. These findings suggest that land development policies that focus on lot coverage should be revisited, and more focus should be placed on preserving native vegetation and soil conditions alongside development.

Opening the Duke electronic health record to apps: Implementing SMART on FHIR.

PubMed

Bloomfield, Richard A; Polo-Wood, Felipe; Mandel, Joshua C; Mandl, Kenneth D

2017-03-01

Recognizing a need for our EHR to be highly interoperable, our team at Duke Health enabled our Epic-based electronic health record to be compatible with the Boston Children's project called Substitutable Medical Apps and Reusable Technologies (SMART), which employed Health Level Seven International's (HL7) Fast Healthcare Interoperability Resources (FHIR), commonly known as SMART on FHIR. We created a custom SMART on FHIR-compatible server infrastructure written in Node.js that served two primary functions. First, it handled API management activities such rate-limiting, authorization, auditing, logging, and analytics. Second, it retrieved the EHR data and made it available in a FHIR-compatible format. Finally, we made required changes to the EHR user interface to allow us to integrate several compatible apps into the provider- and patient-facing EHR workflows. After integrating SMART on FHIR into our Epic-based EHR, we demonstrated several types of apps running on the infrastructure. This included both provider- and patient-facing apps as well as apps that are closed source, open source and internally-developed. We integrated the apps into the testing environment of our desktop EHR as well as our patient portal. We also demonstrated the integration of a native iOS app. In this paper, we demonstrate the successful implementation of the SMART and FHIR technologies on our Epic-based EHR and subsequent integration of several compatible provider- and patient-facing apps. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Open Component Portability Infrastructure (OPENCPI)

DTIC Science & Technology

2013-03-01

8 Figure 2. C Function vs . OpenCL Kernel...10 Figure 3. OpenCL vs . OpenCPI Layering...difference between a simple C function and the analogous OpenCL kernel. Figure 2. C Function vs . OpenCL Kernel These existing example OpenCL

Open | SpeedShop: An Open Source Infrastructure for Parallel Performance Analysis

DOE PAGES

Schulz, Martin; Galarowicz, Jim; Maghrak, Don; ...

2008-01-01

Over the last decades a large number of performance tools has been developed to analyze and optimize high performance applications. Their acceptance by end users, however, has been slow: each tool alone is often limited in scope and comes with widely varying interfaces and workflow constraints, requiring different changes in the often complex build and execution infrastructure of the target application. We started the Open | SpeedShop project about 3 years ago to overcome these limitations and provide efficient, easy to apply, and integrated performance analysis for parallel systems. Open | SpeedShop has two different faces: it provides an interoperable tool set covering themore » most common analysis steps as well as a comprehensive plugin infrastructure for building new tools. In both cases, the tools can be deployed to large scale parallel applications using DPCL/Dyninst for distributed binary instrumentation. Further, all tools developed within or on top of Open | SpeedShop are accessible through multiple fully equivalent interfaces including an easy-to-use GUI as well as an interactive command line interface reducing the usage threshold for those tools.« less

Infrastructure and the Virtual Observatory

NASA Astrophysics Data System (ADS)

Dowler, P.; Gaudet, S.; Schade, D.

2011-07-01

The modern data center is faced with architectural and software engineering challenges that grow along with the challenges facing observatories: massive data flow, distributed computing environments, and distributed teams collaborating on large and small projects. By using VO standards as key components of the infrastructure, projects can take advantage of a decade of intellectual investment by the IVOA community. By their nature, these standards are proven and tested designs that already exist. Adopting VO standards saves considerable design effort, allows projects to take advantage of open-source software and test suites to speed development, and enables the use of third party tools that understand the VO protocols. The evolving CADC architecture now makes heavy use of VO standards. We show examples of how these standards may be used directly, coupled with non-VO standards, or extended with custom capabilities to solve real problems and provide value to our users. In the end, we use VO services as major parts of the core infrastructure to reduce cost rather than as an extra layer with additional cost and we can deliver more general purpose and robust services to our user community.

NFFA-Europe: enhancing European competitiveness in nanoscience research and innovation (Conference Presentation)

NASA Astrophysics Data System (ADS)

Carsughi, Flavio; Fonseca, Luis

2017-06-01

NFFA-EUROPE is an European open access resource for experimental and theoretical nanoscience and sets out a platform to carry out comprehensive projects for multidisciplinary research at the nanoscale extending from synthesis to nanocharacterization to theory and numerical simulation. Advanced infrastructures specialized on growth, nano-lithography, nano-characterization, theory and simulation and fine-analysis with Synchrotron, FEL and Neutron radiation sources are integrated in a multi-site combination to develop frontier research on methods for reproducible nanoscience research and to enable European and international researchers from diverse disciplines to carry out advanced proposals impacting science and innovation. NFFA-EUROPE will enable coordinated access to infrastructures on different aspects of nanoscience research that is not currently available at single specialized ones and without duplicating their specific scopes. Approved user projects will have access to the best suited instruments and support competences for performing the research, including access to analytical large scale facilities, theory and simulation and high-performance computing facilities. Access is offered free of charge to European users and users will receive a financial contribution for their travel, accommodation and subsistence costs. The users access will include several "installations" and will be coordinated through a single entry point portal that will activate an advanced user-infrastructure dialogue to build up a personalized access programme with an increasing return on science and innovation production. The own research activity of NFFA-EUROPE will address key bottlenecks of nanoscience research: nanostructure traceability, protocol reproducibility, in-operando nano-manipulation and analysis, open data.

Highly efficient entanglement swapping and teleportation at telecom wavelength

PubMed Central

Jin, Rui-Bo; Takeoka, Masahiro; Takagi, Utako; Shimizu, Ryosuke; Sasaki, Masahide

2015-01-01

Entanglement swapping at telecom wavelengths is at the heart of quantum networking in optical fiber infrastructures. Although entanglement swapping has been demonstrated experimentally so far using various types of entangled photon sources both in near-infrared and telecom wavelength regions, the rate of swapping operation has been too low to be applied to practical quantum protocols, due to limited efficiency of entangled photon sources and photon detectors. Here we demonstrate drastic improvement of the efficiency at telecom wavelength by using two ultra-bright entangled photon sources and four highly efficient superconducting nanowire single photon detectors. We have attained a four-fold coincidence count rate of 108 counts per second, which is three orders higher than the previous experiments at telecom wavelengths. A raw (net) visibility in a Hong-Ou-Mandel interference between the two independent entangled sources was 73.3 ± 1.0% (85.1 ± 0.8%). We performed the teleportation and entanglement swapping, and obtained a fidelity of 76.3% in the swapping test. Our results on the coincidence count rates are comparable with the ones ever recorded in teleportation/swapping and multi-photon entanglement generation experiments at around 800 nm wavelengths. Our setup opens the way to practical implementation of device-independent quantum key distribution and its distance extension by the entanglement swapping as well as multi-photon entangled state generation in telecom band infrastructures with both space and fiber links. PMID:25791212

Highly efficient entanglement swapping and teleportation at telecom wavelength.

PubMed

Jin, Rui-Bo; Takeoka, Masahiro; Takagi, Utako; Shimizu, Ryosuke; Sasaki, Masahide

2015-03-20

Entanglement swapping at telecom wavelengths is at the heart of quantum networking in optical fiber infrastructures. Although entanglement swapping has been demonstrated experimentally so far using various types of entangled photon sources both in near-infrared and telecom wavelength regions, the rate of swapping operation has been too low to be applied to practical quantum protocols, due to limited efficiency of entangled photon sources and photon detectors. Here we demonstrate drastic improvement of the efficiency at telecom wavelength by using two ultra-bright entangled photon sources and four highly efficient superconducting nanowire single photon detectors. We have attained a four-fold coincidence count rate of 108 counts per second, which is three orders higher than the previous experiments at telecom wavelengths. A raw (net) visibility in a Hong-Ou-Mandel interference between the two independent entangled sources was 73.3 ± 1.0% (85.1 ± 0.8%). We performed the teleportation and entanglement swapping, and obtained a fidelity of 76.3% in the swapping test. Our results on the coincidence count rates are comparable with the ones ever recorded in teleportation/swapping and multi-photon entanglement generation experiments at around 800 nm wavelengths. Our setup opens the way to practical implementation of device-independent quantum key distribution and its distance extension by the entanglement swapping as well as multi-photon entangled state generation in telecom band infrastructures with both space and fiber links.

Sources of Free and Open Source Spatial Data for Natural Disasters and Principles for Use in Developing Country Contexts

NASA Astrophysics Data System (ADS)

Taylor, Faith E.; Malamud, Bruce D.; Millington, James D. A.

2016-04-01

Access to reliable spatial and quantitative datasets (e.g., infrastructure maps, historical observations, environmental variables) at regional and site specific scales can be a limiting factor for understanding hazards and risks in developing country settings. Here we present a 'living database' of >75 freely available data sources relevant to hazard and risk in Africa (and more globally). Data sources include national scientific foundations, non-governmental bodies, crowd-sourced efforts, academic projects, special interest groups and others. The database is available at http://tinyurl.com/africa-datasets and is continually being updated, particularly in the context of broader natural hazards research we are doing in the context of Malawi and Kenya. For each data source, we review the spatiotemporal resolution and extent and make our own assessments of reliability and usability of datasets. Although such freely available datasets are sometimes presented as a panacea to improving our understanding of hazards and risk in developing countries, there are both pitfalls and opportunities unique to using this type of freely available data. These include factors such as resolution, homogeneity, uncertainty, access to metadata and training for usage. Based on our experience, use in the field and grey/peer-review literature, we present a suggested set of guidelines for using these free and open source data in developing country contexts.

Open-Source Electronic Health Record Systems for Low-Resource Settings: Systematic Review

PubMed Central

Zolfo, Maria; Diro, Ermias

2017-01-01

Background Despite the great impact of information and communication technologies on clinical practice and on the quality of health services, this trend has been almost exclusive to developed countries, whereas countries with poor resources suffer from many economic and social issues that have hindered the real benefits of electronic health (eHealth) tools. As a component of eHealth systems, electronic health records (EHRs) play a fundamental role in patient management and effective medical care services. Thus, the adoption of EHRs in regions with a lack of infrastructure, untrained staff, and ill-equipped health care providers is an important task. However, the main barrier to adopting EHR software in low- and middle-income countries is the cost of its purchase and maintenance, which highlights the open-source approach as a good solution for these underserved areas. Objective The aim of this study was to conduct a systematic review of open-source EHR systems based on the requirements and limitations of low-resource settings. Methods First, we reviewed existing literature on the comparison of available open-source solutions. In close collaboration with the University of Gondar Hospital, Ethiopia, we identified common limitations in poor resource environments and also the main requirements that EHRs should support. Then, we extensively evaluated the current open-source EHR solutions, discussing their strengths and weaknesses, and their appropriateness to fulfill a predefined set of features relevant for low-resource settings. Results The evaluation methodology allowed assessment of several key aspects of available solutions that are as follows: (1) integrated applications, (2) configurable reports, (3) custom reports, (4) custom forms, (5) interoperability, (6) coding systems, (7) authentication methods, (8) patient portal, (9) access control model, (10) cryptographic features, (11) flexible data model, (12) offline support, (13) native client, (14) Web client,(15) other clients, (16) code-based language, (17) development activity, (18) modularity, (19) user interface, (20) community support, and (21) customization. The quality of each feature is discussed for each of the evaluated solutions and a final comparison is presented. Conclusions There is a clear demand for open-source, reliable, and flexible EHR systems in low-resource settings. In this study, we have evaluated and compared five open-source EHR systems following a multidimensional methodology that can provide informed recommendations to other implementers, developers, and health care professionals. We hope that the results of this comparison can guide decision making when needing to adopt, install, and maintain an open-source EHR solution in low-resource settings. PMID:29133283

A data protection scheme for medical research networks. Review after five years of operation.

PubMed

Helbing, K; Demiroglu, S Y; Rakebrandt, F; Pommerening, K; Rienhoff, O; Sax, U

2010-01-01

The data protection requirements matured in parallel to new clinical tests generating more personal data since the 1960s. About ten years ago it was recognized that a generic data protection scheme for medical research networks is required, which reinforces patient rights but also allows economically feasible medical research compared to "hand-carved" individual solutions. To give recommendations for more efficient IT infrastructures for medical research networks in compliance with data protection requirements. The IT infrastructures of three medical research networks were reviewed with respect to the relevant data management modules. Recommendations are derived to increase cost efficiency in research networks assessing the consequences of a service provider approach without lowering the data protection level. The existing data protection schemes are very complex. Smaller research networks cannot afford the implementation of such schemes. Larger networks struggle to keep them sustainable. Due to a modular redesign in the medical research network community, a new approach offers opportunities for an efficient sustainable IT infrastructure involving a service provider concept. For standard components 70-80% of the costs could be cut down, for open source components about 37% over a three-year period. Future research networks should switch to a service-oriented approach to achieve a sustainable, cost-efficient IT infrastructure.

Modeling the Hydrologic Effects of Large-Scale Green Infrastructure Projects with GIS

NASA Astrophysics Data System (ADS)

Bado, R. A.; Fekete, B. M.; Khanbilvardi, R.

2015-12-01

Impervious surfaces in urban areas generate excess runoff, which in turn causes flooding, combined sewer overflows, and degradation of adjacent surface waters. Municipal environmental protection agencies have shown a growing interest in mitigating these effects with 'green' infrastructure practices that partially restore the perviousness and water holding capacity of urban centers. Assessment of the performance of current and future green infrastructure projects is hindered by the lack of adequate hydrological modeling tools; conventional techniques fail to account for the complex flow pathways of urban environments, and detailed analyses are difficult to prepare for the very large domains in which green infrastructure projects are implemented. Currently, no standard toolset exists that can rapidly and conveniently predict runoff, consequent inundations, and sewer overflows at a city-wide scale. We demonstrate how streamlined modeling techniques can be used with open-source GIS software to efficiently model runoff in large urban catchments. Hydraulic parameters and flow paths through city blocks, roadways, and sewer drains are automatically generated from GIS layers, and ultimately urban flow simulations can be executed for a variety of rainfall conditions. With this methodology, users can understand the implications of large-scale land use changes and green/gray storm water retention systems on hydraulic loading, peak flow rates, and runoff volumes.

The Application of the Open Pharmacological Concepts Triple Store (Open PHACTS) to Support Drug Discovery Research

PubMed Central

Ratnam, Joseline; Zdrazil, Barbara; Digles, Daniela; Cuadrado-Rodriguez, Emiliano; Neefs, Jean-Marc; Tipney, Hannah; Siebes, Ronald; Waagmeester, Andra; Bradley, Glyn; Chau, Chau Han; Richter, Lars; Brea, Jose; Evelo, Chris T.; Jacoby, Edgar; Senger, Stefan; Loza, Maria Isabel; Ecker, Gerhard F.; Chichester, Christine

2014-01-01

Integration of open access, curated, high-quality information from multiple disciplines in the Life and Biomedical Sciences provides a holistic understanding of the domain. Additionally, the effective linking of diverse data sources can unearth hidden relationships and guide potential research strategies. However, given the lack of consistency between descriptors and identifiers used in different resources and the absence of a simple mechanism to link them, gathering and combining relevant, comprehensive information from diverse databases remains a challenge. The Open Pharmacological Concepts Triple Store (Open PHACTS) is an Innovative Medicines Initiative project that uses semantic web technology approaches to enable scientists to easily access and process data from multiple sources to solve real-world drug discovery problems. The project draws together sources of publicly-available pharmacological, physicochemical and biomolecular data, represents it in a stable infrastructure and provides well-defined information exploration and retrieval methods. Here, we highlight the utility of this platform in conjunction with workflow tools to solve pharmacological research questions that require interoperability between target, compound, and pathway data. Use cases presented herein cover 1) the comprehensive identification of chemical matter for a dopamine receptor drug discovery program 2) the identification of compounds active against all targets in the Epidermal growth factor receptor (ErbB) signaling pathway that have a relevance to disease and 3) the evaluation of established targets in the Vitamin D metabolism pathway to aid novel Vitamin D analogue design. The example workflows presented illustrate how the Open PHACTS Discovery Platform can be used to exploit existing knowledge and generate new hypotheses in the process of drug discovery. PMID:25522365

Cloud Environment Automation: from infrastructure deployment to application monitoring

NASA Astrophysics Data System (ADS)

Aiftimiei, C.; Costantini, A.; Bucchi, R.; Italiano, A.; Michelotto, D.; Panella, M.; Pergolesi, M.; Saletta, M.; Traldi, S.; Vistoli, C.; Zizzi, G.; Salomoni, D.

2017-10-01

The potential offered by the cloud paradigm is often limited by technical issues, rules and regulations. In particular, the activities related to the design and deployment of the Infrastructure as a Service (IaaS) cloud layer can be difficult to apply and time-consuming for the infrastructure maintainers. In this paper the research activity, carried out during the Open City Platform (OCP) research project [1], aimed at designing and developing an automatic tool for cloud-based IaaS deployment is presented. Open City Platform is an industrial research project funded by the Italian Ministry of University and Research (MIUR), started in 2014. It intends to research, develop and test new technological solutions open, interoperable and usable on-demand in the field of Cloud Computing, along with new sustainable organizational models that can be deployed for and adopted by the Public Administrations (PA). The presented work and the related outcomes are aimed at simplifying the deployment and maintenance of a complete IaaS cloud-based infrastructure.

Consolidation and development roadmap of the EMI middleware

NASA Astrophysics Data System (ADS)

Kónya, B.; Aiftimiei, C.; Cecchi, M.; Field, L.; Fuhrmann, P.; Nilsen, J. K.; White, J.

2012-12-01

Scientific research communities have benefited recently from the increasing availability of computing and data infrastructures with unprecedented capabilities for large scale distributed initiatives. These infrastructures are largely defined and enabled by the middleware they deploy. One of the major issues in the current usage of research infrastructures is the need to use similar but often incompatible middleware solutions. The European Middleware Initiative (EMI) is a collaboration of the major European middleware providers ARC, dCache, gLite and UNICORE. EMI aims to: deliver a consolidated set of middleware components for deployment in EGI, PRACE and other Distributed Computing Infrastructures; extend the interoperability between grids and other computing infrastructures; strengthen the reliability of the services; establish a sustainable model to maintain and evolve the middleware; fulfil the requirements of the user communities. This paper presents the consolidation and development objectives of the EMI software stack covering the last two years. The EMI development roadmap is introduced along the four technical areas of compute, data, security and infrastructure. The compute area plan focuses on consolidation of standards and agreements through a unified interface for job submission and management, a common format for accounting, the wide adoption of GLUE schema version 2.0 and the provision of a common framework for the execution of parallel jobs. The security area is working towards a unified security model and lowering the barriers to Grid usage by allowing users to gain access with their own credentials. The data area is focusing on implementing standards to ensure interoperability with other grids and industry components and to reuse already existing clients in operating systems and open source distributions. One of the highlights of the infrastructure area is the consolidation of the information system services via the creation of a common information backbone.

Low Cost, Scalable Proteomics Data Analysis Using Amazon's Cloud Computing Services and Open Source Search Algorithms

PubMed Central

Halligan, Brian D.; Geiger, Joey F.; Vallejos, Andrew K.; Greene, Andrew S.; Twigger, Simon N.

2009-01-01

One of the major difficulties for many laboratories setting up proteomics programs has been obtaining and maintaining the computational infrastructure required for the analysis of the large flow of proteomics data. We describe a system that combines distributed cloud computing and open source software to allow laboratories to set up scalable virtual proteomics analysis clusters without the investment in computational hardware or software licensing fees. Additionally, the pricing structure of distributed computing providers, such as Amazon Web Services, allows laboratories or even individuals to have large-scale computational resources at their disposal at a very low cost per run. We provide detailed step by step instructions on how to implement the virtual proteomics analysis clusters as well as a list of current available preconfigured Amazon machine images containing the OMSSA and X!Tandem search algorithms and sequence databases on the Medical College of Wisconsin Proteomics Center website (http://proteomics.mcw.edu/vipdac). PMID:19358578

Low cost, scalable proteomics data analysis using Amazon's cloud computing services and open source search algorithms.

PubMed

Halligan, Brian D; Geiger, Joey F; Vallejos, Andrew K; Greene, Andrew S; Twigger, Simon N

2009-06-01

One of the major difficulties for many laboratories setting up proteomics programs has been obtaining and maintaining the computational infrastructure required for the analysis of the large flow of proteomics data. We describe a system that combines distributed cloud computing and open source software to allow laboratories to set up scalable virtual proteomics analysis clusters without the investment in computational hardware or software licensing fees. Additionally, the pricing structure of distributed computing providers, such as Amazon Web Services, allows laboratories or even individuals to have large-scale computational resources at their disposal at a very low cost per run. We provide detailed step-by-step instructions on how to implement the virtual proteomics analysis clusters as well as a list of current available preconfigured Amazon machine images containing the OMSSA and X!Tandem search algorithms and sequence databases on the Medical College of Wisconsin Proteomics Center Web site ( http://proteomics.mcw.edu/vipdac ).

Open Source Web-Based Solutions for Disseminating and Analyzing Flood Hazard Information at the Community Level

NASA Astrophysics Data System (ADS)

Santillan, M. M.-M.; Santillan, J. R.; Morales, E. M. O.

2017-09-01

We discuss in this paper the development, including the features and functionalities, of an open source web-based flood hazard information dissemination and analytical system called "Flood EViDEns". Flood EViDEns is short for "Flood Event Visualization and Damage Estimations", an application that was developed by the Caraga State University to address the needs of local disaster managers in the Caraga Region in Mindanao, Philippines in accessing timely and relevant flood hazard information before, during and after the occurrence of flood disasters at the community (i.e., barangay and household) level. The web application made use of various free/open source web mapping and visualization technologies (GeoServer, GeoDjango, OpenLayers, Bootstrap), various geospatial datasets including LiDAR-derived elevation and information products, hydro-meteorological data, and flood simulation models to visualize various scenarios of flooding and its associated damages to infrastructures. The Flood EViDEns application facilitates the release and utilization of this flood-related information through a user-friendly front end interface consisting of web map and tables. A public version of the application can be accessed at http://121.97.192.11:8082/. The application is currently expanded to cover additional sites in Mindanao, Philippines through the "Geo-informatics for the Systematic Assessment of Flood Effects and Risks for a Resilient Mindanao" or the "Geo-SAFER Mindanao" Program.

Auscope: Australian Earth Science Information Infrastructure using Free and Open Source Software

NASA Astrophysics Data System (ADS)

Woodcock, R.; Cox, S. J.; Fraser, R.; Wyborn, L. A.

2013-12-01

Since 2005 the Australian Government has supported a series of initiatives providing researchers with access to major research facilities and information networks necessary for world-class research. Starting with the National Collaborative Research Infrastructure Strategy (NCRIS) the Australian earth science community established an integrated national geoscience infrastructure system called AuScope. AuScope is now in operation, providing a number of components to assist in understanding the structure and evolution of the Australian continent. These include the acquisition of subsurface imaging , earth composition and age analysis, a virtual drill core library, geological process simulation, and a high resolution geospatial reference framework. To draw together information from across the earth science community in academia, industry and government, AuScope includes a nationally distributed information infrastructure. Free and Open Source Software (FOSS) has been a significant enabler in building the AuScope community and providing a range of interoperable services for accessing data and scientific software. A number of FOSS components have been created, adopted or upgraded to create a coherent, OGC compliant Spatial Information Services Stack (SISS). SISS is now deployed at all Australian Geological Surveys, many Universities and the CSIRO. Comprising a set of OGC catalogue and data services, and augmented with new vocabulary and identifier services, the SISS provides a comprehensive package for organisations to contribute their data to the AuScope network. This packaging and a variety of software testing and documentation activities enabled greater trust and notably reduced barriers to adoption. FOSS selection was important, not only for technical capability and robustness, but also for appropriate licensing and community models to ensure sustainability of the infrastructure in the long term. Government agencies were sensitive to these issues and AuScope's careful selection has been rewarded by adoption. In some cases the features provided by the SISS solution are now significantly in advance of COTS offerings which will create expectations that can be passed back from users to their preferred vendors. Using FOSS, AuScope has addressed the challenge of data exchange across organisations nationally. The data standards (e.g. GeosciML) and platforms that underpin AuScope provide important new datasets and multi-agency links independent of underlying software and hardware differences. AuScope has created an infrastructure, a platform of technologies and the opportunity for new ways of working with and integrating disparate data at much lower cost. Research activities are now exploiting the information infrastructure to create virtual laboratories for research ranging from geophysics through water and the environment. Once again the AuScope community is making heavy use of FOSS to provide access to processing software and Cloud computing and HPC. The successful use of FOSS by AuScope, and the efforts made to ensure it is suitable for adoption, have resulted in the SISS being selected as a reference implementation for a number of Australian Government initiatives beyond AuScope in environmental information and bioregional assessments.

An authentication infrastructure for today and tomorrow

DOE Office of Scientific and Technical Information (OSTI.GOV)

Engert, D.E.

1996-06-01

The Open Software Foundation`s Distributed Computing Environment (OSF/DCE) was originally designed to provide a secure environment for distributed applications. By combining it with Kerberos Version 5 from MIT, it can be extended to provide network security as well. This combination can be used to build both an inter and intra organizational infrastructure while providing single sign-on for the user with overall improved security. The ESnet community of the Department of Energy is building just such an infrastructure. ESnet has modified these systems to improve their interoperability, while encouraging the developers to incorporate these changes and work more closely together tomore » continue to improve the interoperability. The success of this infrastructure depends on its flexibility to meet the needs of many applications and network security requirements. The open nature of Kerberos, combined with the vendor support of OSF/DCE, provides the infrastructure for today and tomorrow.« less

BioPortal: An Open-Source Community-Based Ontology Repository

NASA Astrophysics Data System (ADS)

Noy, N.; NCBO Team

2011-12-01

Advances in computing power and new computational techniques have changed the way researchers approach science. In many fields, one of the most fruitful approaches has been to use semantically aware software to break down the barriers among disparate domains, systems, data sources, and technologies. Such software facilitates data aggregation, improves search, and ultimately allows the detection of new associations that were previously not detectable. Achieving these analyses requires software systems that take advantage of the semantics and that can intelligently negotiate domains and knowledge sources, identifying commonality across systems that use different and conflicting vocabularies, while understanding apparent differences that may be concealed by the use of superficially similar terms. An ontology, a semantically rich vocabulary for a domain of interest, is the cornerstone of software for bridging systems, domains, and resources. However, as ontologies become the foundation of all semantic technologies in e-science, we must develop an infrastructure for sharing ontologies, finding and evaluating them, integrating and mapping among them, and using ontologies in applications that help scientists process their data. BioPortal [1] is an open-source on-line community-based ontology repository that has been used as a critical component of semantic infrastructure in several domains, including biomedicine and bio-geochemical data. BioPortal, uses the social approaches in the Web 2.0 style to bring structure and order to the collection of biomedical ontologies. It enables users to provide and discuss a wide array of knowledge components, from submitting the ontologies themselves, to commenting on and discussing classes in the ontologies, to reviewing ontologies in the context of their own ontology-based projects, to creating mappings between overlapping ontologies and discussing and critiquing the mappings. Critically, it provides web-service access to all its content, enabling its integration in semantically enriched applications. [1] Noy, N.F., Shah, N.H., et al., BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Res, 2009. 37(Web Server issue): p. W170-3.

Development of a telemedicine model for emerging countries: a case study on pediatric oncology in Brazil.

PubMed

Hira, A Y; Nebel de Mello, A; Faria, R A; Odone Filho, V; Lopes, R D; Zuffo, M K

2006-01-01

This article discusses a telemedicine model for emerging countries, through the description of ONCONET, a telemedicine initiative applied to pediatric oncology in Brazil. The ONCONET core technology is a Web-based system that offers health information and other services specialized in childhood cancer such as electronic medical records and cooperative protocols for complex treatments. All Web-based services are supported by the use of high performance computing infrastructure based on clusters of commodity computers. The system was fully implemented on an open-source and free-software approach. Aspects of modeling, implementation and integration are covered. A model, both technologically and economically viable, was created through the research and development of in-house solutions adapted to the emerging countries reality and with focus on scalability both in the total number of patients and in the national infrastructure.

A metadata initiative for global information discovery

USGS Publications Warehouse

Christian, E.

2001-01-01

The Global Information Locator Service (GILS) encompasses a global vision framed by the fundamental values of open societies. Societal values such as a free flow of information impose certain requirements on the society's information infrastructure. These requirements in turn shape the various laws, policies, standards, and technologies that determine the infrastructure design. A particular focus of GILS is the requirement to provide the means for people to discover sources of data and information. Information discovery in the GILS vision is designed to be decentralized yet coherent, and globally comprehensive yet useful for detailed data. This article introduces basic concepts and design issues, with emphasis on the techniques by which GILS supports interoperability. It explains the practical implications of GILS for the common roles of organizations involved in handling information, from content provider through system engineer and intermediary to searcher. The article provides examples of GILS initiatives in various types of communities: bibliographic, geographic, environmental, and government. ?? 2001 Elsevier Science Inc.

Pollution magnet: nano-magnetite for arsenic removal from drinking water.

PubMed

Yavuz, Cafer T; Mayo, J T; Suchecki, Carmen; Wang, Jennifer; Ellsworth, Adam Z; D'Couto, Helen; Quevedo, Elizabeth; Prakash, Arjun; Gonzalez, Laura; Nguyen, Christina; Kelty, Christopher; Colvin, Vicki L

2010-08-01

Arsenic contamination in groundwater is a severe global problem, most notably in Southeast Asia where millions suffer from acute and chronic arsenic poisoning. Removing arsenic from groundwater in impoverished rural or urban areas without electricity and with no manufacturing infrastructure remains a significant challenge. Magnetite nanocrystals have proven to be useful in arsenic remediation and could feasibly be synthesized by a thermal decomposition method that employs refluxing of FeOOH and oleic acid in 1-octadecene in a laboratory setup. To reduce the initial cost of production, $US 2600/kg, and make this nanomaterial widely available, we suggest that inexpensive and accessible "everyday" chemicals be used. Here we show that it is possible to create functional and high-quality nanocrystals using methods appropriate for manufacturing in diverse and minimal infrastructure, even those without electricity. We suggest that the transfer of this knowledge is best achieved using an open source concept.

Infrastructure Commons in Economic Perspective

NASA Astrophysics Data System (ADS)

Frischmann, Brett M.

This chapter briefly summarizes a theory (developed in substantial detail elsewhere)1 that explains why there are strong economic arguments for managing and sustaining infrastructure resources in an openly accessible manner. This theory facilitates a better understanding of two related issues: how society benefits from infrastructure resources and how decisions about how to manage or govern infrastructure resources affect a wide variety of public and private interests. The key insights from this analysis are that infrastructure resources generate value as inputs into a wide range of productive processes and that the outputs from these processes are often public goods and nonmarket goods that generate positive externalities that benefit society as a whole. Managing such resources in an openly accessible manner may be socially desirable from an economic perspective because doing so facilitates these downstream productive activities. For example, managing the Internet infrastructure in an openly accessible manner facilitates active citizen involvement in the production and sharing of many different public and nonmarket goods. Over the last decade, this has led to increased opportunities for a wide range of citizens to engage in entrepreneurship, political discourse, social network formation, and community building, among many other activities. The chapter applies these insights to the network neutrality debate and suggests how the debate might be reframed to better account for the wide range of private and public interests at stake.

The Infrastructure of Open Educational Resources

ERIC Educational Resources Information Center

Smith, Marshall S.; Wang, Phoenix M.

2007-01-01

The success of OER is likely to depend on a flexible, extendable infrastructure that will meet the challenges of an evolving World Wide Web. In this article, the authors examine three key dimensions of this infrastructure--technical, legal/cultural/social/political, and research--and discuss possible directions for development. (Contains 1 table…

WebGL Visualisation of 3D Environmental Models Based on Finnish Open Geospatial Data Sets

NASA Astrophysics Data System (ADS)

Krooks, A.; Kahkonen, J.; Lehto, L.; Latvala, P.; Karjalainen, M.; Honkavaara, E.

2014-08-01

Recent developments in spatial data infrastructures have enabled real time GIS analysis and visualization using open input data sources and service interfaces. In this study we present a new concept where metric point clouds derived from national open airborne laser scanning (ALS) and photogrammetric image data are processed, analyzed, finally visualised a through open service interfaces to produce user-driven analysis products from targeted areas. The concept is demonstrated in three environmental applications: assessment of forest storm damages, assessment of volumetric changes in open pit mine and 3D city model visualization. One of the main objectives was to study the usability and requirements of national level photogrammetric imagery in these applications. The results demonstrated that user driven 3D geospatial analyses were possible with the proposed approach and current technology, for instance, the landowner could assess the amount of fallen trees within his property borders after a storm easily using any web browser. On the other hand, our study indicated that there are still many uncertainties especially due to the insufficient standardization of photogrammetric products and processes and their quality indicators.

Space Telecommunications Radio System (STRS) Compliance Testing

NASA Technical Reports Server (NTRS)

Handler, Louis M.

2011-01-01

The Space Telecommunications Radio System (STRS) defines an open architecture for software defined radios. This document describes the testing methodology to aid in determining the degree of compliance to the STRS architecture. Non-compliances are reported to the software and hardware developers as well as the NASA project manager so that any non-compliances may be fixed or waivers issued. Since the software developers may be divided into those that provide the operating environment including the operating system and STRS infrastructure (OE) and those that supply the waveform applications, the tests are divided accordingly. The static tests are also divided by the availability of an automated tool that determines whether the source code and configuration files contain the appropriate items. Thus, there are six separate step-by-step test procedures described as well as the corresponding requirements that they test. The six types of STRS compliance tests are: STRS application automated testing, STRS infrastructure automated testing, STRS infrastructure testing by compiling WFCCN with the infrastructure, STRS configuration file testing, STRS application manual code testing, and STRS infrastructure manual code testing. Examples of the input and output of the scripts are shown in the appendices as well as more specific information about what to configure and test in WFCCN for non-compliance. In addition, each STRS requirement is listed and the type of testing briefly described. Attached is also a set of guidelines on what to look for in addition to the requirements to aid in the document review process.

Multimedia courseware in an open-systems environment: a DoD strategy

NASA Astrophysics Data System (ADS)

Welsch, Lawrence A.

1991-03-01

The federal government is about to invest billions of dollars to develop multimedia training materials for delivery on computer-based interactive training systems. Acquisition of a variety of computers and peripheral devices hosting various operating systems and suites of authoring system software will be necessary to facilitate the development of this courseware. There is no single source that will satisfy all needs. Although high-performance, low-cost interactive training hardware is available, the products have proprietary software interfaces. Because the interfaces are proprietary, expensive reprogramming is usually required to adapt such software products to other platforms. This costly reprogramming could be eliminated by adopting standard software interfaces. DoD's Portable Courseware Project (PORTCO) is typical of projects worldwide that require standard software interfaces. This paper articulates the strategy whereby PORTCO leverages the open systems movement and the new realities of information technology. These realities encompass changes in the pace at which new technology becomes available, changes in organizational goals and philosophy, new roles of vendors and users, changes in the procurement process, and acceleration toward open system environments. The PORTCO strategy is applicable to all projects and systems that require open systems to achieve mission objectives. The federal goal is to facilitate the creation of an environment in which high quality portable courseware is available as commercial off-the-shelf products and is competitively supplied by a variety of vendors. In order to achieve this goal a system architecture incorporating standards to meet the users' needs must be established. The Request for Architecture (RFA) developed cooperatively by DoD and the National Institute of Standards and Technology (NIST) will generate the PORTCO systems architecture. This architecture must freely integrate the courseware and authoring software from the lower levels of machine architecture and systems service implementation. In addition, the systems architecture will establish how the application-specific technologies relate to other technologies. Further, a computer-based interactive training applications profile must be developed. This profile, along with the systems architecture derived as a result of the RFA, provides the basis for identifying the needed standards. NIST will then accelerate the development of these standards using, but not restricted to, existing standards activities within established standards forums. The federal multimedia courseware effort has adopted the Interactive Multimedia Association (INA) Recommended Practices for Interactive Video Portability as the baseline for the migration of computer-based interactive training systems to an open systems environment based upon international standards. The PORTCO strategy includes an evolutionary migration to a standards-based, Open System Environments (OSE). An important aspect of this migration strategy is to move to open systems via stepwise evolution rather than via quantum leaps. Another area of concern is that of infrastructure issues, such as maintaining and supporting the technologies required for computer-based interactive training. The federal multimedia initiative will use the RFA-based architecture to differentiate between those technologies that can be maintained and supported by existing infrastructure mechanisms and those that require new mechanisms. Existing infrastructure mechanisms will be used and where infrastructure mechanisms do not exist, the approach will be to place high priority on establishing the appropriate mechanisms. Establishing an infrastructure mechanism is a nontrivial task requiring sustained investment of resources.

Dynamic Extension of a Virtualized Cluster by using Cloud Resources

NASA Astrophysics Data System (ADS)

Oberst, Oliver; Hauth, Thomas; Kernert, David; Riedel, Stephan; Quast, Günter

2012-12-01

The specific requirements concerning the software environment within the HEP community constrain the choice of resource providers for the outsourcing of computing infrastructure. The use of virtualization in HPC clusters and in the context of cloud resources is therefore a subject of recent developments in scientific computing. The dynamic virtualization of worker nodes in common batch systems provided by ViBatch serves each user with a dynamically virtualized subset of worker nodes on a local cluster. Now it can be transparently extended by the use of common open source cloud interfaces like OpenNebula or Eucalyptus, launching a subset of the virtual worker nodes within the cloud. This paper demonstrates how a dynamically virtualized computing cluster is combined with cloud resources by attaching remotely started virtual worker nodes to the local batch system.

The Neurona at Home project: Simulating a large-scale cellular automata brain in a distributed computing environment

NASA Astrophysics Data System (ADS)

Acedo, L.; Villanueva-Oller, J.; Moraño, J. A.; Villanueva, R.-J.

2013-01-01

The Berkeley Open Infrastructure for Network Computing (BOINC) has become the standard open source solution for grid computing in the Internet. Volunteers use their computers to complete an small part of the task assigned by a dedicated server. We have developed a BOINC project called Neurona@Home whose objective is to simulate a cellular automata random network with, at least, one million neurons. We consider a cellular automata version of the integrate-and-fire model in which excitatory and inhibitory nodes can activate or deactivate neighbor nodes according to a set of probabilistic rules. Our aim is to determine the phase diagram of the model and its behaviour and to compare it with the electroencephalographic signals measured in real brains.

SBSI: an extensible distributed software infrastructure for parameter estimation in systems biology.

PubMed

Adams, Richard; Clark, Allan; Yamaguchi, Azusa; Hanlon, Neil; Tsorman, Nikos; Ali, Shakir; Lebedeva, Galina; Goltsov, Alexey; Sorokin, Anatoly; Akman, Ozgur E; Troein, Carl; Millar, Andrew J; Goryanin, Igor; Gilmore, Stephen

2013-03-01

Complex computational experiments in Systems Biology, such as fitting model parameters to experimental data, can be challenging to perform. Not only do they frequently require a high level of computational power, but the software needed to run the experiment needs to be usable by scientists with varying levels of computational expertise, and modellers need to be able to obtain up-to-date experimental data resources easily. We have developed a software suite, the Systems Biology Software Infrastructure (SBSI), to facilitate the parameter-fitting process. SBSI is a modular software suite composed of three major components: SBSINumerics, a high-performance library containing parallelized algorithms for performing parameter fitting; SBSIDispatcher, a middleware application to track experiments and submit jobs to back-end servers; and SBSIVisual, an extensible client application used to configure optimization experiments and view results. Furthermore, we have created a plugin infrastructure to enable project-specific modules to be easily installed. Plugin developers can take advantage of the existing user-interface and application framework to customize SBSI for their own uses, facilitated by SBSI's use of standard data formats. All SBSI binaries and source-code are freely available from http://sourceforge.net/projects/sbsi under an Apache 2 open-source license. The server-side SBSINumerics runs on any Unix-based operating system; both SBSIVisual and SBSIDispatcher are written in Java and are platform independent, allowing use on Windows, Linux and Mac OS X. The SBSI project website at http://www.sbsi.ed.ac.uk provides documentation and tutorials.

Application of Emerging Open-source Embedded Systems for Enabling Low-cost Wireless Mini-observatory Nodes in the Coastal Zone

NASA Astrophysics Data System (ADS)

Glazer, B. T.

2016-02-01

Here, we describe the development of novel, low-cost, open-source instrumentation to enable wireless data transfer of biogeochemical sensors in the coastal zone. The platform is centered upon the Beaglebone Black single board computer. Process-inquiry in environmental sciences suffers from undersampling; enabling sustained and unattended data collection typically involves expensive instrumentation and infrastructure deployed as cabled observatories with little flexibility in deployment location following initial installation. High cost of commercially-available or custom electronic packages have not only limited the number of sensor node sites that can be targeted by reasonably well-funded academic researchers, but have also entirely prohibited widespread engagement with K-12, public non-profit, and `citizen scientist' STEM audiences. The new platform under development represents a balanced blend of research-grade sensors and low-cost open-source electronics that are easily assembled. Custom, robust, open-source code that remains customizable for specific node configurations can match a specific deployment's measurement needs, depending on the scientific research priorities. We have demonstrated prototype capabilities and versatility through lab testing and field deployments of multiple sensor nodes with multiple sensor inputs, all of which are streaming near-real-time data over wireless RF links to a shore-based base station. On shore, first-pass data processing QA/QC takes place and near-real-time plots are made available on the World Wide Web. Specifically, we have worked closely with an environmental and cultural management and restoration non-profit organization, and middle and high school science classes, engaging their interest in STEM application to local watershed processes. Ultimately, continued successful development of this pilot project can lead to a coastal oceanographic analogue of the popular Weather Underground personal weather station model.

International Workshop on Educational Infrastructure: Conclusions (Summary of Proceedings, Guadalajara, Jalisco, Mexico, February 24-27, 2002).

ERIC Educational Resources Information Center

Organisation for Economic Cooperation and Development, Paris (France). Programme on Educational Building.

This document summarizes themes developed and conclusions from the International Workshop on Educational Infrastructure. The opening topic was "Delivering Education and Training in the Knowledge Society." It was clear to participants that educational infrastructure must go hand-in-hand with reengineering processes to adjust to the needs…

Seqcrawler: biological data indexing and browsing platform.

PubMed

Sallou, Olivier; Bretaudeau, Anthony; Roult, Aurelien

2012-07-24

Seqcrawler takes its roots in software like SRS or Lucegene. It provides an indexing platform to ease the search of data and meta-data in biological banks and it can scale to face the current flow of data. While many biological bank search tools are available on the Internet, mainly provided by large organizations to search their data, there is a lack of free and open source solutions to browse one's own set of data with a flexible query system and able to scale from a single computer to a cloud system. A personal index platform will help labs and bioinformaticians to search their meta-data but also to build a larger information system with custom subsets of data. The software is scalable from a single computer to a cloud-based infrastructure. It has been successfully tested in a private cloud with 3 index shards (pieces of index) hosting ~400 millions of sequence information (whole GenBank, UniProt, PDB and others) for a total size of 600 GB in a fault tolerant architecture (high-availability). It has also been successfully integrated with software to add extra meta-data from blast results to enhance users' result analysis. Seqcrawler provides a complete open source search and store solution for labs or platforms needing to manage large amount of data/meta-data with a flexible and customizable web interface. All components (search engine, visualization and data storage), though independent, share a common and coherent data system that can be queried with a simple HTTP interface. The solution scales easily and can also provide a high availability infrastructure.

TerraFERMA: The Transparent Finite Element Rapid Model Assembler for multiphysics problems in Earth sciences

NASA Astrophysics Data System (ADS)

Wilson, Cian R.; Spiegelman, Marc; van Keken, Peter E.

2017-02-01

We introduce and describe a new software infrastructure TerraFERMA, the Transparent Finite Element Rapid Model Assembler, for the rapid and reproducible description and solution of coupled multiphysics problems. The design of TerraFERMA is driven by two computational needs in Earth sciences. The first is the need for increased flexibility in both problem description and solution strategies for coupled problems where small changes in model assumptions can lead to dramatic changes in physical behavior. The second is the need for software and models that are more transparent so that results can be verified, reproduced, and modified in a manner such that the best ideas in computation and Earth science can be more easily shared and reused. TerraFERMA leverages three advanced open-source libraries for scientific computation that provide high-level problem description (FEniCS), composable solvers for coupled multiphysics problems (PETSc), and an options handling system (SPuD) that allows the hierarchical management of all model options. TerraFERMA integrates these libraries into an interface that organizes the scientific and computational choices required in a model into a single options file from which a custom compiled application is generated and run. Because all models share the same infrastructure, models become more reusable and reproducible, while still permitting the individual researcher considerable latitude in model construction. TerraFERMA solves partial differential equations using the finite element method. It is particularly well suited for nonlinear problems with complex coupling between components. TerraFERMA is open-source and available at http://terraferma.github.io, which includes links to documentation and example input files.

Data management in Oceanography at SOCIB

NASA Astrophysics Data System (ADS)

Joaquin, Tintoré; March, David; Lora, Sebastian; Sebastian, Kristian; Frontera, Biel; Gómara, Sonia; Pau Beltran, Joan

2014-05-01

SOCIB, the Balearic Islands Coastal Ocean Observing and Forecasting System (http://www.socib.es), is a Marine Research Infrastructure, a multiplatform distributed and integrated system, a facility of facilities that extends from the nearshore to the open sea and provides free, open and quality control data. SOCIB is a facility o facilities and has three major infrastructure components: (1) a distributed multiplatform observing system, (2) a numerical forecasting system, and (3) a data management and visualization system. We present the spatial data infrastructure and applications developed at SOCIB. One of the major goals of the SOCIB Data Centre is to provide users with a system to locate and download the data of interest (near real-time and delayed mode) and to visualize and manage the information. Following SOCIB principles, data need to be (1) discoverable and accessible, (2) freely available, and (3) interoperable and standardized. In consequence, SOCIB Data Centre Facility is implementing a general data management system to guarantee international standards, quality assurance and interoperability. The combination of different sources and types of information requires appropriate methods to ingest, catalogue, display, and distribute this information. SOCIB Data Centre is responsible for directing the different stages of data management, ranging from data acquisition to its distribution and visualization through web applications. The system implemented relies on open source solutions. In other words, the data life cycle relies in the following stages: • Acquisition: The data managed by SOCIB mostly come from its own observation platforms, numerical models or information generated from the activities in the SIAS Division. • Processing: Applications developed at SOCIB to deal with all collected platform data performing data calibration, derivation, quality control and standardization. • Archival: Storage in netCDF and spatial databases. • Distribution: Data web services using Thredds, Geoserver and RESTful own services. • Catalogue: Metadata is provided through the ncISO plugin in Thredds and Geonetwork. • Visualization: web and mobile applications to present SOCIB data to different user profiles. SOCIB data services and applications have been developed to provide response to science and society needs (eg. European initiatives such as Emodnet or Copernicus), by targeting different user profiles (eg. researchers, technicians, policy and decision makers, educators, students, and society in general). For example, SOCIB has developed applications to: 1) allow researchers and technicians to access oceanographic information; 2) provide decision support for oil spills response; 3) disseminate information about the coastal state for tourists and recreational users; 4) present coastal research in educational programs; and 5) offer easy and fast access to marine information through mobile devices. In conclusion, the organizational and conceptual structure of SOCIB's Data Centre and the components developed provide an example of marine information systems within the framework of new ocean observatories and/or marine research infrastructures.

Generation of open biomedical datasets through ontology-driven transformation and integration processes.

PubMed

Carmen Legaz-García, María Del; Miñarro-Giménez, José Antonio; Menárguez-Tortosa, Marcos; Fernández-Breis, Jesualdo Tomás

2016-06-03

Biomedical research usually requires combining large volumes of data from multiple heterogeneous sources, which makes difficult the integrated exploitation of such data. The Semantic Web paradigm offers a natural technological space for data integration and exploitation by generating content readable by machines. Linked Open Data is a Semantic Web initiative that promotes the publication and sharing of data in machine readable semantic formats. We present an approach for the transformation and integration of heterogeneous biomedical data with the objective of generating open biomedical datasets in Semantic Web formats. The transformation of the data is based on the mappings between the entities of the data schema and the ontological infrastructure that provides the meaning to the content. Our approach permits different types of mappings and includes the possibility of defining complex transformation patterns. Once the mappings are defined, they can be automatically applied to datasets to generate logically consistent content and the mappings can be reused in further transformation processes. The results of our research are (1) a common transformation and integration process for heterogeneous biomedical data; (2) the application of Linked Open Data principles to generate interoperable, open, biomedical datasets; (3) a software tool, called SWIT, that implements the approach. In this paper we also describe how we have applied SWIT in different biomedical scenarios and some lessons learned. We have presented an approach that is able to generate open biomedical repositories in Semantic Web formats. SWIT is able to apply the Linked Open Data principles in the generation of the datasets, so allowing for linking their content to external repositories and creating linked open datasets. SWIT datasets may contain data from multiple sources and schemas, thus becoming integrated datasets.

Primary care access barriers as reported by nonurgent emergency department users: implications for the US primary care infrastructure.

PubMed

Hefner, Jennifer L; Wexler, Randy; McAlearney, Ann Scheck

2015-01-01

The objective was to explore variation by insurance status in patient-reported barriers to accessing primary care. The authors fielded a brief, anonymous, voluntary survey of nonurgent emergency department (ED) visits at a large academic medical center and conducted descriptive analysis and thematic coding of 349 open-ended survey responses. The privately insured predominantly reported primary care infrastructure barriers-wait time in clinic and for an appointment, constraints related to conventional business hours, and difficulty finding a primary care provider (because of geography or lack of new patient openings). Half of those insured by Medicaid and/or Medicare also reported these infrastructure barriers. In contrast, the uninsured predominantly reported insurance, income, and transportation barriers. Given that insured nonurgent ED users frequently report infrastructure barriers, these should be the focus of patient-level interventions to reduce nonurgent ED use and of health system-level policies to enhance the capacity of the US primary care infrastructure. © 2014 by the American College of Medical Quality.

Quantifying the Benefits of Shallow Posthole Installation for the Future French Permanent Broadband Stations

NASA Astrophysics Data System (ADS)

Vergne, J.; Charade, O.; Bonaime, S.; Louis-Xavier, T.; Arnold, B.

2015-12-01

In the framework of the RESIF (réseau sismologique et géodésique français) infrastructure, more than one hundred new permanent broadband stations have to be deployed in metropolitan France within the forthcoming years. This requires a standardized installation method able to provide good noise level performance at a reasonable cost, especially for the 60 percent of stations that we expect to be settled in open environments. During the last two years we tested various types of sensor's hosting infrastructures with a strong focus on recently released posthole sensors that can be deployed at the bottom of shallow boreholes. Tests were performed at 3 different sites (two GEOSCOPE stations and a dedicated open-field prototype site) with geological conditions spanning from hard rocks to very soft soils. On each site, posthole sensors were deployed at different depths, from the surface to a maximum of 20m deep, and in different types of casing. Moreover, a reference sensor, either installed in a tunnel, a cellar or a seismic vault, has been operated continuously. We present a comprehensive comparison of the seismic noise level measured in the different hosting infrastructures and for several frequency bands corresponding to various sources of noise. At high and low frequencies, seismic noise level in some boreholes equals or outperforms the one obtained for the reference sensors. Between 0.005 and 0.05Hz, we observe a strong decrease of seismic noise level on the horizontal components in the deepest boreholes compared to near surface installations. This improvement can reach up to 30dB and is mostly due to a reduction in tilt noise induced by wind or local pressure variations. However, the absolute noise level that can be achieved clearly depends on the local geology. All these tests, together with estimated installation costs, point toward the deployment of sensors in shallow boreholes at the future French broadband stations located in open environments.

Mesh infrastructure for coupled multiprocess geophysical simulations

DOE PAGES

Garimella, Rao V.; Perkins, William A.; Buksas, Mike W.; ...

2014-01-01

We have developed a sophisticated mesh infrastructure capability to support large scale multiphysics simulations such as subsurface flow and reactive contaminant transport at storage sites as well as the analysis of the effects of a warming climate on the terrestrial arctic. These simulations involve a wide range of coupled processes including overland flow, subsurface flow, freezing and thawing of ice rich soil, accumulation, redistribution and melting of snow, biogeochemical processes involving plant matter and finally, microtopography evolution due to melting and degradation of ice wedges below the surface. In addition to supporting the usual topological and geometric queries about themore » mesh, the mesh infrastructure adds capabilities such as identifying columnar structures in the mesh, enabling deforming of the mesh subject to constraints and enabling the simultaneous use of meshes of different dimensionality for subsurface and surface processes. The generic mesh interface is capable of using three different open source mesh frameworks (MSTK, MOAB and STKmesh) under the hood allowing the developers to directly compare them and choose one that is best suited for the application's needs. We demonstrate the results of some simulations using these capabilities as well as present a comparison of the performance of the different mesh frameworks.« less

The Anatomy of a Grid portal

NASA Astrophysics Data System (ADS)

Licari, Daniele; Calzolari, Federico

2011-12-01

In this paper we introduce a new way to deal with Grid portals referring to our implementation. L-GRID is a light portal to access the EGEE/EGI Grid infrastructure via Web, allowing users to submit their jobs from a common Web browser in a few minutes, without any knowledge about the Grid infrastructure. It provides the control over the complete lifecycle of a Grid Job, from its submission and status monitoring, to the output retrieval. The system, implemented as client-server architecture, is based on the Globus Grid middleware. The client side application is based on a java applet; the server relies on a Globus User Interface. There is no need of user registration on the server side, and the user needs only his own X.509 personal certificate. The system is user-friendly, secure (it uses SSL protocol, mechanism for dynamic delegation and identity creation in public key infrastructures), highly customizable, open source, and easy to install. The X.509 personal certificate does not get out from the local machine. It allows to reduce the time spent for the job submission, granting at the same time a higher efficiency and a better security level in proxy delegation and management.

Multiphysics Application Coupling Toolkit

DOE Office of Scientific and Technical Information (OSTI.GOV)

Campbell, Michael T.

2013-12-02

This particular consortium implementation of the software integration infrastructure will, in large part, refactor portions of the Rocstar multiphysics infrastructure. Development of this infrastructure originated at the University of Illinois DOE ASCI Center for Simulation of Advanced Rockets (CSAR) to support the center's massively parallel multiphysics simulation application, Rocstar, and has continued at IllinoisRocstar, a small company formed near the end of the University-based program. IllinoisRocstar is now licensing these new developments as free, open source, in hopes to help improve their own and others' access to infrastructure which can be readily utilized in developing coupled or composite software systems;more » with particular attention to more rapid production and utilization of multiphysics applications in the HPC environment. There are two major pieces to the consortium implementation, the Application Component Toolkit (ACT), and the Multiphysics Application Coupling Toolkit (MPACT). The current development focus is the ACT, which is (will be) the substrate for MPACT. The ACT itself is built up from the components described in the technical approach. In particular, the ACT has the following major components: 1.The Component Object Manager (COM): The COM package provides encapsulation of user applications, and their data. COM also provides the inter-component function call mechanism. 2.The System Integration Manager (SIM): The SIM package provides constructs and mechanisms for orchestrating composite systems of multiply integrated pieces.« less

Open-Source Electronic Health Record Systems for Low-Resource Settings: Systematic Review.

PubMed

Syzdykova, Assel; Malta, André; Zolfo, Maria; Diro, Ermias; Oliveira, José Luis

2017-11-13

Despite the great impact of information and communication technologies on clinical practice and on the quality of health services, this trend has been almost exclusive to developed countries, whereas countries with poor resources suffer from many economic and social issues that have hindered the real benefits of electronic health (eHealth) tools. As a component of eHealth systems, electronic health records (EHRs) play a fundamental role in patient management and effective medical care services. Thus, the adoption of EHRs in regions with a lack of infrastructure, untrained staff, and ill-equipped health care providers is an important task. However, the main barrier to adopting EHR software in low- and middle-income countries is the cost of its purchase and maintenance, which highlights the open-source approach as a good solution for these underserved areas. The aim of this study was to conduct a systematic review of open-source EHR systems based on the requirements and limitations of low-resource settings. First, we reviewed existing literature on the comparison of available open-source solutions. In close collaboration with the University of Gondar Hospital, Ethiopia, we identified common limitations in poor resource environments and also the main requirements that EHRs should support. Then, we extensively evaluated the current open-source EHR solutions, discussing their strengths and weaknesses, and their appropriateness to fulfill a predefined set of features relevant for low-resource settings. The evaluation methodology allowed assessment of several key aspects of available solutions that are as follows: (1) integrated applications, (2) configurable reports, (3) custom reports, (4) custom forms, (5) interoperability, (6) coding systems, (7) authentication methods, (8) patient portal, (9) access control model, (10) cryptographic features, (11) flexible data model, (12) offline support, (13) native client, (14) Web client,(15) other clients, (16) code-based language, (17) development activity, (18) modularity, (19) user interface, (20) community support, and (21) customization. The quality of each feature is discussed for each of the evaluated solutions and a final comparison is presented. There is a clear demand for open-source, reliable, and flexible EHR systems in low-resource settings. In this study, we have evaluated and compared five open-source EHR systems following a multidimensional methodology that can provide informed recommendations to other implementers, developers, and health care professionals. We hope that the results of this comparison can guide decision making when needing to adopt, install, and maintain an open-source EHR solution in low-resource settings. ©Assel Syzdykova, André Malta, Maria Zolfo, Ermias Diro, José Luis Oliveira. Originally published in JMIR Medical Informatics (http://medinform.jmir.org), 13.11.2017.

Carbon Sequestration through Sustainably Sourced Algal Fertilizer: Deep Ocean Water.

NASA Astrophysics Data System (ADS)

Sherman, M. T.

2014-12-01

Drawing down carbon from the atmosphere happens in the oceans when marine plants are growing due to the use of carbon dioxide for biological processes and by raising the pH of the water. Macro- and microscopic marine photosynthesizers are limited in their growth by the availability of light and nutrients (nitrogen, phosphorous, iron, etc.) Deep ocean water (DOW), oceanic water from bellow about 1000m, is a natural medium for marine algae, which contains all (except in rare circumstances) necessary components for algal growth and represents over 90% of the volume of the ocean. The introduction of DOW to a tropical or summer sea can increase chlorophyll from near zero to 60 mg per M3 or more. The form of the utilization infrastructure for DOW can roughly be divided into two effective types; the unconstrained release and the open pond system. Unconstrained release has the advantage of having relatively low infrastructure investment and is available to any area of the ocean. The open pond system has high infrastructure costs but enables intensive use of DOW for harvesting macro- and microalgae and sustainable mariculture. It also enables greater concomitant production of DOW's other potential products such as electricity or potable water. However, unlike an unconstrained release the open pond system can capture much of the biomaterial from the water and limits the impact to the surrounding ecosystem. The Tidal Irrigation and Electrical System (TIESystem), is an open pond that is to be constructed on a continental shelf. It harnesses the tidal flux to pump DOW into the pond on the rising tide and then uses the falling tide to pump biologically rich material out of the pond. This biomaterial represents fixed CO2 and can be used for biofuel or fertilizers. The TIESystem benefits from an economy of scale that increases at a rate that is roughly equal to the relationship of the circumference of a circle (the barrier that creates the open pond) to the area of the pond multiplied by the tidal flux on that particular area of the continental shelf. Despite the large construction costs of artificial islands and structures robust enough to withstand the conditions of the continental shelf, the system will become economic as it grows in size. However, extensive research will be required to maximize the output of each subsystem and minimize the risk of pollution.

FixO3 : Early progress towards Open Ocean observatory Data Management Harmonisation

NASA Astrophysics Data System (ADS)

Pagnani, Maureen; Huber, Robert; Lampitt, Richard

2014-05-01

Since 2002 there has been a sustained effort, supported as European framework projects, to harmonise both the technology and the data management of Open Ocean fixed observatories run by European nations. FixO3 started in September 2013, and for 4 years will coordinate the convergence of data management best practice across a constellation of moorings in the Atlantic, in both hemispheres, and in the Mediterranean. To ensure the continued existence of these unique sources of oceanographic data as sustained observatories it is vital to improve access to the data collected, both in terms of methods of presentation, real-time availability, long-term archiving and quality assurance. The data management component of FixO3 will improve access to marine observatory data by harmonizing data management standards and workflows covering the complete life cycle of data from real time data acquisition to long-term archiving. Legal and data policy aspects will be examined to identify transnational barriers to open-access to marine observatory data. A harmonised FixO3 data policy is being synthesised from the partner's existing policies, which will overcome the identified barriers, and provide a formal basis for data exchange between FixO3 infrastructures. Presently, the interpretation and implementation of accepted standards has considerable incompatibilities within the observatory community, and these different approaches will be unified into the FixO3 approach. Further, FixO3 aims to harmonise data management and standardisation efforts with other European and international marine data and observatory infrastructures. The FixO3 synthesis will build on the standards established in other European infrastructures such as EDMONET, SEADATANET, PANGAEA, EuroSITES (European contribution to JCOMMP OceanSITES programme), and MyOcean (the Marine Core Service for GMES) infrastructures as well as relevant international infrastructures and data centres such as the ICOS Ocean Thematic Centre. The data management efforts are central to FixO3. Combined with the procedural and technological harmonisation, tackled in separate work packages, the FixO3 network of observatories will efficiently and cost effectively provide a consistent resource of quality controlled accessible oceanographic data The project website www.fixo3.eu is being developed as both a data showcase and single distribution point, and with database driven tools will enable the sharing of information between the observatories in the most smart and cost effective way. The network of knowledge built throughout the project will become a legacy resource that will ensure access to the unique ensemble data sets only achievable at these key observatories.

Data issues in the life sciences.

PubMed

Thessen, Anne E; Patterson, David J

2011-01-01

We review technical and sociological issues facing the Life Sciences as they transform into more data-centric disciplines - the "Big New Biology". Three major challenges are: 1) lack of comprehensive standards; 2) lack of incentives for individual scientists to share data; 3) lack of appropriate infrastructure and support. Technological advances with standards, bandwidth, distributed computing, exemplar successes, and a strong presence in the emerging world of Linked Open Data are sufficient to conclude that technical issues will be overcome in the foreseeable future. While motivated to have a shared open infrastructure and data pool, and pressured by funding agencies in move in this direction, the sociological issues determine progress. Major sociological issues include our lack of understanding of the heterogeneous data cultures within Life Sciences, and the impediments to progress include a lack of incentives to build appropriate infrastructures into projects and institutions or to encourage scientists to make data openly available.

Data issues in the life sciences

PubMed Central

Thessen, Anne E.; Patterson, David J.

2011-01-01

Abstract We review technical and sociological issues facing the Life Sciences as they transform into more data-centric disciplines - the “Big New Biology”. Three major challenges are: 1) lack of comprehensive standards; 2) lack of incentives for individual scientists to share data; 3) lack of appropriate infrastructure and support. Technological advances with standards, bandwidth, distributed computing, exemplar successes, and a strong presence in the emerging world of Linked Open Data are sufficient to conclude that technical issues will be overcome in the foreseeable future. While motivated to have a shared open infrastructure and data pool, and pressured by funding agencies in move in this direction, the sociological issues determine progress. Major sociological issues include our lack of understanding of the heterogeneous data cultures within Life Sciences, and the impediments to progress include a lack of incentives to build appropriate infrastructures into projects and institutions or to encourage scientists to make data openly available. PMID:22207805

Implementation and use of a highly available and innovative IaaS solution: the Cloud Area Padovana

NASA Astrophysics Data System (ADS)

Aiftimiei, C.; Andreetto, P.; Bertocco, S.; Biasotto, M.; Dal Pra, S.; Costa, F.; Crescente, A.; Dorigo, A.; Fantinel, S.; Fanzago, F.; Frizziero, E.; Gulmini, M.; Michelotto, M.; Sgaravatto, M.; Traldi, S.; Venaruzzo, M.; Verlato, M.; Zangrando, L.

2015-12-01

While in the business world the cloud paradigm is typically implemented purchasing resources and services from third party providers (e.g. Amazon), in the scientific environment there's usually the need of on-premises IaaS infrastructures which allow efficient usage of the hardware distributed among (and owned by) different scientific administrative domains. In addition, the requirement of open source adoption has led to the choice of products like OpenStack by many organizations. We describe a use case of the Italian National Institute for Nuclear Physics (INFN) which resulted in the implementation of a unique cloud service, called ’Cloud Area Padovana’, which encompasses resources spread over two different sites: the INFN Legnaro National Laboratories and the INFN Padova division. We describe how this IaaS has been implemented, which technologies have been adopted and how services have been configured in high-availability (HA) mode. We also discuss how identity and authorization management were implemented, adopting a widely accepted standard architecture based on SAML2 and OpenID: by leveraging the versatility of those standards the integration with authentication federations like IDEM was implemented. We also discuss some other innovative developments, such as a pluggable scheduler, implemented as an extension of the native OpenStack scheduler, which allows the allocation of resources according to a fair-share based model and which provides a persistent queuing mechanism for handling user requests that can not be immediately served. Tools, technologies, procedures used to install, configure, monitor, operate this cloud service are also discussed. Finally we present some examples that show how this IaaS infrastructure is being used.

Facilitating NASA Earth Science Data Processing Using Nebula Cloud Computing

NASA Technical Reports Server (NTRS)

Pham, Long; Chen, Aijun; Kempler, Steven; Lynnes, Christopher; Theobald, Michael; Asghar, Esfandiari; Campino, Jane; Vollmer, Bruce

2011-01-01

Cloud Computing has been implemented in several commercial arenas. The NASA Nebula Cloud Computing platform is an Infrastructure as a Service (IaaS) built in 2008 at NASA Ames Research Center and 2010 at GSFC. Nebula is an open source Cloud platform intended to: a) Make NASA realize significant cost savings through efficient resource utilization, reduced energy consumption, and reduced labor costs. b) Provide an easier way for NASA scientists and researchers to efficiently explore and share large and complex data sets. c) Allow customers to provision, manage, and decommission computing capabilities on an as-needed bases

Action Recommendation for Cyber Resilience

DOE Office of Scientific and Technical Information (OSTI.GOV)

Choudhury, Sutanay; Rodriguez, Luke R.; Curtis, Darren S.

2015-09-01

This paper presents an unifying graph-based model for representing the infrastructure, behavior and missions of an enterprise. We describe how the model can be used to achieve resiliency against a wide class of failures and attacks. We introduce an algorithm for recommending resilience establishing actions based on dynamic updates to the models. Without loss of generality, we show the effectiveness of the algorithm for preserving latency based quality of service (QoS). Our models and the recommendation algorithms are implemented in a software framework that we seek to release as an open source framework for simulating resilient cyber systems.

Web catalog of oceanographic data using GeoNetwork

NASA Astrophysics Data System (ADS)

Marinova, Veselka; Stefanov, Asen

2017-04-01

Most of the data collected, analyzed and used by Bulgarian oceanographic data center (BgODC) from scientific cruises, argo floats, ferry boxes and real time operating systems are spatially oriented and need to be displayed on the map. The challenge is to make spatial information more accessible to users, decision makers and scientists. In order to meet this challenge, BgODC concentrate its efforts on improving dynamic and standardized access to their geospatial data as well as those from various related organizations and institutions. BgODC currently is implementing a project to create a geospatial portal for distributing metadata and search, exchange and harvesting spatial data. There are many open source software solutions able to create such spatial data infrastructure (SDI). Finally, the GeoNetwork open source is chosen, as it is already widespread. This software is free, effective and "cheap" solution for implementing SDI at organization level. It is platform independent and runs under many operating systems. Filling of the catalog goes through these practical steps: • Managing and storing data reliably within MS SQL spatial data base; • Registration of maps and data of various formats and sources in GeoServer (most popular open source geospatial server embedded with GeoNetwork) ; • Filling added meta data and publishing geospatial data at the desktop of GeoNetwork. GeoServer and GeoNetwork are based on Java so they require installing of a servlet engine like Tomcat. The experience gained from the use of GeoNetwork Open Source confirms that the catalog meets the requirements for data management and is flexible enough to customize. Building the catalog facilitates sustainable data exchange between end users. The catalog is a big step towards implementation of the INSPIRE directive due to availability of many features necessary for producing "INSPIRE compliant" metadata records. The catalog now contains all available GIS data provided by BgODC for Internet access. Searching data within the catalog is based upon geographic extent, theme type and free text search.

ATLAS (Automatic Tool for Local Assembly Structures) - A Comprehensive Infrastructure for Assembly, Annotation, and Genomic Binning of Metagenomic and Metaranscripomic Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

White, Richard A.; Brown, Joseph M.; Colby, Sean M.

ATLAS (Automatic Tool for Local Assembly Structures) is a comprehensive multiomics data analysis pipeline that is massively parallel and scalable. ATLAS contains a modular analysis pipeline for assembly, annotation, quantification and genome binning of metagenomics and metatranscriptomics data and a framework for reference metaproteomic database construction. ATLAS transforms raw sequence data into functional and taxonomic data at the microbial population level and provides genome-centric resolution through genome binning. ATLAS provides robust taxonomy based on majority voting of protein coding open reading frames rolled-up at the contig level using modified lowest common ancestor (LCA) analysis. ATLAS provides robust taxonomy based onmore » majority voting of protein coding open reading frames rolled-up at the contig level using modified lowest common ancestor (LCA) analysis. ATLAS is user-friendly, easy install through bioconda maintained as open-source on GitHub, and is implemented in Snakemake for modular customizable workflows.« less

Creating an open environment software infrastructure

NASA Technical Reports Server (NTRS)

Jipping, Michael J.

1992-01-01

As the development of complex computer hardware accelerates at increasing rates, the ability of software to keep pace is essential. The development of software design tools, however, is falling behind the development of hardware for several reasons, the most prominent of which is the lack of a software infrastructure to provide an integrated environment for all parts of a software system. The research was undertaken to provide a basis for answering this problem by investigating the requirements of open environments.

Application of large-scale computing infrastructure for diverse environmental research applications using GC3Pie

NASA Astrophysics Data System (ADS)

Maffioletti, Sergio; Dawes, Nicholas; Bavay, Mathias; Sarni, Sofiane; Lehning, Michael

2013-04-01

The Swiss Experiment platform (SwissEx: http://www.swiss-experiment.ch) provides a distributed storage and processing infrastructure for environmental research experiments. The aim of the second phase project (the Open Support Platform for Environmental Research, OSPER, 2012-2015) is to develop the existing infrastructure to provide scientists with an improved workflow. This improved workflow will include pre-defined, documented and connected processing routines. A large-scale computing and data facility is required to provide reliable and scalable access to data for analysis, and it is desirable that such an infrastructure should be free of traditional data handling methods. Such an infrastructure has been developed using the cloud-based part of the Swiss national infrastructure SMSCG (http://www.smscg.ch) and Academic Cloud. The infrastructure under construction supports two main usage models: 1) Ad-hoc data analysis scripts: These scripts are simple processing scripts, written by the environmental researchers themselves, which can be applied to large data sets via the high power infrastructure. Examples of this type of script are spatial statistical analysis scripts (R-based scripts), mostly computed on raw meteorological and/or soil moisture data. These provide processed output in the form of a grid, a plot, or a kml. 2) Complex models: A more intense data analysis pipeline centered (initially) around the physical process model, Alpine3D, and the MeteoIO plugin; depending on the data set, this may require a tightly coupled infrastructure. SMSCG already supports Alpine3D executions as both regular grid jobs and as virtual software appliances. A dedicated appliance with the Alpine3D specific libraries has been created and made available through the SMSCG infrastructure. The analysis pipelines are activated and supervised by simple control scripts that, depending on the data fetched from the meteorological stations, launch new instances of the Alpine3D appliance, execute location-based subroutines at each grid point and store the results back into the central repository for post-processing. An optional extension of this infrastructure will be to provide a 'ring buffer'-type database infrastructure, such that model results (e.g. test runs made to check parameter dependency or for development) can be visualised and downloaded after completion without submitting them to a permanent storage infrastructure. Data organization Data collected from sensors are archived and classified in distributed sites connected with an open-source software middleware, GSN. Publicly available data are available through common web services and via a cloud storage server (based on Swift). Collocation of the data and processing in the cloud would eventually eliminate data transfer requirements. Execution control logic Execution of the data analysis pipelines (for both the R-based analysis and the Alpine3D simulations) has been implemented using the GC3Pie framework developed by UZH. (https://code.google.com/p/gc3pie/). This allows large-scale, fault-tolerant execution of the pipelines to be described in terms of software appliances. GC3Pie also allows supervision of the execution of large campaigns of appliances as a single simulation. This poster will present the fundamental architectural components of the data analysis pipelines together with initial experimental results.

BioBlend: automating pipeline analyses within Galaxy and CloudMan.

PubMed

Sloggett, Clare; Goonasekera, Nuwan; Afgan, Enis

2013-07-01

We present BioBlend, a unified API in a high-level language (python) that wraps the functionality of Galaxy and CloudMan APIs. BioBlend makes it easy for bioinformaticians to automate end-to-end large data analysis, from scratch, in a way that is highly accessible to collaborators, by allowing them to both provide the required infrastructure and automate complex analyses over large datasets within the familiar Galaxy environment. http://bioblend.readthedocs.org/. Automated installation of BioBlend is available via PyPI (e.g. pip install bioblend). Alternatively, the source code is available from the GitHub repository (https://github.com/afgane/bioblend) under the MIT open source license. The library has been tested and is working on Linux, Macintosh and Windows-based systems.

Advancing global marine biogeography research with open-source GIS software and cloud-computing

USGS Publications Warehouse

Fujioka, Ei; Vanden Berghe, Edward; Donnelly, Ben; Castillo, Julio; Cleary, Jesse; Holmes, Chris; McKnight, Sean; Halpin, patrick

2012-01-01

Across many scientific domains, the ability to aggregate disparate datasets enables more meaningful global analyses. Within marine biology, the Census of Marine Life served as the catalyst for such a global data aggregation effort. Under the Census framework, the Ocean Biogeographic Information System was established to coordinate an unprecedented aggregation of global marine biogeography data. The OBIS data system now contains 31.3 million observations, freely accessible through a geospatial portal. The challenges of storing, querying, disseminating, and mapping a global data collection of this complexity and magnitude are significant. In the face of declining performance and expanding feature requests, a redevelopment of the OBIS data system was undertaken. Following an Open Source philosophy, the OBIS technology stack was rebuilt using PostgreSQL, PostGIS, GeoServer and OpenLayers. This approach has markedly improved the performance and online user experience while maintaining a standards-compliant and interoperable framework. Due to the distributed nature of the project and increasing needs for storage, scalability and deployment flexibility, the entire hardware and software stack was built on a Cloud Computing environment. The flexibility of the platform, combined with the power of the application stack, enabled rapid re-development of the OBIS infrastructure, and ensured complete standards-compliance.

Enabling Data Intensive Science through Service Oriented Science: Virtual Laboratories and Science Gateways

NASA Astrophysics Data System (ADS)

Lescinsky, D. T.; Wyborn, L. A.; Evans, B. J. K.; Allen, C.; Fraser, R.; Rankine, T.

2014-12-01

We present collaborative work on a generic, modular infrastructure for virtual laboratories (VLs, similar to science gateways) that combine online access to data, scientific code, and computing resources as services that support multiple data intensive scientific computing needs across a wide range of science disciplines. We are leveraging access to 10+ PB of earth science data on Lustre filesystems at Australia's National Computational Infrastructure (NCI) Research Data Storage Infrastructure (RDSI) node, co-located with NCI's 1.2 PFlop Raijin supercomputer and a 3000 CPU core research cloud. The development, maintenance and sustainability of VLs is best accomplished through modularisation and standardisation of interfaces between components. Our approach has been to break up tightly-coupled, specialised application packages into modules, with identified best techniques and algorithms repackaged either as data services or scientific tools that are accessible across domains. The data services can be used to manipulate, visualise and transform multiple data types whilst the scientific tools can be used in concert with multiple scientific codes. We are currently designing a scalable generic infrastructure that will handle scientific code as modularised services and thereby enable the rapid/easy deployment of new codes or versions of codes. The goal is to build open source libraries/collections of scientific tools, scripts and modelling codes that can be combined in specially designed deployments. Additional services in development include: provenance, publication of results, monitoring, workflow tools, etc. The generic VL infrastructure will be hosted at NCI, but can access alternative computing infrastructures (i.e., public/private cloud, HPC).The Virtual Geophysics Laboratory (VGL) was developed as a pilot project to demonstrate the underlying technology. This base is now being redesigned and generalised to develop a Virtual Hazards Impact and Risk Laboratory (VHIRL); any enhancements and new capabilities will be incorporated into a generic VL infrastructure. At same time, we are scoping seven new VLs and in the process, identifying other common components to prioritise and focus development.

Cybernation : the American infrastructure in the information age : a technical primer on risks and reliability

DOT National Transportation Integrated Search

1997-04-01

The infrastructure on which American society depends, in sectors such as transportation, finance, energy, and telecommunications is becoming increasingly automated as advances in information technology open up new possibilities for improved service, ...

Asterism: an integrated, complete, and open-source approach for running seismologist continuous data-intensive analysis on heterogeneous systems

NASA Astrophysics Data System (ADS)

Ferreira da Silva, R.; Filgueira, R.; Deelman, E.; Atkinson, M.

2016-12-01

We present Asterism, an open source data-intensive framework, which combines the Pegasus and dispel4py workflow systems. Asterism aims to simplify the effort required to develop data-intensive applications that run across multiple heterogeneous resources, without users having to: re-formulate their methods according to different enactment systems; manage the data distribution across systems; parallelize their methods; co-place and schedule their methods with computing resources; and store and transfer large/small volumes of data. Asterism's key element is to leverage the strengths of each workflow system: dispel4py allows developing scientific applications locally and then automatically parallelize and scale them on a wide range of HPC infrastructures with no changes to the application's code; Pegasus orchestrates the distributed execution of applications while providing portability, automated data management, recovery, debugging, and monitoring, without users needing to worry about the particulars of the target execution systems. Asterism leverages the level of abstractions provided by each workflow system to describe hybrid workflows where no information about the underlying infrastructure is required beforehand. The feasibility of Asterism has been evaluated using the seismic ambient noise cross-correlation application, a common data-intensive analysis pattern used by many seismologists. The application preprocesses (Phase1) and cross-correlates (Phase2) traces from several seismic stations. The Asterism workflow is implemented as a Pegasus workflow composed of two tasks (Phase1 and Phase2), where each phase represents a dispel4py workflow. Pegasus tasks describe the in/output data at a logical level, the data dependency between tasks, and the e-Infrastructures and the execution engine to run each dispel4py workflow. We have instantiated the workflow using data from 1000 stations from the IRIS services, and run it across two heterogeneous resources described as Docker containers: MPI (Container2) and Storm (Container3) clusters (Figure 1). Each dispel4py workflow is mapped to a particular execution engine, and data transfers between resources are automatically handled by Pegasus. Asterism is freely available online at http://github.com/dispel4py/pegasus_dispel4py.

The Importance of Biodiversity E-infrastructures for Megadiverse Countries

PubMed Central

Canhos, Dora A. L.; Sousa-Baena, Mariane S.; de Souza, Sidnei; Maia, Leonor C.; Stehmann, João R.; Canhos, Vanderlei P.; De Giovanni, Renato; Bonacelli, Maria B. M.; Los, Wouter; Peterson, A. Townsend

2015-01-01

Addressing the challenges of biodiversity conservation and sustainable development requires global cooperation, support structures, and new governance models to integrate diverse initiatives and achieve massive, open exchange of data, tools, and technology. The traditional paradigm of sharing scientific knowledge through publications is not sufficient to meet contemporary demands that require not only the results but also data, knowledge, and skills to analyze the data. E-infrastructures are key in facilitating access to data and providing the framework for collaboration. Here we discuss the importance of e-infrastructures of public interest and the lack of long-term funding policies. We present the example of Brazil’s speciesLink network, an e-infrastructure that provides free and open access to biodiversity primary data and associated tools. SpeciesLink currently integrates 382 datasets from 135 national institutions and 13 institutions from abroad, openly sharing ~7.4 million records, 94% of which are associated to voucher specimens. Just as important as the data is the network of data providers and users. In 2014, more than 95% of its users were from Brazil, demonstrating the importance of local e-infrastructures in enabling and promoting local use of biodiversity data and knowledge. From the outset, speciesLink has been sustained through project-based funding, normally public grants for 2–4-year periods. In between projects, there are short-term crises in trying to keep the system operational, a fact that has also been observed in global biodiversity portals, as well as in social and physical sciences platforms and even in computing services portals. In the last decade, the open access movement propelled the development of many web platforms for sharing data. Adequate policies unfortunately did not follow the same tempo, and now many initiatives may perish. PMID:26204382

The Importance of Biodiversity E-infrastructures for Megadiverse Countries.

PubMed

Canhos, Dora A L; Sousa-Baena, Mariane S; de Souza, Sidnei; Maia, Leonor C; Stehmann, João R; Canhos, Vanderlei P; De Giovanni, Renato; Bonacelli, Maria B M; Los, Wouter; Peterson, A Townsend

2015-07-01

Addressing the challenges of biodiversity conservation and sustainable development requires global cooperation, support structures, and new governance models to integrate diverse initiatives and achieve massive, open exchange of data, tools, and technology. The traditional paradigm of sharing scientific knowledge through publications is not sufficient to meet contemporary demands that require not only the results but also data, knowledge, and skills to analyze the data. E-infrastructures are key in facilitating access to data and providing the framework for collaboration. Here we discuss the importance of e-infrastructures of public interest and the lack of long-term funding policies. We present the example of Brazil's speciesLink network, an e-infrastructure that provides free and open access to biodiversity primary data and associated tools. SpeciesLink currently integrates 382 datasets from 135 national institutions and 13 institutions from abroad, openly sharing ~7.4 million records, 94% of which are associated to voucher specimens. Just as important as the data is the network of data providers and users. In 2014, more than 95% of its users were from Brazil, demonstrating the importance of local e-infrastructures in enabling and promoting local use of biodiversity data and knowledge. From the outset, speciesLink has been sustained through project-based funding, normally public grants for 2-4-year periods. In between projects, there are short-term crises in trying to keep the system operational, a fact that has also been observed in global biodiversity portals, as well as in social and physical sciences platforms and even in computing services portals. In the last decade, the open access movement propelled the development of many web platforms for sharing data. Adequate policies unfortunately did not follow the same tempo, and now many initiatives may perish.

3D Surveying, Modeling and Geo-Information System of the New Campus of ITB-Indonesia

NASA Astrophysics Data System (ADS)

Suwardhi, D.; Trisyanti, S. W.; Ainiyah, N.; Fajri, M. N.; Hanan, H.; Virtriana, R.; Edmarani, A. A.

2016-10-01

The new campus of ITB-Indonesia, which is located at Jatinangor, requires good facilities and infrastructures to supporting all of campus activities. Those can not be separated from procurement and maintenance activities. Technology for procurement and maintenance of facilities and infrastructures -based computer (information system)- has been known as Building Information Modeling (BIM). Nowadays, that technology is more affordable with some of free software that easy to use and tailored to user needs. BIM has some disadvantages and it requires other technologies to complete it, namely Geographic Information System (GIS). BIM and GIS require surveying data to visualized landscape and buildings on Jatinangor ITB campus. This paper presents the on-going of an internal service program conducted by the researcher, academic staff and students for the university. The program including 3D surveying to support the data requirements for 3D modeling of buildings in CityGML and Industry Foundation Classes (IFC) data model. The entire 3D surveying will produce point clouds that can be used to make 3D model. The 3D modeling is divided into low and high levels of detail modeling. The low levels model is stored in 3D CityGML database, and the high levels model including interiors is stored in BIM Server. 3D model can be used to visualized the building and site of Jatinangor ITB campus. For facility management of campus, an geo-information system is developed that can be used for planning, constructing, and maintaining Jatinangor ITB's facilities and infrastructures. The system uses openMAINT, an open source solution for the Property & Facility Management.

Continuous in-situ methane measurements at paddy fields in a rural area of India with poor electric infrastructure, using a low-cost instrument based on open-path near-IR laser absorption spectroscopy

NASA Astrophysics Data System (ADS)

Hidemori, T.; Matsumi, Y.; Nakayama, T.; Kawasaki, M.; Sasago, H.; Takahashi, K.; Imasu, R.; Takeuchi, W.; Adachi, M.; Machida, T.; Terao, Y.; Nomura, S.; Dhaka, S. K.; Singh, J.

2015-12-01

In southeast and south Asia, the previous satellite observations suggest that the methane emission from rice paddies is significant and important source of methane during rainy season. Since it is difficult to measure methane stably and continuously at rural areas such as the paddy fields in terms of infrastructures and maintenances, there are large uncertainties in quantitative estimation of methane emission in these areas and there are needs for more certification between satellite and ground based measurements. To measure methane concentrations continuously at difficult situations such as the center of paddy fields　and wetlands, we developed the continuous in-situ measurement system, not to look for your lost keys under the streetlight. The methane gas sensor is used an open-path laser based measurement instrument (LaserMethane, ANRITSU CORPORATION), which can quickly and selectively detect average methane concentrations on the optical path of the laser beam. The developed system has the power supply and telecommunication system to run the laser gas sensor in rural areas with poor electricity infrastructure.The methane measurement system was installed at paddy fields of Sonepat, Haryana on the north of Delhi in India and has been operated from the end of 2014. The air sampling along with our measurement has been carried out once a week during daytime to calibrate the laser instrument. We found that the seasonal variation of methane concentrations was different from the satellite observations and there were significant diurnal variations, which it was difficult to detect from occasional air samplings. We will present details of the measurement system and recent results of continuous methane measurements in India.

Centralized Fabric Management Using Puppet, Git, and GLPI

NASA Astrophysics Data System (ADS)

Smith, Jason A.; De Stefano, John S., Jr.; Fetzko, John; Hollowell, Christopher; Ito, Hironori; Karasawa, Mizuki; Pryor, James; Rao, Tejas; Strecker-Kellogg, William

2012-12-01

Managing the infrastructure of a large and complex data center can be extremely difficult without taking advantage of recent technological advances in administrative automation. Puppet is a seasoned open-source tool that is designed for enterprise class centralized configuration management. At the RHIC and ATLAS Computing Facility (RACF) at Brookhaven National Laboratory, we use Puppet along with Git, GLPI, and some custom scripts as part of our centralized configuration management system. In this paper, we discuss how we use these tools for centralized configuration management of our servers and services, change management requiring authorized approval of production changes, a complete version controlled history of all changes made, separation of production, testing and development systems using puppet environments, semi-automated server inventory using GLPI, and configuration change monitoring and reporting using the Puppet dashboard. We will also discuss scalability and performance results from using these tools on a 2,000+ node cluster and 400+ infrastructure servers with an administrative staff of approximately 25 full-time employees (FTEs).

Improving the analysis, storage and sharing of neuroimaging data using relational databases and distributed computing.

PubMed

Hasson, Uri; Skipper, Jeremy I; Wilde, Michael J; Nusbaum, Howard C; Small, Steven L

2008-01-15

The increasingly complex research questions addressed by neuroimaging research impose substantial demands on computational infrastructures. These infrastructures need to support management of massive amounts of data in a way that affords rapid and precise data analysis, to allow collaborative research, and to achieve these aims securely and with minimum management overhead. Here we present an approach that overcomes many current limitations in data analysis and data sharing. This approach is based on open source database management systems that support complex data queries as an integral part of data analysis, flexible data sharing, and parallel and distributed data processing using cluster computing and Grid computing resources. We assess the strengths of these approaches as compared to current frameworks based on storage of binary or text files. We then describe in detail the implementation of such a system and provide a concrete description of how it was used to enable a complex analysis of fMRI time series data.

Evaluating a scalable model for implementing electronic health records in resource-limited settings.

PubMed

Were, Martin C; Emenyonu, Nneka; Achieng, Marion; Shen, Changyu; Ssali, John; Masaba, John P M; Tierney, William M

2010-01-01

Current models for implementing electronic health records (EHRs) in resource-limited settings may not be scalable because they fail to address human-resource and cost constraints. This paper describes an implementation model which relies on shared responsibility between local sites and an external three-pronged support infrastructure consisting of: (1) a national technical expertise center, (2) an implementer's community, and (3) a developer's community. This model was used to implement an open-source EHR in three Ugandan HIV-clinics. Pre-post time-motion study at one site revealed that Primary Care Providers spent a third less time in direct and indirect care of patients (p<0.001) and 40% more time on personal activities (p=0.09) after EHRs implementation. Time spent by previously enrolled patients with non-clinician staff fell by half (p=0.004) and with pharmacy by 63% (p<0.001). Surveyed providers were highly satisfied with the EHRs and its support infrastructure. This model offers a viable approach for broadly implementing EHRs in resource-limited settings.

Community-driven computational biology with Debian Linux.

PubMed

Möller, Steffen; Krabbenhöft, Hajo Nils; Tille, Andreas; Paleino, David; Williams, Alan; Wolstencroft, Katy; Goble, Carole; Holland, Richard; Belhachemi, Dominique; Plessy, Charles

2010-12-21

The Open Source movement and its technologies are popular in the bioinformatics community because they provide freely available tools and resources for research. In order to feed the steady demand for updates on software and associated data, a service infrastructure is required for sharing and providing these tools to heterogeneous computing environments. The Debian Med initiative provides ready and coherent software packages for medical informatics and bioinformatics. These packages can be used together in Taverna workflows via the UseCase plugin to manage execution on local or remote machines. If such packages are available in cloud computing environments, the underlying hardware and the analysis pipelines can be shared along with the software. Debian Med closes the gap between developers and users. It provides a simple method for offering new releases of software and data resources, thus provisioning a local infrastructure for computational biology. For geographically distributed teams it can ensure they are working on the same versions of tools, in the same conditions. This contributes to the world-wide networking of researchers.

Improving the Analysis, Storage and Sharing of Neuroimaging Data using Relational Databases and Distributed Computing

PubMed Central

Hasson, Uri; Skipper, Jeremy I.; Wilde, Michael J.; Nusbaum, Howard C.; Small, Steven L.

2007-01-01

The increasingly complex research questions addressed by neuroimaging research impose substantial demands on computational infrastructures. These infrastructures need to support management of massive amounts of data in a way that affords rapid and precise data analysis, to allow collaborative research, and to achieve these aims securely and with minimum management overhead. Here we present an approach that overcomes many current limitations in data analysis and data sharing. This approach is based on open source database management systems that support complex data queries as an integral part of data analysis, flexible data sharing, and parallel and distributed data processing using cluster computing and Grid computing resources. We assess the strengths of these approaches as compared to current frameworks based on storage of binary or text files. We then describe in detail the implementation of such a system and provide a concrete description of how it was used to enable a complex analysis of fMRI time series data. PMID:17964812

Funding knowledgebases: Towards a sustainable funding model for the UniProt use case

PubMed Central

Gabella, Chiara; Durinx, Christine; Appel, Ron

2018-01-01

Millions of life scientists across the world rely on bioinformatics data resources for their research projects. Data resources can be very expensive, especially those with a high added value as the expert-curated knowledgebases. Despite the increasing need for such highly accurate and reliable sources of scientific information, most of them do not have secured funding over the near future and often depend on short-term grants that are much shorter than their planning horizon. Additionally, they are often evaluated as research projects rather than as research infrastructure components. In this work, twelve funding models for data resources are described and applied on the case study of the Universal Protein Resource (UniProt), a key resource for protein sequences and functional information knowledge. We show that most of the models present inconsistencies with open access or equity policies, and that while some models do not allow to cover the total costs, they could potentially be used as a complementary income source. We propose the Infrastructure Model as a sustainable and equitable model for all core data resources in the life sciences. With this model, funding agencies would set aside a fixed percentage of their research grant volumes, which would subsequently be redistributed to core data resources according to well-defined selection criteria. This model, compatible with the principles of open science, is in agreement with several international initiatives such as the Human Frontiers Science Program Organisation (HFSPO) and the OECD Global Science Forum (GSF) project. Here, we have estimated that less than 1% of the total amount dedicated to research grants in the life sciences would be sufficient to cover the costs of the core data resources worldwide, including both knowledgebases and deposition databases. PMID:29333230

Software Attribution for Geoscience Applications in the Computational Infrastructure for Geodynamics

NASA Astrophysics Data System (ADS)

Hwang, L.; Dumit, J.; Fish, A.; Soito, L.; Kellogg, L. H.; Smith, M.

2015-12-01

Scientific software is largely developed by individual scientists and represents a significant intellectual contribution to the field. As the scientific culture and funding agencies move towards an expectation that software be open-source, there is a corresponding need for mechanisms to cite software, both to provide credit and recognition to developers, and to aid in discoverability of software and scientific reproducibility. We assess the geodynamic modeling community's current citation practices by examining more than 300 predominantly self-reported publications utilizing scientific software in the past 5 years that is available through the Computational Infrastructure for Geodynamics (CIG). Preliminary results indicate that authors cite and attribute software either through citing (in rank order) peer-reviewed scientific publications, a user's manual, and/or a paper describing the software code. Attributions maybe found directly in the text, in acknowledgements, in figure captions, or in footnotes. What is considered citable varies widely. Citations predominantly lack software version numbers or persistent identifiers to find the software package. Versioning may be implied through reference to a versioned user manual. Authors sometimes report code features used and whether they have modified the code. As an open-source community, CIG requests that researchers contribute their modifications to the repository. However, such modifications may not be contributed back to a repository code branch, decreasing the chances of discoverability and reproducibility. Survey results through CIG's Software Attribution for Geoscience Applications (SAGA) project suggest that lack of knowledge, tools, and workflows to cite codes are barriers to effectively implement the emerging citation norms. Generated on-demand attributions on software landing pages and a prototype extensible plug-in to automatically generate attributions in codes are the first steps towards reproducibility.

The Computational Infrastructure for Geodynamics as a Community of Practice

NASA Astrophysics Data System (ADS)

Hwang, L.; Kellogg, L. H.

2016-12-01

Computational Infrastructure for Geodynamics (CIG), geodynamics.org, originated in 2005 out of community recognition that the efforts of individual or small groups of researchers to develop scientifically-sound software is impossible to sustain, duplicates effort, and makes it difficult for scientists to adopt state-of-the art computational methods that promote new discovery. As a community of practice, participants in CIG share an interest in computational modeling in geodynamics and work together on open source software to build the capacity to support complex, extensible, scalable, interoperable, reliable, and reusable software in an effort to increase the return on investment in scientific software development and increase the quality of the resulting software. The group interacts regularly to learn from each other and better their practices formally through webinar series, workshops, and tutorials and informally through listservs and hackathons. Over the past decade, we have learned that successful scientific software development requires at a minimum: collaboration between domain-expert researchers, software developers and computational scientists; clearly identified and committed lead developer(s); well-defined scientific and computational goals that are regularly evaluated and updated; well-defined benchmarks and testing throughout development; attention throughout development to usability and extensibility; understanding and evaluation of the complexity of dependent libraries; and managed user expectations through education, training, and support. CIG's code donation standards provide the basis for recently formalized best practices in software development (geodynamics.org/cig/dev/best-practices/). Best practices include use of version control; widely used, open source software libraries; extensive test suites; portable configuration and build systems; extensive documentation internal and external to the code; and structured, human readable input formats.

Funding knowledgebases: Towards a sustainable funding model for the UniProt use case.

PubMed

Gabella, Chiara; Durinx, Christine; Appel, Ron

2017-01-01

Millions of life scientists across the world rely on bioinformatics data resources for their research projects. Data resources can be very expensive, especially those with a high added value as the expert-curated knowledgebases. Despite the increasing need for such highly accurate and reliable sources of scientific information, most of them do not have secured funding over the near future and often depend on short-term grants that are much shorter than their planning horizon. Additionally, they are often evaluated as research projects rather than as research infrastructure components. In this work, twelve funding models for data resources are described and applied on the case study of the Universal Protein Resource (UniProt), a key resource for protein sequences and functional information knowledge. We show that most of the models present inconsistencies with open access or equity policies, and that while some models do not allow to cover the total costs, they could potentially be used as a complementary income source. We propose the Infrastructure Model as a sustainable and equitable model for all core data resources in the life sciences. With this model, funding agencies would set aside a fixed percentage of their research grant volumes, which would subsequently be redistributed to core data resources according to well-defined selection criteria. This model, compatible with the principles of open science, is in agreement with several international initiatives such as the Human Frontiers Science Program Organisation (HFSPO) and the OECD Global Science Forum (GSF) project. Here, we have estimated that less than 1% of the total amount dedicated to research grants in the life sciences would be sufficient to cover the costs of the core data resources worldwide, including both knowledgebases and deposition databases.

An i2b2-based, generalizable, open source, self-scaling chronic disease registry

PubMed Central

Quan, Justin; Ortiz, David M; Bousvaros, Athos; Ilowite, Norman T; Inman, Christi J; Marsolo, Keith; McMurry, Andrew J; Sandborg, Christy I; Schanberg, Laura E; Wallace, Carol A; Warren, Robert W; Weber, Griffin M; Mandl, Kenneth D

2013-01-01

Objective Registries are a well-established mechanism for obtaining high quality, disease-specific data, but are often highly project-specific in their design, implementation, and policies for data use. In contrast to the conventional model of centralized data contribution, warehousing, and control, we design a self-scaling registry technology for collaborative data sharing, based upon the widely adopted Integrating Biology & the Bedside (i2b2) data warehousing framework and the Shared Health Research Information Network (SHRINE) peer-to-peer networking software. Materials and methods Focusing our design around creation of a scalable solution for collaboration within multi-site disease registries, we leverage the i2b2 and SHRINE open source software to create a modular, ontology-based, federated infrastructure that provides research investigators full ownership and access to their contributed data while supporting permissioned yet robust data sharing. We accomplish these objectives via web services supporting peer-group overlays, group-aware data aggregation, and administrative functions. Results The 56-site Childhood Arthritis & Rheumatology Research Alliance (CARRA) Registry and 3-site Harvard Inflammatory Bowel Diseases Longitudinal Data Repository now utilize i2b2 self-scaling registry technology (i2b2-SSR). This platform, extensible to federation of multiple projects within and between research networks, encompasses >6000 subjects at sites throughout the USA. Discussion We utilize the i2b2-SSR platform to minimize technical barriers to collaboration while enabling fine-grained control over data sharing. Conclusions The implementation of i2b2-SSR for the multi-site, multi-stakeholder CARRA Registry has established a digital infrastructure for community-driven research data sharing in pediatric rheumatology in the USA. We envision i2b2-SSR as a scalable, reusable solution facilitating interdisciplinary research across diseases. PMID:22733975

An i2b2-based, generalizable, open source, self-scaling chronic disease registry.

PubMed

Natter, Marc D; Quan, Justin; Ortiz, David M; Bousvaros, Athos; Ilowite, Norman T; Inman, Christi J; Marsolo, Keith; McMurry, Andrew J; Sandborg, Christy I; Schanberg, Laura E; Wallace, Carol A; Warren, Robert W; Weber, Griffin M; Mandl, Kenneth D

2013-01-01

Registries are a well-established mechanism for obtaining high quality, disease-specific data, but are often highly project-specific in their design, implementation, and policies for data use. In contrast to the conventional model of centralized data contribution, warehousing, and control, we design a self-scaling registry technology for collaborative data sharing, based upon the widely adopted Integrating Biology & the Bedside (i2b2) data warehousing framework and the Shared Health Research Information Network (SHRINE) peer-to-peer networking software. Focusing our design around creation of a scalable solution for collaboration within multi-site disease registries, we leverage the i2b2 and SHRINE open source software to create a modular, ontology-based, federated infrastructure that provides research investigators full ownership and access to their contributed data while supporting permissioned yet robust data sharing. We accomplish these objectives via web services supporting peer-group overlays, group-aware data aggregation, and administrative functions. The 56-site Childhood Arthritis & Rheumatology Research Alliance (CARRA) Registry and 3-site Harvard Inflammatory Bowel Diseases Longitudinal Data Repository now utilize i2b2 self-scaling registry technology (i2b2-SSR). This platform, extensible to federation of multiple projects within and between research networks, encompasses >6000 subjects at sites throughout the USA. We utilize the i2b2-SSR platform to minimize technical barriers to collaboration while enabling fine-grained control over data sharing. The implementation of i2b2-SSR for the multi-site, multi-stakeholder CARRA Registry has established a digital infrastructure for community-driven research data sharing in pediatric rheumatology in the USA. We envision i2b2-SSR as a scalable, reusable solution facilitating interdisciplinary research across diseases.

Putting the Information Infrastructure to Work. Report of the Information Infrastructure Task Force Committee on Applications and Technology. NIST Special Publication 857.

ERIC Educational Resources Information Center

National Inst. of Standards and Technology, Gaithersburg, MD.

An interconnection of computer networks, telecommunications services, and applications, the National Information Infrastructure (NII) can open up new vistas and profoundly change much of American life. This report explores some of the opportunities and obstacles to the use of the NII by people and organizations. The goal is to express how…

Integrating grey and green infrastructure to improve the health and well-being of urban populations

Treesearch

Erika S. Svendsen; Mary E. Northridge; Sara S. Metcalf

2012-01-01

One of the enduring lessons of cities is the essential relationship between grey infrastructure (e.g., streets and buildings) and green infrastructure (e.g., parks and open spaces). The design and management of natural resources to enhance human health and well-being may be traced back thousands of years to the earliest urban civilizations. From the irrigation projects...

The MED-SUV Multidisciplinary Interoperability Infrastructure

NASA Astrophysics Data System (ADS)

Mazzetti, Paolo; D'Auria, Luca; Reitano, Danilo; Papeschi, Fabrizio; Roncella, Roberto; Puglisi, Giuseppe; Nativi, Stefano

2016-04-01

In accordance with the international Supersite initiative concept, the MED-SUV (MEDiterranean SUpersite Volcanoes) European project (http://med-suv.eu/) aims to enable long-term monitoring experiment in two relevant geologically active regions of Europe prone to natural hazards: Mt. Vesuvio/Campi Flegrei and Mt. Etna. This objective requires the integration of existing components, such as monitoring systems and data bases and novel sensors for the measurements of volcanic parameters. Moreover, MED-SUV is also a direct contribution to the Global Earth Observation System of Systems (GEOSS) as one the volcano Supersites recognized by the Group on Earth Observation (GEO). To achieve its goal, MED-SUV set up an advanced e-infrastructure allowing the discovery of and access to heterogeneous data for multidisciplinary applications, and the integration with external systems like GEOSS. The MED-SUV overall infrastructure is conceived as a three layer architecture with the lower layer (Data level) including the identified relevant data sources, the mid-tier (Supersite level) including components for mediation and harmonization , and the upper tier (Global level) composed of the systems that MED-SUV must serve, such as GEOSS and possibly other global/community systems. The Data level is mostly composed of existing data sources, such as space agencies satellite data archives, the UNAVCO system, the INGV-Rome data service. They share data according to different specifications for metadata, data and service interfaces, and cannot be changed. Thus, the only relevant MED-SUV activity at this level was the creation of a MED-SUV local repository based on Web Accessible Folder (WAF) technology, deployed in the INGV site in Catania, and hosting in-situ data and products collected and generated during the project. The Supersite level is at the core of the MED-SUV architecture, since it must mediate between the disparate data sources in the layer below, and provide a harmonized view to the layer above. In order to address data and service heteogeneity, the MED-SUV infrastructure is based on the brokered architecture approach, implemented using the GI-suite Brokering Framework for discovery and access. The GI-Suite Brokering Framework has been extended and configured to broker all the identified relevant data sources. It is also able to publish data according to several de-iure and de-facto standards including OGC CSW and OpenSearch, facilitating the interconnection with external systems. At the Global level, MED-SUV identified the interconnection with GEOSS as the main requirement. Since MED-SUV Supersite level is implemented based on the same technology adopted in the current GEOSS Common Infrastructure (GCI) by the GEO Discovery and Access Broker (GEO DAB), no major interoperability problem is foreseen. The MED-SUV Multidisciplinary Interoperability Infrastructure is complemented by a user portal providing human-to-machine interaction, and enabling data discovery and access. The GI-Suite Brokering Framework APIs and javascript library support machine-to-machine interaction, enabling the creation of mobile and Web applications using information available through the MED-SUV Supersite.

Heterogeneous access and processing of EO-Data on a Cloud based Infrastructure delivering operational Products

NASA Astrophysics Data System (ADS)

Niggemann, F.; Appel, F.; Bach, H.; de la Mar, J.; Schirpke, B.; Dutting, K.; Rucker, G.; Leimbach, D.

2015-04-01

To address the challenges of effective data handling faced by Small and Medium Sized Enterprises (SMEs) a cloud-based infrastructure for accessing and processing of Earth Observation(EO)-data has been developed within the project APPS4GMES(www.apps4gmes.de). To gain homogenous multi mission data access an Input Data Portal (IDP) been implemented on this infrastructure. The IDP consists of an Open Geospatial Consortium (OGC) conformant catalogue, a consolidation module for format conversion and an OGC-conformant ordering framework. Metadata of various EO-sources and with different standards is harvested and transferred to an OGC conformant Earth Observation Product standard and inserted into the catalogue by a Metadata Harvester. The IDP can be accessed for search and ordering of the harvested datasets by the services implemented on the cloud infrastructure. Different land-surface services have been realised by the project partners, using the implemented IDP and cloud infrastructure. Results of these are customer ready products, as well as pre-products (e.g. atmospheric corrected EO data), serving as a basis for other services. Within the IDP an automated access to ESA's Sentinel-1 Scientific Data Hub has been implemented. Searching and downloading of the SAR data can be performed in an automated way. With the implementation of the Sentinel-1 Toolbox and own software, for processing of the datasets for further use, for example for Vista's snow monitoring, delivering input for the flood forecast services, can also be performed in an automated way. For performance tests of the cloud environment a sophisticated model based atmospheric correction and pre-classification service has been implemented. Tests conducted an automated synchronised processing of one entire Landsat 8 (LS-8) coverage for Germany and performance comparisons to standard desktop systems. Results of these tests, showing a performance improvement by the factor of six, proved the high flexibility and computing power of the cloud environment. To make full use of the cloud capabilities a possibility for automated upscaling of the hardware resources has been implemented. Together with the IDP infrastructure fast and automated processing of various satellite sources to deliver market ready products can be realised, thus increasing customer needs and numbers can be satisfied without loss of accuracy and quality.

The Information Superhighway and the National Information Infrastructure (NII).

ERIC Educational Resources Information Center

Griffith, Jane Bortnick; Smith, Marcia S.

1994-01-01

Discusses issues connected with the information superhighway and the National Information Infrastructure (NII). Topics addressed include principles for government action; economic benefits; regulations; applications; information policy; pending federal legislation; private sector/government relationship; open access and universal service; privacy…

iTools: a framework for classification, categorization and integration of computational biology resources.

PubMed

Dinov, Ivo D; Rubin, Daniel; Lorensen, William; Dugan, Jonathan; Ma, Jeff; Murphy, Shawn; Kirschner, Beth; Bug, William; Sherman, Michael; Floratos, Aris; Kennedy, David; Jagadish, H V; Schmidt, Jeanette; Athey, Brian; Califano, Andrea; Musen, Mark; Altman, Russ; Kikinis, Ron; Kohane, Isaac; Delp, Scott; Parker, D Stott; Toga, Arthur W

2008-05-28

The advancement of the computational biology field hinges on progress in three fundamental directions--the development of new computational algorithms, the availability of informatics resource management infrastructures and the capability of tools to interoperate and synergize. There is an explosion in algorithms and tools for computational biology, which makes it difficult for biologists to find, compare and integrate such resources. We describe a new infrastructure, iTools, for managing the query, traversal and comparison of diverse computational biology resources. Specifically, iTools stores information about three types of resources--data, software tools and web-services. The iTools design, implementation and resource meta-data content reflect the broad research, computational, applied and scientific expertise available at the seven National Centers for Biomedical Computing. iTools provides a system for classification, categorization and integration of different computational biology resources across space-and-time scales, biomedical problems, computational infrastructures and mathematical foundations. A large number of resources are already iTools-accessible to the community and this infrastructure is rapidly growing. iTools includes human and machine interfaces to its resource meta-data repository. Investigators or computer programs may utilize these interfaces to search, compare, expand, revise and mine meta-data descriptions of existent computational biology resources. We propose two ways to browse and display the iTools dynamic collection of resources. The first one is based on an ontology of computational biology resources, and the second one is derived from hyperbolic projections of manifolds or complex structures onto planar discs. iTools is an open source project both in terms of the source code development as well as its meta-data content. iTools employs a decentralized, portable, scalable and lightweight framework for long-term resource management. We demonstrate several applications of iTools as a framework for integrated bioinformatics. iTools and the complete details about its specifications, usage and interfaces are available at the iTools web page http://iTools.ccb.ucla.edu.

iTools: A Framework for Classification, Categorization and Integration of Computational Biology Resources

PubMed Central

Dinov, Ivo D.; Rubin, Daniel; Lorensen, William; Dugan, Jonathan; Ma, Jeff; Murphy, Shawn; Kirschner, Beth; Bug, William; Sherman, Michael; Floratos, Aris; Kennedy, David; Jagadish, H. V.; Schmidt, Jeanette; Athey, Brian; Califano, Andrea; Musen, Mark; Altman, Russ; Kikinis, Ron; Kohane, Isaac; Delp, Scott; Parker, D. Stott; Toga, Arthur W.

2008-01-01

The advancement of the computational biology field hinges on progress in three fundamental directions – the development of new computational algorithms, the availability of informatics resource management infrastructures and the capability of tools to interoperate and synergize. There is an explosion in algorithms and tools for computational biology, which makes it difficult for biologists to find, compare and integrate such resources. We describe a new infrastructure, iTools, for managing the query, traversal and comparison of diverse computational biology resources. Specifically, iTools stores information about three types of resources–data, software tools and web-services. The iTools design, implementation and resource meta - data content reflect the broad research, computational, applied and scientific expertise available at the seven National Centers for Biomedical Computing. iTools provides a system for classification, categorization and integration of different computational biology resources across space-and-time scales, biomedical problems, computational infrastructures and mathematical foundations. A large number of resources are already iTools-accessible to the community and this infrastructure is rapidly growing. iTools includes human and machine interfaces to its resource meta-data repository. Investigators or computer programs may utilize these interfaces to search, compare, expand, revise and mine meta-data descriptions of existent computational biology resources. We propose two ways to browse and display the iTools dynamic collection of resources. The first one is based on an ontology of computational biology resources, and the second one is derived from hyperbolic projections of manifolds or complex structures onto planar discs. iTools is an open source project both in terms of the source code development as well as its meta-data content. iTools employs a decentralized, portable, scalable and lightweight framework for long-term resource management. We demonstrate several applications of iTools as a framework for integrated bioinformatics. iTools and the complete details about its specifications, usage and interfaces are available at the iTools web page http://iTools.ccb.ucla.edu. PMID:18509477

Enabling systematic, harmonised and large-scale biofilms data computation: the Biofilms Experiment Workbench.

PubMed

Pérez-Rodríguez, Gael; Glez-Peña, Daniel; Azevedo, Nuno F; Pereira, Maria Olívia; Fdez-Riverola, Florentino; Lourenço, Anália

2015-03-01

Biofilms are receiving increasing attention from the biomedical community. Biofilm-like growth within human body is considered one of the key microbial strategies to augment resistance and persistence during infectious processes. The Biofilms Experiment Workbench is a novel software workbench for the operation and analysis of biofilms experimental data. The goal is to promote the interchange and comparison of data among laboratories, providing systematic, harmonised and large-scale data computation. The workbench was developed with AIBench, an open-source Java desktop application framework for scientific software development in the domain of translational biomedicine. Implementation favours free and open-source third-parties, such as the R statistical package, and reaches for the Web services of the BiofOmics database to enable public experiment deposition. First, we summarise the novel, free, open, XML-based interchange format for encoding biofilms experimental data. Then, we describe the execution of common scenarios of operation with the new workbench, such as the creation of new experiments, the importation of data from Excel spreadsheets, the computation of analytical results, the on-demand and highly customised construction of Web publishable reports, and the comparison of results between laboratories. A considerable and varied amount of biofilms data is being generated, and there is a critical need to develop bioinformatics tools that expedite the interchange and comparison of microbiological and clinical results among laboratories. We propose a simple, open-source software infrastructure which is effective, extensible and easy to understand. The workbench is freely available for non-commercial use at http://sing.ei.uvigo.es/bew under LGPL license. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

A Real-Time Web of Things Framework with Customizable Openness Considering Legacy Devices

PubMed Central

Zhao, Shuai; Yu, Le; Cheng, Bo

2016-01-01

With the development of the Internet of Things (IoT), resources and applications based on it have emerged on a large scale. However, most efforts are “silo” solutions where devices and applications are tightly coupled. Infrastructures are needed to connect sensors to the Internet, open up and break the current application silos and move to a horizontal application mode. Based on the concept of Web of Things (WoT), many infrastructures have been proposed to integrate the physical world with the Web. However, issues such as no real-time guarantee, lack of fine-grained control of data, and the absence of explicit solutions for integrating heterogeneous legacy devices, hinder their widespread and practical use. To address these issues, this paper proposes a WoT resource framework that provides the infrastructures for the customizable openness and sharing of users’ data and resources under the premise of ensuring the real-time behavior of their own applications. The proposed framework is validated by actual systems and experimental evaluations. PMID:27690038

A Real-Time Web of Things Framework with Customizable Openness Considering Legacy Devices.

PubMed

Zhao, Shuai; Yu, Le; Cheng, Bo

2016-09-28

With the development of the Internet of Things (IoT), resources and applications based on it have emerged on a large scale. However, most efforts are "silo" solutions where devices and applications are tightly coupled. Infrastructures are needed to connect sensors to the Internet, open up and break the current application silos and move to a horizontal application mode. Based on the concept of Web of Things (WoT), many infrastructures have been proposed to integrate the physical world with the Web. However, issues such as no real-time guarantee, lack of fine-grained control of data, and the absence of explicit solutions for integrating heterogeneous legacy devices, hinder their widespread and practical use. To address these issues, this paper proposes a WoT resource framework that provides the infrastructures for the customizable openness and sharing of users' data and resources under the premise of ensuring the real-time behavior of their own applications. The proposed framework is validated by actual systems and experimental evaluations.

Traleika Glacier X-Stack Extension Final Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fryman, Joshua

The XStack Extension Project continued along the direction of the XStack program in exploring the software tools and frameworks to support a task-based community runtime towards the goal of Exascale programming. The momentum built as part of the XStack project, with the development of the task-based Open Community Runtime (OCR) and related tools, was carried through during the XStack Extension with the focus areas of easing application development, improving performance and supporting more features. The infrastructure set up for a community-driven open-source development continued to be used towards these areas, with continued co-development of runtime and applications. A variety ofmore » OCR programming environments were studied, as described in Sections Revolutionary Programming Environments & Applications – to assist with application development on OCR, and we develop OCR Translator, a ROSE-based source-to-source compiler that parses high-level annotations in an MPI program to generate equivalent OCR code. Figure 2 compares the number of OCR objects needed to generate the 2D stencil workload using the translator, against manual approaches based on SPMD library or native coding. The rate of increase with the translator, with an increase in number of ranks, is consistent with other approaches. This is explored further in Section OCR Translator.« less

OOI CyberInfrastructure - Next Generation Oceanographic Research

NASA Astrophysics Data System (ADS)

Farcas, C.; Fox, P.; Arrott, M.; Farcas, E.; Klacansky, I.; Krueger, I.; Meisinger, M.; Orcutt, J.

2008-12-01

Software has become a key enabling technology for scientific discovery, observation, modeling, and exploitation of natural phenomena. New value emerges from the integration of individual subsystems into networked federations of capabilities exposed to the scientific community. Such data-intensive interoperability networks are crucial for future scientific collaborative research, as they open up new ways of fusing data from different sources and across various domains, and analysis on wide geographic areas. The recently established NSF OOI program, through its CyberInfrastructure component addresses this challenge by providing broad access from sensor networks for data acquisition up to computational grids for massive computations and binding infrastructure facilitating policy management and governance of the emerging system-of-scientific-systems. We provide insight into the integration core of this effort, namely, a hierarchic service-oriented architecture for a robust, performant, and maintainable implementation. We first discuss the relationship between data management and CI crosscutting concerns such as identity management, policy and governance, which define the organizational contexts for data access and usage. Next, we detail critical services including data ingestion, transformation, preservation, inventory, and presentation. To address interoperability issues between data represented in various formats we employ a semantic framework derived from the Earth System Grid technology, a canonical representation for scientific data based on DAP/OPeNDAP, and related data publishers such as ERDDAP. Finally, we briefly present the underlying transport based on a messaging infrastructure over the AMQP protocol, and the preservation based on a distributed file system through SDSC iRODS.

Open Source software and social networks: disruptive alternatives for medical imaging.

PubMed

Ratib, Osman; Rosset, Antoine; Heuberger, Joris

2011-05-01

In recent decades several major changes in computer and communication technology have pushed the limits of imaging informatics and PACS beyond the traditional system architecture providing new perspectives and innovative approach to a traditionally conservative medical community. Disruptive technologies such as the world-wide-web, wireless networking, Open Source software and recent emergence of cyber communities and social networks have imposed an accelerated pace and major quantum leaps in the progress of computer and technology infrastructure applicable to medical imaging applications. This paper reviews the impact and potential benefits of two major trends in consumer market software development and how they will influence the future of medical imaging informatics. Open Source software is emerging as an attractive and cost effective alternative to traditional commercial software developments and collaborative social networks provide a new model of communication that is better suited to the needs of the medical community. Evidence shows that successful Open Source software tools have penetrated the medical market and have proven to be more robust and cost effective than their commercial counterparts. Developed by developers that are themselves part of the user community, these tools are usually better adapted to the user's need and are more robust than traditional software programs being developed and tested by a large number of contributing users. This context allows a much faster and more appropriate development and evolution of the software platforms. Similarly, communication technology has opened up to the general public in a way that has changed the social behavior and habits adding a new dimension to the way people communicate and interact with each other. The new paradigms have also slowly penetrated the professional market and ultimately the medical community. Secure social networks allowing groups of people to easily communicate and exchange information is a new model that is particularly suitable for some specific groups of healthcare professional and for physicians. It has also changed the expectations of how patients wish to communicate with their physicians. Emerging disruptive technologies and innovative paradigm such as Open Source software are leading the way to a new generation of information systems that slowly will change the way physicians and healthcare providers as well as patients will interact and communicate in the future. The impact of these new technologies is particularly effective in image communication, PACS and teleradiology. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

78 FR 54454 - Open Meeting of the Information Security and Privacy Advisory Board

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-04

... include the following items: --Cybersecurity Executive Order 13636, Improving Critical Infrastructure Cybersecurity (78 FR 11737, February 19, 2013); Development of New Cybersecurity Framework; Request for Information (RFI)--Developing a Framework to Improve Critical Infrastructure Cybersecurity (78 FR 13024...

Opening the Classroom

ERIC Educational Resources Information Center

Watson, Richard T.; Boudreau, Marie-Claude; York, Paul T.; Greiner, Martina; Wynn, Donald E.

2008-01-01

We argue that information systems educators--and others in similarly dynamic professional disciplines--could benefit from an alternative infrastructure for learning. We present an "open classroom" model of education which expands upon Ferris' (2002) collaborative partnership model of education by integrating "open" technologies such as Wiki and…

The role of spatial data infrastructure in disaster recover: An economic case study for Christchurch, New Zealand

NASA Astrophysics Data System (ADS)

Coote, A. M.; Whiteman, B.; Carver, J.; Balakrishnan, A.

2013-12-01

The disastrous earthquake in Christchurch city centre and surrounding parts of the Canterbury region of New Zealand in February 2011 which resulted in over 120 fatalities, highlighted a number of deficiencies in the information systems available to those involved in first response and in the subsequent rebuild. The lack of interoperability of geospatial information systems in particular was highlighted within the Royal Commission report on the disaster. As a result of this high level 'something must be done' call to action, Land Information New Zealand (LINZ), the lead public agency in national geospatial data management, were asked to scope a programme of work to accelerate the creation of a Spatial Data Infrastructure (SDI) for the area. This paper will outline the work undertaken to scope and prioritise a programme addressing the most pressing information infrastructure issues and then prepare the business case setting out the benefit-cost justification for the investment required. The resulting programme encompasses many of the emerging opportunities in the geospatial field including 3D GIS, crowd sourcing and open data leading to challenges in how to evaluate the benefits of innovative and 'ground breaking' solutions. It also considers how to track benefits realisation in a rapidly changing environment requiring an agile approach to programme management.

Web-based access to near real-time and archived high-density time-series data: cyber infrastructure challenges & developments in the open-source Waveform Server

NASA Astrophysics Data System (ADS)

Reyes, J. C.; Vernon, F. L.; Newman, R. L.; Steidl, J. H.

2010-12-01

The Waveform Server is an interactive web-based interface to multi-station, multi-sensor and multi-channel high-density time-series data stored in Center for Seismic Studies (CSS) 3.0 schema relational databases (Newman et al., 2009). In the last twelve months, based on expanded specifications and current user feedback, both the server-side infrastructure and client-side interface have been extensively rewritten. The Python Twisted server-side code-base has been fundamentally modified to now present waveform data stored in cluster-based databases using a multi-threaded architecture, in addition to supporting the pre-existing single database model. This allows interactive web-based access to high-density (broadband @ 40Hz to strong motion @ 200Hz) waveform data that can span multiple years; the common lifetime of broadband seismic networks. The client-side interface expands on it's use of simple JSON-based AJAX queries to now incorporate a variety of User Interface (UI) improvements including standardized calendars for defining time ranges, applying on-the-fly data calibration to display SI-unit data, and increased rendering speed. This presentation will outline the various cyber infrastructure challenges we have faced while developing this application, the use-cases currently in existence, and the limitations of web-based application development.

A modular (almost) automatic set-up for elastic multi-tenants cloud (micro)infrastructures

NASA Astrophysics Data System (ADS)

Amoroso, A.; Astorino, F.; Bagnasco, S.; Balashov, N. A.; Bianchi, F.; Destefanis, M.; Lusso, S.; Maggiora, M.; Pellegrino, J.; Yan, L.; Yan, T.; Zhang, X.; Zhao, X.

2017-10-01

An auto-installing tool on an usb drive can allow for a quick and easy automatic deployment of OpenNebula-based cloud infrastructures remotely managed by a central VMDIRAC instance. A single team, in the main site of an HEP Collaboration or elsewhere, can manage and run a relatively large network of federated (micro-)cloud infrastructures, making an highly dynamic and elastic use of computing resources. Exploiting such an approach can lead to modular systems of cloud-bursting infrastructures addressing complex real-life scenarios.

Policy model for space economy infrastructure

NASA Astrophysics Data System (ADS)

Komerath, Narayanan; Nally, James; Zilin Tang, Elizabeth

2007-12-01

Extraterrestrial infrastructure is key to the development of a space economy. Means for accelerating transition from today's isolated projects to a broad-based economy are considered. A large system integration approach is proposed. The beginnings of an economic simulation model are presented, along with examples of how interactions and coordination bring down costs. A global organization focused on space infrastructure and economic expansion is proposed to plan, coordinate, fund and implement infrastructure construction. This entity also opens a way to raise low-cost capital and solve the legal and public policy issues of access to extraterrestrial resources.

Cyberinfrastructure for the digital brain: spatial standards for integrating rodent brain atlases

PubMed Central

Zaslavsky, Ilya; Baldock, Richard A.; Boline, Jyl

2014-01-01

Biomedical research entails capture and analysis of massive data volumes and new discoveries arise from data-integration and mining. This is only possible if data can be mapped onto a common framework such as the genome for genomic data. In neuroscience, the framework is intrinsically spatial and based on a number of paper atlases. This cannot meet today's data-intensive analysis and integration challenges. A scalable and extensible software infrastructure that is standards based but open for novel data and resources, is required for integrating information such as signal distributions, gene-expression, neuronal connectivity, electrophysiology, anatomy, and developmental processes. Therefore, the International Neuroinformatics Coordinating Facility (INCF) initiated the development of a spatial framework for neuroscience data integration with an associated Digital Atlasing Infrastructure (DAI). A prototype implementation of this infrastructure for the rodent brain is reported here. The infrastructure is based on a collection of reference spaces to which data is mapped at the required resolution, such as the Waxholm Space (WHS), a 3D reconstruction of the brain generated using high-resolution, multi-channel microMRI. The core standards of the digital atlasing service-oriented infrastructure include Waxholm Markup Language (WaxML): XML schema expressing a uniform information model for key elements such as coordinate systems, transformations, points of interest (POI)s, labels, and annotations; and Atlas Web Services: interfaces for querying and updating atlas data. The services return WaxML-encoded documents with information about capabilities, spatial reference systems (SRSs) and structures, and execute coordinate transformations and POI-based requests. Key elements of INCF-DAI cyberinfrastructure have been prototyped for both mouse and rat brain atlas sources, including the Allen Mouse Brain Atlas, UCSD Cell-Centered Database, and Edinburgh Mouse Atlas Project. PMID:25309417

Cyberinfrastructure for the digital brain: spatial standards for integrating rodent brain atlases.

PubMed

Zaslavsky, Ilya; Baldock, Richard A; Boline, Jyl

2014-01-01

Biomedical research entails capture and analysis of massive data volumes and new discoveries arise from data-integration and mining. This is only possible if data can be mapped onto a common framework such as the genome for genomic data. In neuroscience, the framework is intrinsically spatial and based on a number of paper atlases. This cannot meet today's data-intensive analysis and integration challenges. A scalable and extensible software infrastructure that is standards based but open for novel data and resources, is required for integrating information such as signal distributions, gene-expression, neuronal connectivity, electrophysiology, anatomy, and developmental processes. Therefore, the International Neuroinformatics Coordinating Facility (INCF) initiated the development of a spatial framework for neuroscience data integration with an associated Digital Atlasing Infrastructure (DAI). A prototype implementation of this infrastructure for the rodent brain is reported here. The infrastructure is based on a collection of reference spaces to which data is mapped at the required resolution, such as the Waxholm Space (WHS), a 3D reconstruction of the brain generated using high-resolution, multi-channel microMRI. The core standards of the digital atlasing service-oriented infrastructure include Waxholm Markup Language (WaxML): XML schema expressing a uniform information model for key elements such as coordinate systems, transformations, points of interest (POI)s, labels, and annotations; and Atlas Web Services: interfaces for querying and updating atlas data. The services return WaxML-encoded documents with information about capabilities, spatial reference systems (SRSs) and structures, and execute coordinate transformations and POI-based requests. Key elements of INCF-DAI cyberinfrastructure have been prototyped for both mouse and rat brain atlas sources, including the Allen Mouse Brain Atlas, UCSD Cell-Centered Database, and Edinburgh Mouse Atlas Project.

FOSS Tools for Research Data Management

NASA Astrophysics Data System (ADS)

Stender, Vivien; Jankowski, Cedric; Hammitzsch, Martin; Wächter, Joachim

2017-04-01

Established initiatives and organizations, e.g. the Initiative for Scientific Cyberinfrastructures (NSF, 2007) or the European Strategy Forum on Research Infrastructures (ESFRI, 2008), promote and foster the development of sustainable research infrastructures. These infrastructures aim the provision of services supporting scientists to search, visualize and access data, to collaborate and exchange information, as well as to publish data and other results. In this regard, Research Data Management (RDM) gains importance and thus requires the support by appropriate tools integrated in these infrastructures. Different projects provide arbitrary solutions to manage research data. However, within two projects - SUMARIO for land and water management and TERENO for environmental monitoring - solutions to manage research data have been developed based on Free and Open Source Software (FOSS) components. The resulting framework provides essential components for harvesting, storing and documenting research data, as well as for discovering, visualizing and downloading these data on the basis of standardized services stimulated considerably by enhanced data management approaches of Spatial Data Infrastructures (SDI). In order to fully exploit the potentials of these developments for enhancing data management in Geosciences the publication of software components, e.g. via GitHub, is not sufficient. We will use our experience to move these solutions into the cloud e.g. as PaaS or SaaS offerings. Our contribution will present data management solutions for the Geosciences developed in two projects. A sort of construction kit with FOSS components build the backbone for the assembly and implementation of projects specific platforms. Furthermore, an approach is presented to stimulate the reuse of FOSS RDM solutions with cloud concepts. In further projects specific RDM platforms can be set-up much faster, customized to the individual needs and tools can be added during the run-time.

78 FR 25254 - Announcing an Open Meeting of the Information Security and Privacy Advisory Board

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-30

... include the following items: --Cybersecurity Executive Order 13636, Improving Critical Infrastructure Cybersecurity (78 FR 11737, February 19, 2013); Development of New Cybersecurity Framework; Request for Information (RFI)--Developing a Framework to Improve Critical Infrastructure Cybersecurity (78 FR 13024...

Development of an Open Global Oil and Gas Infrastructure Inventory and Geodatabase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rose, Kelly

This submission contains a technical report describing the development process and visual graphics for the Global Oil and Gas Infrastructure database. Access the GOGI database using the following link: https://edx.netl.doe.gov/dataset/global-oil-gas-features-database

Hazards and accessibility: combining and visualizing threat and open infrastructure data for disaster management

NASA Astrophysics Data System (ADS)

Tost, Jordi; Ehmel, Fabian; Heidmann, Frank; Olen, Stephanie M.; Bookhagen, Bodo

2018-05-01

The assessment of natural hazards and risk has traditionally been built upon the estimation of threat maps, which are used to depict potential danger posed by a particular hazard throughout a given area. But when a hazard event strikes, infrastructure is a significant factor that can determine if the situation becomes a disaster. The vulnerability of the population in a region does not only depend on the area's local threat, but also on the geographical accessibility of the area. This makes threat maps by themselves insufficient for supporting real-time decision-making, especially for those tasks that involve the use of the road network, such as management of relief operations, aid distribution, or planning of evacuation routes, among others. To overcome this problem, this paper proposes a multidisciplinary approach divided in two parts. First, data fusion of satellite-based threat data and open infrastructure data from OpenStreetMap, introducing a threat-based routing service. Second, the visualization of this data through cartographic generalization and schematization. This emphasizes critical areas along roads in a simple way and allows users to visually evaluate the impact natural hazards may have on infrastructure. We develop and illustrate this methodology with a case study of landslide threat for an area in Colombia.

dCache, towards Federated Identities & Anonymized Delegation

NASA Astrophysics Data System (ADS)

Ashish, A.; Millar, AP; Mkrtchyan, T.; Fuhrmann, P.; Behrmann, G.; Sahakyan, M.; Adeyemi, O. S.; Starek, J.; Litvintsev, D.; Rossi, A.

2017-10-01

For over a decade, dCache has relied on the authentication and authorization infrastructure (AAI) offered by VOMS, Kerberos, Xrootd etc. Although the established infrastructure has worked well and provided sufficient security, the implementation of procedures and the underlying software is often seen as a burden, especially by smaller communities trying to adopt existing HEP software stacks [1]. Moreover, scientists are increasingly dependent on service portals for data access [2]. In this paper, we describe how federated identity management systems can facilitate the transition from traditional AAI infrastructure to novel solutions like OpenID Connect. We investigate the advantages offered by OpenID Connect in regards to ‘delegation of authentication’ and ‘credential delegation for offline access’. Additionally, we demonstrate how macaroons can provide a more fine-granular authorization mechanism that supports anonymized delegation.

Open Informational Ecosystems: The Missing Link for Sharing Educational Resources

ERIC Educational Resources Information Center

Kerres, Michael; Heinen, Richard

2015-01-01

Open educational resources are not available "as such". Their provision relies on a technological infrastructure of related services that can be described as an informational ecosystem. A closed informational ecosystem keeps educational resources within its boundary. An open informational ecosystem relies on the concurrence of…

The EPOS Legal and Governance Framework : tailoring the infrastructure to fit the needs of the EPOS services

NASA Astrophysics Data System (ADS)

Kohler, Elisabeth; Pedersen, Helle; Kontkanen, Pirjo; Korja, Annakaisa; Lauterjung, Jörn; Haslinger, Florian; Sangianantoni, Agata; Bartolini, Alessandro; Consortium, Epos

2016-04-01

One of the most important issues regarding a pan-European distributed large scale research infrastructure is the setting up of its legal and governance structure as this will shape the very operation of the undertaking, i.e. the decision-making process, the allocation of tasks and resources as well as the relationship between the different bodies. Ensuring long-term operational services requires a robust, coherent and transparent legal and governance framework across all of the EPOS TCS (Thematic Core Services) and ICS (Integrated Core Services) that is well aligned to the EPOS global architecture. The chosen model for the EPOS legal entity is the ERIC (European Research Infrastructure Consortium). While the statutory seat of EPOS-ERIC will be in Rome, Italy, most of the services will be hosted in other countries. Specific agreements between EPOS-ERIC and the legal bodies hosting EPOS services will be implemented to allow proper coordination of activities. The objective is to avoid multiple agreements and, where possible, to standardize them in order to reach a harmonized situation across all services. For the governance careful attention will be paid to the decision-making process, the type of decisions and the voting rights, the definition of responsibilities, rights and duties, the reporting mechanisms, as well as other issues like who within a TCS represents the service to the 'outside' world or who advices the TCS on which subjects. Data policy is another crucial issue as EPOS aims to provide interdisciplinary services to researchers interested in geoscience, including access to data, metadata, data products, software and IT tools. EPOS also provides access to computational resources for visualization and processing. Beyond the general principles of Open Access and Open Source the following questions have to be addressed: scope and nature of data that will be accepted; intellectual property rights in data and terms under which data will be shared; openness and availability of data; data privacy and security; publication and attribution; liability and violations or misuse of data. To support the challenges of the EPOS legal, governance, and also financial framework, EPOS will implement a sophisticated metadata catalog and associated integrated services in its ICT architecture.

ooi: OpenStack OCCI interface

NASA Astrophysics Data System (ADS)

López García, Álvaro; Fernández del Castillo, Enol; Orviz Fernández, Pablo

In this document we present an implementation of the Open Grid Forum's Open Cloud Computing Interface (OCCI) for OpenStack, namely ooi (Openstack occi interface, 2015) [1]. OCCI is an open standard for management tasks over cloud resources, focused on interoperability, portability and integration. ooi aims to implement this open interface for the OpenStack cloud middleware, promoting interoperability with other OCCI-enabled cloud management frameworks and infrastructures. ooi focuses on being non-invasive with a vanilla OpenStack installation, not tied to a particular OpenStack release version.

SBSI: an extensible distributed software infrastructure for parameter estimation in systems biology

PubMed Central

Adams, Richard; Clark, Allan; Yamaguchi, Azusa; Hanlon, Neil; Tsorman, Nikos; Ali, Shakir; Lebedeva, Galina; Goltsov, Alexey; Sorokin, Anatoly; Akman, Ozgur E.; Troein, Carl; Millar, Andrew J.; Goryanin, Igor; Gilmore, Stephen

2013-01-01

Summary: Complex computational experiments in Systems Biology, such as fitting model parameters to experimental data, can be challenging to perform. Not only do they frequently require a high level of computational power, but the software needed to run the experiment needs to be usable by scientists with varying levels of computational expertise, and modellers need to be able to obtain up-to-date experimental data resources easily. We have developed a software suite, the Systems Biology Software Infrastructure (SBSI), to facilitate the parameter-fitting process. SBSI is a modular software suite composed of three major components: SBSINumerics, a high-performance library containing parallelized algorithms for performing parameter fitting; SBSIDispatcher, a middleware application to track experiments and submit jobs to back-end servers; and SBSIVisual, an extensible client application used to configure optimization experiments and view results. Furthermore, we have created a plugin infrastructure to enable project-specific modules to be easily installed. Plugin developers can take advantage of the existing user-interface and application framework to customize SBSI for their own uses, facilitated by SBSI’s use of standard data formats. Availability and implementation: All SBSI binaries and source-code are freely available from http://sourceforge.net/projects/sbsi under an Apache 2 open-source license. The server-side SBSINumerics runs on any Unix-based operating system; both SBSIVisual and SBSIDispatcher are written in Java and are platform independent, allowing use on Windows, Linux and Mac OS X. The SBSI project website at http://www.sbsi.ed.ac.uk provides documentation and tutorials. Contact: stg@inf.ed.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23329415

The EarthServer Federation: State, Role, and Contribution to GEOSS

NASA Astrophysics Data System (ADS)

Merticariu, Vlad; Baumann, Peter

2016-04-01

The intercontinental EarthServer initiative has established a European datacube platform with proven scalability: known databases exceed 100 TB, and single queries have been split across more than 1,000 cloud nodes. Its service interface being rigorously based on the OGC "Big Geo Data" standards, Web Coverage Service (WCS) and Web Coverage Processing Service (WCPS), a series of clients can dock into the services, ranging from open-source OpenLayers and QGIS over open-source NASA WorldWind to proprietary ESRI ArcGIS. Datacube fusion in a "mix and match" style is supported by the platform technolgy, the rasdaman Array Database System, which transparently federates queries so that users simply approach any node of the federation to access any data item, internally optimized for minimal data transfer. Notably, rasdaman is part of GEOSS GCI. NASA is contributing its Web WorldWind virtual globe for user-friendly data extraction, navigation, and analysis. Integrated datacube / metadata queries are contributed by CITE. Current federation members include ESA (managed by MEEO sr.l.), Plymouth Marine Laboratory (PML), the European Centre for Medium-Range Weather Forecast (ECMWF), Australia's National Computational Infrastructure, and Jacobs University (adding in Planetary Science). Further data centers have expressed interest in joining. We present the EarthServer approach, discuss its underlying technology, and illustrate the contribution this datacube platform can make to GEOSS.

OpenROCS: a software tool to control robotic observatories

NASA Astrophysics Data System (ADS)

Colomé, Josep; Sanz, Josep; Vilardell, Francesc; Ribas, Ignasi; Gil, Pere

2012-09-01

We present the Open Robotic Observatory Control System (OpenROCS), an open source software platform developed for the robotic control of telescopes. It acts as a software infrastructure that executes all the necessary processes to implement responses to the system events that appear in the routine and non-routine operations associated to data-flow and housekeeping control. The OpenROCS software design and implementation provides a high flexibility to be adapted to different observatory configurations and event-action specifications. It is based on an abstract model that is independent of the specific hardware or software and is highly configurable. Interfaces to the system components are defined in a simple manner to achieve this goal. We give a detailed description of the version 2.0 of this software, based on a modular architecture developed in PHP and XML configuration files, and using standard communication protocols to interface with applications for hardware monitoring and control, environment monitoring, scheduling of tasks, image processing and data quality control. We provide two examples of how it is used as the core element of the control system in two robotic observatories: the Joan Oró Telescope at the Montsec Astronomical Observatory (Catalonia, Spain) and the SuperWASP Qatar Telescope at the Roque de los Muchachos Observatory (Canary Islands, Spain).

78 FR 40487 - National Infrastructure Advisory Council

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-05

... DEPARTMENT OF HOMELAND SECURITY [Docket No. DHS-2013-0033] National Infrastructure Advisory... (NIAC) will meet Monday, July 29, 2013, at the United States Access Board, 1331 F Street NW., Suite 800, Washington, DC 20004. The meeting will be open to the public. DATES: The NIAC will meet Monday, July 29, 2013...

DEVELOP MULTI-STRESSOR, OPEN ARCHITECTURE MODELING FRAMEWORK FOR ECOLOGICAL EXPOSURE FROM SITE TO WATERSHED SCALE

EPA Science Inventory

A number of multimedia modeling frameworks are currently being developed. The Multimedia Integrated Modeling System (MIMS) is one of these frameworks. A framework should be seen as more of a multimedia modeling infrastructure than a single software system. This infrastructure do...

The Federal Government and Information Technology Standards: Building the National Information Infrastructure.

ERIC Educational Resources Information Center

Radack, Shirley M.

1994-01-01

Examines the role of the National Institute of Standards and Technology (NIST) in the development of the National Information Infrastructure (NII). Highlights include the standards process; voluntary standards; Open Systems Interconnection problems; Internet Protocol Suite; consortia; government's role; and network security. (16 references) (LRW)

Digital data collection in paleoanthropology.

PubMed

Reed, Denné; Barr, W Andrew; Mcpherron, Shannon P; Bobe, René; Geraads, Denis; Wynn, Jonathan G; Alemseged, Zeresenay

2015-01-01

Understanding patterns of human evolution across space and time requires synthesizing data collected by independent research teams, and this effort is part of a larger trend to develop cyber infrastructure and e-science initiatives. At present, paleoanthropology cannot easily answer basic questions about the total number of fossils and artifacts that have been discovered, or exactly how those items were collected. In this paper, we examine the methodological challenges to data integration, with the hope that mitigating the technical obstacles will further promote data sharing. At a minimum, data integration efforts must document what data exist and how the data were collected (discovery), after which we can begin standardizing data collection practices with the aim of achieving combined analyses (synthesis). This paper outlines a digital data collection system for paleoanthropology. We review the relevant data management principles for a general audience and supplement this with technical details drawn from over 15 years of paleontological and archeological field experience in Africa and Europe. The system outlined here emphasizes free open-source software (FOSS) solutions that work on multiple computer platforms; it builds on recent advances in open-source geospatial software and mobile computing. © 2015 Wiley Periodicals, Inc.

SaDA: From Sampling to Data Analysis—An Extensible Open Source Infrastructure for Rapid, Robust and Automated Management and Analysis of Modern Ecological High-Throughput Microarray Data

PubMed Central

Singh, Kumar Saurabh; Thual, Dominique; Spurio, Roberto; Cannata, Nicola

2015-01-01

One of the most crucial characteristics of day-to-day laboratory information management is the collection, storage and retrieval of information about research subjects and environmental or biomedical samples. An efficient link between sample data and experimental results is absolutely important for the successful outcome of a collaborative project. Currently available software solutions are largely limited to large scale, expensive commercial Laboratory Information Management Systems (LIMS). Acquiring such LIMS indeed can bring laboratory information management to a higher level, but most of the times this requires a sufficient investment of money, time and technical efforts. There is a clear need for a light weighted open source system which can easily be managed on local servers and handled by individual researchers. Here we present a software named SaDA for storing, retrieving and analyzing data originated from microorganism monitoring experiments. SaDA is fully integrated in the management of environmental samples, oligonucleotide sequences, microarray data and the subsequent downstream analysis procedures. It is simple and generic software, and can be extended and customized for various environmental and biomedical studies. PMID:26047146

A high-throughput system for high-quality tomographic reconstruction of large datasets at Diamond Light Source

PubMed Central

Atwood, Robert C.; Bodey, Andrew J.; Price, Stephen W. T.; Basham, Mark; Drakopoulos, Michael

2015-01-01

Tomographic datasets collected at synchrotrons are becoming very large and complex, and, therefore, need to be managed efficiently. Raw images may have high pixel counts, and each pixel can be multidimensional and associated with additional data such as those derived from spectroscopy. In time-resolved studies, hundreds of tomographic datasets can be collected in sequence, yielding terabytes of data. Users of tomographic beamlines are drawn from various scientific disciplines, and many are keen to use tomographic reconstruction software that does not require a deep understanding of reconstruction principles. We have developed Savu, a reconstruction pipeline that enables users to rapidly reconstruct data to consistently create high-quality results. Savu is designed to work in an ‘orthogonal’ fashion, meaning that data can be converted between projection and sinogram space throughout the processing workflow as required. The Savu pipeline is modular and allows processing strategies to be optimized for users' purposes. In addition to the reconstruction algorithms themselves, it can include modules for identification of experimental problems, artefact correction, general image processing and data quality assessment. Savu is open source, open licensed and ‘facility-independent’: it can run on standard cluster infrastructure at any institution. PMID:25939626

SaDA: From Sampling to Data Analysis-An Extensible Open Source Infrastructure for Rapid, Robust and Automated Management and Analysis of Modern Ecological High-Throughput Microarray Data.

PubMed

Singh, Kumar Saurabh; Thual, Dominique; Spurio, Roberto; Cannata, Nicola

2015-06-03

One of the most crucial characteristics of day-to-day laboratory information management is the collection, storage and retrieval of information about research subjects and environmental or biomedical samples. An efficient link between sample data and experimental results is absolutely important for the successful outcome of a collaborative project. Currently available software solutions are largely limited to large scale, expensive commercial Laboratory Information Management Systems (LIMS). Acquiring such LIMS indeed can bring laboratory information management to a higher level, but most of the times this requires a sufficient investment of money, time and technical efforts. There is a clear need for a light weighted open source system which can easily be managed on local servers and handled by individual researchers. Here we present a software named SaDA for storing, retrieving and analyzing data originated from microorganism monitoring experiments. SaDA is fully integrated in the management of environmental samples, oligonucleotide sequences, microarray data and the subsequent downstream analysis procedures. It is simple and generic software, and can be extended and customized for various environmental and biomedical studies.

Do It Yourself (DIY) Earth Science Collaboratories Using Best Practices and Breakthrough Technologies

NASA Astrophysics Data System (ADS)

Stephan, E.

2017-12-01

The objective of published earth science study data results and literature on the Web should be to provide a means to integrate discoverable science resources through an open collaborative-Web. At the core of any open science collaborative infrastructure is the ability to discover, manage and ultimately use relevant data accessible to the collaboration. Equally important are the relationships between people, applications, services, and publications, which capture critical contextual knowledge that enable their effective use. While contributions of either irreproducible or costly data can be a great asset the inability of users being able to use the data intelligently or make sense of it, makes these investments not usable. An ability to describe ad-hoc discoverable usage methodologies, provide feedback to data producers, and identify and cite data in a systematic way by leveraging existing Web-enabled off the shelf technology is needed. Fortunately many break-through advancements in data publication best practices and government, open source, and commercial investments support consumers who can provide feedback, share experiences, and contribute back to the earth science ecosystem.

Solving a Health Information Management Problem. An international success story.

PubMed

Hannan, Terry J

2015-01-01

The management of health care delivery requires the availability of effective 'information management' tools based on e-technologies [eHealth]. In developed economies many of these 'tools' are readily available whereas in Low and Middle Income Countries (LMIC) there is limited access to eHealth technologies and this has been defined as the "digital divide". This paper provides a short introduction to the fundamental understanding of what is meant by information management in health care and how it applies to all social economies. The core of the paper describes the successful implementation of appropriate information management tools in a resource poor environment to manage the HIV/AIDS epidemic and other disease states, in sub-Saharan Africa and how the system has evolved to become the largest open source eHealth project in the world and become the health information infrastructure for several national eHealth economies. The system is known as Open MRS [www.openmrs.org). The continuing successful evolution of the OpenMRS project has permitted its key implementers to define core factors that are the foundations for successful eHealth projects.

Exploring the Earth Using Deep Learning Techniques

NASA Astrophysics Data System (ADS)

Larraondo, P. R.; Evans, B. J. K.; Antony, J.

2016-12-01

Research using deep neural networks have significantly matured in recent times, and there is now a surge in interest to apply such methods to Earth systems science and the geosciences. When combined with Big Data, we believe there are opportunities for significantly transforming a number of areas relevant to researchers and policy makers. In particular, by using a combination of data from a range of satellite Earth observations as well as computer simulations from climate models and reanalysis, we can gain new insights into the information that is locked within the data. Global geospatial datasets describe a wide range of physical and chemical parameters, which are mostly available using regular grids covering large spatial and temporal extents. This makes them perfect candidates to apply deep learning methods. So far, these techniques have been successfully applied to image analysis through the use of convolutional neural networks. However, this is only one field of interest, and there is potential for many more use cases to be explored. The deep learning algorithms require fast access to large amounts of data in the form of tensors and make intensive use of CPU in order to train its models. The Australian National Computational Infrastructure (NCI) has recently augmented its Raijin 1.2 PFlop supercomputer with hardware accelerators. Together with NCI's 3000 core high performance OpenStack cloud, these computational systems have direct access to NCI's 10+ PBytes of datasets and associated Big Data software technologies (see http://geonetwork.nci.org.au/ and http://nci.org.au/systems-services/national-facility/nerdip/). To effectively use these computing infrastructures requires that both the data and software are organised in a way that readily supports the deep learning software ecosystem. Deep learning software, such as the open source TensorFlow library, has allowed us to demonstrate the possibility of generating geospatial models by combining information from our different data sources. This opens the door to an exciting new way of generating products and extracting features that have previously been labour intensive. In this paper, we will explore some of these geospatial use cases and share some of the lessons learned from this experience.

Architecture for autonomy

NASA Astrophysics Data System (ADS)

Broten, Gregory S.; Monckton, Simon P.; Collier, Jack; Giesbrecht, Jared

2006-05-01

In 2002 Defence R&D Canada changed research direction from pure tele-operated land vehicles to general autonomy for land, air, and sea craft. The unique constraints of the military environment coupled with the complexity of autonomous systems drove DRDC to carefully plan a research and development infrastructure that would provide state of the art tools without restricting research scope. DRDC's long term objectives for its autonomy program address disparate unmanned ground vehicle (UGV), unattended ground sensor (UGS), air (UAV), and subsea and surface (UUV and USV) vehicles operating together with minimal human oversight. Individually, these systems will range in complexity from simple reconnaissance mini-UAVs streaming video to sophisticated autonomous combat UGVs exploiting embedded and remote sensing. Together, these systems can provide low risk, long endurance, battlefield services assuming they can communicate and cooperate with manned and unmanned systems. A key enabling technology for this new research is a software architecture capable of meeting both DRDC's current and future requirements. DRDC built upon recent advances in the computing science field while developing its software architecture know as the Architecture for Autonomy (AFA). Although a well established practice in computing science, frameworks have only recently entered common use by unmanned vehicles. For industry and government, the complexity, cost, and time to re-implement stable systems often exceeds the perceived benefits of adopting a modern software infrastructure. Thus, most persevere with legacy software, adapting and modifying software when and wherever possible or necessary -- adopting strategic software frameworks only when no justifiable legacy exists. Conversely, academic programs with short one or two year projects frequently exploit strategic software frameworks but with little enduring impact. The open-source movement radically changes this picture. Academic frameworks, open to public scrutiny and modification, now rival commercial frameworks in both quality and economic impact. Further, industry now realizes that open source frameworks can reduce cost and risk of systems engineering. This paper describes the Architecture for Autonomy implemented by DRDC and how this architecture meets DRDC's current needs. It also presents an argument for why this architecture should also satisfy DRDC's future requirements as well.

Demonstrating the value of publishing open data by linking DOI-based citations of source datasets to uses in research and policy

NASA Astrophysics Data System (ADS)

Copas, K.; Legind, J. K.; Hahn, A.; Braak, K.; Høftt, M.; Noesgaard, D.; Robertson, T.; Méndez Hernández, F.; Schigel, D.; Ko, C.

2017-12-01

GBIF—the Global Biodiversity Information Facility—has recently demonstrated a system that tracks publications back to individual datasets, giving data providers demonstrable evidence of the benefit and utility of sharing data to support an array of scholarly topics and practical applications. GBIF is an open-data network and research infrastructure funded by the world's governments. Its community consists of more than 90 formal participants and almost 1,000 data-publishing institutions, which currently make tens of thousands of datasets containing nearly 800 million species occurrence records freely and publicly available for discovery, use and reuse across a wide range of biodiversity-related research and policy investigations. Starting in 2015 with the help of DataONE, GBIF introduced DOIs as persistent identifiers for the datasets shared through its network. This enhancement soon extended to the assignment of DOIs to user downloads from GBIF.org, which typically filter the available records with a variety of taxonomic, geographic, temporal and other search terms. Despite the lack of widely accepted standards for citing data among researchers and publications, this technical infrastructure is beginning to take hold and support open, transparent, persistent and repeatable use and reuse of species occurrence data. These `download DOIs' provide canonical references for the search results researchers process and use in peer-reviewed articles—a practice GBIF encourages by confirming new DOIs with each download and offering guidelines on citation. GBIF has recently started linking these citation results back to dataset and publisher pages, offering more consistent, traceable evidence of the value of sharing data to support others' research. GBIF's experience may be a useful model for other repositories to follow.

Key Lessons in Building "Data Commons": The Open Science Data Cloud Ecosystem

NASA Astrophysics Data System (ADS)

Patterson, M.; Grossman, R.; Heath, A.; Murphy, M.; Wells, W.

2015-12-01

Cloud computing technology has created a shift around data and data analysis by allowing researchers to push computation to data as opposed to having to pull data to an individual researcher's computer. Subsequently, cloud-based resources can provide unique opportunities to capture computing environments used both to access raw data in its original form and also to create analysis products which may be the source of data for tables and figures presented in research publications. Since 2008, the Open Cloud Consortium (OCC) has operated the Open Science Data Cloud (OSDC), which provides scientific researchers with computational resources for storing, sharing, and analyzing large (terabyte and petabyte-scale) scientific datasets. OSDC has provided compute and storage services to over 750 researchers in a wide variety of data intensive disciplines. Recently, internal users have logged about 2 million core hours each month. The OSDC also serves the research community by colocating these resources with access to nearly a petabyte of public scientific datasets in a variety of fields also accessible for download externally by the public. In our experience operating these resources, researchers are well served by "data commons," meaning cyberinfrastructure that colocates data archives, computing, and storage infrastructure and supports essential tools and services for working with scientific data. In addition to the OSDC public data commons, the OCC operates a data commons in collaboration with NASA and is developing a data commons for NOAA datasets. As cloud-based infrastructures for distributing and computing over data become more pervasive, we ask, "What does it mean to publish data in a data commons?" Here we present the OSDC perspective and discuss several services that are key in architecting data commons, including digital identifier services.

SlicerRT: radiation therapy research toolkit for 3D Slicer.

PubMed

Pinter, Csaba; Lasso, Andras; Wang, An; Jaffray, David; Fichtinger, Gabor

2012-10-01

Interest in adaptive radiation therapy research is constantly growing, but software tools available for researchers are mostly either expensive, closed proprietary applications, or free open-source packages with limited scope, extensibility, reliability, or user support. To address these limitations, we propose SlicerRT, a customizable, free, and open-source radiation therapy research toolkit. SlicerRT aspires to be an open-source toolkit for RT research, providing fast computations, convenient workflows for researchers, and a general image-guided therapy infrastructure to assist clinical translation of experimental therapeutic approaches. It is a medium into which RT researchers can integrate their methods and algorithms, and conduct comparative testing. SlicerRT was implemented as an extension for the widely used 3D Slicer medical image visualization and analysis application platform. SlicerRT provides functionality specifically designed for radiation therapy research, in addition to the powerful tools that 3D Slicer offers for visualization, registration, segmentation, and data management. The feature set of SlicerRT was defined through consensus discussions with a large pool of RT researchers, including both radiation oncologists and medical physicists. The development processes used were similar to those of 3D Slicer to ensure software quality. Standardized mechanisms of 3D Slicer were applied for documentation, distribution, and user support. The testing and validation environment was configured to automatically launch a regression test upon each software change and to perform comparison with ground truth results provided by other RT applications. Modules have been created for importing and loading DICOM-RT data, computing and displaying dose volume histograms, creating accumulated dose volumes, comparing dose volumes, and visualizing isodose lines and surfaces. The effectiveness of using 3D Slicer with the proposed SlicerRT extension for radiation therapy research was demonstrated on multiple use cases. A new open-source software toolkit has been developed for radiation therapy research. SlicerRT can import treatment plans from various sources into 3D Slicer for visualization, analysis, comparison, and processing. The provided algorithms are extensively tested and they are accessible through a convenient graphical user interface as well as a flexible application programming interface.

ibex: An open infrastructure software platform to facilitate collaborative work in radiomics

PubMed Central

Zhang, Lifei; Fried, David V.; Fave, Xenia J.; Hunter, Luke A.; Court, Laurence E.

2015-01-01

Purpose: Radiomics, which is the high-throughput extraction and analysis of quantitative image features, has been shown to have considerable potential to quantify the tumor phenotype. However, at present, a lack of software infrastructure has impeded the development of radiomics and its applications. Therefore, the authors developed the imaging biomarker explorer (ibex), an open infrastructure software platform that flexibly supports common radiomics workflow tasks such as multimodality image data import and review, development of feature extraction algorithms, model validation, and consistent data sharing among multiple institutions. Methods: The ibex software package was developed using the matlab and c/c++ programming languages. The software architecture deploys the modern model-view-controller, unit testing, and function handle programming concepts to isolate each quantitative imaging analysis task, to validate if their relevant data and algorithms are fit for use, and to plug in new modules. On one hand, ibex is self-contained and ready to use: it has implemented common data importers, common image filters, and common feature extraction algorithms. On the other hand, ibex provides an integrated development environment on top of matlab and c/c++, so users are not limited to its built-in functions. In the ibex developer studio, users can plug in, debug, and test new algorithms, extending ibex’s functionality. ibex also supports quality assurance for data and feature algorithms: image data, regions of interest, and feature algorithm-related data can be reviewed, validated, and/or modified. More importantly, two key elements in collaborative workflows, the consistency of data sharing and the reproducibility of calculation result, are embedded in the ibex workflow: image data, feature algorithms, and model validation including newly developed ones from different users can be easily and consistently shared so that results can be more easily reproduced between institutions. Results: Researchers with a variety of technical skill levels, including radiation oncologists, physicists, and computer scientists, have found the ibex software to be intuitive, powerful, and easy to use. ibex can be run at any computer with the windows operating system and 1GB RAM. The authors fully validated the implementation of all importers, preprocessing algorithms, and feature extraction algorithms. Windows version 1.0 beta of stand-alone ibex and ibex’s source code can be downloaded. Conclusions: The authors successfully implemented ibex, an open infrastructure software platform that streamlines common radiomics workflow tasks. Its transparency, flexibility, and portability can greatly accelerate the pace of radiomics research and pave the way toward successful clinical translation. PMID:25735289

IBEX: an open infrastructure software platform to facilitate collaborative work in radiomics.

PubMed

Zhang, Lifei; Fried, David V; Fave, Xenia J; Hunter, Luke A; Yang, Jinzhong; Court, Laurence E

2015-03-01

Radiomics, which is the high-throughput extraction and analysis of quantitative image features, has been shown to have considerable potential to quantify the tumor phenotype. However, at present, a lack of software infrastructure has impeded the development of radiomics and its applications. Therefore, the authors developed the imaging biomarker explorer (IBEX), an open infrastructure software platform that flexibly supports common radiomics workflow tasks such as multimodality image data import and review, development of feature extraction algorithms, model validation, and consistent data sharing among multiple institutions. The IBEX software package was developed using the MATLAB and c/c++ programming languages. The software architecture deploys the modern model-view-controller, unit testing, and function handle programming concepts to isolate each quantitative imaging analysis task, to validate if their relevant data and algorithms are fit for use, and to plug in new modules. On one hand, IBEX is self-contained and ready to use: it has implemented common data importers, common image filters, and common feature extraction algorithms. On the other hand, IBEX provides an integrated development environment on top of MATLAB and c/c++, so users are not limited to its built-in functions. In the IBEX developer studio, users can plug in, debug, and test new algorithms, extending IBEX's functionality. IBEX also supports quality assurance for data and feature algorithms: image data, regions of interest, and feature algorithm-related data can be reviewed, validated, and/or modified. More importantly, two key elements in collaborative workflows, the consistency of data sharing and the reproducibility of calculation result, are embedded in the IBEX workflow: image data, feature algorithms, and model validation including newly developed ones from different users can be easily and consistently shared so that results can be more easily reproduced between institutions. Researchers with a variety of technical skill levels, including radiation oncologists, physicists, and computer scientists, have found the IBEX software to be intuitive, powerful, and easy to use. IBEX can be run at any computer with the windows operating system and 1GB RAM. The authors fully validated the implementation of all importers, preprocessing algorithms, and feature extraction algorithms. Windows version 1.0 beta of stand-alone IBEX and IBEX's source code can be downloaded. The authors successfully implemented IBEX, an open infrastructure software platform that streamlines common radiomics workflow tasks. Its transparency, flexibility, and portability can greatly accelerate the pace of radiomics research and pave the way toward successful clinical translation.

Implementing OpenMRS for patient monitoring in an HIV/AIDS care and treatment program in rural Mozambique.

PubMed

Manders, Eric-Jan; José, Eurico; Solis, Manuel; Burlison, Janeen; Nhampossa, José Leopoldo; Moon, Troy

2010-01-01

We have adopted the Open Medical Record System (OpenMRS) framework to implement an electronic patient monitoring system for an HIV care and treatment program in Mozambique. The program provides technical assistance to the Ministry of Health supporting the scale up of integrated HIV care and support services in health facilities in rural resource limited settings. The implementation is in use for adult and pediatric programs, with ongoing roll-out to cover all supported sites. We describe early experiences in adapting the system to the program needs, addressing infrastructure challenges, creating a regional support team, training data entry staff, migrating a legacy database, deployment, and current use. We find that OpenMRS offers excellent prospects for in-country development of health information systems, even in severely resource limited settings. However, it also requires considerable organizational infrastructure investment and technical capacity building to ensure continued local support.

Probability Distributome: A Web Computational Infrastructure for Exploring the Properties, Interrelations, and Applications of Probability Distributions.

PubMed

Dinov, Ivo D; Siegrist, Kyle; Pearl, Dennis K; Kalinin, Alexandr; Christou, Nicolas

2016-06-01

Probability distributions are useful for modeling, simulation, analysis, and inference on varieties of natural processes and physical phenomena. There are uncountably many probability distributions. However, a few dozen families of distributions are commonly defined and are frequently used in practice for problem solving, experimental applications, and theoretical studies. In this paper, we present a new computational and graphical infrastructure, the Distributome , which facilitates the discovery, exploration and application of diverse spectra of probability distributions. The extensible Distributome infrastructure provides interfaces for (human and machine) traversal, search, and navigation of all common probability distributions. It also enables distribution modeling, applications, investigation of inter-distribution relations, as well as their analytical representations and computational utilization. The entire Distributome framework is designed and implemented as an open-source, community-built, and Internet-accessible infrastructure. It is portable, extensible and compatible with HTML5 and Web2.0 standards (http://Distributome.org). We demonstrate two types of applications of the probability Distributome resources: computational research and science education. The Distributome tools may be employed to address five complementary computational modeling applications (simulation, data-analysis and inference, model-fitting, examination of the analytical, mathematical and computational properties of specific probability distributions, and exploration of the inter-distributional relations). Many high school and college science, technology, engineering and mathematics (STEM) courses may be enriched by the use of modern pedagogical approaches and technology-enhanced methods. The Distributome resources provide enhancements for blended STEM education by improving student motivation, augmenting the classical curriculum with interactive webapps, and overhauling the learning assessment protocols.

Probability Distributome: A Web Computational Infrastructure for Exploring the Properties, Interrelations, and Applications of Probability Distributions

PubMed Central

Dinov, Ivo D.; Siegrist, Kyle; Pearl, Dennis K.; Kalinin, Alexandr; Christou, Nicolas

2015-01-01

Probability distributions are useful for modeling, simulation, analysis, and inference on varieties of natural processes and physical phenomena. There are uncountably many probability distributions. However, a few dozen families of distributions are commonly defined and are frequently used in practice for problem solving, experimental applications, and theoretical studies. In this paper, we present a new computational and graphical infrastructure, the Distributome, which facilitates the discovery, exploration and application of diverse spectra of probability distributions. The extensible Distributome infrastructure provides interfaces for (human and machine) traversal, search, and navigation of all common probability distributions. It also enables distribution modeling, applications, investigation of inter-distribution relations, as well as their analytical representations and computational utilization. The entire Distributome framework is designed and implemented as an open-source, community-built, and Internet-accessible infrastructure. It is portable, extensible and compatible with HTML5 and Web2.0 standards (http://Distributome.org). We demonstrate two types of applications of the probability Distributome resources: computational research and science education. The Distributome tools may be employed to address five complementary computational modeling applications (simulation, data-analysis and inference, model-fitting, examination of the analytical, mathematical and computational properties of specific probability distributions, and exploration of the inter-distributional relations). Many high school and college science, technology, engineering and mathematics (STEM) courses may be enriched by the use of modern pedagogical approaches and technology-enhanced methods. The Distributome resources provide enhancements for blended STEM education by improving student motivation, augmenting the classical curriculum with interactive webapps, and overhauling the learning assessment protocols. PMID:27158191

Knowledge Infrastructures and the Inscrutability of Openness in Education

ERIC Educational Resources Information Center

Edwards, Richard

2015-01-01

Openness has a long genealogy in education. Whether through the use of post, radio, television and digital technologies, extending learning opportunities to more and a wider range of people has been a significant aspect of educational history. Transcending barriers to learning has been promoted as the means of opening educational opportunities in…

78 FR 38723 - National Infrastructure Advisory Council; Meetings

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-27

... DEPARTMENT OF HOMELAND SECURITY [Docket No. DHS-2013-0034] National Infrastructure Advisory... (NIAC) will meet July 17, August 14, and September 17, 2013. The meetings will be open to the public. DATES: The NIAC will meet at the following dates and times: July 17, 2013, at 3:00 p.m. to 4:30 p.m...

Air Pollution Abatement Performances of Green Infrastructure in Open Road and Built-up Street Canyon Environments – A Review

EPA Science Inventory

Intensifying the proportion of urban green infrastructure has been considered as one of the remedies for air pollution levels in cities, yet the impact of numerous vegetation types deployed in different built environments has to be fully synthesised and quantified. This review ex...

Cloud computing geospatial application for water resources based on free and open source software and open standards - a prototype

NASA Astrophysics Data System (ADS)

Delipetrev, Blagoj

2016-04-01

Presently, most of the existing software is desktop-based, designed to work on a single computer, which represents a major limitation in many ways, starting from limited computer processing, storage power, accessibility, availability, etc. The only feasible solution lies in the web and cloud. This abstract presents research and development of a cloud computing geospatial application for water resources based on free and open source software and open standards using hybrid deployment model of public - private cloud, running on two separate virtual machines (VMs). The first one (VM1) is running on Amazon web services (AWS) and the second one (VM2) is running on a Xen cloud platform. The presented cloud application is developed using free and open source software, open standards and prototype code. The cloud application presents a framework how to develop specialized cloud geospatial application that needs only a web browser to be used. This cloud application is the ultimate collaboration geospatial platform because multiple users across the globe with internet connection and browser can jointly model geospatial objects, enter attribute data and information, execute algorithms, and visualize results. The presented cloud application is: available all the time, accessible from everywhere, it is scalable, works in a distributed computer environment, it creates a real-time multiuser collaboration platform, the programing languages code and components are interoperable, and it is flexible in including additional components. The cloud geospatial application is implemented as a specialized water resources application with three web services for 1) data infrastructure (DI), 2) support for water resources modelling (WRM), 3) user management. The web services are running on two VMs that are communicating over the internet providing services to users. The application was tested on the Zletovica river basin case study with concurrent multiple users. The application is a state-of-the-art cloud geospatial collaboration platform. The presented solution is a prototype and can be used as a foundation for developing of any specialized cloud geospatial applications. Further research will be focused on distributing the cloud application on additional VMs, testing the scalability and availability of services.

Community-driven computational biology with Debian Linux

PubMed Central

2010-01-01

Background The Open Source movement and its technologies are popular in the bioinformatics community because they provide freely available tools and resources for research. In order to feed the steady demand for updates on software and associated data, a service infrastructure is required for sharing and providing these tools to heterogeneous computing environments. Results The Debian Med initiative provides ready and coherent software packages for medical informatics and bioinformatics. These packages can be used together in Taverna workflows via the UseCase plugin to manage execution on local or remote machines. If such packages are available in cloud computing environments, the underlying hardware and the analysis pipelines can be shared along with the software. Conclusions Debian Med closes the gap between developers and users. It provides a simple method for offering new releases of software and data resources, thus provisioning a local infrastructure for computational biology. For geographically distributed teams it can ensure they are working on the same versions of tools, in the same conditions. This contributes to the world-wide networking of researchers. PMID:21210984

Vehicle-based Methane Mapping Helps Find Natural Gas Leaks and Prioritize Leak Repairs

NASA Astrophysics Data System (ADS)

von Fischer, J. C.; Weller, Z.; Roscioli, J. R.; Lamb, B. K.; Ferrara, T.

2017-12-01

Recently, mobile methane sensing platforms have been developed to detect and locate natural gas (NG) leaks in urban distribution systems and to estimate their size. Although this technology has already been used in targeted deployment for prioritization of NG pipeline infrastructure repair and replacement, one open question regarding this technology is how effective the resulting data are for prioritizing infrastructure repair and replacement. To answer this question we explore the accuracy and precision of the natural gas leak location and emission estimates provided by methane sensors placed on Google Street View (GSV) vehicles. We find that the vast majority (75%) of methane emitting sources detected by these mobile platforms are NG leaks and that the location estimates are effective at identifying the general location of leaks. We also show that the emission rate estimates from mobile detection platforms are able to effectively rank NG leaks for prioritizing leak repair. Our findings establish that mobile sensing platforms are an efficient and effective tool for improving the safety and reducing the environmental impacts of low-pressure NG distribution systems by reducing atmospheric methane emissions.

Department of Energy's Virtual Lab Infrastructure for Integrated Earth System Science Data

NASA Astrophysics Data System (ADS)

Williams, D. N.; Palanisamy, G.; Shipman, G.; Boden, T.; Voyles, J.

2014-12-01

The U.S. Department of Energy (DOE) Office of Biological and Environmental Research (BER) Climate and Environmental Sciences Division (CESD) produces a diversity of data, information, software, and model codes across its research and informatics programs and facilities. This information includes raw and reduced observational and instrumentation data, model codes, model-generated results, and integrated data products. Currently, most of this data and information are prepared and shared for program specific activities, corresponding to CESD organization research. A major challenge facing BER CESD is how best to inventory, integrate, and deliver these vast and diverse resources for the purpose of accelerating Earth system science research. This talk provides a concept for a CESD Integrated Data Ecosystem and an initial roadmap for its implementation to address this integration challenge in the "Big Data" domain. Towards this end, a new BER Virtual Laboratory Infrastructure will be presented, which will include services and software connecting the heterogeneous CESD data holdings, and constructed with open source software based on industry standards, protocols, and state-of-the-art technology.

Use of the Homeland-Defense Operational Planning System (HOPS) for Emergency Management

DOE Office of Scientific and Technical Information (OSTI.GOV)

Durling, Jr., R L; Price, D E

2005-12-16

The Homeland-Defense Operational Planning System (HOPS), is a new operational planning tool leveraging Lawrence Livermore National Laboratory's expertise in weapons systems and in sparse information analysis to support the defense of the U.S. homeland. HOPS provides planners with a basis to make decisions to protect against acts of terrorism, focusing on the defense of facilities critical to U.S. infrastructure. Criticality of facilities, structures, and systems is evaluated on a composite matrix of specific projected casualty, economic, and sociopolitical impact bins. Based on these criteria, significant unidentified vulnerabilities are identified and secured. To provide insight into potential successes by malevolent actors,more » HOPS analysts strive to base their efforts mainly on unclassified open-source data. However, more cooperation is needed between HOPS analysts and facility representatives to provide an advantage to those whose task is to defend these facilities. Evaluated facilities include: refineries, major ports, nuclear power plants and other nuclear licensees, dams, government installations, convention centers, sports stadiums, tourist venues, and public and freight transportation systems. A generalized summary of analyses of U.S. infrastructure facilities will be presented.« less

Risk Assessment Using The Homeland-Defense Operational Planning System (HOPS)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Price, D E; Durling, R L

2005-10-10

The Homeland-Defense Operational Planning System (HOPS), is a new operational planning tool leveraging Lawrence Livermore National Laboratory's expertise in weapons systems and in sparse information analysis to support the defense of the U.S. homeland. HOPS provides planners with a basis to make decisions to protect against acts of terrorism, focusing on the defense of facilities critical to U.S. infrastructure. Criticality of facilities, structures, and systems is evaluated on a composite matrix of specific projected casualty, economic, and sociopolitical impact bins. Based on these criteria, significant unidentified vulnerabilities are identified and secured. To provide insight into potential successes by malevolent actors,more » HOPS analysts strive to base their efforts mainly on unclassified open-source data. However, more cooperation is needed between HOPS analysts and facility representatives to provide an advantage to those whose task is to defend these facilities. Evaluated facilities include: refineries, major ports, nuclear power plants and other nuclear licensees, dams, government installations, convention centers, sports stadiums, tourist venues, and public and freight transportation systems. A generalized summary of analyses of U.S. infrastructure facilities will be presented.« less

Initial steps towards a production platform for DNA sequence analysis on the grid.

PubMed

Luyf, Angela C M; van Schaik, Barbera D C; de Vries, Michel; Baas, Frank; van Kampen, Antoine H C; Olabarriaga, Silvia D

2010-12-14

Bioinformatics is confronted with a new data explosion due to the availability of high throughput DNA sequencers. Data storage and analysis becomes a problem on local servers, and therefore it is needed to switch to other IT infrastructures. Grid and workflow technology can help to handle the data more efficiently, as well as facilitate collaborations. However, interfaces to grids are often unfriendly to novice users. In this study we reused a platform that was developed in the VL-e project for the analysis of medical images. Data transfer, workflow execution and job monitoring are operated from one graphical interface. We developed workflows for two sequence alignment tools (BLAST and BLAT) as a proof of concept. The analysis time was significantly reduced. All workflows and executables are available for the members of the Dutch Life Science Grid and the VL-e Medical virtual organizations All components are open source and can be transported to other grid infrastructures. The availability of in-house expertise and tools facilitates the usage of grid resources by new users. Our first results indicate that this is a practical, powerful and scalable solution to address the capacity and collaboration issues raised by the deployment of next generation sequencers. We currently adopt this methodology on a daily basis for DNA sequencing and other applications. More information and source code is available via http://www.bioinformaticslaboratory.nl/

The Open Gateway: Lunar Exploration in 2050

NASA Technical Reports Server (NTRS)

Lawrence, S.; Neal, C.

2017-01-01

The Moon, with its fundamental science questions and abundant, potentially useful re-sources, is the most viable destination for near-term future human and robotic exploration. Given what we have learned since Apollo, the lunar frontier now presents an entirely new paradigm for planetary exploration. The Lunar Exploration Roadmap [1], which was jointly developed by engineers, planetary scientists, commercial entities, and policymakers, is the cohesive strategic plan for using the Moon and its resources to enable the exploration of all other destinations within the Solar system by leveraging incremental, affordable investments in cislunar infrastructure. Here, we summarize the Lunar Exploration Roadmap, and describe the immense benefits that will arise from its successful implementation.

A coordinated set of ecosystem research platforms open to international research in ecotoxicology, AnaEE-France.

PubMed

Mougin, Christian; Azam, Didier; Caquet, Thierry; Cheviron, Nathalie; Dequiedt, Samuel; Le Galliard, Jean-François; Guillaume, Olivier; Houot, Sabine; Lacroix, Gérard; Lafolie, François; Maron, Pierre-Alain; Michniewicz, Radika; Pichot, Christian; Ranjard, Lionel; Roy, Jacques; Zeller, Bernd; Clobert, Jean; Chanzy, André

2015-10-01

The infrastructure for Analysis and Experimentation on Ecosystems (AnaEE-France) is an integrated network of the major French experimental, analytical, and modeling platforms dedicated to the biological study of continental ecosystems (aquatic and terrestrial). This infrastructure aims at understanding and predicting ecosystem dynamics under global change. AnaEE-France comprises complementary nodes offering access to the best experimental facilities and associated biological resources and data: Ecotrons, seminatural experimental platforms to manipulate terrestrial and aquatic ecosystems, in natura sites equipped for large-scale and long-term experiments. AnaEE-France also provides shared instruments and analytical platforms dedicated to environmental (micro) biology. Finally, AnaEE-France provides users with data bases and modeling tools designed to represent ecosystem dynamics and to go further in coupling ecological, agronomical, and evolutionary approaches. In particular, AnaEE-France offers adequate services to tackle the new challenges of research in ecotoxicology, positioning its various types of platforms in an ecologically advanced ecotoxicology approach. AnaEE-France is a leading international infrastructure, and it is pioneering the construction of AnaEE (Europe) infrastructure in the field of ecosystem research. AnaEE-France infrastructure is already open to the international community of scientists in the field of continental ecotoxicology.

Clinical Bioinformatics: challenges and opportunities

PubMed Central

2012-01-01

Background Network Tools and Applications in Biology (NETTAB) Workshops are a series of meetings focused on the most promising and innovative ICT tools and to their usefulness in Bioinformatics. The NETTAB 2011 workshop, held in Pavia, Italy, in October 2011 was aimed at presenting some of the most relevant methods, tools and infrastructures that are nowadays available for Clinical Bioinformatics (CBI), the research field that deals with clinical applications of bioinformatics. Methods In this editorial, the viewpoints and opinions of three world CBI leaders, who have been invited to participate in a panel discussion of the NETTAB workshop on the next challenges and future opportunities of this field, are reported. These include the development of data warehouses and ICT infrastructures for data sharing, the definition of standards for sharing phenotypic data and the implementation of novel tools to implement efficient search computing solutions. Results Some of the most important design features of a CBI-ICT infrastructure are presented, including data warehousing, modularity and flexibility, open-source development, semantic interoperability, integrated search and retrieval of -omics information. Conclusions Clinical Bioinformatics goals are ambitious. Many factors, including the availability of high-throughput "-omics" technologies and equipment, the widespread availability of clinical data warehouses and the noteworthy increase in data storage and computational power of the most recent ICT systems, justify research and efforts in this domain, which promises to be a crucial leveraging factor for biomedical research. PMID:23095472

Spatial Information Processing: Standards-Based Open Source Visualization Technology

NASA Astrophysics Data System (ADS)

Hogan, P.

2009-12-01

. Spatial information intelligence is a global issue that will increasingly affect our ability to survive as a species. Collectively we must better appreciate the complex relationships that make life on Earth possible. Providing spatial information in its native context can accelerate our ability to process that information. To maximize this ability to process information, three basic elements are required: data delivery (server technology), data access (client technology), and data processing (information intelligence). NASA World Wind provides open source client and server technologies based on open standards. The possibilities for data processing and data sharing are enhanced by this inclusive infrastructure for geographic information. It is interesting that this open source and open standards approach, unfettered by proprietary constraints, simultaneously provides for entirely proprietary use of this same technology. 1. WHY WORLD WIND? NASA World Wind began as a single program with specific functionality, to deliver NASA content. But as the possibilities for virtual globe technology became more apparent, we found that while enabling a new class of information technology, we were also getting in the way. Researchers, developers and even users expressed their desire for World Wind functionality in ways that would service their specific needs. They want it in their web pages. They want to add their own features. They want to manage their own data. They told us that only with this kind of flexibility, could their objectives and the potential for this technology be truly realized. World Wind client technology is a set of development tools, a software development kit (SDK) that allows a software engineer to create applications requiring geographic visualization technology. 2. MODULAR COMPONENTRY Accelerated evolution of a technology requires that the essential elements of that technology be modular components such that each can advance independent of the other elements. World Wind therefore changed its mission from providing a single information browser to enabling a whole class of 3D geographic applications. Instead of creating a single program, World Wind is a suite of components that can be selectively used in any number of programs. World Wind technology can be a part of any application, or it can be a window in a web page. Or it can be extended with additional functionalities by application and web developers. World Wind makes it possible to include virtual globe visualization and server technology in support of any objective. The world community can continually benefit from advances made in the technology by NASA in concert with the world community. 3. OPEN SOURCE AND OPEN STANDARDS NASA World Wind is NASA Open Source software. This means that the source code is fully accessible for anyone to freely use, even in association with proprietary technology. Imagery and other data provided by the World Wind servers reside in the public domain, including the data server technology itself. This allows others to deliver their own geospatial data and to provide custom solutions based on users specific needs.

Towards a Multi-Mission, Airborne Science Data System Environment

NASA Astrophysics Data System (ADS)

Crichton, D. J.; Hardman, S.; Law, E.; Freeborn, D.; Kay-Im, E.; Lau, G.; Oswald, J.

2011-12-01

NASA earth science instruments are increasingly relying on airborne missions. However, traditionally, there has been limited common infrastructure support available to principal investigators in the area of science data systems. As a result, each investigator has been required to develop their own computing infrastructures for the science data system. Typically there is little software reuse and many projects lack sufficient resources to provide a robust infrastructure to capture, process, distribute and archive the observations acquired from airborne flights. At NASA's Jet Propulsion Laboratory (JPL), we have been developing a multi-mission data system infrastructure for airborne instruments called the Airborne Cloud Computing Environment (ACCE). ACCE encompasses the end-to-end lifecycle covering planning, provisioning of data system capabilities, and support for scientific analysis in order to improve the quality, cost effectiveness, and capabilities to enable new scientific discovery and research in earth observation. This includes improving data system interoperability across each instrument. A principal characteristic is being able to provide an agile infrastructure that is architected to allow for a variety of configurations of the infrastructure from locally installed compute and storage services to provisioning those services via the "cloud" from cloud computer vendors such as Amazon.com. Investigators often have different needs that require a flexible configuration. The data system infrastructure is built on the Apache's Object Oriented Data Technology (OODT) suite of components which has been used for a number of spaceborne missions and provides a rich set of open source software components and services for constructing science processing and data management systems. In 2010, a partnership was formed between the ACCE team and the Carbon in Arctic Reservoirs Vulnerability Experiment (CARVE) mission to support the data processing and data management needs. A principal goal is to provide support for the Fourier Transform Spectrometer (FTS) instrument which will produce over 700,000 soundings over the life of their three-year mission. The cost to purchase and operate a cluster-based system in order to generate Level 2 Full Physics products from this data was prohibitive. Through an evaluation of cloud computing solutions, Amazon's Elastic Compute Cloud (EC2) was selected for the CARVE deployment. As the ACCE infrastructure is developed and extended to form an infrastructure for airborne missions, the experience of working with CARVE has provided a number of lessons learned and has proven to be important in reinforcing the unique aspects of airborne missions and the importance of the ACCE infrastructure in developing a cost effective, flexible multi-mission capability that leverages emerging capabilities in cloud computing, workflow management, and distributed computing.

Policy Model of Sustainable Infrastructure Development (Case Study : Bandarlampung City, Indonesia)

NASA Astrophysics Data System (ADS)

Persada, C.; Sitorus, S. R. P.; Marimin; Djakapermana, R. D.

2018-03-01

Infrastructure development does not only affect the economic aspect, but also social and environmental, those are the main dimensions of sustainable development. Many aspects and actors involved in urban infrastructure development requires a comprehensive and integrated policy towards sustainability. Therefore, it is necessary to formulate an infrastructure development policy that considers various dimensions of sustainable development. The main objective of this research is to formulate policy of sustainable infrastructure development. In this research, urban infrastructure covers transportation, water systems (drinking water, storm water, wastewater), green open spaces and solid waste. This research was conducted in Bandarlampung City. This study use a comprehensive modeling, namely the Multi Dimensional Scaling (MDS) with Rapid Appraisal of Infrastructure (Rapinfra), it uses of Analytic Network Process (ANP) and it uses system dynamics model. The findings of the MDS analysis showed that the status of Bandarlampung City infrastructure sustainability is less sustainable. The ANP analysis produces 8 main indicators of the most influential in the development of sustainable infrastructure. The system dynamics model offered 4 scenarios of sustainable urban infrastructure policy model. The best scenario was implemented into 3 policies consist of: the integrated infrastructure management, the population control, and the local economy development.

Abstracting application deployment on Cloud infrastructures

NASA Astrophysics Data System (ADS)

Aiftimiei, D. C.; Fattibene, E.; Gargana, R.; Panella, M.; Salomoni, D.

2017-10-01

Deploying a complex application on a Cloud-based infrastructure can be a challenging task. In this contribution we present an approach for Cloud-based deployment of applications and its present or future implementation in the framework of several projects, such as “!CHAOS: a cloud of controls” [1], a project funded by MIUR (Italian Ministry of Research and Education) to create a Cloud-based deployment of a control system and data acquisition framework, “INDIGO-DataCloud” [2], an EC H2020 project targeting among other things high-level deployment of applications on hybrid Clouds, and “Open City Platform”[3], an Italian project aiming to provide open Cloud solutions for Italian Public Administrations. We considered to use an orchestration service to hide the complex deployment of the application components, and to build an abstraction layer on top of the orchestration one. Through Heat [4] orchestration service, we prototyped a dynamic, on-demand, scalable platform of software components, based on OpenStack infrastructures. On top of the orchestration service we developed a prototype of a web interface exploiting the Heat APIs. The user can start an instance of the application without having knowledge about the underlying Cloud infrastructure and services. Moreover, the platform instance can be customized by choosing parameters related to the application such as the size of a File System or the number of instances of a NoSQL DB cluster. As soon as the desired platform is running, the web interface offers the possibility to scale some infrastructure components. In this contribution we describe the solution design and implementation, based on the application requirements, the details of the development of both the Heat templates and of the web interface, together with possible exploitation strategies of this work in Cloud data centers.

VERCE, Virtual Earthquake and Seismology Research Community in Europe, a new ESFRI initiative integrating data infrastructure, Grid and HPC infrastructures for data integration, data analysis and data modeling in seismology

NASA Astrophysics Data System (ADS)

van Hemert, Jano; Vilotte, Jean-Pierre

2010-05-01

Research in earthquake and seismology addresses fundamental problems in understanding Earth's internal wave sources and structures, and augment applications to societal concerns about natural hazards, energy resources and environmental change. This community is central to the European Plate Observing System (EPOS)—the ESFRI initiative in solid Earth Sciences. Global and regional seismology monitoring systems are continuously operated and are transmitting a growing wealth of data from Europe and from around the world. These tremendous volumes of seismograms, i.e., records of ground motions as a function of time, have a definite multi-use attribute, which puts a great premium on open-access data infrastructures that are integrated globally. In Europe, the earthquake and seismology community is part of the European Integrated Data Archives (EIDA) infrastructure and is structured as "horizontal" data services. On top of this distributed data archive system, the community has developed recently within the EC project NERIES advanced SOA-based web services and a unified portal system. Enabling advanced analysis of these data by utilising a data-aware distributed computing environment is instrumental to fully exploit the cornucopia of data and to guarantee optimal operation of the high-cost monitoring facilities. The strategy of VERCE is driven by the needs of data-intensive applications in data mining and modelling and will be illustrated through a set of applications. It aims to provide a comprehensive architecture and framework adapted to the scale and the diversity of these applications, and to integrate the community data infrastructure with Grid and HPC infrastructures. A first novel aspect is a service-oriented architecture that provides well-equipped integrated workbenches, with an efficient communication layer between data and Grid infrastructures, augmented with bridges to the HPC facilities. A second novel aspect is the coupling between Grid data analysis and HPC data modelling applications through workflow and data sharing mechanisms. VERCE will develop important interactions with the European infrastructure initiatives in Grid and HPC computing. The VERCE team: CNRS-France (IPG Paris, LGIT Grenoble), UEDIN (UK), KNMI-ORFEUS (Holland), EMSC, INGV (Italy), LMU (Germany), ULIV (UK), BADW-LRZ (Germany), SCAI (Germany), CINECA (Italy)

77 FR 61746 - Notice of Intent To Prepare a Supplemental Environmental Impact Statement for the Guam and...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-10-11

... Aircraft Carrier Berthing, and Army Air and Missile Defense Task Force'' dated July 2010. Pursuant to 40... day care), some site-specific training, and open space (e.g., parade grounds, open training areas, and open green space in communities). The proposed action also includes the utilities and infrastructure...

Linking earth science informatics resources into uninterrupted digital value chains

NASA Astrophysics Data System (ADS)

Woodcock, Robert; Angreani, Rini; Cox, Simon; Fraser, Ryan; Golodoniuc, Pavel; Klump, Jens; Rankine, Terry; Robertson, Jess; Vote, Josh

2015-04-01

The CSIRO Mineral Resources Flagship was established to tackle medium- to long-term challenges facing the Australian mineral industry across the value chain from exploration and mining through mineral processing within the framework of an economically, environmentally and socially sustainable minerals industry. This broad portfolio demands collaboration and data exchange with a broad range of participants and data providers across government, research and industry. It is an ideal environment to link geoscience informatics platforms to application across the resource extraction industry and to unlock the value of data integration between traditionally discrete parts of the minerals digital value chain. Despite the potential benefits, data integration remains an elusive goal within research and industry. Many projects use only a subset of available data types in an integrated manner, often maintaining the traditional discipline-based data 'silos'. Integrating data across the entire minerals digital value chain is an expensive proposition involving multiple disciplines and, significantly, multiple data sources both internal and external to any single organisation. Differing vocabularies and data formats, along with access regimes to appropriate analysis software and equipment all hamper the sharing and exchange of information. AuScope has addressed the challenge of data exchange across organisations nationally, and established a national geosciences information infrastructure using open standards-based web services. Federated across a wide variety of organisations, the resulting infrastructure contains a wide variety of live and updated data types. The community data standards and infrastructure platforms that underpin AuScope provide important new datasets and multi-agency links independent of software and hardware differences. AuScope has thus created an infrastructure, a platform of technologies and the opportunity for new ways of working with and integrating disparate data at much lower cost. An early example of this approach is the value generated by combining geological and metallurgical data sets as part of the rapidly growing field of geometallurgy. This not only provides a far better understanding of the impact of geological variability on ore processing but also leads to new thinking on the types and characteristics of data sets collected at various stages of the exploration and mining process. The Minerals Resources Flagship is linking its research activities to the AuScope infrastructure, exploiting the technology internally to create a platform for integrated research across the minerals value chain and improved interaction with industry. Referred to as the 'Early Access Virtual Lab', the system will be fully interoperable with AuScope and international infrastructures using open standards like GeosciML. Secured access is provided to allow confidential collaboration with industry when required. This presentation will discuss how the CSIRO Mineral Resources Flagship is building on the AuScope infrastructure to transform the way that data and data products are identified, shared, integrated, and reused, to unlock the benefits of true integration of research efforts across the minerals digital value chain.

Surface Transportation Security Priority Assessment

DTIC Science & Technology

2010-03-01

intercity buses), and pipelines, and related infrastructure (including roads and highways), that are within the territory of the United States...Modernizing the information technology infrastructure used to vet the identity of travelers and transportation workers  Using terrorist databases to...examination of persons travelling , surface transportation modes tend to operate in a much more open environment, making it difficult to screen workers

Incorporating Green Infrastructure into TMDLs

EPA Pesticide Factsheets

The fact sheet provides examples of how some states describe green infrastructure and low impact development activities in their TMDL implementation sections to address stormwater-source impaired waters.

A Cloud-Based Infrastructure for Near-Real-Time Processing and Dissemination of NPP Data

NASA Astrophysics Data System (ADS)

Evans, J. D.; Valente, E. G.; Chettri, S. S.

2011-12-01

We are building a scalable cloud-based infrastructure for generating and disseminating near-real-time data products from a variety of geospatial and meteorological data sources, including the new National Polar-Orbiting Environmental Satellite System (NPOESS) Preparatory Project (NPP). Our approach relies on linking Direct Broadcast and other data streams to a suite of scientific algorithms coordinated by NASA's International Polar-Orbiter Processing Package (IPOPP). The resulting data products are directly accessible to a wide variety of end-user applications, via industry-standard protocols such as OGC Web Services, Unidata Local Data Manager, or OPeNDAP, using open source software components. The processing chain employs on-demand computing resources from Amazon.com's Elastic Compute Cloud and NASA's Nebula cloud services. Our current prototype targets short-term weather forecasting, in collaboration with NASA's Short-term Prediction Research and Transition (SPoRT) program and the National Weather Service. Direct Broadcast is especially crucial for NPP, whose current ground segment is unlikely to deliver data quickly enough for short-term weather forecasters and other near-real-time users. Direct Broadcast also allows full local control over data handling, from the receiving antenna to end-user applications: this provides opportunities to streamline processes for data ingest, processing, and dissemination, and thus to make interpreted data products (Environmental Data Records) available to practitioners within minutes of data capture at the sensor. Cloud computing lets us grow and shrink computing resources to meet large and rapid fluctuations in data availability (twice daily for polar orbiters) - and similarly large fluctuations in demand from our target (near-real-time) users. This offers a compelling business case for cloud computing: the processing or dissemination systems can grow arbitrarily large to sustain near-real time data access despite surges in data volumes or user demand, but that computing capacity (and hourly costs) can be dropped almost instantly once the surge passes. Cloud computing also allows low-risk experimentation with a variety of machine architectures (processor types; bandwidth, memory, and storage capacities, etc.) and of system configurations (including massively parallel computing patterns). Finally, our service-based approach (in which user applications invoke software processes on a Web-accessible server) facilitates access into datasets of arbitrary size and resolution, and allows users to request and receive tailored products on demand. To maximize the usefulness and impact of our technology, we have emphasized open, industry-standard software interfaces. We are also using and developing open source software to facilitate the widespread adoption of similar, derived, or interoperable systems for processing and serving near-real-time data from NPP and other sources.

Exploring the "what if?" in geology through a RESTful open-source framework for cloud-based simulation and analysis

NASA Astrophysics Data System (ADS)

Klump, Jens; Robertson, Jess

2016-04-01

The spatial and temporal extent of geological phenomena makes experiments in geology difficult to conduct, if not entirely impossible and collection of data is laborious and expensive - so expensive that most of the time we cannot test a hypothesis. The aim, in many cases, is to gather enough data to build a predictive geological model. Even in a mine, where data are abundant, a model remains incomplete because the information at the level of a blasting block is two orders of magnitude larger than the sample from a drill core, and we have to take measurement errors into account. So, what confidence can we have in a model based on sparse data, uncertainties and measurement error? Our framework consist of two layers: (a) a ground-truth layer that contains geological models, which can be statistically based on historical operations data, and (b) a network of RESTful synthetic sensor microservices which can query the ground-truth for underlying properties and produce a simulated measurement to a control layer, which could be a database or LIMS, a machine learner or a companies' existing data infrastructure. Ground truth data are generated by an implicit geological model which serves as a host for nested models of geological processes as smaller scales. Our two layers are implemented using Flask and Gunicorn, which are open source Python web application framework and server, the PyData stack (numpy, scipy etc) and Rabbit MQ (an open-source queuing library). Sensor data is encoded using a JSON-LD version of the SensorML and Observations and Measurements standards. Containerisation of the synthetic sensors using Docker and CoreOS allows rapid and scalable deployment of large numbers of sensors, as well as sensor discovery to form a self-organized dynamic network of sensors. Real-time simulation of data sources can be used to investigate crucial questions such as the potential information gain from future sensing capabilities, or from new sampling strategies, or the combination of both, and it enables us to test many "what if?" questions, both in geology and in data engineering. What would we be able to see if we could obtain data at higher resolution? How would real-time data analysis change sampling strategies? Does our data infrastructure handle many new real-time data streams? What feature engineering can be deducted for machine learning approaches? By providing a 'data sandbox' able to scale to realistic geological scenarios we hope to start answering some of these questions. Faults happen in real world networks. Future work will investigate the effect of failure on dynamic sensor networks and the impact on the predictive capability of machine learning algorithms.

PLOCAN glider portal: a gateway for useful data management and visualization system

NASA Astrophysics Data System (ADS)

Morales, Tania; Lorenzo, Alvaro; Viera, Josue; Barrera, Carlos; José Rueda, María

2014-05-01

Nowadays monitoring ocean behavior and its characteristics involves a wide range of sources able to gather and provide a vast amount of data in spatio-temporal scales. Multiplatform infrastructures, like PLOCAN, hold a variety of autonomous Lagrangian and Eulerian devices addressed to collect information then transferred to land in near-real time. Managing all this data collection in an efficient way is a major issue. Advances in ocean observation technologies, where underwater autonomous gliders play a key role, has brought as a consequence an improvement of spatio-temporal resolution which offers a deeper understanding of the ocean but requires a bigger effort in the data management process. There are general requirements in terms of data management in that kind of environments, such as processing raw data at different levels to obtain valuable information, storing data coherently and providing accurate products to final users according to their specific needs. Managing large amount of data can be certainly tedious and complex without having right tools and operational procedures; hence automating these tasks through software applications saves time and reduces errors. Moreover, data distribution is highly relevant since scientist tent to assimilate different sources for comparison and validation. The use of web applications has boosted the necessary scientific dissemination. Within this argument, PLOCAN has implemented a set of independent but compatible applications to process, store and disseminate information gathered through different oceanographic platforms. These applications have been implemented using open standards, such as HTML and CSS, and open source software, like python as programming language and Django as framework web. More specifically, a glider application has been developed within the framework of FP7-GROOM project. Regarding data management, this project focuses on collecting and making available consistent and quality controlled datasets as well as fostering open access to glider data.

Estimation of the Aral Sea state predictability based on the open data sources and the unique field observations

NASA Astrophysics Data System (ADS)

Izhitskiy, Alexander; Ayzel, Georgy; Zavialov, Peter; Kurbaniyazov, Abilgazi

2016-04-01

The Aral Sea, formerly one of the four largest lakes in the world, has lost over 90% of its volume during the dramatical dessication mainly caused by the severe alteration of water budget of the basin. Shrinkage of the Aral Sea resulted in profound changes of the lake's ecosystem, that became a subject for a number of publications based on a wide range of methods such as field observations, remote sensing data analysis and numerical modeling. However, by the early 21th century, the number of field studies decreased significantly due to almost complete cessation of navigation and displacement of the Aral's shoreline far away from roads and other infrastructure. Thus, only a small amount of field data (salinity, temperature, etc.) for different regions of the lake is available for the last two decades. On the other hand, a set of the open data sources (sea level variability, atmospheric reanalysis) were developed for the region. The main idea of the presented study is to estimate the possibility of prediction of the Aral Sea state using coupled system of basic geoanalysis tools, numerical modeling of hydrological cycle (both for sea and land-surface interactions with atmosphere) and state-of-art machine learning techniques. Firstly, available in situ data, obtained in the Aral Sea by Shirshov Institute and other researchers, are concerned as the "base points of state" for each year within the studied period. Secondly, consistent patterns in the interannual variability of all other available parameters, taken from the open data sources and numerical modeling predictions, are founded out. As a result, such an approach allows predicting the future state of sea basing on the possible climatic scenario.

Using Cloud Computing infrastructure with CloudBioLinux, CloudMan and Galaxy

PubMed Central

Afgan, Enis; Chapman, Brad; Jadan, Margita; Franke, Vedran; Taylor, James

2012-01-01

Cloud computing has revolutionized availability and access to computing and storage resources; making it possible to provision a large computational infrastructure with only a few clicks in a web browser. However, those resources are typically provided in the form of low-level infrastructure components that need to be procured and configured before use. In this protocol, we demonstrate how to utilize cloud computing resources to perform open-ended bioinformatics analyses, with fully automated management of the underlying cloud infrastructure. By combining three projects, CloudBioLinux, CloudMan, and Galaxy into a cohesive unit, we have enabled researchers to gain access to more than 100 preconfigured bioinformatics tools and gigabytes of reference genomes on top of the flexible cloud computing infrastructure. The protocol demonstrates how to setup the available infrastructure and how to use the tools via a graphical desktop interface, a parallel command line interface, and the web-based Galaxy interface. PMID:22700313

Preliminary Identification of Urban Park Infrastructure Resilience in Semarang Central Java

NASA Astrophysics Data System (ADS)

Muzdalifah, Aji Uhfatun; Maryono

2018-02-01

Park is one of the spot green infrastructure. There are two major characteristic of park, first Active parks and second passive park. Those of two open spaces have been significant on the fulfillment of urban environment. To maintenance the urban park, it is very importance to identify the characteristic of active and passive park. The identification also needs to fostering stakeholder effort to increase quality of urban park infrastructure. This study aims to explore and assess the characteristic of urban park infrastructure in Semarang City, Central Java. Data collection methods conduct by review formal document, field observation and interview with key government officer. The study founded that urban active parks infrastructure resilience could be defined by; Park Location, Garden Shape, Vegetation, Support Element, Park Function, and Expected Benefit from Park Existence. Moreover, the vegetation aspect and the supporting elements are the most importance urban park infrastructure in Semarang.

Using cloud computing infrastructure with CloudBioLinux, CloudMan, and Galaxy.

PubMed

Afgan, Enis; Chapman, Brad; Jadan, Margita; Franke, Vedran; Taylor, James

2012-06-01

Cloud computing has revolutionized availability and access to computing and storage resources, making it possible to provision a large computational infrastructure with only a few clicks in a Web browser. However, those resources are typically provided in the form of low-level infrastructure components that need to be procured and configured before use. In this unit, we demonstrate how to utilize cloud computing resources to perform open-ended bioinformatic analyses, with fully automated management of the underlying cloud infrastructure. By combining three projects, CloudBioLinux, CloudMan, and Galaxy, into a cohesive unit, we have enabled researchers to gain access to more than 100 preconfigured bioinformatics tools and gigabytes of reference genomes on top of the flexible cloud computing infrastructure. The protocol demonstrates how to set up the available infrastructure and how to use the tools via a graphical desktop interface, a parallel command-line interface, and the Web-based Galaxy interface.

Final report for the Integrated and Robust Security Infrastructure (IRSI) laboratory directed research and development project

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hutchinson, R.L.; Hamilton, V.A.; Istrail, G.G.

1997-11-01

This report describes the results of a Sandia-funded laboratory-directed research and development project titled {open_quotes}Integrated and Robust Security Infrastructure{close_quotes} (IRSI). IRSI was to provide a broad range of commercial-grade security services to any software application. IRSI has two primary goals: application transparency and manageable public key infrastructure. IRSI must provide its security services to any application without the need to modify the application to invoke the security services. Public key mechanisms are well suited for a network with many end users and systems. There are many issues that make it difficult to deploy and manage a public key infrastructure. IRSImore » addressed some of these issues to create a more manageable public key infrastructure.« less

Energy Exchange NASA Opening Plenary

NASA Technical Reports Server (NTRS)

Marrs, Rick

2017-01-01

Rick Marrs, Deputy Assistant Administrator Office of Strategic Infrastructure NASA Headquarters will be speaking during the 2017 Energy Exchange opening plenary. His presentation showcases the NASA mission, sustainability at NASA, NASA's strategic Sustainability Performance Plan, Existing PV Partnerships, and NASA funded Solar Initiatives at KSC.

The eNanoMapper database for nanomaterial safety information

PubMed Central

Chomenidis, Charalampos; Doganis, Philip; Fadeel, Bengt; Grafström, Roland; Hardy, Barry; Hastings, Janna; Hegi, Markus; Jeliazkov, Vedrin; Kochev, Nikolay; Kohonen, Pekka; Munteanu, Cristian R; Sarimveis, Haralambos; Smeets, Bart; Sopasakis, Pantelis; Tsiliki, Georgia; Vorgrimmler, David; Willighagen, Egon

2015-01-01

Summary Background: The NanoSafety Cluster, a cluster of projects funded by the European Commision, identified the need for a computational infrastructure for toxicological data management of engineered nanomaterials (ENMs). Ontologies, open standards, and interoperable designs were envisioned to empower a harmonized approach to European research in nanotechnology. This setting provides a number of opportunities and challenges in the representation of nanomaterials data and the integration of ENM information originating from diverse systems. Within this cluster, eNanoMapper works towards supporting the collaborative safety assessment for ENMs by creating a modular and extensible infrastructure for data sharing, data analysis, and building computational toxicology models for ENMs. Results: The eNanoMapper database solution builds on the previous experience of the consortium partners in supporting diverse data through flexible data storage, open source components and web services. We have recently described the design of the eNanoMapper prototype database along with a summary of challenges in the representation of ENM data and an extensive review of existing nano-related data models, databases, and nanomaterials-related entries in chemical and toxicogenomic databases. This paper continues with a focus on the database functionality exposed through its application programming interface (API), and its use in visualisation and modelling. Considering the preferred community practice of using spreadsheet templates, we developed a configurable spreadsheet parser facilitating user friendly data preparation and data upload. We further present a web application able to retrieve the experimental data via the API and analyze it with multiple data preprocessing and machine learning algorithms. Conclusion: We demonstrate how the eNanoMapper database is used to import and publish online ENM and assay data from several data sources, how the “representational state transfer” (REST) API enables building user friendly interfaces and graphical summaries of the data, and how these resources facilitate the modelling of reproducible quantitative structure–activity relationships for nanomaterials (NanoQSAR). PMID:26425413

The eNanoMapper database for nanomaterial safety information.

PubMed

Jeliazkova, Nina; Chomenidis, Charalampos; Doganis, Philip; Fadeel, Bengt; Grafström, Roland; Hardy, Barry; Hastings, Janna; Hegi, Markus; Jeliazkov, Vedrin; Kochev, Nikolay; Kohonen, Pekka; Munteanu, Cristian R; Sarimveis, Haralambos; Smeets, Bart; Sopasakis, Pantelis; Tsiliki, Georgia; Vorgrimmler, David; Willighagen, Egon

2015-01-01

The NanoSafety Cluster, a cluster of projects funded by the European Commision, identified the need for a computational infrastructure for toxicological data management of engineered nanomaterials (ENMs). Ontologies, open standards, and interoperable designs were envisioned to empower a harmonized approach to European research in nanotechnology. This setting provides a number of opportunities and challenges in the representation of nanomaterials data and the integration of ENM information originating from diverse systems. Within this cluster, eNanoMapper works towards supporting the collaborative safety assessment for ENMs by creating a modular and extensible infrastructure for data sharing, data analysis, and building computational toxicology models for ENMs. The eNanoMapper database solution builds on the previous experience of the consortium partners in supporting diverse data through flexible data storage, open source components and web services. We have recently described the design of the eNanoMapper prototype database along with a summary of challenges in the representation of ENM data and an extensive review of existing nano-related data models, databases, and nanomaterials-related entries in chemical and toxicogenomic databases. This paper continues with a focus on the database functionality exposed through its application programming interface (API), and its use in visualisation and modelling. Considering the preferred community practice of using spreadsheet templates, we developed a configurable spreadsheet parser facilitating user friendly data preparation and data upload. We further present a web application able to retrieve the experimental data via the API and analyze it with multiple data preprocessing and machine learning algorithms. We demonstrate how the eNanoMapper database is used to import and publish online ENM and assay data from several data sources, how the "representational state transfer" (REST) API enables building user friendly interfaces and graphical summaries of the data, and how these resources facilitate the modelling of reproducible quantitative structure-activity relationships for nanomaterials (NanoQSAR).

FermiGrid - experience and future plans

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chadwick, K.; Berman, E.; Canal, P.

2007-09-01

Fermilab supports a scientific program that includes experiments and scientists located across the globe. In order to better serve this community, Fermilab has placed its production computer resources in a Campus Grid infrastructure called 'FermiGrid'. The FermiGrid infrastructure allows the large experiments at Fermilab to have priority access to their own resources, enables sharing of these resources in an opportunistic fashion, and movement of work (jobs, data) between the Campus Grid and National Grids such as Open Science Grid and the WLCG. FermiGrid resources support multiple Virtual Organizations (VOs), including VOs from the Open Science Grid (OSG), EGEE and themore » Worldwide LHC Computing Grid Collaboration (WLCG). Fermilab also makes leading contributions to the Open Science Grid in the areas of accounting, batch computing, grid security, job management, resource selection, site infrastructure, storage management, and VO services. Through the FermiGrid interfaces, authenticated and authorized VOs and individuals may access our core grid services, the 10,000+ Fermilab resident CPUs, near-petabyte (including CMS) online disk pools and the multi-petabyte Fermilab Mass Storage System. These core grid services include a site wide Globus gatekeeper, VO management services for several VOs, Fermilab site authorization services, grid user mapping services, as well as job accounting and monitoring, resource selection and data movement services. Access to these services is via standard and well-supported grid interfaces. We will report on the user experience of using the FermiGrid campus infrastructure interfaced to a national cyberinfrastructure--the successes and the problems.« less

International Symposium on Grids and Clouds (ISGC) 2017

NASA Astrophysics Data System (ADS)

2017-03-01

The International Symposium on Grids and Clouds (ISGC) 2017 will be held at Academia Sinica in Taipei, Taiwan from 5-10 March 2017, with co- located events and workshops. The main theme of ISGC 2017 is "Global Challenges: From Open Data to Open Science". The unprecedented progress in ICT has transformed the way education is conducted and research is carried out. The emerging global e-Infrastructure, championed by global science communities such as High Energy Physics, Astronomy, and Bio- medicine, must permeate into other sciences. Many areas, such as climate change, disaster mitigation, and human sustainability and well-being, represent global challenges where collaboration over e-Infrastructure will presumably help resolve the common problems of the people who are impacted. Access to global e-Infrastructure helps also the less globally organized, long-tail sciences, with their own collaboration challenges. Open data are not only a political phenomenon serving government transparency; they also create an opportunity to eliminate access barriers to all scientific data, specifically data from global sciences and regional data that concern natural phenomena and people. In this regard, the purpose of open data is to improve sciences, accelerating specifically those that may benefit people. Nevertheless, to eliminate barriers to open data is itself a daunting task and the barriers to individuals, institutions and big collaborations are manifold. Open science is a step beyond open data, where the tools and understanding of scientific data must be made available to whoever is interested to participate in such scientific research. The promotion of open science may change the academic tradition practiced over the past few hundred years. This change of dynamics may contribute to the resolution of common challenges of human sustainability where the current pace of scientific progress is not sufficiently fast. ISGC 2017 created a face-to-face venue where individual communities and national representatives can present and share their contributions to the global puzzle and contribute thus to the solution of global challenges.

The TJO-OAdM robotic observatory: OpenROCS and dome control

NASA Astrophysics Data System (ADS)

Colomé, Josep; Francisco, Xavier; Ribas, Ignasi; Casteels, Kevin; Martín, Jonatan

2010-07-01

The Telescope Joan Oró at the Montsec Astronomical Observatory (TJO - OAdM) is a small-class observatory working in completely unattended control. There are key problems to solve when a robotic control is envisaged, both on hardware and software issues. We present the OpenROCS (ROCS stands for Robotic Observatory Control System), an open source platform developed for the robotic control of the TJO - OAdM and similar astronomical observatories. It is a complex software architecture, composed of several applications for hardware control, event handling, environment monitoring, target scheduling, image reduction pipeline, etc. The code is developed in Java, C++, Python and Perl. The software infrastructure used is based on the Internet Communications Engine (Ice), an object-oriented middleware that provides object-oriented remote procedure call, grid computing, and publish/subscribe functionality. We also describe the subsystem in charge of the dome control: several hardware and software elements developed to specially protect the system at this identified single point of failure. It integrates a redundant control and a rain detector signal for alarm triggering and it responds autonomously in case communication with any of the control elements is lost (watchdog functionality). The self-developed control software suite (OpenROCS) and dome control system have proven to be highly reliable.

Sharing Water-related Information to Tackle Changes in the Hydrosphere - for Operational Needs (SWITCH-ON)

NASA Astrophysics Data System (ADS)

Arheimer, Berit

2015-04-01

Recently, a collaborative EU project started called SWITCH-ON (EU FP7 project No 603587) coordinated by SMHI to support the INSPIRE directive and the Open Data Strategy. The overall goal of the project is to establish a "one-stop-shop" web portal for easy access to European water information. The project will use open data, provide infrastructure for sharing and collaboration, and add value to society and research by repurposing and refining data from various sources. The SWITCH-ON project http://www.water-switch-on.eu/ will establish new forms of water research and facilitate the development of new products and services based on principles of sharing and community building in the water society. The SWITCH-ON objectives are to use open data for implementing: 1) an innovative spatial information platform (SIP) to find, bind, transform and publish data, 2) entirely new forms of collaborative research organised in a Virtual Water-Science Laboratory, open for any research group, 3) fourteen new operational products for water management and awareness, 4) outreach facilities for new water business and knowledge in line with the Europe's smart growth and environmental objectives. This poster will describe the overall project goals and especially the recent progress on developing a Virtual Water-Science Laboratory. Contact: waterswitchon@gmail.com

Arid Green Infrastructure for Water Control and Conservation ...

EPA Pesticide Factsheets

Green infrastructure is an approach to managing wet weather flows using systems and practices that mimic natural processes. It is designed to manage stormwater as close to its source as possible and protect the quality of receiving waters. Although most green infrastructure practices were first developed in temperate climates, green infrastructure also can be a cost-effective approach to stormwater management and water conservation in arid and semi-arid regions, such as those found in the western and southwestern United States. Green infrastructure practices can be applied at the site, neighborhood and watershed scales. In addition to water management and conservation, implementing green infrastructure confers many social and economic benefits and can address issues of environmental justice. The U.S. Environmental Protection Agency (EPA) commissioned a literature review to identify the state-of-the science practices dealing with water control and conservation in arid and semi-arid regions, with emphasis on these regions in the United States. The search focused on stormwater control measures or practices that slow, capture, treat, infiltrate and/or store runoff at its source (i.e., green infrastructure). The material in Chapters 1 through 3 provides background to EPA’s current activities related to the application of green infrastructure practices in arid and semi-arid regions. An introduction to the topic of green infrastructure in arid and semi-arid regions i

An Open Source Tool to Test Interoperability

NASA Astrophysics Data System (ADS)

Bermudez, L. E.

2012-12-01

Scientists interact with information at various levels from gathering of the raw observed data to accessing portrayed processed quality control data. Geoinformatics tools help scientist on the acquisition, storage, processing, dissemination and presentation of geospatial information. Most of the interactions occur in a distributed environment between software components that take the role of either client or server. The communication between components includes protocols, encodings of messages and managing of errors. Testing of these communication components is important to guarantee proper implementation of standards. The communication between clients and servers can be adhoc or follow standards. By following standards interoperability between components increase while reducing the time of developing new software. The Open Geospatial Consortium (OGC), not only coordinates the development of standards but also, within the Compliance Testing Program (CITE), provides a testing infrastructure to test clients and servers. The OGC Web-based Test Engine Facility, based on TEAM Engine, allows developers to test Web services and clients for correct implementation of OGC standards. TEAM Engine is a JAVA open source facility, available at Sourceforge that can be run via command line, deployed in a web servlet container or integrated in developer's environment via MAVEN. The TEAM Engine uses the Compliance Test Language (CTL) and TestNG to test HTTP requests, SOAP services and XML instances against Schemas and Schematron based assertions of any type of web service, not only OGC services. For example, the OGC Web Feature Service (WFS) 1.0.0 test has more than 400 test assertions. Some of these assertions includes conformance of HTTP responses, conformance of GML-encoded data; proper values for elements and attributes in the XML; and, correct error responses. This presentation will provide an overview of TEAM Engine, introduction of how to test via the OGC Testing web site and description of performing local tests. It will also provide information about how to participate in the open source code development of TEAM Engine.

R classes and methods for SNP array data.

PubMed

Scharpf, Robert B; Ruczinski, Ingo

2010-01-01

The Bioconductor project is an "open source and open development software project for the analysis and comprehension of genomic data" (1), primarily based on the R programming language. Infrastructure packages, such as Biobase, are maintained by Bioconductor core developers and serve several key roles to the broader community of Bioconductor software developers and users. In particular, Biobase introduces an S4 class, the eSet, for high-dimensional assay data. Encapsulating the assay data as well as meta-data on the samples, features, and experiment in the eSet class definition ensures propagation of the relevant sample and feature meta-data throughout an analysis. Extending the eSet class promotes code reuse through inheritance as well as interoperability with other R packages and is less error-prone. Recently proposed class definitions for high-throughput SNP arrays extend the eSet class. This chapter highlights the advantages of adopting and extending Biobase class definitions through a working example of one implementation of classes for the analysis of high-throughput SNP arrays.

The ELIXIR channel in F1000Research.

PubMed

Blomberg, Niklas; Oliveira, Arlindo; Mons, Barend; Persson, Bengt; Jonassen, Inge

2015-01-01

ELIXIR, the European life science infrastructure for biological information, is a unique initiative to consolidate Europe's national centres, services, and core bioinformatics resources into a single, coordinated infrastructure. ELIXIR brings together Europe's major life-science data archives and connects these with national bioinformatics infrastructures  - the ELIXIR Nodes. This editorial introduces the ELIXIR channel in F1000Research; the aim of the channel is to collect and present ELIXIR's scientific and operational output, engage with the broad life science community and encourage discussion on proposed infrastructure solutions. Submissions will be assessed by the ELIXIR channel Advisory Board to ensure they are relevant to ELIXIR community, and subjected to F1000Research open peer review process.

The ELIXIR channel in F1000Research

PubMed Central

Blomberg, Niklas; Oliveira, Arlindo; Mons, Barend; Persson, Bengt; Jonassen, Inge

2016-01-01

ELIXIR, the European life science infrastructure for biological information, is a unique initiative to consolidate Europe’s national centres, services, and core bioinformatics resources into a single, coordinated infrastructure. ELIXIR brings together Europe’s major life-science data archives and connects these with national bioinformatics infrastructures  - the ELIXIR Nodes. This editorial introduces the ELIXIR channel in F1000Research; the aim of the channel is to collect and present ELIXIR’s scientific and operational output, engage with the broad life science community and encourage discussion on proposed infrastructure solutions. Submissions will be assessed by the ELIXIR channel Advisory Board to ensure they are relevant to ELIXIR community, and subjected to F1000Research open peer review process. PMID:26913192

Semantic Support for Complex Ecosystem Research Environments

NASA Astrophysics Data System (ADS)

Klawonn, M.; McGuinness, D. L.; Pinheiro, P.; Santos, H. O.; Chastain, K.

2015-12-01

As ecosystems come under increasing stresses from diverse sources, there is growing interest in research efforts aimed at monitoring, modeling, and improving understanding of ecosystems and protection options. We aimed to provide a semantic infrastructure capable of representing data initially related to one large aquatic ecosystem research effort - the Jefferson project at Lake George. This effort includes significant historical observational data, extensive sensor-based monitoring data, experimental data, as well as model and simulation data covering topics including lake circulation, watershed runoff, lake biome food webs, etc. The initial measurement representation has been centered on monitoring data and related provenance. We developed a human-aware sensor network ontology (HASNetO) that leverages existing ontologies (PROV-O, OBOE, VSTO*) in support of measurement annotations. We explicitly support the human-aware aspects of human sensor deployment and collection activity to help capture key provenance that often is lacking. Our foundational ontology has since been generalized into a family of ontologies and used to create our human-aware data collection infrastructure that now supports the integration of measurement data along with simulation data. Interestingly, we have also utilized the same infrastructure to work with partners who have some more specific needs for specifying the environmental conditions where measurements occur, for example, knowing that an air temperature is not an external air temperature, but of the air temperature when windows are shut and curtains are open. We have also leveraged the same infrastructure to work with partners more interested in modeling smart cities with data feeds more related to people, mobility, environment, and living. We will introduce our human-aware data collection infrastructure, and demonstrate how it uses HASNetO and its supporting SOLR-based search platform to support data integration and semantic browsing. Further we will present learnings from its use in three relatively diverse large ecosystem research efforts and highlight some benefits and challenges related to our semantically-enhanced foundation.

Open source challenges for hospital information system (HIS) in developing countries: a pilot project in Mali.

PubMed

Bagayoko, Cheick-Oumar; Dufour, Jean-Charles; Chaacho, Saad; Bouhaddou, Omar; Fieschi, Marius

2010-04-16

We are currently witnessing a significant increase in use of Open Source tools in the field of health. Our study aims to research the potential of these software packages for developing countries. Our experiment was conducted at the Centre Hospitalier Mere Enfant in Mali. After reviewing several Open Source tools in the field of hospital information systems, Mediboard software was chosen for our study. To ensure the completeness of Mediboard in relation to the functionality required for a hospital information system, its features were compared to those of a well-defined comprehensive record management tool set up at the University Hospital "La Timone" of Marseilles in France. It was then installed on two Linux servers: a first server for testing and validation of different modules, and a second one for the deployed full implementation. After several months of use, we have evaluated the usability aspects of the system including feedback from end-users through a questionnaire. Initial results showed the potential of Open Source in the field of health IT for developing countries like Mali.Five main modules have been fully implemented: patient administrative and medical records management of hospital activities, tracking of practitioners' activities, infrastructure management and the billing system. This last component of the system has been fully developed by the local Mali team.The evaluation showed that the system is broadly accepted by all the users who participated in the study. 77% of the participants found the system useful; 85% found it easy; 100% of them believe the system increases the reliability of data. The same proportion encourages the continuation of the experiment and its expansion throughout the hospital. In light of the results, we can conclude that the objective of our study was reached. However, it is important to take into account the recommendations and the challenges discussed here to avoid several potential pitfalls specific to the context of Africa.Our future work will target the full integration of the billing module in Mediboard and an expanded implementation throughout the hospital.

Open source challenges for hospital information system (HIS) in developing countries: a pilot project in Mali

PubMed Central

2010-01-01

Background We are currently witnessing a significant increase in use of Open Source tools in the field of health. Our study aims to research the potential of these software packages for developing countries. Our experiment was conducted at the Centre Hospitalier Mere Enfant in Mali. Methods After reviewing several Open Source tools in the field of hospital information systems, Mediboard software was chosen for our study. To ensure the completeness of Mediboard in relation to the functionality required for a hospital information system, its features were compared to those of a well-defined comprehensive record management tool set up at the University Hospital "La Timone" of Marseilles in France. It was then installed on two Linux servers: a first server for testing and validation of different modules, and a second one for the deployed full implementation. After several months of use, we have evaluated the usability aspects of the system including feedback from end-users through a questionnaire. Results Initial results showed the potential of Open Source in the field of health IT for developing countries like Mali. Five main modules have been fully implemented: patient administrative and medical records management of hospital activities, tracking of practitioners' activities, infrastructure management and the billing system. This last component of the system has been fully developed by the local Mali team. The evaluation showed that the system is broadly accepted by all the users who participated in the study. 77% of the participants found the system useful; 85% found it easy; 100% of them believe the system increases the reliability of data. The same proportion encourages the continuation of the experiment and its expansion throughout the hospital. Conclusions In light of the results, we can conclude that the objective of our study was reached. However, it is important to take into account the recommendations and the challenges discussed here to avoid several potential pitfalls specific to the context of Africa. Our future work will target the full integration of the billing module in Mediboard and an expanded implementation throughout the hospital. PMID:20398366

Globalisation, Consumption and the Learning Business.

ERIC Educational Resources Information Center

Field, John

1995-01-01

Distance open learning represents both an outcome of and a primary factor in globalization. Despite investment in infrastructure, software, and human resources, demand for distance open learning in the European market remains constrained. The European Union's policies conceptualize a "European economic space" that ignores the real…

OpenSoC Fabric

DOE Office of Scientific and Technical Information (OSTI.GOV)

2014-08-21

Recent advancements in technology scaling have shown a trend towards greater integration with large-scale chips containing thousands of processors connected to memories and other I/O devices using non-trivial network topologies. Software simulation proves insufficient to study the tradeoffs in such complex systems due to slow execution time, whereas hardware RTL development is too time-consuming. We present OpenSoC Fabric, an on-chip network generation infrastructure which aims to provide a parameterizable and powerful on-chip network generator for evaluating future high performance computing architectures based on SoC technology. OpenSoC Fabric leverages a new hardware DSL, Chisel, which contains powerful abstractions provided by itsmore » base language, Scala, and generates both software (C++) and hardware (Verilog) models from a single code base. The OpenSoC Fabric2 infrastructure is modeled after existing state-of-the-art simulators, offers large and powerful collections of configuration options, and follows object-oriented design and functional programming to make functionality extension as easy as possible.« less

Arid Green Infrastructure for Water Control and Conservation State of the Science and Research Needs for Arid/Semi-Arid Regions

EPA Science Inventory

Green infrastructure is an approach to managing wet weather flows using systems and practices that mimic natural processes. It is designed to manage stormwater as close to its source as possible and protect the quality of receiving waters. Although most green infrastructure pract...

NiftyNet: a deep-learning platform for medical imaging.

PubMed

Gibson, Eli; Li, Wenqi; Sudre, Carole; Fidon, Lucas; Shakir, Dzhoshkun I; Wang, Guotai; Eaton-Rosen, Zach; Gray, Robert; Doel, Tom; Hu, Yipeng; Whyntie, Tom; Nachev, Parashkev; Modat, Marc; Barratt, Dean C; Ourselin, Sébastien; Cardoso, M Jorge; Vercauteren, Tom

2018-05-01

Medical image analysis and computer-assisted intervention problems are increasingly being addressed with deep-learning-based solutions. Established deep-learning platforms are flexible but do not provide specific functionality for medical image analysis and adapting them for this domain of application requires substantial implementation effort. Consequently, there has been substantial duplication of effort and incompatible infrastructure developed across many research groups. This work presents the open-source NiftyNet platform for deep learning in medical imaging. The ambition of NiftyNet is to accelerate and simplify the development of these solutions, and to provide a common mechanism for disseminating research outputs for the community to use, adapt and build upon. The NiftyNet infrastructure provides a modular deep-learning pipeline for a range of medical imaging applications including segmentation, regression, image generation and representation learning applications. Components of the NiftyNet pipeline including data loading, data augmentation, network architectures, loss functions and evaluation metrics are tailored to, and take advantage of, the idiosyncracies of medical image analysis and computer-assisted intervention. NiftyNet is built on the TensorFlow framework and supports features such as TensorBoard visualization of 2D and 3D images and computational graphs by default. We present three illustrative medical image analysis applications built using NiftyNet infrastructure: (1) segmentation of multiple abdominal organs from computed tomography; (2) image regression to predict computed tomography attenuation maps from brain magnetic resonance images; and (3) generation of simulated ultrasound images for specified anatomical poses. The NiftyNet infrastructure enables researchers to rapidly develop and distribute deep learning solutions for segmentation, regression, image generation and representation learning applications, or extend the platform to new applications. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Public key infrastructure for DOE security research

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aiken, R.; Foster, I.; Johnston, W.E.

This document summarizes the Department of Energy`s Second Joint Energy Research/Defence Programs Security Research Workshop. The workshop, built on the results of the first Joint Workshop which reviewed security requirements represented in a range of mission-critical ER and DP applications, discussed commonalties and differences in ER/DP requirements and approaches, and identified an integrated common set of security research priorities. One significant conclusion of the first workshop was that progress in a broad spectrum of DOE-relevant security problems and applications could best be addressed through public-key cryptography based systems, and therefore depended upon the existence of a robust, broadly deployed public-keymore » infrastructure. Hence, public-key infrastructure ({open_quotes}PKI{close_quotes}) was adopted as a primary focus for the second workshop. The Second Joint Workshop covered a range of DOE security research and deployment efforts, as well as summaries of the state of the art in various areas relating to public-key technologies. Key findings were that a broad range of DOE applications can benefit from security architectures and technologies built on a robust, flexible, widely deployed public-key infrastructure; that there exists a collection of specific requirements for missing or undeveloped PKI functionality, together with a preliminary assessment of how these requirements can be met; that, while commercial developments can be expected to provide many relevant security technologies, there are important capabilities that commercial developments will not address, due to the unique scale, performance, diversity, distributed nature, and sensitivity of DOE applications; that DOE should encourage and support research activities intended to increase understanding of security technology requirements, and to develop critical components not forthcoming from other sources in a timely manner.« less

Developing a European grid infrastructure for cancer research: vision, architecture and services

PubMed Central

Tsiknakis, M; Rueping, S; Martin, L; Sfakianakis, S; Bucur, A; Sengstag, T; Brochhausen, M; Pucaski, J; Graf, N

2007-01-01

Life sciences are currently at the centre of an information revolution. The nature and amount of information now available opens up areas of research that were once in the realm of science fiction. During this information revolution, the data-gathering capabilities have greatly surpassed the data-analysis techniques. Data integration across heterogeneous data sources and data aggregation across different aspects of the biomedical spectrum, therefore, is at the centre of current biomedical and pharmaceutical R&D. This paper reports on original results from the ACGT integrated project, focusing on the design and development of a European Biomedical Grid infrastructure in support of multi-centric, post-genomic clinical trials (CTs) on cancer. Post-genomic CTs use multi-level clinical and genomic data and advanced computational analysis and visualization tools to test hypotheses in trying to identify the molecular reasons for a disease and the stratification of patients in terms of treatment. The paper provides a presentation of the needs of users involved in post-genomic CTs and presents indicative scenarios, which drive the requirements of the engineering phase of the project. Subsequently, the initial architecture specified by the project is presented, and its services are classified and discussed. A range of such key services, including the Master Ontology on sCancer, which lie at the heart of the integration architecture of the project, is presented. Special efforts have been taken to describe the methodological and technological framework of the project, enabling the creation of a legally compliant and trustworthy infrastructure. Finally, a short discussion of the forthcoming work is included, and the potential involvement of the cancer research community in further development or utilization of the infrastructure is described. PMID:22275955

COOPEUS - connecting research infrastructures in environmental sciences

NASA Astrophysics Data System (ADS)

Koop-Jakobsen, Ketil; Waldmann, Christoph; Huber, Robert

2015-04-01

The COOPEUS project was initiated in 2012 bringing together 10 research infrastructures (RIs) in environmental sciences from the EU and US in order to improve the discovery, access, and use of environmental information and data across scientific disciplines and across geographical borders. The COOPEUS mission is to facilitate readily accessible research infrastructure data to advance our understanding of Earth systems through an international community-driven effort, by: Bringing together both user communities and top-down directives to address evolving societal and scientific needs; Removing technical, scientific, cultural and geopolitical barriers for data use; and Coordinating the flow, integrity and preservation of information. A survey of data availability was conducted among the COOPEUS research infrastructures for the purpose of discovering impediments for open international and cross-disciplinary sharing of environmental data. The survey showed that the majority of data offered by the COOPEUS research infrastructures is available via the internet (>90%), but the accessibility to these data differ significantly among research infrastructures; only 45% offer open access on their data, whereas the remaining infrastructures offer restricted access e.g. do not release raw data or sensible data, demand user registration or require permission prior to release of data. These rules and regulations are often installed as a form of standard practice, whereas formal data policies are lacking in 40% of the infrastructures, primarily in the EU. In order to improve this situation COOPEUS has installed a common data-sharing policy, which is agreed upon by all the COOPEUS research infrastructures. To investigate the existing opportunities for improving interoperability among environmental research infrastructures, COOPEUS explored the opportunities with the GEOSS common infrastructure (GCI) by holding a hands-on workshop. Through exercises directly registering resources, the first steps were taken to implement the GCI as a platform for documenting the capabilities of the COOPEUS research infrastructures. COOPEUS recognizes the potential for the GCI to become an important platform promoting cross-disciplinary approaches in the studies of multifaceted environmental challenges. Recommendations from the workshop participants also revealed that in order to attract research infrastructures to use the GCI, the registration process must be simplified and accelerated. However, also the data policies of the individual research infrastructure, or lack thereof, can prevent the use of the GCI or other portals, due to unclarities regarding data management authority and data ownership. COOPEUS shall continue to promote cross-disciplinary data exchange in the environmental field and will in the future expand to also include other geographical areas.

A smarter way to search, share and utilize open-spatial online data for energy R&D - Custom machine learning and GIS tools in U.S. DOE's virtual data library & laboratory, EDX

NASA Astrophysics Data System (ADS)

Rose, K.; Bauer, J.; Baker, D.; Barkhurst, A.; Bean, A.; DiGiulio, J.; Jones, K.; Jones, T.; Justman, D.; Miller, R., III; Romeo, L.; Sabbatino, M.; Tong, A.

2017-12-01

As spatial datasets are increasingly accessible through open, online systems, the opportunity to use these resources to address a range of Earth system questions grows. Simultaneously, there is a need for better infrastructure and tools to find and utilize these resources. We will present examples of advanced online computing capabilities, hosted in the U.S. DOE's Energy Data eXchange (EDX), that address these needs for earth-energy research and development. In one study the computing team developed a custom, machine learning, big data computing tool designed to parse the web and return priority datasets to appropriate servers to develop an open-source global oil and gas infrastructure database. The results of this spatial smart search approach were validated against expert-driven, manual search results which required a team of seven spatial scientists three months to produce. The custom machine learning tool parsed online, open systems, including zip files, ftp sites and other web-hosted resources, in a matter of days. The resulting resources were integrated into a geodatabase now hosted for open access via EDX. Beyond identifying and accessing authoritative, open spatial data resources, there is also a need for more efficient tools to ingest, perform, and visualize multi-variate, spatial data analyses. Within the EDX framework, there is a growing suite of processing, analytical and visualization capabilities that allow multi-user teams to work more efficiently in private, virtual workspaces. An example of these capabilities are a set of 5 custom spatio-temporal models and data tools that form NETL's Offshore Risk Modeling suite that can be used to quantify oil spill risks and impacts. Coupling the data and advanced functions from EDX with these advanced spatio-temporal models has culminated with an integrated web-based decision-support tool. This platform has capabilities to identify and combine data across scales and disciplines, evaluate potential environmental, social, and economic impacts, highlight knowledge or technology gaps, and reduce uncertainty for a range of `what if' scenarios relevant to oil spill prevention efforts. These examples illustrate EDX's growing capabilities for advanced spatial data search and analysis to support geo-data science needs.

Selection of important ecological source patches base on Green Infrastructure theory: A case study of Wuhan city

NASA Astrophysics Data System (ADS)

Ke, Yuanyuan; Yu, Yan; Tong, Yan

2018-01-01

Selecting urban ecological patches is of great significance for constructing urban green infrastructure network, protecting urban biodiversity and ecological environment. With the support of GIS technology, a criterion for selecting sources of patches was developed according to existing planning. Then ecological source patches of terrestrial organism, aquatic and amphibious organism were selected in Wuhan city. To increase the connectivity of the ecological patches and achieve greater ecological protection benefits, the green infrastructure networks in Wuhan city were constructed with the minimum path analysis method. Finally, the characteristics of ecological source patches were analyzed with landscape metrics, and ecological protection importance degree of ecological source patches were evaluated comprehensively. The results showed that there were 23 important ecological source patches in Wuhan city, among which Sushan Temple Forest Patch, Lu Lake and Shangshe Lake Wetland Patch were the most important in all kinds of patches for ecological protection. This study can provide a scientific basis for the preservation of urban ecological space, the delineation of natural conservation areas and the protection of biological diversity.

Screensaver: an open source lab information management system (LIMS) for high throughput screening facilities

PubMed Central

2010-01-01

Background Shared-usage high throughput screening (HTS) facilities are becoming more common in academe as large-scale small molecule and genome-scale RNAi screening strategies are adopted for basic research purposes. These shared facilities require a unique informatics infrastructure that must not only provide access to and analysis of screening data, but must also manage the administrative and technical challenges associated with conducting numerous, interleaved screening efforts run by multiple independent research groups. Results We have developed Screensaver, a free, open source, web-based lab information management system (LIMS), to address the informatics needs of our small molecule and RNAi screening facility. Screensaver supports the storage and comparison of screening data sets, as well as the management of information about screens, screeners, libraries, and laboratory work requests. To our knowledge, Screensaver is one of the first applications to support the storage and analysis of data from both genome-scale RNAi screening projects and small molecule screening projects. Conclusions The informatics and administrative needs of an HTS facility may be best managed by a single, integrated, web-accessible application such as Screensaver. Screensaver has proven useful in meeting the requirements of the ICCB-Longwood/NSRB Screening Facility at Harvard Medical School, and has provided similar benefits to other HTS facilities. PMID:20482787

AutoBayes Program Synthesis System System Internals

NASA Technical Reports Server (NTRS)

Schumann, Johann Martin

2011-01-01

This lecture combines the theoretical background of schema based program synthesis with the hands-on study of a powerful, open-source program synthesis system (Auto-Bayes). Schema-based program synthesis is a popular approach toward program synthesis. The lecture will provide an introduction into this topic and discuss how this technology can be used to generate customized algorithms. The synthesis of advanced numerical algorithms requires the availability of a powerful symbolic (algebra) system. Its task is to symbolically solve equations, simplify expressions, or to symbolically calculate derivatives (among others) such that the synthesized algorithms become as efficient as possible. We will discuss the use and importance of the symbolic system for synthesis. Any synthesis system is a large and complex piece of code. In this lecture, we will study Autobayes in detail. AutoBayes has been developed at NASA Ames and has been made open source. It takes a compact statistical specification and generates a customized data analysis algorithm (in C/C++) from it. AutoBayes is written in SWI Prolog and many concepts from rewriting, logic, functional, and symbolic programming. We will discuss the system architecture, the schema libary and the extensive support infra-structure. Practical hands-on experiments and exercises will enable the student to get insight into a realistic program synthesis system and provides knowledge to use, modify, and extend Autobayes.

Application of Open Source Technologies for Oceanographic Data Analysis

NASA Astrophysics Data System (ADS)

Huang, T.; Gangl, M.; Quach, N. T.; Wilson, B. D.; Chang, G.; Armstrong, E. M.; Chin, T. M.; Greguska, F.

2015-12-01

NEXUS is a data-intensive analysis solution developed with a new approach for handling science data that enables large-scale data analysis by leveraging open source technologies such as Apache Cassandra, Apache Spark, Apache Solr, and Webification. NEXUS has been selected to provide on-the-fly time-series and histogram generation for the Soil Moisture Active Passive (SMAP) mission for Level 2 and Level 3 Active, Passive, and Active Passive products. It also provides an on-the-fly data subsetting capability. NEXUS is designed to scale horizontally, enabling it to handle massive amounts of data in parallel. It takes a new approach on managing time and geo-referenced array data by dividing data artifacts into chunks and stores them in an industry-standard, horizontally scaled NoSQL database. This approach enables the development of scalable data analysis services that can infuse and leverage the elastic computing infrastructure of the Cloud. It is equipped with a high-performance geospatial and indexed data search solution, coupled with a high-performance data Webification solution free from file I/O bottlenecks, as well as a high-performance, in-memory data analysis engine. In this talk, we will focus on the recently funded AIST 2014 project by using NEXUS as the core for oceanographic anomaly detection service and web portal. We call it, OceanXtremes

Screensaver: an open source lab information management system (LIMS) for high throughput screening facilities.

PubMed

Tolopko, Andrew N; Sullivan, John P; Erickson, Sean D; Wrobel, David; Chiang, Su L; Rudnicki, Katrina; Rudnicki, Stewart; Nale, Jennifer; Selfors, Laura M; Greenhouse, Dara; Muhlich, Jeremy L; Shamu, Caroline E

2010-05-18

Shared-usage high throughput screening (HTS) facilities are becoming more common in academe as large-scale small molecule and genome-scale RNAi screening strategies are adopted for basic research purposes. These shared facilities require a unique informatics infrastructure that must not only provide access to and analysis of screening data, but must also manage the administrative and technical challenges associated with conducting numerous, interleaved screening efforts run by multiple independent research groups. We have developed Screensaver, a free, open source, web-based lab information management system (LIMS), to address the informatics needs of our small molecule and RNAi screening facility. Screensaver supports the storage and comparison of screening data sets, as well as the management of information about screens, screeners, libraries, and laboratory work requests. To our knowledge, Screensaver is one of the first applications to support the storage and analysis of data from both genome-scale RNAi screening projects and small molecule screening projects. The informatics and administrative needs of an HTS facility may be best managed by a single, integrated, web-accessible application such as Screensaver. Screensaver has proven useful in meeting the requirements of the ICCB-Longwood/NSRB Screening Facility at Harvard Medical School, and has provided similar benefits to other HTS facilities.

Enabling a systems biology knowledgebase with gaggle and firegoose

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baliga, Nitin S.

The overall goal of this project was to extend the existing Gaggle and Firegoose systems to develop an open-source technology that runs over the web and links desktop applications with many databases and software applications. This technology would enable researchers to incorporate workflows for data analysis that can be executed from this interface to other online applications. The four specific aims were to (1) provide one-click mapping of genes, proteins, and complexes across databases and species; (2) enable multiple simultaneous workflows; (3) expand sophisticated data analysis for online resources; and enhance open-source development of the Gaggle-Firegoose infrastructure. Gaggle is anmore » open-source Java software system that integrates existing bioinformatics programs and data sources into a user-friendly, extensible environment to allow interactive exploration, visualization, and analysis of systems biology data. Firegoose is an extension to the Mozilla Firefox web browser that enables data transfer between websites and desktop tools including Gaggle. In the last phase of this funding period, we have made substantial progress on development and application of the Gaggle integration framework. We implemented the workspace to the Network Portal. Users can capture data from Firegoose and save them to the workspace. Users can create workflows to start multiple software components programmatically and pass data between them. Results of analysis can be saved to the cloud so that they can be easily restored on any machine. We also developed the Gaggle Chrome Goose, a plugin for the Google Chrome browser in tandem with an opencpu server in the Amazon EC2 cloud. This allows users to interactively perform data analysis on a single web page using the R packages deployed on the opencpu server. The cloud-based framework facilitates collaboration between researchers from multiple organizations. We have made a number of enhancements to the cmonkey2 application to enable and improve the integration within different environments, and we have created a new tools pipeline for generating EGRIN2 models in a largely automated way.« less

a Cultural Landscape Information System Developed with Open Source Tools

NASA Astrophysics Data System (ADS)

Chudyk, C.; Müller, H.; Uhler, M.; Würriehausen, F.

2013-07-01

Since 2010, the state of Rhineland-Palatinate in Germany has developed a cultural landscape information system as a process to secure and further enrich aggregate data about its cultural assets. In an open dialogue between governing authorities and citizens, the intention of the project is an active cooperation of public and private actors. A cultural landscape information system called KuLIS was designed as a web platform, combining semantic wiki software with a geographic information system. Based on data sets from public administrations, the information about cultural assets can be extended and enhanced by interested participants. The developed infrastructure facilitates local information accumulation through a crowdsourcing approach. This capability offers new possibilities for e-governance and open data developments. The collaborative approach allows governing authorities to manage and supervise official data, while public participation enables affordable information acquisition. Gathered cultural heritage information can provide incentives for touristic valorisation of communities or concepts for strengthening regional identification. It can also influence political decisions in defining significant cultural regions worth of protecting from industrial influences. The presented cultural landscape information allows citizens to influence the statewide development of cultural landscapes in a democratic way.

Using Rose and Compass for Authentication

DOE Office of Scientific and Technical Information (OSTI.GOV)

White, G

2009-07-09

Many recent non-proliferation software projects include a software authentication component. In this context, 'authentication' is defined as determining that a software package performs only its intended purpose and performs that purpose correctly and reliably over many years. In addition to visual inspection by knowledgeable computer scientists, automated tools are needed to highlight suspicious code constructs both to aid the visual inspection and to guide program development. While many commercial tools are available for portions of the authentication task, they are proprietary, and have limited extensibility. An open-source, extensible tool can be customized to the unique needs of each project. ROSEmore » is an LLNL-developed robust source-to-source analysis and optimization infrastructure currently addressing large, million-line DOE applications in C, C++, and FORTRAN. It continues to be extended to support the automated analysis of binaries (x86, ARM, and PowerPC). We continue to extend ROSE to address a number of security specific requirements and apply it to software authentication for non-proliferation projects. We will give an update on the status of our work.« less

The EGI-Engage EPOS Competence Center - Interoperating heterogeneous AAI mechanisms and Orchestrating distributed computational resources

NASA Astrophysics Data System (ADS)

Bailo, Daniele; Scardaci, Diego; Spinuso, Alessandro; Sterzel, Mariusz; Schwichtenberg, Horst; Gemuend, Andre

2016-04-01

The mission of EGI-Engage project [1] is to accelerate the implementation of the Open Science Commons vision, where researchers from all disciplines have easy and open access to the innovative digital services, data, knowledge and expertise they need for collaborative and excellent research. The Open Science Commons is grounded on three pillars: the e-Infrastructure Commons, an ecosystem of services that constitute the foundation layer of distributed infrastructures; the Open Data Commons, where observations, results and applications are increasingly available for scientific research and for anyone to use and reuse; and the Knowledge Commons, in which communities have shared ownership of knowledge, participate in the co-development of software and are technically supported to exploit state-of-the-art digital services. To develop the Knowledge Commons, EGI-Engage is supporting the work of a set of community-specific Competence Centres, with participants from user communities (scientific institutes), National Grid Initiatives (NGIs), technology and service providers. Competence Centres collect and analyse requirements, integrate community-specific applications into state-of-the-art services, foster interoperability across e-Infrastructures, and evolve services through a user-centric development model. One of these Competence Centres is focussed on the European Plate Observing System (EPOS) [2] as representative of the solid earth science communities. EPOS is a pan-European long-term plan to integrate data, software and services from the distributed (and already existing) Research Infrastructures all over Europe, in the domain of the solid earth science. EPOS will enable innovative multidisciplinary research for a better understanding of the Earth's physical and chemical processes that control earthquakes, volcanic eruptions, ground instability and tsunami as well as the processes driving tectonics and Earth's surface dynamics. EPOS will improve our ability to better manage the use of the subsurface of the Earth. EPOS started its Implementation Phase in October 2015 and is now actively working in order to integrate multidisciplinary data into a single e-infrastructure. Multidisciplinary data are organized and governed by the Thematic Core Services (TCS) - European wide organizations and e-Infrastructure providing community specific data and data products - and are driven by various scientific communities encompassing a wide spectrum of Earth science disciplines. TCS data, data products and services will be integrated into the Integrated Core Services (ICS) system, that will ensure their interoperability and access to these services by the scientific community as well as other users within the society. The EPOS competence center (EPOS CC) goal is to tackle two of the main challenges that the ICS are going to face in the near future, by taking advantage of the technical solutions provided by EGI. In order to do this, we will present the two pilot use cases the EGI-EPOS CC is developing: 1) The AAI pilot, dealing with the provision of transparent and homogeneous access to the ICS infrastructure to users owning different kind of credentials (e.g. eduGain, OpenID Connect, X509 certificates etc.). Here the focus is on the mechanisms which allow the credential delegation. 2) The computational pilot, Improve the back-end services of an existing application in the field of Computational Seismology, developed in the context of the EC funded project VERCE. The application allows the processing and the comparison of data resulting from the simulation of seismic wave propagation following a real earthquake and real measurements recorded by seismographs. While the simulation data is produced directly by the users and stored in a Data Management System, the observations need to be pre-staged from institutional data-services, which are maintained by the community itself. This use case aims at exploiting the EGI FedCloud e-infrastructure for Data Intensive analysis and also explores possible interaction with other Common Data Infrastructure initiatives as EUDAT. In the presentation, the state of the art of the two use cases, together with the open challenges and the future application will be discussed. Also, possible integration of EGI solutions with EPOS and other e-infrastructure providers will be considered. [1] EGI-ENGAGE https://www.egi.eu/about/egi-engage/ [2] EPOS http://www.epos-eu.org/

JACOB: an enterprise framework for computational chemistry.

PubMed

Waller, Mark P; Dresselhaus, Thomas; Yang, Jack

2013-06-15

Here, we present just a collection of beans (JACOB): an integrated batch-based framework designed for the rapid development of computational chemistry applications. The framework expedites developer productivity by handling the generic infrastructure tier, and can be easily extended by user-specific scientific code. Paradigms from enterprise software engineering were rigorously applied to create a scalable, testable, secure, and robust framework. A centralized web application is used to configure and control the operation of the framework. The application-programming interface provides a set of generic tools for processing large-scale noninteractive jobs (e.g., systematic studies), or for coordinating systems integration (e.g., complex workflows). The code for the JACOB framework is open sourced and is available at: www.wallerlab.org/jacob. Copyright © 2013 Wiley Periodicals, Inc.

A bioinformatics roadmap for the human vaccines project.

PubMed

Scheuermann, Richard H; Sinkovits, Robert S; Schenkelberg, Theodore; Koff, Wayne C

2017-06-01

Biomedical research has become a data intensive science in which high throughput experimentation is producing comprehensive data about biological systems at an ever-increasing pace. The Human Vaccines Project is a new public-private partnership, with the goal of accelerating development of improved vaccines and immunotherapies for global infectious diseases and cancers by decoding the human immune system. To achieve its mission, the Project is developing a Bioinformatics Hub as an open-source, multidisciplinary effort with the overarching goal of providing an enabling infrastructure to support the data processing, analysis and knowledge extraction procedures required to translate high throughput, high complexity human immunology research data into biomedical knowledge, to determine the core principles driving specific and durable protective immune responses.

The PO.DAAC Portal and its use of the Drupal Framework

NASA Astrophysics Data System (ADS)

Alarcon, C.; Huang, T.; Bingham, A.; Cosic, S.

2011-12-01

The Physical Oceanography Distributed Active Archive Center portal (http://podaac.jpl.nasa.gov) is the primary interface for discovering and accessing oceanographic datasets collected from the vantage point of space. In addition, it provides information about NASA's satellite missions and operational activities at the data center. Recently the portal underwent a major redesign and deployment utilizing the Drupal framework. The Drupal framework was chosen as the platform for the portal due to its flexibility, open source community, and modular infrastructure. The portal features efficient content addition and management, mailing lists, forums, role based access control, and a faceted dataset browse capability. The dataset browsing was built as a custom Drupal module and integrates with a SOLR search engine.

A Tony Thomas-Inspired Guide to INSPIRE

DOE Office of Scientific and Technical Information (OSTI.GOV)

O'Connell, Heath B.; /Fermilab

2010-04-01

The SPIRES database was created in the late 1960s to catalogue the high energy physics preprints received by the SLAC Library. In the early 1990s it became the first database on the web and the first website outside of Europe. Although indispensible to the HEP community, its aging software infrastructure is becoming a serious liability. In a joint project involving CERN, DESY, Fermilab and SLAC, a new database, INSPIRE, is being created to replace SPIRES using CERN's modern, open-source Invenio database software. INSPIRE will maintain the content and functionality of SPIRES plus many new features. I describe this evolution frommore » the birth of SPIRES to the current day, noting that the career of Tony Thomas spans this timeline.« less

A Simple Technique for Securing Data at Rest Stored in a Computing Cloud

NASA Astrophysics Data System (ADS)

Sedayao, Jeff; Su, Steven; Ma, Xiaohao; Jiang, Minghao; Miao, Kai

"Cloud Computing" offers many potential benefits, including cost savings, the ability to deploy applications and services quickly, and the ease of scaling those application and services once they are deployed. A key barrier for enterprise adoption is the confidentiality of data stored on Cloud Computing Infrastructure. Our simple technique implemented with Open Source software solves this problem by using public key encryption to render stored data at rest unreadable by unauthorized personnel, including system administrators of the cloud computing service on which the data is stored. We validate our approach on a network measurement system implemented on PlanetLab. We then use it on a service where confidentiality is critical - a scanning application that validates external firewall implementations.

Remote Monitoring of Soil Water Content, Temperature, and Heat Flow Using Low-Cost Cellular (3G) IoT Technology

NASA Astrophysics Data System (ADS)

Ham, J. M.

2016-12-01

New microprocessor boards, open-source sensors, and cloud infrastructure developed for the Internet of Things (IoT) can be used to create low-cost monitoring systems for environmental research. This project describes two applications in soil science and hydrology: 1) remote monitoring of the soil temperature regime near oil and gas operations to detect the thermal signature associated with the natural source zone degradation of hydrocarbon contaminants in the vadose zone, and 2) remote monitoring of soil water content near the surface as part of a global citizen science network. In both cases, prototype data collection systems were built around the cellular (2G/3G) "Electron" microcontroller (www.particle.io). This device allows connectivity to the cloud using a low-cost global SIM and data plan. The systems have cellular connectivity in over 100 countries and data can be logged to the cloud for storage. Users can view data real time over any internet connection or via their smart phone. For both projects, data logging, storage, and visualization was done using IoT services like Thingspeak (thingspeak.com). The soil thermal monitoring system was tested on experimental plots in Colorado USA to evaluate the accuracy and reliability of different temperature sensors and 3D printed housings. The soil water experiment included comparison opens-source capacitance-based sensors to commercial versions. Results demonstrate the power of leveraging IoT technology for field research.

VERCE: a productive e-Infrastructure and e-Science environment for data-intensive seismology research

NASA Astrophysics Data System (ADS)

Vilotte, J. P.; Atkinson, M.; Spinuso, A.; Rietbrock, A.; Michelini, A.; Igel, H.; Frank, A.; Carpené, M.; Schwichtenberg, H.; Casarotti, E.; Filgueira, R.; Garth, T.; Germünd, A.; Klampanos, I.; Krause, A.; Krischer, L.; Leong, S. H.; Magnoni, F.; Matser, J.; Moguilny, G.

2015-12-01

Seismology addresses both fundamental problems in understanding the Earth's internal wave sources and structures and augmented societal applications, like earthquake and tsunami hazard assessment and risk mitigation; and puts a premium on open-data accessible by the Federated Digital Seismological Networks. The VERCE project, "Virtual Earthquake and seismology Research Community e-science environment in Europe", has initiated a virtual research environment to support complex orchestrated workflows combining state-of-art wave simulation codes and data analysis tools on distributed computing and data infrastructures (DCIs) along with multiple sources of observational data and new capabilities to combine simulation results with observational data. The VERCE Science Gateway provides a view of all the available resources, supporting collaboration with shared data and methods, with data access controls. The mapping to DCIs handles identity management, authority controls, transformations between representations and controls, and access to resources. The framework for computational science that provides simulation codes, like SPECFEM3D, democratizes their use by getting data from multiple sources, managing Earth models and meshes, distilling them as input data, and capturing results with meta-data. The dispel4py data-intensive framework allows for developing data-analysis applications using Python and the ObsPy library, which can be executed on different DCIs. A set of tools allows coupling with seismology and external data services. Provenance driven tools validate results and show relationships between data to facilitate method improvement. Lessons learned from VERCE training lead us to conclude that solid-Earth scientists could make significant progress by using VERCE e-science environment. VERCE has already contributed to the European Plate Observation System (EPOS), and is part of the EPOS implementation phase. Its cross-disciplinary capabilities are being extended for the EPOS implantation phase.

Patient-controlled sharing of medical imaging data across unaffiliated healthcare organizations

PubMed Central

Ahn, David K; Unde, Bhagyashree; Gage, H Donald; Carr, J Jeffrey

2013-01-01

Background Current image sharing is carried out by manual transportation of CDs by patients or organization-coordinated sharing networks. The former places a significant burden on patients and providers. The latter faces challenges to patient privacy. Objective To allow healthcare providers efficient access to medical imaging data acquired at other unaffiliated healthcare facilities while ensuring strong protection of patient privacy and minimizing burden on patients, providers, and the information technology infrastructure. Methods An image sharing framework is described that involves patients as an integral part of, and with full control of, the image sharing process. Central to this framework is the Patient Controlled Access-key REgistry (PCARE) which manages the access keys issued by image source facilities. When digitally signed by patients, the access keys are used by any requesting facility to retrieve the associated imaging data from the source facility. A centralized patient portal, called a PCARE patient control portal, allows patients to manage all the access keys in PCARE. Results A prototype of the PCARE framework has been developed by extending open-source technology. The results for feasibility, performance, and user assessments are encouraging and demonstrate the benefits of patient-controlled image sharing. Discussion The PCARE framework is effective in many important clinical cases of image sharing and can be used to integrate organization-coordinated sharing networks. The same framework can also be used to realize a longitudinal virtual electronic health record. Conclusion The PCARE framework allows prior imaging data to be shared among unaffiliated healthcare facilities while protecting patient privacy with minimal burden on patients, providers, and infrastructure. A prototype has been implemented to demonstrate the feasibility and benefits of this approach. PMID:22886546

Strengthening Software Authentication with the ROSE Software Suite

DOE Office of Scientific and Technical Information (OSTI.GOV)

White, G

2006-06-15

Many recent nonproliferation and arms control software projects include a software authentication regime. These include U.S. Government-sponsored projects both in the United States and in the Russian Federation (RF). This trend toward requiring software authentication is only accelerating. Demonstrating assurance that software performs as expected without hidden ''backdoors'' is crucial to a project's success. In this context, ''authentication'' is defined as determining that a software package performs only its intended purpose and performs said purpose correctly and reliably over the planned duration of an agreement. In addition to visual inspections by knowledgeable computer scientists, automated tools are needed to highlightmore » suspicious code constructs, both to aid visual inspection and to guide program development. While many commercial tools are available for portions of the authentication task, they are proprietary and not extensible. An open-source, extensible tool can be customized to the unique needs of each project (projects can have both common and custom rules to detect flaws and security holes). Any such extensible tool has to be based on a complete language compiler. ROSE is precisely such a compiler infrastructure developed within the Department of Energy (DOE) and targeted at the optimization of scientific applications and user-defined libraries within large-scale applications (typically applications of a million lines of code). ROSE is a robust, source-to-source analysis and optimization infrastructure currently addressing large, million-line DOE applications in C and C++ (handling the full C, C99, C++ languages and with current collaborations to support Fortran90). We propose to extend ROSE to address a number of security-specific requirements, and apply it to software authentication for nonproliferation and arms control projects.« less

The Virtual Geophysics Laboratory (VGL): Scientific Workflows Operating Across Organizations and Across Infrastructures

NASA Astrophysics Data System (ADS)

Cox, S. J.; Wyborn, L. A.; Fraser, R.; Rankine, T.; Woodcock, R.; Vote, J.; Evans, B.

2012-12-01

The Virtual Geophysics Laboratory (VGL) is web portal that provides geoscientists with an integrated online environment that: seamlessly accesses geophysical and geoscience data services from the AuScope national geoscience information infrastructure; loosely couples these data to a variety of gesocience software tools; and provides large scale processing facilities via cloud computing. VGL is a collaboration between CSIRO, Geoscience Australia, National Computational Infrastructure, Monash University, Australian National University and the University of Queensland. The VGL provides a distributed system whereby a user can enter an online virtual laboratory to seamlessly connect to OGC web services for geoscience data. The data is supplied in open standards formats using international standards like GeoSciML. A VGL user uses a web mapping interface to discover and filter the data sources using spatial and attribute filters to define a subset. Once the data is selected the user is not required to download the data. VGL collates the service query information for later in the processing workflow where it will be staged directly to the computing facilities. The combination of deferring data download and access to Cloud computing enables VGL users to access their data at higher resolutions and to undertake larger scale inversions, more complex models and simulations than their own local computing facilities might allow. Inside the Virtual Geophysics Laboratory, the user has access to a library of existing models, complete with exemplar workflows for specific scientific problems based on those models. For example, the user can load a geological model published by Geoscience Australia, apply a basic deformation workflow provided by a CSIRO scientist, and have it run in a scientific code from Monash. Finally the user can publish these results to share with a colleague or cite in a paper. This opens new opportunities for access and collaboration as all the resources (models, code, data, processing) are shared in the one virtual laboratory. VGL provides end users with access to an intuitive, user-centered interface that leverages cloud storage and cloud and cluster processing from both the research communities and commercial suppliers (e.g. Amazon). As the underlying data and information services are agnostic of the scientific domain, they can support many other data types. This fundamental characteristic results in a highly reusable virtual laboratory infrastructure that could also be used for example natural hazards, satellite processing, soil geochemistry, climate modeling, agriculture crop modeling.

Insights and Challenges to Integrating Data from Diverse Ecological Networks

NASA Astrophysics Data System (ADS)

Peters, D. P. C.

2014-12-01

Many of the most dramatic and surprising effects of global change occur across large spatial extents, from regions to continents, that impact multiple ecosystem types across a range of interacting spatial and temporal scales. The ability of ecologists and inter-disciplinary scientists to understand and predict these dynamics depend, in large part, on existing site-based research infrastructures that developed in response to historic events. Integrating these diverse sources of data is critical to addressing these broad-scale questions. A conceptual approach is presented to synthesize and integrate diverse sources and types of data from different networks of research sites. This approach focuses on developing derived data products through spatial and temporal aggregation that allow datasets collected with different methods to be compared. The approach is illustrated through the integration, analysis, and comparison of hundreds of long-term datasets from 50 ecological sites in the US that represent ecosystem types commonly found globally. New insights were found by comparing multiple sites using common derived data. In addition to "bringing to light" many dark data in a standardized, open access, easy-to-use format, a suite of lessons were learned that can be applied to up and coming research networks in the US and internationally. These lessons will be described along with the challenges, including cyber-infrastructure, cultural, and behavioral constraints associated with the use of big and little data, that may keep ecologists and inter-disciplinary scientists from taking full advantage of the vast amounts of existing and yet-to-be exposed data.

Web-based spatial analysis with the ILWIS open source GIS software and satellite images from GEONETCast

NASA Astrophysics Data System (ADS)

Lemmens, R.; Maathuis, B.; Mannaerts, C.; Foerster, T.; Schaeffer, B.; Wytzisk, A.

2009-12-01

This paper involves easy accessible integrated web-based analysis of satellite images with a plug-in based open source software. The paper is targeted to both users and developers of geospatial software. Guided by a use case scenario, we describe the ILWIS software and its toolbox to access satellite images through the GEONETCast broadcasting system. The last two decades have shown a major shift from stand-alone software systems to networked ones, often client/server applications using distributed geo-(web-)services. This allows organisations to combine without much effort their own data with remotely available data and processing functionality. Key to this integrated spatial data analysis is a low-cost access to data from within a user-friendly and flexible software. Web-based open source software solutions are more often a powerful option for developing countries. The Integrated Land and Water Information System (ILWIS) is a PC-based GIS & Remote Sensing software, comprising a complete package of image processing, spatial analysis and digital mapping and was developed as commercial software from the early nineties onwards. Recent project efforts have migrated ILWIS into a modular, plug-in-based open source software, and provide web-service support for OGC-based web mapping and processing. The core objective of the ILWIS Open source project is to provide a maintainable framework for researchers and software developers to implement training components, scientific toolboxes and (web-) services. The latest plug-ins have been developed for multi-criteria decision making, water resources analysis and spatial statistics analysis. The development of this framework is done since 2007 in the context of 52°North, which is an open initiative that advances the development of cutting edge open source geospatial software, using the GPL license. GEONETCast, as part of the emerging Global Earth Observation System of Systems (GEOSS), puts essential environmental data at the fingertips of users around the globe. This user-friendly and low-cost information dissemination provides global information as a basis for decision-making in a number of critical areas, including public health, energy, agriculture, weather, water, climate, natural disasters and ecosystems. GEONETCast makes available satellite images via Digital Video Broadcast (DVB) technology. An OGC WMS interface and plug-ins which convert GEONETCast data streams allow an ILWIS user to integrate various distributed data sources with data locally stored on his machine. Our paper describes a use case in which ILWIS is used with GEONETCast satellite imagery for decision making processes in Ghana. We also explain how the ILWIS software can be extended with additional functionality by means of building plug-ins and unfold our plans to implement other OGC standards, such as WCS and WPS in the same context. Especially, the latter one can be seen as a major step forward in terms of moving well-proven desktop based processing functionality to the web. This enables the embedding of ILWIS functionality in Spatial Data Infrastructures or even the execution in scalable and on-demand cloud computing environments.

Clinical Knowledge Governance Framework for Nationwide Data Infrastructure Projects.

PubMed

Wulff, Antje; Haarbrandt, Birger; Marschollek, Michael

2018-01-01

The availability of semantically-enriched and interoperable clinical information models is crucial for reusing once collected data across institutions like aspired in the German HiGHmed project. Funded by the Federal Ministry of Education and Research, this nationwide data infrastructure project adopts the openEHR approach for semantic modelling. Here, strong governance is required to define high-quality and reusable models. Design of a clinical knowledge governance framework for openEHR modelling in cross-institutional settings like HiGHmed. Analysis of successful practices from international projects, published ideas on archetype governance and own modelling experiences as well as modelling of BPMN processes. We designed a framework by presenting archetype variations, roles and responsibilities, IT support and modelling workflows. Our framework has great potential to make the openEHR modelling efforts manageable. Because practical experiences are rare, prospectively our work will be predestinated to evaluate the benefits of such structured governance approaches.

Proceedings Second Annual Cyber Security and Information Infrastructure Research Workshop

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sheldon, Frederick T; Krings, Axel; Yoo, Seong-Moo

2006-01-01

The workshop theme is Cyber Security: Beyond the Maginot Line Recently the FBI reported that computer crime has skyrocketed costing over $67 billion in 2005 alone and affecting 2.8M+ businesses and organizations. Attack sophistication is unprecedented along with availability of open source concomitant tools. Private, academic, and public sectors invest significant resources in cyber security. Industry primarily performs cyber security research as an investment in future products and services. While the public sector also funds cyber security R&D, the majority of this activity focuses on the specific mission(s) of the funding agency. Thus, broad areas of cyber security remain neglectedmore » or underdeveloped. Consequently, this workshop endeavors to explore issues involving cyber security and related technologies toward strengthening such areas and enabling the development of new tools and methods for securing our information infrastructure critical assets. We aim to assemble new ideas and proposals about robust models on which we can build the architecture of a secure cyberspace including but not limited to: * Knowledge discovery and management * Critical infrastructure protection * De-obfuscating tools for the validation and verification of tamper-proofed software * Computer network defense technologies * Scalable information assurance strategies * Assessment-driven design for trust * Security metrics and testing methodologies * Validation of security and survivability properties * Threat assessment and risk analysis * Early accurate detection of the insider threat * Security hardened sensor networks and ubiquitous computing environments * Mobile software authentication protocols * A new "model" of the threat to replace the "Maginot Line" model and more . . .« less

Insecurity of Wireless Networks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sheldon, Frederick T; Weber, John Mark; Yoo, Seong-Moo

Wireless is a powerful core technology enabling our global digital infrastructure. Wi-Fi networks are susceptible to attacks on Wired Equivalency Privacy, Wi-Fi Protected Access (WPA), and WPA2. These attack signatures can be profiled into a system that defends against such attacks on the basis of their inherent characteristics. Wi-Fi is the standard protocol for wireless networks used extensively in US critical infrastructures. Since the Wired Equivalency Privacy (WEP) security protocol was broken, the Wi-Fi Protected Access (WPA) protocol has been considered the secure alternative compatible with hardware developed for WEP. However, in November 2008, researchers developed an attack on WPA,more » allowing forgery of Address Resolution Protocol (ARP) packets. Subsequent enhancements have enabled ARP poisoning, cryptosystem denial of service, and man-in-the-middle attacks. Open source systems and methods (OSSM) have long been used to secure networks against such attacks. This article reviews OSSMs and the results of experimental attacks on WPA. These experiments re-created current attacks in a laboratory setting, recording both wired and wireless traffic. The article discusses methods of intrusion detection and prevention in the context of cyber physical protection of critical Internet infrastructure. The basis for this research is a specialized (and undoubtedly incomplete) taxonomy of Wi-Fi attacks and their adaptations to existing countermeasures and protocol revisions. Ultimately, this article aims to provide a clearer picture of how and why wireless protection protocols and encryption must achieve a more scientific basis for detecting and preventing such attacks.« less

Managing an Open Access, Multi-Institutional, International Digital Library: The Digital Library of the Caribbean

ERIC Educational Resources Information Center

Wooldridge, Brooke; Taylor, Laurie; Sullivan, Mark

2009-01-01

Developing an Open Access, multi-institutional, multilingual, international digital library requires robust technological and institutional infrastructures that support both the needs of individual institutions alongside the needs of the growing partnership and ensure continuous communication and development of the shared vision for the digital…

Road infrastructure, spatial spillover and county economic growth

NASA Astrophysics Data System (ADS)

Hu, Zhenhua; Luo, Shuang

2017-09-01

This paper analyzes the spatial spillover effect of road infrastructure on the economic growth of poverty-stricken counties, based on the spatial Durbin model, by using the panel data of 37 poor counties in Hunan province from 2006 to 2015. The results showed that there is a significant spatial dependence of economic growth in Poor Counties. Road infrastructure has a positive impact on economic growth, and the results will be overestimated without considering spatial factors. Considering the spatial factors, the road infrastructure will promote the economic growth of the surrounding areas through the spillover effect, but the spillover effect is restricted by the distance factor. Capital investment is the biggest factor of economic growth in poor counties, followed by urbanization, labor force and regional openness.

MOBBED: a computational data infrastructure for handling large collections of event-rich time series datasets in MATLAB

PubMed Central

Cockfield, Jeremy; Su, Kyungmin; Robbins, Kay A.

2013-01-01

Experiments to monitor human brain activity during active behavior record a variety of modalities (e.g., EEG, eye tracking, motion capture, respiration monitoring) and capture a complex environmental context leading to large, event-rich time series datasets. The considerable variability of responses within and among subjects in more realistic behavioral scenarios requires experiments to assess many more subjects over longer periods of time. This explosion of data requires better computational infrastructure to more systematically explore and process these collections. MOBBED is a lightweight, easy-to-use, extensible toolkit that allows users to incorporate a computational database into their normal MATLAB workflow. Although capable of storing quite general types of annotated data, MOBBED is particularly oriented to multichannel time series such as EEG that have event streams overlaid with sensor data. MOBBED directly supports access to individual events, data frames, and time-stamped feature vectors, allowing users to ask questions such as what types of events or features co-occur under various experimental conditions. A database provides several advantages not available to users who process one dataset at a time from the local file system. In addition to archiving primary data in a central place to save space and avoid inconsistencies, such a database allows users to manage, search, and retrieve events across multiple datasets without reading the entire dataset. The database also provides infrastructure for handling more complex event patterns that include environmental and contextual conditions. The database can also be used as a cache for expensive intermediate results that are reused in such activities as cross-validation of machine learning algorithms. MOBBED is implemented over PostgreSQL, a widely used open source database, and is freely available under the GNU general public license at http://visual.cs.utsa.edu/mobbed. Source and issue reports for MOBBED are maintained at http://vislab.github.com/MobbedMatlab/ PMID:24124417

MOBBED: a computational data infrastructure for handling large collections of event-rich time series datasets in MATLAB.

PubMed

Cockfield, Jeremy; Su, Kyungmin; Robbins, Kay A

2013-01-01

Experiments to monitor human brain activity during active behavior record a variety of modalities (e.g., EEG, eye tracking, motion capture, respiration monitoring) and capture a complex environmental context leading to large, event-rich time series datasets. The considerable variability of responses within and among subjects in more realistic behavioral scenarios requires experiments to assess many more subjects over longer periods of time. This explosion of data requires better computational infrastructure to more systematically explore and process these collections. MOBBED is a lightweight, easy-to-use, extensible toolkit that allows users to incorporate a computational database into their normal MATLAB workflow. Although capable of storing quite general types of annotated data, MOBBED is particularly oriented to multichannel time series such as EEG that have event streams overlaid with sensor data. MOBBED directly supports access to individual events, data frames, and time-stamped feature vectors, allowing users to ask questions such as what types of events or features co-occur under various experimental conditions. A database provides several advantages not available to users who process one dataset at a time from the local file system. In addition to archiving primary data in a central place to save space and avoid inconsistencies, such a database allows users to manage, search, and retrieve events across multiple datasets without reading the entire dataset. The database also provides infrastructure for handling more complex event patterns that include environmental and contextual conditions. The database can also be used as a cache for expensive intermediate results that are reused in such activities as cross-validation of machine learning algorithms. MOBBED is implemented over PostgreSQL, a widely used open source database, and is freely available under the GNU general public license at http://visual.cs.utsa.edu/mobbed. Source and issue reports for MOBBED are maintained at http://vislab.github.com/MobbedMatlab/

[Life cycle assessment of the infrastructure for hydrogen sources of fuel cell vehicles].

PubMed

Feng, Wen; Wang, Shujuan; Ni, Weidou; Chen, Changhe

2003-05-01

In order to promote the application of life cycle assessment and provide references for China to make the project of infrastructure for hydrogen sources of fuel cell vehicles in the near future, 10 feasible plans of infrastructure for hydrogen sources of fuel cell vehicles were designed according to the current technologies of producing, storing and transporting hydrogen. Then life cycle assessment was used as a tool to evaluate the environmental performances of the 10 plans. The standard indexes of classified environmental impacts of every plan were gotten and sensitivity analysis for several parameters were carried out. The results showed that the best plan was that hydrogen will be produced by natural gas steam reforming in central factory, then transported to refuelling stations through pipelines, and filled to fuel cell vehicles using hydrogen gas at last.

Embodied Energy and GHG Emissions from Material Use in Conventional and Unconventional Oil and Gas Operations.

PubMed

Brandt, Adam R

2015-11-03

Environmental impacts embodied in oilfield capital equipment have not been thoroughly studied. In this paper, we present the first open-source model which computes the embodied energy and greenhouse gas (GHG) emissions associated with materials consumed in constructing oil and gas wells and associated infrastructure. The model includes well casing, wellbore cement, drilling mud, processing equipment, gas compression, and transport infrastructure. Default case results show that consumption of materials in constructing oilfield equipment consumes ∼0.014 MJ of primary energy per MJ of oil produced, and results in ∼1.3 gCO2-eq GHG emissions per MJ (lower heating value) of crude oil produced, an increase of 15% relative to upstream emissions assessed in earlier OPGEE model versions, and an increase of 1-1.5% of full life cycle emissions. A case study of a hydraulically fractured well in the Bakken formation of North Dakota suggests lower energy intensity (0.011 MJ/MJ) and emissions intensity (1.03 gCO2-eq/MJ) due to the high productivity of hydraulically fractured wells. Results are sensitive to per-well productivity, the complexity of wellbore casing design, and the energy and emissions intensity per kg of material consumed.

COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access.

PubMed

Salek, Reza M; Neumann, Steffen; Schober, Daniel; Hummel, Jan; Billiau, Kenny; Kopka, Joachim; Correa, Elon; Reijmers, Theo; Rosato, Antonio; Tenori, Leonardo; Turano, Paola; Marin, Silvia; Deborde, Catherine; Jacob, Daniel; Rolin, Dominique; Dartigues, Benjamin; Conesa, Pablo; Haug, Kenneth; Rocca-Serra, Philippe; O'Hagan, Steve; Hao, Jie; van Vliet, Michael; Sysi-Aho, Marko; Ludwig, Christian; Bouwman, Jildau; Cascante, Marta; Ebbels, Timothy; Griffin, Julian L; Moing, Annick; Nikolski, Macha; Oresic, Matej; Sansone, Susanna-Assunta; Viant, Mark R; Goodacre, Royston; Günther, Ulrich L; Hankemeier, Thomas; Luchinat, Claudio; Walther, Dirk; Steinbeck, Christoph

Metabolomics has become a crucial phenotyping technique in a range of research fields including medicine, the life sciences, biotechnology and the environmental sciences. This necessitates the transfer of experimental information between research groups, as well as potentially to publishers and funders. After the initial efforts of the metabolomics standards initiative, minimum reporting standards were proposed which included the concepts for metabolomics databases. Built by the community, standards and infrastructure for metabolomics are still needed to allow storage, exchange, comparison and re-utilization of metabolomics data. The Framework Programme 7 EU Initiative 'coordination of standards in metabolomics' (COSMOS) is developing a robust data infrastructure and exchange standards for metabolomics data and metadata. This is to support workflows for a broad range of metabolomics applications within the European metabolomics community and the wider metabolomics and biomedical communities' participation. Here we announce our concepts and efforts asking for re-engagement of the metabolomics community, academics and industry, journal publishers, software and hardware vendors, as well as those interested in standardisation worldwide (addressing missing metabolomics ontologies, complex-metadata capturing and XML based open source data exchange format), to join and work towards updating and implementing metabolomics standards.

Open Data, Open Specifications and Free and Open Source Software: A powerful mix to create distributed Web-based water information systems

NASA Astrophysics Data System (ADS)

Arias, Carolina; Brovelli, Maria Antonia; Moreno, Rafael

2015-04-01

We are in an age when water resources are increasingly scarce and the impacts of human activities on them are ubiquitous. These problems don't respect administrative or political boundaries and they must be addressed integrating information from multiple sources at multiple spatial and temporal scales. Communication, coordination and data sharing are critical for addressing the water conservation and management issues of the 21st century. However, different countries, provinces, local authorities and agencies dealing with water resources have diverse organizational, socio-cultural, economic, environmental and information technology (IT) contexts that raise challenges to the creation of information systems capable of integrating and distributing information across their areas of responsibility in an efficient and timely manner. Tight and disparate financial resources, and dissimilar IT infrastructures (data, hardware, software and personnel expertise) further complicate the creation of these systems. There is a pressing need for distributed interoperable water information systems that are user friendly, easily accessible and capable of managing and sharing large volumes of spatial and non-spatial data. In a distributed system, data and processes are created and maintained in different locations each with competitive advantages to carry out specific activities. Open Data (data that can be freely distributed) is available in the water domain, and it should be further promoted across countries and organizations. Compliance with Open Specifications for data collection, storage and distribution is the first step toward the creation of systems that are capable of interacting and exchanging data in a seamlessly (interoperable) way. The features of Free and Open Source Software (FOSS) offer low access cost that facilitate scalability and long-term viability of information systems. The World Wide Web (the Web) will be the platform of choice to deploy and access these systems. Geospatial capabilities for mapping, visualization, and spatial analysis will be important components of these new generation of Web-based interoperable information systems in the water domain. The purpose of this presentation is to increase the awareness of scientists, IT personnel and agency managers about the advantages offered by the combined use of Open Data, Open Specifications for geospatial and water-related data collection, storage and sharing, as well as mature FOSS projects for the creation of interoperable Web-based information systems in the water domain. A case study is used to illustrate how these principles and technologies can be integrated to create a system with the previously mentioned characteristics for managing and responding to flood events.

Aging infrastructure creates opportunities for cost-efficient restoration of aquatic ecosystem connectivity.

PubMed

Neeson, Thomas M; Moody, Allison T; O'Hanley, Jesse R; Diebel, Matthew; Doran, Patrick J; Ferris, Michael C; Colling, Timothy; McIntyre, Peter B

2018-06-09

A hallmark of industrialization is the construction of dams for water management and roads for transportation, leading to fragmentation of aquatic ecosystems. Many nations are striving to address both maintenance backlogs and mitigation of environmental impacts as their infrastructure ages. Here, we test whether accounting for road repair needs could offer opportunities to boost conservation efficiency by piggybacking connectivity restoration projects on infrastructure maintenance. Using optimization models to align fish passage restoration sites with likely road repair priorities, we find potential increases in conservation return-on-investment ranging from 17% to 25%. Importantly, these gains occur without compromising infrastructure or conservation priorities; simply communicating openly about objectives and candidate sites enables greater accomplishment at current funding levels. Society embraces both reliable roads and thriving fisheries, so overcoming this coordination challenge should be feasible. Given deferred maintenance crises for many types of infrastructure, there could be widespread opportunities to enhance the cost effectiveness of conservation investments by coordinating with infrastructure renewal efforts. © 2018 by the Ecological Society of America.

MarDRe: efficient MapReduce-based removal of duplicate DNA reads in the cloud.

PubMed

Expósito, Roberto R; Veiga, Jorge; González-Domínguez, Jorge; Touriño, Juan

2017-09-01

This article presents MarDRe, a de novo cloud-ready duplicate and near-duplicate removal tool that can process single- and paired-end reads from FASTQ/FASTA datasets. MarDRe takes advantage of the widely adopted MapReduce programming model to fully exploit Big Data technologies on cloud-based infrastructures. Written in Java to maximize cross-platform compatibility, MarDRe is built upon the open-source Apache Hadoop project, the most popular distributed computing framework for scalable Big Data processing. On a 16-node cluster deployed on the Amazon EC2 cloud platform, MarDRe is up to 8.52 times faster than a representative state-of-the-art tool. Source code in Java and Hadoop as well as a user's guide are freely available under the GNU GPLv3 license at http://mardre.des.udc.es . rreye@udc.es. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

The Matsu Wheel: A Cloud-Based Framework for Efficient Analysis and Reanalysis of Earth Satellite Imagery

NASA Technical Reports Server (NTRS)

Patterson, Maria T.; Anderson, Nicholas; Bennett, Collin; Bruggemann, Jacob; Grossman, Robert L.; Handy, Matthew; Ly, Vuong; Mandl, Daniel J.; Pederson, Shane; Pivarski, James;

Climate Change Studies over Bangalore using Multi-source Remote Sensing Data and GIS

NASA Astrophysics Data System (ADS)

B, S.; Gouda, K. C.; Laxmikantha, B. P.; Bhat, N.

2014-12-01

Urbanization is a form of metropolitan growth that is a response to often bewildering sets of economic, social, and political forces and to the physical geography of an area. Some of the causes of the sprawl include - population growth, economy, patterns of infrastructure initiatives like the construction of roads and the provision of infrastructure using public money encouraging development. The direct implication of such urban sprawl is the change in land use and land cover of the region. In this study the long term climate data from multiple sources like NCEP reanalysis, IMD observations and various satellite derived products from MAIRS, IMD, ERSL and TRMM are considered and analyzed using the developed algorithms for the better understanding of the variability in the climate parameters over Bangalore. These products are further mathematically analyzed to arrive at desired results by extracting land surface temperature (LST), Potential evapo-transmission (PET), Rainfall, Humidity etc. Various satellites products are derived from NASA (National Aeronautics Space Agency), Indian meteorological satellites and global satellites are helpful in massive study of urban issues at global and regional scale. Climate change analysis is well studied by using either single source data such as Temperature or Rainfall from IMD (Indian Meteorological Department) or combined data products available as in case of MAIRS (Monsoon Asia Integrated Regional Scale) program to get rainfall at regional scale. Finally all the above said parameters are normalized and analyzed with the help of various open source available software's for pre and post processing our requirements to obtain desired results. A sample of analysis i.e. the Inter annual variability of annual averaged Temperature over Bangalore is presented in figure 1, which clearly shows the rising trend of the temperature (0.06oC/year). Also the Land use and land cover (LULC) analysis over Bangalore, Day light hours from satellite derived products are analyzed and the correlation of climate parameters with LULC are presented.

NCI's Distributed Geospatial Data Server

NASA Astrophysics Data System (ADS)

Larraondo, P. R.; Evans, B. J. K.; Antony, J.

2016-12-01

Earth systems, environmental and geophysics datasets are an extremely valuable source of information about the state and evolution of the Earth. However, different disciplines and applications require this data to be post-processed in different ways before it can be used. For researchers experimenting with algorithms across large datasets or combining multiple data sets, the traditional approach to batch data processing and storing all the output for later analysis rapidly becomes unfeasible, and often requires additional work to publish for others to use. Recent developments on distributed computing using interactive access to significant cloud infrastructure opens the door for new ways of processing data on demand, hence alleviating the need for storage space for each individual copy of each product. The Australian National Computational Infrastructure (NCI) has developed a highly distributed geospatial data server which supports interactive processing of large geospatial data products, including satellite Earth Observation data and global model data, using flexible user-defined functions. This system dynamically and efficiently distributes the required computations among cloud nodes and thus provides a scalable analysis capability. In many cases this completely alleviates the need to preprocess and store the data as products. This system presents a standards-compliant interface, allowing ready accessibility for users of the data. Typical data wrangling problems such as handling different file formats and data types, or harmonising the coordinate projections or temporal and spatial resolutions, can now be handled automatically by this service. The geospatial data server exposes functionality for specifying how the data should be aggregated and transformed. The resulting products can be served using several standards such as the Open Geospatial Consortium's (OGC) Web Map Service (WMS) or Web Feature Service (WFS), Open Street Map tiles, or raw binary arrays under different conventions. We will show some cases where we have used this new capability to provide a significant improvement over previous approaches.

Safety impacts of bicycle infrastructure: A critical review.

PubMed

DiGioia, Jonathan; Watkins, Kari Edison; Xu, Yanzhi; Rodgers, Michael; Guensler, Randall

2017-06-01

This paper takes a critical look at the present state of bicycle infrastructure treatment safety research, highlighting data needs. Safety literature relating to 22 bicycle treatments is examined, including findings, study methodologies, and data sources used in the studies. Some preliminary conclusions related to research efficacy are drawn from the available data and findings in the research. While the current body of bicycle safety literature points toward some defensible conclusions regarding the safety and effectiveness of certain bicycle treatments, such as bike lanes and removal of on-street parking, the vast majority treatments are still in need of rigorous research. Fundamental questions arise regarding appropriate exposure measures, crash measures, and crash data sources. This research will aid transportation departments with regard to decisions about bicycle infrastructure and guide future research efforts toward understanding safety impacts of bicycle infrastructure. Copyright © 2017 Elsevier Ltd and National Safety Council. All rights reserved.

The Chandra Source Catalog: Processing and Infrastructure

NASA Astrophysics Data System (ADS)

Evans, Janet; Evans, Ian N.; Glotfelty, Kenny J.; Hain, Roger; Hall, Diane M.; Miller, Joseph B.; Plummer, David A.; Zografou, Panagoula; Primini, Francis A.; Anderson, Craig S.; Bonaventura, Nina R.; Chen, Judy C.; Davis, John E.; Doe, Stephen M.; Fabbiano, Giuseppina; Galle, Elizabeth C.; Gibbs, Danny G., II; Grier, John D.; Harbo, Peter N.; He, Xiang Qun (Helen); Houck, John C.; Karovska, Margarita; Kashyap, Vinay L.; Lauer, Jennifer; McCollough, Michael L.; McDowell, Jonathan C.; Mitschang, Arik W.; Morgan, Douglas L.; Mossman, Amy E.; Nichols, Joy S.; Nowak, Michael A.; Refsdal, Brian L.; Rots, Arnold H.; Siemiginowska, Aneta L.; Sundheim, Beth A.; Tibbetts, Michael S.; van Stone, David W.; Winkelman, Sherry L.

2009-09-01

Chandra Source Catalog processing recalibrates each observation using the latest available calibration data, and employs a wavelet-based source detection algorithm to identify all the X-ray sources in the field of view. Source properties are then extracted from each detected source that is a candidate for inclusion in the catalog. Catalog processing is completed by matching sources across multiple observations, merging common detections, and applying quality assurance checks. The Chandra Source Catalog processing system shares a common processing infrastructure and utilizes much of the functionality that is built into the Standard Data Processing (SDP) pipeline system that provides calibrated Chandra data to end-users. Other key components of the catalog processing system have been assembled from the portable CIAO data analysis package. Minimal new software tool development has been required to support the science algorithms needed for catalog production. Since processing pipelines must be instantiated for each detected source, the number of pipelines that are run during catalog construction is a factor of order 100 times larger than for SDP. The increased computational load, and inherent parallel nature of the processing, is handled by distributing the workload across a multi-node Beowulf cluster. Modifications to the SDP automated processing application to support catalog processing, and extensions to Chandra Data Archive software to ingest and retrieve catalog products, complete the upgrades to the infrastructure to support catalog processing.

Extensions to Traditional Spatial Data Infrastructures: Integration of Social Media, Synchronization of Datasets, and Data on the Go in GeoPackages

NASA Astrophysics Data System (ADS)

Simonis, Ingo

2015-04-01

Traditional Spatial Data Infrastructures focus on aspects such as description and discovery of geospatial data, integration of these data into processing workflows, and representation of fusion or other data analysis results. Though lots of interoperability agreements still need to be worked out to achieve a satisfying level of interoperability within large scale initiatives such as INSPIRE, new technologies, use cases and requirements are constantly emerging from the user community. This paper focuses on three aspects that came up recently: The integration of social media data into SDIs, synchronization aspects between datasets used by field workers in shared resources environments, and the generation and maintenance of data for mixed mode online/offline situations that can be easily packed, delivered, modified, and synchronized with reference data sets. The work described in this paper results from the latest testbed executed by the Open Geospatial Consortium, OGC. The testbed is part of the interoperability program (IP), which constitutes a significant part of the OGC standards development process. The IP has a number of instruments to enhance geospatial standards and technologies, such as Testbeds, Pilot Projects, Interoperability Experiments, and Interoperability Expert Services. These activities are designed to encourage rapid development, testing, validation, demonstration and adoption of open, consensus based standards and best practices. The latest global activity, testbed-11, aims at exploring new technologies and architectural approaches to enrich and extend traditional spatial data infrastructures with data from Social Media, improved data synchronization, and the capability to take data to the field in new synchronized data containers called GeoPackages. Social media sources are a valuable supplement to providing up to date information in distributed environments. Following an uncoordinated crowdsourcing approach, social media data can be both overwhelming in volume and questionable in its accuracy and legitimacy. Testbed-11 explores how best to make use of such sources of information and how to deal with immanent issues with data from platforms such as OpenStreetMap, Twitter, tumblr, flickr, Snapchat, Facebook, Instagram, YouTube, Vimeo, Panoramio, Pinterest, Picasa or storyful. Further important aspects highlighted here are the synchronization of data and the capability to take complex data sets of any size on mobile devices to the field - and keeping them in sync with reference data stores. In particular in emergency management situations, it is crucial to ensure properly synchronized data sets across different types of data stores and applications. Often data is taken to the field on mobile devices, where it gets updated or annotated. Though bandwidth permanently improves, requirements on data quality and complexity grow in parallel. Intermitted connectivity is paired with high security requirements that have to be fulfilled. This paper discusses the latest approaches using synchronization services and synchronized GeoPackages, the new container format for geospatial data.

The cost of getting CCS wrong: Uncertainty, infrastructure design, and stranded CO 2

DOE PAGES

Middleton, Richard Stephen; Yaw, Sean Patrick

2018-01-11

Carbon capture, and storage (CCS) infrastructure will require industry—such as fossil-fuel power, ethanol production, and oil and gas extraction—to make massive investment in infrastructure. The cost of getting these investments wrong will be substantial and will impact the success of CCS technology. Multiple factors can and will impact the success of commercial-scale CCS, including significant uncertainties regarding capture, transport, and injection-storage decisions. Uncertainties throughout the CCS supply chain include policy, technology, engineering performance, economics, and market forces. In particular, large uncertainties exist for the injection and storage of CO 2. Even taking into account upfront investment in site characterization, themore » final performance of the storage phase is largely unknown until commercial-scale injection has started. We explore and quantify the impact of getting CCS infrastructure decisions wrong based on uncertain injection rates and uncertain CO 2 storage capacities using a case study managing CO 2 emissions from the Canadian oil sands industry in Alberta. We use SimCCS, a widely used CCS infrastructure design framework, to develop multiple CCS infrastructure scenarios. Each scenario consists of a CCS infrastructure network that connects CO 2 sources (oil sands extraction and processing) with CO 2 storage reservoirs (acid gas storage reservoirs) using a dedicated CO 2 pipeline network. Each scenario is analyzed under a range of uncertain storage estimates and infrastructure performance is assessed and quantified in terms of cost to build additional infrastructure to store all CO 2. We also include the role of stranded CO 2, CO 2 that a source was expecting to but cannot capture due substandard performance in the transport and storage infrastructure. Results show that the cost of getting the original infrastructure design wrong are significant and that comprehensive planning will be required to ensure that CCS becomes a successful climate mitigation technology. Here, we show that the concept of stranded CO 2 can transform a seemingly high-performing infrastructure design into the worst case scenario.« less

The cost of getting CCS wrong: Uncertainty, infrastructure design, and stranded CO 2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Middleton, Richard Stephen; Yaw, Sean Patrick

Carbon capture, and storage (CCS) infrastructure will require industry—such as fossil-fuel power, ethanol production, and oil and gas extraction—to make massive investment in infrastructure. The cost of getting these investments wrong will be substantial and will impact the success of CCS technology. Multiple factors can and will impact the success of commercial-scale CCS, including significant uncertainties regarding capture, transport, and injection-storage decisions. Uncertainties throughout the CCS supply chain include policy, technology, engineering performance, economics, and market forces. In particular, large uncertainties exist for the injection and storage of CO 2. Even taking into account upfront investment in site characterization, themore » final performance of the storage phase is largely unknown until commercial-scale injection has started. We explore and quantify the impact of getting CCS infrastructure decisions wrong based on uncertain injection rates and uncertain CO 2 storage capacities using a case study managing CO 2 emissions from the Canadian oil sands industry in Alberta. We use SimCCS, a widely used CCS infrastructure design framework, to develop multiple CCS infrastructure scenarios. Each scenario consists of a CCS infrastructure network that connects CO 2 sources (oil sands extraction and processing) with CO 2 storage reservoirs (acid gas storage reservoirs) using a dedicated CO 2 pipeline network. Each scenario is analyzed under a range of uncertain storage estimates and infrastructure performance is assessed and quantified in terms of cost to build additional infrastructure to store all CO 2. We also include the role of stranded CO 2, CO 2 that a source was expecting to but cannot capture due substandard performance in the transport and storage infrastructure. Results show that the cost of getting the original infrastructure design wrong are significant and that comprehensive planning will be required to ensure that CCS becomes a successful climate mitigation technology. Here, we show that the concept of stranded CO 2 can transform a seemingly high-performing infrastructure design into the worst case scenario.« less

The Fallacies of Open: Participatory Design, Infrastructuring, and the Pursuit of Radical Possibility

ERIC Educational Resources Information Center

West-Puckett, Stephanie; Smith, Anna; Cantrill, Christina; Zamora, Mia

2018-01-01

To better understand the impacts of participatory design in English language arts teacher education, this critical case study focuses on the National Writing Project's Connected Learning Massive, Open, Online Collaboration (CLMOOC) that engaged educators in playing with the connected learning framework. The authors draw from 5 years of interaction…

Identity federation in OpenStack - an introduction to hybrid clouds

NASA Astrophysics Data System (ADS)

Denis, Marek; Castro Leon, Jose; Ormancey, Emmanuel; Tedesco, Paolo

2015-12-01

We are evaluating cloud identity federation available in the OpenStack ecosystem that allows for on premise bursting into remote clouds with use of local identities (i.e. domain accounts). Further enhancements to identity federation are a clear way to hybrid cloud architectures - virtualized infrastructures layered across independent private and public clouds.

An Open Computing Infrastructure that Facilitates Integrated Product and Process Development from a Decision-Based Perspective

NASA Technical Reports Server (NTRS)

Hale, Mark A.

1996-01-01

Computer applications for design have evolved rapidly over the past several decades, and significant payoffs are being achieved by organizations through reductions in design cycle times. These applications are overwhelmed by the requirements imposed during complex, open engineering systems design. Organizations are faced with a number of different methodologies, numerous legacy disciplinary tools, and a very large amount of data. Yet they are also faced with few interdisciplinary tools for design collaboration or methods for achieving the revolutionary product designs required to maintain a competitive advantage in the future. These organizations are looking for a software infrastructure that integrates current corporate design practices with newer simulation and solution techniques. Such an infrastructure must be robust to changes in both corporate needs and enabling technologies. In addition, this infrastructure must be user-friendly, modular and scalable. This need is the motivation for the research described in this dissertation. The research is focused on the development of an open computing infrastructure that facilitates product and process design. In addition, this research explicitly deals with human interactions during design through a model that focuses on the role of a designer as that of decision-maker. The research perspective here is taken from that of design as a discipline with a focus on Decision-Based Design, Theory of Languages, Information Science, and Integration Technology. Given this background, a Model of IPPD is developed and implemented along the lines of a traditional experimental procedure: with the steps of establishing context, formalizing a theory, building an apparatus, conducting an experiment, reviewing results, and providing recommendations. Based on this Model, Design Processes and Specification can be explored in a structured and implementable architecture. An architecture for exploring design called DREAMS (Developing Robust Engineering Analysis Models and Specifications) has been developed which supports the activities of both meta-design and actual design execution. This is accomplished through a systematic process which is comprised of the stages of Formulation, Translation, and Evaluation. During this process, elements from a Design Specification are integrated into Design Processes. In addition, a software infrastructure was developed and is called IMAGE (Intelligent Multidisciplinary Aircraft Generation Environment). This represents a virtual apparatus in the Design Experiment conducted in this research. IMAGE is an innovative architecture because it explicitly supports design-related activities. This is accomplished through a GUI driven and Agent-based implementation of DREAMS. A HSCT design has been adopted from the Framework for Interdisciplinary Design Optimization (FIDO) and is implemented in IMAGE. This problem shows how Design Processes and Specification interact in a design system. In addition, the problem utilizes two different solution models concurrently: optimal and satisfying. The satisfying model allows for more design flexibility and allows a designer to maintain design freedom. As a result of following this experimental procedure, this infrastructure is an open system that it is robust to changes in both corporate needs and computer technologies. The development of this infrastructure leads to a number of significant intellectual contributions: 1) A new approach to implementing IPPD with the aid of a computer; 2) A formal Design Experiment; 3) A combined Process and Specification architecture that is language-based; 4) An infrastructure for exploring design; 5) An integration strategy for implementing computer resources; and 6) A seamless modeling language. The need for these contributions is emphasized by the demand by industry and government agencies for the development of these technologies.

Analysis of CERN computing infrastructure and monitoring data

NASA Astrophysics Data System (ADS)

Nieke, C.; Lassnig, M.; Menichetti, L.; Motesnitsalis, E.; Duellmann, D.

2015-12-01

Optimizing a computing infrastructure on the scale of LHC requires a quantitative understanding of a complex network of many different resources and services. For this purpose the CERN IT department and the LHC experiments are collecting a large multitude of logs and performance probes, which are already successfully used for short-term analysis (e.g. operational dashboards) within each group. The IT analytics working group has been created with the goal to bring data sources from different services and on different abstraction levels together and to implement a suitable infrastructure for mid- to long-term statistical analysis. It further provides a forum for joint optimization across single service boundaries and the exchange of analysis methods and tools. To simplify access to the collected data, we implemented an automated repository for cleaned and aggregated data sources based on the Hadoop ecosystem. This contribution describes some of the challenges encountered, such as dealing with heterogeneous data formats, selecting an efficient storage format for map reduce and external access, and will describe the repository user interface. Using this infrastructure we were able to quantitatively analyze the relationship between CPU/wall fraction, latency/throughput constraints of network and disk and the effective job throughput. In this contribution we will first describe the design of the shared analysis infrastructure and then present a summary of first analysis results from the combined data sources.

FixO3: Advancement towards Open Ocean Observatory Data Management Harmonisation

NASA Astrophysics Data System (ADS)

Behnken, Andree; Pagnani, Maureen; Huber, Robert; Lampitt, Richard

2015-04-01

Since 2002 there has been a sustained effort, supported as European framework projects, to harmonise both the technology and the data management of Open Ocean fixed observatories run by European nations. FixO3 started in September 2013, and for 3 more years will coordinate the convergence of data management best practice across a constellation of moorings in the Atlantic, in both hemispheres, and in the Mediterranean. To ensure the continued existence of these unique sources of oceanographic data as sustained observatories it is vital to improve access to the data collected, both in terms of methods of presentation, real-time availability, long-term archiving and quality assurance. The data management component of FixO3 improves access to marine observatory data by harmonising data management standards, formats and workflows covering the complete life cycle of data from real time data acquisition to long-term archiving. Legal and data policy aspects have been examined and discussed to identify transnational barriers to open-access to marine observatory data. As a result, a harmonised FixO3 data policy was drafted, which provides a formal basis for data exchange between FixO3 infrastructures, and also enables open access to data for the general public. FixO3 interacts with other European infrastructures such as EMODnet, SeaDataNet, PANGAEA, and especially aims to harmonise efforts with OceanSites and MyOcean. The project landing page (www.fixo3.eu) offers detailed information about every observatory as well as data visualisations and direct downloads. In addition to this, metadata for all FixO3 - relevant data are available from the searchable FixO3 metadata catalogue, which is also accessible from the project web page. This catalogue is hosted by PANGAEA and receives updates in regular intervals. The FixO3 Standards & Services registry ties in with the GEOSS Components and Services Registry (CSR) and provides additional observatory information. The data management efforts are central to FixO3. As a result of the procedural and technological harmonisation efforts undertaken in the project, the FixO3 network of observatories is accumulating unique, quality controlled data sets that will develop into a legacy repository of openly accessible oceanographic data.

Easy research data handling with an OpenEarth DataLab for geo-monitoring research

NASA Astrophysics Data System (ADS)

Vanderfeesten, Maurice; van der Kuil, Annemiek; Prinčič, Alenka; den Heijer, Kees; Rombouts, Jeroen

2015-04-01

OpenEarth DataLab is an open source-based collaboration and processing platform to enable streamlined research data management from raw data ingest and transformation to interoperable distribution. It enables geo-scientists to easily synchronise, share, compute and visualise the dynamic and most up-to-date research data, scripts and models in multi-stakeholder geo-monitoring programs. This DataLab is developed by the Research Data Services team of TU Delft Library and 3TU.Datacentrum together with coastal engineers of Delft University of Technology and Deltares. Based on the OpenEarth software stack an environment has been developed to orchestrate numerous geo-related open source software components that can empower researchers and increase the overall research quality by managing research data; enabling automatic and interoperable data workflows between all the components with track & trace, hit & run data transformation processing in cloud infrastructure using MatLab and Python, synchronisation of data and scripts (SVN), and much more. Transformed interoperable data products (KML, NetCDF, PostGIS) can be used by ready-made OpenEarth tools for further analyses and visualisation, and can be distributed via interoperable channels such as THREDDS (OpenDAP) and GeoServer. An example of a successful application of OpenEarth DataLab is the Sand Motor, an innovative method for coastal protection in the Netherlands. The Sand Motor is a huge volume of sand that has been applied along the coast to be spread naturally by wind, waves and currents. Different research disciplines are involved concerned with: weather, waves and currents, sand distribution, water table and water quality, flora and fauna, recreation and management. Researchers share and transform their data in the OpenEarth DataLab, that makes it possible to combine their data and to see influence of different aspects of the coastal protection on their models. During the project the data are available only for the researchers involved. After the project a large part of the data and scripts will be published with DOI in the Data Archive of 3TU.Datacentrum for reuse in new research. For the 83 project members of the Sand Motor, the OpenEarth DataLab is available on www.zandmotordata.nl. The OpenEarth DataLab not only saves time and increases quality, but has the potential to open new frontiers for exploring cross-domain analysis and visualisations, revealing new scientific insights.

B-HIT - A Tool for Harvesting and Indexing Biodiversity Data

PubMed Central

Barker, Katharine; Braak, Kyle; Cawsey, E. Margaret; Coddington, Jonathan; Robertson, Tim; Whitacre, Jamie

2015-01-01

With the rapidly growing number of data publishers, the process of harvesting and indexing information to offer advanced search and discovery becomes a critical bottleneck in globally distributed primary biodiversity data infrastructures. The Global Biodiversity Information Facility (GBIF) implemented a Harvesting and Indexing Toolkit (HIT), which largely automates data harvesting activities for hundreds of collection and observational data providers. The team of the Botanic Garden and Botanical Museum Berlin-Dahlem has extended this well-established system with a range of additional functions, including improved processing of multiple taxon identifications, the ability to represent associations between specimen and observation units, new data quality control and new reporting capabilities. The open source software B-HIT can be freely installed and used for setting up thematic networks serving the demands of particular user groups. PMID:26544980

B-HIT - A Tool for Harvesting and Indexing Biodiversity Data.

PubMed

Kelbert, Patricia; Droege, Gabriele; Barker, Katharine; Braak, Kyle; Cawsey, E Margaret; Coddington, Jonathan; Robertson, Tim; Whitacre, Jamie; Güntsch, Anton

2015-01-01

With the rapidly growing number of data publishers, the process of harvesting and indexing information to offer advanced search and discovery becomes a critical bottleneck in globally distributed primary biodiversity data infrastructures. The Global Biodiversity Information Facility (GBIF) implemented a Harvesting and Indexing Toolkit (HIT), which largely automates data harvesting activities for hundreds of collection and observational data providers. The team of the Botanic Garden and Botanical Museum Berlin-Dahlem has extended this well-established system with a range of additional functions, including improved processing of multiple taxon identifications, the ability to represent associations between specimen and observation units, new data quality control and new reporting capabilities. The open source software B-HIT can be freely installed and used for setting up thematic networks serving the demands of particular user groups.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Corey Thuen

The On-Device Dynamic Analysis of Mobile Applications (ODAMA) project was started in an effort to protect mobile devices used in Industrial Control Systems (ICS) from cyber attack. Because mobile devices hide as much of the “computer” as possible, the user’s ability to assess the software running on their system is limited. The research team chose Google’s Android platform for this initial research because it is open source and it would give us freedom in our approach, including the ability to modify the mobile device’s operating system itself. The research team concluded that a Privileged Application was the right approach, andmore » the result was ODAMA. This project is an important piece of the work to secure the expanding use of mobile devices with our nation’s critical infrastructure.« less

OpenFIRE - A Web GIS Service for Distributing the Finnish Reflection Experiment Datasets

NASA Astrophysics Data System (ADS)

Väkevä, Sakari; Aalto, Aleksi; Heinonen, Aku; Heikkinen, Pekka; Korja, Annakaisa

2017-04-01

The Finnish Reflection Experiment (FIRE) is a land-based deep seismic reflection survey conducted between 2001 and 2003 by a research consortium of the Universities of Helsinki and Oulu, the Geological Survey of Finland, and a Russian state-owned enterprise SpetsGeofysika. The dataset consists of 2100 kilometers of high-resolution profiles across the Archaean and Proterozoic nuclei of the Fennoscandian Shield. Although FIRE data have been available on request since 2009, the data have remained underused outside the original research consortium. The original FIRE data have been quality-controlled. The shot gathers have been cross-checked and comprehensive errata has been created. The brute stacks provided by the Russian seismic contractor have been reprocessed into seismic sections and replotted. A complete documentation of the intermediate processing steps is provided together with guidelines for setting up a computing environment and plotting the data. An open access web service "OpenFIRE" for the visualization and the downloading of FIRE data has been created. The service includes a mobile-responsive map application capable of enriching seismic sections with data from other sources such as open data from the National Land Survey and the Geological Survey of Finland. The AVAA team of the Finnish Open Science and Research Initiative has provided a tailored Liferay portal with necessary web components such as an API (Application Programming Interface) for download requests. INSPIRE (Infrastructure for Spatial Information in Europe) -compliant discovery metadata have been produced and geospatial data will be exposed as Open Geospatial Consortium standard services. The technical guidelines of the European Plate Observing System have been followed and the service could be considered as a reference application for sharing reflection seismic data. The OpenFIRE web service is available at www.seismo.helsinki.fi/openfire

Android and ODK based data collection framework to aid in epidemiological analysis

PubMed Central

Raja, A.; Tridane, A.; Gaffar, A.; Lindquist, T.; Pribadi, K.

2014-01-01

Periodic collection of field data, analysis and interpretation of data are key to a good healthcare service. This data is used by the subsequent decision makers to recognize preventive measures, provide timely support to the affected and to help measure the effects of their interventions. While the resources required for good disease surveillance and proactive healthcare are available more readily in developed countries, the lack of these in developing countries may compromise the quality of service provided. This combined with the critical nature of some diseases makes this an essential issue to be addressed. Taking advantage of the rapid growth of cell phone usage and related infrastructure in developed as well as developing countries, several systems have been established to address the gaps in data collection. Android, being an open sourced platform, has gained considerable popularity in this aspect. Open data kit is one such tool developed to aid in data collection. The aim of this paper is to present a prototype framework built using few such existing tools and technologies to address data collection for seasonal influenza, commonly referred to as the flu. PMID:24678381

The development of an application for data privacy by applying an audit repository based on IHE ATNA.

PubMed

Bresser, Laura; Köhler, Steffen; Schwaab, Christoph

2014-01-01

It is necessary to optimize workflows and communication between institutions involved in patients' treatment to improve quality and efficiency of the German healthcare. To achieve these in the Metropolregion Rhein-Neckar, a personal, cross-institutional patient record (PEPA) is used. Given the immense sensitivity of health-related information saved in the PEPA, it is imperative to obey the data protection regulations in Germany. One important aspect is the logging of access to personal health data and all other safety-related events. For gathering audit information, the IHE profile ATNA can be used, because it provides a flexible and standardized infrastructure. There are already existing solutions for gathering the audit information based on ATNA. In this article one solution (OpenATNA) is evaluated, which uses the method of evaluation defined by Peter Baumgartner. In addition, a user interface for a privacy officer is necessary to support the examination of the audit information. Therefore, we will describe a method to develop an application in Liferay (an OpenSource enterprise portal project) which supports examinations on the gathered audit information.

49 CFR 15.5 - Sensitive security information.

Code of Federal Regulations, 2014 CFR

2014-10-01

... sources and methods used to gather or develop threat information, including threats against cyber infrastructure. (8) Security measures. Specific details of aviation or maritime transportation security measures... infrastructure asset information. Any list identifying systems or assets, whether physical or virtual, so vital...

49 CFR 15.5 - Sensitive security information.

Code of Federal Regulations, 2011 CFR

2011-10-01

... sources and methods used to gather or develop threat information, including threats against cyber infrastructure. (8) Security measures. Specific details of aviation or maritime transportation security measures... infrastructure asset information. Any list identifying systems or assets, whether physical or virtual, so vital...

49 CFR 15.5 - Sensitive security information.

Code of Federal Regulations, 2013 CFR

2013-10-01

... sources and methods used to gather or develop threat information, including threats against cyber infrastructure. (8) Security measures. Specific details of aviation or maritime transportation security measures... infrastructure asset information. Any list identifying systems or assets, whether physical or virtual, so vital...

49 CFR 15.5 - Sensitive security information.

Code of Federal Regulations, 2012 CFR

2012-10-01

... sources and methods used to gather or develop threat information, including threats against cyber infrastructure. (8) Security measures. Specific details of aviation or maritime transportation security measures... infrastructure asset information. Any list identifying systems or assets, whether physical or virtual, so vital...

Impacts of transportation infrastructure on storm water and surfaces waters in Chittenden County, Vermont, USA.

DOT National Transportation Integrated Search

2014-06-01

Transportation infrastructure is a major source of stormwater runoff that can alter hydrology and : contribute significant loading of nutrients, sediment, and other pollutants to surface waters. These : increased loads can contribute to impairment of...

Hybrid cloud: bridging of private and public cloud computing

NASA Astrophysics Data System (ADS)

Aryotejo, Guruh; Kristiyanto, Daniel Y.; Mufadhol

2018-05-01

Cloud Computing is quickly emerging as a promising paradigm in the recent years especially for the business sector. In addition, through cloud service providers, cloud computing is widely used by Information Technology (IT) based startup company to grow their business. However, the level of most businesses awareness on data security issues is low, since some Cloud Service Provider (CSP) could decrypt their data. Hybrid Cloud Deployment Model (HCDM) has characteristic as open source, which is one of secure cloud computing model, thus HCDM may solve data security issues. The objective of this study is to design, deploy and evaluate a HCDM as Infrastructure as a Service (IaaS). In the implementation process, Metal as a Service (MAAS) engine was used as a base to build an actual server and node. Followed by installing the vsftpd application, which serves as FTP server. In comparison with HCDM, public cloud was adopted through public cloud interface. As a result, the design and deployment of HCDM was conducted successfully, instead of having good security, HCDM able to transfer data faster than public cloud significantly. To the best of our knowledge, Hybrid Cloud Deployment model is one of secure cloud computing model due to its characteristic as open source. Furthermore, this study will serve as a base for future studies about Hybrid Cloud Deployment model which may relevant for solving big security issues of IT-based startup companies especially in Indonesia.

ROSE::FTTransform - A Source-to-Source Translation Framework for Exascale Fault-Tolerance Research

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lidman, J; Quinlan, D; Liao, C

2012-03-26

Exascale computing systems will require sufficient resilience to tolerate numerous types of hardware faults while still assuring correct program execution. Such extreme-scale machines are expected to be dominated by processors driven at lower voltages (near the minimum 0.5 volts for current transistors). At these voltage levels, the rate of transient errors increases dramatically due to the sensitivity to transient and geographically localized voltage drops on parts of the processor chip. To achieve power efficiency, these processors are likely to be streamlined and minimal, and thus they cannot be expected to handle transient errors entirely in hardware. Here we present anmore » open, compiler-based framework to automate the armoring of High Performance Computing (HPC) software to protect it from these types of transient processor errors. We develop an open infrastructure to support research work in this area, and we define tools that, in the future, may provide more complete automated and/or semi-automated solutions to support software resiliency on future exascale architectures. Results demonstrate that our approach is feasible, pragmatic in how it can be separated from the software development process, and reasonably efficient (0% to 30% overhead for the Jacobi iteration on common hardware; and 20%, 40%, 26%, and 2% overhead for a randomly selected subset of benchmarks from the Livermore Loops [1]).« less

Resilient workflows for computational mechanics platforms

NASA Astrophysics Data System (ADS)

Nguyên, Toàn; Trifan, Laurentiu; Désidéri, Jean-Antoine

2010-06-01

Workflow management systems have recently been the focus of much interest and many research and deployment for scientific applications worldwide [26, 27]. Their ability to abstract the applications by wrapping application codes have also stressed the usefulness of such systems for multidiscipline applications [23, 24]. When complex applications need to provide seamless interfaces hiding the technicalities of the computing infrastructures, their high-level modeling, monitoring and execution functionalities help giving production teams seamless and effective facilities [25, 31, 33]. Software integration infrastructures based on programming paradigms such as Python, Mathlab and Scilab have also provided evidence of the usefulness of such approaches for the tight coupling of multidisciplne application codes [22, 24]. Also high-performance computing based on multi-core multi-cluster infrastructures open new opportunities for more accurate, more extensive and effective robust multi-discipline simulations for the decades to come [28]. This supports the goal of full flight dynamics simulation for 3D aircraft models within the next decade, opening the way to virtual flight-tests and certification of aircraft in the future [23, 24, 29].

Elastic extension of a local analysis facility on external clouds for the LHC experiments

NASA Astrophysics Data System (ADS)

Ciaschini, V.; Codispoti, G.; Rinaldi, L.; Aiftimiei, D. C.; Bonacorsi, D.; Calligola, P.; Dal Pra, S.; De Girolamo, D.; Di Maria, R.; Grandi, C.; Michelotto, D.; Panella, M.; Taneja, S.; Semeria, F.

2017-10-01

The computing infrastructures serving the LHC experiments have been designed to cope at most with the average amount of data recorded. The usage peaks, as already observed in Run-I, may however originate large backlogs, thus delaying the completion of the data reconstruction and ultimately the data availability for physics analysis. In order to cope with the production peaks, the LHC experiments are exploring the opportunity to access Cloud resources provided by external partners or commercial providers. In this work we present the proof of concept of the elastic extension of a local analysis facility, specifically the Bologna Tier-3 Grid site, for the LHC experiments hosted at the site, on an external OpenStack infrastructure. We focus on the Cloud Bursting of the Grid site using DynFarm, a newly designed tool that allows the dynamic registration of new worker nodes to LSF. In this approach, the dynamically added worker nodes instantiated on an OpenStack infrastructure are transparently accessed by the LHC Grid tools and at the same time they serve as an extension of the farm for the local usage.

Services for domain specific developments in the Cloud

NASA Astrophysics Data System (ADS)

Schwichtenberg, Horst; Gemuend, André

2015-04-01

We will discuss and demonstrate the possibilities of new Cloud Services where the complete development of code is in the Cloud. We will discuss the possibilities of such services where the complete development cycle from programing to testing is in the cloud. This can be also combined with dedicated research domain specific services and hide the burden of accessing available infrastructures. As an example, we will show a service that is intended to complement the services of the VERCE projects infrastructure, a service that utilizes Cloud resources to offer simplified execution of data pre- and post-processing scripts. It offers users access to the ObsPy seismological toolbox for processing data with the Python programming language, executed on virtual Cloud resources in a secured sandbox. The solution encompasses a frontend with a modern graphical user interface, a messaging infrastructure as well as Python worker nodes for background processing. All components are deployable in the Cloud and have been tested on different environments based on OpenStack and OpenNebula. Deployments on commercial, public Clouds will be tested in the future.

Unbundled infrastructure firms: Competition and continuing regulation

NASA Astrophysics Data System (ADS)

Hogendorn, Christiaan Paul

Unbundled infrastructure firms provide conduits for electricity transmission, residential communications, etc. but are vertically disintegrated from "content" functions such as electricity generation or world-wide-web pages. These conduits are being deregulated, and this dissertation examines whether the deregulated conduits will behave in an efficient and competitive manner. The dissertation presents three essays, each of which develops a theoretical model of the behavior of conduit firms in a market environment. The first essay considers the prospects for competition between multiple conduits in the emerging market for broadband (high-speed) residential Internet access. It finds that such competition is likely to emerge as demand for these services increase. The second essay shows how a monopoly electricity or natural gas transmission conduit can facilitate collusion between suppliers of the good. It shows that this is an inefficient effect of standard price-cap regulation. The third essay considers the supply chain of residential Internet access and evaluates proposed "open access" regulation that would allow more than one firm to serve customers over the same physical infrastructure. It shows that the amount of content available to consumers does not necessarily increase under open access.

Evaluation of Free Platforms for Delivery of Massive Open Online Courses (MOOCS)

ERIC Educational Resources Information Center

Zancanaro, Airton; Nunes, Carolina Schmitt; Domingues, Maria Jose Carvalho de Souza

2017-01-01

For the hosting, management and delivery of Massive Open Online Courses (MOOC) it is necessary a technological infrastructure that supports it. Various educational institutions do not have or do not wish to invest in such a structure, possibly because MOOCs are not yet part of official programs of universities, but initiatives by a particular…

Delivery of Open, Distance, and E-Learning in Kenya

ERIC Educational Resources Information Center

Nyerere, Jackline Anyona; Gravenir, Frederick Q.; Mse, Godfrey S.

2012-01-01

The increased demand and need for continuous learning have led to the introduction of open, distance, and e-learning (ODeL) in Kenya. Provision of this mode of education has, however, been faced with various challenges, among them infrastructural ones. This study was a survey conducted in two public universities offering major components of ODeL,…

Developing Mathematics Teacher Knowledge: The Paradidactic Infrastructure of "Open Lesson" in Japan

ERIC Educational Resources Information Center

Miyakawa, Takeshi; Winslow, Carl

2013-01-01

In this paper, we first present a theoretical approach to study mathematics teacher knowledge and the conditions for developing it, which is firmly rooted in a systemic approach to didactic phenomena at large, namely the anthropological theory of the didactic. Then, a case of open lesson is presented and analysed, using this theoretical approach,…

OSI and TCP/IP

NASA Technical Reports Server (NTRS)

Randolph, Lynwood P.

1994-01-01

The Open Systems Interconnection Transmission Control Protocol/Internet Protocol (OSI TCP/IP) and the Government Open Systems Interconnection Profile (GOSIP) are compared and described in terms of Federal internetworking. The organization and functions of the Federal Internetworking Requirements Panel (FIRP) are discussed and the panel's conclusions and recommendations with respect to the standards and implementation of the National Information Infrastructure (NII) are presented.

The European Bioinformatics Institute in 2017: data coordination and integration

PubMed Central

Cochrane, Guy; Apweiler, Rolf; Birney, Ewan

2018-01-01

Abstract The European Bioinformatics Institute (EMBL-EBI) supports life-science research throughout the world by providing open data, open-source software and analytical tools, and technical infrastructure (https://www.ebi.ac.uk). We accommodate an increasingly diverse range of data types and integrate them, so that biologists in all disciplines can explore life in ever-increasing detail. We maintain over 40 data resources, many of which are run collaboratively with partners in 16 countries (https://www.ebi.ac.uk/services). Submissions continue to increase exponentially: our data storage has doubled in less than two years to 120 petabytes. Recent advances in cellular imaging and single-cell sequencing techniques are generating a vast amount of high-dimensional data, bringing to light new cell types and new perspectives on anatomy. Accordingly, one of our main focus areas is integrating high-quality information from bioimaging, biobanking and other types of molecular data. This is reflected in our deep involvement in Open Targets, stewarding of plant phenotyping standards (MIAPPE) and partnership in the Human Cell Atlas data coordination platform, as well as the 2017 launch of the Omics Discovery Index. This update gives a birds-eye view of EMBL-EBI’s approach to data integration and service development as genomics begins to enter the clinic. PMID:29186510

Rheticus: a cloud-based Geo-Information Service for the Detection and Monitoring of Geohazards and Infrastructural Instabilities

NASA Astrophysics Data System (ADS)

Chiaradia, M. T.; Samarelli, S.; Massimi, V.; Nutricato, R.; Nitti, D. O.; Morea, A.; Tijani, K.

2017-12-01

Geospatial information is today essential for organizations and professionals working in several industries. More and more, huge information is collected from multiple data sources and is freely available to anyone as open data. Rheticus® is an innovative cloud-based data and services hub able to deliver Earth Observation added-value products through automatic complex processes and, if appropriate, a minimum interaction with human operators. This target is achieved by means of programmable components working as different software layers in a modern enterprise system which relies on SOA (Service-Oriented-Architecture) model. Due to its spread architecture, where every functionality is defined and encapsulated in a standalone component, Rheticus is potentially highly scalable and distributable allowing different configurations depending on the user needs. This approach makes the system very flexible with respect to the services implementation, ensuring the ability to rethink and redesign the whole process with little effort. In this work, we outline the overall cloud-based platform and focus on the "Rheticus Displacement" service, aimed at providing accurate information to monitor movements occurring across landslide features or structural instabilities that could affect buildings or infrastructures. Using Sentinel-1 (S1) open data images and Multi-Temporal SAR Interferometry techniques (MTInSAR), the service is complementary to traditional survey methods, providing a long-term solution to slope instability monitoring. Rheticus automatically browses and accesses (on a weekly basis) the products of the rolling archive of ESA S1 Scientific Data Hub. S1 data are then processed by SPINUA (Stable Point Interferometry even in Unurbanized Areas), a robust MTInSAR algorithm, which is responsible of producing displacement maps immediately usable to measure movements of point and distributed scatterers, with sub-centimetric precision. We outline the automatic generation process of displacement maps and we provide examples of the detection and monitoring of geohazard and infrastructure instabilities. ACK: Rheticus® is a registered trademark of Planetek Italia srl. Study carried out in the framework of the FAST4MAP project (ASI Contract n. 2015-020-R.0). Sentinel-1A products provided by ESA.

Maximizing the use of EO products: how to leverage the potential of open geospatial service architectures

NASA Astrophysics Data System (ADS)

Usländer, Thomas

2012-10-01

The demand for the rapid provision of EO products with well-defined characteristics in terms of temporal, spatial, image-specific and thematic criteria is increasing. Examples are products to support near real-time damage assessment after a natural disaster event, e.g. an earthquake. However, beyond the organizational and economic questions, there are technological and systemic barriers to enable a comfortable search, order, delivery or even combination of EO products. Most portals of space agencies and EO product providers require sophisticated satellite and product knowledge and, even worse, are all different and not interoperable. This paper gives an overview about the use cases and the architectural solutions that aim at an open and flexible EO mission infrastructure with application-oriented user interfaces and well-defined service interfaces based upon open standards. It presents corresponding international initiatives such as INSPIRE (Infrastructure for Spatial Information in the European Community), GMES (Global Monitoring for Environment and Security), GEOSS (Global Earth Observation System of Systems) and HMA (Heterogeneous Missions Accessibility) and their associated infrastructure approaches. The paper presents a corresponding analysis and design methodology and two examples how such architectures are already successfully used in early warning systems for geo-hazards and toolsets for environmentallyinduced health risks. Finally, the paper concludes with an outlook how these ideas relate to the vision of the Future Internet.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hale, Rebecca L.; Turnbull, Laura; Earl, Stevan

Urban watersheds are often sources of nitrogen (N) to downstream systems, contributing to poor water quality. However, it is unknown which components (e.g., land cover and stormwater infrastructure type) of urban watersheds contribute to N export and which may be sites of retention. In this study we investigated which watershed characteristics control N sourcing, biogeochemical processing of nitrate (NO3–) during storms, and the amount of rainfall N that is retained within urban watersheds. We used triple isotopes of NO3– (δ15N, δ18O, and Δ17O) to identify sources and transformations of NO3– during storms from 10 nested arid urban watersheds that variedmore » in stormwater infrastructure type and drainage area. Stormwater infrastructure and land cover—retention basins, pipes, and grass cover—dictated the sourcing of NO3– in runoff. Urban watersheds can be strong sinks or sources of N to stormwater depending on the proportion of rainfall that leaves the watershed as runoff, but we found no evidence that denitrification occurred during storms. Our results suggest that watershed characteristics control the sources and transport of inorganic N in urban stormwater but that retention of inorganic N at the timescale of individual runoff events is controlled by hydrologic, rather than biogeochemical, mechanisms.« less

Data Quality Assurance and Provenance Tracking in ICOADS Release 3.0

NASA Astrophysics Data System (ADS)

Cram, T.; Worley, S. J.; Ji, Z.; Schuster, D.

2017-12-01

The International Comprehensive Ocean-Atmosphere Data Set (ICOADS) Release 3.0 (R3.0) is the world's most extensive collection of global surface marine meteorological in situ observational data. Managed under an international partnership, it contains over 455 million unique multi-parameter records, dates back to 1662, and is updated monthly in near real-time. It is a foundational dataset for weather and climate research that has been used by thousands of users. By using rigorous data preparation methods, new IT infrastructure, and International Maritime Meteorological Archive (IMMA) format enhancements, ICOADS R3.0 is exemplary in data quality assurance, provenance tracking, and capturing user feedback. The features in this data lifecycle management will be presented and include, but are not limited to, written data translation specification for each data source being added to ICOADS, assignment of data source identification parameters, attachment of the original data in the IMMA format to support future re-evaluation if necessary, permanently assigned unique identification on every record making data development and community collaborations easily possible using a relational database infrastructure, and extensible capacity of the IMMA format to augment the data richness beyond the primary scope of marine surface data. Some recent augmentations are more completely specified ocean observations from profiling observing systems, feedback data submitted by the atmospheric and oceanographic reanalysis providers, higher quality edited cloud reports, and community provided data value adjustments with uncertainty estimates. Highlights covering these ICOADS value-added features will be explained and the open free access from NCAR will be briefly described.

Determining the Financial Impact of Flood Hazards in Ungaged Basins

NASA Astrophysics Data System (ADS)

Cotterman, K. A.; Gutenson, J. L.; Pradhan, N. R.; Byrd, A.

2017-12-01

Many portions of the Earth lack adequate authoritative or in situ data that is of great value in determining natural hazard vulnerability from both anthropogenic and physical perspective. Such locations include the majority of developing nations, which do not possess adequate warning systems and protective infrastructure. The lack of warning and protection from natural hazards make these nations vulnerable to the destructive power of events such as floods. The goal of this research is to demonstrate an initial workflow with which to characterize flood financial hazards with global datasets and crowd-sourced, non-authoritative data in ungagged river basins. This workflow includes the hydrologic and hydraulic response of the watershed to precipitation, characterized by the physics-based modeling application Gridded Surface-Subsurface Hydrologic Analysis (GSSHA) model. In addition, data infrastructure and resources are available to approximate the human impact of flooding. Open source, volunteer geographic information (VGI) data can provide global coverage of elements at risk of flooding. Additional valuation mechanisms can then translate flood exposure into percentage and financial damage to each building. The combinations of these tools allow the authors to remotely assess flood hazards with minimal computational, temporal, and financial overhead. This combination of deterministic and stochastic modeling provides the means to quickly characterize watershed flood vulnerability and will allow emergency responders and planners to better understand the implications of flooding, both spatially and financially. In either a planning, real-time, or forecasting scenario, the system will assist the user in understanding basin flood vulnerability and increasing community resiliency and preparedness.

Developing a Web-based system by integrating VGI and SDI for real estate management and marketing

NASA Astrophysics Data System (ADS)

Salajegheh, J.; Hakimpour, F.; Esmaeily, A.

2014-10-01

Property importance of various aspects, especially the impact on various sectors of the economy and the country's macroeconomic is clear. Because of the real, multi-dimensional and heterogeneous nature of housing as a commodity, the lack of an integrated system includes comprehensive information of property, the lack of awareness of some actors in this field about comprehensive information about property and the lack of clear and comprehensive rules and regulations for the trading and pricing, several problems arise for the people involved in this field. In this research implementation of a crowd-sourced Web-based real estate support system is desired. Creating a Spatial Data Infrastructure (SDI) in this system for collecting, updating and integrating all official data about property is also desired in this study. In this system a Web2.0 broker and technologies such as Web services and service composition has been used. This work aims to provide comprehensive and diverse information about property from different sources. For this purpose five-level real estate support system architecture is used. PostgreSql DBMS is used to implement the desired system. Geoserver software is also used as map server and reference implementation of OGC (Open Geospatial Consortium) standards. And Apache server is used to run web pages and user interfaces. Integration introduced methods and technologies provide a proper environment for various users to use the system and share their information. This goal is only achieved by cooperation between all involved organizations in real estate with implementation their required infrastructures in interoperability Web services format.

Runtime Detection of C-Style Errors in UPC Code

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pirkelbauer, P; Liao, C; Panas, T

2011-09-29

Unified Parallel C (UPC) extends the C programming language (ISO C 99) with explicit parallel programming support for the partitioned global address space (PGAS), which provides a global memory space with localized partitions to each thread. Like its ancestor C, UPC is a low-level language that emphasizes code efficiency over safety. The absence of dynamic (and static) safety checks allows programmer oversights and software flaws that can be hard to spot. In this paper, we present an extension of a dynamic analysis tool, ROSE-Code Instrumentation and Runtime Monitor (ROSECIRM), for UPC to help programmers find C-style errors involving the globalmore » address space. Built on top of the ROSE source-to-source compiler infrastructure, the tool instruments source files with code that monitors operations and keeps track of changes to the system state. The resulting code is linked to a runtime monitor that observes the program execution and finds software defects. We describe the extensions to ROSE-CIRM that were necessary to support UPC. We discuss complications that arise from parallel code and our solutions. We test ROSE-CIRM against a runtime error detection test suite, and present performance results obtained from running error-free codes. ROSE-CIRM is released as part of the ROSE compiler under a BSD-style open source license.« less

Cultural and Technological Issues and Solutions for Geodynamics Software Citation

NASA Astrophysics Data System (ADS)

Heien, E. M.; Hwang, L.; Fish, A. E.; Smith, M.; Dumit, J.; Kellogg, L. H.

2014-12-01

Computational software and custom-written codes play a key role in scientific research and teaching, providing tools to perform data analysis and forward modeling through numerical computation. However, development of these codes is often hampered by the fact that there is no well-defined way for the authors to receive credit or professional recognition for their work through the standard methods of scientific publication and subsequent citation of the work. This in turn may discourage researchers from publishing their codes or making them easier for other scientists to use. We investigate the issues involved in citing software in a scientific context, and introduce features that should be components of a citation infrastructure, particularly oriented towards the codes and scientific culture in the area of geodynamics research. The codes used in geodynamics are primarily specialized numerical modeling codes for continuum mechanics problems; they may be developed by individual researchers, teams of researchers, geophysicists in collaboration with computational scientists and applied mathematicians, or by coordinated community efforts such as the Computational Infrastructure for Geodynamics. Some but not all geodynamics codes are open-source. These characteristics are common to many areas of geophysical software development and use. We provide background on the problem of software citation and discuss some of the barriers preventing adoption of such citations, including social/cultural barriers, insufficient technological support infrastructure, and an overall lack of agreement about what a software citation should consist of. We suggest solutions in an initial effort to create a system to support citation of software and promotion of scientific software development.

Compilation of geospatial data for the mineral industries and related infrastructure of Latin America and the Caribbean

USGS Publications Warehouse

Baker, Michael S.; Buteyn, Spencer D.; Freeman, Philip A.; Trippi, Michael H.; Trimmer III, Loyd M.

2017-07-31

This report describes the U.S. Geological Survey’s (USGS) ongoing commitment to its mission of understanding the nature and distribution of global mineral commodity supply chains by updating and publishing the georeferenced locations of mineral commodity production and processing facilities, mineral exploration and development sites, and mineral commodity exporting ports in Latin America and the Caribbean. The report includes an overview of data sources and an explanation of the geospatial PDF map format.The geodatabase and geospatial data layers described in this report create a new geographic information product in the form of a geospatial portable document format (PDF) map. The geodatabase contains additional data layers from USGS, foreign governmental, and open-source sources as follows: (1) coal occurrence areas, (2) electric power generating facilities, (3) electric power transmission lines, (4) hydrocarbon resource cumulative production data, (5) liquefied natural gas terminals, (6) oil and gas concession leasing areas, (7) oil and gas field center points, (8) oil and gas pipelines, (9) USGS petroleum provinces, (10) railroads, (11) recoverable proven plus probable hydrocarbon resources, (12) major cities, (13) major rivers, and (14) undiscovered porphyry copper tracts.

Building a multidisciplinary e-infrastructure for the NextData Community

NASA Astrophysics Data System (ADS)

Nativi, Stefano; Rorro, Marco; Mazzetti, Paolo; Fiameni, Giuseppe; Papeschi, Fabrizio; Carpenè, Michele

2014-05-01

In 2012, Italy decided to launch a national initiative called NextData (http://www.nextdataproject.it/): a national system for the retrieval, storage, access and diffusion of environmental and climate data from mountain and marine areas. NextData is funded by the Research and University Ministry, as a "Project of Interest". In 2013, NextData funded a "special project", the NextData System of Systems Infrastructure project (ND-SoS-Ina). The main objective is to design, build and operate in production the NextData multidisciplinary and multi-organizational e-infrastructure for the publication and sharing of its resources (e.g. data, services, vocabularies, models). SoS-Ina realizes the NextData general portal implementing the interoperability among the data archives carried out by NextData. The Florentine Division of the Institute of Atmospheric Pollution Research of CNR (CNR-IIA) and CINECA run the project. SoS-Ina (http://essi-lab.eu/nextdata/sosina/) decided to adopt a "System of Systems" (SoS) approach based on a brokering architecture. This has been pursued by applying the brokering technology first developed by the EC-FP7 EuroGEOSS project (http://www.eurogeoss.eu/broker/Pages/AbouttheEuroGEOSSBroker.aspx) and more recently consolidated by the international programme GEOSS (Global Earth Observation System of Systems) of GEO (Group oh Earth Observation) -see http://www.earthobservations.org/documents/geo_ix/20111122_geoss_implementation_highlights.pdf. The NextData general Portal architecture definition will proceed accordingly with the requirements elicited by user communities. The portal will rely on services and interfaces being offered by the brokering middleware and will be based on Liferay (http://www.liferay.com/). Liferay is free and open source, it provides many built-in applications for social collaboration, content and document management. Liferay is also configurable for high availability. The project considers three distinct phases and related milestones: (a) the first prototype of the NextData SoS infrastructure, implementing the core functionalities; (b) the consolidated version of the NextData SoS infrastructure, implementing advanced functionalities; (c) the final and operative NextData SoS infrastructure for data and information sharing and publication. An important outcome of the project will be the performances and scalability advancement of the current brokering and portal technologies, exploiting resources and middleware services provided by CINECA.

Normalization and standardization of electronic health records for high-throughput phenotyping: the SHARPn consortium

PubMed Central

Pathak, Jyotishman; Bailey, Kent R; Beebe, Calvin E; Bethard, Steven; Carrell, David S; Chen, Pei J; Dligach, Dmitriy; Endle, Cory M; Hart, Lacey A; Haug, Peter J; Huff, Stanley M; Kaggal, Vinod C; Li, Dingcheng; Liu, Hongfang; Marchant, Kyle; Masanz, James; Miller, Timothy; Oniki, Thomas A; Palmer, Martha; Peterson, Kevin J; Rea, Susan; Savova, Guergana K; Stancl, Craig R; Sohn, Sunghwan; Solbrig, Harold R; Suesse, Dale B; Tao, Cui; Taylor, David P; Westberg, Les; Wu, Stephen; Zhuo, Ning; Chute, Christopher G

2013-01-01

Research objective To develop scalable informatics infrastructure for normalization of both structured and unstructured electronic health record (EHR) data into a unified, concept-based model for high-throughput phenotype extraction. Materials and methods Software tools and applications were developed to extract information from EHRs. Representative and convenience samples of both structured and unstructured data from two EHR systems—Mayo Clinic and Intermountain Healthcare—were used for development and validation. Extracted information was standardized and normalized to meaningful use (MU) conformant terminology and value set standards using Clinical Element Models (CEMs). These resources were used to demonstrate semi-automatic execution of MU clinical-quality measures modeled using the Quality Data Model (QDM) and an open-source rules engine. Results Using CEMs and open-source natural language processing and terminology services engines—namely, Apache clinical Text Analysis and Knowledge Extraction System (cTAKES) and Common Terminology Services (CTS2)—we developed a data-normalization platform that ensures data security, end-to-end connectivity, and reliable data flow within and across institutions. We demonstrated the applicability of this platform by executing a QDM-based MU quality measure that determines the percentage of patients between 18 and 75 years with diabetes whose most recent low-density lipoprotein cholesterol test result during the measurement year was <100 mg/dL on a randomly selected cohort of 273 Mayo Clinic patients. The platform identified 21 and 18 patients for the denominator and numerator of the quality measure, respectively. Validation results indicate that all identified patients meet the QDM-based criteria. Conclusions End-to-end automated systems for extracting clinical information from diverse EHR systems require extensive use of standardized vocabularies and terminologies, as well as robust information models for storing, discovering, and processing that information. This study demonstrates the application of modular and open-source resources for enabling secondary use of EHR data through normalization into standards-based, comparable, and consistent format for high-throughput phenotyping to identify patient cohorts. PMID:24190931

A Development of Lightweight Grid Interface

NASA Astrophysics Data System (ADS)

Iwai, G.; Kawai, Y.; Sasaki, T.; Watase, Y.

2011-12-01

In order to help a rapid development of Grid/Cloud aware applications, we have developed API to abstract the distributed computing infrastructures based on SAGA (A Simple API for Grid Applications). SAGA, which is standardized in the OGF (Open Grid Forum), defines API specifications to access distributed computing infrastructures, such as Grid, Cloud and local computing resources. The Universal Grid API (UGAPI), which is a set of command line interfaces (CLI) and APIs, aims to offer simpler API to combine several SAGA interfaces with richer functionalities. These CLIs of the UGAPI offer typical functionalities required by end users for job management and file access to the different distributed computing infrastructures as well as local computing resources. We have also built a web interface for the particle therapy simulation and demonstrated the large scale calculation using the different infrastructures at the same time. In this paper, we would like to present how the web interface based on UGAPI and SAGA achieve more efficient utilization of computing resources over the different infrastructures with technical details and practical experiences.

An analysis of water data systems to inform the Open Water Data Initiative

USGS Publications Warehouse

Blodgett, David L.; Read, Emily K.; Lucido, Jessica M.; Slawecki, Tad; Young, Dwane

2016-01-01

Improving access to data and fostering open exchange of water information is foundational to solving water resources issues. In this vein, the Department of the Interior's Assistant Secretary for Water and Science put forward the charge to undertake an Open Water Data Initiative (OWDI) that would prioritize and accelerate work toward better water data infrastructure. The goal of the OWDI is to build out the Open Water Web (OWW). We therefore considered the OWW in terms of four conceptual functions: water data cataloging, water data as a service, enriching water data, and community for water data. To describe the current state of the OWW and identify areas needing improvement, we conducted an analysis of existing systems using a standard model for describing distributed systems and their business requirements. Our analysis considered three OWDI-focused use cases—flooding, drought, and contaminant transport—and then examined the landscape of other existing applications that support the Open Water Web. The analysis, which includes a discussion of observed successful practices of cataloging, serving, enriching, and building community around water resources data, demonstrates that we have made significant progress toward the needed infrastructure, although challenges remain. The further development of the OWW can be greatly informed by the interpretation and findings of our analysis.

Development of an expert analysis tool based on an interactive subsidence hazard map for urban land use in the city of Celaya, Mexico

NASA Astrophysics Data System (ADS)

Alloy, A.; Gonzalez Dominguez, F.; Nila Fonseca, A. L.; Ruangsirikulchai, A.; Gentle, J. N., Jr.; Cabral, E.; Pierce, S. A.

2016-12-01

Land Subsidence as a result of groundwater extraction in central Mexico's larger urban centers initiated in the 80's as a result of population and economic growth. The city of Celaya has undergone subsidence for a few decades and a consequence is the development of an active normal fault system that affects its urban infrastructure and residential areas. To facilitate its analysis and a land use decision-making process we created an online interactive map enabling users to easily obtain information associated with land subsidence. Geological and socioeconomic data of the city was collected, including fault location, population data, and other important infrastructure and structural data has been obtained from fieldwork as part of a study abroad interchange undergraduate course. The subsidence and associated faulting hazard map was created using an InSAR derived subsidence velocity map and population data from INEGI to identify hazard zones using a subsidence gradient spatial analysis approach based on a subsidence gradient and population risk matrix. This interactive map provides a simple perspective of different vulnerable urban elements. As an accessible visualization tool, it will enhance communication between scientific and socio-economic disciplines. Our project also lays the groundwork for a future expert analysis system with an open source and easily accessible Python coded, SQLite database driven website which archives fault and subsidence data along with visual damage documentation to civil structures. This database takes field notes and provides an entry form for uniform datasets, which are used to generate a JSON. Such a database is useful because it allows geoscientists to have a centralized repository and access to their observations over time. Because of the widespread presence of the subsidence phenomena throughout cities in central Mexico, the spatial analysis has been automated using the open source software R. Raster, rgeos, shapefiles, and rgdal libraries have been used to develop the script which permits to obtain the raster maps of horizontal gradient and population density. An advantage is that this analysis can be automated for periodic updates or repurposed for similar analysis in other cities, providing an easily accessible tool for land subsidence hazard assessments.

Summary report on transportation of nuclear fuel materials in Japan : transportation infrastructure, threats identified in open literature, and physical protection regulations.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cochran, John Russell; Ouchi, Yuichiro; Furaus, James Phillip

2008-03-01

This report summarizes the results of three detailed studies of the physical protection systems for the protection of nuclear materials transport in Japan, with an emphasis on the transportation of mixed oxide fuel materials1. The Japanese infrastructure for transporting nuclear fuel materials is addressed in the first section. The second section of this report presents a summary of baseline data from the open literature on the threats of sabotage and theft during the transport of nuclear fuel materials in Japan. The third section summarizes a review of current International Atomic Energy Agency, Japanese and United States guidelines and regulations concerningmore » the physical protection for the transportation of nuclear fuel materials.« less

Framework for Real-Time All-Hazards Global Situational Awareness

DOE Office of Scientific and Technical Information (OSTI.GOV)

Omitaomu, Olufemi A; Fernandez, Steven J; Bhaduri, Budhendra L

Information systems play a pivotal role in emergency response by making consequence analysis models based on up-to-date data available to decision makers. While consequence analysis models have been used for years on local scales, their application on national and global scales has been constrained by lack of non-proprietary data. This chapter describes how this has changed using a framework for real-time all-hazards situational awareness called the Energy Awareness and Resiliency Standardized Services (EARSS) as an example. EARSS is a system of systems developed to collect non-proprietary data from diverse open content sources to develop a geodatabase of critical infrastructures allmore » over the world. The EARSS system shows that it is feasible to provide global disaster alerts by producing valuable information such as texting messages about detected hazards, emailing reports about affected areas, estimating an expected number of impacted people and their demographic characteristics, identifying critical infrastructures that may be affected, and analyzing potential downstream effects. This information is provided in real-time to federal agencies and subscribers all over the world for decision making in humanitarian assistance and emergency response. The system also uses live streams of power outages, weather, and satellite surveillance data as events unfold. This, in turn, is combined with other public domain or open content information, such as media reports and postings on social networking websites, for complete coverage of the situation as events unfold. Working with up-to-date information from the EARSS system, emergency responders on the ground could pre-position their staff and resources, such as emergency generators and ice, where they are most needed.« less

GISpark: A Geospatial Distributed Computing Platform for Spatiotemporal Big Data

NASA Astrophysics Data System (ADS)

Wang, S.; Zhong, E.; Wang, E.; Zhong, Y.; Cai, W.; Li, S.; Gao, S.

2016-12-01

Geospatial data are growing exponentially because of the proliferation of cost effective and ubiquitous positioning technologies such as global remote-sensing satellites and location-based devices. Analyzing large amounts of geospatial data can provide great value for both industrial and scientific applications. Data- and compute- intensive characteristics inherent in geospatial big data increasingly pose great challenges to technologies of data storing, computing and analyzing. Such challenges require a scalable and efficient architecture that can store, query, analyze, and visualize large-scale spatiotemporal data. Therefore, we developed GISpark - a geospatial distributed computing platform for processing large-scale vector, raster and stream data. GISpark is constructed based on the latest virtualized computing infrastructures and distributed computing architecture. OpenStack and Docker are used to build multi-user hosting cloud computing infrastructure for GISpark. The virtual storage systems such as HDFS, Ceph, MongoDB are combined and adopted for spatiotemporal data storage management. Spark-based algorithm framework is developed for efficient parallel computing. Within this framework, SuperMap GIScript and various open-source GIS libraries can be integrated into GISpark. GISpark can also integrated with scientific computing environment (e.g., Anaconda), interactive computing web applications (e.g., Jupyter notebook), and machine learning tools (e.g., TensorFlow/Orange). The associated geospatial facilities of GISpark in conjunction with the scientific computing environment, exploratory spatial data analysis tools, temporal data management and analysis systems make up a powerful geospatial computing tool. GISpark not only provides spatiotemporal big data processing capacity in the geospatial field, but also provides spatiotemporal computational model and advanced geospatial visualization tools that deals with other domains related with spatial property. We tested the performance of the platform based on taxi trajectory analysis. Results suggested that GISpark achieves excellent run time performance in spatiotemporal big data applications.

Escript: Open Source Environment For Solving Large-Scale Geophysical Joint Inversion Problems in Python

NASA Astrophysics Data System (ADS)

Gross, Lutz; Altinay, Cihan; Fenwick, Joel; Smith, Troy

2014-05-01

The program package escript has been designed for solving mathematical modeling problems using python, see Gross et al. (2013). Its development and maintenance has been funded by the Australian Commonwealth to provide open source software infrastructure for the Australian Earth Science community (recent funding by the Australian Geophysical Observing System EIF (AGOS) and the AuScope Collaborative Research Infrastructure Scheme (CRIS)). The key concepts of escript are based on the terminology of spatial functions and partial differential equations (PDEs) - an approach providing abstraction from the underlying spatial discretization method (i.e. the finite element method (FEM)). This feature presents a programming environment to the user which is easy to use even for complex models. Due to the fact that implementations are independent from data structures simulations are easily portable across desktop computers and scalable compute clusters without modifications to the program code. escript has been successfully applied in a variety of applications including modeling mantel convection, melting processes, volcanic flow, earthquakes, faulting, multi-phase flow, block caving and mineralization (see Poulet et al. 2013). The recent escript release (see Gross et al. (2013)) provides an open framework for solving joint inversion problems for geophysical data sets (potential field, seismic and electro-magnetic). The strategy bases on the idea to formulate the inversion problem as an optimization problem with PDE constraints where the cost function is defined by the data defect and the regularization term for the rock properties, see Gross & Kemp (2013). This approach of first-optimize-then-discretize avoids the assemblage of the - in general- dense sensitivity matrix as used in conventional approaches where discrete programming techniques are applied to the discretized problem (first-discretize-then-optimize). In this paper we will discuss the mathematical framework for inversion and appropriate solution schemes in escript. We will also give a brief introduction into escript's open framework for defining and solving geophysical inversion problems. Finally we will show some benchmark results to demonstrate the computational scalability of the inversion method across a large number of cores and compute nodes in a parallel computing environment. References: - L. Gross et al. (2013): Escript Solving Partial Differential Equations in Python Version 3.4, The University of Queensland, https://launchpad.net/escript-finley - L. Gross and C. Kemp (2013) Large Scale Joint Inversion of Geophysical Data using the Finite Element Method in escript. ASEG Extended Abstracts 2013, http://dx.doi.org/10.1071/ASEG2013ab306 - T. Poulet, L. Gross, D. Georgiev, J. Cleverley (2012): escript-RT: Reactive transport simulation in Python using escript, Computers & Geosciences, Volume 45, 168-176. http://dx.doi.org/10.1016/j.cageo.2011.11.005.

Network Interdependency Modeling for Risk Assessment on Built Infrastructure Systems

DTIC Science & Technology

2013-10-01

does begin to address infrastructure decay as a source of risk comes from the Department of Homeland Security (DHS). In 2009, the DHS Science and...network of connected edges and nodes. The National Research Council (2005) reported that the study of networks as a science and applications of...principles from this science are still in its early stages. As modern infrastructures have become more interlinked, knowledge of an infrastructure’s network

A Smart City Lighting Case Study on an OpenStack-Powered Infrastructure.

PubMed

Merlino, Giovanni; Bruneo, Dario; Distefano, Salvatore; Longo, Francesco; Puliafito, Antonio; Al-Anbuky, Adnan

2015-07-06

The adoption of embedded systems, mobile devices and other smart devices keeps rising globally, and the scope of their involvement broadens, for instance, in smart city-like scenarios. In light of this, a pressing need emerges to tame such complexity and reuse as much tooling as possible without resorting to vertical ad hoc solutions, while at the same time taking into account valid options with regard to infrastructure management and other more advanced functionalities. Existing solutions mainly focus on core mechanisms and do not allow one to scale by leveraging infrastructure or adapt to a variety of scenarios, especially if actuators are involved in the loop. A new, more flexible, cloud-based approach, able to provide device-focused workflows, is required. In this sense, a widely-used and competitive framework for infrastructure as a service, such as OpenStack, with its breadth in terms of feature coverage and expanded scope, looks to fit the bill, replacing current application-specific approaches with an innovative application-agnostic one. This work thus describes the rationale, efforts and results so far achieved for an integration of IoT paradigms and resource ecosystems with such a kind of cloud-oriented device-centric environment, by focusing on a smart city scenario, namely a park smart lighting example, and featuring data collection, data visualization, event detection and coordinated reaction, as example use cases of such integration.

Integrating multiple scientific computing needs via a Private Cloud infrastructure

NASA Astrophysics Data System (ADS)

Bagnasco, S.; Berzano, D.; Brunetti, R.; Lusso, S.; Vallero, S.

2014-06-01

In a typical scientific computing centre, diverse applications coexist and share a single physical infrastructure. An underlying Private Cloud facility eases the management and maintenance of heterogeneous use cases such as multipurpose or application-specific batch farms, Grid sites catering to different communities, parallel interactive data analysis facilities and others. It allows to dynamically and efficiently allocate resources to any application and to tailor the virtual machines according to the applications' requirements. Furthermore, the maintenance of large deployments of complex and rapidly evolving middleware and application software is eased by the use of virtual images and contextualization techniques; for example, rolling updates can be performed easily and minimizing the downtime. In this contribution we describe the Private Cloud infrastructure at the INFN-Torino Computer Centre, that hosts a full-fledged WLCG Tier-2 site and a dynamically expandable PROOF-based Interactive Analysis Facility for the ALICE experiment at the CERN LHC and several smaller scientific computing applications. The Private Cloud building blocks include the OpenNebula software stack, the GlusterFS filesystem (used in two different configurations for worker- and service-class hypervisors) and the OpenWRT Linux distribution (used for network virtualization). A future integration into a federated higher-level infrastructure is made possible by exposing commonly used APIs like EC2 and by using mainstream contextualization tools like CloudInit.

A Smart City Lighting Case Study on an OpenStack-Powered Infrastructure

PubMed Central

Merlino, Giovanni; Bruneo, Dario; Distefano, Salvatore; Longo, Francesco; Puliafito, Antonio; Al-Anbuky, Adnan

2015-01-01

The adoption of embedded systems, mobile devices and other smart devices keeps rising globally, and the scope of their involvement broadens, for instance, in smart city-like scenarios. In light of this, a pressing need emerges to tame such complexity and reuse as much tooling as possible without resorting to vertical ad hoc solutions, while at the same time taking into account valid options with regard to infrastructure management and other more advanced functionalities. Existing solutions mainly focus on core mechanisms and do not allow one to scale by leveraging infrastructure or adapt to a variety of scenarios, especially if actuators are involved in the loop. A new, more flexible, cloud-based approach, able to provide device-focused workflows, is required. In this sense, a widely-used and competitive framework for infrastructure as a service, such as OpenStack, with its breadth in terms of feature coverage and expanded scope, looks to fit the bill, replacing current application-specific approaches with an innovative application-agnostic one. This work thus describes the rationale, efforts and results so far achieved for an integration of IoT paradigms and resource ecosystems with such a kind of cloud-oriented device-centric environment, by focusing on a smart city scenario, namely a park smart lighting example, and featuring data collection, data visualization, event detection and coordinated reaction, as example use cases of such integration. PMID:26153775

Mobilising Open Access to Research Data: Recommendations from the RECODE project

NASA Astrophysics Data System (ADS)

Finn, Rachel; Sveinsdottir, Thordis

2015-04-01

This paper will introduce the findings and policy recommendations from the FP7 project RECODE (Policy RECommendations for Open Access to Research Data in Europe) which aims to leverage existing networks, communities and projects to address challenges within the open access and data dissemination and preservation sector. We will introduce the key recommendations, which provide solutions relevant to opening access to PSI. The project is built on case study research of five scientific disciplines with the aim of recognizing and working with disciplinary fragmentation associated with open access to research data. The RECODE findings revealed that the mobilisation of open access to research data requires a partnership approach for developing a coherent and flexible ecosystem that is easy and transparent to embed in research practice and process. As such, the development of open access to research data needs to be: • Informed by research practices and processes in different fields • Supported by an integrated institutional and technological data infrastructure and guided by ethical and regulatory frameworks • Underpinned by infrastructure and guiding frameworks that allow for differences in disciplinary research and data management practices • Characterised by a partnership approach involving the key stakeholders, researchers, and institutions The proposed presentation will examine each of these aspects in detail and use information and good practices from the RECODE project to consider how stakeholders within the PSI movement might action each of these points. It will also highlight areas where RECODE findings and good practice recommendations have clear relevance for the PSI sector.

78 FR 20934 - National Infrastructure Advisory Council; Notice of Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-08

.... Both mandate comprehensive consultation with stakeholders in very short time lines for implementation... Members III. Opening Remarks and Introductions IV. NIAC Presentation on Regional Resilience Working Group...

Analyzing existing conventional soil information sources to be incorporated in thematic Spatial Data Infrastructures

NASA Astrophysics Data System (ADS)

Pascual-Aguilar, J. A.; Rubio, J. L.; Domínguez, J.; Andreu, V.

2012-04-01

New information technologies give the possibility of widespread dissemination of spatial information to different geographical scales from continental to local by means of Spatial Data Infrastructures. Also administrative awareness on the need for open access information services has allowed the citizens access to this spatial information through development of legal documents, such as the INSPIRE Directive of the European Union, adapted by national laws as in the case of Spain. The translation of the general criteria of generic Spatial Data Infrastructures (SDI) to thematic ones is a crucial point for the progress of these instruments as large tool for the dissemination of information. In such case, it must be added to the intrinsic criteria of digital information, such as the harmonization information and the disclosure of metadata, the own environmental information characteristics and the techniques employed in obtaining it. In the case of inventories and mapping of soils, existing information obtained by traditional means, prior to the digital technologies, is considered to be a source of valid information, as well as unique, for the development of thematic SDI. In this work, an evaluation of existing and accessible information that constitutes the basis for building a thematic SDI of soils in Spain is undertaken. This information framework has common features to other European Union states. From a set of more than 1,500 publications corresponding to the national territory of Spain, the study was carried out in those documents (94) found for five autonomous regions of northern Iberian Peninsula (Asturias, Cantabria, Basque Country, Navarra and La Rioja). The analysis was performed taking into account the criteria of soil mapping and inventories. The results obtained show a wide variation in almost all the criteria: geographic representation (projections, scales) and geo-referencing the location of the profiles, map location of profiles integrated with edaphic units, description and taxonomic classification systems of soils (FAO, Soil taxonomy, etc.), amount and type of soil analysis parameters and dates of the inventories. In conclusion, the construction of thematic SDI on soil should take into account, prior to the integration of all maps and inventories, a series of processes of harmonization that allows spatial continuity between existing information and also temporal identification of the inventories and maps. This should require the development of at least two types of integration tools: (1) enabling spatial continuity without contradictions between maps made at different times and with different criteria and (2) the development of information systems data (metadata) to highlight the characteristics of information and connection possibilities with other sources that comprise the Spatial Data Infrastructure. Acknowledgements This research has financed by the European Union within the framework of the GS Soil project (eContentplus Programme ECP-2008-GEO-318004).

Shackleton Energy enabling Space Resources Exploitation on the Moon within a Decade

NASA Astrophysics Data System (ADS)

Keravala, J.; Stone, B.; Tietz, D.; Frischauf, N.

2013-09-01

Access to in-space natural resources is a key requirement for increasing exploration and expansion of humanity off Earth. In particular, making use of the Moon's resources in the form of lunar polar ice to fuel propellant depots at key locations in near Earth space enables dramatic reductions in the cost of access and operations in space, while simultaneously leveraging reusable in-space transporters essential to opening the newspace highway system. Success of this private venture will provide for a sustained balance of our terrestrial economy and the growth of our civilisation. Establishing the cis-Lunar highway required to access lunar sourced water from the cold traps of the polar craters provides the backbone infrastructure for an exponential growth of a space-based economy. With that core infrastructure in place, space-based solar power generation systems, debris mitigation capabilities and planetary protection systems plus scientific and exploratory missions, among others, can become commercial realities in our lifetime. Shackleton Energy was founded from the space, mining, energy and exploration sectors to meet this challenge as a fully private venture. Following successful robotic precursor missions, our industrial astronauts combined with a robotic mining capability will make first landings at the South Pole of the Moon and begin deliveries of propellant to our depots in within a decade. Customers, partners, technologies and most importantly, the investor classes aligned with the risk profiles involved, have been identified and all the components for a viable business are available. Infrastructure investment in space programs has traditionally been the province of governments, but sustainable expansion requires commercial leadership and this is now the responsibility of a dynamic new industry. The technologies and know-how are ready to be applied. Launch services to LEO are available and the industrial capability exists in the aerospace, mining and energy sectors to enable Shackleton Energy to build an in-orbit and Lunar infrastructure on a fully commercial basis.

[caCORE: core architecture of bioinformation on cancer research in America].

PubMed

Gao, Qin; Zhang, Yan-lei; Xie, Zhi-yun; Zhang, Qi-peng; Hu, Zhang-zhi

2006-04-18

A critical factor in the advancement of biomedical research is the ease with which data can be integrated, redistributed and analyzed both within and across domains. This paper summarizes the Biomedical Information Core Infrastructure built by National Cancer Institute Center for Bioinformatics in America (NCICB). The main product from the Core Infrastructure is caCORE--cancer Common Ontologic Reference Environment, which is the infrastructure backbone supporting data management and application development at NCICB. The paper explains the structure and function of caCORE: (1) Enterprise Vocabulary Services (EVS). They provide controlled vocabulary, dictionary and thesaurus services, and EVS produces the NCI Thesaurus and the NCI Metathesaurus; (2) The Cancer Data Standards Repository (caDSR). It provides a metadata registry for common data elements. (3) Cancer Bioinformatics Infrastructure Objects (caBIO). They provide Java, Simple Object Access Protocol and HTTP-XML application programming interfaces. The vision for caCORE is to provide a common data management framework that will support the consistency, clarity, and comparability of biomedical research data and information. In addition to providing facilities for data management and redistribution, caCORE helps solve problems of data integration. All NCICB-developed caCORE components are distributed under open-source licenses that support unrestricted usage by both non-profit and commercial entities, and caCORE has laid the foundation for a number of scientific and clinical applications. Based on it, the paper expounds caCORE-base applications simply in several NCI projects, of which one is CMAP (Cancer Molecular Analysis Project), and the other is caBIG (Cancer Biomedical Informatics Grid). In the end, the paper also gives good prospects of caCORE, and while caCORE was born out of the needs of the cancer research community, it is intended to serve as a general resource. Cancer research has historically contributed to many areas beyond tumor biology. At the same time, the paper makes some suggestions about the study at the present time on biomedical informatics in China.

Building climate adaptation capabilities through technology and community

NASA Astrophysics Data System (ADS)

Murray, D.; McWhirter, J.; Intsiful, J. D.; Cozzini, S.

2011-12-01

To effectively plan for adaptation to changes in climate, decision makers require infrastructure and tools that will provide them with timely access to current and future climate information. For example, climate scientists and operational forecasters need to access global and regional model projections and current climate information that they can use to prepare monitoring products and reports and then publish these for the decision makers. Through the UNDP African Adaption Programme, an infrastructure is being built across Africa that will provide multi-tiered access to such information. Web accessible servers running RAMADDA, an open source content management system for geoscience information, will provide access to the information at many levels: from the raw and processed climate model output to real-time climate conditions and predictions to documents and presentation for government officials. Output from regional climate models (e.g. RegCM4) and downscaled global climate models will be accessible through RAMADDA. The Integrated Data Viewer (IDV) is being used by scientists to create visualizations that assist the understanding of climate processes and projections, using the data on these as well as external servers. Since RAMADDA is more than a data server, it is also being used as a publishing platform for the generated material that will be available and searchable by the decision makers. Users can wade through the enormous volumes of information and extract subsets for their region or project of interest. Participants from 20 countries attended workshops at ICTP during 2011. They received training on setting up and installing the servers and necessary software and are now working on deploying the systems in their respective countries. This is the first time an integrated and comprehensive approach to climate change adaptation has been widely applied in Africa. It is expected that this infrastructure will enhance North-South collaboration and improve the delivery of technical support and services. This improved infrastructure will enhance the capacity of countries to provide a wide range of robust products and services in a timely manner.

Swiss Experiment: Design, implemention and use of a cross-disciplinary infrastructure for data intensive science

NASA Astrophysics Data System (ADS)

Dawes, N.; Salehi, A.; Clifton, A.; Bavay, M.; Aberer, K.; Parlange, M. B.; Lehning, M.

2010-12-01

It has long been known that environmental processes are cross-disciplinary, but data has continued to be acquired and held for a single purpose. Swiss Experiment is a rapidly evolving cross-disciplinary, distributed sensor data infrastructure, where tools for the environmental science community stem directly from computer science research. The platform uses the bleeding edge of computer science to acquire, store and distribute data and metadata from all environmental science disciplines at a variety of temporal and spatial resolutions. SwissEx is simultaneously developing new technologies to allow low cost, high spatial and temporal resolution measurements such that small areas can be intensely monitored. This data is then combined with existing widespread, low density measurements in the cross-disciplinary platform to provide well documented datasets, which are of use to multiple research disciplines. We present a flexible, generic infrastructure at an advanced stage of development. The infrastructure makes the most of Web 2.0 technologies for a collaborative working environment and as a user interface for a metadata database. This environment is already closely integrated with GSN, an open-source database middleware developed under Swiss Experiment for acquisition and storage of generic time-series data (2D and 3D). GSN can be queried directly by common data processing packages and makes data available in real-time to models and 3rd party software interfaces via its web service interface. It also provides real-time push or pull data exchange between instances, a user management system which leaves data owners in charge of their data, advanced real-time processing and much more. The SwissEx interface is increasingly gaining users and supporting environmental science in Switzerland. It is also an integral part of environmental education projects ClimAtscope and O3E, where the technologies can provide rapid feedback of results for children of all ages and where the data from their own stations can be compared to national data networks.

Combating AIDS in South Africa and Mozambique: The Role of Open, Distance, and Flexible Learning

ERIC Educational Resources Information Center

Pridmore, Pat; Yates, Chris

2005-01-01

This article examines the potential for open, distance, and flexible learning (ODFL) to mitigate the impact of HIV and AIDS on young people. Based on experience from a field study in Mozambique and South Africa, the authors show how ODFL can support and extend the work of existing infrastructures supporting vulnerable youth. As neighboring…

The Place of Multiple Intelligence in Achieving the Objectives and Goals of Open and Distance Learning Institutions: A Critical Analysis

ERIC Educational Resources Information Center

Ojo, Olugbenga David; Olakulehin, Felix Kayode

2006-01-01

This paper examined the nature of open and distance learning institutions as organizations where synergy of efforts of all personnel is required in order to achieve the aims and objectives of the institution. It explored the huge infrastructural and personnel requirements of distance learning institutions, especially at inception, and the…

MaTrace: tracing the fate of materials over time and across products in open-loop recycling.

PubMed

Nakamura, Shinichiro; Kondo, Yasushi; Kagawa, Shigemi; Matsubae, Kazuyo; Nakajima, Kenichi; Nagasaka, Tetsuya

2014-07-01

Even for metals, open-loop recycling is more common than closed-loop recycling due, among other factors, to the degradation of quality in the end-of-life (EoL) phase. Open-loop recycling is subject to loss of functionality of original materials, dissipation in forms that are difficult to recover, and recovered metals might need dilution with primary metals to meet quality requirements. Sustainable management of metal resources calls for the minimization of these losses. Imperative to this is quantitative tracking of the fate of materials across different stages, products, and losses. A new input-output analysis (IO) based model of dynamic material flow analysis (MFA) is presented that can trace the fate of materials over time and across products in open-loop recycling taking explicit consideration of losses and the quality of scrap into account. Application to car steel recovered from EoL vehicles (ELV) showed that after 50 years around 80% of the steel is used in products, mostly buildings and civil engineering (infrastructure), with the rest mostly resided in unrecovered obsolete infrastructure and refinery losses. Sensitivity analysis was conducted to evaluate the effects of changes in product lifespan, and the quality of scrap.

Municipal solid waste management in Rasht City, Iran.

PubMed

Alavi Moghadam, M R; Mokhtarani, N; Mokhtarani, B

2009-01-01

Pollution and health risks generated by improper solid waste management are important issues concerning environmental management in developing countries. In most cities, the use of open dumps is common for the disposal of wastes, resulting in soil and water resource contamination by leachate in addition to odors and fires. Solid waste management infrastructure and services in developing countries are far from achieving basic standards in terms of hygiene and efficient collection and disposal. This paper presents an overview of current municipal solid waste management in Rasht city, Gilan Province, Iran, and provides recommendations for system improvement. The collected data of different MSW functional elements were based on data from questionnaires, visual observations of the authors, available reports and several interviews and meetings with responsible persons. Due to an increase in population and changes in lifestyle, the quantity and quality of MSW in Rasht city has changed. Lack of resources, infrastructure, suitable planning, leadership, and public awareness are the main challenges of MSW management of Rasht city. However, the present situation of solid waste management in this city, which generates more than 400tons/d, has been improved since the establishment of an organization responsible only for solid waste management. Source separation of wastes and construction of a composting plant are the two main activities of the Rasht Municipality in recent years.

Self-service for software development projects and HPC activities

NASA Astrophysics Data System (ADS)

Husejko, M.; Høimyr, N.; Gonzalez, A.; Koloventzos, G.; Asbury, D.; Trzcinska, A.; Agtzidis, I.; Botrel, G.; Otto, J.

2014-05-01

This contribution describes how CERN has implemented several essential tools for agile software development processes, ranging from version control (Git) to issue tracking (Jira) and documentation (Wikis). Running such services in a large organisation like CERN requires many administrative actions both by users and service providers, such as creating software projects, managing access rights, users and groups, and performing tool-specific customisation. Dealing with these requests manually would be a time-consuming task. Another area of our CERN computing services that has required dedicated manual support has been clusters for specific user communities with special needs. Our aim is to move all our services to a layered approach, with server infrastructure running on the internal cloud computing infrastructure at CERN. This contribution illustrates how we plan to optimise the management of our of services by means of an end-user facing platform acting as a portal into all the related services for software projects, inspired by popular portals for open-source developments such as Sourceforge, GitHub and others. Furthermore, the contribution will discuss recent activities with tests and evaluations of High Performance Computing (HPC) applications on different hardware and software stacks, and plans to offer a dynamically scalable HPC service at CERN, based on affordable hardware.

LifeWatch - a Large-scale eScience Infrastructure to Assist in Understanding and Managing our Planet's Biodiversity

NASA Astrophysics Data System (ADS)

Hernández Ernst, Vera; Poigné, Axel; Los, Walter

2010-05-01

Understanding and managing the complexity of the biodiversity system in relation to global changes concerning land use and climate change with their social and economic implications is crucial to mitigate species loss and biodiversity changes in general. The sustainable development and exploitation of existing biodiversity resources require flexible and powerful infrastructures offering, on the one hand, the access to large-scale databases of observations and measures, to advanced analytical and modelling software, and to high performance computing environments and, on the other hand, the interlinkage of European scientific communities among each others and with national policies. The European Strategy Forum on Research Infrastructures (ESFRI) selected the "LifeWatch e-science and technology infrastructure for biodiversity research" as a promising development to construct facilities to contribute to meet those challenges. LifeWatch collaborates with other selected initiatives (e.g. ICOS, ANAEE, NOHA, and LTER-Europa) to achieve the integration of the infrastructures at landscape and regional scales. This should result in a cooperating cluster of such infrastructures supporting an integrated approach for data capture and transmission, data management and harmonisation. Besides, facilities for exploration, forecasting, and presentation using heterogeneous and distributed data and tools should allow the interdisciplinary scientific research at any spatial and temporal scale. LifeWatch is an example of a new generation of interoperable research infrastructures based on standards and a service-oriented architecture that allow for linkage with external resources and associated infrastructures. External data sources will be established data aggregators as the Global Biodiversity Information Facility (GBIF) for species occurrences and other EU Networks of Excellence like the Long-Term Ecological Research Network (LTER), GMES, and GEOSS for terrestrial monitoring, the MARBEF network for marine data, and the Consortium for European Taxonomic Facilities (CETAF) and its European Distributed Institute for Taxonomy (EDIT) for taxonomic data. But also "smaller" networks and "volunteer scientists" may send data (e.g. GPS supported species observations) to a LifeWatch repository. Autonomous operating wireless environmental sensors and other smart hand-held devices will contribute to increase data capture activities. In this way LifeWatch will directly underpin the development of GEOBON, the biodiversity component if GEOSS, the Global Earth observation System. To overcome all major technical difficulties imposed by the variety of currently and future technologies, protocols, data formats, etc., LifeWatch will define and use common open interfaces. For this purpose, the LifeWatch Reference Model was developed during the preparatory phase specifying the service-oriented architecture underlying the ICT-infrastructure. The Reference Model identifies key requirements and key architectural concepts to support workflows for scientific in-silico experiments, tracking of provenance, and semantic enhancement, besides meeting the functional requirements mentioned before. It provides guidelines for the specification and implementation of services and information models, defining as well a number of generic services and models. Another key issue addressed by the Reference Model is that the cooperation of many developer teams residing in many European countries has to be organized to obtain compatible results in that conformance with the specifications and policies of the Reference Model will be required. The LifeWatch Reference Model is based on the ORCHESTRA Reference Model for geospatial-oriented architectures and services networks that provides a generic framework and has been endorsed as best practice by the Open Geospatial Consortium (OGC). The LifeWatch Infrastructure will allow (interdisciplinary) scientific researchers to collaborate by creating e-Laboratories or by composing e-Services which can be shared and jointly developed. For it a long-term vision for the LifeWatch Biodiversity Workbench Portal has been developed as a one-stop application for the LifeWatch infrastructure based on existing and emerging technologies. There the user can find all available resources such as data, workflows, tools, etc. and access LifeWatch applications that integrate different resource and provides key capabilities like resource discovery and visualisation, creation of workflows, creation and management of provenance, and the support of collaborative activities. While LifeWatch developers will construct components for solving generic LifeWatch tasks, users may add their own facilities to fulfil individual needs. Examples for application of the LifeWatch Reference Model and the LifeWatch Biodiversity Workbench Portal will be given.

Whole earth modeling: developing and disseminating scientific software for computational geophysics.

NASA Astrophysics Data System (ADS)

Kellogg, L. H.

2016-12-01

Historically, a great deal of specialized scientific software for modeling and data analysis has been developed by individual researchers or small groups of scientists working on their own specific research problems. As the magnitude of available data and computer power has increased, so has the complexity of scientific problems addressed by computational methods, creating both a need to sustain existing scientific software, and expand its development to take advantage of new algorithms, new software approaches, and new computational hardware. To that end, communities like the Computational Infrastructure for Geodynamics (CIG) have been established to support the use of best practices in scientific computing for solid earth geophysics research and teaching. Working as a scientific community enables computational geophysicists to take advantage of technological developments, improve the accuracy and performance of software, build on prior software development, and collaborate more readily. The CIG community, and others, have adopted an open-source development model, in which code is developed and disseminated by the community in an open fashion, using version control and software repositories like Git. One emerging issue is how to adequately identify and credit the intellectual contributions involved in creating open source scientific software. The traditional method of disseminating scientific ideas, peer reviewed publication, was not designed for review or crediting scientific software, although emerging publication strategies such software journals are attempting to address the need. We are piloting an integrated approach in which authors are identified and credited as scientific software is developed and run. Successful software citation requires integration with the scholarly publication and indexing mechanisms as well, to assign credit, ensure discoverability, and provide provenance for software.

Sharing Water-related Information to Tackle Changes in the Hydrosphere - for Operational Needs (SWITCH-ON)

NASA Astrophysics Data System (ADS)

Arheimer, Berit

2014-05-01

A recently started EU project (FP7 project No 603587) called SWITCH-ON will establish new infrastructure for water research in Europe. The overall goal of the project is to make use of open data, and add value to society by repurposing and refining data from various sources. SWITCH-ON will establish new forms of water research and facilitate the development of new products and services based on principles of sharing and community building. The basic for this work is a virtual water-science laboratory, which consists of open data, dedicated software tools and a set of protocols, hosted at the "SWITCH-ON water information" portal at http://water-switch-on.eu/. The laboratory will seamlessly integrate the open data with harmonised modelling tools and facilities the performance of virtual experiments of comparative science. Comparative science is a new form of research, which will advance science by contrasting water related processes in different environments and help understand complex processes in a more holistic way than individual studies The SWITCH-ON objectives are to use open data for implementing: 1) an innovative spatial information platform with open data tailored for direct water assessments, 2) an entirely new form of collaborative research for water-related sciences, 3) fourteen new operational products and services dedicated to appointed end-users, 4) new business and knowledge to inform individual and collective decisions in line with the Europe's smart growth and environmental objectives. The SWITCH-ON project will be one trigger in a contemporary global movement to better address environmental and societal challenges through openness and collaboration. The poster will present the project visions and achievements so far, and invite more research groups to use the virtual water-science laboratory.

UNH Data Cooperative: A Cyber Infrastructure for Earth System Studies

NASA Astrophysics Data System (ADS)

Braswell, B. H.; Fekete, B. M.; Prusevich, A.; Gliden, S.; Magill, A.; Vorosmarty, C. J.

2007-12-01

Earth system scientists and managers have a continuously growing demand for a wide array of earth observations derived from various data sources including (a) modern satellite retrievals, (b) "in-situ" records, (c) various simulation outputs, and (d) assimilated data products combining model results with observational records. The sheer quantity of data, and formatting inconsistencies make it difficult for users to take full advantage of this important information resource. Thus the system could benefit from a thorough retooling of our current data processing procedures and infrastructure. Emerging technologies, like OPeNDAP and OGC map services, open standard data formats (NetCDF, HDF) data cataloging systems (NASA-Echo, Global Change Master Directory, etc.) are providing the basis for a new approach in data management and processing, where web- services are increasingly designed to serve computer-to-computer communications without human interactions and complex analysis can be carried out over distributed computer resources interconnected via cyber infrastructure. The UNH Earth System Data Collaborative is designed to utilize the aforementioned emerging web technologies to offer new means of access to earth system data. While the UNH Data Collaborative serves a wide array of data ranging from weather station data (Climate Portal) to ocean buoy records and ship tracks (Portsmouth Harbor Initiative) to land cover characteristics, etc. the underlaying data architecture shares common components for data mining and data dissemination via web-services. Perhaps the most unique element of the UNH Data Cooperative's IT infrastructure is its prototype modeling environment for regional ecosystem surveillance over the Northeast corridor, which allows the integration of complex earth system model components with the Cooperative's data services. While the complexity of the IT infrastructure to perform complex computations is continuously increasing, scientists are often forced to spend considerable amount of time to solve basic data management and preprocessing tasks and deal with low level computational design problems like parallelization of model codes. Our modeling infrastructure is designed to take care the bulk of the common tasks found in complex earth system models like I/O handling, computational domain and time management, parallel execution of the modeling tasks, etc. The modeling infrastructure allows scientists to focus on the numerical implementation of the physical processes on a single computational objects(typically grid cells) while the framework takes care of the preprocessing of input data, establishing of the data exchange between computation objects and the execution of the science code. In our presentation, we will discuss the key concepts of our modeling infrastructure. We will demonstrate integration of our modeling framework with data services offered by the UNH Earth System Data Collaborative via web interfaces. We will layout the road map to turn our prototype modeling environment into a truly community framework for wide range of earth system scientists and environmental managers.

Multi-Level Data-Security and Data-Protection in a Distributed Search Infrastructure for Digital Medical Samples.

PubMed

Witt, Michael; Krefting, Dagmar

2016-01-01

Human sample data is stored in biobanks with software managing digital derived sample data. When these stand-alone components are connected and a search infrastructure is employed users become able to collect required research data from different data sources. Data protection, patient rights, data heterogeneity and access control are major challenges for such an infrastructure. This dissertation will investigate concepts for a multi-level security architecture to comply with these requirements.

NASA Remote Sensing Observations for Water Resource and Infrastructure Management

NASA Astrophysics Data System (ADS)

Granger, S. L.; Armstrong, L.; Farr, T.; Geller, G.; Heath, E.; Hyon, J.; Lavoie, S.; McDonald, K.; Realmuto, V.; Stough, T.; Szana, K.

2008-12-01

Decision support tools employed by water resource and infrastructure managers often utilize data products obtained from local sources or national/regional databases of historic surveys and observations. Incorporation of data from these sources can be laborious and time consuming as new products must be identified, cleaned and archived for each new study site. Adding remote sensing observations to the list of sources holds promise for a timely, consistent, global product to aid decision support at regional and global scales by providing global observations of geophysical parameters including soil moisture, precipitation, atmospheric temperature, derived evapotranspiration, and snow extent needed for hydrologic models and decision support tools. However, issues such as spatial and temporal resolution arise when attempting to integrate remote sensing observations into existing decision support tools. We are working to overcome these and other challenges through partnerships with water resource managers, tool developers and other stakeholders. We are developing a new data processing framework, enabled by a core GIS server, to seamlessly pull together observations from disparate sources for synthesis into information products and visualizations useful to the water resources community. A case study approach is being taken to develop the system by working closely with water infrastructure and resource managers to integrate remote observations into infrastructure, hydrologic and water resource decision tools. We present the results of a case study utilizing observations from the PALS aircraft instrument as a proxy for NASA's upcoming Soil Moisture Active Passive (SMAP) mission and an existing commercial decision support tool.

International Convergence on Geoscience Cyberinfrastructure

NASA Astrophysics Data System (ADS)

Allison, M. L.; Atkinson, R.; Arctur, D. K.; Cox, S.; Jackson, I.; Nativi, S.; Wyborn, L. A.

2012-04-01

There is growing international consensus on addressing the challenges to cyber(e)-infrastructure for the geosciences. These challenges include: Creating common standards and protocols; Engaging the vast number of distributed data resources; Establishing practices for recognition of and respect for intellectual property; Developing simple data and resource discovery and access systems; Building mechanisms to encourage development of web service tools and workflows for data analysis; Brokering the diverse disciplinary service buses; Creating sustainable business models for maintenance and evolution of information resources; Integrating the data management life-cycle into the practice of science. Efforts around the world are converging towards de facto creation of an integrated global digital data network for the geosciences based on common standards and protocols for data discovery and access, and a shared vision of distributed, web-based, open source interoperable data access and integration. Commonalities include use of Open Geospatial Consortium (OGC) and ISO specifications and standardized data interchange mechanisms. For multidisciplinarity, mediation, adaptation, and profiling services have been successfully introduced to leverage the geosciences standards which are commonly used by the different geoscience communities -introducing a brokering approach which extends the basic SOA archetype. Principal challenges are less technical than cultural, social, and organizational. Before we can make data interoperable, we must make people interoperable. These challenges are being met by increased coordination of development activities (technical, organizational, social) among leaders and practitioners in national and international efforts across the geosciences to foster commonalities across disparate networks. In doing so, we will 1) leverage and share resources, and developments, 2) facilitate and enhance emerging technical and structural advances, 3) promote interoperability across scientific domains, 4) support the promulgation and institutionalization of agreed-upon standards, protocols, and practice, and 5) enhance knowledge transfer not only across the community, but into the domain sciences, 6) lower existing entry barriers for users and data producers, 7) build on the existing disciplinary infrastructures leveraging their service buses. . All of these objectives are required for establishing a permanent and sustainable cyber(e)-infrastructure for the geosciences. The rationale for this approach is well articulated in the AuScope mission statement: "Many of these problems can only be solved on a national, if not global scale. No single researcher, research institution, discipline or jurisdiction can provide the solutions. We increasingly need to embrace e-Research techniques and use the internet not only to access nationally distributed datasets, instruments and compute infrastructure, but also to build online, 'virtual' communities of globally dispersed researchers." Multidisciplinary interoperability can be successfully pursued by adopting a "system of systems" or a "Network of Networks" philosophy. This approach aims to: (a) supplement but not supplant systems mandates and governance arrangements; (b) keep the existing capacities as autonomous as possible; (c) lower entry barriers; (d) Build incrementally on existing infrastructures (information systems); (e) incorporate heterogeneous resources by introducing distribution and mediation functionalities. This approach has been adopted by the European INSPIRE (Infrastructure for Spatial Information in the European Community) initiative and by the international GEOSS (Global Earth Observation System of Systems) programme.

Volcanic hazards at distant critical infrastructure: A method for bespoke, multi-disciplinary assessment

NASA Astrophysics Data System (ADS)

Odbert, H. M.; Aspinall, W.; Phillips, J.; Jenkins, S.; Wilson, T. M.; Scourse, E.; Sheldrake, T.; Tucker, P.; Nakeshree, K.; Bernardara, P.; Fish, K.

2015-12-01

Societies rely on critical services such as power, water, transport networks and manufacturing. Infrastructure may be sited to minimise exposure to natural hazards but not all can be avoided. The probability of long-range transport of a volcanic plume to a site is comparable to other external hazards that must be considered to satisfy safety assessments. Recent advances in numerical models of plume dispersion and stochastic modelling provide a formalized and transparent approach to probabilistic assessment of hazard distribution. To understand the risks to critical infrastructure far from volcanic sources, it is necessary to quantify their vulnerability to different hazard stressors. However, infrastructure assets (e.g. power plantsand operational facilities) are typically complex systems in themselves, with interdependent components that may differ in susceptibility to hazard impact. Usually, such complexity means that risk either cannot be estimated formally or that unsatisfactory simplifying assumptions are prerequisite to building a tractable risk model. We present a new approach to quantifying risk by bridging expertise of physical hazard modellers and infrastructure engineers. We use a joint expert judgment approach to determine hazard model inputs and constrain associated uncertainties. Model outputs are chosen on the basis of engineering or operational concerns. The procedure facilitates an interface between physical scientists, with expertise in volcanic hazards, and infrastructure engineers, with insight into vulnerability to hazards. The result is a joined-up approach to estimating risk from low-probability hazards to critical infrastructure. We describe our methodology and show preliminary results for vulnerability to volcanic hazards at a typical UK industrial facility. We discuss our findings in the context of developing bespoke assessment of hazards from distant sources in collaboration with key infrastructure stakeholders.

A spatial model to aggregate point-source and nonpoint-source water-quality data for large areas

USGS Publications Warehouse

White, D.A.; Smith, R.A.; Price, C.V.; Alexander, R.B.; Robinson, K.W.

1992-01-01

More objective and consistent methods are needed to assess water quality for large areas. A spatial model, one that capitalizes on the topologic relationships among spatial entities, to aggregate pollution sources from upstream drainage areas is described that can be implemented on land surfaces having heterogeneous water-pollution effects. An infrastructure of stream networks and drainage basins, derived from 1:250,000-scale digital-elevation models, define the hydrologic system in this spatial model. The spatial relationships between point- and nonpoint pollution sources and measurement locations are referenced to the hydrologic infrastructure with the aid of a geographic information system. A maximum-branching algorithm has been developed to simulate the effects of distance from a pollutant source to an arbitrary downstream location, a function traditionally employed in deterministic water quality models. ?? 1992.

OPM: The Open Porous Media Initiative

NASA Astrophysics Data System (ADS)

Flemisch, B.; Flornes, K. M.; Lie, K.; Rasmussen, A.

2011-12-01

The principal objective of the Open Porous Media (OPM) initiative is to develop a simulation suite that is capable of modeling industrially and scientifically relevant flow and transport processes in porous media and bridge the gap between the different application areas of porous media modeling, including reservoir mechanics, CO2 sequestration, biological systems, and product development of engineered media. The OPM initiative will provide a long-lasting, efficient, and well-maintained open-source software for flow and transport in porous media built on modern software principles. The suite is released under the GNU General Public License (GPL). Our motivation is to provide a means to unite industry and public research on simulation of flow and transport in porous media. For academic users, we seek to provide a software infrastructure that facilitates testing of new ideas on models with industry-standard complexity, while at the same time giving the researcher control over discretization and solvers. Similarly, we aim to accelerate the technology transfer from academic institutions to professional companies by making new research results available as free software of professional standard. The OPM initiative is currently supported by six research groups in Norway and Germany and funded by existing grants from public research agencies as well as from Statoil Petroleum and Total E&P Norge. However, a full-scale development of the OPM initiative requires substantially more funding and involvement of more research groups and potential end users. In this talk, we will provide an overview of the current activities in the OPM initiative. Special emphasis will be given to the demonstration of the synergies achieved by combining the strengths of individual open-source software components. In particular, a new fully implicit solver developed within the DUNE-based simulator DuMux could be enhanced by the ability to read industry-standard Eclipse input files and to run on grids given in corner-point format. Examples taken from the SPE comparative solution projects and CO2 sequestration benchmarks illustrate the current capabilities of the simulation suite.

keep your models up-to-date: connecting community mapping data to complex urban flood modelling

NASA Astrophysics Data System (ADS)

Winsemius, Hessel; Eilander, Dirk; Ward, Philip; Diaz Loaiza, Andres; Iliffe, Mark; Mawanda, Shaban; Luo, Tianyi; Kimacha, Nyambiri; Chen, Jorik

2017-04-01

The world is urbanizing rapidly. According to the United Nation's World Urbanization Prospect, 50% of the global population already lives in urban areas today. This number is expected to grow to 66% by 2050. The rapid changes in these urban environments go hand in hand with rapid changes in natural hazard risks, in particular in informal unplanned neighbourhoods. In Dar Es Salaam - Tanzania, flood risk dominates and given the rapid changes in the city, continuous updates of detailed street level hazard and risk mapping are needed to adequately support decision making for urban planning, infrastructure design and disaster response. Over the past years, the Ramani Huria and Zuia Mafuriko projects have mapped the most flood prone neighbourhoods, including roads, buildings, drainage and land use and contributed data to the open-source OpenStreetMap database. In this contribution, we will demonstrate how we mobilize these contributed data to establish dynamic flood models for Dar Es Salaam and keep these up-to-date by making a direct link between the data, and model schematization. The tools automatically establish a sound 1D drainage network as well as a high resolution terrain dataset, by fusing the OpenStreetMap data with existing lower resolution terrain data such as the globally available satellite based SRTM 30. It then translates these fully automatically into the inputs required for the D-HYDRO modeling suite. Our tools are built such that community and stakeholder knowledge can be included in the model details through workshops with the tools so that missing essential information about the city's details can be augmented on-the-fly. This process creates a continuous dialogue between members of the community that collect data, and stakeholders requiring data for flood models. Moreover, used taxonomy and data filtering can be configured to conditions in other cities, making the tools generic and scalable. The tools are made available open-source.

GATECloud.net: a platform for large-scale, open-source text processing on the cloud.

PubMed

Tablan, Valentin; Roberts, Ian; Cunningham, Hamish; Bontcheva, Kalina

2013-01-28

Cloud computing is increasingly being regarded as a key enabler of the 'democratization of science', because on-demand, highly scalable cloud computing facilities enable researchers anywhere to carry out data-intensive experiments. In the context of natural language processing (NLP), algorithms tend to be complex, which makes their parallelization and deployment on cloud platforms a non-trivial task. This study presents a new, unique, cloud-based platform for large-scale NLP research--GATECloud. net. It enables researchers to carry out data-intensive NLP experiments by harnessing the vast, on-demand compute power of the Amazon cloud. Important infrastructural issues are dealt with by the platform, completely transparently for the researcher: load balancing, efficient data upload and storage, deployment on the virtual machines, security and fault tolerance. We also include a cost-benefit analysis and usage evaluation.

Laying the Groundwork for Enterprise-Wide Medical Language Processing Services: Architecture and Process

PubMed Central

Chen, Elizabeth S.; Maloney, Francine L.; Shilmayster, Eugene; Goldberg, Howard S.

2009-01-01

A systematic and standard process for capturing information within free-text clinical documents could facilitate opportunities for improving quality and safety of patient care, enhancing decision support, and advancing data warehousing across an enterprise setting. At Partners HealthCare System, the Medical Language Processing (MLP) services project was initiated to establish a component-based architectural model and processes to facilitate putting MLP functionality into production for enterprise consumption, promote sharing of components, and encourage reuse. Key objectives included exploring the use of an open-source framework called the Unstructured Information Management Architecture (UIMA) and leveraging existing MLP-related efforts, terminology, and document standards. This paper describes early experiences in defining the infrastructure and standards for extracting, encoding, and structuring clinical observations from a variety of clinical documents to serve enterprise-wide needs. PMID:20351830

Laying the groundwork for enterprise-wide medical language processing services: architecture and process.

PubMed

Chen, Elizabeth S; Maloney, Francine L; Shilmayster, Eugene; Goldberg, Howard S

2009-11-14

A systematic and standard process for capturing information within free-text clinical documents could facilitate opportunities for improving quality and safety of patient care, enhancing decision support, and advancing data warehousing across an enterprise setting. At Partners HealthCare System, the Medical Language Processing (MLP) services project was initiated to establish a component-based architectural model and processes to facilitate putting MLP functionality into production for enterprise consumption, promote sharing of components, and encourage reuse. Key objectives included exploring the use of an open-source framework called the Unstructured Information Management Architecture (UIMA) and leveraging existing MLP-related efforts, terminology, and document standards. This paper describes early experiences in defining the infrastructure and standards for extracting, encoding, and structuring clinical observations from a variety of clinical documents to serve enterprise-wide needs.

40 CFR Table 3 to Subpart Wwww of... - Organic HAP Emissions Limits for Existing Open Molding Sources, New Open Molding Sources Emitting...

Code of Federal Regulations, 2010 CFR

2010-07-01

... Existing Open Molding Sources, New Open Molding Sources Emitting Less Than 100 TPY of HAP, and New and... CATEGORIES National Emissions Standards for Hazardous Air Pollutants: Reinforced Plastic Composites... Existing Open Molding Sources, New Open Molding Sources Emitting Less Than 100 TPY of HAP, and New and...

Alternative Fuels Data Center

Science.gov Websites

legislation dates back to the Clean Air Act of 1970, which created initiatives to reduce mobile sources of acts also include provisions related to alternative fuel vehicles (AFVs) and infrastructure. The Energy alternative fuel use and infrastructure development. The Energy Independence and Security Act of 2007 included

Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R.

PubMed

McCarthy, Davis J; Campbell, Kieran R; Lun, Aaron T L; Wills, Quin F

2017-04-15

Single-cell RNA sequencing (scRNA-seq) is increasingly used to study gene expression at the level of individual cells. However, preparing raw sequence data for further analysis is not a straightforward process. Biases, artifacts and other sources of unwanted variation are present in the data, requiring substantial time and effort to be spent on pre-processing, quality control (QC) and normalization. We have developed the R/Bioconductor package scater to facilitate rigorous pre-processing, quality control, normalization and visualization of scRNA-seq data. The package provides a convenient, flexible workflow to process raw sequencing reads into a high-quality expression dataset ready for downstream analysis. scater provides a rich suite of plotting tools for single-cell data and a flexible data structure that is compatible with existing tools and can be used as infrastructure for future software development. The open-source code, along with installation instructions, vignettes and case studies, is available through Bioconductor at http://bioconductor.org/packages/scater . davis@ebi.ac.uk. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

76 FR 55693 - Critical Infrastructure Partnership Advisory Council

Federal Register 2010, 2011, 2012, 2013, 2014

2011-09-08

...) Plenary Meeting will be held on Thursday, October 6, 2011, at the Renaissance Washington Downtown Hotel... Washington Downtown Hotel, 999 Ninth Street, NW., Washington, DC 20001. While this meeting is open to the...

Access Control Management for SCADA Systems

NASA Astrophysics Data System (ADS)

Hong, Seng-Phil; Ahn, Gail-Joon; Xu, Wenjuan

The information technology revolution has transformed all aspects of our society including critical infrastructures and led a significant shift from their old and disparate business models based on proprietary and legacy environments to more open and consolidated ones. Supervisory Control and Data Acquisition (SCADA) systems have been widely used not only for industrial processes but also for some experimental facilities. Due to the nature of open environments, managing SCADA systems should meet various security requirements since system administrators need to deal with a large number of entities and functions involved in critical infrastructures. In this paper, we identify necessary access control requirements in SCADA systems and articulate access control policies for the simulated SCADA systems. We also attempt to analyze and realize those requirements and policies in the context of role-based access control that is suitable for simplifying administrative tasks in large scale enterprises.

The open science grid

NASA Astrophysics Data System (ADS)

Pordes, Ruth; OSG Consortium; Petravick, Don; Kramer, Bill; Olson, Doug; Livny, Miron; Roy, Alain; Avery, Paul; Blackburn, Kent; Wenaus, Torre; Würthwein, Frank; Foster, Ian; Gardner, Rob; Wilde, Mike; Blatecky, Alan; McGee, John; Quick, Rob

2007-07-01

The Open Science Grid (OSG) provides a distributed facility where the Consortium members provide guaranteed and opportunistic access to shared computing and storage resources. OSG provides support for and evolution of the infrastructure through activities that cover operations, security, software, troubleshooting, addition of new capabilities, and support for existing and engagement with new communities. The OSG SciDAC-2 project provides specific activities to manage and evolve the distributed infrastructure and support it's use. The innovative aspects of the project are the maintenance and performance of a collaborative (shared & common) petascale national facility over tens of autonomous computing sites, for many hundreds of users, transferring terabytes of data a day, executing tens of thousands of jobs a day, and providing robust and usable resources for scientific groups of all types and sizes. More information can be found at the OSG web site: www.opensciencegrid.org.

The deegree framework - Spatial Data Infrastructure solution for end-users and developers

NASA Astrophysics Data System (ADS)

Kiehle, Christian; Poth, Andreas

2010-05-01

The open source software framework deegree is a comprehensive implementa­tion of standards as defined by ISO and Open Geospatial Consortium (OGC). It has been developed with two goals in mind: provide a uniform framework for implementing Spatial Data Infrastructures (SDI) and adhering to standards as strictly as possible. Although being open source software (Lesser GNU Public Li­cense, LGPL), deegree has been developed with a business model in mind: providing the general building blocks of SDIs without license fees and offer cus­tomization, consulting and tailoring by specialized companies. The core of deegree is a comprehensive Java Application Programming Inter­face (API) offering access to spatial features, analysis, metadata and coordinate reference systems. As a library, deegree can and has been integrated as a core module inside spatial information systems. It is reference implementation for several OGC standards and based on an ISO 19107 geometry model. For end users, deegree is shipped as a web application providing easy-to-set-up components for web mapping and spatial analysis. Since 2000, deegree has been the backbone of many productive SDIs, first and foremost for governmental stakeholders (e.g. Federal Agency for Cartography and Geodesy in Germany, the Ministry of Housing, Spatial Planning and the En­vironment in the Netherlands, etc.) as well as for research and development projects as an early adoption of standards, drafts and discussion papers. Be­sides mature standards like Web Map Service, Web Feature Service and Cata­logue Services, deegree also implements rather new standards like the Sensor Observation Service, the Web Processing Service and the Web Coordinate Transformation Service (WCTS). While a robust background in standardization (knowledge and implementation) is a must for consultancy, standard-compliant services and encodings alone do not provide solutions for customers. The added value is comprised by a sophistic­ated set of client software, desktop and web environments. A focus lies on different client solutions for specific standards like the Web Pro­cessing Service and the Web Coordinate Transformation Service. On the other hand, complex geoportal solutions comprised of multiple standards and en­hanced by components for user management, security and map client function­ality show the demanding requirements of real world solutions. The XPlan-GML-standard as defined by the German spatial planing authorities is a good ex­ample of how complex real-world requirements can get. XPlan-GML is intended to provide a framework for digital spatial planning documents and requires complex Geography Markup Language (GML) features along with Symbology Encoding (SE), Filter Encoding (FE), Web Map Services (WMS), Web Feature Services (WFS). This complex in­frastructure should be used by urban and spatial planners and therefore re­quires a user-friendly graphical interface hiding the complexity of the underly­ing infrastructure. Based on challenges faced within customer projects, the importance of easy to use software components is focused. SDI solution should be build upon ISO/OGC-standards, but more important, should be user-friendly and support the users in spatial data management and analysis.

Putting Teeth into Open Architectures: Infrastructure for Reducing the Need for Retesting

DTIC Science & Technology

2007-04-30

the test and evaluation team. This paper outlines new approaches to quality assurance and testing that are better suited for providing...reconfiguration. Testing of reusable subsystems is also subject to the above considerations and, similarly, requires new methods for effectively achieving...architectural model. Thus, fully realizing the open architecture vision requires a new paradigm for test and evaluation. We propose such a

Institutional Change for Improving Accessibility in the Design and Delivery of Distance Learning--The Role of Faculty Accessibility Specialists at the Open University

ERIC Educational Resources Information Center

Slater, Rachel; Pearson, Victoria K.; Warren, James P.; Forbes, Tina

2015-01-01

The Open University (OU) has an established infrastructure for supporting disabled students. Historically, the thrust of this has focused on providing accessible adjustments post-production. In 2012, the OU implemented securing greater accessibility (SeGA) to raise awareness and bring about an institutional change to curriculum design so that the…