mmpdb: An Open-Source Matched Molecular Pair Platform for Large Multiproperty Data Sets.

PubMed

Dalke, Andrew; Hert, Jérôme; Kramer, Christian

2018-05-29

Matched molecular pair analysis (MMPA) enables the automated and systematic compilation of medicinal chemistry rules from compound/property data sets. Here we present mmpdb, an open-source matched molecular pair (MMP) platform to create, compile, store, retrieve, and use MMP rules. mmpdb is suitable for the large data sets typically found in pharmaceutical and agrochemical companies and provides new algorithms for fragment canonicalization and stereochemistry handling. The platform is written in Python and based on the RDKit toolkit. It is freely available from https://github.com/rdkit/mmpdb .

Specification Patent Management for Web Application Platform Ecosystem

NASA Astrophysics Data System (ADS)

Fukami, Yoshiaki; Isshiki, Masao; Takeda, Hideaki; Ohmukai, Ikki; Kokuryo, Jiro

Diversified usage of web applications has encouraged disintegration of web platform into management of identification and applications. Users make use of various kinds of data linked to their identity with multiple applications on certain social web platforms such as Facebook or MySpace. There has emerged competition among web application platforms. Platformers can design relationship with developers by controlling patent of their own specification and adopt open technologies developed external organizations. Platformers choose a way to open according to feature of the specification and their position. Patent management of specification come to be a key success factor to build competitive web application platforms. Each way to attract external developers such as standardization, open source has not discussed and analyzed all together.

An Embedded Systems Course for Engineering Students Using Open-Source Platforms in Wireless Scenarios

ERIC Educational Resources Information Center

Rodriguez-Sanchez, M. C.; Torrado-Carvajal, Angel; Vaquero, Joaquin; Borromeo, Susana; Hernandez-Tamames, Juan A.

2016-01-01

This paper presents a case study analyzing the advantages and disadvantages of using project-based learning (PBL) combined with collaborative learning (CL) and industry best practices, integrated with information communication technologies, open-source software, and open-source hardware tools, in a specialized microcontroller and embedded systems…

Next Stop: OpenSim!

ERIC Educational Resources Information Center

Korolov, Maria

2011-01-01

Unhappy with conditions in Second Life, educators are migrating to a developing virtual world that offers them greater autonomy and a safer platform for their students at far less a cost. OpenSimulator is an open source virtual world platform that schools can run for free on their own servers or can get cheaply and quickly--the space can be up and…

Open source OCR framework using mobile devices

NASA Astrophysics Data System (ADS)

Zhou, Steven Zhiying; Gilani, Syed Omer; Winkler, Stefan

2008-02-01

Mobile phones have evolved from passive one-to-one communication device to powerful handheld computing device. Today most new mobile phones are capable of capturing images, recording video, and browsing internet and do much more. Exciting new social applications are emerging on mobile landscape, like, business card readers, sing detectors and translators. These applications help people quickly gather the information in digital format and interpret them without the need of carrying laptops or tablet PCs. However with all these advancements we find very few open source software available for mobile phones. For instance currently there are many open source OCR engines for desktop platform but, to our knowledge, none are available on mobile platform. Keeping this in perspective we propose a complete text detection and recognition system with speech synthesis ability, using existing desktop technology. In this work we developed a complete OCR framework with subsystems from open source desktop community. This includes a popular open source OCR engine named Tesseract for text detection & recognition and Flite speech synthesis module, for adding text-to-speech ability.

Open Energy Info (OpenEI) (Fact Sheet)

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

Not Available

2010-12-01

The Open Energy Information (OpenEI.org) initiative is a free, open-source, knowledge-sharing platform. OpenEI was created to provide access to data, models, tools, and information that accelerate the transition to clean energy systems through informed decisions.

Open-Source 3D-Printable Optics Equipment

PubMed Central

Zhang, Chenlong; Anzalone, Nicholas C.; Faria, Rodrigo P.; Pearce, Joshua M.

2013-01-01

Just as the power of the open-source design paradigm has driven down the cost of software to the point that it is accessible to most people, the rise of open-source hardware is poised to drive down the cost of doing experimental science to expand access to everyone. To assist in this aim, this paper introduces a library of open-source 3-D-printable optics components. This library operates as a flexible, low-cost public-domain tool set for developing both research and teaching optics hardware. First, the use of parametric open-source designs using an open-source computer aided design package is described to customize the optics hardware for any application. Second, details are provided on the use of open-source 3-D printers (additive layer manufacturing) to fabricate the primary mechanical components, which are then combined to construct complex optics-related devices. Third, the use of the open-source electronics prototyping platform are illustrated as control for optical experimental apparatuses. This study demonstrates an open-source optical library, which significantly reduces the costs associated with much optical equipment, while also enabling relatively easily adapted customizable designs. The cost reductions in general are over 97%, with some components representing only 1% of the current commercial investment for optical products of similar function. The results of this study make its clear that this method of scientific hardware development enables a much broader audience to participate in optical experimentation both as research and teaching platforms than previous proprietary methods. PMID:23544104

Open-source 3D-printable optics equipment.

PubMed

Zhang, Chenlong; Anzalone, Nicholas C; Faria, Rodrigo P; Pearce, Joshua M

2013-01-01

Just as the power of the open-source design paradigm has driven down the cost of software to the point that it is accessible to most people, the rise of open-source hardware is poised to drive down the cost of doing experimental science to expand access to everyone. To assist in this aim, this paper introduces a library of open-source 3-D-printable optics components. This library operates as a flexible, low-cost public-domain tool set for developing both research and teaching optics hardware. First, the use of parametric open-source designs using an open-source computer aided design package is described to customize the optics hardware for any application. Second, details are provided on the use of open-source 3-D printers (additive layer manufacturing) to fabricate the primary mechanical components, which are then combined to construct complex optics-related devices. Third, the use of the open-source electronics prototyping platform are illustrated as control for optical experimental apparatuses. This study demonstrates an open-source optical library, which significantly reduces the costs associated with much optical equipment, while also enabling relatively easily adapted customizable designs. The cost reductions in general are over 97%, with some components representing only 1% of the current commercial investment for optical products of similar function. The results of this study make its clear that this method of scientific hardware development enables a much broader audience to participate in optical experimentation both as research and teaching platforms than previous proprietary methods.

Maritime Analytics Prototype: Final Development Report

DTIC Science & Technology

2014-04-01

access management platform OpenAM , support for multiple instances of the same type of widget and support for installation specific configuration files to...et de la gestion de l’accès OpenAM , le support pour plusieurs instances du même type de widget et le support des fichiers d’installation de...open source authentication and access management platform OpenAM , support for multiple instances of the same type of widget and support for

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

A case study in open source innovation: developing the Tidepool Platform for interoperability in type 1 diabetes management.

PubMed

Neinstein, Aaron; Wong, Jenise; Look, Howard; Arbiter, Brandon; Quirk, Kent; McCanne, Steve; Sun, Yao; Blum, Michael; Adi, Saleh

2016-03-01

Develop a device-agnostic cloud platform to host diabetes device data and catalyze an ecosystem of software innovation for type 1 diabetes (T1D) management. An interdisciplinary team decided to establish a nonprofit company, Tidepool, and build open-source software. Through a user-centered design process, the authors created a software platform, the Tidepool Platform, to upload and host T1D device data in an integrated, device-agnostic fashion, as well as an application ("app"), Blip, to visualize the data. Tidepool's software utilizes the principles of modular components, modern web design including REST APIs and JavaScript, cloud computing, agile development methodology, and robust privacy and security. By consolidating the currently scattered and siloed T1D device data ecosystem into one open platform, Tidepool can improve access to the data and enable new possibilities and efficiencies in T1D clinical care and research. The Tidepool Platform decouples diabetes apps from diabetes devices, allowing software developers to build innovative apps without requiring them to design a unique back-end (e.g., database and security) or unique ways of ingesting device data. It allows people with T1D to choose to use any preferred app regardless of which device(s) they use. The authors believe that the Tidepool Platform can solve two current problems in the T1D device landscape: 1) limited access to T1D device data and 2) poor interoperability of data from different devices. If proven effective, Tidepool's open source, cloud model for health data interoperability is applicable to other healthcare use cases. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association.

A case study in open source innovation: developing the Tidepool Platform for interoperability in type 1 diabetes management

PubMed Central

Wong, Jenise; Look, Howard; Arbiter, Brandon; Quirk, Kent; McCanne, Steve; Sun, Yao; Blum, Michael; Adi, Saleh

2016-01-01

Objective Develop a device-agnostic cloud platform to host diabetes device data and catalyze an ecosystem of software innovation for type 1 diabetes (T1D) management. Materials and Methods An interdisciplinary team decided to establish a nonprofit company, Tidepool, and build open-source software. Results Through a user-centered design process, the authors created a software platform, the Tidepool Platform, to upload and host T1D device data in an integrated, device-agnostic fashion, as well as an application (“app”), Blip, to visualize the data. Tidepool’s software utilizes the principles of modular components, modern web design including REST APIs and JavaScript, cloud computing, agile development methodology, and robust privacy and security. Discussion By consolidating the currently scattered and siloed T1D device data ecosystem into one open platform, Tidepool can improve access to the data and enable new possibilities and efficiencies in T1D clinical care and research. The Tidepool Platform decouples diabetes apps from diabetes devices, allowing software developers to build innovative apps without requiring them to design a unique back-end (e.g., database and security) or unique ways of ingesting device data. It allows people with T1D to choose to use any preferred app regardless of which device(s) they use. Conclusion The authors believe that the Tidepool Platform can solve two current problems in the T1D device landscape: 1) limited access to T1D device data and 2) poor interoperability of data from different devices. If proven effective, Tidepool’s open source, cloud model for health data interoperability is applicable to other healthcare use cases. PMID:26338218

Fiji: an open-source platform for biological-image analysis.

PubMed

Schindelin, Johannes; Arganda-Carreras, Ignacio; Frise, Erwin; Kaynig, Verena; Longair, Mark; Pietzsch, Tobias; Preibisch, Stephan; Rueden, Curtis; Saalfeld, Stephan; Schmid, Benjamin; Tinevez, Jean-Yves; White, Daniel James; Hartenstein, Volker; Eliceiri, Kevin; Tomancak, Pavel; Cardona, Albert

2012-06-28

Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.

SIG Contribution in the Making of Geotechnical Maps in Urban Areas

NASA Astrophysics Data System (ADS)

Monteiro, António; Pais, Luís Andrade; Rodrigues, Carlos; Carvalho, Paulo

2017-10-01

The use of Geographic Information Systems (GIS) has spread to several science areas, from oceanography to geotechnics. Its application in the urban mapping was intensified in the last century, which allowed a great development, due to the use of geographic database, new analysis tools and, more recently, free open source software. Geotechnical cartography struggle with a permanent and large environment re-organization in urban area, due to new building construction, trenching and the drilling of sampling wells and holes. This creates an extra important and largest volume of data at any pre-existence geological map. The main problem results on the fact that the natural environment is covered with buildings and communications system. The purpose of this work is to create a viable geographic information base for geotechnical mapping through a free GIS computer program and open source, with non-traditional cartographic sources, giving preference to open platforms. QGIS was used as software and “Google Maps”, “Bing Maps” and “OpenStreetMap” were applied as cartographic sources using the “OpenLayers plugin” module. Finally, we also pretend to identify and delimit the degree of granite’s change and fracturing areas using a “Streetview” platform. This model has cartographic input which are a geological map study area, open cartographic web archives and the use of “Streetview” platform. The output has several layouts, such as topography intersection (roads, borders, etc.), with geological map and the bordering area of Guarda Urban Zone. The use of this platform types decrease the collect data time and, sometimes, a careful observation of pictures that were taken during excavations may reveal important details for geological mapping in the study area.

moocRP: Enabling Open Learning Analytics with an Open Source Platform for Data Distribution, Analysis, and Visualization

ERIC Educational Resources Information Center

Pardos, Zachary A.; Whyte, Anthony; Kao, Kevin

2016-01-01

In this paper, we address issues of transparency, modularity, and privacy with the introduction of an open source, web-based data repository and analysis tool tailored to the Massive Open Online Course community. The tool integrates data request/authorization and distribution workflow features as well as provides a simple analytics module upload…

OpenSesame: an open-source, graphical experiment builder for the social sciences.

PubMed

Mathôt, Sebastiaan; Schreij, Daniel; Theeuwes, Jan

2012-06-01

In the present article, we introduce OpenSesame, a graphical experiment builder for the social sciences. OpenSesame is free, open-source, and cross-platform. It features a comprehensive and intuitive graphical user interface and supports Python scripting for complex tasks. Additional functionality, such as support for eyetrackers, input devices, and video playback, is available through plug-ins. OpenSesame can be used in combination with existing software for creating experiments.

RMG An Open Source Electronic Structure Code for Multi-Petaflops Calculations

NASA Astrophysics Data System (ADS)

Briggs, Emil; Lu, Wenchang; Hodak, Miroslav; Bernholc, Jerzy

RMG (Real-space Multigrid) is an open source, density functional theory code for quantum simulations of materials. It solves the Kohn-Sham equations on real-space grids, which allows for natural parallelization via domain decomposition. Either subspace or Davidson diagonalization, coupled with multigrid methods, are used to accelerate convergence. RMG is a cross platform open source package which has been used in the study of a wide range of systems, including semiconductors, biomolecules, and nanoscale electronic devices. It can optionally use GPU accelerators to improve performance on systems where they are available. The recently released versions (>2.0) support multiple GPU's per compute node, have improved performance and scalability, enhanced accuracy and support for additional hardware platforms. New versions of the code are regularly released at http://www.rmgdft.org. The releases include binaries for Linux, Windows and MacIntosh systems, automated builds for clusters using cmake, as well as versions adapted to the major supercomputing installations and platforms. Several recent, large-scale applications of RMG will be discussed.

Raspberry Pi-powered imaging for plant phenotyping.

PubMed

Tovar, Jose C; Hoyer, J Steen; Lin, Andy; Tielking, Allison; Callen, Steven T; Elizabeth Castillo, S; Miller, Michael; Tessman, Monica; Fahlgren, Noah; Carrington, James C; Nusinow, Dmitri A; Gehan, Malia A

2018-03-01

Image-based phenomics is a powerful approach to capture and quantify plant diversity. However, commercial platforms that make consistent image acquisition easy are often cost-prohibitive. To make high-throughput phenotyping methods more accessible, low-cost microcomputers and cameras can be used to acquire plant image data. We used low-cost Raspberry Pi computers and cameras to manage and capture plant image data. Detailed here are three different applications of Raspberry Pi-controlled imaging platforms for seed and shoot imaging. Images obtained from each platform were suitable for extracting quantifiable plant traits (e.g., shape, area, height, color) en masse using open-source image processing software such as PlantCV. This protocol describes three low-cost platforms for image acquisition that are useful for quantifying plant diversity. When coupled with open-source image processing tools, these imaging platforms provide viable low-cost solutions for incorporating high-throughput phenomics into a wide range of research programs.

Open Source in Education

ERIC Educational Resources Information Center

Lakhan, Shaheen E.; Jhunjhunwala, Kavita

2008-01-01

Educational institutions have rushed to put their academic resources and services online, beginning the global community onto a common platform and awakening the interest of investors. Despite continuing technical challenges, online education shows great promise. Open source software offers one approach to addressing the technical problems in…

OpenMS: a flexible open-source software platform for mass spectrometry data analysis.

PubMed

Röst, Hannes L; Sachsenberg, Timo; Aiche, Stephan; Bielow, Chris; Weisser, Hendrik; Aicheler, Fabian; Andreotti, Sandro; Ehrlich, Hans-Christian; Gutenbrunner, Petra; Kenar, Erhan; Liang, Xiao; Nahnsen, Sven; Nilse, Lars; Pfeuffer, Julianus; Rosenberger, George; Rurik, Marc; Schmitt, Uwe; Veit, Johannes; Walzer, Mathias; Wojnar, David; Wolski, Witold E; Schilling, Oliver; Choudhary, Jyoti S; Malmström, Lars; Aebersold, Ruedi; Reinert, Knut; Kohlbacher, Oliver

2016-08-30

High-resolution mass spectrometry (MS) has become an important tool in the life sciences, contributing to the diagnosis and understanding of human diseases, elucidating biomolecular structural information and characterizing cellular signaling networks. However, the rapid growth in the volume and complexity of MS data makes transparent, accurate and reproducible analysis difficult. We present OpenMS 2.0 (http://www.openms.de), a robust, open-source, cross-platform software specifically designed for the flexible and reproducible analysis of high-throughput MS data. The extensible OpenMS software implements common mass spectrometric data processing tasks through a well-defined application programming interface in C++ and Python and through standardized open data formats. OpenMS additionally provides a set of 185 tools and ready-made workflows for common mass spectrometric data processing tasks, which enable users to perform complex quantitative mass spectrometric analyses with ease.

Developing an Intelligent Diagnosis and Assessment E-Learning Tool for Introductory Programming

ERIC Educational Resources Information Center

Huang, Chenn-Jung; Chen, Chun-Hua; Luo, Yun-Cheng; Chen, Hong-Xin; Chuang, Yi-Ta

2008-01-01

Recently, a lot of open source e-learning platforms have been offered for free in the Internet. We thus incorporate the intelligent diagnosis and assessment tool into an open software e-learning platform developed for programming language courses, wherein the proposed learning diagnosis assessment tools based on text mining and machine learning…

GridAPPS-D

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

2017-03-28

GridAPPS-D is an open-source, open architecture, standards based platform for development of advanced electric power system planning and operations applications. GridAPPS-D provides a documented data abstraction for the application developer enabling creation of applications that can be run in any compliant system or platform. This enables development of applications that are platform vendor independent applications and applications that take advantage of the possibility of data rich and data driven applications based on deployment of smart grid devices and systems.

Performance Evaluation of Block Acquisition and Tracking Algorithms Using an Open Source GPS Receiver Platform

NASA Technical Reports Server (NTRS)

Ramachandran, Ganesh K.; Akopian, David; Heckler, Gregory W.; Winternitz, Luke B.

2011-01-01

Location technologies have many applications in wireless communications, military and space missions, etc. US Global Positioning System (GPS) and other existing and emerging Global Navigation Satellite Systems (GNSS) are expected to provide accurate location information to enable such applications. While GNSS systems perform very well in strong signal conditions, their operation in many urban, indoor, and space applications is not robust or even impossible due to weak signals and strong distortions. The search for less costly, faster and more sensitive receivers is still in progress. As the research community addresses more and more complicated phenomena there exists a demand on flexible multimode reference receivers, associated SDKs, and development platforms which may accelerate and facilitate the research. One of such concepts is the software GPS/GNSS receiver (GPS SDR) which permits a facilitated access to algorithmic libraries and a possibility to integrate more advanced algorithms without hardware and essential software updates. The GNU-SDR and GPS-SDR open source receiver platforms are such popular examples. This paper evaluates the performance of recently proposed block-corelator techniques for acquisition and tracking of GPS signals using open source GPS-SDR platform.

SolarPILOT Feature Requests and Collaboration | Concentrating Solar Power |

Science.gov Websites

DOE of the CSP community's needs. As of March 2018, SolarPILOT is also available as an open source project. While not every project benefits from an open source approach, several factors influenced this , but lack of availability has, in some cases, prevented widespread adoption of a common platform. Open

Command & Control in Virtual Environments: Designing a Virtual Environment for Experimentation

DTIC Science & Technology

2010-06-01

proceed with the research: Second Life/ OpenSim A popular leader in the desktop virtual worlds revolution, for many Second Life has become...prototype environments and adapt them quickly within the world. OpenSim is an open-source community built around upon the Second Life platform...functionality natively present in Second Life and the Opensim platform. With the recent release of Second Life Viewer 2.0, which contains a complete

Architecture Design and Experimental Platform Demonstration of Optical Network based on OpenFlow Protocol

NASA Astrophysics Data System (ADS)

Xing, Fangyuan; Wang, Honghuan; Yin, Hongxi; Li, Ming; Luo, Shenzi; Wu, Chenguang

2016-02-01

With the extensive application of cloud computing and data centres, as well as the constantly emerging services, the big data with the burst characteristic has brought huge challenges to optical networks. Consequently, the software defined optical network (SDON) that combines optical networks with software defined network (SDN), has attracted much attention. In this paper, an OpenFlow-enabled optical node employed in optical cross-connect (OXC) and reconfigurable optical add/drop multiplexer (ROADM), is proposed. An open source OpenFlow controller is extended on routing strategies. In addition, the experiment platform based on OpenFlow protocol for software defined optical network, is designed. The feasibility and availability of the OpenFlow-enabled optical nodes and the extended OpenFlow controller are validated by the connectivity test, protection switching and load balancing experiments in this test platform.

What Can OpenEI Do For You?

ScienceCinema

None

2018-02-06

Open Energy Information (OpenEI) is an open source web platform—similar to the one used by Wikipedia—developed by the US Department of Energy (DOE) and the National Renewable Energy Laboratory (NREL) to make the large amounts of energy-related data and information more easily searched, accessed, and used both by people and automated machine processes. Built utilizing the standards and practices of the Linked Open Data community, the OpenEI platform is much more robust and powerful than typical web sites and databases. As an open platform, all users can search, edit, add, and access data in OpenEI for free. The user community contributes the content and ensures its accuracy and relevance; as the community expands, so does the content's comprehensiveness and quality. The data are structured and tagged with descriptors to enable cross-linking among related data sets, advanced search functionality, and consistent, usable formatting. Data input protocols and quality standards help ensure the content is structured and described properly and derived from a credible source. Although DOE/NREL is developing OpenEI and seeding it with initial data, it is designed to become a true community model with millions of users, a large core of active contributors, and numerous sponsors.

Building a Billion Spatio-Temporal Object Search and Visualization Platform

NASA Astrophysics Data System (ADS)

Kakkar, D.; Lewis, B.

2017-10-01

With funding from the Sloan Foundation and Harvard Dataverse, the Harvard Center for Geographic Analysis (CGA) has developed a prototype spatio-temporal visualization platform called the Billion Object Platform or BOP. The goal of the project is to lower barriers for scholars who wish to access large, streaming, spatio-temporal datasets. The BOP is now loaded with the latest billion geo-tweets, and is fed a real-time stream of about 1 million tweets per day. The geo-tweets are enriched with sentiment and census/admin boundary codes when they enter the system. The system is open source and is currently hosted on Massachusetts Open Cloud (MOC), an OpenStack environment with all components deployed in Docker orchestrated by Kontena. This paper will provide an overview of the BOP architecture, which is built on an open source stack consisting of Apache Lucene, Solr, Kafka, Zookeeper, Swagger, scikit-learn, OpenLayers, and AngularJS. The paper will further discuss the approach used for harvesting, enriching, streaming, storing, indexing, visualizing and querying a billion streaming geo-tweets.

An Open Source Model for Open Access Journal Publication

PubMed Central

Blesius, Carl R.; Williams, Michael A.; Holzbach, Ana; Huntley, Arthur C.; Chueh, Henry

2005-01-01

We describe an electronic journal publication infrastructure that allows a flexible publication workflow, academic exchange around different forms of user submissions, and the exchange of articles between publishers and archives using a common XML based standard. This web-based application is implemented on a freely available open source software stack. This publication demonstrates the Dermatology Online Journal's use of the platform for non-biased independent open access publication. PMID:16779183

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.

Implementation of a near-real time cross-border web-mapping platform on airborne particulate matter (PM) concentration with open-source software

NASA Astrophysics Data System (ADS)

Knörchen, Achim; Ketzler, Gunnar; Schneider, Christoph

2015-01-01

Although Europe has been growing together for the past decades, cross-border information platforms on environmental issues are still scarce. With regard to the establishment of a web-mapping tool on airborne particulate matter (PM) concentration for the Euregio Meuse-Rhine located in the border region of Belgium, Germany and the Netherlands, this article describes the research on methodical and technical backgrounds implementing such a platform. An open-source solution was selected for presenting the data in a Web GIS (OpenLayers/GeoExt; both JavaScript-based), applying other free tools for data handling (Python), data management (PostgreSQL), geo-statistical modelling (Octave), geoprocessing (GRASS GIS/GDAL) and web mapping (MapServer). The multilingual, made-to-order online platform provides access to near-real time data on PM concentration as well as additional background information. In an open data section, commented configuration files for the Web GIS client are being made available for download. Furthermore, all geodata generated by the project is being published under public domain and can be retrieved in various formats or integrated into Desktop GIS as Web Map Services (WMS).

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.

OpenQuake, a platform for collaborative seismic hazard and risk assessment

NASA Astrophysics Data System (ADS)

Henshaw, Paul; Burton, Christopher; Butler, Lars; Crowley, Helen; Danciu, Laurentiu; Nastasi, Matteo; Monelli, Damiano; Pagani, Marco; Panzeri, Luigi; Simionato, Michele; Silva, Vitor; Vallarelli, Giuseppe; Weatherill, Graeme; Wyss, Ben

2013-04-01

Sharing of data and risk information, best practices, and approaches across the globe is key to assessing risk more effectively. Through global projects, open-source IT development and collaborations with more than 10 regions, leading experts are collaboratively developing unique global datasets, best practice, tools and models for global seismic hazard and risk assessment, within the context of the Global Earthquake Model (GEM). Guided by the needs and experiences of governments, companies and international organisations, all contributions are being integrated into OpenQuake: a web-based platform that - together with other resources - will become accessible in 2014. With OpenQuake, stakeholders worldwide will be able to calculate, visualize and investigate earthquake hazard and risk, capture new data and share findings for joint learning. The platform is envisaged as a collaborative hub for earthquake risk assessment, used at global and local scales, around which an active network of users has formed. OpenQuake will comprise both online and offline tools, many of which can also be used independently. One of the first steps in OpenQuake development was the creation of open-source software for advanced seismic hazard and risk calculations at any scale, the OpenQuake Engine. Although in continuous development, a command-line version of the software is already being test-driven and used by hundreds worldwide; from non-profits in Central Asia, seismologists in sub-Saharan Africa and companies in South Asia to the European seismic hazard harmonization programme (SHARE). In addition, several technical trainings were organized with scientists from different regions of the world (sub-Saharan Africa, Central Asia, Asia-Pacific) to introduce the engine and other OpenQuake tools to the community, something that will continue to happen over the coming years. Other tools that are being developed of direct interest to the hazard community are: • OpenQuake Modeller; fundamental instruments for the creation of seismogenic input models for seismic hazard assessment, a critical input to the OpenQuake Engine. OpenQuake Modeller will consist of a suite of tools (Hazard Modellers Toolkit) for characterizing the seismogenic sources of earthquakes and their models of earthquakes recurrence. An earthquake catalogue homogenization tool, for integration, statistical comparison and user-defined harmonization of multiple catalogues of earthquakes is also included in the OpenQuake modeling tools. • A data capture tool for active faults; a tool that allows geologists to draw (new) fault discoveries on a map in an intuitive GIS-environment and add details on the fault through the tool. This data, once quality checked, can then be integrated with the global active faults database, which will increase in value with every new fault insertion. Building on many ongoing efforts and the knowledge of scientists worldwide, GEM will for the first time integrate state-of-the-art data, models, results and open-source tools into a single platform. The platform will continue to increase in value, in particular for use in local contexts, through contributions from and collaborations with scientists and organisations worldwide. This presentation will showcase the OpenQuake Platform, focusing on the IT solutions that have been adopted as well as the added value that the platform will bring to scientists worldwide.

A Platform for Scalable Satellite and Geospatial Data Analysis

NASA Astrophysics Data System (ADS)

Beneke, C. M.; Skillman, S.; Warren, M. S.; Kelton, T.; Brumby, S. P.; Chartrand, R.; Mathis, M.

2017-12-01

At Descartes Labs, we use the commercial cloud to run global-scale machine learning applications over satellite imagery. We have processed over 5 Petabytes of public and commercial satellite imagery, including the full Landsat and Sentinel archives. By combining open-source tools with a FUSE-based filesystem for cloud storage, we have enabled a scalable compute platform that has demonstrated reading over 200 GB/s of satellite imagery into cloud compute nodes. In one application, we generated global 15m Landsat-8, 20m Sentinel-1, and 10m Sentinel-2 composites from 15 trillion pixels, using over 10,000 CPUs. We recently created a public open-source Python client library that can be used to query and access preprocessed public satellite imagery from within our platform, and made this platform available to researchers for non-commercial projects. In this session, we will describe how you can use the Descartes Labs Platform for rapid prototyping and scaling of geospatial analyses and demonstrate examples in land cover classification.

An ontology based information system for the management of institutional repository's collections

NASA Astrophysics Data System (ADS)

Tsolakidis, A.; Kakoulidis, P.; Skourlas, C.

2015-02-01

In this paper we discuss a simple methodological approach to create, and customize institutional repositories for the domain of the technological education. The use of the open source software platform of DSpace is proposed to build up the repository application and provide access to digital resources including research papers, dissertations, administrative documents, educational material, etc. Also the use of owl ontologies is proposed for indexing and accessing the various, heterogeneous items stored in the repository. Customization and operation of a platform for the selection and use of terms or parts of similar existing owl ontologies is also described. This platform could be based on the open source software Protégé that supports owl, is widely used, and also supports visualization, SPARQL etc. The combined use of the owl platform and the DSpace repository form a basis for creating customized ontologies, accommodating the semantic metadata of items and facilitating searching.

An open-source platform to study uniaxial stress effects on nanoscale devices

NASA Astrophysics Data System (ADS)

Signorello, G.; Schraff, M.; Zellekens, P.; Drechsler, U.; Bürge, M.; Steinauer, H. R.; Heller, R.; Tschudy, M.; Riel, H.

2017-05-01

We present an automatic measurement platform that enables the characterization of nanodevices by electrical transport and optical spectroscopy as a function of the uniaxial stress. We provide insights into and detailed descriptions of the mechanical device, the substrate design and fabrication, and the instrument control software, which is provided under open-source license. The capability of the platform is demonstrated by characterizing the piezo-resistance of an InAs nanowire device using a combination of electrical transport and Raman spectroscopy. The advantages of this measurement platform are highlighted by comparison with state-of-the-art piezo-resistance measurements in InAs nanowires. We envision that the systematic application of this methodology will provide new insights into the physics of nanoscale devices and novel materials for electronics, and thus contribute to the assessment of the potential of strain as a technology booster for nanoscale electronics.

ProteoCloud: a full-featured open source proteomics cloud computing pipeline.

PubMed

Muth, Thilo; Peters, Julian; Blackburn, Jonathan; Rapp, Erdmann; Martens, Lennart

2013-08-02

We here present the ProteoCloud pipeline, a freely available, full-featured cloud-based platform to perform computationally intensive, exhaustive searches in a cloud environment using five different peptide identification algorithms. ProteoCloud is entirely open source, and is built around an easy to use and cross-platform software client with a rich graphical user interface. This client allows full control of the number of cloud instances to initiate and of the spectra to assign for identification. It also enables the user to track progress, and to visualize and interpret the results in detail. Source code, binaries and documentation are all available at http://proteocloud.googlecode.com. Copyright © 2012 Elsevier B.V. All rights reserved.

Stories from OpenAQ, a Global and Grassroots Open Air Quality Community

NASA Astrophysics Data System (ADS)

Hasenkopf, C. A.; Flasher, J. C.; Veerman, O.; Scalamogna, A.; Silva, D.; Salmon, M.; Buuralda, D.; DeWitt, L. H.

2016-12-01

Air pollution, responsible for more deaths each year than HIV/AIDS and malaria, combined, is a global public health crisis. Yet many scientific questions, including those directly relevant for policy, remain unanswered when it comes to the impact of air pollution on health in highly polluted environments. Often, specific solutions to improving air quality are local and sustained through public engagement, policy and monitoring. Both the overarching science of air quality and health and local solutions rely on access to reliable, timely air quality data. Over the past year, the OpenAQ community has opened up existing disparate air quality data in 24 countries through an open source platform (openaq.org) so that communities around the world can use it to advance science, public engagement, and policy. We will share stories of communities, from Delhi to Ulaanbaatar and from scientists to journalists, using open air quality data from our platform to advance their fight against air inequality. We will share recent research we have conducted on best practices for engaging different communities and building tools that enable the public to fully unleash the power of open air quality data to fight air inequality. The subsequent open-source tools (github.com/openaq) we have developed from this research and our entire data-sharing platform may be of interest to other open data communities.

Real-time implementation of logo detection on open source BeagleBoard

NASA Astrophysics Data System (ADS)

George, M.; Kehtarnavaz, N.; Estevez, L.

2011-03-01

This paper presents the real-time implementation of our previously developed logo detection and tracking algorithm on the open source BeagleBoard mobile platform. This platform has an OMAP processor that incorporates an ARM Cortex processor. The algorithm combines Scale Invariant Feature Transform (SIFT) with k-means clustering, online color calibration and moment invariants to robustly detect and track logos in video. Various optimization steps that are carried out to allow the real-time execution of the algorithm on BeagleBoard are discussed. The results obtained are compared to the PC real-time implementation results.

Open chemistry registry and mapping platform based on open source cheminformatics toolkits (ACS Fall meeting)

EPA Science Inventory

TheOpen PHACTS project (openphacts.org) is a European initiative, constituting a public–private partnership to enable easier, cheaper and faster drug discovery [1]. The project is supported by the Open PHACTS Foundation (www.openphactsfoundation.org) and funded by contributions f...

OpenHealth Platform for Interactive Contextualization of Population Health Open Data.

PubMed

Almeida, Jonas S; Hajagos, Janos; Crnosija, Ivan; Kurc, Tahsin; Saltz, Mary; Saltz, Joel

The financial incentives for data science applications leading to improved health outcomes, such as DSRIP (bit.ly/dsrip), are well-aligned with the broad adoption of Open Data by State and Federal agencies. This creates entirely novel opportunities for analytical applications that make exclusive use of the pervasive Web Computing platform. The framework described here explores this new avenue to contextualize Health data in a manner that relies exclusively on the native JavaScript interpreter and data processing resources of the ubiquitous Web Browser. The OpenHealth platform is made publicly available, and is publicly hosted with version control and open source, at https://github.com/mathbiol/openHealth. The different data/analytics workflow architectures explored are accompanied with live applications ranging from DSRIP, such as Hospital Inpatient Prevention Quality Indicators at http://bit.ly/pqiSuffolk, to The Cancer Genome Atlas (TCGA) as illustrated by http://bit.ly/tcgascopeGBM.

Psynteract: A flexible, cross-platform, open framework for interactive experiments.

PubMed

Henninger, Felix; Kieslich, Pascal J; Hilbig, Benjamin E

2017-10-01

We introduce a novel platform for interactive studies, that is, any form of study in which participants' experiences depend not only on their own responses, but also on those of other participants who complete the same study in parallel, for example a prisoner's dilemma or an ultimatum game. The software thus especially serves the rapidly growing field of strategic interaction research within psychology and behavioral economics. In contrast to all available software packages, our platform does not handle stimulus display and response collection itself. Instead, we provide a mechanism to extend existing experimental software to incorporate interactive functionality. This approach allows us to draw upon the capabilities already available, such as accuracy of temporal measurement, integration with auxiliary hardware such as eye-trackers or (neuro-)physiological apparatus, and recent advances in experimental software, for example capturing response dynamics through mouse-tracking. Through integration with OpenSesame, an open-source graphical experiment builder, studies can be assembled via a drag-and-drop interface requiring little or no further programming skills. In addition, by using the same communication mechanism across software packages, we also enable interoperability between systems. Our source code, which provides support for all major operating systems and several popular experimental packages, can be freely used and distributed under an open source license. The communication protocols underlying its functionality are also well documented and easily adapted to further platforms. Code and documentation are available at https://github.com/psynteract/ .

Open-WiSe: a solar powered wireless sensor network platform.

PubMed

González, Apolinar; Aquino, Raúl; Mata, Walter; Ochoa, Alberto; Saldaña, Pedro; Edwards, Arthur

2012-01-01

Because battery-powered nodes are required in wireless sensor networks and energy consumption represents an important design consideration, alternate energy sources are needed to provide more effective and optimal function. The main goal of this work is to present an energy harvesting wireless sensor network platform, the Open Wireless Sensor node (WiSe). The design and implementation of the solar powered wireless platform is described including the hardware architecture, firmware, and a POSIX Real-Time Kernel. A sleep and wake up strategy was implemented to prolong the lifetime of the wireless sensor network. This platform was developed as a tool for researchers investigating Wireless sensor network or system integrators.

OSIRIX: open source multimodality image navigation software

NASA Astrophysics Data System (ADS)

Rosset, Antoine; Pysher, Lance; Spadola, Luca; Ratib, Osman

2005-04-01

The goal of our project is to develop a completely new software platform that will allow users to efficiently and conveniently navigate through large sets of multidimensional data without the need of high-end expensive hardware or software. We also elected to develop our system on new open source software libraries allowing other institutions and developers to contribute to this project. OsiriX is a free and open-source imaging software designed manipulate and visualize large sets of medical images: http://homepage.mac.com/rossetantoine/osirix/

Open Ephys: an open-source, plugin-based platform for multichannel electrophysiology.

PubMed

Siegle, Joshua H; López, Aarón Cuevas; Patel, Yogi A; Abramov, Kirill; Ohayon, Shay; Voigts, Jakob

2017-08-01

Closed-loop experiments, in which causal interventions are conditioned on the state of the system under investigation, have become increasingly common in neuroscience. Such experiments can have a high degree of explanatory power, but they require a precise implementation that can be difficult to replicate across laboratories. We sought to overcome this limitation by building open-source software that makes it easier to develop and share algorithms for closed-loop control. We created the Open Ephys GUI, an open-source platform for multichannel electrophysiology experiments. In addition to the standard 'open-loop' visualization and recording functionality, the GUI also includes modules for delivering feedback in response to events detected in the incoming data stream. Importantly, these modules can be built and shared as plugins, which makes it possible for users to extend the functionality of the GUI through a simple API, without having to understand the inner workings of the entire application. In combination with low-cost, open-source hardware for amplifying and digitizing neural signals, the GUI has been used for closed-loop experiments that perturb the hippocampal theta rhythm in a phase-specific manner. The Open Ephys GUI is the first widely used application for multichannel electrophysiology that leverages a plugin-based workflow. We hope that it will lower the barrier to entry for electrophysiologists who wish to incorporate real-time feedback into their research.

Open Ephys: an open-source, plugin-based platform for multichannel electrophysiology

NASA Astrophysics Data System (ADS)

Siegle, Joshua H.; Cuevas López, Aarón; Patel, Yogi A.; Abramov, Kirill; Ohayon, Shay; Voigts, Jakob

2017-08-01

Objective. Closed-loop experiments, in which causal interventions are conditioned on the state of the system under investigation, have become increasingly common in neuroscience. Such experiments can have a high degree of explanatory power, but they require a precise implementation that can be difficult to replicate across laboratories. We sought to overcome this limitation by building open-source software that makes it easier to develop and share algorithms for closed-loop control. Approach. We created the Open Ephys GUI, an open-source platform for multichannel electrophysiology experiments. In addition to the standard ‘open-loop’ visualization and recording functionality, the GUI also includes modules for delivering feedback in response to events detected in the incoming data stream. Importantly, these modules can be built and shared as plugins, which makes it possible for users to extend the functionality of the GUI through a simple API, without having to understand the inner workings of the entire application. Main results. In combination with low-cost, open-source hardware for amplifying and digitizing neural signals, the GUI has been used for closed-loop experiments that perturb the hippocampal theta rhythm in a phase-specific manner. Significance. The Open Ephys GUI is the first widely used application for multichannel electrophysiology that leverages a plugin-based workflow. We hope that it will lower the barrier to entry for electrophysiologists who wish to incorporate real-time feedback into their research.

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.

Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools.

PubMed

Ham, Timothy S; Dmytriv, Zinovii; Plahar, Hector; Chen, Joanna; Hillson, Nathan J; Keasling, Jay D

2012-10-01

The Joint BioEnergy Institute Inventory of Composable Elements (JBEI-ICEs) is an open source registry platform for managing information about biological parts. It is capable of recording information about 'legacy' parts, such as plasmids, microbial host strains and Arabidopsis seeds, as well as DNA parts in various assembly standards. ICE is built on the idea of a web of registries and thus provides strong support for distributed interconnected use. The information deposited in an ICE installation instance is accessible both via a web browser and through the web application programming interfaces, which allows automated access to parts via third-party programs. JBEI-ICE includes several useful web browser-based graphical applications for sequence annotation, manipulation and analysis that are also open source. As with open source software, users are encouraged to install, use and customize JBEI-ICE and its components for their particular purposes. As a web application programming interface, ICE provides well-developed parts storage functionality for other synthetic biology software projects. A public instance is available at public-registry.jbei.org, where users can try out features, upload parts or simply use it for their projects. The ICE software suite is available via Google Code, a hosting site for community-driven open source projects.

OpenAQ: A Platform to Aggregate and Freely Share Global Air Quality Data

NASA Astrophysics Data System (ADS)

Hasenkopf, C. A.; Flasher, J. C.; Veerman, O.; DeWitt, H. L.

2015-12-01

Thousands of ground-based air quality monitors around the world publicly publish real-time air quality data; however, researchers and the public do not have access to this information in the ways most useful to them. Often, air quality data are posted on obscure websites showing only current values, are programmatically inaccessible, and/or are in inconsistent data formats across sites. Yet, historical and programmatic access to such a global dataset would be transformative to several scientific fields, from epidemiology to low-cost sensor technologies to estimates of ground-level aerosol by satellite retrievals. To increase accessibility and standardize this disparate dataset, we have built OpenAQ, an innovative, open platform created by a group of scientists and open data programmers. The source code for the platform is viewable at github.com/openaq. Currently, we are aggregating, storing, and making publicly available real-time air quality data (PM2.5, PM10, SO2, NO2, and O3) via an Application Program Interface (API). We will present the OpenAQ platform, which currently has the following specific capabilities: A continuous ingest mechanism for some of the most polluted cities, generalizable to more sources An API providing data-querying, including ability to filter by location, measurement type and value and date, as well as custom sort options A generalized, chart-based visualization tool to explore data accessible via the API At this stage, we are seeking wider participation and input from multiple research communities in expanding our data retrieval sites, standardizing our protocols, receiving feedback on quality issues, and creating tools that can be built on top of this open platform.

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

Apte, A; Veeraraghavan, H; Oh, J

Purpose: To present an open source and free platform to facilitate radiomics research — The “Radiomics toolbox” in CERR. Method: There is scarcity of open source tools that support end-to-end modeling of image features to predict patient outcomes. The “Radiomics toolbox” strives to fill the need for such a software platform. The platform supports (1) import of various kinds of image modalities like CT, PET, MR, SPECT, US. (2) Contouring tools to delineate structures of interest. (3) Extraction and storage of image based features like 1st order statistics, gray-scale co-occurrence and zonesize matrix based texture features and shape features andmore » (4) Statistical Analysis. Statistical analysis of the extracted features is supported with basic functionality that includes univariate correlations, Kaplan-Meir curves and advanced functionality that includes feature reduction and multivariate modeling. The graphical user interface and the data management are performed with Matlab for the ease of development and readability of code and features for wide audience. Open-source software developed with other programming languages is integrated to enhance various components of this toolbox. For example: Java-based DCM4CHE for import of DICOM, R for statistical analysis. Results: The Radiomics toolbox will be distributed as an open source, GNU copyrighted software. The toolbox was prototyped for modeling Oropharyngeal PET dataset at MSKCC. The analysis will be presented in a separate paper. Conclusion: The Radiomics Toolbox provides an extensible platform for extracting and modeling image features. To emphasize new uses of CERR for radiomics and image-based research, we have changed the name from the “Computational Environment for Radiotherapy Research” to the “Computational Environment for Radiological Research”.« less

Open Targets: a platform for therapeutic target identification and validation

PubMed Central

Koscielny, Gautier; An, Peter; Carvalho-Silva, Denise; Cham, Jennifer A.; Fumis, Luca; Gasparyan, Rippa; Hasan, Samiul; Karamanis, Nikiforos; Maguire, Michael; Papa, Eliseo; Pierleoni, Andrea; Pignatelli, Miguel; Platt, Theo; Rowland, Francis; Wankar, Priyanka; Bento, A. Patrícia; Burdett, Tony; Fabregat, Antonio; Forbes, Simon; Gaulton, Anna; Gonzalez, Cristina Yenyxe; Hermjakob, Henning; Hersey, Anne; Jupe, Steven; Kafkas, Şenay; Keays, Maria; Leroy, Catherine; Lopez, Francisco-Javier; Magarinos, Maria Paula; Malone, James; McEntyre, Johanna; Munoz-Pomer Fuentes, Alfonso; O'Donovan, Claire; Papatheodorou, Irene; Parkinson, Helen; Palka, Barbara; Paschall, Justin; Petryszak, Robert; Pratanwanich, Naruemon; Sarntivijal, Sirarat; Saunders, Gary; Sidiropoulos, Konstantinos; Smith, Thomas; Sondka, Zbyslaw; Stegle, Oliver; Tang, Y. Amy; Turner, Edward; Vaughan, Brendan; Vrousgou, Olga; Watkins, Xavier; Martin, Maria-Jesus; Sanseau, Philippe; Vamathevan, Jessica; Birney, Ewan; Barrett, Jeffrey; Dunham, Ian

2017-01-01

We have designed and developed a data integration and visualization platform that provides evidence about the association of known and potential drug targets with diseases. The platform is designed to support identification and prioritization of biological targets for follow-up. Each drug target is linked to a disease using integrated genome-wide data from a broad range of data sources. The platform provides either a target-centric workflow to identify diseases that may be associated with a specific target, or a disease-centric workflow to identify targets that may be associated with a specific disease. Users can easily transition between these target- and disease-centric workflows. The Open Targets Validation Platform is accessible at https://www.targetvalidation.org. PMID:27899665

OpenCFU, a new free and open-source software to count cell colonies and other circular objects.

PubMed

Geissmann, Quentin

2013-01-01

Counting circular objects such as cell colonies is an important source of information for biologists. Although this task is often time-consuming and subjective, it is still predominantly performed manually. The aim of the present work is to provide a new tool to enumerate circular objects from digital pictures and video streams. Here, I demonstrate that the created program, OpenCFU, is very robust, accurate and fast. In addition, it provides control over the processing parameters and is implemented in an intuitive and modern interface. OpenCFU is a cross-platform and open-source software freely available at http://opencfu.sourceforge.net.

Development and validation of an open source quantification tool for DSC-MRI studies.

PubMed

Gordaliza, P M; Mateos-Pérez, J M; Montesinos, P; Guzmán-de-Villoria, J A; Desco, M; Vaquero, J J

2015-03-01

This work presents the development of an open source tool for the quantification of dynamic susceptibility-weighted contrast-enhanced (DSC) perfusion studies. The development of this tool is motivated by the lack of open source tools implemented on open platforms to allow external developers to implement their own quantification methods easily and without the need of paying for a development license. This quantification tool was developed as a plugin for the ImageJ image analysis platform using the Java programming language. A modular approach was used in the implementation of the components, in such a way that the addition of new methods can be done without breaking any of the existing functionalities. For the validation process, images from seven patients with brain tumors were acquired and quantified with the presented tool and with a widely used clinical software package. The resulting perfusion parameters were then compared. Perfusion parameters and the corresponding parametric images were obtained. When no gamma-fitting is used, an excellent agreement with the tool used as a gold-standard was obtained (R(2)>0.8 and values are within 95% CI limits in Bland-Altman plots). An open source tool that performs quantification of perfusion studies using magnetic resonance imaging has been developed and validated using a clinical software package. It works as an ImageJ plugin and the source code has been published with an open source license. Copyright © 2015 Elsevier Ltd. All rights reserved.

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

Peffer, Therese; Blumstein, Carl; Culler, David

The Project uses state-of-the-art computer science to extend the benefits of Building Automation Systems (BAS) typically found in large buildings (>100,000 square foot) to medium-sized commercial buildings (<50,000 sq ft). The BAS developed in this project, termed OpenBAS, uses an open-source and open software architecture platform, user interface, and plug-and-play control devices to facilitate adoption of energy efficiency strategies in the commercial building sector throughout the United States. At the heart of this “turn key” BAS is the platform with three types of controllers—thermostat, lighting controller, and general controller—that are easily “discovered” by the platform in a plug-and-play fashion. Themore » user interface showcases the platform and provides the control system set-up, system status display and means of automatically mapping the control points in the system.« less

Open-WiSe: A Solar Powered Wireless Sensor Network Platform

PubMed Central

González, Apolinar; Aquino, Raúl; Mata, Walter; Ochoa, Alberto; Saldaña, Pedro; Edwards, Arthur

2012-01-01

Because battery-powered nodes are required in wireless sensor networks and energy consumption represents an important design consideration, alternate energy sources are needed to provide more effective and optimal function. The main goal of this work is to present an energy harvesting wireless sensor network platform, the Open Wireless Sensor node (WiSe). The design and implementation of the solar powered wireless platform is described including the hardware architecture, firmware, and a POSIX Real-Time Kernel. A sleep and wake up strategy was implemented to prolong the lifetime of the wireless sensor network. This platform was developed as a tool for researchers investigating Wireless sensor network or system integrators. PMID:22969396

The Role of Semantics in Open-World, Integrative, Collaborative Science Data Platforms

NASA Astrophysics Data System (ADS)

Fox, Peter; Chen, Yanning; Wang, Han; West, Patrick; Erickson, John; Ma, Marshall

2014-05-01

As collaborative science spreads into more and more Earth and space science fields, both participants and funders are expressing stronger needs for highly functional data and information capabilities. Characteristics include a) easy to use, b) highly integrated, c) leverage investments, d) accommodate rapid technical change, and e) do not incur undue expense or time to build or maintain - these are not a small set of requirements. Based on our accumulated experience over the last ~ decade and several key technical approaches, we adapt, extend, and integrate several open source applications and frameworks to handle major portions of functionality for these platforms. This includes: an object-type repository, collaboration tools, identity management, all within a portal managing diverse content and applications. In this contribution, we present our methods and results of information models, adaptation, integration and evolution of a networked data science architecture based on several open source technologies (Drupal, VIVO, the Comprehensive Knowledge Archive Network; CKAN, and the Global Handle System; GHS). In particular we present the Deep Carbon Observatory - a platform for international science collaboration. We present and discuss key functional and non-functional attributes, and discuss the general applicability of the platform.

OpenDrop: An Integrated Do-It-Yourself Platform for Personal Use of Biochips

PubMed Central

Alistar, Mirela; Gaudenz, Urs

2017-01-01

Biochips, or digital labs-on-chip, are developed with the purpose of being used by laboratory technicians or biologists in laboratories or clinics. In this article, we expand this vision with the goal of enabling everyone, regardless of their expertise, to use biochips for their own personal purposes. We developed OpenDrop, an integrated electromicrofluidic platform that allows users to develop and program their own bio-applications. We address the main challenges that users may encounter: accessibility, bio-protocol design and interaction with microfluidics. OpenDrop consists of a do-it-yourself biochip, an automated software tool with visual interface and a detailed technique for at-home operations of microfluidics. We report on two years of use of OpenDrop, released as an open-source platform. Our platform attracted a highly diverse user base with participants originating from maker communities, academia and industry. Our findings show that 47% of attempts to replicate OpenDrop were successful, the main challenge remaining the assembly of the device. In terms of usability, the users managed to operate their platforms at home and are working on designing their own bio-applications. Our work provides a step towards a future in which everyone will be able to create microfluidic devices for their personal applications, thereby democratizing parts of health care. PMID:28952524

tranSMART: An Open Source and Community-Driven Informatics and Data Sharing Platform for Clinical and Translational Research.

PubMed

Athey, Brian D; Braxenthaler, Michael; Haas, Magali; Guo, Yike

2013-01-01

tranSMART is an emerging global open source public private partnership community developing a comprehensive informatics-based analysis and data-sharing cloud platform for clinical and translational research. The tranSMART consortium includes pharmaceutical and other companies, not-for-profits, academic entities, patient advocacy groups, and government stakeholders. The tranSMART value proposition relies on the concept that the global community of users, developers, and stakeholders are the best source of innovation for applications and for useful data. Continued development and use of the tranSMART platform will create a means to enable "pre-competitive" data sharing broadly, saving money and, potentially accelerating research translation to cures. Significant transformative effects of tranSMART includes 1) allowing for all its user community to benefit from experts globally, 2) capturing the best of innovation in analytic tools, 3) a growing 'big data' resource, 4) convergent standards, and 5) new informatics-enabled translational science in the pharma, academic, and not-for-profit sectors.

Bioclipse: an open source workbench for chemo- and bioinformatics.

PubMed

Spjuth, Ola; Helmus, Tobias; Willighagen, Egon L; Kuhn, Stefan; Eklund, Martin; Wagener, Johannes; Murray-Rust, Peter; Steinbeck, Christoph; Wikberg, Jarl E S

2007-02-22

There is a need for software applications that provide users with a complete and extensible toolkit for chemo- and bioinformatics accessible from a single workbench. Commercial packages are expensive and closed source, hence they do not allow end users to modify algorithms and add custom functionality. Existing open source projects are more focused on providing a framework for integrating existing, separately installed bioinformatics packages, rather than providing user-friendly interfaces. No open source chemoinformatics workbench has previously been published, and no successful attempts have been made to integrate chemo- and bioinformatics into a single framework. Bioclipse is an advanced workbench for resources in chemo- and bioinformatics, such as molecules, proteins, sequences, spectra, and scripts. It provides 2D-editing, 3D-visualization, file format conversion, calculation of chemical properties, and much more; all fully integrated into a user-friendly desktop application. Editing supports standard functions such as cut and paste, drag and drop, and undo/redo. Bioclipse is written in Java and based on the Eclipse Rich Client Platform with a state-of-the-art plugin architecture. This gives Bioclipse an advantage over other systems as it can easily be extended with functionality in any desired direction. Bioclipse is a powerful workbench for bio- and chemoinformatics as well as an advanced integration platform. The rich functionality, intuitive user interface, and powerful plugin architecture make Bioclipse the most advanced and user-friendly open source workbench for chemo- and bioinformatics. Bioclipse is released under Eclipse Public License (EPL), an open source license which sets no constraints on external plugin licensing; it is totally open for both open source plugins as well as commercial ones. Bioclipse is freely available at http://www.bioclipse.net.

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.

OpenICE medical device interoperability platform overview and requirement analysis.

PubMed

Arney, David; Plourde, Jeffrey; Goldman, Julian M

2018-02-23

We give an overview of OpenICE, an open source implementation of the ASTM standard F2761 for the Integrated Clinical Environment (ICE) that leverages medical device interoperability, together with an analysis of the clinical and non-functional requirements and community process that inspired its design.

The SCEC Broadband Platform: A Collaborative Open-Source Software Package for Strong Ground Motion Simulation and Validation

NASA Astrophysics Data System (ADS)

Silva, F.; Maechling, P. J.; Goulet, C. A.; Somerville, P.; Jordan, T. H.

2014-12-01

The Southern California Earthquake Center (SCEC) Broadband Platform is a collaborative software development project involving geoscientists, earthquake engineers, graduate students, and the SCEC Community Modeling Environment. The SCEC Broadband Platform (BBP) is open-source scientific software that can generate broadband (0-100Hz) ground motions for earthquakes, integrating complex scientific modules that implement rupture generation, low and high-frequency seismogram synthesis, non-linear site effects calculation, and visualization into a software system that supports easy on-demand computation of seismograms. The Broadband Platform operates in two primary modes: validation simulations and scenario simulations. In validation mode, the Platform runs earthquake rupture and wave propagation modeling software to calculate seismograms for a well-observed historical earthquake. Then, the BBP calculates a number of goodness of fit measurements that quantify how well the model-based broadband seismograms match the observed seismograms for a certain event. Based on these results, the Platform can be used to tune and validate different numerical modeling techniques. In scenario mode, the Broadband Platform can run simulations for hypothetical (scenario) earthquakes. In this mode, users input an earthquake description, a list of station names and locations, and a 1D velocity model for their region of interest, and the Broadband Platform software then calculates ground motions for the specified stations. Working in close collaboration with scientists and research engineers, the SCEC software development group continues to add new capabilities to the Broadband Platform and to release new versions as open-source scientific software distributions that can be compiled and run on many Linux computer systems. Our latest release includes 5 simulation methods, 7 simulation regions covering California, Japan, and Eastern North America, the ability to compare simulation results against GMPEs, and several new data products, such as map and distance-based goodness of fit plots. As the number and complexity of scenarios simulated using the Broadband Platform increases, we have added batching utilities to substantially improve support for running large-scale simulations on computing clusters.

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.

Sensing Slow Mobility and Interesting Locations for Lombardy Region (italy): a Case Study Using Pointwise Geolocated Open Data

NASA Astrophysics Data System (ADS)

Brovelli, M. A.; Oxoli, D.; Zurbarán, M. A.

2016-06-01

During the past years Web 2.0 technologies have caused the emergence of platforms where users can share data related to their activities which in some cases are then publicly released with open licenses. Popular categories for this include community platforms where users can upload GPS tracks collected during slow travel activities (e.g. hiking, biking and horse riding) and platforms where users share their geolocated photos. However, due to the high heterogeneity of the information available on the Web, the sole use of these user-generated contents makes it an ambitious challenge to understand slow mobility flows as well as to detect the most visited locations in a region. Exploiting the available data on community sharing websites allows to collect near real-time open data streams and enables rigorous spatial-temporal analysis. This work presents an approach for collecting, unifying and analysing pointwise geolocated open data available from different sources with the aim of identifying the main locations and destinations of slow mobility activities. For this purpose, we collected pointwise open data from the Wikiloc platform, Twitter, Flickr and Foursquare. The analysis was confined to the data uploaded in Lombardy Region (Northern Italy) - corresponding to millions of pointwise data. Collected data was processed through the use of Free and Open Source Software (FOSS) in order to organize them into a suitable database. This allowed to run statistical analyses on data distribution in both time and space by enabling the detection of users' slow mobility preferences as well as places of interest at a regional scale.

Developing and Benchmarking Native Linux Applications on Android

NASA Astrophysics Data System (ADS)

Batyuk, Leonid; Schmidt, Aubrey-Derrick; Schmidt, Hans-Gunther; Camtepe, Ahmet; Albayrak, Sahin

Smartphones get increasingly popular where more and more smartphone platforms emerge. Special attention was gained by the open source platform Android which was presented by the Open Handset Alliance (OHA) hosting members like Google, Motorola, and HTC. Android uses a Linux kernel and a stripped-down userland with a custom Java VM set on top. The resulting system joins the advantages of both environments, while third-parties are intended to develop only Java applications at the moment.

OpenCFU, a New Free and Open-Source Software to Count Cell Colonies and Other Circular Objects

PubMed Central

Geissmann, Quentin

2013-01-01

Counting circular objects such as cell colonies is an important source of information for biologists. Although this task is often time-consuming and subjective, it is still predominantly performed manually. The aim of the present work is to provide a new tool to enumerate circular objects from digital pictures and video streams. Here, I demonstrate that the created program, OpenCFU, is very robust, accurate and fast. In addition, it provides control over the processing parameters and is implemented in an intuitive and modern interface. OpenCFU is a cross-platform and open-source software freely available at http://opencfu.sourceforge.net. PMID:23457446

Crowd Sourcing for Challenging Technical Problems and Business Model

NASA Technical Reports Server (NTRS)

Davis, Jeffrey R.; Richard, Elizabeth

2011-01-01

Crowd sourcing may be defined as the act of outsourcing tasks that are traditionally performed by an employee or contractor to an undefined, generally large group of people or community (a crowd) in the form of an open call. The open call may be issued by an organization wishing to find a solution to a particular problem or complete a task, or by an open innovation service provider on behalf of that organization. In 2008, the Space Life Sciences Directorate (SLSD), with the support of Wyle Integrated Science and Engineering, established and implemented pilot projects in open innovation (crowd sourcing) to determine if these new internet-based platforms could indeed find solutions to difficult technical challenges. These unsolved technical problems were converted to problem statements, also called "Challenges" or "Technical Needs" by the various open innovation service providers, and were then posted externally to seek solutions. In addition, an open call was issued internally to NASA employees Agency wide (10 Field Centers and NASA HQ) using an open innovation service provider crowd sourcing platform to post NASA challenges from each Center for the others to propose solutions). From 2008 to 2010, the SLSD issued 34 challenges, 14 externally and 20 internally. The 14 external problems or challenges were posted through three different vendors: InnoCentive, Yet2.com and TopCoder. The 20 internal challenges were conducted using the InnoCentive crowd sourcing platform designed for internal use by an organization. This platform was customized for NASA use and promoted as NASA@Work. The results were significant. Of the seven InnoCentive external challenges, two full and five partial awards were made in complex technical areas such as predicting solar flares and long-duration food packaging. Similarly, the TopCoder challenge yielded an optimization algorithm for designing a lunar medical kit. The Yet2.com challenges yielded many new industry and academic contacts in bone imaging, microbial detection and even the use of pharmaceuticals for radiation protection. The internal challenges through NASA@Work drew over 6000 participants across all NASA centers. Challenges conducted by each NASA center elicited ideas and solutions from several other NASA centers and demonstrated rapid and efficient participation from employees at multiple centers to contribute to problem solving. Finally, on January 19, 2011, the SLSD conducted a workshop on open collaboration and innovation strategies and best practices through the newly established NASA Human Health and Performance Center (NHHPC). Initial projects will be described leading to a new business model for SLSD.

Plenario: An Open Data Discovery and Exploration Platform for Urban Science

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

Catlett, Charlie; Malik, Tanu; Goldstein, Brett J.

2014-12-01

The past decade has seen the widespread release of open data concerning city services, conditions, and activities by government bodies and public institutions of all sizes. Hundreds of open data portals now host thousands of datasets of many different types. These new data sources represent enormous po- tential for improved understanding of urban dynamics and processes—and, ultimately, for more livable, efficient, and prosperous communities. However, those who seek to realize this potential quickly discover that discovering and applying those data relevant to any particular question can be extraordinarily dif- ficult, due to decentralized storage, heterogeneous formats, and poor documentation. Inmore » this context, we introduce Plenario, a platform designed to automating time-consuming tasks associated with the discovery, exploration, and application of open city data—and, in so doing, reduce barriers to data use for researchers, policymakers, service providers, journalists, and members of the general public. Key innovations include a geospatial data warehouse that allows data from many sources to be registered into a common spatial and temporal frame; simple and intuitive interfaces that permit rapid discovery and exploration of data subsets pertaining to a particular area and time, regardless of type and source; easy export of such data subsets for further analysis; a user-configurable data ingest framework for automated importing and periodic updating of new datasets into the data warehouse; cloud hosting for elastic scaling and rapid creation of new Plenario instances; and an open source implementation to enable community contributions. We describe here the architecture and implementation of the Plenario platform, discuss lessons learned from its use by several communities, and outline plans for future work.« less

Open source Modeling and optimization tools for Planning

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

Peles, S.

Open source modeling and optimization tools for planning The existing tools and software used for planning and analysis in California are either expensive, difficult to use, or not generally accessible to a large number of participants. These limitations restrict the availability of participants for larger scale energy and grid studies in the state. The proposed initiative would build upon federal and state investments in open source software, and create and improve open source tools for use in the state planning and analysis activities. Computational analysis and simulation frameworks in development at national labs and universities can be brought forward tomore » complement existing tools. An open source platform would provide a path for novel techniques and strategies to be brought into the larger community and reviewed by a broad set of stakeholders.« less

Incomplete Intelligence: Is the Information Sharing Environment an Effective Platform?

DTIC Science & Technology

2012-09-01

Initiative NYFD New York Fire Department NYPD New York Police Department OLAP On Line Analytics Processing OSINT Open Source Intelligence...Intelligence ( OSINT ), from public websites, media sources, and other unclassified events and reports. Although some of these sources do not have a direct

Towards Networked Knowledge: The Learning Registry, an Infrastructure for Sharing Online Learning Resources

ERIC Educational Resources Information Center

Lee, Ashley; Hobson, Joe; Bienkowski, Marie; Midgley, Steve; Currier, Sarah; Campbell, Lorna M.; Novoselova, Tatiana

2012-01-01

In this article, the authors describe an open-source, open-data digital infrastructure for sharing information about open educational resources (OERs) across disparate systems and platforms. The Learning Registry, which began as a project funded by the U.S. Departments of Education and Defense, currently has an active international community…

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.

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.

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;

MRMer, an interactive open source and cross-platform system for data extraction and visualization of multiple reaction monitoring experiments.

PubMed

Martin, Daniel B; Holzman, Ted; May, Damon; Peterson, Amelia; Eastham, Ashley; Eng, Jimmy; McIntosh, Martin

2008-11-01

Multiple reaction monitoring (MRM) mass spectrometry identifies and quantifies specific peptides in a complex mixture with very high sensitivity and speed and thus has promise for the high throughput screening of clinical samples for candidate biomarkers. We have developed an interactive software platform, called MRMer, for managing highly complex MRM-MS experiments, including quantitative analyses using heavy/light isotopic peptide pairs. MRMer parses and extracts information from MS files encoded in the platform-independent mzXML data format. It extracts and infers precursor-product ion transition pairings, computes integrated ion intensities, and permits rapid visual curation for analyses exceeding 1000 precursor-product pairs. Results can be easily output for quantitative comparison of consecutive runs. Additionally MRMer incorporates features that permit the quantitative analysis experiments including heavy and light isotopic peptide pairs. MRMer is open source and provided under the Apache 2.0 license.

Efficient Comparison between Windows and Linux Platform Applicable in a Virtual Architectural Walkthrough Application

NASA Astrophysics Data System (ADS)

Thubaasini, P.; Rusnida, R.; Rohani, S. M.

This paper describes Linux, an open source platform used to develop and run a virtual architectural walkthrough application. It proposes some qualitative reflections and observations on the nature of Linux in the concept of Virtual Reality (VR) and on the most popular and important claims associated with the open source approach. The ultimate goal of this paper is to measure and evaluate the performance of Linux used to build the virtual architectural walkthrough and develop a proof of concept based on the result obtain through this project. Besides that, this study reveals the benefits of using Linux in the field of virtual reality and reflects a basic comparison and evaluation between Windows and Linux base operating system. Windows platform is use as a baseline to evaluate the performance of Linux. The performance of Linux is measured based on three main criteria which is frame rate, image quality and also mouse motion.

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.

Increasing Flight Software Reuse with OpenSatKit

NASA Technical Reports Server (NTRS)

McComas, David C.

2018-01-01

In January 2015 the NASA Goddard Space Flight Center (GSFC) released the Core Flight System (cFS) as open source under the NASA Open Source Agreement (NOSA) license. The cFS is based on flight software (FSW) developed for 12 spacecraft spanning nearly two decades of effort and it can provide about a third of the FSW functionality for a low-earth orbiting scientific spacecraft. The cFS is a FSW framework that is portable, configurable, and extendable using a product line deployment model. However, the components are maintained separately so the user must configure, integrate, and deploy them as a cohesive functional system. This can be very challenging especially for organizations such as universities building cubesats that have minimal experience developing FSW. Supporting universities was one of the primary motivators for releasing the cFS under NOSA. This paper describes the OpenSatKit that was developed to address the cFS deployment challenges and to serve as a cFS training platform for new users. It provides a fully functional out-of-the box software system that includes NASA's cFS, Ball Aerospace's command and control system COSMOS, and a NASA dynamic simulator called 42. The kit is freely available since all of the components have been released as open source. The kit runs on a Linux platform, includes 8 cFS applications, several kit-specific applications, and built in demos illustrating how to use key application features. It also includes the software necessary to port the cFS to a Raspberry Pi and instructions for configuring COSMOS to communicate with the target. All of the demos and test scripts can be rerun unchanged with the cFS running on the Raspberry Pi. The cFS uses a 3-tiered layered architecture including a platform abstraction layer, a Core Flight Executive (cFE) middle layer, and an application layer. Similar to smart phones, the cFS application layer is the key architectural feature for users to extend the FSW functionality to meet their mission-specific requirements. The platform abstraction layer and the cFE layers go a step further than smart phones by providing a platform-agnostic Application Programmer Interface (API) that allows applications to run unchanged on different platforms. OpenSatKit can serve two significant architectural roles that will further help the adoption of the cFS and help create a community of users that can share assets. First, the kit is being enhanced to automate the integration of applications with the goal of creating a virtual cFS "App Store".. Second, a platform certification test suite can be developed that would allow users to verify the port of the cFS to a new platform. This paper will describe the current state of these efforts and future plans.

Biomechanical ToolKit: Open-source framework to visualize and process biomechanical data.

PubMed

Barre, Arnaud; Armand, Stéphane

2014-04-01

C3D file format is widely used in the biomechanical field by companies and laboratories to store motion capture systems data. However, few software packages can visualize and modify the integrality of the data in the C3D file. Our objective was to develop an open-source and multi-platform framework to read, write, modify and visualize data from any motion analysis systems using standard (C3D) and proprietary file formats (used by many companies producing motion capture systems). The Biomechanical ToolKit (BTK) was developed to provide cost-effective and efficient tools for the biomechanical community to easily deal with motion analysis data. A large panel of operations is available to read, modify and process data through C++ API, bindings for high-level languages (Matlab, Octave, and Python), and standalone application (Mokka). All these tools are open-source and cross-platform and run on all major operating systems (Windows, Linux, MacOS X). Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Crux: Rapid Open Source Protein Tandem Mass Spectrometry Analysis

PubMed Central

2015-01-01

Efficiently and accurately analyzing big protein tandem mass spectrometry data sets requires robust software that incorporates state-of-the-art computational, machine learning, and statistical methods. The Crux mass spectrometry analysis software toolkit (http://cruxtoolkit.sourceforge.net) is an open source project that aims to provide users with a cross-platform suite of analysis tools for interpreting protein mass spectrometry data. PMID:25182276

T-Check in Technologies for Interoperability: Web Services and Security--Single Sign-On

DTIC Science & Technology

2007-12-01

following tools: • Apache Tomcat 6.0—a Java Servlet container to host the Web services and a simple Web client application [Apache 2007a] • Apache Axis...Eclipse. Eclipse – an open development platform. http://www.eclipse.org/ (2007) [Hunter 2001] Hunter, Jason. Java Servlet Programming, 2nd Edition...Citation SAML 1.1 Java Toolkit SAML Ping Identity’s SAML-1.1 implementation [SourceID 2006] OpenSAML SAML An open source implementation of SAML 1.1

The successes and challenges of open-source biopharmaceutical innovation.

PubMed

Allarakhia, Minna

2014-05-01

Increasingly, open-source-based alliances seek to provide broad access to data, research-based tools, preclinical samples and downstream compounds. The challenge is how to create value from open-source biopharmaceutical innovation. This value creation may occur via transparency and usage of data across the biopharmaceutical value chain as stakeholders move dynamically between open source and open innovation. In this article, several examples are used to trace the evolution of biopharmaceutical open-source initiatives. The article specifically discusses the technological challenges associated with the integration and standardization of big data; the human capacity development challenges associated with skill development around big data usage; and the data-material access challenge associated with data and material access and usage rights, particularly as the boundary between open source and open innovation becomes more fluid. It is the author's opinion that the assessment of when and how value creation will occur, through open-source biopharmaceutical innovation, is paramount. The key is to determine the metrics of value creation and the necessary technological, educational and legal frameworks to support the downstream outcomes of now big data-based open-source initiatives. The continued focus on the early-stage value creation is not advisable. Instead, it would be more advisable to adopt an approach where stakeholders transform open-source initiatives into open-source discovery, crowdsourcing and open product development partnerships on the same platform.

Implementation and performance test of cloud platform based on Hadoop

NASA Astrophysics Data System (ADS)

Xu, Jingxian; Guo, Jianhong; Ren, Chunlan

2018-01-01

Hadoop, as an open source project for the Apache foundation, is a distributed computing framework that deals with large amounts of data and has been widely used in the Internet industry. Therefore, it is meaningful to study the implementation of Hadoop platform and the performance of test platform. The purpose of this subject is to study the method of building Hadoop platform and to study the performance of test platform. This paper presents a method to implement Hadoop platform and a test platform performance method. Experimental results show that the proposed test performance method is effective and it can detect the performance of Hadoop platform.

A multi-purpose open-source triggering platform for magnetic resonance

NASA Astrophysics Data System (ADS)

Ruytenberg, T.; Webb, A. G.; Beenakker, J. W. M.

2014-10-01

Many MR scans need to be synchronised with external events such as the cardiac or respiratory cycles. For common physiological functions commercial trigger equipment exists, but for more experimental inputs these are not available. This paper describes the design of a multi-purpose open-source trigger platform for MR systems. The heart of the system is an open-source Arduino Due microcontroller. This microcontroller samples an analogue input and digitally processes these data to determine the trigger. The output of the microcontroller is programmed to mimic a physiological signal which is fed into the electrocardiogram (ECG) or pulse oximeter port of MR scanner. The microcontroller is connected to a Bluetooth dongle that allows wireless monitoring and control outside the scanner room. This device can be programmed to generate a trigger based on various types of input. As one example, this paper describes how it can be used as an acoustic cardiac triggering unit. For this, a plastic stethoscope is connected to a microphone which is used as an input for the system. This test setup was used to acquire retrospectively-triggered cardiac scans in ten volunteers. Analysis showed that this platform produces a reliable trigger (>99% triggers are correct) with a small average 8 ms variation between the exact trigger points.

A multi-purpose open-source triggering platform for magnetic resonance.

PubMed

Ruytenberg, T; Webb, A G; Beenakker, J W M

2014-10-01

Many MR scans need to be synchronised with external events such as the cardiac or respiratory cycles. For common physiological functions commercial trigger equipment exists, but for more experimental inputs these are not available. This paper describes the design of a multi-purpose open-source trigger platform for MR systems. The heart of the system is an open-source Arduino Due microcontroller. This microcontroller samples an analogue input and digitally processes these data to determine the trigger. The output of the microcontroller is programmed to mimic a physiological signal which is fed into the electrocardiogram (ECG) or pulse oximeter port of MR scanner. The microcontroller is connected to a Bluetooth dongle that allows wireless monitoring and control outside the scanner room. This device can be programmed to generate a trigger based on various types of input. As one example, this paper describes how it can be used as an acoustic cardiac triggering unit. For this, a plastic stethoscope is connected to a microphone which is used as an input for the system. This test setup was used to acquire retrospectively-triggered cardiac scans in ten volunteers. Analysis showed that this platform produces a reliable trigger (>99% triggers are correct) with a small average 8 ms variation between the exact trigger points. Copyright © 2014 Elsevier Inc. All rights reserved.

Jenkins-CI, an Open-Source Continuous Integration System, as a Scientific Data and Image-Processing Platform.

PubMed

Moutsatsos, Ioannis K; Hossain, Imtiaz; Agarinis, Claudia; Harbinski, Fred; Abraham, Yann; Dobler, Luc; Zhang, Xian; Wilson, Christopher J; Jenkins, Jeremy L; Holway, Nicholas; Tallarico, John; Parker, Christian N

2017-03-01

High-throughput screening generates large volumes of heterogeneous data that require a diverse set of computational tools for management, processing, and analysis. Building integrated, scalable, and robust computational workflows for such applications is challenging but highly valuable. Scientific data integration and pipelining facilitate standardized data processing, collaboration, and reuse of best practices. We describe how Jenkins-CI, an "off-the-shelf," open-source, continuous integration system, is used to build pipelines for processing images and associated data from high-content screening (HCS). Jenkins-CI provides numerous plugins for standard compute tasks, and its design allows the quick integration of external scientific applications. Using Jenkins-CI, we integrated CellProfiler, an open-source image-processing platform, with various HCS utilities and a high-performance Linux cluster. The platform is web-accessible, facilitates access and sharing of high-performance compute resources, and automates previously cumbersome data and image-processing tasks. Imaging pipelines developed using the desktop CellProfiler client can be managed and shared through a centralized Jenkins-CI repository. Pipelines and managed data are annotated to facilitate collaboration and reuse. Limitations with Jenkins-CI (primarily around the user interface) were addressed through the selection of helper plugins from the Jenkins-CI community.

Jenkins-CI, an Open-Source Continuous Integration System, as a Scientific Data and Image-Processing Platform

PubMed Central

Moutsatsos, Ioannis K.; Hossain, Imtiaz; Agarinis, Claudia; Harbinski, Fred; Abraham, Yann; Dobler, Luc; Zhang, Xian; Wilson, Christopher J.; Jenkins, Jeremy L.; Holway, Nicholas; Tallarico, John; Parker, Christian N.

2016-01-01

High-throughput screening generates large volumes of heterogeneous data that require a diverse set of computational tools for management, processing, and analysis. Building integrated, scalable, and robust computational workflows for such applications is challenging but highly valuable. Scientific data integration and pipelining facilitate standardized data processing, collaboration, and reuse of best practices. We describe how Jenkins-CI, an “off-the-shelf,” open-source, continuous integration system, is used to build pipelines for processing images and associated data from high-content screening (HCS). Jenkins-CI provides numerous plugins for standard compute tasks, and its design allows the quick integration of external scientific applications. Using Jenkins-CI, we integrated CellProfiler, an open-source image-processing platform, with various HCS utilities and a high-performance Linux cluster. The platform is web-accessible, facilitates access and sharing of high-performance compute resources, and automates previously cumbersome data and image-processing tasks. Imaging pipelines developed using the desktop CellProfiler client can be managed and shared through a centralized Jenkins-CI repository. Pipelines and managed data are annotated to facilitate collaboration and reuse. Limitations with Jenkins-CI (primarily around the user interface) were addressed through the selection of helper plugins from the Jenkins-CI community. PMID:27899692

The Prodiguer Messaging Platform

NASA Astrophysics Data System (ADS)

Greenslade, Mark; Denvil, Sebastien; Raciazek, Jerome; Carenton, Nicolas; Levavasseur, Guillame

2014-05-01

CONVERGENCE is a French multi-partner national project designed to gather HPC and informatics expertise to innovate in the context of running French climate models with differing grids and at differing resolutions. Efficient and reliable execution of these models and the management and dissemination of model output (data and meta-data) are just some of the complexities that CONVERGENCE aims to resolve. The Institut Pierre Simon Laplace (IPSL) is responsible for running climate simulations upon a set of heterogenous HPC environments within France. With heterogeneity comes added complexity in terms of simulation instrumentation and control. Obtaining a global perspective upon the state of all simulations running upon all HPC environments has hitherto been problematic. In this presentation we detail how, within the context of CONVERGENCE, the implementation of the Prodiguer messaging platform resolves complexity and permits the development of real-time applications such as: 1. a simulation monitoring dashboard; 2. a simulation metrics visualizer; 3. an automated simulation runtime notifier; 4. an automated output data & meta-data publishing pipeline; The Prodiguer messaging platform leverages a widely used open source message broker software called RabbitMQ. RabbitMQ itself implements the Advanced Message Queue Protocol (AMPQ). Hence it will be demonstrated that the Prodiguer messaging platform is built upon both open source and open standards.

Applying open source data visualization tools to standard based medical data.

PubMed

Kopanitsa, Georgy; Taranik, Maxim

2014-01-01

Presentation of medical data in personal health records (PHRs) requires flexible platform independent tools to ensure easy access to the information. Different backgrounds of the patients, especially elder people require simple graphical presentation of the data. Data in PHRs can be collected from heterogeneous sources. Application of standard based medical data allows development of generic visualization methods. Focusing on the deployment of Open Source Tools, in this paper we applied Java Script libraries to create data presentations for standard based medical data.

Performance Assessment of Network Intrusion-Alert Prediction

DTIC Science & Technology

2012-09-01

the threats. In this thesis, we use Snort to generate the intrusion detection alerts. 2. SNORT Snort is an open source network intrusion...standard for IPS. (Snort, 2012) We choose Snort because it is an open source product that is free to download and can be deployed cross-platform...Learning & prediction in relational time series: A survey. 21st Behavior Representation in Modeling & Simulation ( BRIMS ) Conference 2012, 93–100. Tan

The digital code driven autonomous synthesis of ibuprofen automated in a 3D-printer-based robot.

PubMed

Kitson, Philip J; Glatzel, Stefan; Cronin, Leroy

2016-01-01

An automated synthesis robot was constructed by modifying an open source 3D printing platform. The resulting automated system was used to 3D print reaction vessels (reactionware) of differing internal volumes using polypropylene feedstock via a fused deposition modeling 3D printing approach and subsequently make use of these fabricated vessels to synthesize the nonsteroidal anti-inflammatory drug ibuprofen via a consecutive one-pot three-step approach. The synthesis of ibuprofen could be achieved on different scales simply by adjusting the parameters in the robot control software. The software for controlling the synthesis robot was written in the python programming language and hard-coded for the synthesis of ibuprofen by the method described, opening possibilities for the sharing of validated synthetic 'programs' which can run on similar low cost, user-constructed robotic platforms towards an 'open-source' regime in the area of chemical synthesis.

What Can OpenEI Do For You?

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

None

2010-12-10

Open Energy Information (OpenEI) is an open source web platform—similar to the one used by Wikipedia—developed by the US Department of Energy (DOE) and the National Renewable Energy Laboratory (NREL) to make the large amounts of energy-related data and information more easily searched, accessed, and used both by people and automated machine processes. Built utilizing the standards and practices of the Linked Open Data community, the OpenEI platform is much more robust and powerful than typical web sites and databases. As an open platform, all users can search, edit, add, and access data in OpenEI for free. The user communitymore » contributes the content and ensures its accuracy and relevance; as the community expands, so does the content's comprehensiveness and quality. The data are structured and tagged with descriptors to enable cross-linking among related data sets, advanced search functionality, and consistent, usable formatting. Data input protocols and quality standards help ensure the content is structured and described properly and derived from a credible source. Although DOE/NREL is developing OpenEI and seeding it with initial data, it is designed to become a true community model with millions of users, a large core of active contributors, and numerous sponsors.« less

Tatool: a Java-based open-source programming framework for psychological studies.

PubMed

von Bastian, Claudia C; Locher, André; Ruflin, Michael

2013-03-01

Tatool (Training and Testing Tool) was developed to assist researchers with programming training software, experiments, and questionnaires. Tatool is Java-based, and thus is a platform-independent and object-oriented framework. The architecture was designed to meet the requirements of experimental designs and provides a large number of predefined functions that are useful in psychological studies. Tatool comprises features crucial for training studies (e.g., configurable training schedules, adaptive training algorithms, and individual training statistics) and allows for running studies online via Java Web Start. The accompanying "Tatool Online" platform provides the possibility to manage studies and participants' data easily with a Web-based interface. Tatool is published open source under the GNU Lesser General Public License, and is available at www.tatool.ch.

The Generation Challenge Programme Platform: Semantic Standards and Workbench for Crop Science

PubMed Central

Bruskiewich, Richard; Senger, Martin; Davenport, Guy; Ruiz, Manuel; Rouard, Mathieu; Hazekamp, Tom; Takeya, Masaru; Doi, Koji; Satoh, Kouji; Costa, Marcos; Simon, Reinhard; Balaji, Jayashree; Akintunde, Akinnola; Mauleon, Ramil; Wanchana, Samart; Shah, Trushar; Anacleto, Mylah; Portugal, Arllet; Ulat, Victor Jun; Thongjuea, Supat; Braak, Kyle; Ritter, Sebastian; Dereeper, Alexis; Skofic, Milko; Rojas, Edwin; Martins, Natalia; Pappas, Georgios; Alamban, Ryan; Almodiel, Roque; Barboza, Lord Hendrix; Detras, Jeffrey; Manansala, Kevin; Mendoza, Michael Jonathan; Morales, Jeffrey; Peralta, Barry; Valerio, Rowena; Zhang, Yi; Gregorio, Sergio; Hermocilla, Joseph; Echavez, Michael; Yap, Jan Michael; Farmer, Andrew; Schiltz, Gary; Lee, Jennifer; Casstevens, Terry; Jaiswal, Pankaj; Meintjes, Ayton; Wilkinson, Mark; Good, Benjamin; Wagner, James; Morris, Jane; Marshall, David; Collins, Anthony; Kikuchi, Shoshi; Metz, Thomas; McLaren, Graham; van Hintum, Theo

2008-01-01

The Generation Challenge programme (GCP) is a global crop research consortium directed toward crop improvement through the application of comparative biology and genetic resources characterization to plant breeding. A key consortium research activity is the development of a GCP crop bioinformatics platform to support GCP research. This platform includes the following: (i) shared, public platform-independent domain models, ontology, and data formats to enable interoperability of data and analysis flows within the platform; (ii) web service and registry technologies to identify, share, and integrate information across diverse, globally dispersed data sources, as well as to access high-performance computational (HPC) facilities for computationally intensive, high-throughput analyses of project data; (iii) platform-specific middleware reference implementations of the domain model integrating a suite of public (largely open-access/-source) databases and software tools into a workbench to facilitate biodiversity analysis, comparative analysis of crop genomic data, and plant breeding decision making. PMID:18483570

Managing multicentre clinical trials with open source.

PubMed

Raptis, Dimitri Aristotle; Mettler, Tobias; Fischer, Michael Alexander; Patak, Michael; Lesurtel, Mickael; Eshmuminov, Dilmurodjon; de Rougemont, Olivier; Graf, Rolf; Clavien, Pierre-Alain; Breitenstein, Stefan

2014-03-01

Multicentre clinical trials are challenged by high administrative burden, data management pitfalls and costs. This leads to a reduced enthusiasm and commitment of the physicians involved and thus to a reluctance in conducting multicentre clinical trials. The purpose of this study was to develop a web-based open source platform to support a multi-centre clinical trial. We developed on Drupal, an open source software distributed under the terms of the General Public License, a web-based, multi-centre clinical trial management system with the design science research approach. This system was evaluated by user-testing and well supported several completed and on-going clinical trials and is available for free download. Open source clinical trial management systems are capable in supporting multi-centre clinical trials by enhancing efficiency, quality of data management and collaboration.

Development of an Open Source, Air-Deployable Weather Station

NASA Astrophysics Data System (ADS)

Krejci, A.; Lopez Alcala, J. M.; Nelke, M.; Wagner, J.; Udell, C.; Higgins, C. W.; Selker, J. S.

2017-12-01

We created a packaged weather station intended to be deployed in the air on tethered systems. The device incorporates lightweight sensors and parts and runs for up to 24 hours off of lithium polymer batteries, allowing the entire package to be supported by a thin fiber. As the fiber does not provide a stable platform, additional data (pitch and roll) from typical weather parameters (e.g. temperature, pressure, humidity, wind speed, and wind direction) are determined using an embedded inertial motion unit. All designs are open sourced including electronics, CAD drawings, and descriptions of assembly and can be found on the OPEnS lab website at http://www.open-sensing.org/lowcost-weather-station/. The Openly Published Environmental Sensing Lab (OPEnS: Open-Sensing.org) expands the possibilities of scientific observation of our Earth, transforming the technology, methods, and culture by combining open-source development and cutting-edge technology. New OPEnS labs are now being established in India, France, Switzerland, the Netherlands, and Ghana.

Breaking Away

ERIC Educational Resources Information Center

Panettieri, Joseph C.

2007-01-01

This article discusses open source projects which may free universities from expensive, rigid commercial software. But will the rewards outweigh the potential risks? The Kuali Project involves multiple universities writing and sharing code for their financial and operational systems. Another, the Sakai Project, is a community source platform for…

Plenario: A Spatio-Temporal Platform for Discovery and Exploration of Urban Science Data

NASA Astrophysics Data System (ADS)

Engler, W. H.; Malik, T.; Catlett, C.; Foster, I.; Goldstein, B.

2015-12-01

The past decade has seen the widespread release of open data concerning city services, conditions, and activities by government bodies and public institutions of all sizes. Hundreds of open data portals now host thousands of datasets of many different types. These new data sources represent enormous potential for improved understanding of urban dynamics and processes—and, ultimately, for more livable, efficient, and prosperous communities. However, those who seek to realize this potential quickly discover that discovering and applying those data relevant to any particular question can be extraordinarily difficult, due to decentralized storage, heterogeneous formats, and poor documentation. In this context, we introduce Plenario, a platform designed to automating time-consuming tasks associated with the discovery, exploration, and application of open city data—and, in so doing, reduce barriers to data use for researchers, policymakers, service providers, journalists, and members of the general public. Key innovations include a geospatial data warehouse that allows data from many sources to be registered into a common spatial and temporal frame; simple and intuitive interfaces that permit rapid discovery and exploration of data subsets pertaining to a particular area and time, regardless of type and source; easy export of such data subsets for further analysis; a user-configurable data ingest framework for automated importing and periodic updating of new datasets into the data warehouse; cloud hosting for elastic scaling and rapid creation of new Plenario instances; and an open source implementation to enable community contributions. We describe here the architecture and implementation of the Plenario platform, discuss lessons learned from its use by several communities, and outline plans for future work.

PaaS for web applications with OpenShift Origin

NASA Astrophysics Data System (ADS)

Lossent, A.; Rodriguez Peon, A.; Wagner, A.

2017-10-01

The CERN Web Frameworks team has deployed OpenShift Origin to facilitate deployment of web applications and to improving efficiency in terms of computing resource usage. OpenShift leverages Docker containers and Kubernetes orchestration to provide a Platform-as-a-service solution oriented for web applications. We will review use cases and how OpenShift was integrated with other services such as source control, web site management and authentication services.

Development of a software for quantitative evaluation radiotherapy target and organ-at-risk segmentation comparison.

PubMed

Kalpathy-Cramer, Jayashree; Awan, Musaddiq; Bedrick, Steven; Rasch, Coen R N; Rosenthal, David I; Fuller, Clifton D

2014-02-01

Modern radiotherapy requires accurate region of interest (ROI) inputs for plan optimization and delivery. Target delineation, however, remains operator-dependent and potentially serves as a major source of treatment delivery error. In order to optimize this critical, yet observer-driven process, a flexible web-based platform for individual and cooperative target delineation analysis and instruction was developed in order to meet the following unmet needs: (1) an open-source/open-access platform for automated/semiautomated quantitative interobserver and intraobserver ROI analysis and comparison, (2) a real-time interface for radiation oncology trainee online self-education in ROI definition, and (3) a source for pilot data to develop and validate quality metrics for institutional and cooperative group quality assurance efforts. The resultant software, Target Contour Testing/Instructional Computer Software (TaCTICS), developed using Ruby on Rails, has since been implemented and proven flexible, feasible, and useful in several distinct analytical and research applications.

Increasing Flight Software Reuse with OpenSatKit

NASA Technical Reports Server (NTRS)

McComas, David

2018-01-01

In January 2015 the NASA Goddard Space Flight Center (GSFC) released the Core Flight System (cFS) as open source under the NASA Open Source Agreement (NOSA) license. The cFS is based on flight software (FSW) developed for 12 spacecraft spanning nearly two decades of effort and it can provide about a third of the FSW functionality for a low-earth orbiting scientific spacecraft. The cFS is a FSW framework that is portable, configurable, and extendable using a product line deployment model. However, the components are maintained separately so the user must configure, integrate, and deploy them as a cohesive functional system. This can be very challenging especially for organizations such as universities building cubesats that have minimal experience developing FSW. Supporting universities was one of the primary motivators for releasing the cFS under NOSA. This paper describes the OpenSatKit that was developed to address the cFS deployment challenges and to serve as a cFS training platform for new users. It provides a fully functional out-of-the box software system that includes NASA's cFS, Ball Aerospaceâ€"TM"s command and control system COSMOS, and a NASA dynamic simulator called 42. The kit is freely available since all of the components have been released as open source. The kit runs on a Linux platform, includes 8 cFS applications, several kit-specific applications, and built in demos illustrating how to use key application features. It also includes the software necessary to port the cFS to a Raspberry Pi and instructions for configuring COSMOS to communicate with the target. All of the demos and test scripts can be rerun unchanged with the cFS running on the Raspberry Pi. The cFS uses a 3-tiered layered architecture including a platform abstraction layer, a Core Flight Executive (cFE) middle layer, and an application layer. Similar to smart phones, the cFS application layer is the key architectural feature for userâ€"TM"s to extend the FSW functionality to meet their mission-specific requirements. The platform abstraction layer and the cFE layers go a step further than smart phones by providing a platform-agnostic Application Programmer Interface (API) that allows applications to run unchanged on different platforms. OpenSatKit can serve two significant architectural roles that will further help the adoption of the cFS and help create a community of users that can share assets. First, the kit is being enhanced to automate the integration of applications with the goal of creating a virtual cFS 'App Store'. Second, a platform certification test suite can be developed that would allow users to verify the port of the cFS to a new platform. This paper will describe the current state of these efforts and future plans.

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.

78 FR 45565 - Notice Pursuant to the National Cooperative Research and Production Act of 1993 -- tranSMART...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-29

... activities are to enable effective sharing, integration, standardization, and analysis of heterogeneous data from collaborative translational research by mobilizing the tranSMART open- source and open-data...: (a) Establish and sustain tranSMART as the preferred data sharing and analytics platform for...

Web Platform for Sharing Modeling Software in the Field of Nonlinear Optics

NASA Astrophysics Data System (ADS)

Dubenskaya, Julia; Kryukov, Alexander; Demichev, Andrey

2018-02-01

We describe the prototype of a Web platform intended for sharing software programs for computer modeling in the rapidly developing field of the nonlinear optics phenomena. The suggested platform is built on the top of the HUBZero open-source middleware. In addition to the basic HUBZero installation we added to our platform the capability to run Docker containers via an external application server and to send calculation programs to those containers for execution. The presented web platform provides a wide range of features and might be of benefit to nonlinear optics researchers.

RADIOMICS.io | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

RADIOMICS.io is a open source platform for informatics developments for radiographic phenotyping using automated algorithms, such as engineered features or using deep learning technologies. With this platform, we aim to establish a reference standard for radiomic analyses, provide a tested and maintained resource, and to grow the community of radiomic developers addressing critical needs in cancer research.

WaveformECG: A Platform for Visualizing, Annotating, and Analyzing ECG Data

PubMed Central

Winslow, Raimond L.; Granite, Stephen; Jurado, Christian

2017-01-01

The electrocardiogram (ECG) is the most commonly collected data in cardiovascular research because of the ease with which it can be measured and because changes in ECG waveforms reflect underlying aspects of heart disease. Accessed through a browser, WaveformECG is an open source platform supporting interactive analysis, visualization, and annotation of ECGs. PMID:28642673

ACQ4: an open-source software platform for data acquisition and analysis in neurophysiology research.

PubMed

Campagnola, Luke; Kratz, Megan B; Manis, Paul B

2014-01-01

The complexity of modern neurophysiology experiments requires specialized software to coordinate multiple acquisition devices and analyze the collected data. We have developed ACQ4, an open-source software platform for performing data acquisition and analysis in experimental neurophysiology. This software integrates the tasks of acquiring, managing, and analyzing experimental data. ACQ4 has been used primarily for standard patch-clamp electrophysiology, laser scanning photostimulation, multiphoton microscopy, intrinsic imaging, and calcium imaging. The system is highly modular, which facilitates the addition of new devices and functionality. The modules included with ACQ4 provide for rapid construction of acquisition protocols, live video display, and customizable analysis tools. Position-aware data collection allows automated construction of image mosaics and registration of images with 3-dimensional anatomical atlases. ACQ4 uses free and open-source tools including Python, NumPy/SciPy for numerical computation, PyQt for the user interface, and PyQtGraph for scientific graphics. Supported hardware includes cameras, patch clamp amplifiers, scanning mirrors, lasers, shutters, Pockels cells, motorized stages, and more. ACQ4 is available for download at http://www.acq4.org.

Pulseq-Graphical Programming Interface: Open source visual environment for prototyping pulse sequences and integrated magnetic resonance imaging algorithm development.

PubMed

Ravi, Keerthi Sravan; Potdar, Sneha; Poojar, Pavan; Reddy, Ashok Kumar; Kroboth, Stefan; Nielsen, Jon-Fredrik; Zaitsev, Maxim; Venkatesan, Ramesh; Geethanath, Sairam

2018-03-11

To provide a single open-source platform for comprehensive MR algorithm development inclusive of simulations, pulse sequence design and deployment, reconstruction, and image analysis. We integrated the "Pulseq" platform for vendor-independent pulse programming with Graphical Programming Interface (GPI), a scientific development environment based on Python. Our integrated platform, Pulseq-GPI, permits sequences to be defined visually and exported to the Pulseq file format for execution on an MR scanner. For comparison, Pulseq files using either MATLAB only ("MATLAB-Pulseq") or Python only ("Python-Pulseq") were generated. We demonstrated three fundamental sequences on a 1.5 T scanner. Execution times of the three variants of implementation were compared on two operating systems. In vitro phantom images indicate equivalence with the vendor supplied implementations and MATLAB-Pulseq. The examples demonstrated in this work illustrate the unifying capability of Pulseq-GPI. The execution times of all the three implementations were fast (a few seconds). The software is capable of user-interface based development and/or command line programming. The tool demonstrated here, Pulseq-GPI, integrates the open-source simulation, reconstruction and analysis capabilities of GPI Lab with the pulse sequence design and deployment features of Pulseq. Current and future work includes providing an ISMRMRD interface and incorporating Specific Absorption Ratio and Peripheral Nerve Stimulation computations. Copyright © 2018 Elsevier Inc. All rights reserved.

Platform for Quantitative Evaluation of Spatial Intratumoral Heterogeneity in Multiplexed Fluorescence Images.

PubMed

Spagnolo, Daniel M; Al-Kofahi, Yousef; Zhu, Peihong; Lezon, Timothy R; Gough, Albert; Stern, Andrew M; Lee, Adrian V; Ginty, Fiona; Sarachan, Brion; Taylor, D Lansing; Chennubhotla, S Chakra

2017-11-01

We introduce THRIVE (Tumor Heterogeneity Research Interactive Visualization Environment), an open-source tool developed to assist cancer researchers in interactive hypothesis testing. The focus of this tool is to quantify spatial intratumoral heterogeneity (ITH), and the interactions between different cell phenotypes and noncellular constituents. Specifically, we foresee applications in phenotyping cells within tumor microenvironments, recognizing tumor boundaries, identifying degrees of immune infiltration and epithelial/stromal separation, and identification of heterotypic signaling networks underlying microdomains. The THRIVE platform provides an integrated workflow for analyzing whole-slide immunofluorescence images and tissue microarrays, including algorithms for segmentation, quantification, and heterogeneity analysis. THRIVE promotes flexible deployment, a maintainable code base using open-source libraries, and an extensible framework for customizing algorithms with ease. THRIVE was designed with highly multiplexed immunofluorescence images in mind, and, by providing a platform to efficiently analyze high-dimensional immunofluorescence signals, we hope to advance these data toward mainstream adoption in cancer research. Cancer Res; 77(21); e71-74. ©2017 AACR . ©2017 American Association for Cancer Research.

radR: an open-source platform for acquiring and analysing data on biological targets observed by surveillance radar.

PubMed

Taylor, Philip D; Brzustowski, John M; Matkovich, Carolyn; Peckford, Michael L; Wilson, Dave

2010-10-26

Radar has been used for decades to study movement of insects, birds and bats. In spite of this, there are few readily available software tools for the acquisition, storage and processing of such data. Program radR was developed to solve this problem. Program radR is an open source software tool for the acquisition, storage and analysis of data from marine radars operating in surveillance mode. radR takes time series data with a two-dimensional spatial component as input from some source (typically a radar digitizing card) and extracts and retains information of biological relevance (i.e. moving targets). Low-level data processing is implemented in "C" code, but user-defined functions written in the "R" statistical programming language can be called at pre-defined steps in the calculations. Output data formats are designed to allow for future inclusion of additional data items without requiring change to C code. Two brands of radar digitizing card are currently supported as data sources. We also provide an overview of the basic considerations of setting up and running a biological radar study. Program radR provides a convenient, open source platform for the acquisition and analysis of radar data of biological targets.

radR: an open-source platform for acquiring and analysing data on biological targets observed by surveillance radar

PubMed Central

2010-01-01

Background Radar has been used for decades to study movement of insects, birds and bats. In spite of this, there are few readily available software tools for the acquisition, storage and processing of such data. Program radR was developed to solve this problem. Results Program radR is an open source software tool for the acquisition, storage and analysis of data from marine radars operating in surveillance mode. radR takes time series data with a two-dimensional spatial component as input from some source (typically a radar digitizing card) and extracts and retains information of biological relevance (i.e. moving targets). Low-level data processing is implemented in "C" code, but user-defined functions written in the "R" statistical programming language can be called at pre-defined steps in the calculations. Output data formats are designed to allow for future inclusion of additional data items without requiring change to C code. Two brands of radar digitizing card are currently supported as data sources. We also provide an overview of the basic considerations of setting up and running a biological radar study. Conclusions Program radR provides a convenient, open source platform for the acquisition and analysis of radar data of biological targets. PMID:20977735

GIS-Based Noise Simulation Open Source Software: N-GNOIS

NASA Astrophysics Data System (ADS)

Vijay, Ritesh; Sharma, A.; Kumar, M.; Shende, V.; Chakrabarti, T.; Gupta, Rajesh

2015-12-01

Geographical information system (GIS)-based noise simulation software (N-GNOIS) has been developed to simulate the noise scenario due to point and mobile sources considering the impact of geographical features and meteorological parameters. These have been addressed in the software through attenuation modules of atmosphere, vegetation and barrier. N-GNOIS is a user friendly, platform-independent and open geospatial consortia (OGC) compliant software. It has been developed using open source technology (QGIS) and open source language (Python). N-GNOIS has unique features like cumulative impact of point and mobile sources, building structure and honking due to traffic. Honking is the most common phenomenon in developing countries and is frequently observed on any type of roads. N-GNOIS also helps in designing physical barrier and vegetation cover to check the propagation of noise and acts as a decision making tool for planning and management of noise component in environmental impact assessment (EIA) studies.

General Mission Analysis Tool (GMAT) Architectural Specification. Draft

NASA Technical Reports Server (NTRS)

Hughes, Steven P.; Conway, Darrel, J.

2007-01-01

Early in 2002, Goddard Space Flight Center (GSFC) began to identify requirements for the flight dynamics software needed to fly upcoming missions that use formations of spacecraft to collect data. These requirements ranged from low level modeling features to large scale interoperability requirements. In 2003 we began work on a system designed to meet these requirement; this system is GMAT. The General Mission Analysis Tool (GMAT) is a general purpose flight dynamics modeling tool built on open source principles. The GMAT code is written in C++, and uses modern C++ constructs extensively. GMAT can be run through either a fully functional Graphical User Interface (GUI) or as a command line program with minimal user feedback. The system is built and runs on Microsoft Windows, Linux, and Macintosh OS X platforms. The GMAT GUI is written using wxWidgets, a cross platform library of components that streamlines the development and extension of the user interface Flight dynamics modeling is performed in GMAT by building components that represent the players in the analysis problem that is being modeled. These components interact through the sequential execution of instructions, embodied in the GMAT Mission Sequence. A typical Mission Sequence will model the trajectories of a set of spacecraft evolving over time, calculating relevant parameters during this propagation, and maneuvering individual spacecraft to maintain a set of mission constraints as established by the mission analyst. All of the elements used in GMAT for mission analysis can be viewed in the GMAT GUI or through a custom scripting language. Analysis problems modeled in GMAT are saved as script files, and these files can be read into GMAT. When a script is read into the GMAT GUI, the corresponding user interface elements are constructed in the GMAT GUI. The GMAT system was developed from the ground up to run in a platform agnostic environment. The source code compiles on numerous different platforms, and is regularly exercised running on Windows, Linux and Macintosh computers by the development and analysis teams working on the project. The system can be run using either a graphical user interface, written using the open source wxWidgets framework, or from a text console. The GMAT source code was written using open source tools. GSFC has released the code using the NASA open source license.

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.

Language Geography from Microblogging Platforms

NASA Astrophysics Data System (ADS)

Mocanu, Delia; Baronchelli, Andrea; Perra, Nicola; Gonçalves, Bruno; Vespignani, Alessandro

2013-03-01

Microblogging platforms have now become major open source indicators for complex social interactions. With the advent of smartphones, the everincreasing mobile Internet traffic gives us the unprecedented opportunity to complement studies of complex social phenomena with real-time location information. In this work, we show that the data nowadays accessible allows for detailed studies at different scales, ranging from country-level aggregate analysis to the analysis of linguistic communities withing specific neighborhoods. The high resolution and coverage of this data permits us to investigate such issues as the linguistic homogeneity of different countries, touristic seasonal patterns within countries, and the geographical distribution of different languages in bilingual regions. This work highlights the potentialities of geolocalized studies of open data sources that can provide an extremely detailed picture of the language geography.

Open-source colorimeter.

PubMed

Anzalone, Gerald C; Glover, Alexandra G; Pearce, Joshua M

2013-04-19

The high cost of what have historically been sophisticated research-related sensors and tools has limited their adoption to a relatively small group of well-funded researchers. This paper provides a methodology for applying an open-source approach to design and development of a colorimeter. A 3-D printable, open-source colorimeter utilizing only open-source hardware and software solutions and readily available discrete components is discussed and its performance compared to a commercial portable colorimeter. Performance is evaluated with commercial vials prepared for the closed reflux chemical oxygen demand (COD) method. This approach reduced the cost of reliable closed reflux COD by two orders of magnitude making it an economic alternative for the vast majority of potential users. The open-source colorimeter demonstrated good reproducibility and serves as a platform for further development and derivation of the design for other, similar purposes such as nephelometry. This approach promises unprecedented access to sophisticated instrumentation based on low-cost sensors by those most in need of it, under-developed and developing world laboratories.

Open-Source Colorimeter

PubMed Central

Anzalone, Gerald C.; Glover, Alexandra G.; Pearce, Joshua M.

2013-01-01

The high cost of what have historically been sophisticated research-related sensors and tools has limited their adoption to a relatively small group of well-funded researchers. This paper provides a methodology for applying an open-source approach to design and development of a colorimeter. A 3-D printable, open-source colorimeter utilizing only open-source hardware and software solutions and readily available discrete components is discussed and its performance compared to a commercial portable colorimeter. Performance is evaluated with commercial vials prepared for the closed reflux chemical oxygen demand (COD) method. This approach reduced the cost of reliable closed reflux COD by two orders of magnitude making it an economic alternative for the vast majority of potential users. The open-source colorimeter demonstrated good reproducibility and serves as a platform for further development and derivation of the design for other, similar purposes such as nephelometry. This approach promises unprecedented access to sophisticated instrumentation based on low-cost sensors by those most in need of it, under-developed and developing world laboratories. PMID:23604032

SPIM-fluid: open source light-sheet based platform for high-throughput imaging

PubMed Central

Gualda, Emilio J.; Pereira, Hugo; Vale, Tiago; Estrada, Marta Falcão; Brito, Catarina; Moreno, Nuno

2015-01-01

Light sheet fluorescence microscopy has recently emerged as the technique of choice for obtaining high quality 3D images of whole organisms/embryos with low photodamage and fast acquisition rates. Here we present an open source unified implementation based on Arduino and Micromanager, which is capable of operating Light Sheet Microscopes for automatized 3D high-throughput imaging on three-dimensional cell cultures and model organisms like zebrafish, oriented to massive drug screening. PMID:26601007

Web-Based Portfolio Assessment: Validation of an Open Source Platform

ERIC Educational Resources Information Center

Collins, Regina; Elliot, Norbert; Klobucar, Andrew; Deek, Fadi P.

2013-01-01

Assessment of educational outcomes through purchased tests is commonplace in the evaluation of individual student ability and of educational programs. Focusing on the assessment of writing performance in a longitudinal study of first-time, full-time students (n = 598), this research describes the design, use, and assessment of an open-source…

Biosignal PI, an Affordable Open-Source ECG and Respiration Measurement System

PubMed Central

Abtahi, Farhad; Snäll, Jonatan; Aslamy, Benjamin; Abtahi, Shirin; Seoane, Fernando; Lindecrantz, Kaj

2015-01-01

Bioimedical pilot projects e.g., telemedicine, homecare, animal and human trials usually involve several physiological measurements. Technical development of these projects is time consuming and in particular costly. A versatile but affordable biosignal measurement platform can help to reduce time and risk while keeping the focus on the important goal and making an efficient use of resources. In this work, an affordable and open source platform for development of physiological signals is proposed. As a first step an 8–12 leads electrocardiogram (ECG) and respiration monitoring system is developed. Chips based on iCoupler technology have been used to achieve electrical isolation as required by IEC 60601 for patient safety. The result shows the potential of this platform as a base for prototyping compact, affordable, and medically safe measurement systems. Further work involves both hardware and software development to develop modules. These modules may require development of front-ends for other biosignals or just collect data wirelessly from different devices e.g., blood pressure, weight, bioimpedance spectrum, blood glucose, e.g., through Bluetooth. All design and development documents, files and source codes will be available for non-commercial use through project website, BiosignalPI.org. PMID:25545268

Macedonian journal of chemistry and chemical engineering: open journal systems--editor's perspective.

PubMed

Zdravkovski, Zoran

2014-01-01

The development and availability of personal computers and software as well as printing techniques in the last twenty years have made a profound change in the publication of scientific journals. Additionally, the Internet in the last decade has revolutionized the publication process to the point of changing the basic paradigm of printed journals. The Macedonian Journal of Chemistry and Chemical Engineering in its 40-year history has adopted and adapted to all these transformations. In order to keep up with the inevitable changes, as editor-in-chief I felt my responsibility was to introduce an electronic editorial managing of the journal. The choice was between commercial and open source platforms, and because of the limited funding of the journal we chose the latter. We decided on Open Journal Systems, which provided online submission and management of all content, had flexible configuration--requirements, sections, review process, etc., had options for comprehensive indexing, offered various reading tools, had email notification and commenting ability for readers, had an option for thesis abstracts and was installed locally. However, since there is limited support it requires a moderate computer knowledge/skills and effort in order to set up. Overall, it is an excellent editorial platform and a convenient solution for journals with a low budget or journals that do not want to spend their resources on commercial platforms or simply support the idea of open source software.

An Extensible Sensing and Control Platform for Building Energy Management

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

Rowe, Anthony; Berges, Mario; Martin, Christopher

2016-04-03

The goal of this project is to develop Mortar.io, an open-source BAS platform designed to simplify data collection, archiving, event scheduling and coordination of cross-system interactions. Mortar.io is optimized for (1) robustness to network outages, (2) ease of installation using plug-and-play and (3) scalable support for small to large buildings and campuses.

The Use of Distance Learning in the Educational Process Content and Structure of Educational Platforms--Analysis of the Platform Educans

ERIC Educational Resources Information Center

Igado, Manuel Fandos

2010-01-01

This work provides some considerations that complements the scarcity of researches this field of knowledge of the e-learning specifically referred to secondary education. Distance training programmes (both open source code and not) are becoming increasingly more popular, especially in higher level education. However, there are very few cases of…

A Real-Time Linux for Multicore Platforms

DTIC Science & Technology

2013-12-20

under ARO support) to obtain a fully-functional OS for supporting real-time workloads on multicore platforms. This system, called LITMUS -RT...to be specified as plugin components. LITMUS -RT is open-source software (available at The views, opinions and/or findings contained in this report... LITMUS -RT (LInux Testbed for MUltiprocessor Scheduling in Real-Time systems), allows different multiprocessor real-time scheduling and

Open-source telemedicine platform for wireless medical video communication.

PubMed

Panayides, A; Eleftheriou, I; Pantziaris, M

2013-01-01

An m-health system for real-time wireless communication of medical video based on open-source software is presented. The objective is to deliver a low-cost telemedicine platform which will allow for reliable remote diagnosis m-health applications such as emergency incidents, mass population screening, and medical education purposes. The performance of the proposed system is demonstrated using five atherosclerotic plaque ultrasound videos. The videos are encoded at the clinically acquired resolution, in addition to lower, QCIF, and CIF resolutions, at different bitrates, and four different encoding structures. Commercially available wireless local area network (WLAN) and 3.5G high-speed packet access (HSPA) wireless channels are used to validate the developed platform. Objective video quality assessment is based on PSNR ratings, following calibration using the variable frame delay (VFD) algorithm that removes temporal mismatch between original and received videos. Clinical evaluation is based on atherosclerotic plaque ultrasound video assessment protocol. Experimental results show that adequate diagnostic quality wireless medical video communications are realized using the designed telemedicine platform. HSPA cellular networks provide for ultrasound video transmission at the acquired resolution, while VFD algorithm utilization bridges objective and subjective ratings.

An Open Source Software and Web-GIS Based Platform for Airborne SAR Remote Sensing Data Management, Distribution and Sharing

NASA Astrophysics Data System (ADS)

Changyong, Dou; Huadong, Guo; Chunming, Han; Ming, Liu

2014-03-01

With more and more Earth observation data available to the community, how to manage and sharing these valuable remote sensing datasets is becoming an urgent issue to be solved. The web based Geographical Information Systems (GIS) technology provides a convenient way for the users in different locations to share and make use of the same dataset. In order to efficiently use the airborne Synthetic Aperture Radar (SAR) remote sensing data acquired in the Airborne Remote Sensing Center of the Institute of Remote Sensing and Digital Earth (RADI), Chinese Academy of Sciences (CAS), a Web-GIS based platform for airborne SAR data management, distribution and sharing was designed and developed. The major features of the system include map based navigation search interface, full resolution imagery shown overlaid the map, and all the software adopted in the platform are Open Source Software (OSS). The functions of the platform include browsing the imagery on the map navigation based interface, ordering and downloading data online, image dataset and user management, etc. At present, the system is under testing in RADI and will come to regular operation soon.

Open-Source Telemedicine Platform for Wireless Medical Video Communication

PubMed Central

Panayides, A.; Eleftheriou, I.; Pantziaris, M.

2013-01-01

An m-health system for real-time wireless communication of medical video based on open-source software is presented. The objective is to deliver a low-cost telemedicine platform which will allow for reliable remote diagnosis m-health applications such as emergency incidents, mass population screening, and medical education purposes. The performance of the proposed system is demonstrated using five atherosclerotic plaque ultrasound videos. The videos are encoded at the clinically acquired resolution, in addition to lower, QCIF, and CIF resolutions, at different bitrates, and four different encoding structures. Commercially available wireless local area network (WLAN) and 3.5G high-speed packet access (HSPA) wireless channels are used to validate the developed platform. Objective video quality assessment is based on PSNR ratings, following calibration using the variable frame delay (VFD) algorithm that removes temporal mismatch between original and received videos. Clinical evaluation is based on atherosclerotic plaque ultrasound video assessment protocol. Experimental results show that adequate diagnostic quality wireless medical video communications are realized using the designed telemedicine platform. HSPA cellular networks provide for ultrasound video transmission at the acquired resolution, while VFD algorithm utilization bridges objective and subjective ratings. PMID:23573082

Open Source Next Generation Visualization Software for Interplanetary Missions

NASA Technical Reports Server (NTRS)

Trimble, Jay; Rinker, George

2016-01-01

Mission control is evolving quickly, driven by the requirements of new missions, and enabled by modern computing capabilities. Distributed operations, access to data anywhere, data visualization for spacecraft analysis that spans multiple data sources, flexible reconfiguration to support multiple missions, and operator use cases, are driving the need for new capabilities. NASA's Advanced Multi-Mission Operations System (AMMOS), Ames Research Center (ARC) and the Jet Propulsion Laboratory (JPL) are collaborating to build a new generation of mission operations software for visualization, to enable mission control anywhere, on the desktop, tablet and phone. The software is built on an open source platform that is open for contributions (http://nasa.github.io/openmct).

Free and open source software for the manipulation of digital images.

PubMed

Solomon, Robert W

2009-06-01

Free and open source software is a type of software that is nearly as powerful as commercial software but is freely downloadable. This software can do almost everything that the expensive programs can. GIMP (gnu image manipulation program) is the free program that is comparable to Photoshop, and versions are available for Windows, Macintosh, and Linux platforms. This article briefly describes how GIMP can be installed and used to manipulate radiology images. It is no longer necessary to budget large amounts of money for high-quality software to achieve the goals of image processing and document creation because free and open source software is available for the user to download at will.

Low Cost and Flexible UAV Deployment of Sensors

PubMed Central

Sørensen, Lars Yndal; Jacobsen, Lars Toft; Hansen, John Paulin

2017-01-01

This paper presents a platform for airborne sensor applications using low-cost, open-source components carried by an easy-to-fly unmanned aircraft vehicle (UAV). The system, available in open-source , is designed for researchers, students and makers for a broad range of exploration and data-collection needs. The main contribution is the extensible architecture for modularized airborne sensor deployment and real-time data visualisation. Our open-source Android application provides data collection, flight path definition and map tools. Total cost of the system is below 800 dollars. The flexibility of the system is illustrated by mapping the location of Bluetooth beacons (iBeacons) on a ground field and by measuring water temperature in a lake. PMID:28098819

Low Cost and Flexible UAV Deployment of Sensors.

PubMed

Sørensen, Lars Yndal; Jacobsen, Lars Toft; Hansen, John Paulin

2017-01-14

This paper presents a platform for airborne sensor applications using low-cost, open-source components carried by an easy-to-fly unmanned aircraft vehicle (UAV). The system, available in open-source , is designed for researchers, students and makers for a broad range of exploration and data-collection needs. The main contribution is the extensible architecture for modularized airborne sensor deployment and real-time data visualisation. Our open-source Android application provides data collection, flight path definition and map tools. Total cost of the system is below 800 dollars. The flexibility of the system is illustrated by mapping the location of Bluetooth beacons (iBeacons) on a ground field and by measuring water temperature in a lake.

Development of an IHE MRRT-compliant open-source web-based reporting platform.

PubMed

Pinto Dos Santos, Daniel; Klos, G; Kloeckner, R; Oberle, R; Dueber, C; Mildenberger, P

2017-01-01

To develop a platform that uses structured reporting templates according to the IHE Management of Radiology Report Templates (MRRT) profile, and to implement this platform into clinical routine. The reporting platform uses standard web technologies (HTML / JavaScript and PHP / MySQL) only. Several freely available external libraries were used to simplify the programming. The platform runs on a standard web server, connects with the radiology information system (RIS) and PACS, and is easily accessible via a standard web browser. A prototype platform that allows structured reporting to be easily incorporated into the clinical routine was developed and successfully tested. To date, 797 reports were generated using IHE MRRT-compliant templates (many of them downloaded from the RSNA's radreport.org website). Reports are stored in a MySQL database and are easily accessible for further analyses. Development of an IHE MRRT-compliant platform for structured reporting is feasible using only standard web technologies. All source code will be made available upon request under a free license, and the participation of other institutions in further development is welcome. • A platform for structured reporting using IHE MRRT-compliant templates is presented. • Incorporating structured reporting into clinical routine is feasible. • Full source code will be provided upon request under a free license.

Technical Communications in OSS Content Management Systems: An Academic Institutional Case Study

ERIC Educational Resources Information Center

Cripps, Michael J.

2011-01-01

Single sourcing through a content management system (CMS) is altering technical communication practices in many organizations, including institutions of higher education. Open source software (OSS) solutions are currently among the most popular content management platforms adopted by colleges and universities in the United States and abroad. The…

Mobile service for open data visualization on geo-based images

NASA Astrophysics Data System (ADS)

Lee, Kiwon; Kim, Kwangseob; Kang, Sanggoo

2015-12-01

Since the early 2010s, governments in most countries have adopted and promoted open data policy and open data platform. Korea are in the same situation, and government and public organizations have operated the public-accessible open data portal systems since 2011. The number of open data and data type have been increasing every year. These trends are more expandable or extensible on mobile environments. The purpose of this study is to design and implement a mobile application service to visualize various typed or formatted public open data with geo-based images on the mobile web. Open data cover downloadable data sets or open-accessible data application programming interface API. Geo-based images mean multi-sensor satellite imageries which are referred in geo-coordinates and matched with digital map sets. System components for mobile service are fully based on open sources and open development environments without any commercialized tools: PostgreSQL for database management system, OTB for remote sensing image processing, GDAL for data conversion, GeoServer for application server, OpenLayers for mobile web mapping, R for data analysis and D3.js for web-based data graphic processing. Mobile application in client side was implemented by using HTML5 for cross browser and cross platform. The result shows many advantageous points such as linking open data and geo-based data, integrating open data and open source, and demonstrating mobile applications with open data. It is expected that this approach is cost effective and process efficient implementation strategy for intelligent earth observing data.

Clinician accessible tools for GUI computational models of transcranial electrical stimulation: BONSAI and SPHERES.

PubMed

Truong, Dennis Q; Hüber, Mathias; Xie, Xihe; Datta, Abhishek; Rahman, Asif; Parra, Lucas C; Dmochowski, Jacek P; Bikson, Marom

2014-01-01

Computational models of brain current flow during transcranial electrical stimulation (tES), including transcranial direct current stimulation (tDCS) and transcranial alternating current stimulation (tACS), are increasingly used to understand and optimize clinical trials. We propose that broad dissemination requires a simple graphical user interface (GUI) software that allows users to explore and design montages in real-time, based on their own clinical/experimental experience and objectives. We introduce two complimentary open-source platforms for this purpose: BONSAI and SPHERES. BONSAI is a web (cloud) based application (available at neuralengr.com/bonsai) that can be accessed through any flash-supported browser interface. SPHERES (available at neuralengr.com/spheres) is a stand-alone GUI application that allow consideration of arbitrary montages on a concentric sphere model by leveraging an analytical solution. These open-source tES modeling platforms are designed go be upgraded and enhanced. Trade-offs between open-access approaches that balance ease of access, speed, and flexibility are discussed. Copyright © 2014 Elsevier Inc. All rights reserved.

Knowledge Discovery for Smart Grid Operation, Control, and Situation Awareness -- A Big Data Visualization Platform

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

Gu, Yi; Jiang, Huaiguang; Zhang, Yingchen

In this paper, a big data visualization platform is designed to discover the hidden useful knowledge for smart grid (SG) operation, control and situation awareness. The spawn of smart sensors at both grid side and customer side can provide large volume of heterogeneous data that collect information in all time spectrums. Extracting useful knowledge from this big-data poll is still challenging. In this paper, the Apache Spark, an open source cluster computing framework, is used to process the big-data to effectively discover the hidden knowledge. A high-speed communication architecture utilizing the Open System Interconnection (OSI) model is designed to transmitmore » the data to a visualization platform. This visualization platform uses Google Earth, a global geographic information system (GIS) to link the geological information with the SG knowledge and visualize the information in user defined fashion. The University of Denver's campus grid is used as a SG test bench and several demonstrations are presented for the proposed platform.« less

pytc: Open-Source Python Software for Global Analyses of Isothermal Titration Calorimetry Data.

PubMed

Duvvuri, Hiranmayi; Wheeler, Lucas C; Harms, Michael J

2018-05-08

Here we describe pytc, an open-source Python package for global fits of thermodynamic models to multiple isothermal titration calorimetry experiments. Key features include simplicity, the ability to implement new thermodynamic models, a robust maximum likelihood fitter, a fast Bayesian Markov-Chain Monte Carlo sampler, rigorous implementation, extensive documentation, and full cross-platform compatibility. pytc fitting can be done using an application program interface or via a graphical user interface. It is available for download at https://github.com/harmslab/pytc .

An open-source java platform for automated reaction mapping.

PubMed

Crabtree, John D; Mehta, Dinesh P; Kouri, Tina M

2010-09-27

This article presents software applications that have been built upon a modular, open-source, reaction mapping library that can be used in both cheminformatics and bioinformatics research. We first describe the theoretical underpinnings and modular architecture of the core software library. We then describe two applications that have been built upon that core. The first is a generic reaction viewer and mapper, and the second classifies reactions according to rules that can be modified by end users with little or no programming skills.

Analyzing huge pathology images with open source software.

PubMed

Deroulers, Christophe; Ameisen, David; Badoual, Mathilde; Gerin, Chloé; Granier, Alexandre; Lartaud, Marc

2013-06-06

Digital pathology images are increasingly used both for diagnosis and research, because slide scanners are nowadays broadly available and because the quantitative study of these images yields new insights in systems biology. However, such virtual slides build up a technical challenge since the images occupy often several gigabytes and cannot be fully opened in a computer's memory. Moreover, there is no standard format. Therefore, most common open source tools such as ImageJ fail at treating them, and the others require expensive hardware while still being prohibitively slow. We have developed several cross-platform open source software tools to overcome these limitations. The NDPITools provide a way to transform microscopy images initially in the loosely supported NDPI format into one or several standard TIFF files, and to create mosaics (division of huge images into small ones, with or without overlap) in various TIFF and JPEG formats. They can be driven through ImageJ plugins. The LargeTIFFTools achieve similar functionality for huge TIFF images which do not fit into RAM. We test the performance of these tools on several digital slides and compare them, when applicable, to standard software. A statistical study of the cells in a tissue sample from an oligodendroglioma was performed on an average laptop computer to demonstrate the efficiency of the tools. Our open source software enables dealing with huge images with standard software on average computers. They are cross-platform, independent of proprietary libraries and very modular, allowing them to be used in other open source projects. They have excellent performance in terms of execution speed and RAM requirements. They open promising perspectives both to the clinician who wants to study a single slide and to the research team or data centre who do image analysis of many slides on a computer cluster. The virtual slide(s) for this article can be found here:http://www.diagnosticpathology.diagnomx.eu/vs/5955513929846272.

Analyzing huge pathology images with open source software

PubMed Central

2013-01-01

Background Digital pathology images are increasingly used both for diagnosis and research, because slide scanners are nowadays broadly available and because the quantitative study of these images yields new insights in systems biology. However, such virtual slides build up a technical challenge since the images occupy often several gigabytes and cannot be fully opened in a computer’s memory. Moreover, there is no standard format. Therefore, most common open source tools such as ImageJ fail at treating them, and the others require expensive hardware while still being prohibitively slow. Results We have developed several cross-platform open source software tools to overcome these limitations. The NDPITools provide a way to transform microscopy images initially in the loosely supported NDPI format into one or several standard TIFF files, and to create mosaics (division of huge images into small ones, with or without overlap) in various TIFF and JPEG formats. They can be driven through ImageJ plugins. The LargeTIFFTools achieve similar functionality for huge TIFF images which do not fit into RAM. We test the performance of these tools on several digital slides and compare them, when applicable, to standard software. A statistical study of the cells in a tissue sample from an oligodendroglioma was performed on an average laptop computer to demonstrate the efficiency of the tools. Conclusions Our open source software enables dealing with huge images with standard software on average computers. They are cross-platform, independent of proprietary libraries and very modular, allowing them to be used in other open source projects. They have excellent performance in terms of execution speed and RAM requirements. They open promising perspectives both to the clinician who wants to study a single slide and to the research team or data centre who do image analysis of many slides on a computer cluster. Virtual slides The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/5955513929846272 PMID:23829479

OPAL: An Open-Source MPI-IO Library over Cray XT

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

Yu, Weikuan; Vetter, Jeffrey S; Canon, Richard Shane

Parallel IO over Cray XT is supported by a vendor-supplied MPI-IO package. This package contains a proprietary ADIO implementation built on top of the sysio library. While it is reasonable to maintain a stable code base for application scientists' convenience, it is also very important to the system developers and researchers to analyze and assess the effectiveness of parallel IO software, and accordingly, tune and optimize the MPI-IO implementation. A proprietary parallel IO code base relinquishes such flexibilities. On the other hand, a generic UFS-based MPI-IO implementation is typically used on many Linux-based platforms. We have developed an open-source MPI-IOmore » package over Lustre, referred to as OPAL (OPportunistic and Adaptive MPI-IO Library over Lustre). OPAL provides a single source-code base for MPI-IO over Lustre on Cray XT and Linux platforms. Compared to Cray implementation, OPAL provides a number of good features, including arbitrary specification of striping patterns and Lustre-stripe aligned file domain partitioning. This paper presents the performance comparisons between OPAL and Cray's proprietary implementation. Our evaluation demonstrates that OPAL achieves the performance comparable to the Cray implementation. We also exemplify the benefits of an open source package in revealing the underpinning of the parallel IO performance.« less

DStat: A Versatile, Open-Source Potentiostat for Electroanalysis and Integration.

PubMed

Dryden, Michael D M; Wheeler, Aaron R

2015-01-01

Most electroanalytical techniques require the precise control of the potentials in an electrochemical cell using a potentiostat. Commercial potentiostats function as "black boxes," giving limited information about their circuitry and behaviour which can make development of new measurement techniques and integration with other instruments challenging. Recently, a number of lab-built potentiostats have emerged with various design goals including low manufacturing cost and field-portability, but notably lacking is an accessible potentiostat designed for general lab use, focusing on measurement quality combined with ease of use and versatility. To fill this gap, we introduce DStat (http://microfluidics.utoronto.ca/dstat), an open-source, general-purpose potentiostat for use alone or integrated with other instruments. DStat offers picoampere current measurement capabilities, a compact USB-powered design, and user-friendly cross-platform software. DStat is easy and inexpensive to build, may be modified freely, and achieves good performance at low current levels not accessible to other lab-built instruments. In head-to-head tests, DStat's voltammetric measurements are much more sensitive than those of "CheapStat" (a popular open-source potentiostat described previously), and are comparable to those of a compact commercial "black box" potentiostat. Likewise, in head-to-head tests, DStat's potentiometric precision is similar to that of a commercial pH meter. Most importantly, the versatility of DStat was demonstrated through integration with the open-source DropBot digital microfluidics platform. In sum, we propose that DStat is a valuable contribution to the "open source" movement in analytical science, which is allowing users to adapt their tools to their experiments rather than alter their experiments to be compatible with their tools.

AZOrange - High performance open source machine learning for QSAR modeling in a graphical programming environment

PubMed Central

2011-01-01

Background Machine learning has a vast range of applications. In particular, advanced machine learning methods are routinely and increasingly used in quantitative structure activity relationship (QSAR) modeling. QSAR data sets often encompass tens of thousands of compounds and the size of proprietary, as well as public data sets, is rapidly growing. Hence, there is a demand for computationally efficient machine learning algorithms, easily available to researchers without extensive machine learning knowledge. In granting the scientific principles of transparency and reproducibility, Open Source solutions are increasingly acknowledged by regulatory authorities. Thus, an Open Source state-of-the-art high performance machine learning platform, interfacing multiple, customized machine learning algorithms for both graphical programming and scripting, to be used for large scale development of QSAR models of regulatory quality, is of great value to the QSAR community. Results This paper describes the implementation of the Open Source machine learning package AZOrange. AZOrange is specially developed to support batch generation of QSAR models in providing the full work flow of QSAR modeling, from descriptor calculation to automated model building, validation and selection. The automated work flow relies upon the customization of the machine learning algorithms and a generalized, automated model hyper-parameter selection process. Several high performance machine learning algorithms are interfaced for efficient data set specific selection of the statistical method, promoting model accuracy. Using the high performance machine learning algorithms of AZOrange does not require programming knowledge as flexible applications can be created, not only at a scripting level, but also in a graphical programming environment. Conclusions AZOrange is a step towards meeting the needs for an Open Source high performance machine learning platform, supporting the efficient development of highly accurate QSAR models fulfilling regulatory requirements. PMID:21798025

AZOrange - High performance open source machine learning for QSAR modeling in a graphical programming environment.

PubMed

Stålring, Jonna C; Carlsson, Lars A; Almeida, Pedro; Boyer, Scott

2011-07-28

Machine learning has a vast range of applications. In particular, advanced machine learning methods are routinely and increasingly used in quantitative structure activity relationship (QSAR) modeling. QSAR data sets often encompass tens of thousands of compounds and the size of proprietary, as well as public data sets, is rapidly growing. Hence, there is a demand for computationally efficient machine learning algorithms, easily available to researchers without extensive machine learning knowledge. In granting the scientific principles of transparency and reproducibility, Open Source solutions are increasingly acknowledged by regulatory authorities. Thus, an Open Source state-of-the-art high performance machine learning platform, interfacing multiple, customized machine learning algorithms for both graphical programming and scripting, to be used for large scale development of QSAR models of regulatory quality, is of great value to the QSAR community. This paper describes the implementation of the Open Source machine learning package AZOrange. AZOrange is specially developed to support batch generation of QSAR models in providing the full work flow of QSAR modeling, from descriptor calculation to automated model building, validation and selection. The automated work flow relies upon the customization of the machine learning algorithms and a generalized, automated model hyper-parameter selection process. Several high performance machine learning algorithms are interfaced for efficient data set specific selection of the statistical method, promoting model accuracy. Using the high performance machine learning algorithms of AZOrange does not require programming knowledge as flexible applications can be created, not only at a scripting level, but also in a graphical programming environment. AZOrange is a step towards meeting the needs for an Open Source high performance machine learning platform, supporting the efficient development of highly accurate QSAR models fulfilling regulatory requirements.

A Far Cry from School History: Massive Online Open Courses as a Generative Source for Historical Research

ERIC Educational Resources Information Center

Gallagher, Silvia; Wallace, Ciaran

2016-01-01

Current research into Massive Online Open Courses (MOOCs) has neglected the potential of using learner comments for discipline-specific analysis. This article explores how MOOCs, within the historical discipline, can be used to generate, investigate, and document personal narratives, and argues that they serve as a rich platform for historical…

Tools to Analyze Morphology and Spatially Mapped Molecular Data | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

This project is to develop, deploy, and disseminate a suite of open source tools and integrated informatics platform that will facilitate multi-scale, correlative analyses of high resolution whole slide tissue image data, spatially mapped genetics and molecular data for cancer research. This platform will play an essential role in supporting studies of tumor initiation, development, heterogeneity, invasion, and metastasis.

SmartR: an open-source platform for interactive visual analytics for translational research data

PubMed Central

Herzinger, Sascha; Gu, Wei; Satagopam, Venkata; Eifes, Serge; Rege, Kavita; Barbosa-Silva, Adriano; Schneider, Reinhard

2017-01-01

Abstract Summary: In translational research, efficient knowledge exchange between the different fields of expertise is crucial. An open platform that is capable of storing a multitude of data types such as clinical, pre-clinical or OMICS data combined with strong visual analytical capabilities will significantly accelerate the scientific progress by making data more accessible and hypothesis generation easier. The open data warehouse tranSMART is capable of storing a variety of data types and has a growing user community including both academic institutions and pharmaceutical companies. tranSMART, however, currently lacks interactive and dynamic visual analytics and does not permit any post-processing interaction or exploration. For this reason, we developed SmartR, a plugin for tranSMART, that equips the platform not only with several dynamic visual analytical workflows, but also provides its own framework for the addition of new custom workflows. Modern web technologies such as D3.js or AngularJS were used to build a set of standard visualizations that were heavily improved with dynamic elements. Availability and Implementation: The source code is licensed under the Apache 2.0 License and is freely available on GitHub: https://github.com/transmart/SmartR. Contact: reinhard.schneider@uni.lu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:28334291

NASA World Wind, Open Source 4D Geospatial Visualization Platform: *.NET & Java* for EDUCATION

NASA Astrophysics Data System (ADS)

Hogan, P.; Kuehnel, F.

2006-12-01

NASA World Wind has only one goal, to provide the maximum opportunity for geospatial information to be experienced, be it education, science, research, business, or government. The benefits to understanding for information delivered in the context of its 4D virtual reality are extraordinary. The NASA World Wind visualization platform is open source and therefore lends itself well to being extended to service *any* requirements, be they proprietary and commercial or simply available. Data accessibility is highly optimized using standard formats including internationally certified open standards (W*S). Although proprietary applications can be built based on World Wind, and proprietary data delivered that leverage World Wind, there is nothing proprietary about the visualization platform itself or the multiple planetary data sets readily available, including global animations of live weather. NASA World Wind is being used by NASA research teams as well as being a formal part of high school and university curriculum. The National Guard uses World Wind for emergency response activities and State governments have incorporated high resolution imagery for GIS management as well as for their cross-agency emergency response activities. The U.S. federal government uses NASA World Wind for a myriad of GIS and security-related issues (NSA, NGA, DOE, FAA, etc.).

NASA World Wind, Open Source 4D Geospatial Visualization Platform: *.NET & Java*

NASA Astrophysics Data System (ADS)

Hogan, P.; Coughlan, J.

2006-12-01

NASA World Wind has only one goal, to provide the maximum opportunity for geospatial information to be experienced, be it education, science, research, business, or government. The benefits to understanding for information delivered in the context of its 4D virtual reality are extraordinary. The NASA World Wind visualization platform is open source and therefore lends itself well to being extended to service *any* requirements, be they proprietary and commercial or simply available. Data accessibility is highly optimized using standard formats including internationally certified open standards (W*S). Although proprietary applications can be built based on World Wind, and proprietary data delivered that leverage World Wind, there is nothing proprietary about the visualization platform itself or the multiple planetary data sets readily available, including global animations of live weather. NASA World Wind is being used by NASA research teams as well as being a formal part of high school and university curriculum. The National Guard uses World Wind for emergency response activities and State governments have incorporated high resolution imagery for GIS management as well as for their cross-agency emergency response activities. The U.S. federal government uses NASA World Wind for a myriad of GIS and security-related issues (NSA, NGA, DOE, FAA, etc.).

SmartR: an open-source platform for interactive visual analytics for translational research data.

PubMed

Herzinger, Sascha; Gu, Wei; Satagopam, Venkata; Eifes, Serge; Rege, Kavita; Barbosa-Silva, Adriano; Schneider, Reinhard

2017-07-15

In translational research, efficient knowledge exchange between the different fields of expertise is crucial. An open platform that is capable of storing a multitude of data types such as clinical, pre-clinical or OMICS data combined with strong visual analytical capabilities will significantly accelerate the scientific progress by making data more accessible and hypothesis generation easier. The open data warehouse tranSMART is capable of storing a variety of data types and has a growing user community including both academic institutions and pharmaceutical companies. tranSMART, however, currently lacks interactive and dynamic visual analytics and does not permit any post-processing interaction or exploration. For this reason, we developed SmartR , a plugin for tranSMART, that equips the platform not only with several dynamic visual analytical workflows, but also provides its own framework for the addition of new custom workflows. Modern web technologies such as D3.js or AngularJS were used to build a set of standard visualizations that were heavily improved with dynamic elements. The source code is licensed under the Apache 2.0 License and is freely available on GitHub: https://github.com/transmart/SmartR . reinhard.schneider@uni.lu. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Open source platform for collaborative construction of wearable sensor datasets for human motion analysis and an application for gait analysis.

PubMed

Llamas, César; González, Manuel A; Hernández, Carmen; Vegas, Jesús

2016-10-01

Nearly every practical improvement in modeling human motion is well founded in a properly designed collection of data or datasets. These datasets must be made publicly available for the community could validate and accept them. It is reasonable to concede that a collective, guided enterprise could serve to devise solid and substantial datasets, as a result of a collaborative effort, in the same sense as the open software community does. In this way datasets could be complemented, extended and expanded in size with, for example, more individuals, samples and human actions. For this to be possible some commitments must be made by the collaborators, being one of them sharing the same data acquisition platform. In this paper, we offer an affordable open source hardware and software platform based on inertial wearable sensors in a way that several groups could cooperate in the construction of datasets through common software suitable for collaboration. Some experimental results about the throughput of the overall system are reported showing the feasibility of acquiring data from up to 6 sensors with a sampling frequency no less than 118Hz. Also, a proof-of-concept dataset is provided comprising sampled data from 12 subjects suitable for gait analysis. Copyright © 2016 Elsevier Inc. All rights reserved.

An inexpensive Arduino-based LED stimulator system for vision research.

PubMed

Teikari, Petteri; Najjar, Raymond P; Malkki, Hemi; Knoblauch, Kenneth; Dumortier, Dominique; Gronfier, Claude; Cooper, Howard M

2012-11-15

Light emitting diodes (LEDs) are being used increasingly as light sources in life sciences applications such as in vision research, fluorescence microscopy and in brain-computer interfacing. Here we present an inexpensive but effective visual stimulator based on light emitting diodes (LEDs) and open-source Arduino microcontroller prototyping platform. The main design goal of our system was to use off-the-shelf and open-source components as much as possible, and to reduce design complexity allowing use of the system to end-users without advanced electronics skills. The main core of the system is a USB-connected Arduino microcontroller platform designed initially with a specific emphasis on the ease-of-use creating interactive physical computing environments. The pulse-width modulation (PWM) signal of Arduino was used to drive LEDs allowing linear light intensity control. The visual stimulator was demonstrated in applications such as murine pupillometry, rodent models for cognitive research, and heterochromatic flicker photometry in human psychophysics. These examples illustrate some of the possible applications that can be easily implemented and that are advantageous for students, educational purposes and universities with limited resources. The LED stimulator system was developed as an open-source project. Software interface was developed using Python with simplified examples provided for Matlab and LabVIEW. Source code and hardware information are distributed under the GNU General Public Licence (GPL, version 3). Copyright © 2012 Elsevier B.V. All rights reserved.

A novel low-cost open-hardware platform for monitoring soil water content and multiple soil-air-vegetation parameters.

PubMed

Bitella, Giovanni; Rossi, Roberta; Bochicchio, Rocco; Perniola, Michele; Amato, Mariana

2014-10-21

Monitoring soil water content at high spatio-temporal resolution and coupled to other sensor data is crucial for applications oriented towards water sustainability in agriculture, such as precision irrigation or phenotyping root traits for drought tolerance. The cost of instrumentation, however, limits measurement frequency and number of sensors. The objective of this work was to design a low cost "open hardware" platform for multi-sensor measurements including water content at different depths, air and soil temperatures. The system is based on an open-source ARDUINO microcontroller-board, programmed in a simple integrated development environment (IDE). Low cost high-frequency dielectric probes were used in the platform and lab tested on three non-saline soils (ECe1: 2.5 < 0.1 mS/cm). Empirical calibration curves were subjected to cross-validation (leave-one-out method), and normalized root mean square error (NRMSE) were respectively 0.09 for the overall model, 0.09 for the sandy soil, 0.07 for the clay loam and 0.08 for the sandy loam. The overall model (pooled soil data) fitted the data very well (R2 = 0.89) showing a high stability, being able to generate very similar RMSEs during training and validation (RMSE(training) = 2.63; RMSE(validation) = 2.61). Data recorded on the card were automatically sent to a remote server allowing repeated field-data quality checks. This work provides a framework for the replication and upgrading of a customized low cost platform, consistent with the open source approach whereby sharing information on equipment design and software facilitates the adoption and continuous improvement of existing technologies.

A Novel Low-Cost Open-Hardware Platform for Monitoring Soil Water Content and Multiple Soil-Air-Vegetation Parameters

PubMed Central

Bitella, Giovanni; Rossi, Roberta; Bochicchio, Rocco; Perniola, Michele; Amato, Mariana

2014-01-01

Monitoring soil water content at high spatio-temporal resolution and coupled to other sensor data is crucial for applications oriented towards water sustainability in agriculture, such as precision irrigation or phenotyping root traits for drought tolerance. The cost of instrumentation, however, limits measurement frequency and number of sensors. The objective of this work was to design a low cost “open hardware” platform for multi-sensor measurements including water content at different depths, air and soil temperatures. The system is based on an open-source ARDUINO microcontroller-board, programmed in a simple integrated development environment (IDE). Low cost high-frequency dielectric probes were used in the platform and lab tested on three non-saline soils (ECe1: 2.5 < 0.1 mS/cm). Empirical calibration curves were subjected to cross-validation (leave-one-out method), and normalized root mean square error (NRMSE) were respectively 0.09 for the overall model, 0.09 for the sandy soil, 0.07 for the clay loam and 0.08 for the sandy loam. The overall model (pooled soil data) fitted the data very well (R2 = 0.89) showing a high stability, being able to generate very similar RMSEs during training and validation (RMSEtraining = 2.63; RMSEvalidation = 2.61). Data recorded on the card were automatically sent to a remote server allowing repeated field-data quality checks. This work provides a framework for the replication and upgrading of a customized low cost platform, consistent with the open source approach whereby sharing information on equipment design and software facilitates the adoption and continuous improvement of existing technologies. PMID:25337742

PLUS: open-source toolkit for ultrasound-guided intervention systems.

PubMed

Lasso, Andras; Heffter, Tamas; Rankin, Adam; Pinter, Csaba; Ungi, Tamas; Fichtinger, Gabor

2014-10-01

A variety of advanced image analysis methods have been under the development for ultrasound-guided interventions. Unfortunately, the transition from an image analysis algorithm to clinical feasibility trials as part of an intervention system requires integration of many components, such as imaging and tracking devices, data processing algorithms, and visualization software. The objective of our paper is to provide a freely available open-source software platform-PLUS: Public software Library for Ultrasound-to facilitate rapid prototyping of ultrasound-guided intervention systems for translational clinical research. PLUS provides a variety of methods for interventional tool pose and ultrasound image acquisition from a wide range of tracking and imaging devices, spatial and temporal calibration, volume reconstruction, simulated image generation, and recording and live streaming of the acquired data. This paper introduces PLUS, explains its functionality and architecture, and presents typical uses and performance in ultrasound-guided intervention systems. PLUS fulfills the essential requirements for the development of ultrasound-guided intervention systems and it aspires to become a widely used translational research prototyping platform. PLUS is freely available as open source software under BSD license and can be downloaded from http://www.plustoolkit.org.

Sirepo for Synchrotron Radiation Workshop

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

Nagler, Robert; Moeller, Paul; Rakitin, Maksim

Sirepo is an open source framework for cloud computing. The graphical user interface (GUI) for Sirepo, also known as the client, executes in any HTML5 compliant web browser on any computing platform, including tablets. The client is built in JavaScript, making use of the following open source libraries: Bootstrap, which is fundamental for cross-platform web applications; AngularJS, which provides a model–view–controller (MVC) architecture and GUI components; and D3.js, which provides interactive plots and data-driven transformations. The Sirepo server is built on the following Python technologies: Flask, which is a lightweight framework for web development; Jinja, which is a secure andmore » widely used templating language; and Werkzeug, a utility library that is compliant with the WSGI standard. We use Nginx as the HTTP server and proxy, which provides a scalable event-driven architecture. The physics codes supported by Sirepo execute inside a Docker container. One of the codes supported by Sirepo is the Synchrotron Radiation Workshop (SRW). SRW computes synchrotron radiation from relativistic electrons in arbitrary magnetic fields and propagates the radiation wavefronts through optical beamlines. SRW is open source and is primarily supported by Dr. Oleg Chubar of NSLS-II at Brookhaven National Laboratory.« less

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.

ACQ4: an open-source software platform for data acquisition and analysis in neurophysiology research

PubMed Central

Campagnola, Luke; Kratz, Megan B.; Manis, Paul B.

2014-01-01

The complexity of modern neurophysiology experiments requires specialized software to coordinate multiple acquisition devices and analyze the collected data. We have developed ACQ4, an open-source software platform for performing data acquisition and analysis in experimental neurophysiology. This software integrates the tasks of acquiring, managing, and analyzing experimental data. ACQ4 has been used primarily for standard patch-clamp electrophysiology, laser scanning photostimulation, multiphoton microscopy, intrinsic imaging, and calcium imaging. The system is highly modular, which facilitates the addition of new devices and functionality. The modules included with ACQ4 provide for rapid construction of acquisition protocols, live video display, and customizable analysis tools. Position-aware data collection allows automated construction of image mosaics and registration of images with 3-dimensional anatomical atlases. ACQ4 uses free and open-source tools including Python, NumPy/SciPy for numerical computation, PyQt for the user interface, and PyQtGraph for scientific graphics. Supported hardware includes cameras, patch clamp amplifiers, scanning mirrors, lasers, shutters, Pockels cells, motorized stages, and more. ACQ4 is available for download at http://www.acq4.org. PMID:24523692

openBIS ELN-LIMS: an open-source database for academic laboratories.

PubMed

Barillari, Caterina; Ottoz, Diana S M; Fuentes-Serna, Juan Mariano; Ramakrishnan, Chandrasekhar; Rinn, Bernd; Rudolf, Fabian

2016-02-15

The open-source platform openBIS (open Biology Information System) offers an Electronic Laboratory Notebook and a Laboratory Information Management System (ELN-LIMS) solution suitable for the academic life science laboratories. openBIS ELN-LIMS allows researchers to efficiently document their work, to describe materials and methods and to collect raw and analyzed data. The system comes with a user-friendly web interface where data can be added, edited, browsed and searched. The openBIS software, a user guide and a demo instance are available at https://openbis-eln-lims.ethz.ch. The demo instance contains some data from our laboratory as an example to demonstrate the possibilities of the ELN-LIMS (Ottoz et al., 2014). For rapid local testing, a VirtualBox image of the ELN-LIMS is also available. © The Author 2015. Published by Oxford University Press.

PLUME and research sotware

NASA Astrophysics Data System (ADS)

Baudin, Veronique; Gomez-Diaz, Teresa

2013-04-01

The PLUME open platform (https://www.projet-plume.org) has as first goal to share competences and to value the knowledge of software experts within the French higher education and research communities. The project proposes in its platform the access to more than 380 index cards describing useful and economic software for this community, with open access to everybody. The second goal of PLUME focuses on to improve the visibility of software produced by research laboratories within the higher education and research communities. The "development-ESR" index cards briefly describe the main features of the software, including references to research publications associated to it. The platform counts more than 300 cards describing research software, where 89 cards have an English version. In this talk we describe the theme classification and the taxonomy of the index cards and the evolution with new themes added to the project. We will also focus on the organisation of PLUME as an open project and its interests in the promotion of free/open source software from and for research, contributing to the creation of a community of shared knowledge.

OpenChrom: a cross-platform open source software for the mass spectrometric analysis of chromatographic data.

PubMed

Wenig, Philip; Odermatt, Juergen

2010-07-30

Today, data evaluation has become a bottleneck in chromatographic science. Analytical instruments equipped with automated samplers yield large amounts of measurement data, which needs to be verified and analyzed. Since nearly every GC/MS instrument vendor offers its own data format and software tools, the consequences are problems with data exchange and a lack of comparability between the analytical results. To challenge this situation a number of either commercial or non-profit software applications have been developed. These applications provide functionalities to import and analyze several data formats but have shortcomings in terms of the transparency of the implemented analytical algorithms and/or are restricted to a specific computer platform. This work describes a native approach to handle chromatographic data files. The approach can be extended in its functionality such as facilities to detect baselines, to detect, integrate and identify peaks and to compare mass spectra, as well as the ability to internationalize the application. Additionally, filters can be applied on the chromatographic data to enhance its quality, for example to remove background and noise. Extended operations like do, undo and redo are supported. OpenChrom is a software application to edit and analyze mass spectrometric chromatographic data. It is extensible in many different ways, depending on the demands of the users or the analytical procedures and algorithms. It offers a customizable graphical user interface. The software is independent of the operating system, due to the fact that the Rich Client Platform is written in Java. OpenChrom is released under the Eclipse Public License 1.0 (EPL). There are no license constraints regarding extensions. They can be published using open source as well as proprietary licenses. OpenChrom is available free of charge at http://www.openchrom.net.

The SCEC Broadband Platform: A Collaborative Open-Source Software Package for Strong Ground Motion Simulation and Validation

NASA Astrophysics Data System (ADS)

Silva, F.; Maechling, P. J.; Goulet, C.; Somerville, P.; Jordan, T. H.

2013-12-01

The Southern California Earthquake Center (SCEC) Broadband Platform is a collaborative software development project involving SCEC researchers, graduate students, and the SCEC Community Modeling Environment. The SCEC Broadband Platform is open-source scientific software that can generate broadband (0-100Hz) ground motions for earthquakes, integrating complex scientific modules that implement rupture generation, low and high-frequency seismogram synthesis, non-linear site effects calculation, and visualization into a software system that supports easy on-demand computation of seismograms. The Broadband Platform operates in two primary modes: validation simulations and scenario simulations. In validation mode, the Broadband Platform runs earthquake rupture and wave propagation modeling software to calculate seismograms of a historical earthquake for which observed strong ground motion data is available. Also in validation mode, the Broadband Platform calculates a number of goodness of fit measurements that quantify how well the model-based broadband seismograms match the observed seismograms for a certain event. Based on these results, the Platform can be used to tune and validate different numerical modeling techniques. During the past year, we have modified the software to enable the addition of a large number of historical events, and we are now adding validation simulation inputs and observational data for 23 historical events covering the Eastern and Western United States, Japan, Taiwan, Turkey, and Italy. In scenario mode, the Broadband Platform can run simulations for hypothetical (scenario) earthquakes. In this mode, users input an earthquake description, a list of station names and locations, and a 1D velocity model for their region of interest, and the Broadband Platform software then calculates ground motions for the specified stations. By establishing an interface between scientific modules with a common set of input and output files, the Broadband Platform facilitates the addition of new scientific methods, which are written by earth scientists in a number of languages such as C, C++, Fortran, and Python. The Broadband Platform's modular design also supports the reuse of existing software modules as building blocks to create new scientific methods. Additionally, the Platform implements a wrapper around each scientific module, converting input and output files to and from the specific formats required (or produced) by individual scientific codes. Working in close collaboration with scientists and research engineers, the SCEC software development group continues to add new capabilities to the Broadband Platform and to release new versions as open-source scientific software distributions that can be compiled and run on many Linux computer systems. Our latest release includes the addition of 3 new simulation methods and several new data products, such as map and distance-based goodness of fit plots. Finally, as the number and complexity of scenarios simulated using the Broadband Platform increase, we have added batching utilities to substantially improve support for running large-scale simulations on computing clusters.

SMART Platforms: Building the App Store for Biosurveillance

PubMed Central

Mandl, Kenneth D.

2013-01-01

Objective To enable public health departments to develop “apps” to run on electronic health records (EHRs) for (1) biosurveillance and case reporting and (2) delivering alerts to the point of care. We describe a novel health information technology platform with substitutable apps constructed around core services enabling EHRs to function as iPhone-like platforms. Introduction Health care information is a fundamental source of data for biosurveillance, yet configuring EHRs to report relevant data to health departments is technically challenging, labor intensive, and often requires custom solutions for each installation. Public health agencies wishing to deliver alerts to clinicians also must engage in an endless array of one-off systems integrations. Despite a $48B investment in HIT, and meaningful use criteria requiring reporting to biosurveillance systems, most vendor electronic health records are architected monolithically, making modification difficult for hospitals and physician practices. An alternative approach is to reimagine EHRs as iPhone-like platforms supporting substitutable apps-based functionality. Substitutability is the capability inherent in a system of replacing one application with another of similar functionality. Methods Substitutability requires that the purchaser of an app can replace one application with another without being technically expert, without requiring re-engineering other applications that they are using, and without having to consult or require assistance of any of the vendors of previously installed or currently installed applications. Apps necessarily compete with each other promoting progress and adaptability. The Substitutable Medical Applications, Reusable Technologies (SMART) Platforms project is funded by a $15M grant from Office of the National Coordinator of Health Information Technology’s Strategic Health IT Advanced Research Projects (SHARP) Program. All SMART standards are open and the core software is open source. The SMART project promotes substitutability through an application programming interface (API) that can be adopted as part of a “container” built around by a wide variety of HIT, providing readonly access to the underlying data model and a software development toolkit to readily create apps. SMART containers are HIT systems, that have implemented the SMART API or a portion of it. Containers marshal data sources and present them consistently across the SMART API. SMART applications consume the API and are substitutable. Results SMART provides a common platform supporting an “app store for biosurveillance” as an approach to enabling one stop shopping for public health departments—to create an app once, and distribute it everywhere. Further, such apps can be readily updated or created—for example, in the case of an emerging infection, an app may be designed to collect additional data at emergency department triage. Or a public health department may widely distribute an app, interoperable with any SMART-enabled EMR, that delivers contextualized alerts when patient electronic records are opened, or through background processes. SMART has sparked an ecosystem of apps developers and attracted existing health information technology platforms to adopt the SMART API—including, traditional, open source, and next generation EHRs, patient-facing platforms and health information exchanges. SMART-enabled platforms to date include the Cerner EMR, the WorldVista EHR, the OpenMRS EHR, the i2b2 analytic platform, and the Indivo X personal health record. The SMART team is working with the Mirth Corporation, to SMART-enable the HealthBridge and Redwood MedNet Health Information Exchanges. We have demonstrated that a single SMART app can run, unmodified, in all of these environments, as long as the underlying platform collects the required data types. Major EHR vendors are currently adapting the SMART API for their products. Conclusions The SMART system enables nimble customization of any electronic health record system to create either a reporting function (outgoing communication) or an alerting function (incoming communication) establishing a technology for a robust linkage between public health and clinical environments.

From Oss CAD to Bim for Cultural Heritage Digital Representation

NASA Astrophysics Data System (ADS)

Logothetis, S.; Karachaliou, E.; Stylianidis, E.

2017-02-01

The paper illustrates the use of open source Computer-aided design (CAD) environments in order to develop Building Information Modelling (BIM) tools able to manage 3D models in the field of cultural heritage. Nowadays, the development of Free and Open Source Software (FOSS) has been rapidly growing and their use tends to be consolidated. Although BIM technology is widely known and used, there is a lack of integrated open source platforms able to support all stages of Historic Building Information Modelling (HBIM) processes. The present research aims to use a FOSS CAD environment in order to develop BIM plug-ins which will be able to import and edit digital representations of cultural heritage models derived by photogrammetric methods.

Development of an open-source web-based intervention for Brazilian smokers - Viva sem Tabaco.

PubMed

Gomide, H P; Bernardino, H S; Richter, K; Martins, L F; Ronzani, T M

2016-08-02

Web-based interventions for smoking cessation available in Portuguese do not adhere to evidence-based treatment guidelines. Besides, all existing web-based interventions are built on proprietary platforms that developing countries often cannot afford. We aimed to describe the development of "Viva sem Tabaco", an open-source web-based intervention. The development of the intervention included the selection of content from evidence-based guidelines for smoking cessation, the design of the first layout, conduction of 2 focus groups to identify potential features, refinement of the layout based on focus groups and correction of content based on feedback provided by specialists on smoking cessation. At the end, we released the source-code and intervention on the Internet and translated it into Spanish and English. The intervention developed fills gaps in the information available in Portuguese and the lack of open-source interventions for smoking cessation. The open-source licensing format and its translation system may help researchers from different countries deploying evidence-based interventions for smoking cessation.

Open Source Platform Application to Groundwater Characterization and Monitoring

NASA Astrophysics Data System (ADS)

Ntarlagiannis, D.; Day-Lewis, F. D.; Falzone, S.; Lane, J. W., Jr.; Slater, L. D.; Robinson, J.; Hammett, S.

2017-12-01

Groundwater characterization and monitoring commonly rely on the use of multiple point sensors and human labor. Due to the number of sensors, labor, and other resources needed, establishing and maintaining an adequate groundwater monitoring network can be both labor intensive and expensive. To improve and optimize the monitoring network design, open source software and hardware components could potentially provide the platform to control robust and efficient sensors thereby reducing costs and labor. This work presents early attempts to create a groundwater monitoring system incorporating open-source software and hardware that will control the remote operation of multiple sensors along with data management and file transfer functions. The system is built around a Raspberry PI 3, that controls multiple sensors in order to perform on-demand, continuous or `smart decision' measurements while providing flexibility to incorporate additional sensors to meet the demands of different projects. The current objective of our technology is to monitor exchange of ionic tracers between mobile and immobile porosity using a combination of fluid and bulk electrical-conductivity measurements. To meet this objective, our configuration uses four sensors (pH, specific conductance, pressure, temperature) that can monitor the fluid electrical properties of interest and guide the bulk electrical measurement. This system highlights the potential of using open source software and hardware components for earth sciences applications. The versatility of the system makes it ideal for use in a large number of applications, and the low cost allows for high resolution (spatially and temporally) monitoring.

A-Track: Detecting Moving Objects in FITS images

NASA Astrophysics Data System (ADS)

Atay, T.; Kaplan, M.; Kilic, Y.; Karapinar, N.

2017-04-01

A-Track is a fast, open-source, cross-platform pipeline for detecting moving objects (asteroids and comets) in sequential telescope images in FITS format. The moving objects are detected using a modified line detection algorithm.

PR-PR: Cross-Platform Laboratory Automation System

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

Linshiz, G; Stawski, N; Goyal, G

To enable protocol standardization, sharing, and efficient implementation across laboratory automation platforms, we have further developed the PR-PR open-source high-level biology-friendly robot programming language as a cross-platform laboratory automation system. Beyond liquid-handling robotics, PR-PR now supports microfluidic and microscopy platforms, as well as protocol translation into human languages, such as English. While the same set of basic PR-PR commands and features are available for each supported platform, the underlying optimization and translation modules vary from platform to platform. Here, we describe these further developments to PR-PR, and demonstrate the experimental implementation and validation of PR-PR protocols for combinatorial modified Goldenmore » Gate DNA assembly across liquid-handling robotic, microfluidic, and manual platforms. To further test PR-PR cross-platform performance, we then implement and assess PR-PR protocols for Kunkel DNA mutagenesis and hierarchical Gibson DNA assembly for microfluidic and manual platforms.« less

PR-PR: cross-platform laboratory automation system.

PubMed

Linshiz, Gregory; Stawski, Nina; Goyal, Garima; Bi, Changhao; Poust, Sean; Sharma, Monica; Mutalik, Vivek; Keasling, Jay D; Hillson, Nathan J

2014-08-15

To enable protocol standardization, sharing, and efficient implementation across laboratory automation platforms, we have further developed the PR-PR open-source high-level biology-friendly robot programming language as a cross-platform laboratory automation system. Beyond liquid-handling robotics, PR-PR now supports microfluidic and microscopy platforms, as well as protocol translation into human languages, such as English. While the same set of basic PR-PR commands and features are available for each supported platform, the underlying optimization and translation modules vary from platform to platform. Here, we describe these further developments to PR-PR, and demonstrate the experimental implementation and validation of PR-PR protocols for combinatorial modified Golden Gate DNA assembly across liquid-handling robotic, microfluidic, and manual platforms. To further test PR-PR cross-platform performance, we then implement and assess PR-PR protocols for Kunkel DNA mutagenesis and hierarchical Gibson DNA assembly for microfluidic and manual platforms.

MSiReader: an open-source interface to view and analyze high resolving power MS imaging files on Matlab platform.

PubMed

Robichaud, Guillaume; Garrard, Kenneth P; Barry, Jeremy A; Muddiman, David C

2013-05-01

During the past decade, the field of mass spectrometry imaging (MSI) has greatly evolved, to a point where it has now been fully integrated by most vendors as an optional or dedicated platform that can be purchased with their instruments. However, the technology is not mature and multiple research groups in both academia and industry are still very actively studying the fundamentals of imaging techniques, adapting the technology to new ionization sources, and developing new applications. As a result, there important varieties of data file formats used to store mass spectrometry imaging data and, concurrent to the development of MSi, collaborative efforts have been undertaken to introduce common imaging data file formats. However, few free software packages to read and analyze files of these different formats are readily available. We introduce here MSiReader, a free open source application to read and analyze high resolution MSI data from the most common MSi data formats. The application is built on the Matlab platform (Mathworks, Natick, MA, USA) and includes a large selection of data analysis tools and features. People who are unfamiliar with the Matlab language will have little difficult navigating the user-friendly interface, and users with Matlab programming experience can adapt and customize MSiReader for their own needs.

MSiReader: An Open-Source Interface to View and Analyze High Resolving Power MS Imaging Files on Matlab Platform

NASA Astrophysics Data System (ADS)

Robichaud, Guillaume; Garrard, Kenneth P.; Barry, Jeremy A.; Muddiman, David C.

2013-05-01

During the past decade, the field of mass spectrometry imaging (MSI) has greatly evolved, to a point where it has now been fully integrated by most vendors as an optional or dedicated platform that can be purchased with their instruments. However, the technology is not mature and multiple research groups in both academia and industry are still very actively studying the fundamentals of imaging techniques, adapting the technology to new ionization sources, and developing new applications. As a result, there important varieties of data file formats used to store mass spectrometry imaging data and, concurrent to the development of MSi, collaborative efforts have been undertaken to introduce common imaging data file formats. However, few free software packages to read and analyze files of these different formats are readily available. We introduce here MSiReader, a free open source application to read and analyze high resolution MSI data from the most common MSi data formats. The application is built on the Matlab platform (Mathworks, Natick, MA, USA) and includes a large selection of data analysis tools and features. People who are unfamiliar with the Matlab language will have little difficult navigating the user-friendly interface, and users with Matlab programming experience can adapt and customize MSiReader for their own needs.

Adaptation of a web-based, open source electronic medical record system platform to support a large study of tuberculosis epidemiology

PubMed Central

2012-01-01

Background In 2006, we were funded by the US National Institutes of Health to implement a study of tuberculosis epidemiology in Peru. The study required a secure information system to manage data from a target goal of 16,000 subjects who needed to be followed for at least one year. With previous experience in the development and deployment of web-based medical record systems for TB treatment in Peru, we chose to use the OpenMRS open source electronic medical record system platform to develop the study information system. Supported by a core technical and management team and a large and growing worldwide community, OpenMRS is now being used in more than 40 developing countries. We adapted the OpenMRS platform to better support foreign languages. We added a new module to support double data entry, linkage to an existing laboratory information system, automatic upload of GPS data from handheld devices, and better security and auditing of data changes. We added new reports for study managers, and developed data extraction tools for research staff and statisticians. Further adaptation to handle direct entry of laboratory data occurred after the study was launched. Results Data collection in the OpenMRS system began in September 2009. By August 2011 a total of 9,256 participants had been enrolled, 102,274 forms and 13,829 laboratory results had been entered, and there were 208 users. The system is now entirely supported by the Peruvian study staff and programmers. Conclusions The information system served the study objectives well despite requiring some significant adaptations mid-stream. OpenMRS has more tools and capabilities than it did in 2008, and requires less adaptations for future projects. OpenMRS can be an effective research data system in resource poor environments, especially for organizations using or considering it for clinical care as well as research. PMID:23131180

ProteoWizard: open source software for rapid proteomics tools development.

PubMed

Kessner, Darren; Chambers, Matt; Burke, Robert; Agus, David; Mallick, Parag

2008-11-01

The ProteoWizard software project provides a modular and extensible set of open-source, cross-platform tools and libraries. The tools perform proteomics data analyses; the libraries enable rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and performs standard proteomics and LCMS dataset computations. The library contains readers and writers of the mzML data format, which has been written using modern C++ techniques and design principles and supports a variety of platforms with native compilers. The software has been specifically released under the Apache v2 license to ensure it can be used in both academic and commercial projects. In addition to the library, we also introduce a rapidly growing set of companion tools whose implementation helps to illustrate the simplicity of developing applications on top of the ProteoWizard library. Cross-platform software that compiles using native compilers (i.e. GCC on Linux, MSVC on Windows and XCode on OSX) is available for download free of charge, at http://proteowizard.sourceforge.net. This website also provides code examples, and documentation. It is our hope the ProteoWizard project will become a standard platform for proteomics development; consequently, code use, contribution and further development are strongly encouraged.

Image Harvest: an open-source platform for high-throughput plant image processing and analysis

PubMed Central

Knecht, Avi C.; Campbell, Malachy T.; Caprez, Adam; Swanson, David R.; Walia, Harkamal

2016-01-01

High-throughput plant phenotyping is an effective approach to bridge the genotype-to-phenotype gap in crops. Phenomics experiments typically result in large-scale image datasets, which are not amenable for processing on desktop computers, thus creating a bottleneck in the image-analysis pipeline. Here, we present an open-source, flexible image-analysis framework, called Image Harvest (IH), for processing images originating from high-throughput plant phenotyping platforms. Image Harvest is developed to perform parallel processing on computing grids and provides an integrated feature for metadata extraction from large-scale file organization. Moreover, the integration of IH with the Open Science Grid provides academic researchers with the computational resources required for processing large image datasets at no cost. Image Harvest also offers functionalities to extract digital traits from images to interpret plant architecture-related characteristics. To demonstrate the applications of these digital traits, a rice (Oryza sativa) diversity panel was phenotyped and genome-wide association mapping was performed using digital traits that are used to describe different plant ideotypes. Three major quantitative trait loci were identified on rice chromosomes 4 and 6, which co-localize with quantitative trait loci known to regulate agronomically important traits in rice. Image Harvest is an open-source software for high-throughput image processing that requires a minimal learning curve for plant biologists to analyzephenomics datasets. PMID:27141917

Open Source Hbim for Cultural Heritage: a Project Proposal

NASA Astrophysics Data System (ADS)

Diara, F.; Rinaudo, F.

2018-05-01

Actual technologies are changing Cultural Heritage research, analysis, conservation and development ways, allowing new innovative approaches. The possibility of integrating Cultural Heritage data, like archaeological information, inside a three-dimensional environment system (like a Building Information Modelling) involve huge benefits for its management, monitoring and valorisation. Nowadays there are many commercial BIM solutions. However, these tools are thought and developed mostly for architecture design or technical installations. An example of better solution could be a dynamic and open platform that might consider Cultural Heritage needs as priority. Suitable solution for better and complete data usability and accessibility could be guaranteed by open source protocols. This choice would allow adapting software to Cultural Heritage needs and not the opposite, thus avoiding methodological stretches. This work will focus exactly on analysis and experimentations about specific characteristics of these kind of open source software (DBMS, CAD, Servers) applied to a Cultural Heritage example, in order to verifying their flexibility, reliability and then creating a dynamic HBIM open source prototype. Indeed, it might be a starting point for a future creation of a complete HBIM open source solution that we could adapt to others Cultural Heritage researches and analysis.

Mapping urban green open space in Bontang city using QGIS and cloud computing

NASA Astrophysics Data System (ADS)

Agus, F.; Ramadiani; Silalahi, W.; Armanda, A.; Kusnandar

2018-04-01

Digital mapping techniques are available freely and openly so that map-based application development is easier, faster and cheaper. A rapid development of Cloud Computing Geographic Information System makes this system can help the needs of the community for the provision of geospatial information online. The presence of urban Green Open Space (GOS) provide great benefits as an oxygen supplier, carbon-binding agent and can contribute to providing comfort and beauty of city life. This study aims to propose a platform application of GIS Cloud Computing (CC) of Bontang City GOS mapping. The GIS-CC platform uses the basic map available that’s free and open source. The research used survey method to collect GOS data obtained from Bontang City Government, while application developing works Quantum GIS-CC. The result section describes the existence of GOS Bontang City and the design of GOS mapping application.

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.

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

An open source web interface for linking models to infrastructure system databases

NASA Astrophysics Data System (ADS)

Knox, S.; Mohamed, K.; Harou, J. J.; Rheinheimer, D. E.; Medellin-Azuara, J.; Meier, P.; Tilmant, A.; Rosenberg, D. E.

2016-12-01

Models of networked engineered resource systems such as water or energy systems are often built collaboratively with developers from different domains working at different locations. These models can be linked to large scale real world databases, and they are constantly being improved and extended. As the development and application of these models becomes more sophisticated, and the computing power required for simulations and/or optimisations increases, so has the need for online services and tools which enable the efficient development and deployment of these models. Hydra Platform is an open source, web-based data management system, which allows modellers of network-based models to remotely store network topology and associated data in a generalised manner, allowing it to serve multiple disciplines. Hydra Platform uses a web API using JSON to allow external programs (referred to as `Apps') to interact with its stored networks and perform actions such as importing data, running models, or exporting the networks to different formats. Hydra Platform supports multiple users accessing the same network and has a suite of functions for managing users and data. We present ongoing development in Hydra Platform, the Hydra Web User Interface, through which users can collaboratively manage network data and models in a web browser. The web interface allows multiple users to graphically access, edit and share their networks, run apps and view results. Through apps, which are located on the server, the web interface can give users access to external data sources and models without the need to install or configure any software. This also ensures model results can be reproduced by removing platform or version dependence. Managing data and deploying models via the web interface provides a way for multiple modellers to collaboratively manage data, deploy and monitor model runs and analyse results.

An open-source computational and data resource to analyze digital maps of immunopeptidomes

DOE PAGES

Caron, Etienne; Espona, Lucia; Kowalewski, Daniel J.; ...

2015-07-08

We present a novel mass spectrometry-based high-throughput workflow and an open-source computational and data resource to reproducibly identify and quantify HLA-associated peptides. Collectively, the resources support the generation of HLA allele-specific peptide assay libraries consisting of consensus fragment ion spectra, and the analysis of quantitative digital maps of HLA peptidomes generated from a range of biological sources by SWATH mass spectrometry (MS). This study represents the first community-based effort to develop a robust platform for the reproducible and quantitative measurement of the entire repertoire of peptides presented by HLA molecules, an essential step towards the design of efficient immunotherapies.

DStat: A Versatile, Open-Source Potentiostat for Electroanalysis and Integration

PubMed Central

Dryden, Michael D. M.; Wheeler, Aaron R.

2015-01-01

Most electroanalytical techniques require the precise control of the potentials in an electrochemical cell using a potentiostat. Commercial potentiostats function as “black boxes,” giving limited information about their circuitry and behaviour which can make development of new measurement techniques and integration with other instruments challenging. Recently, a number of lab-built potentiostats have emerged with various design goals including low manufacturing cost and field-portability, but notably lacking is an accessible potentiostat designed for general lab use, focusing on measurement quality combined with ease of use and versatility. To fill this gap, we introduce DStat (http://microfluidics.utoronto.ca/dstat), an open-source, general-purpose potentiostat for use alone or integrated with other instruments. DStat offers picoampere current measurement capabilities, a compact USB-powered design, and user-friendly cross-platform software. DStat is easy and inexpensive to build, may be modified freely, and achieves good performance at low current levels not accessible to other lab-built instruments. In head-to-head tests, DStat’s voltammetric measurements are much more sensitive than those of “CheapStat” (a popular open-source potentiostat described previously), and are comparable to those of a compact commercial “black box” potentiostat. Likewise, in head-to-head tests, DStat’s potentiometric precision is similar to that of a commercial pH meter. Most importantly, the versatility of DStat was demonstrated through integration with the open-source DropBot digital microfluidics platform. In sum, we propose that DStat is a valuable contribution to the “open source” movement in analytical science, which is allowing users to adapt their tools to their experiments rather than alter their experiments to be compatible with their tools. PMID:26510100

plas.io: Open Source, Browser-based WebGL Point Cloud Visualization

NASA Astrophysics Data System (ADS)

Butler, H.; Finnegan, D. C.; Gadomski, P. J.; Verma, U. K.

2014-12-01

Point cloud data, in the form of Light Detection and Ranging (LiDAR), RADAR, or semi-global matching (SGM) image processing, are rapidly becoming a foundational data type to quantify and characterize geospatial processes. Visualization of these data, due to overall volume and irregular arrangement, is often difficult. Technological advancement in web browsers, in the form of WebGL and HTML5, have made interactivity and visualization capabilities ubiquitously available which once only existed in desktop software. plas.io is an open source JavaScript application that provides point cloud visualization, exploitation, and compression features in a web-browser platform, reducing the reliance for client-based desktop applications. The wide reach of WebGL and browser-based technologies mean plas.io's capabilities can be delivered to a diverse list of devices -- from phones and tablets to high-end workstations -- with very little custom software development. These properties make plas.io an ideal open platform for researchers and software developers to communicate visualizations of complex and rich point cloud data to devices to which everyone has easy access.

A prospective international cooperative information technology platform built using open-source tools for improving the access to and safety of bone marrow transplantation in low- and middle-income countries.

PubMed

Agarwal, Rajat Kumar; Sedai, Amit; Dhimal, Sunil; Ankita, Kumari; Clemente, Luigi; Siddique, Sulman; Yaqub, Naila; Khalid, Sadaf; Itrat, Fatima; Khan, Anwar; Gilani, Sarah Khan; Marwah, Priya; Soni, Rajpreet; Missiry, Mohamed El; Hussain, Mohamed Hamed; Uderzo, Cornelio; Faulkner, Lawrence

2014-01-01

Jagriti Innovations developed a collaboration tool in partnership with the Cure2Children Foundation that has been used by health professionals in Italy, Pakistan, and India for the collaborative management of patients undergoing bone marrow transplantation (BMT) for thalassemia major since August 2008. This online open-access database covers data recording, analyzing, and reporting besides enabling knowledge exchange, telemedicine, capacity building, and quality assurance. As of February 2014, over 2400 patients have been registered and 112 BMTs have been performed with outcomes comparable to international standards, but at a fraction of the cost. This approach avoids medical emigration and contributes to local healthcare strengthening and competitiveness. This paper presents the experience and clinical outcomes associated with the use of this platform built using open-source tools and focusing on a locally pertinent tertiary care procedure-BMT. 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.

Hard real-time closed-loop electrophysiology with the Real-Time eXperiment Interface (RTXI)

PubMed Central

George, Ansel; Dorval, Alan D.; Christini, David J.

2017-01-01

The ability to experimentally perturb biological systems has traditionally been limited to static pre-programmed or operator-controlled protocols. In contrast, real-time control allows dynamic probing of biological systems with perturbations that are computed on-the-fly during experimentation. Real-time control applications for biological research are available; however, these systems are costly and often restrict the flexibility and customization of experimental protocols. The Real-Time eXperiment Interface (RTXI) is an open source software platform for achieving hard real-time data acquisition and closed-loop control in biological experiments while retaining the flexibility needed for experimental settings. RTXI has enabled users to implement complex custom closed-loop protocols in single cell, cell network, animal, and human electrophysiology studies. RTXI is also used as a free and open source, customizable electrophysiology platform in open-loop studies requiring online data acquisition, processing, and visualization. RTXI is easy to install, can be used with an extensive range of external experimentation and data acquisition hardware, and includes standard modules for implementing common electrophysiology protocols. PMID:28557998

Free-access open-source e-learning in comprehensive neurosurgery skills training.

PubMed

Jotwani, Payal; Srivastav, Vinkle; Tripathi, Manjul; Deo, Rama Chandra; Baby, Britty; Damodaran, Natesan; Singh, Ramandeep; Suri, Ashish; Bettag, Martin; Roy, Tara Sankar; Busert, Christoph; Mehlitz, Marcus; Lalwani, Sanjeev; Garg, Kanwaljeet; Paul, Kolin; Prasad, Sanjiva; Banerjee, Subhashis; Kalra, Prem; Kumar, Subodh; Sharma, Bhavani Shankar; Mahapatra, Ashok Kumar

2014-01-01

Since the end of last century, technology has taken a front seat in dispersion of medical education. Advancements of technology in neurosurgery and traditional training methods are now being challenged by legal and ethical concerns of patient safety, resident work-hour restriction and cost of operating-room time. To supplement the existing neurosurgery education pattern, various e-learning platforms are introduced as structured, interactive learning system. This study focuses on the concept, formulation, development and impact of web based learning platforms dedicated to neurosurgery discipline to disseminate education, supplement surgical knowledge and improve skills of neurosurgeons. 'Neurosurgery Education and Training School (NETS), e-learning platform' has integration of web-based technologies like 'Content Management System' for organizing the education material and 'Learning Management System' for updating neurosurgeons. NETS discussion forum networks neurosurgeons, neuroscientists and neuro-technologists across the globe facilitating collaborative translational research. Multi-authored neurosurgical e-learning material supplements the deficiencies of regular time-bound education. Interactive open-source, global, free-access e-learning platform of NETS has around 1) 425 visitors/month from 73 countries; ratio of new visitors to returning visitors 42.3; 57.7 (2); 64,380 views from 190 subscribers for surgical videos, 3-D animation, graphics based training modules (3); average 402 views per post. The e-Learning platforms provide updated educational content that make them "quick, surf, find and extract" resources. e-Learning tools like web-based education, social interactive platform and question-answer forum will save unnecessary expenditure of time and travel of neurosurgeons seeking knowledge. The need for free access platforms is more pronounced for the neurosurgeons and patients in developing nations.

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

DCO-VIVO: A Collaborative Data Platform for the Deep Carbon Science Communities

NASA Astrophysics Data System (ADS)

Wang, H.; Chen, Y.; West, P.; Erickson, J. S.; Ma, X.; Fox, P. A.

2014-12-01

Deep Carbon Observatory (DCO) is a decade-long scientific endeavor to understand carbon in the complex deep Earth system. Thousands of DCO scientists from institutions across the globe are organized into communities representing four domains of exploration: Extreme Physics and Chemistry, Reservoirs and Fluxes, Deep Energy, and Deep Life. Cross-community and cross-disciplinary collaboration is one of the most distinctive features in DCO's flexible research framework. VIVO is an open-source Semantic Web platform that facilitates cross-institutional researcher and research discovery. it includes a number of standard ontologies that interconnect people, organizations, publications, activities, locations, and other entities of research interest to enable browsing, searching, visualizing, and generating Linked Open (research) Data. The DCO-VIVO solution expedites research collaboration between DCO scientists and communities. Based on DCO's specific requirements, the DCO Data Science team developed a series of extensions to the VIVO platform including extending the VIVO information model, extended query over the semantic information within VIVO, integration with other open source collaborative environments and data management systems, using single sign-on, assigning of unique Handles to DCO objects, and publication and dataset ingesting extensions using existing publication systems. We present here the iterative development of these requirements that are now in daily use by the DCO community of scientists for research reporting, information sharing, and resource discovery in support of research activities and program management.

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.

Neural ensemble communities: open-source approaches to hardware for large-scale electrophysiology.

PubMed

Siegle, Joshua H; Hale, Gregory J; Newman, Jonathan P; Voigts, Jakob

2015-06-01

One often-overlooked factor when selecting a platform for large-scale electrophysiology is whether or not a particular data acquisition system is 'open' or 'closed': that is, whether or not the system's schematics and source code are available to end users. Open systems have a reputation for being difficult to acquire, poorly documented, and hard to maintain. With the arrival of more powerful and compact integrated circuits, rapid prototyping services, and web-based tools for collaborative development, these stereotypes must be reconsidered. We discuss some of the reasons why multichannel extracellular electrophysiology could benefit from open-source approaches and describe examples of successful community-driven tool development within this field. In order to promote the adoption of open-source hardware and to reduce the need for redundant development efforts, we advocate a move toward standardized interfaces that connect each element of the data processing pipeline. This will give researchers the flexibility to modify their tools when necessary, while allowing them to continue to benefit from the high-quality products and expertise provided by commercial vendors. Copyright © 2014 Elsevier Ltd. All rights reserved.

Summary and evaluation of the Strategic Defense Initiative Space Power Architecture Study

NASA Technical Reports Server (NTRS)

Edenburn, M. (Editor); Smith, J. M. (Editor)

1989-01-01

The Space Power Architecture Study (SPAS) identified and evaluated power subsystem options for multimegawatt electric (MMWE) space based weapons and surveillance platforms for the Strategic Defense Initiative (SDI) applications. Steady state requirements of less than 1 MMWE are adequately covered by the SP-100 nuclear space power program and hence were not addressed in the SPAS. Four steady state power systems less than 1 MMWE were investigated with little difference between them on a mass basis. The majority of the burst power systems utilized H(2) from the weapons and were either closed (no effluent), open (effluent release) or steady state with storage (no effluent). Closed systems used nuclear or combustion heat source with thermionic, Rankine, turboalternator, fuel cell and battery conversion devices. Open systems included nuclear or combustion heat sources using turboalternator, magnetohydrodynamic, fuel cell or battery power conversion devices. The steady state systems with storage used the SP-100 or Star-M reactors as energy sources and flywheels, fuel cells or batteries to store energy for burst applications. As with other studies the open systems are by far the lightest, most compact and simplist (most reliable) systems. However, unlike other studies the SPAS studied potential platform operational problems caused by effluents or vibration.

Sirepo - Warp

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

Nagler, Robert; Moeller, Paul

Sirepo is an open source framework for cloud computing. The graphical user interface (GUI) for Sirepo, also known as the client, executes in any HTML5 compliant web browser on any computing platform, including tablets. The client is built in JavaScript, making use of the following open source libraries: Bootstrap, which is fundamental for cross-platform web applications; AngularJS, which provides a model–view–controller (MVC) architecture and GUI components; and D3.js, which provides interactive plots and data-driven transformations. The Sirepo server is built on the following Python technologies: Flask, which is a lightweight framework for web development; Jin-ja, which is a secure andmore » widely used templating language; and Werkzeug, a utility library that is compliant with the WSGI standard. We use Nginx as the HTTP server and proxy, which provides a scalable event-driven architecture. The physics codes supported by Sirepo execute inside a Docker container. One of the codes supported by Sirepo is Warp. Warp is a particle-in-cell (PIC) code de-signed to simulate high-intensity charged particle beams and plasmas in both the electrostatic and electromagnetic regimes, with a wide variety of integrated physics models and diagnostics. At pre-sent, Sirepo supports a small subset of Warp’s capabilities. Warp is open source and is part of the Berkeley Lab Accelerator Simulation Toolkit.« less

FreeSASA: An open source C library for solvent accessible surface area calculations.

PubMed

Mitternacht, Simon

2016-01-01

Calculating solvent accessible surface areas (SASA) is a run-of-the-mill calculation in structural biology. Although there are many programs available for this calculation, there are no free-standing, open-source tools designed for easy tool-chain integration. FreeSASA is an open source C library for SASA calculations that provides both command-line and Python interfaces in addition to its C API. The library implements both Lee and Richards' and Shrake and Rupley's approximations, and is highly configurable to allow the user to control molecular parameters, accuracy and output granularity. It only depends on standard C libraries and should therefore be easy to compile and install on any platform. The library is well-documented, stable and efficient. The command-line interface can easily replace closed source legacy programs, with comparable or better accuracy and speed, and with some added functionality.

OpenSim: open-source software to create and analyze dynamic simulations of movement.

PubMed

Delp, Scott L; Anderson, Frank C; Arnold, Allison S; Loan, Peter; Habib, Ayman; John, Chand T; Guendelman, Eran; Thelen, Darryl G

2007-11-01

Dynamic simulations of movement allow one to study neuromuscular coordination, analyze athletic performance, and estimate internal loading of the musculoskeletal system. Simulations can also be used to identify the sources of pathological movement and establish a scientific basis for treatment planning. We have developed a freely available, open-source software system (OpenSim) that lets users develop models of musculoskeletal structures and create dynamic simulations of a wide variety of movements. We are using this system to simulate the dynamics of individuals with pathological gait and to explore the biomechanical effects of treatments. OpenSim provides a platform on which the biomechanics community can build a library of simulations that can be exchanged, tested, analyzed, and improved through a multi-institutional collaboration. Developing software that enables a concerted effort from many investigators poses technical and sociological challenges. Meeting those challenges will accelerate the discovery of principles that govern movement control and improve treatments for individuals with movement pathologies.

Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application.

PubMed

Hanwell, Marcus D; de Jong, Wibe A; Harris, Christopher J

2017-10-30

An end-to-end platform for chemical science research has been developed that integrates data from computational and experimental approaches through a modern web-based interface. The platform offers an interactive visualization and analytics environment that functions well on mobile, laptop and desktop devices. It offers pragmatic solutions to ensure that large and complex data sets are more accessible. Existing desktop applications/frameworks were extended to integrate with high-performance computing resources, and offer command-line tools to automate interaction-connecting distributed teams to this software platform on their own terms. The platform was developed openly, and all source code hosted on the GitHub platform with automated deployment possible using Ansible coupled with standard Ubuntu-based machine images deployed to cloud machines. The platform is designed to enable teams to reap the benefits of the connected web-going beyond what conventional search and analytics platforms offer in this area. It also has the goal of offering federated instances, that can be customized to the sites/research performed. Data gets stored using JSON, extending upon previous approaches using XML, building structures that support computational chemistry calculations. These structures were developed to make it easy to process data across different languages, and send data to a JavaScript-based web client.

Specifications and implementation of the RT MHD control system for the EC launcher of FTU

NASA Astrophysics Data System (ADS)

Galperti, C.; Alessi, E.; Boncagni, L.; Bruschi, A.; Granucci, G.; Grosso, A.; Iannone, F.; Marchetto, C.; Nowak, S.; Panella, M.; Sozzi, C.; Tilia, B.

2012-09-01

To perform real time plasma control experiments using EC heating waves by using the new fast launcher installed on FTU a dedicated data acquisition and elaboration system has been designed recently. A prototypical version of the acquisition/control system has been recently developed and will be tested on FTU machine in its next experimental campaign. The open-source framework MARTe (Multi-threaded Application Real-Time executor) on Linux/RTAI real-time operating system has been chosen as software platform to realize the control system. Standard open-architecture industrial PCs, based either on VME bus and CompactPCI bus equipped with standard input/output cards are the chosen hardware platform.

RAPID and DDS

NASA Technical Reports Server (NTRS)

Utz, Hans Heinrich

2011-01-01

This talk gives an overview of the the Robot Applications Programmers Interface Delegate (RAPID) as well as the distributed systems middleware Data Distribution Service (DDS). DDS is an open software standard, RAPID is cleared for open-source release under NOSA. RAPID specifies data-structures and semantics for high-level telemetry published by NASA robotic software. These data-structures are supported by multiple robotic platforms at Johnson Space Center (JSC), Jet Propulsion Laboratory (JPL) and Ames Research Center (ARC), providing high-level interoperability between those platforms. DDS is used as the middleware for data transfer. The feature set of the middleware heavily influences the design decision made in the RAPID specification. So it is appropriate to discuss both in this introductory talk.

Integrated genome browser: visual analytics platform for genomics.

PubMed

Freese, Nowlan H; Norris, David C; Loraine, Ann E

2016-07-15

Genome browsers that support fast navigation through vast datasets and provide interactive visual analytics functions can help scientists achieve deeper insight into biological systems. Toward this end, we developed Integrated Genome Browser (IGB), a highly configurable, interactive and fast open source desktop genome browser. Here we describe multiple updates to IGB, including all-new capabilities to display and interact with data from high-throughput sequencing experiments. To demonstrate, we describe example visualizations and analyses of datasets from RNA-Seq, ChIP-Seq and bisulfite sequencing experiments. Understanding results from genome-scale experiments requires viewing the data in the context of reference genome annotations and other related datasets. To facilitate this, we enhanced IGB's ability to consume data from diverse sources, including Galaxy, Distributed Annotation and IGB-specific Quickload servers. To support future visualization needs as new genome-scale assays enter wide use, we transformed the IGB codebase into a modular, extensible platform for developers to create and deploy all-new visualizations of genomic data. IGB is open source and is freely available from http://bioviz.org/igb aloraine@uncc.edu. © The Author 2016. Published by Oxford University Press.

Neuroimaging Data Sharing on the Neuroinformatics Database Platform

PubMed Central

Book, Gregory A; Stevens, Michael; Assaf, Michal; Glahn, David; Pearlson, Godfrey D

2015-01-01

We describe the Neuroinformatics Database (NiDB), an open-source database platform for archiving, analysis, and sharing of neuroimaging data. Data from the multi-site projects Autism Brain Imaging Data Exchange (ABIDE), Bipolar-Schizophrenia Network on Intermediate Phenotypes parts one and two (B-SNIP1, B-SNIP2), and Monetary Incentive Delay task (MID) are available for download from the public instance of NiDB, with more projects sharing data as it becomes available. As demonstrated by making several large datasets available, NiDB is an extensible platform appropriately suited to archive and distribute shared neuroimaging data. PMID:25888923

Moodle 2.0: Shifting from a Learning Toolkit to a Open Learning Platform

NASA Astrophysics Data System (ADS)

Alier, Marc; Casañ, María José; Piguillem, Jordi

Learning Management Systems (LMS) have reached a plateau of maturity in features, application to teaching practices and wide adoption by learning institutions. But the Web 2.0 carries new kinds of tools, services and ways of using the web; personally and socially. Some educators and learners have started to advocate for a new approach to frame one's learning sources, from the LMS course space towards Personal Learning Environments (PLE). But PLE's are characterized by its absence of structure, just what is provided by open standards and mashup techniques. Based on 5 years of participative observation research, this article explains the changes in architecture performed on the second version of Moodle, why did these changes happen and what should be the next steps so Moodle can shift from being a learning tool to a true open learning platform.

Global review of open access risk assessment software packages valid for global or continental scale analysis

NASA Astrophysics Data System (ADS)

Daniell, James; Simpson, Alanna; Gunasekara, Rashmin; Baca, Abigail; Schaefer, Andreas; Ishizawa, Oscar; Murnane, Rick; Tijssen, Annegien; Deparday, Vivien; Forni, Marc; Himmelfarb, Anne; Leder, Jan

2015-04-01

Over the past few decades, a plethora of open access software packages for the calculation of earthquake, volcanic, tsunami, storm surge, wind and flood have been produced globally. As part of the World Bank GFDRR Review released at the Understanding Risk 2014 Conference, over 80 such open access risk assessment software packages were examined. Commercial software was not considered in the evaluation. A preliminary analysis was used to determine whether the 80 models were currently supported and if they were open access. This process was used to select a subset of 31 models that include 8 earthquake models, 4 cyclone models, 11 flood models, and 8 storm surge/tsunami models for more detailed analysis. By using multi-criteria analysis (MCDA) and simple descriptions of the software uses, the review allows users to select a few relevant software packages for their own testing and development. The detailed analysis evaluated the models on the basis of over 100 criteria and provides a synopsis of available open access natural hazard risk modelling tools. In addition, volcano software packages have since been added making the compendium of risk software tools in excess of 100. There has been a huge increase in the quality and availability of open access/source software over the past few years. For example, private entities such as Deltares now have an open source policy regarding some flood models (NGHS). In addition, leaders in developing risk models in the public sector, such as Geoscience Australia (EQRM, TCRM, TsuDAT, AnuGA) or CAPRA (ERN-Flood, Hurricane, CRISIS2007 etc.), are launching and/or helping many other initiatives. As we achieve greater interoperability between modelling tools, we will also achieve a future wherein different open source and open access modelling tools will be increasingly connected and adapted towards unified multi-risk model platforms and highly customised solutions. It was seen that many software tools could be improved by enabling user-defined exposure and vulnerability. Without this function, many tools can only be used regionally and not at global or continental scale. It is becoming increasingly easy to use multiple packages for a single region and/or hazard to characterize the uncertainty in the risk, or use as checks for the sensitivities in the analysis. There is a potential for valuable synergy between existing software. A number of open source software packages could be combined to generate a multi-risk model with multiple views of a hazard. This extensive review has simply attempted to provide a platform for dialogue between all open source and open access software packages and to hopefully inspire collaboration between developers, given the great work done by all open access and open source developers.

OpenMebius: an open source software for isotopically nonstationary 13C-based metabolic flux analysis.

PubMed

Kajihata, Shuichi; Furusawa, Chikara; Matsuda, Fumio; Shimizu, Hiroshi

2014-01-01

The in vivo measurement of metabolic flux by (13)C-based metabolic flux analysis ((13)C-MFA) provides valuable information regarding cell physiology. Bioinformatics tools have been developed to estimate metabolic flux distributions from the results of tracer isotopic labeling experiments using a (13)C-labeled carbon source. Metabolic flux is determined by nonlinear fitting of a metabolic model to the isotopic labeling enrichment of intracellular metabolites measured by mass spectrometry. Whereas (13)C-MFA is conventionally performed under isotopically constant conditions, isotopically nonstationary (13)C metabolic flux analysis (INST-(13)C-MFA) has recently been developed for flux analysis of cells with photosynthetic activity and cells at a quasi-steady metabolic state (e.g., primary cells or microorganisms under stationary phase). Here, the development of a novel open source software for INST-(13)C-MFA on the Windows platform is reported. OpenMebius (Open source software for Metabolic flux analysis) provides the function of autogenerating metabolic models for simulating isotopic labeling enrichment from a user-defined configuration worksheet. Analysis using simulated data demonstrated the applicability of OpenMebius for INST-(13)C-MFA. Confidence intervals determined by INST-(13)C-MFA were less than those determined by conventional methods, indicating the potential of INST-(13)C-MFA for precise metabolic flux analysis. OpenMebius is the open source software for the general application of INST-(13)C-MFA.

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

ERDDAP: Reducing Data Friction with an Open Source Data Platform

NASA Astrophysics Data System (ADS)

O'Brien, K.

2017-12-01

Data friction is not just an issue facing interdisciplinary research. Often times, even within disciplines, significant data friction can exist. Issues of differing formats, limited metadata and non-existent machine-to-machine data access are all issues that exist within disciplines and make it that much harder for successful interdisciplinary cooperation. Therefore, reducing data friction within disciplines is crucial first step in providing better overall collaboration. ERDDAP, an open source data platform developed at NOAA's Southwest Fisheries Center, is well poised to improve data useability and understanding and reduce data friction, both in single and multi-disciplinary research. By virtue of its ability to integrate data of varying formats and provide RESTful-based user access to data and metadata, use of ERDDAP has grown substantially throughout the ocean data community. ERDDAP also supports standards such as the DAP data protocol, the Climate and Forecast (CF) metadata conventions and the Bagit document standard for data archival. In this presentation, we will discuss the advantages of using ERDDAP as a data platform. We will also show specific use cases where utilizing ERDDAP has reduced friction within a single discipline (physical oceanography) and improved interdisciplinary collaboration as well.

Open-source platform to benchmark fingerprints for ligand-based virtual screening

PubMed Central

2013-01-01

Similarity-search methods using molecular fingerprints are an important tool for ligand-based virtual screening. A huge variety of fingerprints exist and their performance, usually assessed in retrospective benchmarking studies using data sets with known actives and known or assumed inactives, depends largely on the validation data sets used and the similarity measure used. Comparing new methods to existing ones in any systematic way is rather difficult due to the lack of standard data sets and evaluation procedures. Here, we present a standard platform for the benchmarking of 2D fingerprints. The open-source platform contains all source code, structural data for the actives and inactives used (drawn from three publicly available collections of data sets), and lists of randomly selected query molecules to be used for statistically valid comparisons of methods. This allows the exact reproduction and comparison of results for future studies. The results for 12 standard fingerprints together with two simple baseline fingerprints assessed by seven evaluation methods are shown together with the correlations between methods. High correlations were found between the 12 fingerprints and a careful statistical analysis showed that only the two baseline fingerprints were different from the others in a statistically significant way. High correlations were also found between six of the seven evaluation methods, indicating that despite their seeming differences, many of these methods are similar to each other. PMID:23721588

Unified, Cross-Platform, Open-Source Library Package for High-Performance Computing

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

Kozacik, Stephen

Compute power is continually increasing, but this increased performance is largely found in sophisticated computing devices and supercomputer resources that are difficult to use, resulting in under-utilization. We developed a unified set of programming tools that will allow users to take full advantage of the new technology by allowing them to work at a level abstracted away from the platform specifics, encouraging the use of modern computing systems, including government-funded supercomputer facilities.

Image Harvest: an open-source platform for high-throughput plant image processing and analysis.

PubMed

Knecht, Avi C; Campbell, Malachy T; Caprez, Adam; Swanson, David R; Walia, Harkamal

2016-05-01

High-throughput plant phenotyping is an effective approach to bridge the genotype-to-phenotype gap in crops. Phenomics experiments typically result in large-scale image datasets, which are not amenable for processing on desktop computers, thus creating a bottleneck in the image-analysis pipeline. Here, we present an open-source, flexible image-analysis framework, called Image Harvest (IH), for processing images originating from high-throughput plant phenotyping platforms. Image Harvest is developed to perform parallel processing on computing grids and provides an integrated feature for metadata extraction from large-scale file organization. Moreover, the integration of IH with the Open Science Grid provides academic researchers with the computational resources required for processing large image datasets at no cost. Image Harvest also offers functionalities to extract digital traits from images to interpret plant architecture-related characteristics. To demonstrate the applications of these digital traits, a rice (Oryza sativa) diversity panel was phenotyped and genome-wide association mapping was performed using digital traits that are used to describe different plant ideotypes. Three major quantitative trait loci were identified on rice chromosomes 4 and 6, which co-localize with quantitative trait loci known to regulate agronomically important traits in rice. Image Harvest is an open-source software for high-throughput image processing that requires a minimal learning curve for plant biologists to analyzephenomics datasets. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Open Source Hardware for DIY Environmental Sensing

NASA Astrophysics Data System (ADS)

Aufdenkampe, A. K.; Hicks, S. D.; Damiano, S. G.; Montgomery, D. S.

2014-12-01

The Arduino open source electronics platform has been very popular within the DIY (Do It Yourself) community for several years, and it is now providing environmental science researchers with an inexpensive alternative to commercial data logging and transmission hardware. Here we present the designs for our latest series of custom Arduino-based dataloggers, which include wireless communication options like self-meshing radio networks and cellular phone modules. The main Arduino board uses a custom interface board to connect to various research-grade sensors to take readings of turbidity, dissolved oxygen, water depth and conductivity, soil moisture, solar radiation, and other parameters. Sensors with SDI-12 communications can be directly interfaced to the logger using our open Arduino-SDI-12 software library (https://github.com/StroudCenter/Arduino-SDI-12). Different deployment options are shown, like rugged enclosures to house the loggers and rigs for mounting the sensors in both fresh water and marine environments. After the data has been collected and transmitted by the logger, the data is received by a mySQL-PHP stack running on a web server that can be accessed from anywhere in the world. Once there, the data can be visualized on web pages or served though REST requests and Water One Flow (WOF) services. Since one of the main benefits of using open source hardware is the easy collaboration between users, we are introducing a new web platform for discussion and sharing of ideas and plans for hardware and software designs used with DIY environmental sensors and data loggers.

psiTurk: An open-source framework for conducting replicable behavioral experiments online.

PubMed

Gureckis, Todd M; Martin, Jay; McDonnell, John; Rich, Alexander S; Markant, Doug; Coenen, Anna; Halpern, David; Hamrick, Jessica B; Chan, Patricia

2016-09-01

Online data collection has begun to revolutionize the behavioral sciences. However, conducting carefully controlled behavioral experiments online introduces a number of new of technical and scientific challenges. The project described in this paper, psiTurk, is an open-source platform which helps researchers develop experiment designs which can be conducted over the Internet. The tool primarily interfaces with Amazon's Mechanical Turk, a popular crowd-sourcing labor market. This paper describes the basic architecture of the system and introduces new users to the overall goals. psiTurk aims to reduce the technical hurdles for researchers developing online experiments while improving the transparency and collaborative nature of the behavioral sciences.

DeNovoGUI: An Open Source Graphical User Interface for de Novo Sequencing of Tandem Mass Spectra

PubMed Central

2013-01-01

De novo sequencing is a popular technique in proteomics for identifying peptides from tandem mass spectra without having to rely on a protein sequence database. Despite the strong potential of de novo sequencing algorithms, their adoption threshold remains quite high. We here present a user-friendly and lightweight graphical user interface called DeNovoGUI for running parallelized versions of the freely available de novo sequencing software PepNovo+, greatly simplifying the use of de novo sequencing in proteomics. Our platform-independent software is freely available under the permissible Apache2 open source license. Source code, binaries, and additional documentation are available at http://denovogui.googlecode.com. PMID:24295440

DeNovoGUI: an open source graphical user interface for de novo sequencing of tandem mass spectra.

PubMed

Muth, Thilo; Weilnböck, Lisa; Rapp, Erdmann; Huber, Christian G; Martens, Lennart; Vaudel, Marc; Barsnes, Harald

2014-02-07

De novo sequencing is a popular technique in proteomics for identifying peptides from tandem mass spectra without having to rely on a protein sequence database. Despite the strong potential of de novo sequencing algorithms, their adoption threshold remains quite high. We here present a user-friendly and lightweight graphical user interface called DeNovoGUI for running parallelized versions of the freely available de novo sequencing software PepNovo+, greatly simplifying the use of de novo sequencing in proteomics. Our platform-independent software is freely available under the permissible Apache2 open source license. Source code, binaries, and additional documentation are available at http://denovogui.googlecode.com .

The Biopsychology-Toolbox: a free, open-source Matlab-toolbox for the control of behavioral experiments.

PubMed

Rose, Jonas; Otto, Tobias; Dittrich, Lars

2008-10-30

The Biopsychology-Toolbox is a free, open-source Matlab-toolbox for the control of behavioral experiments. The major aim of the project was to provide a set of basic tools that allow programming novices to control basic hardware used for behavioral experimentation without limiting the power and flexibility of the underlying programming language. The modular design of the toolbox allows portation of parts as well as entire paradigms between different types of hardware. In addition to the toolbox, this project offers a platform for the exchange of functions, hardware solutions and complete behavioral paradigms.

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

Mashup Scheme Design of Map Tiles Using Lightweight Open Source Webgis Platform

NASA Astrophysics Data System (ADS)

Hu, T.; Fan, J.; He, H.; Qin, L.; Li, G.

2018-04-01

To address the difficulty involved when using existing commercial Geographic Information System platforms to integrate multi-source image data fusion, this research proposes the loading of multi-source local tile data based on CesiumJS and examines the tile data organization mechanisms and spatial reference differences of the CesiumJS platform, as well as various tile data sources, such as Google maps, Map World, and Bing maps. Two types of tile data loading schemes have been designed for the mashup of tiles, the single data source loading scheme and the multi-data source loading scheme. The multi-sources of digital map tiles used in this paper cover two different but mainstream spatial references, the WGS84 coordinate system and the Web Mercator coordinate system. According to the experimental results, the single data source loading scheme and the multi-data source loading scheme with the same spatial coordinate system showed favorable visualization effects; however, the multi-data source loading scheme was prone to lead to tile image deformation when loading multi-source tile data with different spatial references. The resulting method provides a low cost and highly flexible solution for small and medium-scale GIS programs and has a certain potential for practical application values. The problem of deformation during the transition of different spatial references is an important topic for further research.

CompactPCI/Linux Platform in FTU Slow Control System

NASA Astrophysics Data System (ADS)

Iannone, F.; Wang, L.; Centioli, C.; Panella, M.; Mazza, G.; Vitale, V.

2004-12-01

In large fusion experiments, such as tokamak devices, there is a common trend for slow control systems. Because of complexity of the plants, the so-called `Standard Model' (SM) in slow control has been adopted on several tokamak machines. This model is based on a three-level hierarchical control: 1) High-Level Control (HLC) with a supervisory function; 2) Medium-Level Control (MLC) to interface and concentrate I/O field equipments; 3) Low-Level Control (LLC) with hard real-time I/O function, often managed by PLCs. FTU control system designed with SM concepts has underwent several stages of developments in its fifteen years duration of runs. The latest evolution was inevitable, due to the obsolescence of the MLC CPUs, based on VME-MOTOROLA 68030 with OS9 operating system. A large amount of C code was developed for that platform to route the data flow from LLC, which is constituted by 24 Westinghouse Numalogic PC-700 PLCs with about 8000 field-points, to HLC, based on a commercial Object-Oriented Real-Time database on Alpha/CompaqTru64 platform. Therefore, we have to look for cost-effective solutions and finally a CompactPCI-Intel x86 platform with Linux operating system was chosen. A software porting has been done, taking into account the differences between OS9 and Linux operating system in terms of Inter/Network Processes Communications and I/O multi-ports serial driver. This paper describes the hardware/software architecture of the new MLC system, emphasizing the reliability and the low costs of the open source solutions. Moreover, a huge amount of software packages available in open source environment will assure a less painful maintenance, and will open the way to further improvements of the system itself.

Enhancing participatory approach in water resources management: development of a survey to evaluate stakeholders needs and priorities related to software capabilities

NASA Astrophysics Data System (ADS)

Foglia, L.; Rossetto, R.; Borsi, I.; Josef, S.; Boukalova, Z.; Triana, F.; Ghetta, M.; Sabbatini, T.; Bonari, E.; Cannata, M.; De Filippis, G.

2016-12-01

The EU H2020 FREEWAT project (FREE and open source software tools for WATer resource management) aims at simplifying the application of EU-water related Directives, by developing an open source and public domain, GIS-integrated platform for planning and management of ground- and surface-water resources. The FREEWAT platform is conceived as a canvas, where several distributed and physically-based simulation codes are virtually integrated. The choice of such codes was supported by the result of a survey performed by means of questionnaires distributed to 14 case study FREEWAT project partners and several stakeholders. This was performed in the first phase of the project within the WP 6 (Enhanced science and participatory approach evidence-based decision making), Task 6.1 (Definition of a "needs/tools" evaluation grid). About 30% among all the invited entities and institutions from several EU and non-EU Countries expressed their interest in contributing to the survey. Most of them were research institutions, government and geoenvironmental companies and river basin authorities.The result of the questionnaire provided a spectrum of needs and priorities of partners/stakeholders, which were addressed during the development phase of the FREEWAT platform. The main needs identified were related to ground- and surface-water quality, sustainable water management, interaction between groundwater/surface-water bodies, and design and management of Managed Aquifer Recharge schemes. Needs and priorities were then connected to the specific EU Directives and Regulations to be addressed.One of the main goals of the questionnaires was to collect information and suggestions regarding the use of existing commercial/open-source software tools to address needs and priorities, and regarding the needs to address specific water-related processes/problems.

Open source 3D printers: an appropriate technology for building low cost optics labs for the developing communities

NASA Astrophysics Data System (ADS)

Gwamuri, J.; Pearce, Joshua M.

2017-08-01

The recent introduction of RepRap (self-replicating rapid prototyper) 3-D printers and the resultant open source technological improvements have resulted in affordable 3-D printing, enabling low-cost distributed manufacturing for individuals. This development and others such as the rise of open source-appropriate technology (OSAT) and solar powered 3-D printing are moving 3-D printing from an industry based technology to one that could be used in the developing world for sustainable development. In this paper, we explore some specific technological improvements and how distributed manufacturing with open-source 3-D printing can be used to provide open-source 3-D printable optics components for developing world communities through the ability to print less expensive and customized products. This paper presents an open-source low cost optical equipment library which enables relatively easily adapted customizable designs with the potential of changing the way optics is taught in resource constraint communities. The study shows that this method of scientific hardware development has a potential to enables a much broader audience to participate in optical experimentation both as research and teaching platforms. Conclusions on the technical viability of 3-D printing to assist in development and recommendations on how developing communities can fully exploit this technology to improve the learning of optics through hands-on methods have been outlined.

A Scalable, Open Source Platform for Data Processing, Archiving and Dissemination

DTIC Science & Technology

2016-01-01

Object Oriented Data Technology (OODT) big data toolkit developed by NASA and the Work-flow INstance Generation and Selection (WINGS) scientific work...to several challenge big data problems and demonstrated the utility of OODT-WINGS in addressing them. Specific demonstrated analyses address i...source software, Apache, Object Oriented Data Technology, OODT, semantic work-flows, WINGS, big data , work- flow management 16. SECURITY CLASSIFICATION OF

Building Energy Management Open Source Software

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

This is the repository for Building Energy Management Open Source Software (BEMOSS), which is an open source operating system that is engineered to improve sensing and control of equipment in small- and medium-sized commercial buildings. BEMOSS offers the following key features: (1) Open source, open architecture – BEMOSS is an open source operating system that is built upon VOLTTRON – a distributed agent platform developed by Pacific Northwest National Laboratory (PNNL). BEMOSS was designed to make it easy for hardware manufacturers to seamlessly interface their devices with BEMOSS. Software developers can also contribute to adding additional BEMOSS functionalities and applications.more » (2) Plug & play – BEMOSS was designed to automatically discover supported load controllers (including smart thermostats, VAV/RTUs, lighting load controllers and plug load controllers) in commercial buildings. (3) Interoperability – BEMOSS was designed to work with load control devices form different manufacturers that operate on different communication technologies and data exchange protocols. (4) Cost effectiveness – Implementation of BEMOSS deemed to be cost-effective as it was built upon a robust open source platform that can operate on a low-cost single-board computer, such as Odroid. This feature could contribute to its rapid deployment in small- or medium-sized commercial buildings. (5) Scalability and ease of deployment – With its multi-node architecture, BEMOSS provides a distributed architecture where load controllers in a multi-floor and high occupancy building could be monitored and controlled by multiple single-board computers hosting BEMOSS. This makes it possible for a building engineer to deploy BEMOSS in one zone of a building, be comfortable with its operation, and later on expand the deployment to the entire building to make it more energy efficient. (6) Ability to provide local and remote monitoring – BEMOSS provides both local and remote monitoring ability with role-based access control. (7) Security – In addition to built-in security features provided by VOLTTRON, BEMOSS provides enhanced security features, including BEMOSS discovery approval process, encrypted core-to-node communication, thermostat anti-tampering feature and many more. (8) Support from the Advisory Committee – BEMOSS was developed in consultation with an advisory committee from the beginning of the project. BEMOSS advisory committee comprises representatives from 22 organizations from government and industry.« less

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.

Steady-state capabilities for hydroturbines with OpenFOAM

NASA Astrophysics Data System (ADS)

Page, M.; Beaudoin, M.; Giroux, A. M.

2010-08-01

The availability of a high quality Open Source CFD simulation platform like OpenFOAM offers new R&D opportunities by providing direct access to models and solver implementation details. Efforts have been made by Hydro-Québec to adapt OpenFOAM to hydroturbines for the development of steady-state capabilities. The paper describes the developments that have been made to implement new turbomachinery related capabilities: Multiple Frame of Reference solver, domain coupling interfaces (GGI, cyclicGGI and mixing plane) and specialized boundary conditions. Practical use of the new turbomachinery capabilities are demonstrated for the analysis of a 195-MW Francis hydroturbine.

Climate Signals: An On-Line Digital Platform for Mapping Climate Change Impacts in Real Time

NASA Astrophysics Data System (ADS)

Cutting, H.

2016-12-01

Climate Signals is an on-line digital platform for cataloging and mapping the impacts of climate change. The CS platform specifies and details the chains of connections between greenhouse gas emissions and individual climate events. Currently in open-beta release, the platform is designed to to engage and serve the general public, news media, and policy-makers, particularly in real-time during extreme climate events. Climate Signals consists of a curated relational database of events and their links to climate change, a mapping engine, and a gallery of climate change monitors offering real-time data. For each event in the database, an infographic engine provides a custom attribution "tree" that illustrates the connections to climate change. In addition, links to key contextual resources are aggregated and curated for each event. All event records are fully annotated with detailed source citations and corresponding hyper links. The system of attribution used to link events to climate change in real-time is detailed here. This open-beta release is offered for public user testing and engagement. Launched in May 2016, the operation of this platform offers lessons for public engagement in climate change impacts.

Performance evaluation of OpenFOAM on many-core architectures

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

Brzobohatý, Tomáš; Říha, Lubomír; Karásek, Tomáš, E-mail: tomas.karasek@vsb.cz

In this article application of Open Source Field Operation and Manipulation (OpenFOAM) C++ libraries for solving engineering problems on many-core architectures is presented. Objective of this article is to present scalability of OpenFOAM on parallel platforms solving real engineering problems of fluid dynamics. Scalability test of OpenFOAM is performed using various hardware and different implementation of standard PCG and PBiCG Krylov iterative methods. Speed up of various implementations of linear solvers using GPU and MIC accelerators are presented in this paper. Numerical experiments of 3D lid-driven cavity flow for several cases with various number of cells are presented.

Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application

DOE PAGES

Hanwell, Marcus D.; de Jong, Wibe A.; Harris, Christopher J.

2017-10-30

An end-to-end platform for chemical science research has been developed that integrates data from computational and experimental approaches through a modern web-based interface. The platform offers an interactive visualization and analytics environment that functions well on mobile, laptop and desktop devices. It offers pragmatic solutions to ensure that large and complex data sets are more accessible. Existing desktop applications/frameworks were extended to integrate with high-performance computing resources, and offer command-line tools to automate interaction - connecting distributed teams to this software platform on their own terms. The platform was developed openly, and all source code hosted on the GitHub platformmore » with automated deployment possible using Ansible coupled with standard Ubuntu-based machine images deployed to cloud machines. The platform is designed to enable teams to reap the benefits of the connected web - going beyond what conventional search and analytics platforms offer in this area. It also has the goal of offering federated instances, that can be customized to the sites/research performed. Data gets stored using JSON, extending upon previous approaches using XML, building structures that support computational chemistry calculations. These structures were developed to make it easy to process data across different languages, and send data to a JavaScript-based web client.« less

Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application

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

Hanwell, Marcus D.; de Jong, Wibe A.; Harris, Christopher J.

An end-to-end platform for chemical science research has been developed that integrates data from computational and experimental approaches through a modern web-based interface. The platform offers an interactive visualization and analytics environment that functions well on mobile, laptop and desktop devices. It offers pragmatic solutions to ensure that large and complex data sets are more accessible. Existing desktop applications/frameworks were extended to integrate with high-performance computing resources, and offer command-line tools to automate interaction - connecting distributed teams to this software platform on their own terms. The platform was developed openly, and all source code hosted on the GitHub platformmore » with automated deployment possible using Ansible coupled with standard Ubuntu-based machine images deployed to cloud machines. The platform is designed to enable teams to reap the benefits of the connected web - going beyond what conventional search and analytics platforms offer in this area. It also has the goal of offering federated instances, that can be customized to the sites/research performed. Data gets stored using JSON, extending upon previous approaches using XML, building structures that support computational chemistry calculations. These structures were developed to make it easy to process data across different languages, and send data to a JavaScript-based web client.« less

A Standard Platform for Testing and Comparison of MDAO Architectures

NASA Technical Reports Server (NTRS)

Gray, Justin S.; Moore, Kenneth T.; Hearn, Tristan A.; Naylor, Bret A.

2012-01-01

The Multidisciplinary Design Analysis and Optimization (MDAO) community has developed a multitude of algorithms and techniques, called architectures, for performing optimizations on complex engineering systems which involve coupling between multiple discipline analyses. These architectures seek to efficiently handle optimizations with computationally expensive analyses including multiple disciplines. We propose a new testing procedure that can provide a quantitative and qualitative means of comparison among architectures. The proposed test procedure is implemented within the open source framework, OpenMDAO, and comparative results are presented for five well-known architectures: MDF, IDF, CO, BLISS, and BLISS-2000. We also demonstrate how using open source soft- ware development methods can allow the MDAO community to submit new problems and architectures to keep the test suite relevant.

Development of an open-source cloud-connected sensor-monitoring platform

USDA-ARS?s Scientific Manuscript database

Rapid advances in electronics and communications technologies offer continuously evolving options for sensing and awareness of the physical environment. Many of these advances are becoming increasingly available to “non-professionals,” that is, those without formal training or expertise in discipli...

Design of a Community-Engaged Health Informatics Platform with an Architecture of Participation.

PubMed

Millery, Mari; Ramos, Wilson; Lien, Chueh; Aguirre, Alejandra N; Kukafka, Rita

2015-01-01

Community-engaged health informatics (CEHI) applies information technology and participatory approaches to improve the health of communities. Our objective was to translate the concept of CEHI into a usable and replicable informatics platform that will facilitate community-engaged practice and research. The setting is a diverse urban neighborhood in New York City. The methods included community asset mapping, stakeholder interviews, logic modeling, analysis of affordances in open-source tools, elicitation of use cases and requirements, and a survey of early adopters. Based on synthesis of data collected, GetHealthyHeigths.org (GHH) was developed using open-source LAMP stack and Drupal content management software. Drupal's organic groups module was used for novel participatory functionality, along with detailed user roles and permissions. Future work includes evaluation of GHH and its impact on agency and service networks. We plan to expand GHH with additional functionality to further support CEHI by combining informatics solutions with community engagement to improve health.

Design of a Community-Engaged Health Informatics Platform with an Architecture of Participation

PubMed Central

Millery, Mari; Ramos, Wilson; Lien, Chueh; Aguirre, Alejandra N.; Kukafka, Rita

2015-01-01

Community-engaged health informatics (CEHI) applies information technology and participatory approaches to improve the health of communities. Our objective was to translate the concept of CEHI into a usable and replicable informatics platform that will facilitate community-engaged practice and research. The setting is a diverse urban neighborhood in New York City. The methods included community asset mapping, stakeholder interviews, logic modeling, analysis of affordances in open-source tools, elicitation of use cases and requirements, and a survey of early adopters. Based on synthesis of data collected, GetHealthyHeigths.org (GHH) was developed using open-source LAMP stack and Drupal content management software. Drupal’s organic groups module was used for novel participatory functionality, along with detailed user roles and permissions. Future work includes evaluation of GHH and its impact on agency and service networks. We plan to expand GHH with additional functionality to further support CEHI by combining informatics solutions with community engagement to improve health. PMID:26958227

The Digital Slide Archive: A Software Platform for Management, Integration, and Analysis of Histology for Cancer Research.

PubMed

Gutman, David A; Khalilia, Mohammed; Lee, Sanghoon; Nalisnik, Michael; Mullen, Zach; Beezley, Jonathan; Chittajallu, Deepak R; Manthey, David; Cooper, Lee A D

2017-11-01

Tissue-based cancer studies can generate large amounts of histology data in the form of glass slides. These slides contain important diagnostic, prognostic, and biological information and can be digitized into expansive and high-resolution whole-slide images using slide-scanning devices. Effectively utilizing digital pathology data in cancer research requires the ability to manage, visualize, share, and perform quantitative analysis on these large amounts of image data, tasks that are often complex and difficult for investigators with the current state of commercial digital pathology software. In this article, we describe the Digital Slide Archive (DSA), an open-source web-based platform for digital pathology. DSA allows investigators to manage large collections of histologic images and integrate them with clinical and genomic metadata. The open-source model enables DSA to be extended to provide additional capabilities. Cancer Res; 77(21); e75-78. ©2017 AACR . ©2017 American Association for Cancer Research.

PIVOT: platform for interactive analysis and visualization of transcriptomics data.

PubMed

Zhu, Qin; Fisher, Stephen A; Dueck, Hannah; Middleton, Sarah; Khaladkar, Mugdha; Kim, Junhyong

2018-01-05

Many R packages have been developed for transcriptome analysis but their use often requires familiarity with R and integrating results of different packages requires scripts to wrangle the datatypes. Furthermore, exploratory data analyses often generate multiple derived datasets such as data subsets or data transformations, which can be difficult to track. Here we present PIVOT, an R-based platform that wraps open source transcriptome analysis packages with a uniform user interface and graphical data management that allows non-programmers to interactively explore transcriptomics data. PIVOT supports more than 40 popular open source packages for transcriptome analysis and provides an extensive set of tools for statistical data manipulations. A graph-based visual interface is used to represent the links between derived datasets, allowing easy tracking of data versions. PIVOT further supports automatic report generation, publication-quality plots, and program/data state saving, such that all analysis can be saved, shared and reproduced. PIVOT will allow researchers with broad background to easily access sophisticated transcriptome analysis tools and interactively explore transcriptome datasets.

Supporting Building Portfolio Investment and Policy Decision Making through an Integrated Building Utility Data Platform

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

Aziz, Azizan; Lasternas, Bertrand; Alschuler, Elena

The American Recovery and Reinvestment Act stimulus funding of 2009 for smart grid projects resulted in the tripling of smart meters deployment. In 2012, the Green Button initiative provided utility customers with access to their real-time1 energy usage. The availability of finely granular data provides an enormous potential for energy data analytics and energy benchmarking. The sheer volume of time-series utility data from a large number of buildings also poses challenges in data collection, quality control, and database management for rigorous and meaningful analyses. In this paper, we will describe a building portfolio-level data analytics tool for operational optimization, businessmore » investment and policy assessment using 15-minute to monthly intervals utility data. The analytics tool is developed on top of the U.S. Department of Energy’s Standard Energy Efficiency Data (SEED) platform, an open source software application that manages energy performance data of large groups of buildings. To support the significantly large volume of granular interval data, we integrated a parallel time-series database to the existing relational database. The time-series database improves on the current utility data input, focusing on real-time data collection, storage, analytics and data quality control. The fully integrated data platform supports APIs for utility apps development by third party software developers. These apps will provide actionable intelligence for building owners and facilities managers. Unlike a commercial system, this platform is an open source platform funded by the U.S. Government, accessible to the public, researchers and other developers, to support initiatives in reducing building energy consumption.« less

Operational use of open satellite data for marine water quality monitoring

NASA Astrophysics Data System (ADS)

Symeonidis, Panagiotis; Vakkas, Theodoros

2017-09-01

The purpose of this study was to develop an operational platform for marine water quality monitoring using near real time satellite data. The developed platform utilizes free and open satellite data available from different data sources like COPERNICUS, the European Earth Observation Initiative, or NASA, from different satellites and instruments. The quality of the marine environment is operationally evaluated using parameters like chlorophyll-a concentration, water color and Sea Surface Temperature (SST). For each parameter, there are more than one dataset available, from different data sources or satellites, to allow users to select the most appropriate dataset for their area or time of interest. The above datasets are automatically downloaded from the data provider's services and ingested to the central, spatial engine. The spatial data platform uses the Postgresql database with the PostGIS extension for spatial data storage and Geoserver for the provision of the spatial data services. The system provides daily, 10 days and monthly maps and time series of the above parameters. The information is provided using a web client which is based on the GET SDI PORTAL, an easy to use and feature rich geospatial visualization and analysis platform. The users can examine the temporal variation of the parameters using a simple time animation tool. In addition, with just one click on the map, the system provides an interactive time series chart for any of the parameters of the available datasets. The platform can be offered as Software as a Service (SaaS) to any area in the Mediterranean region.

Power Watch - A global, open database of power plants that supports research on climate, water and air pollution impact of the global power sector.

NASA Astrophysics Data System (ADS)

Friedrich, J.; Kressig, A.; Van Groenou, S.; McCormick, C.

2017-12-01

Challenge The lack of transparent, accessible, and centralized power sector data inhibits the ability to research the impact of the global power sector. information gaps for citizens, analysts, and decision makers worldwide create barriers to sustainable development efforts. The need for transparent, accessible, and centralized information is especially important to enhance the commitments outlined in the recently adopted Paris Agreement and Sustainable Development Goals. Offer Power Watch will address this challenge by creating a comprehensive, open-source platform on the world's power systems. The platform hosts data on 85% of global installed electrical capacity and for each power plant will include data points on installed capacity, fuel type, annual generation, commissioning year, with more characteristics like emissions, particulate matter, annual water demand and more added over time. Most of the data is reported from national level sources, but annual generation and other operational characteristiscs are estimated via Machine Learning modeling and remotely sensed data when not officially reported. In addition, Power Watch plans to provide a suite of tools that address specific decision maker needs, such as water risk assessments and air pollution modeling. Impact Through open data, the platform and its tools will allow reserachers to do more analysis of power sector impacts and perform energy modeling. It will help catalyze accountability for policy makers, businesses, and investors and will inform and drive the transition to a clean energy future while reaching development targets.

Real time wind farm emulation using SimWindFarm toolbox

NASA Astrophysics Data System (ADS)

Topor, Marcel

2016-06-01

This paper presents a wind farm emulation solution using an open source Matlab/Simulink toolbox and the National Instruments cRIO platform. This work is based on the Aeolus SimWindFarm (SWF) toolbox models developed at Aalborg university, Denmark. Using the Matlab Simulink models developed in SWF, the modeling code can be exported to a real time model using the NI Veristand model framework and the resulting code is integrated as a hardware in the loop control on the NI 9068 platform.

The digital code driven autonomous synthesis of ibuprofen automated in a 3D-printer-based robot

PubMed Central

Kitson, Philip J; Glatzel, Stefan

2016-01-01

An automated synthesis robot was constructed by modifying an open source 3D printing platform. The resulting automated system was used to 3D print reaction vessels (reactionware) of differing internal volumes using polypropylene feedstock via a fused deposition modeling 3D printing approach and subsequently make use of these fabricated vessels to synthesize the nonsteroidal anti-inflammatory drug ibuprofen via a consecutive one-pot three-step approach. The synthesis of ibuprofen could be achieved on different scales simply by adjusting the parameters in the robot control software. The software for controlling the synthesis robot was written in the python programming language and hard-coded for the synthesis of ibuprofen by the method described, opening possibilities for the sharing of validated synthetic ‘programs’ which can run on similar low cost, user-constructed robotic platforms towards an ‘open-source’ regime in the area of chemical synthesis. PMID:28144350

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.

LOVD: easy creation of a locus-specific sequence variation database using an "LSDB-in-a-box" approach.

PubMed

Fokkema, Ivo F A C; den Dunnen, Johan T; Taschner, Peter E M

2005-08-01

The completion of the human genome project has initiated, as well as provided the basis for, the collection and study of all sequence variation between individuals. Direct access to up-to-date information on sequence variation is currently provided most efficiently through web-based, gene-centered, locus-specific databases (LSDBs). We have developed the Leiden Open (source) Variation Database (LOVD) software approaching the "LSDB-in-a-Box" idea for the easy creation and maintenance of a fully web-based gene sequence variation database. LOVD is platform-independent and uses PHP and MySQL open source software only. The basic gene-centered and modular design of the database follows the recommendations of the Human Genome Variation Society (HGVS) and focuses on the collection and display of DNA sequence variations. With minimal effort, the LOVD platform is extendable with clinical data. The open set-up should both facilitate and promote functional extension with scripts written by the community. The LOVD software is freely available from the Leiden Muscular Dystrophy pages (www.DMD.nl/LOVD/). To promote the use of LOVD, we currently offer curators the possibility to set up an LSDB on our Leiden server. (c) 2005 Wiley-Liss, Inc.

The Importance of Artificial Intelligence for Naval Intelligence Training Simulations

DTIC Science & Technology

2006-09-01

experimental investigation described later. B. SYSTEM ARCHITECTURE The game-based simulator was created using NetBeans , which is an open source integrated...development environment (IDE) written entirely in Java using the NetBeans Platform. NetBeans is based upon the Java language which contains the...involved within the simulation are conducted in a GUI built within the NetBeans IDE. The opening display allows the user to setup the simulation

Neural ensemble communities: Open-source approaches to hardware for large-scale electrophysiology

PubMed Central

Siegle, Joshua H.; Hale, Gregory J.; Newman, Jonathan P.; Voigts, Jakob

2014-01-01

One often-overlooked factor when selecting a platform for large-scale electrophysiology is whether or not a particular data acquisition system is “open” or “closed”: that is, whether or not the system’s schematics and source code are available to end users. Open systems have a reputation for being difficult to acquire, poorly documented, and hard to maintain. With the arrival of more powerful and compact integrated circuits, rapid prototyping services, and web-based tools for collaborative development, these stereotypes must be reconsidered. We discuss some of the reasons why multichannel extracellular electrophysiology could benefit from open-source approaches and describe examples of successful community-driven tool development within this field. In order to promote the adoption of open-source hardware and to reduce the need for redundant development efforts, we advocate a move toward standardized interfaces that connect each element of the data processing pipeline. This will give researchers the flexibility to modify their tools when necessary, while allowing them to continue to benefit from the high-quality products and expertise provided by commercial vendors. PMID:25528614

Development of a web application for water resources based on open source software

NASA Astrophysics Data System (ADS)

Delipetrev, Blagoj; Jonoski, Andreja; Solomatine, Dimitri P.

2014-01-01

This article presents research and development of a prototype web application for water resources using latest advancements in Information and Communication Technologies (ICT), open source software and web GIS. The web application has three web services for: (1) managing, presenting and storing of geospatial data, (2) support of water resources modeling and (3) water resources optimization. The web application is developed using several programming languages (PhP, Ajax, JavaScript, Java), libraries (OpenLayers, JQuery) and open source software components (GeoServer, PostgreSQL, PostGIS). The presented web application has several main advantages: it is available all the time, it is accessible from everywhere, it creates a real time multi-user collaboration platform, the programing languages code and components are interoperable and designed to work in a distributed computer environment, it is flexible for adding additional components and services and, it is scalable depending on the workload. The application was successfully tested on a case study with concurrent multi-users access.

GO2OGS 1.0: a versatile workflow to integrate complex geological information with fault data into numerical simulation models

NASA Astrophysics Data System (ADS)

Fischer, T.; Naumov, D.; Sattler, S.; Kolditz, O.; Walther, M.

2015-11-01

We offer a versatile workflow to convert geological models built with the ParadigmTM GOCAD© (Geological Object Computer Aided Design) software into the open-source VTU (Visualization Toolkit unstructured grid) format for usage in numerical simulation models. Tackling relevant scientific questions or engineering tasks often involves multidisciplinary approaches. Conversion workflows are needed as a way of communication between the diverse tools of the various disciplines. Our approach offers an open-source, platform-independent, robust, and comprehensible method that is potentially useful for a multitude of environmental studies. With two application examples in the Thuringian Syncline, we show how a heterogeneous geological GOCAD model including multiple layers and faults can be used for numerical groundwater flow modeling, in our case employing the OpenGeoSys open-source numerical toolbox for groundwater flow simulations. The presented workflow offers the chance to incorporate increasingly detailed data, utilizing the growing availability of computational power to simulate numerical models.

Leveraging Open Standards and Technologies to Enhance Community Access to Earth Science Lidar Data

NASA Astrophysics Data System (ADS)

Crosby, C. J.; Nandigam, V.; Krishnan, S.; Cowart, C.; Baru, C.; Arrowsmith, R.

2011-12-01

Lidar (Light Detection and Ranging) data, collected from space, airborne and terrestrial platforms, have emerged as an invaluable tool for a variety of Earth science applications ranging from ice sheet monitoring to modeling of earth surface processes. However, lidar present a unique suite of challenges from the perspective of building cyberinfrastructure systems that enable the scientific community to access these valuable research datasets. Lidar data are typically characterized by millions to billions of individual measurements of x,y,z position plus attributes; these "raw" data are also often accompanied by derived raster products and are frequently terabytes in size. As a relatively new and rapidly evolving data collection technology, relevant open data standards and software projects are immature compared to those for other remote sensing platforms. The NSF-funded OpenTopography Facility project has developed an online lidar data access and processing system that co-locates data with on-demand processing tools to enable users to access both raw point cloud data as well as custom derived products and visualizations. OpenTopography is built on a Service Oriented Architecture (SOA) in which applications and data resources are deployed as standards compliant (XML and SOAP) Web services with the open source Opal Toolkit. To develop the underlying applications for data access, filtering and conversion, and various processing tasks, OpenTopography has heavily leveraged existing open source software efforts for both lidar and raster data. Operating on the de facto LAS binary point cloud format (maintained by ASPRS), open source libLAS and LASlib libraries provide OpenTopography data ingestion, query and translation capabilities. Similarly, raster data manipulation is performed through a suite of services built on the Geospatial Data Abstraction Library (GDAL). OpenTopography has also developed our own algorithm for high-performance gridding of lidar point cloud data, Points2Grid, and have released the code as an open source project. An emerging conversation that the lidar community and OpenTopography are actively engaged in is the need for open, community supported standards and metadata for both full waveform and terrestrial (waveform and discrete return) lidar data. Further, given the immature nature of many lidar data archives and limited online access to public domain data, there is an opportunity to develop interoperable data catalogs based on an open standard such as the OGC CSW specification to facilitate discovery and access to Earth science oriented lidar data.

Long distance education for croatian nurses with open source software.

PubMed

Radenovic, Aleksandar; Kalauz, Sonja

2006-01-01

Croatian Nursing Informatics Association (CNIA) has been established as result of continuing work on promoting nursing informatics in Croatia. Main goals of CNIA are promoting nursing informatics and education of nurses about nursing informatics and using information technology in nursing process. CNIA in start of work is developed three courses from nursing informatics all designed with support of long distance education with open source software. Courses are: A - 'From Data to Wisdom', B - 'Introduction to Nursing Informatics' and C - 'Nursing Informatics I'. Courses A and B are obligatory for C course. Technology used to implement these online courses is based on the open source Learning Management System (LMS), Claroline, free online collaborative learning platform. Courses are divided in two modules/days. First module/day participants have classical approach to education and second day with E-learning from home. These courses represent first courses from nursing informatics' and first long distance education for nurses also.

CymeR: cytometry analysis using KNIME, docker and R

PubMed Central

Muchmore, B.; Alarcón-Riquelme, M.E.

2017-01-01

Abstract Summary: Here we present open-source software for the analysis of high-dimensional cytometry data using state of the art algorithms. Importantly, use of the software requires no programming ability, and output files can either be interrogated directly in CymeR or they can be used downstream with any other cytometric data analysis platform. Also, because we use Docker to integrate the multitude of components that form the basis of CymeR, we have additionally developed a proof-of-concept of how future open-source bioinformatic programs with graphical user interfaces could be developed. Availability and Implementation: CymeR is open-source software that ties several components into a single program that is perhaps best thought of as a self-contained data analysis operating system. Please see https://github.com/bmuchmore/CymeR/wiki for detailed installation instructions. Contact: brian.muchmore@genyo.es or marta.alarcon@genyo.es PMID:27998935

CymeR: cytometry analysis using KNIME, docker and R.

PubMed

Muchmore, B; Alarcón-Riquelme, M E

2017-03-01

Here we present open-source software for the analysis of high-dimensional cytometry data using state of the art algorithms. Importantly, use of the software requires no programming ability, and output files can either be interrogated directly in CymeR or they can be used downstream with any other cytometric data analysis platform. Also, because we use Docker to integrate the multitude of components that form the basis of CymeR, we have additionally developed a proof-of-concept of how future open-source bioinformatic programs with graphical user interfaces could be developed. CymeR is open-source software that ties several components into a single program that is perhaps best thought of as a self-contained data analysis operating system. Please see https://github.com/bmuchmore/CymeR/wiki for detailed installation instructions. brian.muchmore@genyo.es or marta.alarcon@genyo.es. © The Author 2016. Published by Oxford University Press.

Implementation and Testing of Low Cost Uav Platform for Orthophoto Imaging

NASA Astrophysics Data System (ADS)

Brucas, D.; Suziedelyte-Visockiene, J.; Ragauskas, U.; Berteska, E.; Rudinskas, D.

2013-08-01

Implementation of Unmanned Aerial Vehicles for civilian applications is rapidly increasing. Technologies which were expensive and available only for military use have recently spread on civilian market. There is a vast number of low cost open source components and systems for implementation on UAVs available. Using of low cost hobby and open source components ensures considerable decrease of UAV price, though in some cases compromising its reliability. In Space Science and Technology Institute (SSTI) in collaboration with Vilnius Gediminas Technical University (VGTU) researches have been performed in field of constructing and implementation of small UAVs composed of low cost open source components (and own developments). Most obvious and simple implementation of such UAVs - orthophoto imaging with data download and processing after the flight. The construction, implementation of UAVs, flight experience, data processing and data implementation will be further covered in the paper and presentation.

THE BERKELEY DATA ANALYSIS SYSTEM (BDAS): AN OPEN SOURCE PLATFORM FOR BIG DATA ANALYTICS

DTIC Science & Technology

2017-09-01

Evan Sparks, Oliver Zahn, Michael J. Franklin, David A. Patterson, Saul Perlmutter. Scientific Computing Meets Big Data Technology: An Astronomy ...Processing Astronomy Imagery Using Big Data Technology. IEEE Transaction on Big Data, 2016. Approved for Public Release; Distribution Unlimited. 22 [93

Environmental and Landscape Remote Sensing Using Free and Open Source Image Processing Tools

EPA Science Inventory

As global climate change and human activities impact the environment, there is a growing need for scientific tools to monitor and measure environmental conditions that support human and ecological health. Remotely sensed imagery from satellite and airborne platforms provides a g...

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

Lee, Seyong; Kim, Jungwon; Vetter, Jeffrey S

This paper presents a directive-based, high-level programming framework for high-performance reconfigurable computing. It takes a standard, portable OpenACC C program as input and generates a hardware configuration file for execution on FPGAs. We implemented this prototype system using our open-source OpenARC compiler; it performs source-to-source translation and optimization of the input OpenACC program into an OpenCL code, which is further compiled into a FPGA program by the backend Altera Offline OpenCL compiler. Internally, the design of OpenARC uses a high- level intermediate representation that separates concerns of program representation from underlying architectures, which facilitates portability of OpenARC. In fact, thismore » design allowed us to create the OpenACC-to-FPGA translation framework with minimal extensions to our existing system. In addition, we show that our proposed FPGA-specific compiler optimizations and novel OpenACC pragma extensions assist the compiler in generating more efficient FPGA hardware configuration files. Our empirical evaluation on an Altera Stratix V FPGA with eight OpenACC benchmarks demonstrate the benefits of our strategy. To demonstrate the portability of OpenARC, we show results for the same benchmarks executing on other heterogeneous platforms, including NVIDIA GPUs, AMD GPUs, and Intel Xeon Phis. This initial evidence helps support the goal of using a directive-based, high-level programming strategy for performance portability across heterogeneous HPC architectures.« less

An open-source computational and data resource to analyze digital maps of immunopeptidomes

PubMed Central

Caron, Etienne; Espona, Lucia; Kowalewski, Daniel J; Schuster, Heiko; Ternette, Nicola; Alpízar, Adán; Schittenhelm, Ralf B; Ramarathinam, Sri H; Lindestam Arlehamn, Cecilia S; Chiek Koh, Ching; Gillet, Ludovic C; Rabsteyn, Armin; Navarro, Pedro; Kim, Sangtae; Lam, Henry; Sturm, Theo; Marcilla, Miguel; Sette, Alessandro; Campbell, David S; Deutsch, Eric W; Moritz, Robert L; Purcell, Anthony W; Rammensee, Hans-Georg; Stevanovic, Stefan; Aebersold, Ruedi

2015-01-01

We present a novel mass spectrometry-based high-throughput workflow and an open-source computational and data resource to reproducibly identify and quantify HLA-associated peptides. Collectively, the resources support the generation of HLA allele-specific peptide assay libraries consisting of consensus fragment ion spectra, and the analysis of quantitative digital maps of HLA peptidomes generated from a range of biological sources by SWATH mass spectrometry (MS). This study represents the first community-based effort to develop a robust platform for the reproducible and quantitative measurement of the entire repertoire of peptides presented by HLA molecules, an essential step towards the design of efficient immunotherapies. DOI: http://dx.doi.org/10.7554/eLife.07661.001 PMID:26154972

A Lightweight Remote Parallel Visualization Platform for Interactive Massive Time-varying Climate Data Analysis

NASA Astrophysics Data System (ADS)

Li, J.; Zhang, T.; Huang, Q.; Liu, Q.

2014-12-01

Today's climate datasets are featured with large volume, high degree of spatiotemporal complexity and evolving fast overtime. As visualizing large volume distributed climate datasets is computationally intensive, traditional desktop based visualization applications fail to handle the computational intensity. Recently, scientists have developed remote visualization techniques to address the computational issue. Remote visualization techniques usually leverage server-side parallel computing capabilities to perform visualization tasks and deliver visualization results to clients through network. In this research, we aim to build a remote parallel visualization platform for visualizing and analyzing massive climate data. Our visualization platform was built based on Paraview, which is one of the most popular open source remote visualization and analysis applications. To further enhance the scalability and stability of the platform, we have employed cloud computing techniques to support the deployment of the platform. In this platform, all climate datasets are regular grid data which are stored in NetCDF format. Three types of data access methods are supported in the platform: accessing remote datasets provided by OpenDAP servers, accessing datasets hosted on the web visualization server and accessing local datasets. Despite different data access methods, all visualization tasks are completed at the server side to reduce the workload of clients. As a proof of concept, we have implemented a set of scientific visualization methods to show the feasibility of the platform. Preliminary results indicate that the framework can address the computation limitation of desktop based visualization applications.

The importance of using open source technologies and common standards for interoperability within eHealth: Perspectives from the Millennium Villages Project

PubMed Central

Borland, Rob; Barasa, Mourice; Iiams-Hauser, Casey; Velez, Olivia; Kaonga, Nadi Nina; Berg, Matt

2013-01-01

The purpose of this paper is to illustrate the importance of using open source technologies and common standards for interoperability when implementing eHealth systems and illustrate this through case studies, where possible. The sources used to inform this paper draw from the implementation and evaluation of the eHealth Program in the context of the Millennium Villages Project (MVP). As the eHealth Team was tasked to deploy an eHealth architecture, the Millennium Villages Global-Network (MVG-Net), across all fourteen of the MVP sites in Sub-Saharan Africa, the team recognized the need for standards and uniformity but also realized that context would be an important factor. Therefore, the team decided to utilize open source solutions. The MVP implementation of MVG-Net provides a model for those looking to implement informatics solutions across disciplines and countries. Furthermore, there are valuable lessons learned that the eHealth community can benefit from. By sharing lessons learned and developing an accessible, open-source eHealth platform, we believe that we can more efficiently and rapidly achieve the health-related and collaborative Millennium Development Goals (MDGs). PMID:22894051

Avionics and Power Management for Low-Cost High-Altitude Balloon Science Platforms

NASA Technical Reports Server (NTRS)

Chin, Jeffrey; Roberts, Anthony; McNatt, Jeremiah

2016-01-01

High-altitude balloons (HABs) have become popular as educational and scientific platforms for planetary research. This document outlines key components for missions where low cost and rapid development are desired. As an alternative to ground-based vacuum and thermal testing, these systems can be flight tested at comparable costs. Communication, solar, space, and atmospheric sensing experiments often require environments where ground level testing can be challenging or impossible in certain cases. When performing HAB research the ability to monitor the status of the platform and gather data is key for both scientific and recoverability aspects of the mission. A few turnkey platform solutions are outlined that leverage rapidly evolving open-source engineering ecosystems. Rather than building custom components from scratch, these recommendations attempt to maximize simplicity and cost of HAB platforms to make launches more accessible to everyone.

The Open Microscopy Environment: open image informatics for the biological sciences

NASA Astrophysics Data System (ADS)

Blackburn, Colin; Allan, Chris; Besson, Sébastien; Burel, Jean-Marie; Carroll, Mark; Ferguson, Richard K.; Flynn, Helen; Gault, David; Gillen, Kenneth; Leigh, Roger; Leo, Simone; Li, Simon; Lindner, Dominik; Linkert, Melissa; Moore, Josh; Moore, William J.; Ramalingam, Balaji; Rozbicki, Emil; Rustici, Gabriella; Tarkowska, Aleksandra; Walczysko, Petr; Williams, Eleanor; Swedlow, Jason R.

2016-07-01

Despite significant advances in biological imaging and analysis, major informatics challenges remain unsolved: file formats are proprietary, storage and analysis facilities are lacking, as are standards for sharing image data and results. While the open FITS file format is ubiquitous in astronomy, astronomical imaging shares many challenges with biological imaging, including the need to share large image sets using secure, cross-platform APIs, and the need for scalable applications for processing and visualization. The Open Microscopy Environment (OME) is an open-source software framework developed to address these challenges. OME tools include: an open data model for multidimensional imaging (OME Data Model); an open file format (OME-TIFF) and library (Bio-Formats) enabling free access to images (5D+) written in more than 145 formats from many imaging domains, including FITS; and a data management server (OMERO). The Java-based OMERO client-server platform comprises an image metadata store, an image repository, visualization and analysis by remote access, allowing sharing and publishing of image data. OMERO provides a means to manage the data through a multi-platform API. OMERO's model-based architecture has enabled its extension into a range of imaging domains, including light and electron microscopy, high content screening, digital pathology and recently into applications using non-image data from clinical and genomic studies. This is made possible using the Bio-Formats library. The current release includes a single mechanism for accessing image data of all types, regardless of original file format, via Java, C/C++ and Python and a variety of applications and environments (e.g. ImageJ, Matlab and R).

Shipping Science Worldwide with Open Source Containers

NASA Astrophysics Data System (ADS)

Molineaux, J. P.; McLaughlin, B. D.; Pilone, D.; Plofchan, P. G.; Murphy, K. J.

2014-12-01

Scientific applications often present difficult web-hosting needs. Their compute- and data-intensive nature, as well as an increasing need for high-availability and distribution, combine to create a challenging set of hosting requirements. In the past year, advancements in container-based virtualization and related tooling have offered new lightweight and flexible ways to accommodate diverse applications with all the isolation and portability benefits of traditional virtualization. This session will introduce and demonstrate an open-source, single-interface, Platform-as-a-Serivce (PaaS) that empowers application developers to seamlessly leverage geographically distributed, public and private compute resources to achieve highly-available, performant hosting for scientific applications.

ImagePy: an open-source, Python-based and platform-independent software package for boimage analysis.

PubMed

Wang, Anliang; Yan, Xiaolong; Wei, Zhijun

2018-04-27

This note presents the design of a scalable software package named ImagePy for analysing biological images. Our contribution is concentrated on facilitating extensibility and interoperability of the software through decoupling the data model from the user interface. Especially with assistance from the Python ecosystem, this software framework makes modern computer algorithms easier to be applied in bioimage analysis. ImagePy is free and open source software, with documentation and code available at https://github.com/Image-Py/imagepy under the BSD license. It has been tested on the Windows, Mac and Linux operating systems. wzjdlut@dlut.edu.cn or yxdragon@imagepy.org.

3-D interactive visualisation tools for Hi spectral line imaging

NASA Astrophysics Data System (ADS)

van der Hulst, J. M.; Punzo, D.; Roerdink, J. B. T. M.

2017-06-01

Upcoming HI surveys will deliver such large datasets that automated processing using the full 3-D information to find and characterize HI objects is unavoidable. Full 3-D visualization is an essential tool for enabling qualitative and quantitative inspection and analysis of the 3-D data, which is often complex in nature. Here we present SlicerAstro, an open-source extension of 3DSlicer, a multi-platform open source software package for visualization and medical image processing, which we developed for the inspection and analysis of HI spectral line data. We describe its initial capabilities, including 3-D filtering, 3-D selection and comparative modelling.

Closed-Loop, Multichannel Experimentation Using the Open-Source NeuroRighter Electrophysiology Platform

PubMed Central

Newman, Jonathan P.; Zeller-Townson, Riley; Fong, Ming-Fai; Arcot Desai, Sharanya; Gross, Robert E.; Potter, Steve M.

2013-01-01

Single neuron feedback control techniques, such as voltage clamp and dynamic clamp, have enabled numerous advances in our understanding of ion channels, electrochemical signaling, and neural dynamics. Although commercially available multichannel recording and stimulation systems are commonly used for studying neural processing at the network level, they provide little native support for real-time feedback. We developed the open-source NeuroRighter multichannel electrophysiology hardware and software platform for closed-loop multichannel control with a focus on accessibility and low cost. NeuroRighter allows 64 channels of stimulation and recording for around US $10,000, along with the ability to integrate with other software and hardware. Here, we present substantial enhancements to the NeuroRighter platform, including a redesigned desktop application, a new stimulation subsystem allowing arbitrary stimulation patterns, low-latency data servers for accessing data streams, and a new application programming interface (API) for creating closed-loop protocols that can be inserted into NeuroRighter as plugin programs. This greatly simplifies the design of sophisticated real-time experiments without sacrificing the power and speed of a compiled programming language. Here we present a detailed description of NeuroRighter as a stand-alone application, its plugin API, and an extensive set of case studies that highlight the system’s abilities for conducting closed-loop, multichannel interfacing experiments. PMID:23346047

Stewardship and management challenges within a cloud-based open data ecosystem (Invited Paper 211863)

NASA Astrophysics Data System (ADS)

Kearns, E. J.

2017-12-01

NOAA's Big Data Project is conducting an experiment in the collaborative distribution of open government data to non-governmental cloud-based systems. Through Cooperative Research and Development Agreements signed in 2015 between NOAA and Amazon Web Services, Google Cloud Platform, IBM, Microsoft Azure, and the Open Commons Consortium, NOAA is distributing open government data to a wide community of potential users. There are a number of significant advantages related to the use of open data on commercial cloud platforms, but through this experiment NOAA is also discovering significant challenges for those stewarding and maintaining NOAA's data resources in support of users in the wider open data ecosystem. Among the challenges that will be discussed are: the need to provide effective interpretation of the data content to enable their use by data scientists from other expert communities; effective maintenance of Collaborators' open data stores through coordinated publication of new data and new versions of older data; the provenance and verification of open data as authentic NOAA-sourced data across multiple management boundaries and analytical tools; and keeping pace with the accelerating expectations of users with regard to improved quality control, data latency, availability, and discoverability. Suggested strategies to address these challenges will also be described.

Postgraduate Students as OER Capacitators

ERIC Educational Resources Information Center

King, Thomas William

2017-01-01

A comprehensive theoretical, legal and practical basis for OER has been developed over the past fifteen years, supported by the expansion of open source curation platforms and the work of advocacy groups and international bodies. OER's potential has been sufficiently documented; the question remains how best to support, integrate and normalise OER…

Engaging Language Learners through Technology Integration: Theory, Applications, and Outcomes

ERIC Educational Resources Information Center

Li, Shuai, Ed.; Swanson, Peter, Ed.

2014-01-01

Web 2.0 technologies, open source software platforms, and mobile applications have transformed teaching and learning of second and foreign languages. Language teaching has transitioned from a teacher-centered approach to a student-centered approach through the use of Computer-Assisted Language Learning (CALL) and new teaching approaches.…

SpiceyPy, a Python Wrapper for SPICE

NASA Astrophysics Data System (ADS)

Annex, A.

2017-06-01

SpiceyPy is an open source Python wrapper for the NAIF SPICE toolkit. It is available for macOS, Linux, and Windows platforms and for Python versions 2.7.x and 3.x as well as Anaconda. SpiceyPy can be installed by running: “pip install spiceypy.”

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…

Integrating an Awareness of Selfhood and Society into Virtual Learning

ERIC Educational Resources Information Center

Stricker, Andrew, Ed.; Calongne, Cynthia, Ed.; Truman, Barbara, Ed.; Arenas, Fil, Ed.

2017-01-01

Recent technological advances have opened new platforms for learning and teaching. By utilizing virtual spaces, more educational opportunities are created for students who cannot attend a physical classroom environment. "Integrating an Awareness of Selfhood and Society into Virtual Learning" is a pivotal reference source that discusses…

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/

NASA's Earth Imagery Service as Open Source Software

NASA Astrophysics Data System (ADS)

De Cesare, C.; Alarcon, C.; Huang, T.; Roberts, J. T.; Rodriguez, J.; Cechini, M. F.; Boller, R. A.; Baynes, K.

2016-12-01

The NASA Global Imagery Browse Service (GIBS) is a software system that provides access to an archive of historical and near-real-time Earth imagery from NASA-supported satellite instruments. The imagery itself is open data, and is accessible via standards such as the Open Geospatial Consortium (OGC)'s Web Map Tile Service (WMTS) protocol. GIBS includes three core software projects: The Imagery Exchange (TIE), OnEarth, and the Meta Raster Format (MRF) project. These projects are developed using a variety of open source software, including: Apache HTTPD, GDAL, Mapserver, Grails, Zookeeper, Eclipse, Maven, git, and Apache Commons. TIE has recently been released for open source, and is now available on GitHub. OnEarth, MRF, and their sub-projects have been on GitHub since 2014, and the MRF project in particular receives many external contributions from the community. Our software has been successful beyond the scope of GIBS: the PO.DAAC State of the Ocean and COVERAGE visualization projects reuse components from OnEarth. The MRF source code has recently been incorporated into GDAL, which is a core library in many widely-used GIS software such as QGIS and GeoServer. This presentation will describe the challenges faced in incorporating open software and open data into GIBS, and also showcase GIBS as a platform on which scientists and the general public can build their own applications.

Harvesting rockfall hazard evaluation parameters from Google Earth Street View

NASA Astrophysics Data System (ADS)

Partsinevelos, Panagiotis; Agioutantis, Zacharias; Tripolitsiotis, Achilles; Steiakakis, Chrysanthos; Mertikas, Stelios

2015-04-01

Rockfall incidents along highways and railways prove extremely dangerous for properties, infrastructures and human lives. Several qualitative metrics such as the Rockfall Hazard Rating System (RHRS) and the Colorado Rockfall Hazard Rating System (CRHRS) have been established to estimate rockfall potential and provide risk maps in order to control and monitor rockfall incidents. The implementation of such metrics for efficient and reliable risk modeling require accurate knowledge of multi-parametric attributes such as the geological, geotechnical, topographic parameters of the study area. The Missouri Rockfall Hazard Rating System (MORH RS) identifies the most potentially problematic areas using digital video logging for the determination of parameters like slope height and angle, face irregularities, etc. This study aims to harvest in a semi-automated approach geometric and qualitative measures through open source platforms that may provide 3-dimensional views of the areas of interest. More specifically, the Street View platform from Google Maps, is hereby used to provide essential information that can be used towards 3-dimensional reconstruction of slopes along highways. The potential of image capturing along a programmable virtual route to provide the input data for photogrammetric processing is also evaluated. Moreover, qualitative characterization of the geological and geotechnical status, based on the Street View images, is performed. These attributes are then integrated to deliver a GIS-based rockfall hazard map. The 3-dimensional models are compared to actual photogrammetric measures in a rockfall prone area in Crete, Greece while in-situ geotechnical characterization is also used to compare and validate the hazard risk. This work is considered as the first step towards the exploitation of open source platforms to improve road safety and the development of an operational system where authorized agencies (i.e., civil protection) will be able to acquire near-real time hazard maps based on video images retrieved either by open source platforms, operational unmanned aerial vehicles, and/or simple video recordings from users. This work has been performed under the framework of the "Cooperation 2011" project ISTRIA (11_SYN_9_13989) funded from the Operational Program "Competitiveness and Entrepreneurship" (co-funded by the European Regional Development Fund (ERDF)) and managed by the Greek General Secretariat for Research and Technology.

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.

Using OpenOffice as a Portable Interface to JAVA-Based Applications

NASA Astrophysics Data System (ADS)

Comeau, T.; Garrett, B.; Richon, J.; Romelfanger, F.

2004-07-01

STScI previously used Microsoft Word and Microsoft Access, a Sybase ODBC driver, and the Adobe Acrobat PDF writer, along with a substantial amount of Visual Basic, to generate a variety of documents for the internal Space Telescope Grants Administration System (STGMS). While investigating an upgrade to Microsoft Office XP, we began considering alternatives, ultimately selecting an open source product, OpenOffice.org. This reduces the total number of products required to operate the internal STGMS system, simplifies the build system, and opens the possibility of moving to a non-Windows platform. We describe the experience of moving from Microsoft Office to OpenOffice.org, and our other internal uses of OpenOffice.org in our development environment.

Technological choices for mobile clinical applications.

PubMed

Ehrler, Frederic; Issom, David; Lovis, Christian

2011-01-01

The rise of cheaper and more powerful mobile devices make them a new and attractive platform for clinical applications. The interaction paradigm and portability of the device facilitates bedside human-machine interactions. The better accessibility to information and decision-support anywhere in the hospital improves the efficiency and the safety of care processes. In this study, we attempt to find out what are the most appropriate Operating System (OS) and Software Development Kit (SDK) to support the development of clinical applications on mobile devices. The Android platform is a Linux-based, open source platform that has many advantages. Two main SDKs are available on this platform: the native Android and the Adobe Flex SDK. Both of them have interesting features, but the latter has been preferred due its portability at comparable performance and ease of development.

MetaNET--a web-accessible interactive platform for biological metabolic network analysis.

PubMed

Narang, Pankaj; Khan, Shawez; Hemrom, Anmol Jaywant; Lynn, Andrew Michael

2014-01-01

Metabolic reactions have been extensively studied and compiled over the last century. These have provided a theoretical base to implement models, simulations of which are used to identify drug targets and optimize metabolic throughput at a systemic level. While tools for the perturbation of metabolic networks are available, their applications are limited and restricted as they require varied dependencies and often a commercial platform for full functionality. We have developed MetaNET, an open source user-friendly platform-independent and web-accessible resource consisting of several pre-defined workflows for metabolic network analysis. MetaNET is a web-accessible platform that incorporates a range of functions which can be combined to produce different simulations related to metabolic networks. These include (i) optimization of an objective function for wild type strain, gene/catalyst/reaction knock-out/knock-down analysis using flux balance analysis. (ii) flux variability analysis (iii) chemical species participation (iv) cycles and extreme paths identification and (v) choke point reaction analysis to facilitate identification of potential drug targets. The platform is built using custom scripts along with the open-source Galaxy workflow and Systems Biology Research Tool as components. Pre-defined workflows are available for common processes, and an exhaustive list of over 50 functions are provided for user defined workflows. MetaNET, available at http://metanet.osdd.net , provides a user-friendly rich interface allowing the analysis of genome-scale metabolic networks under various genetic and environmental conditions. The framework permits the storage of previous results, the ability to repeat analysis and share results with other users over the internet as well as run different tools simultaneously using pre-defined workflows, and user-created custom workflows.

Unified Framework for Development, Deployment and Robust Testing of Neuroimaging Algorithms

PubMed Central

Joshi, Alark; Scheinost, Dustin; Okuda, Hirohito; Belhachemi, Dominique; Murphy, Isabella; Staib, Lawrence H.; Papademetris, Xenophon

2011-01-01

Developing both graphical and command-line user interfaces for neuroimaging algorithms requires considerable effort. Neuroimaging algorithms can meet their potential only if they can be easily and frequently used by their intended users. Deployment of a large suite of such algorithms on multiple platforms requires consistency of user interface controls, consistent results across various platforms and thorough testing. We present the design and implementation of a novel object-oriented framework that allows for rapid development of complex image analysis algorithms with many reusable components and the ability to easily add graphical user interface controls. Our framework also allows for simplified yet robust nightly testing of the algorithms to ensure stability and cross platform interoperability. All of the functionality is encapsulated into a software object requiring no separate source code for user interfaces, testing or deployment. This formulation makes our framework ideal for developing novel, stable and easy-to-use algorithms for medical image analysis and computer assisted interventions. The framework has been both deployed at Yale and released for public use in the open source multi-platform image analysis software—BioImage Suite (bioimagesuite.org). PMID:21249532

Millstone: software for multiplex microbial genome analysis and engineering

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

Goodman, Daniel B.; Kuznetsov, Gleb; Lajoie, Marc J.

Inexpensive DNA sequencing and advances in genome editing have made computational analysis a major rate-limiting step in adaptive laboratory evolution and microbial genome engineering. Here, we describe Millstone, a web-based platform that automates genotype comparison and visualization for projects with up to hundreds of genomic samples. To enable iterative genome engineering, Millstone allows users to design oligonucleotide libraries and create successive versions of reference genomes. Millstone is open source and easily deployable to a cloud platform, local cluster, or desktop, making it a scalable solution for any lab.

Millstone: software for multiplex microbial genome analysis and engineering.

PubMed

Goodman, Daniel B; Kuznetsov, Gleb; Lajoie, Marc J; Ahern, Brian W; Napolitano, Michael G; Chen, Kevin Y; Chen, Changping; Church, George M

2017-05-25

Inexpensive DNA sequencing and advances in genome editing have made computational analysis a major rate-limiting step in adaptive laboratory evolution and microbial genome engineering. We describe Millstone, a web-based platform that automates genotype comparison and visualization for projects with up to hundreds of genomic samples. To enable iterative genome engineering, Millstone allows users to design oligonucleotide libraries and create successive versions of reference genomes. Millstone is open source and easily deployable to a cloud platform, local cluster, or desktop, making it a scalable solution for any lab.

Millstone: software for multiplex microbial genome analysis and engineering

DOE PAGES

Goodman, Daniel B.; Kuznetsov, Gleb; Lajoie, Marc J.; ...

2017-05-25

Inexpensive DNA sequencing and advances in genome editing have made computational analysis a major rate-limiting step in adaptive laboratory evolution and microbial genome engineering. Here, we describe Millstone, a web-based platform that automates genotype comparison and visualization for projects with up to hundreds of genomic samples. To enable iterative genome engineering, Millstone allows users to design oligonucleotide libraries and create successive versions of reference genomes. Millstone is open source and easily deployable to a cloud platform, local cluster, or desktop, making it a scalable solution for any lab.

An integrated, open-source set of tools for urban vulnerability monitoring from Earth observation data

NASA Astrophysics Data System (ADS)

De Vecchi, Daniele; Harb, Mostapha; Dell'Acqua, Fabio; Aurelio Galeazzo, Daniel

2015-04-01

Aim: The paper introduces an integrated set of open-source tools designed to process medium and high-resolution imagery with the aim to extract vulnerability indicators [1]. Problem: In the context of risk monitoring [2], a series of vulnerability proxies can be defined, such as the extension of a built-up area or buildings regularity [3]. Different open-source C and Python libraries are already available for image processing and geospatial information (e.g. OrfeoToolbox, OpenCV and GDAL). They include basic processing tools but not vulnerability-oriented workflows. Therefore, it is of significant importance to provide end-users with a set of tools capable to return information at a higher level. Solution: The proposed set of python algorithms is a combination of low-level image processing and geospatial information handling tools along with high-level workflows. In particular, two main products are released under the GPL license: source code, developers-oriented, and a QGIS plugin. These tools were produced within the SENSUM project framework (ended December 2014) where the main focus was on earthquake and landslide risk. Further development and maintenance is guaranteed by the decision to include them in the platform designed within the FP 7 RASOR project . Conclusion: With the lack of a unified software suite for vulnerability indicators extraction, the proposed solution can provide inputs for already available models like the Global Earthquake Model. The inclusion of the proposed set of algorithms within the RASOR platforms can guarantee support and enlarge the community of end-users. Keywords: Vulnerability monitoring, remote sensing, optical imagery, open-source software tools References [1] M. Harb, D. De Vecchi, F. Dell'Acqua, "Remote sensing-based vulnerability proxies in the EU FP7 project SENSUM", Symposium on earthquake and landslide risk in Central Asia and Caucasus: exploiting remote sensing and geo-spatial information management, 29-30th January 2014, Bishkek, Kyrgyz Republic. [2] UNISDR, "Living with Risk", Geneva, Switzerland, 2004. [3] P. Bisch, E. Carvalho, H. Degree, P. Fajfar, M. Fardis, P. Franchin, M. Kreslin, A. Pecker, "Eurocode 8: Seismic Design of Buildings", Lisbon, 2011. (SENSUM: www.sensum-project.eu, grant number: 312972 ) (RASOR: www.rasor-project.eu, grant number: 606888 )

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.

Review assessment support in Open Journal System using TextRank

NASA Astrophysics Data System (ADS)

Manalu, S. R.; Willy; Sundjaja, A. M.; Noerlina

2017-01-01

In this paper, a review assessment support in Open Journal System (OJS) using TextRank is proposed. OJS is an open-source journal management platform that provides a streamlined journal publishing workflow. TextRank is an unsupervised, graph-based ranking model commonly used as extractive auto summarization of text documents. This study applies the TextRank algorithm to summarize 50 article reviews from an OJS-based international journal. The resulting summaries are formed using the most representative sentences extracted from the reviews. The summaries are then used to help OJS editors in assessing a review’s quality.

Development of a Web-Based Visualization Platform for Climate Research Using Google Earth

NASA Technical Reports Server (NTRS)

Sun, Xiaojuan; Shen, Suhung; Leptoukh, Gregory G.; Wang, Panxing; Di, Liping; Lu, Mingyue

2011-01-01

Recently, it has become easier to access climate data from satellites, ground measurements, and models from various data centers, However, searching. accessing, and prc(essing heterogeneous data from different sources are very tim -consuming tasks. There is lack of a comprehensive visual platform to acquire distributed and heterogeneous scientific data and to render processed images from a single accessing point for climate studies. This paper. documents the design and implementation of a Web-based visual, interoperable, and scalable platform that is able to access climatological fields from models, satellites, and ground stations from a number of data sources using Google Earth (GE) as a common graphical interface. The development is based on the TCP/IP protocol and various data sharing open sources, such as OPeNDAP, GDS, Web Processing Service (WPS), and Web Mapping Service (WMS). The visualization capability of integrating various measurements into cE extends dramatically the awareness and visibility of scientific results. Using embedded geographic information in the GE, the designed system improves our understanding of the relationships of different elements in a four dimensional domain. The system enables easy and convenient synergistic research on a virtual platform for professionals and the general public, gr$tly advancing global data sharing and scientific research collaboration.

Evaporation from Lake Mead, Arizona and Nevada, 1997-99

USGS Publications Warehouse

Westenburg, Craig L.; DeMeo, Guy A.; Tanko, Daron J.

2006-01-01

Lake Mead is one of a series of large Colorado River reservoirs operated and maintained by the Bureau of Reclamation. The Colorado River system of reservoirs and diversions is an important source of water for millions of people in seven Western States and Mexico. The U.S. Geological Survey, in cooperation with the Bureau of Reclamation, conducted a study from 1997 to 1999 to estimate evaporation from Lake Mead. For this study, micrometeorological and hydrologic data were collected continually from instrumented platforms deployed at four locations on the lake, open-water areas of Boulder Basin, Virgin Basin, and Overton Arm and a protected cove in Boulder Basin. Data collected at the platforms were used to estimate Lake Mead evaporation by solving an energy-budget equation. The average annual evaporation rate at open-water stations from January 1998 to December 1999 was 7.5 feet. Because the spatial variation of monthly and annual evaporation rates was minimal for the open-water stations, a single open-water station in Boulder Basin would provide data that are adequate to estimate evaporation from Lake Mead.

Numerical tools to predict the environmental loads for offshore structures under extreme weather conditions

NASA Astrophysics Data System (ADS)

Wu, Yanling

2018-05-01

In this paper, the extreme waves were generated using the open source computational fluid dynamic (CFD) tools — OpenFOAM and Waves2FOAM — using linear and nonlinear NewWave input. They were used to conduct the numerical simulation of the wave impact process. Numerical tools based on first-order (with and without stretching) and second-order NewWave are investigated. The simulation to predict force loading for the offshore platform under the extreme weather condition is implemented and compared.

Oscillation Baselining and Analysis Tool

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

PNNL developed a new tool for oscillation analysis and baselining. This tool has been developed under a new DOE Grid Modernization Laboratory Consortium (GMLC) Project (GM0072 - “Suite of open-source applications and models for advanced synchrophasor analysis”) and it is based on the open platform for PMU analysis. The Oscillation Baselining and Analysis Tool (OBAT) performs the oscillation analysis and identifies modes of oscillations (frequency, damping, energy, and shape). The tool also does oscillation event baselining (fining correlation between oscillations characteristics and system operating conditions).

Visualization of Vgi Data Through the New NASA Web World Wind Virtual Globe

NASA Astrophysics Data System (ADS)

Brovelli, M. A.; Kilsedar, C. E.; Zamboni, G.

2016-06-01

GeoWeb 2.0, laying the foundations of Volunteered Geographic Information (VGI) systems, has led to platforms where users can contribute to the geographic knowledge that is open to access. Moreover, as a result of the advancements in 3D visualization, virtual globes able to visualize geographic data even on browsers emerged. However the integration of VGI systems and virtual globes has not been fully realized. The study presented aims to visualize volunteered data in 3D, considering also the ease of use aspects for general public, using Free and Open Source Software (FOSS). The new Application Programming Interface (API) of NASA, Web World Wind, written in JavaScript and based on Web Graphics Library (WebGL) is cross-platform and cross-browser, so that the virtual globe created using this API can be accessible through any WebGL supported browser on different operating systems and devices, as a result not requiring any installation or configuration on the client-side, making the collected data more usable to users, which is not the case with the World Wind for Java as installation and configuration of the Java Virtual Machine (JVM) is required. Furthermore, the data collected through various VGI platforms might be in different formats, stored in a traditional relational database or in a NoSQL database. The project developed aims to visualize and query data collected through Open Data Kit (ODK) platform and a cross-platform application, where data is stored in a relational PostgreSQL and NoSQL CouchDB databases respectively.

FIRE: an open-software suite for real-time 2D/3D image registration for image guided radiotherapy research

NASA Astrophysics Data System (ADS)

Furtado, H.; Gendrin, C.; Spoerk, J.; Steiner, E.; Underwood, T.; Kuenzler, T.; Georg, D.; Birkfellner, W.

2016-03-01

Radiotherapy treatments have changed at a tremendously rapid pace. Dose delivered to the tumor has escalated while organs at risk (OARs) are better spared. The impact of moving tumors during dose delivery has become higher due to very steep dose gradients. Intra-fractional tumor motion has to be managed adequately to reduce errors in dose delivery. For tumors with large motion such as tumors in the lung, tracking is an approach that can reduce position uncertainty. Tumor tracking approaches range from purely image intensity based techniques to motion estimation based on surrogate tracking. Research efforts are often based on custom designed software platforms which take too much time and effort to develop. To address this challenge we have developed an open software platform especially focusing on tumor motion management. FLIRT is a freely available open-source software platform. The core method for tumor tracking is purely intensity based 2D/3D registration. The platform is written in C++ using the Qt framework for the user interface. The performance critical methods are implemented on the graphics processor using the CUDA extension. One registration can be as fast as 90ms (11Hz). This is suitable to track tumors moving due to respiration (~0.3Hz) or heartbeat (~1Hz). Apart from focusing on high performance, the platform is designed to be flexible and easy to use. Current use cases range from tracking feasibility studies, patient positioning and method validation. Such a framework has the potential of enabling the research community to rapidly perform patient studies or try new methods.

openECA Detailed Design Document

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

Robertson, Russell

This document describes the functional and non-functional requirements for: The openECA platform The included analytic systems that will: Validate the operational readiness and performance of the openECA platform Provide out-of-box value to those that implement the openECA platform with an initial collection of analytics

Getting started with Open-Hardware: Development and Control of Microfluidic Devices

PubMed Central

da Costa, Eric Tavares; Mora, Maria F.; Willis, Peter A.; do Lago, Claudimir L.; Jiao, Hong; Garcia, Carlos D.

2014-01-01

Understanding basic concepts of electronics and computer programming allows researchers to get the most out of the equipment found in their laboratories. Although a number of platforms have been specifically designed for the general public and are supported by a vast array of on-line tutorials, this subject is not normally included in university chemistry curricula. Aiming to provide the basic concepts of hardware and software, this article is focused on the design and use of a simple module to control a series of PDMS-based valves. The module is based on a low-cost microprocessor (Teensy) and open-source software (Arduino). The microvalves were fabricated using thin sheets of PDMS and patterned using CO2 laser engraving, providing a simple and efficient way to fabricate devices without the traditional photolithographic process or facilities. Synchronization of valve control enabled the development of two simple devices to perform injection (1.6 ± 0.4 μL/stroke) and mixing of different solutions. Furthermore, a practical demonstration of the utility of this system for microscale chemical sample handling and analysis was achieved performing an on-chip acid-base titration, followed by conductivity detection with an open-source low-cost detection system. Overall, the system provided a very reproducible (98%) platform to perform fluid delivery at the microfluidic scale. PMID:24823494

Global Health Innovation Technology Models.

PubMed

Harding, Kimberly

2016-01-01

Chronic technology and business process disparities between High Income, Low Middle Income and Low Income (HIC, LMIC, LIC) research collaborators directly prevent the growth of sustainable Global Health innovation for infectious and rare diseases. There is a need for an Open Source-Open Science Architecture Framework to bridge this divide. We are proposing such a framework for consideration by the Global Health community, by utilizing a hybrid approach of integrating agnostic Open Source technology and healthcare interoperability standards and Total Quality Management principles. We will validate this architecture framework through our programme called Project Orchid. Project Orchid is a conceptual Clinical Intelligence Exchange and Virtual Innovation platform utilizing this approach to support clinical innovation efforts for multi-national collaboration that can be locally sustainable for LIC and LMIC research cohorts. The goal is to enable LIC and LMIC research organizations to accelerate their clinical trial process maturity in the field of drug discovery, population health innovation initiatives and public domain knowledge networks. When sponsored, this concept will be tested by 12 confirmed clinical research and public health organizations in six countries. The potential impact of this platform is reduced drug discovery and public health innovation lag time and improved clinical trial interventions, due to reliable clinical intelligence and bio-surveillance across all phases of the clinical innovation process.

Global Health Innovation Technology Models

PubMed Central

Harding, Kimberly

2016-01-01

Chronic technology and business process disparities between High Income, Low Middle Income and Low Income (HIC, LMIC, LIC) research collaborators directly prevent the growth of sustainable Global Health innovation for infectious and rare diseases. There is a need for an Open Source-Open Science Architecture Framework to bridge this divide. We are proposing such a framework for consideration by the Global Health community, by utilizing a hybrid approach of integrating agnostic Open Source technology and healthcare interoperability standards and Total Quality Management principles. We will validate this architecture framework through our programme called Project Orchid. Project Orchid is a conceptual Clinical Intelligence Exchange and Virtual Innovation platform utilizing this approach to support clinical innovation efforts for multi-national collaboration that can be locally sustainable for LIC and LMIC research cohorts. The goal is to enable LIC and LMIC research organizations to accelerate their clinical trial process maturity in the field of drug discovery, population health innovation initiatives and public domain knowledge networks. When sponsored, this concept will be tested by 12 confirmed clinical research and public health organizations in six countries. The potential impact of this platform is reduced drug discovery and public health innovation lag time and improved clinical trial interventions, due to reliable clinical intelligence and bio-surveillance across all phases of the clinical innovation process.

Open-Source GIS

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

Vatsavai, Raju; Burk, Thomas E; Lime, Steve

2012-01-01

The components making up an Open Source GIS are explained in this chapter. A map server (Sect. 30.1) can broadly be defined as a software platform for dynamically generating spatially referenced digital map products. The University of Minnesota MapServer (UMN Map Server) is one such system. Its basic features are visualization, overlay, and query. Section 30.2 names and explains many of the geospatial open source libraries, such as GDAL and OGR. The other libraries are FDO, JTS, GEOS, JCS, MetaCRS, and GPSBabel. The application examples include derived GIS-software and data format conversions. Quantum GIS, its origin and its applications explainedmore » in detail in Sect. 30.3. The features include a rich GUI, attribute tables, vector symbols, labeling, editing functions, projections, georeferencing, GPS support, analysis, and Web Map Server functionality. Future developments will address mobile applications, 3-D, and multithreading. The origins of PostgreSQL are outlined and PostGIS discussed in detail in Sect. 30.4. It extends PostgreSQL by implementing the Simple Feature standard. Section 30.5 details the most important open source licenses such as the GPL, the LGPL, the MIT License, and the BSD License, as well as the role of the Creative Commons.« less

Integrating an Educational Game in Moodle LMS

ERIC Educational Resources Information Center

Minovic, Miroslav; Milovanovic, Milos; Minovic, Jelena; Starcevic, Dusan

2012-01-01

The authors present a learning platform based on a computer game. Learning games combine two industries: education and entertainment, which is often called "Edutainment." The game is realized as a strategic game (similar to Risk[TM]), implemented as a module for Moodle CMS, utilizing Java Applet technology. Moodle is an open-source course…

Automatic System for Producing and Distributing Lecture Recordings and Livestreams Using Opencast Matterhorn

ERIC Educational Resources Information Center

Jonach, Rafael; Ebner, Martin; Grigoriadis, Ypatios

2015-01-01

Lectures of courses at universities are increasingly being recorded and offered through various distribution channels to support students' learning activities. This research work aims to create an automatic system for producing and distributing high quality lecture recordings. Opencast Matterhorn is an open source platform for automated video…

Developing Digital Competences Using an Educational Software. A Pedagogical Research

ERIC Educational Resources Information Center

Magdas, Ioana; Bontea, Timea

2011-01-01

Many teachers and people in educational institutions consider it necessary to prepare children for living in a computerized society. The Internet offers an incredible number of opportunities for teachers. The Web offer of e-learning open source platforms reached an impressive configuration. In this article, we present an educational software for…

VAGUE: a graphical user interface for the Velvet assembler.

PubMed

Powell, David R; Seemann, Torsten

2013-01-15

Velvet is a popular open-source de novo genome assembly software tool, which is run from the Unix command line. Most of the problems experienced by new users of Velvet revolve around constructing syntactically and semantically correct command lines, getting input files into acceptable formats and assessing the output. Here, we present Velvet Assembler Graphical User Environment (VAGUE), a multi-platform graphical front-end for Velvet. VAGUE aims to make sequence assembly accessible to a wider audience and to facilitate better usage amongst existing users of Velvet. VAGUE is implemented in JRuby and targets the Java Virtual Machine. It is available under an open-source GPLv2 licence from http://www.vicbioinformatics.com/. torsten.seemann@monash.edu.

Development of Thread-compatible Open Source Stack

NASA Astrophysics Data System (ADS)

Zimmermann, Lukas; Mars, Nidhal; Schappacher, Manuel; Sikora, Axel

2017-07-01

The Thread protocol is a recent development based on 6LoWPAN (IPv6 over IEEE 802.15.4), but with extensions regarding a more media independent approach, which - additionally - also promises true interoperability. To evaluate and analyse the operation of a Thread network a given open source 6LoWPAN stack for embedded devices (emb::6) has been extended in order to comply with the Thread specification. The implementation covers Mesh Link Establishment (MLE) and network layer functionality as well as 6LoWPAN mesh under routing mechanism based on MAC short addresses. The development has been verified on a virtualization platform and allows dynamical establishment of network topologies based on Thread’s partitioning algorithm.

Spatial Dmbs Architecture for a Free and Open Source Bim

NASA Astrophysics Data System (ADS)

Logothetis, S.; Valari, E.; Karachaliou, E.; Stylianidis, E.

2017-08-01

Recent research on the field of Building Information Modelling (BIM) technology, revealed that except of a few, accessible and free BIM viewers there is a lack of Free & Open Source Software (FOSS) BIM software for the complete BIM process. With this in mind and considering BIM as the technological advancement of Computer-Aided Design (CAD) systems, the current work proposes the use of a FOSS CAD software in order to extend its capabilities and transform it gradually into a FOSS BIM platform. Towards this undertaking, a first approach on developing a spatial Database Management System (DBMS) able to store, organize and manage the overall amount of information within a single application, is presented.

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.

Using Open and Interoperable Ways to Publish and Access LANCE AIRS Near-Real Time Data

NASA Technical Reports Server (NTRS)

Zhao, Peisheng; Lynnes, Christopher; Vollmer, Bruce; Savtchenko, Andrey; Theobald, Michael; Yang, Wenli

2011-01-01

The Atmospheric Infrared Sounder (AIRS) Near-Real Time (NRT) data from the Land Atmosphere Near real-time Capability for EOS (LANCE) element at the Goddard Earth Sciences Data and Information Services Center (GES DISC) provides information on the global and regional atmospheric state, with very low temporal latency, to support climate research and improve weather forecasting. An open and interoperable platform is useful to facilitate access to, and integration of, LANCE AIRS NRT data. As Web services technology has matured in recent years, a new scalable Service-Oriented Architecture (SOA) is emerging as the basic platform for distributed computing and large networks of interoperable applications. Following the provide-register-discover-consume SOA paradigm, this presentation discusses how to use open-source geospatial software components to build Web services for publishing and accessing AIRS NRT data, explore the metadata relevant to registering and discovering data and services in the catalogue systems, and implement a Web portal to facilitate users' consumption of the data and services.

Open Ephys electroencephalography (Open Ephys  +  EEG): a modular, low-cost, open-source solution to human neural recording

NASA Astrophysics Data System (ADS)

Black, Christopher; Voigts, Jakob; Agrawal, Uday; Ladow, Max; Santoyo, Juan; Moore, Christopher; Jones, Stephanie

2017-06-01

Objective. Electroencephalography (EEG) offers a unique opportunity to study human neural activity non-invasively with millisecond resolution using minimal equipment in or outside of a lab setting. EEG can be combined with a number of techniques for closed-loop experiments, where external devices are driven by specific neural signals. However, reliable, commercially available EEG systems are expensive, often making them impractical for individual use and research development. Moreover, by design, a majority of these systems cannot be easily altered to the specification needed by the end user. We focused on mitigating these issues by implementing open-source tools to develop a new EEG platform to drive down research costs and promote collaboration and innovation. Approach. Here, we present methods to expand the open-source electrophysiology system, Open Ephys (www.openephys.org), to include human EEG recordings. We describe the equipment and protocol necessary to interface various EEG caps with the Open Ephys acquisition board, and detail methods for processing data. We present applications of Open Ephys  +  EEG as a research tool and discuss how this innovative EEG technology lays a framework for improved closed-loop paradigms and novel brain-computer interface experiments. Main results. The Open Ephys  +  EEG system can record reliable human EEG data, as well as human EMG data. A side-by-side comparison of eyes closed 8-14 Hz activity between the Open Ephys  +  EEG system and the Brainvision ActiCHamp EEG system showed similar average power and signal to noise. Significance. Open Ephys  +  EEG enables users to acquire high-quality human EEG data comparable to that of commercially available systems, while maintaining the price point and extensibility inherent to open-source systems.

Open Ephys electroencephalography (Open Ephys  +  EEG): a modular, low-cost, open-source solution to human neural recording.

PubMed

Black, Christopher; Voigts, Jakob; Agrawal, Uday; Ladow, Max; Santoyo, Juan; Moore, Christopher; Jones, Stephanie

2017-06-01

Electroencephalography (EEG) offers a unique opportunity to study human neural activity non-invasively with millisecond resolution using minimal equipment in or outside of a lab setting. EEG can be combined with a number of techniques for closed-loop experiments, where external devices are driven by specific neural signals. However, reliable, commercially available EEG systems are expensive, often making them impractical for individual use and research development. Moreover, by design, a majority of these systems cannot be easily altered to the specification needed by the end user. We focused on mitigating these issues by implementing open-source tools to develop a new EEG platform to drive down research costs and promote collaboration and innovation. Here, we present methods to expand the open-source electrophysiology system, Open Ephys (www.openephys.org), to include human EEG recordings. We describe the equipment and protocol necessary to interface various EEG caps with the Open Ephys acquisition board, and detail methods for processing data. We present applications of Open Ephys  +  EEG as a research tool and discuss how this innovative EEG technology lays a framework for improved closed-loop paradigms and novel brain-computer interface experiments. The Open Ephys  +  EEG system can record reliable human EEG data, as well as human EMG data. A side-by-side comparison of eyes closed 8-14 Hz activity between the Open Ephys  +  EEG system and the Brainvision ActiCHamp EEG system showed similar average power and signal to noise. Open Ephys  +  EEG enables users to acquire high-quality human EEG data comparable to that of commercially available systems, while maintaining the price point and extensibility inherent to open-source systems.

Building an Open-source Simulation Platform of Acoustic Radiation Force-based Breast Elastography

PubMed Central

Wang, Yu; Peng, Bo; Jiang, Jingfeng

2017-01-01

Ultrasound-based elastography including strain elastography (SE), acoustic radiation force Impulse (ARFI) imaging, point shear wave elastography (pSWE) and supersonic shear imaging (SSI) have been used to differentiate breast tumors among other clinical applications. The objective of this study is to extend a previously published virtual simulation platform built for ultrasound quasi-static breast elastography toward acoustic radiation force-based breast elastography. Consequently, the extended virtual breast elastography simulation platform can be used to validate image pixels with known underlying soft tissue properties (i.e. “ground truth”) in complex, heterogeneous media, enhancing confidence in elastographic image interpretations. The proposed virtual breast elastography system inherited four key components from the previously published virtual simulation platform: an ultrasound simulator (Field II), a mesh generator (Tetgen), a finite element solver (FEBio) and a visualization and data processing package (VTK). Using a simple message passing mechanism, functionalities have now been extended to acoustic radiation force-based elastography simulations. Examples involving three different numerical breast models with increasing complexity – one uniform model, one simple inclusion model and one virtual complex breast model derived from magnetic resonance imaging data, were used to demonstrate capabilities of this extended virtual platform. Overall, simulation results were compared with the published results. In the uniform model, the estimated shear wave speed (SWS) values were within 4% compared to the predetermined SWS values. In the simple inclusion and the complex breast models, SWS values of all hard inclusions in soft backgrounds were slightly underestimated, similar to what has been reported. The elastic contrast values and visual observation show that ARFI images have higher spatial resolution, while SSI images can provide higher inclusion-to-background contrast. In summary, our initial results were consistent with our expectations and what have been reported in the literature. The proposed (open-source) simulation platform can serve as a single gateway to perform many elastographic simulations in a transparent manner, thereby promoting collaborative developments. PMID:28075330

Building an open-source simulation platform of acoustic radiation force-based breast elastography

NASA Astrophysics Data System (ADS)

Wang, Yu; Peng, Bo; Jiang, Jingfeng

2017-03-01

Ultrasound-based elastography including strain elastography, acoustic radiation force impulse (ARFI) imaging, point shear wave elastography and supersonic shear imaging (SSI) have been used to differentiate breast tumors among other clinical applications. The objective of this study is to extend a previously published virtual simulation platform built for ultrasound quasi-static breast elastography toward acoustic radiation force-based breast elastography. Consequently, the extended virtual breast elastography simulation platform can be used to validate image pixels with known underlying soft tissue properties (i.e. ‘ground truth’) in complex, heterogeneous media, enhancing confidence in elastographic image interpretations. The proposed virtual breast elastography system inherited four key components from the previously published virtual simulation platform: an ultrasound simulator (Field II), a mesh generator (Tetgen), a finite element solver (FEBio) and a visualization and data processing package (VTK). Using a simple message passing mechanism, functionalities have now been extended to acoustic radiation force-based elastography simulations. Examples involving three different numerical breast models with increasing complexity—one uniform model, one simple inclusion model and one virtual complex breast model derived from magnetic resonance imaging data, were used to demonstrate capabilities of this extended virtual platform. Overall, simulation results were compared with the published results. In the uniform model, the estimated shear wave speed (SWS) values were within 4% compared to the predetermined SWS values. In the simple inclusion and the complex breast models, SWS values of all hard inclusions in soft backgrounds were slightly underestimated, similar to what has been reported. The elastic contrast values and visual observation show that ARFI images have higher spatial resolution, while SSI images can provide higher inclusion-to-background contrast. In summary, our initial results were consistent with our expectations and what have been reported in the literature. The proposed (open-source) simulation platform can serve as a single gateway to perform many elastographic simulations in a transparent manner, thereby promoting collaborative developments.

Progress in Open-World, Integrative, Collaborative Science Data Platforms (Invited)

NASA Astrophysics Data System (ADS)

Fox, P. A.

2013-12-01

As collaborative, or network science spreads into more Earth and space science fields, both the participants and their funders have expressed a very strong desire for highly functional data and information capabilities that are a) easy to use, b) integrated in a variety of ways, c) leverage prior investments and keep pace with rapid technical change, and d) are not expensive or time-consuming to build or maintain. In response, and based on our accumulated experience over the last decade and a maturing of several key technical approaches, we have adapted, extended, and integrated several open source applications and frameworks that handle major portions of functionality for these platforms. At minimum, these functions include: an object-type repository, collaboration tools, an ability to identify and manage all key entities in the platform, and an integrated portal to manage diverse content and applications, with varied access levels and privacy options. At a conceptual level, science networks (even small ones) deal with people, and many intellectual artifacts produced or consumed in research, organizational and/our outreach activities, as well as the relations among them. Increasingly these networks are modeled as knowledge networks, i.e. graphs with named and typed relations among the 'nodes'. Nodes can be people, organizations, datasets, events, presentations, publications, videos, meetings, reports, groups, and more. In this heterogeneous ecosystem, it is also important to use a set of common informatics approaches to co-design and co-evolve the needed science data platforms based on what real people want to use them for. In this contribution, we present our methods and results for information modeling, adapting, integrating and evolving a networked data science and information architecture based on several open source technologies (Drupal, VIVO, the Comprehensive Knowledge Archive Network; CKAN, and the Global Handle System; GHS). In particular we present both the instantiation of this data platform for the Deep Carbon Observatory, including key functional and non-functional attributes, how the smart mediation among the components is modeled and managed, and discuss its general applicability.

APEX/SPIN: a free test platform to measure speech intelligibility.

PubMed

Francart, Tom; Hofmann, Michael; Vanthornhout, Jonas; Van Deun, Lieselot; van Wieringen, Astrid; Wouters, Jan

2017-02-01

Measuring speech intelligibility in quiet and noise is important in clinical practice and research. An easy-to-use free software platform for conducting speech tests is presented, called APEX/SPIN. The APEX/SPIN platform allows the use of any speech material in combination with any noise. A graphical user interface provides control over a large range of parameters, such as number of loudspeakers, signal-to-noise ratio and parameters of the procedure. An easy-to-use graphical interface is provided for calibration and storage of calibration values. To validate the platform, perception of words in quiet and sentences in noise were measured both with APEX/SPIN and with an audiometer and CD player, which is a conventional setup in current clinical practice. Five normal-hearing listeners participated in the experimental evaluation. Speech perception results were similar for the APEX/SPIN platform and conventional procedures. APEX/SPIN is a freely available and open source platform that allows the administration of all kinds of custom speech perception tests and procedures.

The use of open source bioinformatics tools to dissect transcriptomic data.

PubMed

Nitsche, Benjamin M; Ram, Arthur F J; Meyer, Vera

2012-01-01

Microarrays are a valuable technology to study fungal physiology on a transcriptomic level. Various microarray platforms are available comprising both single and two channel arrays. Despite different technologies, preprocessing of microarray data generally includes quality control, background correction, normalization, and summarization of probe level data. Subsequently, depending on the experimental design, diverse statistical analysis can be performed, including the identification of differentially expressed genes and the construction of gene coexpression networks.We describe how Bioconductor, a collection of open source and open development packages for the statistical programming language R, can be used for dissecting microarray data. We provide fundamental details that facilitate the process of getting started with R and Bioconductor. Using two publicly available microarray datasets from Aspergillus niger, we give detailed protocols on how to identify differentially expressed genes and how to construct gene coexpression networks.

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.

Open Source Cloud-Based Technologies for Bim

NASA Astrophysics Data System (ADS)

Logothetis, S.; Karachaliou, E.; Valari, E.; Stylianidis, E.

2018-05-01

This paper presents a Cloud-based open source system for storing and processing data from a 3D survey approach. More specifically, we provide an online service for viewing, storing and analysing BIM. Cloud technologies were used to develop a web interface as a BIM data centre, which can handle large BIM data using a server. The server can be accessed by many users through various electronic devices anytime and anywhere so they can view online 3D models using browsers. Nowadays, the Cloud computing is engaged progressively in facilitating BIM-based collaboration between the multiple stakeholders and disciplinary groups for complicated Architectural, Engineering and Construction (AEC) projects. Besides, the development of Open Source Software (OSS) has been rapidly growing and their use tends to be united. Although BIM and Cloud technologies are extensively known and used, there is a lack of integrated open source Cloud-based platforms able to support all stages of BIM processes. The present research aims to create an open source Cloud-based BIM system that is able to handle geospatial data. In this effort, only open source tools will be used; from the starting point of creating the 3D model with FreeCAD to its online presentation through BIMserver. Python plug-ins will be developed to link the two software which will be distributed and freely available to a large community of professional for their use. The research work will be completed by benchmarking four Cloud-based BIM systems: Autodesk BIM 360, BIMserver, Graphisoft BIMcloud and Onuma System, which present remarkable results.

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.

Survey of Non-Rigid Registration Tools in Medicine.

PubMed

Keszei, András P; Berkels, Benjamin; Deserno, Thomas M

2017-02-01

We catalogue available software solutions for non-rigid image registration to support scientists in selecting suitable tools for specific medical registration purposes. Registration tools were identified using non-systematic search in Pubmed, Web of Science, IEEE Xplore® Digital Library, Google Scholar, and through references in identified sources (n = 22). Exclusions are due to unavailability or inappropriateness. The remaining (n = 18) tools were classified by (i) access and technology, (ii) interfaces and application, (iii) living community, (iv) supported file formats, and (v) types of registration methodologies emphasizing the similarity measures implemented. Out of the 18 tools, (i) 12 are open source, 8 are released under a permissive free license, which imposes the least restrictions on the use and further development of the tool, 8 provide graphical processing unit (GPU) support; (ii) 7 are built on software platforms, 5 were developed for brain image registration; (iii) 6 are under active development but only 3 have had their last update in 2015 or 2016; (iv) 16 support the Analyze format, while 7 file formats can be read with only one of the tools; and (v) 6 provide multiple registration methods and 6 provide landmark-based registration methods. Based on open source, licensing, GPU support, active community, several file formats, algorithms, and similarity measures, the tools Elastics and Plastimatch are chosen for the platform ITK and without platform requirements, respectively. Researchers in medical image analysis already have a large choice of registration tools freely available. However, the most recently published algorithms may not be included in the tools, yet.

Innovation in engineering education through computer assisted learning and virtual university model

NASA Astrophysics Data System (ADS)

Raicu, A.; Raicu, G.

2015-11-01

The paper presents the most important aspects of innovation in Engineering Education using Computer Assisted Learning. The authors propose to increase the quality of Engineering Education programs of study at European standards. The use of computer assisted learning methodologies in all studies is becoming an important resource in Higher Education. We intend to improve the concept of e-Learning using virtual terminals, online support and assisting special training through live seminars and interactive labs to develop a virtual university model. We intend to encourage computer assisted learning and innovation as sources of competitive advantage, to permit vision and learning analysis, identifies new sources of technology and ideas. Our work is based on our university datasets collected during last fifteen years using several e-Learning systems. In Constanta Maritime University (CMU), using eLearning and Knowledge Management Services (KMS) is very important and we apply it effectively to achieve strategic objectives, such as collaboration, sharing and good practice. We have experience in this field since 2000 year using Moodle as KMS in our university. The term KMS can be associated to Open Source Software, Open Standards, Open Protocols and Open Knowledge licenses, initiatives and policies. In CMU Virtual Campus we have today over 12500 active users. Another experience of the authors is the implementation of MariTrainer Wiki educational platform based on Dokeos and DekiWiki under MARICOMP and MEP Leonardo da Vinci Project. We'll also present in this paper a case study under EU funded project POSDRU, where the authors implemented other educational platform in Technological High Schools from Romania used over 1000 teachers. Based on large datasets the study tries to improve the concept of e-Learning teaching using the revolutionary technologies. The new concept present in this paper is that the teaching and learning will be interactive and live. The new and modern techniques are the flexible learning courses, the production of learning demonstrators and testing. All the information from the virtual educational platform remain open space, communication between participants and continued after graduation, so we can talk about creating and maintaining a community of graduates, a partnership with them. Every European University must have a department which aims to provide computer assisted learning using knowledge creation through learning, capture and explication, sharing and collaborative communication, access, use and reuse and knowledge archiving.

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

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.

Analysis of vehicular traffic flow in the major areas of Kuala Lumpur utilizing open-traffic

NASA Astrophysics Data System (ADS)

Manogaran, Saargunawathy; Ali, Muhammad; Yusof, Kamaludin Mohamad; Suhaili, Ramdhan

2017-09-01

Vehicular traffic congestion occurs when a large number of drivers are overcrowded on the road and the traffic flow does not run smoothly. Traffic congestion causes chaos on the road and interruption to daily activities of users. Time consumed on road give lots of negative effects on productivity, social behavior, environmental and cost to economy. Congestion is worsens and leads to havoc during the emergency such as flood, accidents, road maintenance and etc., where behavior of traffic flow is always unpredictable and uncontrollable. Real-time and historical traffic data are critical inputs for most traffic flow analysis applications. Researcher attempt to predict traffic using simulations as there is no exact model of traffic flow exists due to its high complexity. Open Traffic is an open source platform available for traffic data analysis linked to Open Street Map (OSM). This research is aimed to study and understand the Open Traffic platform. The real-time traffic flow pattern in Kuala Lumpur area was successfully been extracted and analyzed using Open Traffic. It was observed that the congestion occurs on every major road in Kuala Lumpur and most of it owes to the offices and the economic and commercial centers during rush hours. At some roads the congestion occurs at night due to the tourism activities.

Swan: A tool for porting CUDA programs to OpenCL

NASA Astrophysics Data System (ADS)

Harvey, M. J.; De Fabritiis, G.

2011-04-01

The use of modern, high-performance graphical processing units (GPUs) for acceleration of scientific computation has been widely reported. The majority of this work has used the CUDA programming model supported exclusively by GPUs manufactured by NVIDIA. An industry standardisation effort has recently produced the OpenCL specification for GPU programming. This offers the benefits of hardware-independence and reduced dependence on proprietary tool-chains. Here we describe a source-to-source translation tool, "Swan" for facilitating the conversion of an existing CUDA code to use the OpenCL model, as a means to aid programmers experienced with CUDA in evaluating OpenCL and alternative hardware. While the performance of equivalent OpenCL and CUDA code on fixed hardware should be comparable, we find that a real-world CUDA application ported to OpenCL exhibits an overall 50% increase in runtime, a reduction in performance attributable to the immaturity of contemporary compilers. The ported application is shown to have platform independence, running on both NVIDIA and AMD GPUs without modification. We conclude that OpenCL is a viable platform for developing portable GPU applications but that the more mature CUDA tools continue to provide best performance. Program summaryProgram title: Swan Catalogue identifier: AEIH_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEIH_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU Public License version 2 No. of lines in distributed program, including test data, etc.: 17 736 No. of bytes in distributed program, including test data, etc.: 131 177 Distribution format: tar.gz Programming language: C Computer: PC Operating system: Linux RAM: 256 Mbytes Classification: 6.5 External routines: NVIDIA CUDA, OpenCL Nature of problem: Graphical Processing Units (GPUs) from NVIDIA are preferentially programed with the proprietary CUDA programming toolkit. An alternative programming model promoted as an industry standard, OpenCL, provides similar capabilities to CUDA and is also supported on non-NVIDIA hardware (including multicore ×86 CPUs, AMD GPUs and IBM Cell processors). The adaptation of a program from CUDA to OpenCL is relatively straightforward but laborious. The Swan tool facilitates this conversion. Solution method:Swan performs a translation of CUDA kernel source code into an OpenCL equivalent. It also generates the C source code for entry point functions, simplifying kernel invocation from the host program. A concise host-side API abstracts the CUDA and OpenCL APIs. A program adapted to use Swan has no dependency on the CUDA compiler for the host-side program. The converted program may be built for either CUDA or OpenCL, with the selection made at compile time. Restrictions: No support for CUDA C++ features Running time: Nominal

Instrumentino: An Open-Source Software for Scientific Instruments.

PubMed

Koenka, Israel Joel; Sáiz, Jorge; Hauser, Peter C

2015-01-01

Scientists often need to build dedicated computer-controlled experimental systems. For this purpose, it is becoming common to employ open-source microcontroller platforms, such as the Arduino. These boards and associated integrated software development environments provide affordable yet powerful solutions for the implementation of hardware control of transducers and acquisition of signals from detectors and sensors. It is, however, a challenge to write programs that allow interactive use of such arrangements from a personal computer. This task is particularly complex if some of the included hardware components are connected directly to the computer and not via the microcontroller. A graphical user interface framework, Instrumentino, was therefore developed to allow the creation of control programs for complex systems with minimal programming effort. By writing a single code file, a powerful custom user interface is generated, which enables the automatic running of elaborate operation sequences and observation of acquired experimental data in real time. The framework, which is written in Python, allows extension by users, and is made available as an open source project.

Evaluating open-source cloud computing solutions for geosciences

NASA Astrophysics Data System (ADS)

Huang, Qunying; Yang, Chaowei; Liu, Kai; Xia, Jizhe; Xu, Chen; Li, Jing; Gui, Zhipeng; Sun, Min; Li, Zhenglong

2013-09-01

Many organizations start to adopt cloud computing for better utilizing computing resources by taking advantage of its scalability, cost reduction, and easy to access characteristics. Many private or community cloud computing platforms are being built using open-source cloud solutions. However, little has been done to systematically compare and evaluate the features and performance of open-source solutions in supporting Geosciences. This paper provides a comprehensive study of three open-source cloud solutions, including OpenNebula, Eucalyptus, and CloudStack. We compared a variety of features, capabilities, technologies and performances including: (1) general features and supported services for cloud resource creation and management, (2) advanced capabilities for networking and security, and (3) the performance of the cloud solutions in provisioning and operating the cloud resources as well as the performance of virtual machines initiated and managed by the cloud solutions in supporting selected geoscience applications. Our study found that: (1) no significant performance differences in central processing unit (CPU), memory and I/O of virtual machines created and managed by different solutions, (2) OpenNebula has the fastest internal network while both Eucalyptus and CloudStack have better virtual machine isolation and security strategies, (3) Cloudstack has the fastest operations in handling virtual machines, images, snapshots, volumes and networking, followed by OpenNebula, and (4) the selected cloud computing solutions are capable for supporting concurrent intensive web applications, computing intensive applications, and small-scale model simulations without intensive data communication.

The Confluence of GIS, Cloud and Open Source, Enabling Big Raster Data Applications

NASA Astrophysics Data System (ADS)

Plesea, L.; Emmart, C. B.; Boller, R. A.; Becker, P.; Baynes, K.

2016-12-01

The rapid evolution of available cloud services is profoundly changing the way applications are being developed and used. Massive object stores, service scalability, continuous integration are some of the most important cloud technology advances that directly influence science applications and GIS. At the same time, more and more scientists are using GIS platforms in their day to day research. Yet with new opportunities there are always some challenges. Given the large amount of data commonly required in science applications, usually large raster datasets, connectivity is one of the biggest problems. Connectivity has two aspects, one being the limited bandwidth and latency of the communication link due to the geographical location of the resources, the other one being the interoperability and intrinsic efficiency of the interface protocol used to connect. NASA and Esri are actively helping each other and collaborating on a few open source projects, aiming to provide some of the core technology components to directly address the GIS enabled data connectivity problems. Last year Esri contributed LERC, a very fast and efficient compression algorithm to the GDAL/MRF format, which itself is a NASA/Esri collaboration project. The MRF raster format has some cloud aware features that make it possible to build high performance web services on cloud platforms, as some of the Esri projects demonstrate. Currently, another NASA open source project, the high performance OnEarth WMTS server is being refactored and enhanced to better integrate with MRF, GDAL and Esri software. Taken together, the GDAL, MRF and OnEarth form the core of an open source CloudGIS toolkit that is already showing results. Since it is well integrated with GDAL, which is the most common interoperability component of GIS applications, this approach should improve the connectivity and performance of many science and GIS applications in the cloud.

OpenStereo: Open Source, Cross-Platform Software for Structural Geology Analysis

NASA Astrophysics Data System (ADS)

Grohmann, C. H.; Campanha, G. A.

2010-12-01

Free and open source software (FOSS) are increasingly seen as synonyms of innovation and progress. Freedom to run, copy, distribute, study, change and improve the software (through access to the source code) assure a high level of positive feedback between users and developers, which results in stable, secure and constantly updated systems. Several software packages for structural geology analysis are available to the user, with commercial licenses or that can be downloaded at no cost from the Internet. Some provide basic tools of stereographic projections such as plotting poles, great circles, density contouring, eigenvector analysis, data rotation etc, while others perform more specific tasks, such as paleostress or geotechnical/rock stability analysis. This variety also means a wide range of data formating for input, Graphical User Interface (GUI) design and graphic export format. The majority of packages is built for MS-Windows and even though there are packages for the UNIX-based MacOS, there aren't native packages for *nix (UNIX, Linux, BSD etc) Operating Systems (OS), forcing the users to run these programs with emulators or virtual machines. Those limitations lead us to develop OpenStereo, an open source, cross-platform software for stereographic projections and structural geology. The software is written in Python, a high-level, cross-platform programming language and the GUI is designed with wxPython, which provide a consistent look regardless the OS. Numeric operations (like matrix and linear algebra) are performed with the Numpy module and all graphic capabilities are provided by the Matplolib library, including on-screen plotting and graphic exporting to common desktop formats (emf, eps, ps, pdf, png, svg). Data input is done with simple ASCII text files, with values of dip direction and dip/plunge separated by spaces, tabs or commas. The user can open multiple file at the same time (or the same file more than once), and overlay different elements of each dataset (poles, great circles etc). The GUI shows the opened files in a tree structure, similar to “layers” of many illustration software, where the vertical order of the files in the tree reflects the drawing order of the selected elements. At this stage, the software performs plotting operations of poles to planes, lineations, great circles, density contours and rose diagrams. A set of statistics is calculated for each file and its eigenvalues and eigenvectors are used to suggest if the data is clustered about a mean value or distributed along a girdle. Modified Flinn, Triangular and histograms plots are also available. Next step of development will focus on tools as merging and rotation of datasets, possibility to save 'projects' and paleostress analysis. In its current state, OpenStereo requires Python, wxPython, Numpy and Matplotlib installed in the system. We recommend installing PythonXY or the Enthought Python Distribution on MS-Windows and MacOS machines, since all dependencies are provided. Most Linux distributions provide an easy way to install all dependencies through software repositories. OpenStereo is released under the GNU General Public License. Programmers willing to contribute are encouraged to contact the authors directly. FAPESP Grant #09/17675-5

Research on private cloud computing based on analysis on typical opensource platform: a case study with Eucalyptus and Wavemaker

NASA Astrophysics Data System (ADS)

Yu, Xiaoyuan; Yuan, Jian; Chen, Shi

2013-03-01

Cloud computing is one of the most popular topics in the IT industry and is recently being adopted by many companies. It has four development models, as: public cloud, community cloud, hybrid cloud and private cloud. Except others, private cloud can be implemented in a private network, and delivers some benefits of cloud computing without pitfalls. This paper makes a comparison of typical open source platforms through which we can implement a private cloud. After this comparison, we choose Eucalyptus and Wavemaker to do a case study on the private cloud. We also do some performance estimation of cloud platform services and development of prototype software as cloud services.

Wireless energy transfer platform for medical sensors and implantable devices.

PubMed

Zhang, Fei; Hackworth, Steven A; Liu, Xiaoyu; Chen, Haiyan; Sclabassi, Robert J; Sun, Mingui

2009-01-01

Witricity is a newly developed technique for wireless energy transfer. This paper presents a frequency adjustable witricity system to power medical sensors and implantable devices. New witricity resonators are designed for both energy transmission and reception. A prototype platform is described, including an RF power source, two resonators with new structures, and inductively coupled input and output stages. In vitro experiments, both in open air and using a human head phantom consisting of simulated tissues, are employed to verify the feasibility of this platform. An animal model is utilized to evaluate in vivo energy transfer within the body of a laboratory pig. Our experiments indicate that witricity is an effective new tool for providing a variety of medical sensors and devices with power.

ESTEST: An Open Science Platform for Electronic Structure Research

ERIC Educational Resources Information Center

Yuan, Gary

2012-01-01

Open science platforms in support of data generation, analysis, and dissemination are becoming indispensible tools for conducting research. These platforms use informatics and information technologies to address significant problems in open science data interoperability, verification & validation, comparison, analysis, post-processing,…

The General Mission Analysis Tool (GMAT): Current Features And Adding Custom Functionality

NASA Technical Reports Server (NTRS)

Conway, Darrel J.; Hughes, Steven P.

2010-01-01

The General Mission Analysis Tool (GMAT) is a software system for trajectory optimization, mission analysis, trajectory estimation, and prediction developed by NASA, the Air Force Research Lab, and private industry. GMAT's design and implementation are based on four basic principles: open source visibility for both the source code and design documentation; platform independence; modular design; and user extensibility. The system, released under the NASA Open Source Agreement, runs on Windows, Mac and Linux. User extensions, loaded at run time, have been built for optimization, trajectory visualization, force model extension, and estimation, by parties outside of GMAT's development group. The system has been used to optimize maneuvers for the Lunar Crater Observation and Sensing Satellite (LCROSS) and ARTEMIS missions and is being used for formation design and analysis for the Magnetospheric Multiscale Mission (MMS).

Open source data logger for low-cost environmental monitoring

PubMed Central

2014-01-01

Abstract The increasing transformation of biodiversity into a data-intensive science has seen numerous independent systems linked and aggregated into the current landscape of biodiversity informatics. This paper outlines how we can move forward with this programme, incorporating real time environmental monitoring into our methodology using low-power and low-cost computing platforms. PMID:24855446

Investigating Advances in the Acquisition of Secure Systems Based on Open Architectures

DTIC Science & Technology

2012-08-30

markets (Guertin & Womble, 2012), efficient testing of component‐based OA...workalike of the closed‐source Second Life VW platform. Second Life (2012) is the current market leader in rapid virtual world development and...Strong Copyleft GPL, AGPL Many rights; obligations on “nearby” works Proprietary CTL , EULAs, TOSs Few rights Typical rights

How Educational Ideas Catch On: The Promotion of Popular Education Innovations and the Role of Evidence

ERIC Educational Resources Information Center

Carrier, Nathalie

2017-01-01

Background: Within the wider education industry, a large quantity of ideas, practices and products are routinely promoted as useful innovations. These innovations span many forms such as software applications, open source courseware, online learning platforms and web 2.0 technologies. Coupled with this promotion, there is increasing interest and…

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

Katipamula, Srinivas; Gowri, Krishnan; Hernandez, George

This paper describes one such reference process that can be deployed to provide continuous automated conditioned-based maintenance management for buildings that have BIM, a building automation system (BAS) and a computerized maintenance management software (CMMS) systems. The process can be deployed using an open source transactional network platform, VOLTTRON™, designed for distributed sensing and controls and supports both energy efficiency and grid services.

A Computer Simulation Using Spreadsheets for Learning Concept of Steady-State Equilibrium

ERIC Educational Resources Information Center

Sharda, Vandana; Sastri, O. S. K. S.; Bhardwaj, Jyoti; Jha, Arbind K.

2016-01-01

In this paper, we present a simple spreadsheet based simulation activity that can be performed by students at the undergraduate level. This simulation is implemented in free open source software (FOSS) LibreOffice Calc, which is available for both Windows and Linux platform. This activity aims at building the probability distribution for the…

Joint Intelligence Operations Center (JIOC) Baseline Business Process Model & Capabilities Evaluation Methodology

DTIC Science & Technology

2012-03-01

Targeting Review Board OPLAN Operations Plan OPORD Operations Order OPSIT Operational Situation OSINT Open Source Intelligence OV...Analysis Evaluate FLTREPs MISREPs Unit Assign Assets Feedback Asset Shortfalls Multi-Int Collection Political & Embasy Law Enforcement HUMINT OSINT ...Embassy Information OSINT Manage Theater HUMINT Law Enforcement Collection Sort Requests Platform Information Agency Information M-I Collect

Design and construction of a first-generation high-throughput integrated robotic molecular biology platform for bioenergy applications

USDA-ARS?s Scientific Manuscript database

The molecular biological techniques for plasmid-based assembly and cloning of gene open reading frames are essential for elucidating the function of the proteins encoded by the genes. These techniques involve the production of full-length cDNA libraries as a source of plasmid-based clones to expres...

Cloud-based Jupyter Notebooks for Water Data Analysis

NASA Astrophysics Data System (ADS)

Castronova, A. M.; Brazil, L.; Seul, M.

2017-12-01

The development and adoption of technologies by the water science community to improve our ability to openly collaborate and share workflows will have a transformative impact on how we address the challenges associated with collaborative and reproducible scientific research. Jupyter notebooks offer one solution by providing an open-source platform for creating metadata-rich toolchains for modeling and data analysis applications. Adoption of this technology within the water sciences, coupled with publicly available datasets from agencies such as USGS, NASA, and EPA enables researchers to easily prototype and execute data intensive toolchains. Moreover, implementing this software stack in a cloud-based environment extends its native functionality to provide researchers a mechanism to build and execute toolchains that are too large or computationally demanding for typical desktop computers. Additionally, this cloud-based solution enables scientists to disseminate data processing routines alongside journal publications in an effort to support reproducibility. For example, these data collection and analysis toolchains can be shared, archived, and published using the HydroShare platform or downloaded and executed locally to reproduce scientific analysis. This work presents the design and implementation of a cloud-based Jupyter environment and its application for collecting, aggregating, and munging various datasets in a transparent, sharable, and self-documented manner. The goals of this work are to establish a free and open source platform for domain scientists to (1) conduct data intensive and computationally intensive collaborative research, (2) utilize high performance libraries, models, and routines within a pre-configured cloud environment, and (3) enable dissemination of research products. This presentation will discuss recent efforts towards achieving these goals, and describe the architectural design of the notebook server in an effort to support collaborative and reproducible science.

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

Aerosol and trace gas flux measurements from a mobile car platform on the highway

NASA Astrophysics Data System (ADS)

Gordon, M.; Miller, S. J.; Staebler, R. M.; Taylor, P.

2016-12-01

Mobile flux measurements of aerosols and trace gases at the surface can provide valuable information about the vertical transport of these compounds from near-surface sources. These measurements can be complimentary to stationary tower measurements or elevated mobile measurements from aircraft and unmanned aerial systems (UAS). In July, 2016 a mobile platform (Toyota Highlander), outfitted with a sonic anemometer (ATI), an open path CO2/H2O analyzer (Licor), and an ultrafine particle sizer (DMT), was driven on highways as part of a chasing study to investigate vehicle-induced turbulence and mixing. The open path analyzer and particle sizer inlet were co-located with the anemometer in order to investigate the feasibility of making flux measurements of heat, momentum, water vapour, CO2, and sub-micron aerosols on the highway. These highway flux measurements are compared to stationary platform measurements made upwind and downwind of the highway. Statistical and spectral analyses are used to demonstrate the validity of the mobile measurements. Uncertainties due to flow distortion around the vehicle, under-sampling, and heterogeneity of the vertical temperature and concentrations are investigated and discussed.

Advances and current state of the security and privacy in electronic health records: survey from a social perspective.

PubMed

Tejero, Antonio; de la Torre, Isabel

2012-10-01

E-Health systems are experiencing an impulse in these last years, when many medical agencies began to include digital solutions into their platforms. Electronic Health Records (EHRs) are one of the most important improvements, being in its most part a patient-oriented tool. To achieve a completely operational EHR platform, security and privacy problems have to be resolved, due to the importance of the data included within these records. But given all the different methods to address security and privacy, they still remain in most cases as an open issue. This paper studies existing and proposed solutions included in different scenarios, in order to offer an overview of the current state in EHR systems. Bibliographic material has been obtained mainly from MEDLINE and SCOPUS sources, and over 30 publications have been analyzed. Many EHR platforms are being developed, but most of them present weaknesses when they are opened to the public. These architectures gain significance when they cover all the requisites related to security and privacy.

Lattice QCD simulations using the OpenACC platform

NASA Astrophysics Data System (ADS)

Majumdar, Pushan

2016-10-01

In this article we will explore the OpenACC platform for programming Graphics Processing Units (GPUs). The OpenACC platform offers a directive based programming model for GPUs which avoids the detailed data flow control and memory management necessary in a CUDA programming environment. In the OpenACC model, programs can be written in high level languages with OpenMP like directives. We present some examples of QCD simulation codes using OpenACC and discuss their performance on the Fermi and Kepler GPUs.

PRESTO-Tango as an open-source resource for interrogation of the druggable human GPCRome.

PubMed

Kroeze, Wesley K; Sassano, Maria F; Huang, Xi-Ping; Lansu, Katherine; McCorvy, John D; Giguère, Patrick M; Sciaky, Noah; Roth, Bryan L

2015-05-01

G protein-coupled receptors (GPCRs) are essential mediators of cellular signaling and are important targets of drug action. Of the approximately 350 nonolfactory human GPCRs, more than 100 are still considered to be 'orphans' because their endogenous ligands remain unknown. Here, we describe a unique open-source resource that allows interrogation of the druggable human GPCRome via a G protein-independent β-arrestin-recruitment assay. We validate this unique platform at more than 120 nonorphan human GPCR targets, demonstrate its utility for discovering new ligands for orphan human GPCRs and describe a method (parallel receptorome expression and screening via transcriptional output, with transcriptional activation following arrestin translocation (PRESTO-Tango)) for the simultaneous and parallel interrogation of the entire human nonolfactory GPCRome.

Kekule.js: An Open Source JavaScript Chemoinformatics Toolkit.

PubMed

Jiang, Chen; Jin, Xi; Dong, Ying; Chen, Ming

2016-06-27

Kekule.js is an open-source, object-oriented JavaScript toolkit for chemoinformatics. It provides methods for many common tasks in molecular informatics, including chemical data input/output (I/O), two- and three-dimensional (2D/3D) rendering of chemical structure, stereo identification, ring perception, structure comparison, and substructure search. Encapsulated widgets to display and edit chemical structures directly in web context are also supplied. Developed with web standards, the toolkit is ideal for building chemoinformatics applications over the Internet. Moreover, it is highly platform-independent and can also be used in desktop or mobile environments. Some initial applications, such as plugins for inputting chemical structures on the web and uses in chemistry education, have been developed based on the toolkit.

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.

BioImageXD: an open, general-purpose and high-throughput image-processing platform.

PubMed

Kankaanpää, Pasi; Paavolainen, Lassi; Tiitta, Silja; Karjalainen, Mikko; Päivärinne, Joacim; Nieminen, Jonna; Marjomäki, Varpu; Heino, Jyrki; White, Daniel J

2012-06-28

BioImageXD puts open-source computer science tools for three-dimensional visualization and analysis into the hands of all researchers, through a user-friendly graphical interface tuned to the needs of biologists. BioImageXD has no restrictive licenses or undisclosed algorithms and enables publication of precise, reproducible and modifiable workflows. It allows simple construction of processing pipelines and should enable biologists to perform challenging analyses of complex processes. We demonstrate its performance in a study of integrin clustering in response to selected inhibitors.

Architecture and Implementation of OpenPET Firmware and Embedded Software

PubMed Central

Abu-Nimeh, Faisal T.; Ito, Jennifer; Moses, William W.; Peng, Qiyu; Choong, Woon-Seng

2016-01-01

OpenPET is an open source, modular, extendible, and high-performance platform suitable for multi-channel data acquisition and analysis. Due to the flexibility of the hardware, firmware, and software architectures, the platform is capable of interfacing with a wide variety of detector modules not only in medical imaging but also in homeland security applications. Analog signals from radiation detectors share similar characteristics – a pulse whose area is proportional to the deposited energy and whose leading edge is used to extract a timing signal. As a result, a generic design method of the platform is adopted for the hardware, firmware, and software architectures and implementations. The analog front-end is hosted on a module called a Detector Board, where each board can filter, combine, timestamp, and process multiple channels independently. The processed data is formatted and sent through a backplane bus to a module called Support Board, where 1 Support Board can host up to eight Detector Board modules. The data in the Support Board, coming from 8 Detector Board modules, can be aggregated or correlated (if needed) depending on the algorithm implemented or runtime mode selected. It is then sent out to a computer workstation for further processing. The number of channels (detector modules), to be processed, mandates the overall OpenPET System Configuration, which is designed to handle up to 1,024 channels using 16-channel Detector Boards in the Standard System Configuration and 16,384 channels using 32-channel Detector Boards in the Large System Configuration. PMID:27110034

Efficient Sensor Integration on Platforms (NeXOS)

NASA Astrophysics Data System (ADS)

Memè, S.; Delory, E.; Del Rio, J.; Jirka, S.; Toma, D. M.; Martinez, E.; Frommhold, L.; Barrera, C.; Pearlman, J.

2016-12-01

In-situ ocean observing platforms provide power and information transmission capability to sensors. Ocean observing platforms can be mobile, such as ships, autonomous underwater vehicles, drifters and profilers, or fixed, such as buoys, moorings and cabled observatories. The process of integrating sensors on platforms can imply substantial engineering time and resources. Constraints range from stringent mechanical constraints to proprietary communication and control firmware. In NeXOS, the implementation of a PUCK plug and play capability is being done with applications to multiple sensors and platforms. This is complemented with a sensor web enablement that addresses the flow of information from sensor to user. Open standards are being tested in order to assess their costs and benefits in existing and future observing systems. Part of the testing implied open-source coding and hardware prototyping of specific control devices in particular for closed commercial platforms where firmware upgrading is not straightforward or possible without prior agreements or service fees. Some platform manufacturers such as European companies ALSEAMAR[1] and NKE Instruments [2] are currently upgrading their control and communication firmware as part of their activities in NeXOS. The sensor development companies Sensorlab[3] SMID[4] and TRIOS [5]upgraded their firmware with this plug and play functionality. Other industrial players in Europe and the US have been sent NeXOS sensors emulators to test the new protocol on their platforms. We are currently demonstrating that with little effort, it is also possible to have such middleware implemented on very low-cost compact computers such as the open Raspberry Pi[6], and have a full end-to-end interoperable communication path from sensor to user with sensor plug and play capability. The result is an increase in sensor integration cost-efficiency and the demonstration will be used to highlight the benefit to users and ocean observatory operators. [1] http://www.alseamar-alcen.com [2] http://www.nke-instrumentation.com [3] http://sensorlab.es [4] http://www.smidtechnology.it/ [5] http://www.trios.de/en/products/ [6] Raspberry Pi is a trademark of the Raspberry Pi Foundation

A Cloud-based, Open-Source, Command-and-Control Software Paradigm for Space Situational Awareness (SSA)

NASA Astrophysics Data System (ADS)

Melton, R.; Thomas, J.

With the rapid growth in the number of space actors, there has been a marked increase in the complexity and diversity of software systems utilized to support SSA target tracking, indication, warning, and collision avoidance. Historically, most SSA software has been constructed with "closed" proprietary code, which limits interoperability, inhibits the code transparency that some SSA customers need to develop domain expertise, and prevents the rapid injection of innovative concepts into these systems. Open-source aerospace software, a rapidly emerging, alternative trend in code development, is based on open collaboration, which has the potential to bring greater transparency, interoperability, flexibility, and reduced development costs. Open-source software is easily adaptable, geared to rapidly changing mission needs, and can generally be delivered at lower costs to meet mission requirements. This paper outlines Ball's COSMOS C2 system, a fully open-source, web-enabled, command-and-control software architecture which provides several unique capabilities to move the current legacy SSA software paradigm to an open source model that effectively enables pre- and post-launch asset command and control. Among the unique characteristics of COSMOS is the ease with which it can integrate with diverse hardware. This characteristic enables COSMOS to serve as the command-and-control platform for the full life-cycle development of SSA assets, from board test, to box test, to system integration and test, to on-orbit operations. The use of a modern scripting language, Ruby, also permits automated procedures to provide highly complex decision making for the tasking of SSA assets based on both telemetry data and data received from outside sources. Detailed logging enables quick anomaly detection and resolution. Integrated real-time and offline data graphing renders the visualization of the both ground and on-orbit assets simple and straightforward.

An open-source framework for testing tracking devices using Lego Mindstorms

NASA Astrophysics Data System (ADS)

Jomier, Julien; Ibanez, Luis; Enquobahrie, Andinet; Pace, Danielle; Cleary, Kevin

2009-02-01

In this paper, we present an open-source framework for testing tracking devices in surgical navigation applications. At the core of image-guided intervention systems is the tracking interface that handles communication with the tracking device and gathers tracking information. Given that the correctness of tracking information is critical for protecting patient safety and for ensuring the successful execution of an intervention, the tracking software component needs to be thoroughly tested on a regular basis. Furthermore, with widespread use of extreme programming methodology that emphasizes continuous and incremental testing of application components, testing design becomes critical. While it is easy to automate most of the testing process, it is often more difficult to test components that require manual intervention such as tracking device. Our framework consists of a robotic arm built from a set of Lego Mindstorms and an open-source toolkit written in C++ to control the robot movements and assess the accuracy of the tracking devices. The application program interface (API) is cross-platform and runs on Windows, Linux and MacOS. We applied this framework for the continuous testing of the Image-Guided Surgery Toolkit (IGSTK), an open-source toolkit for image-guided surgery and shown that regression testing on tracking devices can be performed at low cost and improve significantly the quality of the software.

Open Source High Content Analysis Utilizing Automated Fluorescence Lifetime Imaging Microscopy.

PubMed

Görlitz, Frederik; Kelly, Douglas J; Warren, Sean C; Alibhai, Dominic; West, Lucien; Kumar, Sunil; Alexandrov, Yuriy; Munro, Ian; Garcia, Edwin; McGinty, James; Talbot, Clifford; Serwa, Remigiusz A; Thinon, Emmanuelle; da Paola, Vincenzo; Murray, Edward J; Stuhmeier, Frank; Neil, Mark A A; Tate, Edward W; Dunsby, Christopher; French, Paul M W

2017-01-18

We present an open source high content analysis instrument utilizing automated fluorescence lifetime imaging (FLIM) for assaying protein interactions using Förster resonance energy transfer (FRET) based readouts of fixed or live cells in multiwell plates. This provides a means to screen for cell signaling processes read out using intramolecular FRET biosensors or intermolecular FRET of protein interactions such as oligomerization or heterodimerization, which can be used to identify binding partners. We describe here the functionality of this automated multiwell plate FLIM instrumentation and present exemplar data from our studies of HIV Gag protein oligomerization and a time course of a FRET biosensor in live cells. A detailed description of the practical implementation is then provided with reference to a list of hardware components and a description of the open source data acquisition software written in µManager. The application of FLIMfit, an open source MATLAB-based client for the OMERO platform, to analyze arrays of multiwell plate FLIM data is also presented. The protocols for imaging fixed and live cells are outlined and a demonstration of an automated multiwell plate FLIM experiment using cells expressing fluorescent protein-based FRET constructs is presented. This is complemented by a walk-through of the data analysis for this specific FLIM FRET data set.

HydroDesktop as a Community Designed and Developed Resource for Hydrologic Data Discovery and Analysis

NASA Astrophysics Data System (ADS)

Ames, D. P.

2013-12-01

As has been seen in other informatics fields, well-documented and appropriately licensed open source software tools have the potential to significantly increase both opportunities and motivation for inter-institutional science and technology collaboration. The CUAHSI HIS (and related HydroShare) projects have aimed to foster such activities in hydrology resulting in the development of many useful community software components including the HydroDesktop software application. HydroDesktop is an open source, GIS-based, scriptable software application for discovering data on the CUAHSI Hydrologic Information System and related resources. It includes a well-defined plugin architecture and interface to allow 3rd party developers to create extensions and add new functionality without requiring recompiling of the full source code. HydroDesktop is built in the C# programming language and uses the open source DotSpatial GIS engine for spatial data management. Capabilities include data search, discovery, download, visualization, and export. An extension that integrates the R programming language with HydroDesktop provides scripting and data automation capabilities and an OpenMI plugin provides the ability to link models. Current revision and updates to HydroDesktop include migration of core business logic to cross platform, scriptable Python code modules that can be executed in any operating system or linked into other software front-end applications.

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/.

Open Source High Content Analysis Utilizing Automated Fluorescence Lifetime Imaging Microscopy

PubMed Central

Warren, Sean C.; Alibhai, Dominic; West, Lucien; Kumar, Sunil; Alexandrov, Yuriy; Munro, Ian; Garcia, Edwin; McGinty, James; Talbot, Clifford; Serwa, Remigiusz A.; Thinon, Emmanuelle; da Paola, Vincenzo; Murray, Edward J.; Stuhmeier, Frank; Neil, Mark A. A.; Tate, Edward W.; Dunsby, Christopher; French, Paul M. W.

2017-01-01

We present an open source high content analysis instrument utilizing automated fluorescence lifetime imaging (FLIM) for assaying protein interactions using Förster resonance energy transfer (FRET) based readouts of fixed or live cells in multiwell plates. This provides a means to screen for cell signaling processes read out using intramolecular FRET biosensors or intermolecular FRET of protein interactions such as oligomerization or heterodimerization, which can be used to identify binding partners. We describe here the functionality of this automated multiwell plate FLIM instrumentation and present exemplar data from our studies of HIV Gag protein oligomerization and a time course of a FRET biosensor in live cells. A detailed description of the practical implementation is then provided with reference to a list of hardware components and a description of the open source data acquisition software written in µManager. The application of FLIMfit, an open source MATLAB-based client for the OMERO platform, to analyze arrays of multiwell plate FLIM data is also presented. The protocols for imaging fixed and live cells are outlined and a demonstration of an automated multiwell plate FLIM experiment using cells expressing fluorescent protein-based FRET constructs is presented. This is complemented by a walk-through of the data analysis for this specific FLIM FRET data set. PMID:28190060

Real-Time Processing Library for Open-Source Hardware Biomedical Sensors

PubMed Central

Castro-García, Juan A.; Lebrato-Vázquez, Clara

2018-01-01

Applications involving data acquisition from sensors need samples at a preset frequency rate, the filtering out of noise and/or analysis of certain frequency components. We propose a novel software architecture based on open-software hardware platforms which allows programmers to create data streams from input channels and easily implement filters and frequency analysis objects. The performances of the different classes given in the size of memory allocated and execution time (number of clock cycles) were analyzed in the low-cost platform Arduino Genuino. In addition, 11 people took part in an experiment in which they had to implement several exercises and complete a usability test. Sampling rates under 250 Hz (typical for many biomedical applications) makes it feasible to implement filters, sliding windows and Fourier analysis, operating in real time. Participants rated software usability at 70.2 out of 100 and the ease of use when implementing several signal processing applications was rated at just over 4.4 out of 5. Participants showed their intention of using this software because it was percieved as useful and very easy to use. The performances of the library showed that it may be appropriate for implementing small biomedical real-time applications or for human movement monitoring, even in a simple open-source hardware device like Arduino Genuino. The general perception about this library is that it is easy to use and intuitive. PMID:29596394

Getting started with open-hardware: development and control of microfluidic devices.

PubMed

da Costa, Eric Tavares; Mora, Maria F; Willis, Peter A; do Lago, Claudimir L; Jiao, Hong; Garcia, Carlos D

2014-08-01

Understanding basic concepts of electronics and computer programming allows researchers to get the most out of the equipment found in their laboratories. Although a number of platforms have been specifically designed for the general public and are supported by a vast array of on-line tutorials, this subject is not normally included in university chemistry curricula. Aiming to provide the basic concepts of hardware and software, this article is focused on the design and use of a simple module to control a series of PDMS-based valves. The module is based on a low-cost microprocessor (Teensy) and open-source software (Arduino). The microvalves were fabricated using thin sheets of PDMS and patterned using CO2 laser engraving, providing a simple and efficient way to fabricate devices without the traditional photolithographic process or facilities. Synchronization of valve control enabled the development of two simple devices to perform injection (1.6 ± 0.4 μL/stroke) and mixing of different solutions. Furthermore, a practical demonstration of the utility of this system for microscale chemical sample handling and analysis was achieved performing an on-chip acid-base titration, followed by conductivity detection with an open-source low-cost detection system. Overall, the system provided a very reproducible (98%) platform to perform fluid delivery at the microfluidic scale. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Real-Time Processing Library for Open-Source Hardware Biomedical Sensors.

PubMed

Molina-Cantero, Alberto J; Castro-García, Juan A; Lebrato-Vázquez, Clara; Gómez-González, Isabel M; Merino-Monge, Manuel

2018-03-29

Applications involving data acquisition from sensors need samples at a preset frequency rate, the filtering out of noise and/or analysis of certain frequency components. We propose a novel software architecture based on open-software hardware platforms which allows programmers to create data streams from input channels and easily implement filters and frequency analysis objects. The performances of the different classes given in the size of memory allocated and execution time (number of clock cycles) were analyzed in the low-cost platform Arduino Genuino. In addition, 11 people took part in an experiment in which they had to implement several exercises and complete a usability test. Sampling rates under 250 Hz (typical for many biomedical applications) makes it feasible to implement filters, sliding windows and Fourier analysis, operating in real time. Participants rated software usability at 70.2 out of 100 and the ease of use when implementing several signal processing applications was rated at just over 4.4 out of 5. Participants showed their intention of using this software because it was percieved as useful and very easy to use. The performances of the library showed that it may be appropriate for implementing small biomedical real-time applications or for human movement monitoring, even in a simple open-source hardware device like Arduino Genuino. The general perception about this library is that it is easy to use and intuitive.

Crossing the Virtual World Barrier with OpenAvatar

NASA Technical Reports Server (NTRS)

Joy, Bruce; Kavle, Lori; Tan, Ian

2012-01-01

There are multiple standards and formats for 3D models in virtual environments. The problem is that there is no open source platform for generating models out of discrete parts; this results in the process of having to "reinvent the wheel" when new games, virtual worlds and simulations want to enable their users to create their own avatars or easily customize in-world objects. OpenAvatar is designed to provide a framework to allow artists and programmers to create reusable assets which can be used by end users to generate vast numbers of complete models that are unique and functional. OpenAvatar serves as a framework which facilitates the modularization of 3D models allowing parts to be interchanged within a set of logical constraints.

Common Approach to Geoprocessing of Uav Data across Application Domains

NASA Astrophysics Data System (ADS)

Percivall, G. S.; Reichardt, M.; Taylor, T.

2015-08-01

UAVs are a disruptive technology bringing new geographic data and information to many application domains. UASs are similar to other geographic imagery systems so existing frameworks are applicable. But the diversity of UAVs as platforms along with the diversity of available sensors are presenting challenges in the processing and creation of geospatial products. Efficient processing and dissemination of the data is achieved using software and systems that implement open standards. The challenges identified point to the need for use of existing standards and extending standards. Results from the use of the OGC Sensor Web Enablement set of standards are presented. Next steps in the progress of UAVs and UASs may follow the path of open data, open source and open standards.

Open-source platforms for navigated image-guided interventions.

PubMed

Ungi, Tamas; Lasso, Andras; Fichtinger, Gabor

2016-10-01

Navigation technology is changing the clinical standards in medical interventions by making existing procedures more accurate, and new procedures possible. Navigation is based on preoperative or intraoperative imaging combined with 3-dimensional position tracking of interventional tools registered to the images. Research of navigation technology in medical interventions requires significant engineering efforts. The difficulty of developing such complex systems has been limiting the clinical translation of new methods and ideas. A key to the future success of this field is to provide researchers with platforms that allow rapid implementation of applications with minimal resources spent on reimplementing existing system features. A number of platforms have been already developed that can share data in real time through standard interfaces. Complete navigation systems can be built using these platforms using a layered software architecture. In this paper, we review the most popular platforms, and show an effective way to take advantage of them through an example surgical navigation application. Copyright © 2016 Elsevier B.V. All rights reserved.

Harvest: an open platform for developing web-based biomedical data discovery and reporting applications.

PubMed

Pennington, Jeffrey W; Ruth, Byron; Italia, Michael J; Miller, Jeffrey; Wrazien, Stacey; Loutrel, Jennifer G; Crenshaw, E Bryan; White, Peter S

2014-01-01

Biomedical researchers share a common challenge of making complex data understandable and accessible as they seek inherent relationships between attributes in disparate data types. Data discovery in this context is limited by a lack of query systems that efficiently show relationships between individual variables, but without the need to navigate underlying data models. We have addressed this need by developing Harvest, an open-source framework of modular components, and using it for the rapid development and deployment of custom data discovery software applications. Harvest incorporates visualizations of highly dimensional data in a web-based interface that promotes rapid exploration and export of any type of biomedical information, without exposing researchers to underlying data models. We evaluated Harvest with two cases: clinical data from pediatric cardiology and demonstration data from the OpenMRS project. Harvest's architecture and public open-source code offer a set of rapid application development tools to build data discovery applications for domain-specific biomedical data repositories. All resources, including the OpenMRS demonstration, can be found at http://harvest.research.chop.edu.

Harvest: an open platform for developing web-based biomedical data discovery and reporting applications

PubMed Central

Pennington, Jeffrey W; Ruth, Byron; Italia, Michael J; Miller, Jeffrey; Wrazien, Stacey; Loutrel, Jennifer G; Crenshaw, E Bryan; White, Peter S

2014-01-01

Biomedical researchers share a common challenge of making complex data understandable and accessible as they seek inherent relationships between attributes in disparate data types. Data discovery in this context is limited by a lack of query systems that efficiently show relationships between individual variables, but without the need to navigate underlying data models. We have addressed this need by developing Harvest, an open-source framework of modular components, and using it for the rapid development and deployment of custom data discovery software applications. Harvest incorporates visualizations of highly dimensional data in a web-based interface that promotes rapid exploration and export of any type of biomedical information, without exposing researchers to underlying data models. We evaluated Harvest with two cases: clinical data from pediatric cardiology and demonstration data from the OpenMRS project. Harvest's architecture and public open-source code offer a set of rapid application development tools to build data discovery applications for domain-specific biomedical data repositories. All resources, including the OpenMRS demonstration, can be found at http://harvest.research.chop.edu PMID:24131510

An Online Prediction Platform to Support the Environmental ...

EPA Pesticide Factsheets

Historical QSAR models are currently utilized across a broad range of applications within the U.S. Environmental Protection Agency (EPA). These models predict basic physicochemical properties (e.g., logP, aqueous solubility, vapor pressure), which are then incorporated into exposure, fate and transport models. Whereas the classical manner of publishing results in peer-reviewed journals remains appropriate, there are substantial benefits to be gained by providing enhanced, open access to the training data sets and resulting models. Benefits include improved transparency, more flexibility to expand training sets and improve model algorithms, and greater ability to independently characterize model performance both globally and in local areas of chemistry. We have developed a web-based prediction platform that uses open-source descriptors and modeling algorithms, employs modern cheminformatics technologies, and is tailored for ease of use by the toxicology and environmental regulatory community. This tool also provides web-services to meet both EPA’s projects and the modeling community at-large. The platform hosts models developed within EPA’s National Center for Computational Toxicology, as well as those developed by other EPA scientists and the outside scientific community. Recognizing that there are other on-line QSAR model platforms currently available which have additional capabilities, we connect to such services, where possible, to produce an integrated

Open access resources for genome-wide association mapping in rice

PubMed Central

McCouch, Susan R.; Wright, Mark H.; Tung, Chih-Wei; Maron, Lyza G.; McNally, Kenneth L.; Fitzgerald, Melissa; Singh, Namrata; DeClerck, Genevieve; Agosto-Perez, Francisco; Korniliev, Pavel; Greenberg, Anthony J.; Naredo, Ma. Elizabeth B.; Mercado, Sheila Mae Q.; Harrington, Sandra E.; Shi, Yuxin; Branchini, Darcy A.; Kuser-Falcão, Paula R.; Leung, Hei; Ebana, Kowaru; Yano, Masahiro; Eizenga, Georgia; McClung, Anna; Mezey, Jason

2016-01-01

Increasing food production is essential to meet the demands of a growing human population, with its rising income levels and nutritional expectations. To address the demand, plant breeders seek new sources of genetic variation to enhance the productivity, sustainability and resilience of crop varieties. Here we launch a high-resolution, open-access research platform to facilitate genome-wide association mapping in rice, a staple food crop. The platform provides an immortal collection of diverse germplasm, a high-density single-nucleotide polymorphism data set tailored for gene discovery, well-documented analytical strategies, and a suite of bioinformatics resources to facilitate biological interpretation. Using grain length, we demonstrate the power and resolution of our new high-density rice array, the accompanying genotypic data set, and an expanded diversity panel for detecting major and minor effect QTLs and subpopulation-specific alleles, with immediate implications for rice improvement. PMID:26842267

ADMS State of the Industry and Gap Analysis

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

Agalgaonkar, Yashodhan P.; Marinovici, Maria C.; Vadari, Subramanian V.

2016-03-31

An Advanced distribution management system (ADMS) is a platform for optimized distribution system operational management. This platform comprises of distribution management system (DMS) applications, supervisory control and data acquisition (SCADA), outage management system (OMS), and distributed energy resource management system (DERMS). One of the primary objectives of this work is to study and analyze several ADMS component and auxiliary systems. All the important component and auxiliary systems, SCADA, GISs, DMSs, AMRs/AMIs, OMSs, and DERMS, are discussed in this report. Their current generation technologies are analyzed, and their integration (or evolution) with an ADMS technology is discussed. An ADMS technology statemore » of the art and gap analysis is also presented. There are two technical gaps observed. The integration challenge between the component operational systems is the single largest challenge for ADMS design and deployment. Another significant challenge noted is concerning essential ADMS applications, for instance, fault location, isolation, and service restoration (FLISR), volt-var optimization (VVO), etc. There are a relatively small number of ADMS application developers as ADMS software platform is not open source. There is another critical gap and while not being technical in nature (when compared the two above) is still important to consider. The data models currently residing in utility GIS systems are either incomplete or inaccurate or both. This data is essential for planning and operations because it is typically one of the primary sources from which power system model are created. To achieve the full potential of ADMS, the ability to execute acute Power Flow solution is an important pre-requisite. These critical gaps are hindering wider Utility adoption of an ADMS technology. The development of an open architecture platform can eliminate many of these barriers and also aid seamless integration of distribution Utility legacy systems with an ADMS.« less

A ROSE-based OpenMP 3.0 Research Compiler Supporting Multiple Runtime Libraries

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

Liao, C; Quinlan, D; Panas, T

2010-01-25

OpenMP is a popular and evolving programming model for shared-memory platforms. It relies on compilers for optimal performance and to target modern hardware architectures. A variety of extensible and robust research compilers are key to OpenMP's sustainable success in the future. In this paper, we present our efforts to build an OpenMP 3.0 research compiler for C, C++, and Fortran; using the ROSE source-to-source compiler framework. Our goal is to support OpenMP research for ourselves and others. We have extended ROSE's internal representation to handle all of the OpenMP 3.0 constructs and facilitate their manipulation. Since OpenMP research is oftenmore » complicated by the tight coupling of the compiler translations and the runtime system, we present a set of rules to define a common OpenMP runtime library (XOMP) on top of multiple runtime libraries. These rules additionally define how to build a set of translations targeting XOMP. Our work demonstrates how to reuse OpenMP translations across different runtime libraries. This work simplifies OpenMP research by decoupling the problematic dependence between the compiler translations and the runtime libraries. We present an evaluation of our work by demonstrating an analysis tool for OpenMP correctness. We also show how XOMP can be defined using both GOMP and Omni and present comparative performance results against other OpenMP compilers.« less

TERRA REF: Advancing phenomics with high resolution, open access sensor and genomics data

NASA Astrophysics Data System (ADS)

LeBauer, D.; Kooper, R.; Burnette, M.; Willis, C.

2017-12-01

Automated plant measurement has the potential to improve understanding of genetic and environmental controls on plant traits (phenotypes). The application of sensors and software in the automation of high throughput phenotyping reflects a fundamental shift from labor intensive hand measurements to drone, tractor, and robot mounted sensing platforms. These tools are expected to speed the rate of crop improvement by enabling plant breeders to more accurately select plants with improved yields, resource use efficiency, and stress tolerance. However, there are many challenges facing high throughput phenomics: sensors and platforms are expensive, currently there are few standard methods of data collection and storage, and the analysis of large data sets requires high performance computers and automated, reproducible computing pipelines. To overcome these obstacles and advance the science of high throughput phenomics, the TERRA Phenotyping Reference Platform (TERRA-REF) team is developing an open-access database of high resolution sensor data. TERRA REF is an integrated field and greenhouse phenotyping system that includes: a reference field scanner with fifteen sensors that can generate terrabytes of data each day at mm resolution; UAV, tractor, and fixed field sensing platforms; and an automated controlled-environment scanner. These platforms will enable investigation of diverse sensing modalities, and the investigation of traits under controlled and field environments. It is the goal of TERRA REF to lower the barrier to entry for academic and industry researchers by providing high-resolution data, open source software, and online computing resources. Our project is unique in that all data will be made fully public in November 2018, and is already available to early adopters through the beta-user program. We will describe the datasets and how to use them as well as the databases and computing pipeline and how these can be reused and remixed in other phenomics pipelines. Finally, we will describe the National Data Service workbench, a cloud computing platform that can access the petabyte scale data while supporting reproducible research.

FloorspaceJS - A New, Open Source, Web-Based Geometry Editor for Building Energy Modeling (BEM): Preprint

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

Macumber, Daniel L; Horowitz, Scott G; Schott, Marjorie

Across most industries, desktop applications are being rapidly migrated to web applications for a variety of reasons. Web applications are inherently cross platform, mobile, and easier to distribute than desktop applications. Fueling this trend are a wide range of free, open source libraries and frameworks that make it incredibly easy to develop powerful web applications. The building energy modeling community is just beginning to pick up on these larger trends, with a small but growing number of building energy modeling applications starting on or moving to the web. This paper presents a new, open source, web based geometry editor formore » Building Energy Modeling (BEM). The editor is written completely in JavaScript and runs in a modern web browser. The editor works on a custom JSON file format and is designed to be integrated into a variety of web and desktop applications. The web based editor is available to use as a standalone web application at: https://nrel.github.io/openstudio-geometry-editor/. An example integration is demonstrated with the OpenStudio desktop application. Finally, the editor can be easily integrated with a wide range of possible building energy modeling web applications.« less

Opening Health Data: What Do Researchers Want? Early Experiences With New York's Open Health Data Platform.

PubMed

Martin, Erika G; Helbig, Natalie; Birkhead, Guthrie S

2015-01-01

Governments are rapidly developing open data platforms to improve transparency and make information more accessible. New York is a leader, with currently the only state platform devoted to health. Although these platforms could build public health departments' capabilities to serve more researchers, agencies have little guidance on releasing meaningful and usable data. Structured focus groups with researchers and practitioners collected stakeholder feedback on potential uses of open health data and New York's open data strategy. Researchers and practitioners attended a 1-day November 2013 workshop on New York State's open health data resources. After learning about the state's open data platform and vision for open health data, participants were organized into 7 focus groups to discuss the essential elements of open data sets, practical challenges to obtaining and using health data, and potential uses of open data. Participants included 33 quantitative health researchers from State University of New York campuses and private partners and 10 practitioners from the New York State Department of Health. There was low awareness of open data, with 67% of researchers reporting never using open data portals prior to the workshop. Participants were interested in data sets that were geocoded, longitudinal, or aggregated to small area granularity and capabilities to link multiple data sets. Multiple environmental conditions and barriers hinder their capacity to use health data for research. Although open data platforms cannot address all barriers, they provide multiple opportunities for public health research and practice, and participants were overall positive about the state's efforts to release open data. Open data are not ideal for some researchers because they do not contain individually identifiable data, indicating a need for tiered data release strategies. However, they do provide important new opportunities to facilitate research and foster collaborations among agencies, researchers, and practitioners.

Automated Gait Analysis Through Hues and Areas (AGATHA): a method to characterize the spatiotemporal pattern of rat gait

PubMed Central

Kloefkorn, Heidi E.; Pettengill, Travis R.; Turner, Sara M. F.; Streeter, Kristi A.; Gonzalez-Rothi, Elisa J.; Fuller, David D.; Allen, Kyle D.

2016-01-01

While rodent gait analysis can quantify the behavioral consequences of disease, significant methodological differences exist between analysis platforms and little validation has been performed to understand or mitigate these sources of variance. By providing the algorithms used to quantify gait, open-source gait analysis software can be validated and used to explore methodological differences. Our group is introducing, for the first time, a fully-automated, open-source method for the characterization of rodent spatiotemporal gait patterns, termed Automated Gait Analysis Through Hues and Areas (AGATHA). This study describes how AGATHA identifies gait events, validates AGATHA relative to manual digitization methods, and utilizes AGATHA to detect gait compensations in orthopaedic and spinal cord injury models. To validate AGATHA against manual digitization, results from videos of rodent gait, recorded at 1000 frames per second (fps), were compared. To assess one common source of variance (the effects of video frame rate), these 1000 fps videos were re-sampled to mimic several lower fps and compared again. While spatial variables were indistinguishable between AGATHA and manual digitization, low video frame rates resulted in temporal errors for both methods. At frame rates over 125 fps, AGATHA achieved a comparable accuracy and precision to manual digitization for all gait variables. Moreover, AGATHA detected unique gait changes in each injury model. These data demonstrate AGATHA is an accurate and precise platform for the analysis of rodent spatiotemporal gait patterns. PMID:27554674

Automated Gait Analysis Through Hues and Areas (AGATHA): A Method to Characterize the Spatiotemporal Pattern of Rat Gait.

PubMed

Kloefkorn, Heidi E; Pettengill, Travis R; Turner, Sara M F; Streeter, Kristi A; Gonzalez-Rothi, Elisa J; Fuller, David D; Allen, Kyle D

2017-03-01

While rodent gait analysis can quantify the behavioral consequences of disease, significant methodological differences exist between analysis platforms and little validation has been performed to understand or mitigate these sources of variance. By providing the algorithms used to quantify gait, open-source gait analysis software can be validated and used to explore methodological differences. Our group is introducing, for the first time, a fully-automated, open-source method for the characterization of rodent spatiotemporal gait patterns, termed Automated Gait Analysis Through Hues and Areas (AGATHA). This study describes how AGATHA identifies gait events, validates AGATHA relative to manual digitization methods, and utilizes AGATHA to detect gait compensations in orthopaedic and spinal cord injury models. To validate AGATHA against manual digitization, results from videos of rodent gait, recorded at 1000 frames per second (fps), were compared. To assess one common source of variance (the effects of video frame rate), these 1000 fps videos were re-sampled to mimic several lower fps and compared again. While spatial variables were indistinguishable between AGATHA and manual digitization, low video frame rates resulted in temporal errors for both methods. At frame rates over 125 fps, AGATHA achieved a comparable accuracy and precision to manual digitization for all gait variables. Moreover, AGATHA detected unique gait changes in each injury model. These data demonstrate AGATHA is an accurate and precise platform for the analysis of rodent spatiotemporal gait patterns.

Implementation of Web-Based Education in Egypt through Cloud Computing Technologies and Its Effect on Higher Education

ERIC Educational Resources Information Center

El-Seoud, M. Samir Abou; El-Sofany, Hosam F.; Taj-Eddin, Islam A. T. F.; Nosseir, Ann; El-Khouly, Mahmoud M.

2013-01-01

The information technology educational programs at most universities in Egypt face many obstacles that can be overcome using technology enhanced learning. An open source Moodle eLearning platform has been implemented at many public and private universities in Egypt, as an aid to deliver e-content and to provide the institution with various…

Core Flight System (cFS) a Low Cost Solution for SmallSats

NASA Technical Reports Server (NTRS)

McComas, David; Strege, Susanne; Wilmot, Jonathan

2015-01-01

The cFS is a FSW product line that uses a layered architecture and compile-time configuration parameters which make it portable and scalable for a wide range of platforms. The software layers that defined the application run-time environment are now under a NASA-wide configuration control board with the goal of sustaining an open-source application ecosystem.

Design and construction of a first-generation high-throughput integrated molecular biology platform for production of optimized synthetic genes and improved industrial strains

USDA-ARS?s Scientific Manuscript database

The molecular biological techniques for plasmid-based assembly and cloning of synthetic assembled gene open reading frames are essential for elucidating the function of the proteins encoded by the genes. These techniques involve the production of full-length cDNA libraries as a source of plasmid-bas...

Mobile Learning Environment with Short Messaging Service: Application to a Campus Environment in a Developing Country

ERIC Educational Resources Information Center

Premadasa, H. K. Salinda; Meegama, R. Gayan N.

2013-01-01

Purpose: The purpose of this paper is to discuss how to integrate secure, open-source and mobile-based system with the Moodle learning management system (MLMS) then describe the implementation of a campus-wide mobile learning environment with short messaging system (SMS) and how this platform is incorporated with the student's learning…

Open Source Eportfolio: Development and Implementation of an Institution-Wide Electronic Portfolio Platform for Students

ERIC Educational Resources Information Center

Meeus, Wil; Questier, Frederik; Derks, Thea

2006-01-01

This article provides a general overview of how portfolio is used in education and then goes on to discuss the development of a generic, institution-wide portfolio for students. We further provide a succinct summary and critical analysis of the educational principles underlying the use of portfolio in higher education. This is followed by an…

Multidisciplinary Tool for Systems Analysis of Planetary Entry, Descent, and Landing

NASA Technical Reports Server (NTRS)

Samareh, Jamshid A.

2011-01-01

Systems analysis of a planetary entry (SAPE), descent, and landing (EDL) is a multidisciplinary activity in nature. SAPE improves the performance of the systems analysis team by automating and streamlining the process, and this improvement can reduce the errors that stem from manual data transfer among discipline experts. SAPE is a multidisciplinary tool for systems analysis of planetary EDL for Venus, Earth, Mars, Jupiter, Saturn, Uranus, Neptune, and Titan. It performs EDL systems analysis for any planet, operates cross-platform (i.e., Windows, Mac, and Linux operating systems), uses existing software components and open-source software to avoid software licensing issues, performs low-fidelity systems analysis in one hour on a computer that is comparable to an average laptop, and keeps discipline experts in the analysis loop. SAPE uses Python, a platform-independent, open-source language, for integration and for the user interface. Development has relied heavily on the object-oriented programming capabilities that are available in Python. Modules are provided to interface with commercial and government off-the-shelf software components (e.g., thermal protection systems and finite-element analysis). SAPE currently includes the following analysis modules: geometry, trajectory, aerodynamics, aerothermal, thermal protection system, and interface for structural sizing.

McIDAS-V: Data Analysis and Visualization for NPOESS and GOES-R

NASA Astrophysics Data System (ADS)

Rink, T.; Achtor, T. H.

2009-12-01

McIDAS-V, the next-generation McIDAS, is being built on top a modern, cross-platform software framework which supports development of 4-D, interactive displays and integration of wide-array of geophysical data. As the replacement of McIDAS, the development emphasis is on future satellite observation platforms such as NPOESS and GOES-R. Data interrogation, analysis and visualization capabilities have been developed for multi- and hyper-spectral instruments like MODIS, AIRS and IASI, and are being extended for application to VIIRS and CrIS. Compatibility with GOES-R ABI level1 and level2 product storage formats has been demonstrated. The abstract data model, which can internalize most any geophysical data, opens up new possibilities for data fusion techniques, for example, polar and geostationary, (LEO/GEO), synergy for research and validation. McIDAS-V follows an object-oriented design model, using the Java programming language, allowing specialized extensions for for new sources of data, and novel displays and interactive behavior. The reference application, what the user sees on startup, can be customized, and the system has a persistence mechanism allowing sharing of the application state across the internet. McIDAS-V is open-source, and free to the public.

Bonn eXperimental System (BoXS): An open-source platform for interactive experiments in psychology and economics.

PubMed

Seithe, Mirko; Morina, Jeronim; Glöckner, Andreas

2016-12-01

The increased interest in complex-interactive behavior on the one hand and the cognitive and affective processes underlying behavior on the other are a challenge for researchers in psychology and behavioral economics. Research often necessitates that participants strategically interact with each other in dyads or groups. At the same time, to investigate the underlying cognitive and affective processes in a fine-grained manner, not only choices but also other variables such as decision time, information search, and pupil dilation should be recorded. The Bonn eXperimental System (BoXS) introduced in this article is an open-source platform that allows interactive as well as non-interactive experiments to be conducted while recording process measures very efficiently and completely browser-based. In the current version, BoXS has particularly been extended to enable conducting interactive eye-tracking and mouse-tracking experiments. One core advantage of BoXS is its simplicity. Using BoXS does not require prior installation for both experimenters and participants, which allows for running studies outside the laboratory and over the internet. Learning to program for BoXS is easy even for researchers without previous programming experience.

Collaborative development of predictive toxicology applications

PubMed Central

2010-01-01

OpenTox provides an interoperable, standards-based Framework for the support of predictive toxicology data management, algorithms, modelling, validation and reporting. It is relevant to satisfying the chemical safety assessment requirements of the REACH legislation as it supports access to experimental data, (Quantitative) Structure-Activity Relationship models, and toxicological information through an integrating platform that adheres to regulatory requirements and OECD validation principles. Initial research defined the essential components of the Framework including the approach to data access, schema and management, use of controlled vocabularies and ontologies, architecture, web service and communications protocols, and selection and integration of algorithms for predictive modelling. OpenTox provides end-user oriented tools to non-computational specialists, risk assessors, and toxicological experts in addition to Application Programming Interfaces (APIs) for developers of new applications. OpenTox actively supports public standards for data representation, interfaces, vocabularies and ontologies, Open Source approaches to core platform components, and community-based collaboration approaches, so as to progress system interoperability goals. The OpenTox Framework includes APIs and services for compounds, datasets, features, algorithms, models, ontologies, tasks, validation, and reporting which may be combined into multiple applications satisfying a variety of different user needs. OpenTox applications are based on a set of distributed, interoperable OpenTox API-compliant REST web services. The OpenTox approach to ontology allows for efficient mapping of complementary data coming from different datasets into a unifying structure having a shared terminology and representation. Two initial OpenTox applications are presented as an illustration of the potential impact of OpenTox for high-quality and consistent structure-activity relationship modelling of REACH-relevant endpoints: ToxPredict which predicts and reports on toxicities for endpoints for an input chemical structure, and ToxCreate which builds and validates a predictive toxicity model based on an input toxicology dataset. Because of the extensible nature of the standardised Framework design, barriers of interoperability between applications and content are removed, as the user may combine data, models and validation from multiple sources in a dependable and time-effective way. PMID:20807436

Collaborative development of predictive toxicology applications.

PubMed

Hardy, Barry; Douglas, Nicki; Helma, Christoph; Rautenberg, Micha; Jeliazkova, Nina; Jeliazkov, Vedrin; Nikolova, Ivelina; Benigni, Romualdo; Tcheremenskaia, Olga; Kramer, Stefan; Girschick, Tobias; Buchwald, Fabian; Wicker, Joerg; Karwath, Andreas; Gütlein, Martin; Maunz, Andreas; Sarimveis, Haralambos; Melagraki, Georgia; Afantitis, Antreas; Sopasakis, Pantelis; Gallagher, David; Poroikov, Vladimir; Filimonov, Dmitry; Zakharov, Alexey; Lagunin, Alexey; Gloriozova, Tatyana; Novikov, Sergey; Skvortsova, Natalia; Druzhilovsky, Dmitry; Chawla, Sunil; Ghosh, Indira; Ray, Surajit; Patel, Hitesh; Escher, Sylvia

2010-08-31

OpenTox provides an interoperable, standards-based Framework for the support of predictive toxicology data management, algorithms, modelling, validation and reporting. It is relevant to satisfying the chemical safety assessment requirements of the REACH legislation as it supports access to experimental data, (Quantitative) Structure-Activity Relationship models, and toxicological information through an integrating platform that adheres to regulatory requirements and OECD validation principles. Initial research defined the essential components of the Framework including the approach to data access, schema and management, use of controlled vocabularies and ontologies, architecture, web service and communications protocols, and selection and integration of algorithms for predictive modelling. OpenTox provides end-user oriented tools to non-computational specialists, risk assessors, and toxicological experts in addition to Application Programming Interfaces (APIs) for developers of new applications. OpenTox actively supports public standards for data representation, interfaces, vocabularies and ontologies, Open Source approaches to core platform components, and community-based collaboration approaches, so as to progress system interoperability goals.The OpenTox Framework includes APIs and services for compounds, datasets, features, algorithms, models, ontologies, tasks, validation, and reporting which may be combined into multiple applications satisfying a variety of different user needs. OpenTox applications are based on a set of distributed, interoperable OpenTox API-compliant REST web services. The OpenTox approach to ontology allows for efficient mapping of complementary data coming from different datasets into a unifying structure having a shared terminology and representation.Two initial OpenTox applications are presented as an illustration of the potential impact of OpenTox for high-quality and consistent structure-activity relationship modelling of REACH-relevant endpoints: ToxPredict which predicts and reports on toxicities for endpoints for an input chemical structure, and ToxCreate which builds and validates a predictive toxicity model based on an input toxicology dataset. Because of the extensible nature of the standardised Framework design, barriers of interoperability between applications and content are removed, as the user may combine data, models and validation from multiple sources in a dependable and time-effective way.

AI based HealthCare Platform for Real Time, Predictive and Prescriptive Analytics using Reactive Programming

NASA Astrophysics Data System (ADS)

Kaur, Jagreet; Singh Mann, Kulwinder, Dr.

2018-01-01

AI in Healthcare needed to bring real, actionable insights and Individualized insights in real time for patients and Doctors to support treatment decisions., We need a Patient Centred Platform for integrating EHR Data, Patient Data, Prescriptions, Monitoring, Clinical research and Data. This paper proposes a generic architecture for enabling AI based healthcare analytics Platform by using open sources Technologies Apache beam, Apache Flink Apache Spark, Apache NiFi, Kafka, Tachyon, Gluster FS, NoSQL- Elasticsearch, Cassandra. This paper will show the importance of applying AI based predictive and prescriptive analytics techniques in Health sector. The system will be able to extract useful knowledge that helps in decision making and medical monitoring in real-time through an intelligent process analysis and big data processing.

a Public Platform for Geospatial Data Sharing for Disaster Risk Management

NASA Astrophysics Data System (ADS)

Balbo, S.; Boccardo, P.; Dalmasso, S.; Pasquali, P.

2013-01-01

Several studies have been conducted in Africa to assist local governments in addressing the risk situation related to natural hazards. Geospatial data containing information on vulnerability, impacts, climate change, disaster risk reduction is usually part of the output of such studies and is valuable to national and international organizations to reduce the risks and mitigate the impacts of disasters. Nevertheless this data isn't efficiently widely distributed and often resides in remote storage solutions hardly reachable. Spatial Data Infrastructures are technical solutions capable to solve this issue, by storing geospatial data and making them widely available through the internet. Among these solutions, GeoNode, an open source online platform for geospatial data sharing, has been developed in recent years. GeoNode is a platform for the management and publication of geospatial data. It brings together mature and stable open-source software projects under a consistent and easy-to-use interface allowing users, with little training, to quickly and easily share data and create interactive maps. GeoNode data management tools allow for integrated creation of data, metadata, and map visualizations. Each dataset in the system can be shared publicly or restricted to allow access to only specific users. Social features like user profiles and commenting and rating systems allow for the development of communities around each platform to facilitate the use, management, and quality control of the data the GeoNode instance contains (http://geonode.org/). This paper presents a case study scenario of setting up a Web platform based on GeoNode. It is a public platform called MASDAP and promoted by the Government of Malawi in order to support development of the country and build resilience against natural disasters. A substantial amount of geospatial data has already been collected about hydrogeological risk, as well as several other-disasters related information. Moreover this platform will help to ensure that the data created by a number of past or ongoing projects is maintained and that this information remains accessible and useful. An Integrated Flood Risk Management Plan for a river basin has already been included in the platform and other data from future disaster risk management projects will be added as well.

Assessment of grid optimisation measures for the German transmission grid using open source grid data

NASA Astrophysics Data System (ADS)

Böing, F.; Murmann, A.; Pellinger, C.; Bruckmeier, A.; Kern, T.; Mongin, T.

2018-02-01

The expansion of capacities in the German transmission grid is a necessity for further integration of renewable energy sources into the electricity sector. In this paper, the grid optimisation measures ‘Overhead Line Monitoring’, ‘Power-to-Heat’ and ‘Demand Response in the Industry’ are evaluated and compared against conventional grid expansion for the year 2030. Initially, the methodical approach of the simulation model is presented and detailed descriptions of the grid model and the used grid data, which partly originates from open-source platforms, are provided. Further, this paper explains how ‘Curtailment’ and ‘Redispatch’ can be reduced by implementing grid optimisation measures and how the depreciation of economic costs can be determined considering construction costs. The developed simulations show that the conventional grid expansion is more efficient and implies more grid relieving effects than the evaluated grid optimisation measures.

KiT: a MATLAB package for kinetochore tracking.

PubMed

Armond, Jonathan W; Vladimirou, Elina; McAinsh, Andrew D; Burroughs, Nigel J

2016-06-15

During mitosis, chromosomes are attached to the mitotic spindle via large protein complexes called kinetochores. The motion of kinetochores throughout mitosis is intricate and automated quantitative tracking of their motion has already revealed many surprising facets of their behaviour. Here, we present 'KiT' (Kinetochore Tracking)-an easy-to-use, open-source software package for tracking kinetochores from live-cell fluorescent movies. KiT supports 2D, 3D and multi-colour movies, quantification of fluorescence, integrated deconvolution, parallel execution and multiple algorithms for particle localization. KiT is free, open-source software implemented in MATLAB and runs on all MATLAB supported platforms. KiT can be downloaded as a package from http://www.mechanochemistry.org/mcainsh/software.php The source repository is available at https://bitbucket.org/jarmond/kit and under continuing development. Supplementary data are available at Bioinformatics online. jonathan.armond@warwick.ac.uk. © The Author 2016. Published by Oxford University Press.

Robotics-assisted mass spectrometry assay platform enabled by open-source electronics.

PubMed

Chiu, Shih-Hao; Urban, Pawel L

2015-02-15

Mass spectrometry (MS) is an important analytical technique with numerous applications in clinical analysis, biochemistry, environmental analysis, geology and physics. Its success builds on the ability of MS to determine molecular weights of analytes, and elucidate their structures. However, sample handling prior to MS requires a lot of attention and labor. In this work we were aiming to automate processing samples for MS so that analyses could be conducted without much supervision of experienced analysts. The goal of this study was to develop a robotics and information technology-oriented platform that could control the whole analysis process including sample delivery, reaction-based assay, data acquisition, and interaction with the analyst. The proposed platform incorporates a robotic arm for handling sample vials delivered to the laboratory, and several auxiliary devices which facilitate and secure the analysis process. They include: multi-relay board, infrared sensors, photo-interrupters, gyroscopes, force sensors, fingerprint scanner, barcode scanner, touch screen panel, and internet interface. The control of all the building blocks is achieved through implementation of open-source electronics (Arduino), and enabled by custom-written programs in C language. The advantages of the proposed system include: low cost, simplicity, small size, as well as facile automation of sample delivery and processing without the intervention of the analyst. It is envisaged that this simple robotic system may be the forerunner of automated laboratories dedicated to mass spectrometric analysis of biological samples. Copyright © 2014 Elsevier B.V. All rights reserved.

The ImageJ ecosystem: an open platform for biomedical image analysis

PubMed Central

Schindelin, Johannes; Rueden, Curtis T.; Hiner, Mark C.; Eliceiri, Kevin W.

2015-01-01

Technology in microscopy advances rapidly, enabling increasingly affordable, faster, and more precise quantitative biomedical imaging, which necessitates correspondingly more-advanced image processing and analysis techniques. A wide range of software is available – from commercial to academic, special-purpose to Swiss army knife, small to large–but a key characteristic of software that is suitable for scientific inquiry is its accessibility. Open-source software is ideal for scientific endeavors because it can be freely inspected, modified, and redistributed; in particular, the open-software platform ImageJ has had a huge impact on life sciences, and continues to do so. From its inception, ImageJ has grown significantly due largely to being freely available and its vibrant and helpful user community. Scientists as diverse as interested hobbyists, technical assistants, students, scientific staff, and advanced biology researchers use ImageJ on a daily basis, and exchange knowledge via its dedicated mailing list. Uses of ImageJ range from data visualization and teaching to advanced image processing and statistical analysis. The software's extensibility continues to attract biologists at all career stages as well as computer scientists who wish to effectively implement specific image-processing algorithms. In this review, we use the ImageJ project as a case study of how open-source software fosters its suites of software tools, making multitudes of image-analysis technology easily accessible to the scientific community. We specifically explore what makes ImageJ so popular, how it impacts life science, how it inspires other projects, and how it is self-influenced by coevolving projects within the ImageJ ecosystem. PMID:26153368

The ImageJ ecosystem: An open platform for biomedical image analysis.

PubMed

Schindelin, Johannes; Rueden, Curtis T; Hiner, Mark C; Eliceiri, Kevin W

2015-01-01

Technology in microscopy advances rapidly, enabling increasingly affordable, faster, and more precise quantitative biomedical imaging, which necessitates correspondingly more-advanced image processing and analysis techniques. A wide range of software is available-from commercial to academic, special-purpose to Swiss army knife, small to large-but a key characteristic of software that is suitable for scientific inquiry is its accessibility. Open-source software is ideal for scientific endeavors because it can be freely inspected, modified, and redistributed; in particular, the open-software platform ImageJ has had a huge impact on the life sciences, and continues to do so. From its inception, ImageJ has grown significantly due largely to being freely available and its vibrant and helpful user community. Scientists as diverse as interested hobbyists, technical assistants, students, scientific staff, and advanced biology researchers use ImageJ on a daily basis, and exchange knowledge via its dedicated mailing list. Uses of ImageJ range from data visualization and teaching to advanced image processing and statistical analysis. The software's extensibility continues to attract biologists at all career stages as well as computer scientists who wish to effectively implement specific image-processing algorithms. In this review, we use the ImageJ project as a case study of how open-source software fosters its suites of software tools, making multitudes of image-analysis technology easily accessible to the scientific community. We specifically explore what makes ImageJ so popular, how it impacts the life sciences, how it inspires other projects, and how it is self-influenced by coevolving projects within the ImageJ ecosystem. © 2015 Wiley Periodicals, Inc.

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.

Open-source approaches for the repurposing of existing or failed candidate drugs: learning from and applying the lessons across diseases

PubMed Central

Allarakhia, Minna

2013-01-01

Repurposing has the objective of targeting existing drugs and failed, abandoned, or yet-to-be-pursued clinical candidates to new disease areas. The open-source model permits for the sharing of data, resources, compounds, clinical molecules, small libraries, and screening platforms to cost-effectively advance old drugs and/or candidates into clinical re-development. Clearly, at the core of drug-repurposing activities is collaboration, in many cases progressing beyond the open sharing of resources, technology, and intellectual property, to the sharing of facilities and joint program development to foster drug-repurposing human-capacity development. A variety of initiatives under way for drug repurposing, including those targeting rare and neglected diseases, are discussed in this review and provide insight into the stakeholders engaged in drug-repurposing discovery, the models of collaboration used, the intellectual property-management policies crafted, and human capacity developed. In the case of neglected tropical diseases, it is suggested that the development of human capital be a central aspect of drug-repurposing programs. Open-source models can support human-capital development through collaborative data generation, open compound access, open and collaborative screening, preclinical and possibly clinical studies. Given the urgency of drug development for neglected tropical diseases, the review suggests elements from current repurposing programs be extended to the neglected tropical diseases arena. PMID:23966771

Open-source approaches for the repurposing of existing or failed candidate drugs: learning from and applying the lessons across diseases.

PubMed

Allarakhia, Minna

2013-01-01

Repurposing has the objective of targeting existing drugs and failed, abandoned, or yet-to-be-pursued clinical candidates to new disease areas. The open-source model permits for the sharing of data, resources, compounds, clinical molecules, small libraries, and screening platforms to cost-effectively advance old drugs and/or candidates into clinical re-development. Clearly, at the core of drug-repurposing activities is collaboration, in many cases progressing beyond the open sharing of resources, technology, and intellectual property, to the sharing of facilities and joint program development to foster drug-repurposing human-capacity development. A variety of initiatives under way for drug repurposing, including those targeting rare and neglected diseases, are discussed in this review and provide insight into the stakeholders engaged in drug-repurposing discovery, the models of collaboration used, the intellectual property-management policies crafted, and human capacity developed. In the case of neglected tropical diseases, it is suggested that the development of human capital be a central aspect of drug-repurposing programs. Open-source models can support human-capital development through collaborative data generation, open compound access, open and collaborative screening, preclinical and possibly clinical studies. Given the urgency of drug development for neglected tropical diseases, the review suggests elements from current repurposing programs be extended to the neglected tropical diseases arena.

VOLTTRON™: Tech-to-Market Best-Practices Guide for Small- and Medium-Sized Commercial Buildings

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

Cort, Katherine A.; Haack, Jereme N.; Katipamula, Srinivas

VOLTTRON™ is an open-source distributed control and sensing platform developed by Pacific Northwest National Laboratory for the U.S. Department of Energy. It was developed to be used by the Office of Energy Efficiency and Renewable Energy to support transactive controls research and deployment activities. VOLTTRON is designed to be an overarching integration platform that could be used to bring together vendors, users, and developers and enable rapid application development and testing. The platform is designed to support modern control strategies, including the use of agent- and transaction-based controls. It also is designed to support the management of a wide rangemore » of applications, including heating, ventilation, and air-conditioning systems; electric vehicles; and distributed-energy and whole-building loads. This report was completed as part of the Building Technologies Office’s Technology-to-Market Initiative for VOLTTRON’s Market Validation and Business Case Development efforts. The report provides technology-to-market guidance and best practices related to VOLTTRON platform deployments and commercialization activities for use by entities serving small- and medium-sized commercial buildings. The report characterizes the platform ecosystem within the small- and medium-sized commercial building market and articulates the value proposition of VOLTTRON for three core participants in this ecosystem: 1) platform owners/adopters, 2) app developers, and 3) end-users. The report also identifies key market drivers and opportunities for open platform deployments in the small- and medium-sized commercial building market. Possible pathways to the market are described—laboratory testing to market adoption to commercialization. We also identify and address various technical and market barriers that could hinder deployment of VOLTTRON. Finally, we provide “best practice” tech-to-market guidance for building energy-related deployment efforts serving small- and medium-sized commercial buildings.« less

Aerodynamics and Control of Quadrotors

NASA Astrophysics Data System (ADS)

Bangura, Moses

Quadrotors are aerial vehicles with a four motor-rotor assembly for generating lift and controllability. Their light weight, ease of design and simple dynamics have increased their use in aerial robotics research. There are many quadrotors that are commercially available or under development. Commercial off-the-shelf quadrotors usually lack the ability to be reprogrammed and are unsuitable for use as research platforms. The open-source code developed in this thesis differs from other open-source systems by focusing on the key performance road blocks in implementing high performance experimental quadrotor platforms for research: motor-rotor control for thrust regulation, velocity and attitude estimation, and control for position regulation and trajectory tracking. In all three of these fundamental subsystems, code sub modules for implementation on commonly available hardware are provided. In addition, the thesis provides guidance on scoping and commissioning open-source hardware components to build a custom quadrotor. A key contribution of the thesis is then a design methodology for the development of experimental quadrotor platforms from open-source or commercial off-the-shelf software and hardware components that have active community support. Quadrotors built following the methodology allows the user access to the operation of the subsystems and, in particular, the user can tune the gains of the observers and controllers in order to push the overall system to its performance limits. This enables the quadrotor framework to be used for a variety of applications such as heavy lifting and high performance aggressive manoeuvres by both the hobby and academic communities. To address the question of thrust control, momentum and blade element theories are used to develop aerodynamic models for rotor blades specific to quadrotors. With the aerodynamic models, a novel thrust estimation and control scheme that improves on existing RPM (revolutions per minute) control of rotors is proposed. The approach taken uses the measured electrical power into the rotors compensating for electrical loses, to estimate changing aerodynamic conditions around a rotor as well as the aerodynamic thrust force. The resulting control algorithms are implemented in real-time on the embedded electronic speed controller (ESC) hardware. Using the estimates of the aerodynamic conditions around the rotor at this level improves the dynamic response to gust as the low-level thrust control is the fastest dynamic level on the vehicle. The aerodynamic estimation scheme enables the vehicle to react almost instantaneously to aerodynamic changes in the environment without affecting the overall dynamic performance of the vehicle. (Abstract shortened by ProQuest.).

myChEMBL: a virtual machine implementation of open data and cheminformatics tools.

PubMed

Ochoa, Rodrigo; Davies, Mark; Papadatos, George; Atkinson, Francis; Overington, John P

2014-01-15

myChEMBL is a completely open platform, which combines public domain bioactivity data with open source database and cheminformatics technologies. myChEMBL consists of a Linux (Ubuntu) Virtual Machine featuring a PostgreSQL schema with the latest version of the ChEMBL database, as well as the latest RDKit cheminformatics libraries. In addition, a self-contained web interface is available, which can be modified and improved according to user specifications. The VM is available at: ftp://ftp.ebi.ac.uk/pub/databases/chembl/VM/myChEMBL/current. The web interface and web services code is available at: https://github.com/rochoa85/myChEMBL.

49 CFR 231.13 - Passenger-train cars with open-end platforms.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 4 2010-10-01 2010-10-01 false Passenger-train cars with open-end platforms. 231... Passenger-train cars with open-end platforms. (a) Hand brakes—(1) Number. Each passenger-train car shall be...) Location. Each hand brake shall be so located that it can be safely operated while car is in motion. (b...

49 CFR 231.13 - Passenger-train cars with open-end platforms.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 49 Transportation 4 2012-10-01 2012-10-01 false Passenger-train cars with open-end platforms. 231... Passenger-train cars with open-end platforms. (a) Hand brakes—(1) Number. Each passenger-train car shall be...) Location. Each hand brake shall be so located that it can be safely operated while car is in motion. (b...

49 CFR 231.13 - Passenger-train cars with open-end platforms.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 4 2011-10-01 2011-10-01 false Passenger-train cars with open-end platforms. 231... Passenger-train cars with open-end platforms. (a) Hand brakes—(1) Number. Each passenger-train car shall be...) Location. Each hand brake shall be so located that it can be safely operated while car is in motion. (b...

49 CFR 231.13 - Passenger-train cars with open-end platforms.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 49 Transportation 4 2013-10-01 2013-10-01 false Passenger-train cars with open-end platforms. 231... Passenger-train cars with open-end platforms. (a) Hand brakes—(1) Number. Each passenger-train car shall be...) Location. Each hand brake shall be so located that it can be safely operated while car is in motion. (b...

49 CFR 231.13 - Passenger-train cars with open-end platforms.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 49 Transportation 4 2014-10-01 2014-10-01 false Passenger-train cars with open-end platforms. 231... Passenger-train cars with open-end platforms. (a) Hand brakes—(1) Number. Each passenger-train car shall be...) Location. Each hand brake shall be so located that it can be safely operated while car is in motion. (b...

SNPConvert: SNP Array Standardization and Integration in Livestock Species.

PubMed

Nicolazzi, Ezequiel Luis; Marras, Gabriele; Stella, Alessandra

2016-06-09

One of the main advantages of single nucleotide polymorphism (SNP) array technology is providing genotype calls for a specific number of SNP markers at a relatively low cost. Since its first application in animal genetics, the number of available SNP arrays for each species has been constantly increasing. However, conversely to that observed in whole genome sequence data analysis, SNP array data does not have a common set of file formats or coding conventions for allele calling. Therefore, the standardization and integration of SNP array data from multiple sources have become an obstacle, especially for users with basic or no programming skills. Here, we describe the difficulties related to handling SNP array data, focusing on file formats, SNP allele coding, and mapping. We also present SNPConvert suite, a multi-platform, open-source, and user-friendly set of tools to overcome these issues. This tool, which can be integrated with open-source and open-access tools already available, is a first step towards an integrated system to standardize and integrate any type of raw SNP array data. The tool is available at: https://github. com/nicolazzie/SNPConvert.git.

NeuroPG: open source software for optical pattern generation and data acquisition

PubMed Central

Avants, Benjamin W.; Murphy, Daniel B.; Dapello, Joel A.; Robinson, Jacob T.

2015-01-01

Patterned illumination using a digital micromirror device (DMD) is a powerful tool for optogenetics. Compared to a scanning laser, DMDs are inexpensive and can easily create complex illumination patterns. Combining these complex spatiotemporal illumination patterns with optogenetics allows DMD-equipped microscopes to probe neural circuits by selectively manipulating the activity of many individual cells or many subcellular regions at the same time. To use DMDs to study neural activity, scientists must develop specialized software to coordinate optical stimulation patterns with the acquisition of electrophysiological and fluorescence data. To meet this growing need we have developed an open source optical pattern generation software for neuroscience—NeuroPG—that combines, DMD control, sample visualization, and data acquisition in one application. Built on a MATLAB platform, NeuroPG can also process, analyze, and visualize data. The software is designed specifically for the Mightex Polygon400; however, as an open source package, NeuroPG can be modified to incorporate any data acquisition, imaging, or illumination equipment that is compatible with MATLAB’s Data Acquisition and Image Acquisition toolboxes. PMID:25784873

TOPSAN: a dynamic web database for structural genomics.

PubMed

Ellrott, Kyle; Zmasek, Christian M; Weekes, Dana; Sri Krishna, S; Bakolitsa, Constantina; Godzik, Adam; Wooley, John

2011-01-01

The Open Protein Structure Annotation Network (TOPSAN) is a web-based collaboration platform for exploring and annotating structures determined by structural genomics efforts. Characterization of those structures presents a challenge since the majority of the proteins themselves have not yet been characterized. Responding to this challenge, the TOPSAN platform facilitates collaborative annotation and investigation via a user-friendly web-based interface pre-populated with automatically generated information. Semantic web technologies expand and enrich TOPSAN's content through links to larger sets of related databases, and thus, enable data integration from disparate sources and data mining via conventional query languages. TOPSAN can be found at http://www.topsan.org.

Integrative structure modeling with the Integrative Modeling Platform.

PubMed

Webb, Benjamin; Viswanath, Shruthi; Bonomi, Massimiliano; Pellarin, Riccardo; Greenberg, Charles H; Saltzberg, Daniel; Sali, Andrej

2018-01-01

Building models of a biological system that are consistent with the myriad data available is one of the key challenges in biology. Modeling the structure and dynamics of macromolecular assemblies, for example, can give insights into how biological systems work, evolved, might be controlled, and even designed. Integrative structure modeling casts the building of structural models as a computational optimization problem, for which information about the assembly is encoded into a scoring function that evaluates candidate models. Here, we describe our open source software suite for integrative structure modeling, Integrative Modeling Platform (https://integrativemodeling.org), and demonstrate its use. © 2017 The Protein Society.

A microcontroller platform for the rapid prototyping of functional electrical stimulation-based gait neuroprostheses.

PubMed

Luzio de Melo, Paulo; da Silva, Miguel Tavares; Martins, Jorge; Newman, Dava

2015-05-01

Functional electrical stimulation (FES) has been used over the last decades as a method to rehabilitate lost motor functions of individuals with spinal cord injury, multiple sclerosis, and post-stroke hemiparesis. Within this field, researchers in need of developing FES-based control solutions for specific disabilities often have to choose between either the acquisition and integration of high-performance industry-level systems, which are rather expensive and hardly portable, or develop custom-made portable solutions, which despite their lower cost, usually require expert-level electronic skills. Here, a flexible low-cost microcontroller-based platform for rapid prototyping of FES neuroprostheses is presented, designed for reduced execution complexity, development time, and production cost. For this reason, the Arduino open-source microcontroller platform was used, together with off-the-shelf components whenever possible. The developed system enables the rapid deployment of portable FES-based gait neuroprostheses, being flexible enough to allow simple open-loop strategies but also more complex closed-loop solutions. The system is based on a modular architecture that allows the development of optimized solutions depending on the desired FES applications, even though the design and testing of the platform were focused toward drop foot correction. The flexibility of the system was demonstrated using two algorithms targeting drop foot condition within different experimental setups. Successful bench testing of the device in healthy subjects demonstrated these neuroprosthesis platform capabilities to correct drop foot. Copyright © 2015 International Center for Artificial Organs and Transplantation and Wiley Periodicals, Inc.

A Geospatial Information Grid Framework for Geological Survey.

PubMed

Wu, Liang; Xue, Lei; Li, Chaoling; Lv, Xia; Chen, Zhanlong; Guo, Mingqiang; Xie, Zhong

2015-01-01

The use of digital information in geological fields is becoming very important. Thus, informatization in geological surveys should not stagnate as a result of the level of data accumulation. The integration and sharing of distributed, multi-source, heterogeneous geological information is an open problem in geological domains. Applications and services use geological spatial data with many features, including being cross-region and cross-domain and requiring real-time updating. As a result of these features, desktop and web-based geographic information systems (GISs) experience difficulties in meeting the demand for geological spatial information. To facilitate the real-time sharing of data and services in distributed environments, a GIS platform that is open, integrative, reconfigurable, reusable and elastic would represent an indispensable tool. The purpose of this paper is to develop a geological cloud-computing platform for integrating and sharing geological information based on a cloud architecture. Thus, the geological cloud-computing platform defines geological ontology semantics; designs a standard geological information framework and a standard resource integration model; builds a peer-to-peer node management mechanism; achieves the description, organization, discovery, computing and integration of the distributed resources; and provides the distributed spatial meta service, the spatial information catalog service, the multi-mode geological data service and the spatial data interoperation service. The geological survey information cloud-computing platform has been implemented, and based on the platform, some geological data services and geological processing services were developed. Furthermore, an iron mine resource forecast and an evaluation service is introduced in this paper.

A Geospatial Information Grid Framework for Geological Survey

PubMed Central

Wu, Liang; Xue, Lei; Li, Chaoling; Lv, Xia; Chen, Zhanlong; Guo, Mingqiang; Xie, Zhong

2015-01-01

The use of digital information in geological fields is becoming very important. Thus, informatization in geological surveys should not stagnate as a result of the level of data accumulation. The integration and sharing of distributed, multi-source, heterogeneous geological information is an open problem in geological domains. Applications and services use geological spatial data with many features, including being cross-region and cross-domain and requiring real-time updating. As a result of these features, desktop and web-based geographic information systems (GISs) experience difficulties in meeting the demand for geological spatial information. To facilitate the real-time sharing of data and services in distributed environments, a GIS platform that is open, integrative, reconfigurable, reusable and elastic would represent an indispensable tool. The purpose of this paper is to develop a geological cloud-computing platform for integrating and sharing geological information based on a cloud architecture. Thus, the geological cloud-computing platform defines geological ontology semantics; designs a standard geological information framework and a standard resource integration model; builds a peer-to-peer node management mechanism; achieves the description, organization, discovery, computing and integration of the distributed resources; and provides the distributed spatial meta service, the spatial information catalog service, the multi-mode geological data service and the spatial data interoperation service. The geological survey information cloud-computing platform has been implemented, and based on the platform, some geological data services and geological processing services were developed. Furthermore, an iron mine resource forecast and an evaluation service is introduced in this paper. PMID:26710255

Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit

PubMed Central

O'Boyle, Noel M; Morley, Chris; Hutchison, Geoffrey R

2008-01-01

Background Scripting languages such as Python are ideally suited to common programming tasks in cheminformatics such as data analysis and parsing information from files. However, for reasons of efficiency, cheminformatics toolkits such as the OpenBabel toolkit are often implemented in compiled languages such as C++. We describe Pybel, a Python module that provides access to the OpenBabel toolkit. Results Pybel wraps the direct toolkit bindings to simplify common tasks such as reading and writing molecular files and calculating fingerprints. Extensive use is made of Python iterators to simplify loops such as that over all the molecules in a file. A Pybel Molecule can be easily interconverted to an OpenBabel OBMol to access those methods or attributes not wrapped by Pybel. Conclusion Pybel allows cheminformaticians to rapidly develop Python scripts that manipulate chemical information. It is open source, available cross-platform, and offers the power of the OpenBabel toolkit to Python programmers. PMID:18328109

Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit.

PubMed

O'Boyle, Noel M; Morley, Chris; Hutchison, Geoffrey R

2008-03-09

Scripting languages such as Python are ideally suited to common programming tasks in cheminformatics such as data analysis and parsing information from files. However, for reasons of efficiency, cheminformatics toolkits such as the OpenBabel toolkit are often implemented in compiled languages such as C++. We describe Pybel, a Python module that provides access to the OpenBabel toolkit. Pybel wraps the direct toolkit bindings to simplify common tasks such as reading and writing molecular files and calculating fingerprints. Extensive use is made of Python iterators to simplify loops such as that over all the molecules in a file. A Pybel Molecule can be easily interconverted to an OpenBabel OBMol to access those methods or attributes not wrapped by Pybel. Pybel allows cheminformaticians to rapidly develop Python scripts that manipulate chemical information. It is open source, available cross-platform, and offers the power of the OpenBabel toolkit to Python programmers.

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.

Celeris: A GPU-accelerated open source software with a Boussinesq-type wave solver for real-time interactive simulation and visualization

NASA Astrophysics Data System (ADS)

Tavakkol, Sasan; Lynett, Patrick

2017-08-01

In this paper, we introduce an interactive coastal wave simulation and visualization software, called Celeris. Celeris is an open source software which needs minimum preparation to run on a Windows machine. The software solves the extended Boussinesq equations using a hybrid finite volume-finite difference method and supports moving shoreline boundaries. The simulation and visualization are performed on the GPU using Direct3D libraries, which enables the software to run faster than real-time. Celeris provides a first-of-its-kind interactive modeling platform for coastal wave applications and it supports simultaneous visualization with both photorealistic and colormapped rendering capabilities. We validate our software through comparison with three standard benchmarks for non-breaking and breaking waves.

ChiMS: Open-source instrument control software platform on LabVIEW for imaging/depth profiling mass spectrometers.

PubMed

Cui, Yang; Hanley, Luke

2015-06-01

ChiMS is an open-source data acquisition and control software program written within LabVIEW for high speed imaging and depth profiling mass spectrometers. ChiMS can also transfer large datasets from a digitizer to computer memory at high repetition rate, save data to hard disk at high throughput, and perform high speed data processing. The data acquisition mode generally simulates a digital oscilloscope, but with peripheral devices integrated for control as well as advanced data sorting and processing capabilities. Customized user-designed experiments can be easily written based on several included templates. ChiMS is additionally well suited to non-laser based mass spectrometers imaging and various other experiments in laser physics, physical chemistry, and surface science.

ChiMS: Open-source instrument control software platform on LabVIEW for imaging/depth profiling mass spectrometers

PubMed Central

Cui, Yang; Hanley, Luke

2015-01-01

ChiMS is an open-source data acquisition and control software program written within LabVIEW for high speed imaging and depth profiling mass spectrometers. ChiMS can also transfer large datasets from a digitizer to computer memory at high repetition rate, save data to hard disk at high throughput, and perform high speed data processing. The data acquisition mode generally simulates a digital oscilloscope, but with peripheral devices integrated for control as well as advanced data sorting and processing capabilities. Customized user-designed experiments can be easily written based on several included templates. ChiMS is additionally well suited to non-laser based mass spectrometers imaging and various other experiments in laser physics, physical chemistry, and surface science. PMID:26133872

Advanced capabilities for materials modelling with Quantum ESPRESSO

NASA Astrophysics Data System (ADS)

Giannozzi, P.; Andreussi, O.; Brumme, T.; Bunau, O.; Buongiorno Nardelli, M.; Calandra, M.; Car, R.; Cavazzoni, C.; Ceresoli, D.; Cococcioni, M.; Colonna, N.; Carnimeo, I.; Dal Corso, A.; de Gironcoli, S.; Delugas, P.; DiStasio, R. A., Jr.; Ferretti, A.; Floris, A.; Fratesi, G.; Fugallo, G.; Gebauer, R.; Gerstmann, U.; Giustino, F.; Gorni, T.; Jia, J.; Kawamura, M.; Ko, H.-Y.; Kokalj, A.; Küçükbenli, E.; Lazzeri, M.; Marsili, M.; Marzari, N.; Mauri, F.; Nguyen, N. L.; Nguyen, H.-V.; Otero-de-la-Roza, A.; Paulatto, L.; Poncé, S.; Rocca, D.; Sabatini, R.; Santra, B.; Schlipf, M.; Seitsonen, A. P.; Smogunov, A.; Timrov, I.; Thonhauser, T.; Umari, P.; Vast, N.; Wu, X.; Baroni, S.

2017-11-01

Quantum EXPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the-art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory, and many-body perturbation theory, within the plane-wave pseudopotential and projector-augmented-wave approaches. Quantum EXPRESSO owes its popularity to the wide variety of properties and processes it allows to simulate, to its performance on an increasingly broad array of hardware architectures, and to a community of researchers that rely on its capabilities as a core open-source development platform to implement their ideas. In this paper we describe recent extensions and improvements, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software.

Advanced capabilities for materials modelling with Quantum ESPRESSO.

PubMed

Giannozzi, P; Andreussi, O; Brumme, T; Bunau, O; Buongiorno Nardelli, M; Calandra, M; Car, R; Cavazzoni, C; Ceresoli, D; Cococcioni, M; Colonna, N; Carnimeo, I; Dal Corso, A; de Gironcoli, S; Delugas, P; DiStasio, R A; Ferretti, A; Floris, A; Fratesi, G; Fugallo, G; Gebauer, R; Gerstmann, U; Giustino, F; Gorni, T; Jia, J; Kawamura, M; Ko, H-Y; Kokalj, A; Küçükbenli, E; Lazzeri, M; Marsili, M; Marzari, N; Mauri, F; Nguyen, N L; Nguyen, H-V; Otero-de-la-Roza, A; Paulatto, L; Poncé, S; Rocca, D; Sabatini, R; Santra, B; Schlipf, M; Seitsonen, A P; Smogunov, A; Timrov, I; Thonhauser, T; Umari, P; Vast, N; Wu, X; Baroni, S

2017-10-24

Quantum EXPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the-art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory, and many-body perturbation theory, within the plane-wave pseudopotential and projector-augmented-wave approaches. Quantum EXPRESSO owes its popularity to the wide variety of properties and processes it allows to simulate, to its performance on an increasingly broad array of hardware architectures, and to a community of researchers that rely on its capabilities as a core open-source development platform to implement their ideas. In this paper we describe recent extensions and improvements, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software.

Advanced capabilities for materials modelling with Quantum ESPRESSO.

PubMed

Andreussi, Oliviero; Brumme, Thomas; Bunau, Oana; Buongiorno Nardelli, Marco; Calandra, Matteo; Car, Roberto; Cavazzoni, Carlo; Ceresoli, Davide; Cococcioni, Matteo; Colonna, Nicola; Carnimeo, Ivan; Dal Corso, Andrea; de Gironcoli, Stefano; Delugas, Pietro; DiStasio, Robert; Ferretti, Andrea; Floris, Andrea; Fratesi, Guido; Fugallo, Giorgia; Gebauer, Ralph; Gerstmann, Uwe; Giustino, Feliciano; Gorni, Tommaso; Jia, Junteng; Kawamura, Mitsuaki; Ko, Hsin-Yu; Kokalj, Anton; Küçükbenli, Emine; Lazzeri, Michele; Marsili, Margherita; Marzari, Nicola; Mauri, Francesco; Nguyen, Ngoc Linh; Nguyen, Huy-Viet; Otero-de-la-Roza, Alberto; Paulatto, Lorenzo; Poncé, Samuel; Giannozzi, Paolo; Rocca, Dario; Sabatini, Riccardo; Santra, Biswajit; Schlipf, Martin; Seitsonen, Ari Paavo; Smogunov, Alexander; Timrov, Iurii; Thonhauser, Timo; Umari, Paolo; Vast, Nathalie; Wu, Xifan; Baroni, Stefano

2017-09-27

Quantum ESPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory, and many-body perturbation theory, within the plane-wave pseudo-potential and projector-augmented-wave approaches. Quantum ESPRESSO owes its popularity to the wide variety of properties and processes it allows to simulate, to its performance on an increasingly broad array of hardware architectures, and to a community of researchers that rely on its capabilities as a core open-source development platform to implement theirs ideas. In this paper we describe recent extensions and improvements, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software. © 2017 IOP Publishing Ltd.

An efficient approach to the deployment of complex open source information systems

PubMed Central

Cong, Truong Van Chi; Groeneveld, Eildert

2011-01-01

Complex open source information systems are usually implemented as component-based software to inherit the available functionality of existing software packages developed by third parties. Consequently, the deployment of these systems not only requires the installation of operating system, application framework and the configuration of services but also needs to resolve the dependencies among components. The problem becomes more challenging when the application must be installed and used on different platforms such as Linux and Windows. To address this, an efficient approach using the virtualization technology is suggested and discussed in this paper. The approach has been applied in our project to deploy a web-based integrated information system in molecular genetics labs. It is a low-cost solution to benefit both software developers and end-users. PMID:22102770

ChiMS: Open-source instrument control software platform on LabVIEW for imaging/depth profiling mass spectrometers

NASA Astrophysics Data System (ADS)

Cui, Yang; Hanley, Luke

2015-06-01

ChiMS is an open-source data acquisition and control software program written within LabVIEW for high speed imaging and depth profiling mass spectrometers. ChiMS can also transfer large datasets from a digitizer to computer memory at high repetition rate, save data to hard disk at high throughput, and perform high speed data processing. The data acquisition mode generally simulates a digital oscilloscope, but with peripheral devices integrated for control as well as advanced data sorting and processing capabilities. Customized user-designed experiments can be easily written based on several included templates. ChiMS is additionally well suited to non-laser based mass spectrometers imaging and various other experiments in laser physics, physical chemistry, and surface science.

OpenARC: Extensible OpenACC Compiler Framework for Directive-Based Accelerator Programming Study

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

Lee, Seyong; Vetter, Jeffrey S

2014-01-01

Directive-based, accelerator programming models such as OpenACC have arisen as an alternative solution to program emerging Scalable Heterogeneous Computing (SHC) platforms. However, the increased complexity in the SHC systems incurs several challenges in terms of portability and productivity. This paper presents an open-sourced OpenACC compiler, called OpenARC, which serves as an extensible research framework to address those issues in the directive-based accelerator programming. This paper explains important design strategies and key compiler transformation techniques needed to implement the reference OpenACC compiler. Moreover, this paper demonstrates the efficacy of OpenARC as a research framework for directive-based programming study, by proposing andmore » implementing OpenACC extensions in the OpenARC framework to 1) support hybrid programming of the unified memory and separate memory and 2) exploit architecture-specific features in an abstract manner. Porting thirteen standard OpenACC programs and three extended OpenACC programs to CUDA GPUs shows that OpenARC performs similarly to a commercial OpenACC compiler, while it serves as a high-level research framework.« less

Open-source point-of-care electronic medical records for use in resource-limited settings: systematic review and questionnaire surveys

PubMed Central

Bru, Juan; Berger, Christopher A

2012-01-01

Background Point-of-care electronic medical records (EMRs) are a key tool to manage chronic illness. Several EMRs have been developed for use in treating HIV and tuberculosis, but their applicability to primary care, technical requirements and clinical functionalities are largely unknown. Objectives This study aimed to address the needs of clinicians from resource-limited settings without reliable internet access who are considering adopting an open-source EMR. Study eligibility criteria Open-source point-of-care EMRs suitable for use in areas without reliable internet access. Study appraisal and synthesis methods The authors conducted a comprehensive search of all open-source EMRs suitable for sites without reliable internet access. The authors surveyed clinician users and technical implementers from a single site and technical developers of each software product. The authors evaluated availability, cost and technical requirements. Results The hardware and software for all six systems is easily available, but they vary considerably in proprietary components, installation requirements and customisability. Limitations This study relied solely on self-report from informants who developed and who actively use the included products. Conclusions and implications of key findings Clinical functionalities vary greatly among the systems, and none of the systems yet meet minimum requirements for effective implementation in a primary care resource-limited setting. The safe prescribing of medications is a particular concern with current tools. The dearth of fully functional EMR systems indicates a need for a greater emphasis by global funding agencies to move beyond disease-specific EMR systems and develop a universal open-source health informatics platform. PMID:22763661

MicMac GIS application: free open source

NASA Astrophysics Data System (ADS)

Duarte, L.; Moutinho, O.; Teodoro, A.

2016-10-01

The use of Remotely Piloted Aerial System (RPAS) for remote sensing applications is becoming more frequent as the technologies on on-board cameras and the platform itself are becoming a serious contender to satellite and airplane imagery. MicMac is a photogrammetric tool for image matching that can be used in different contexts. It is an open source software and it can be used as a command line or with a graphic interface (for each command). The main objective of this work was the integration of MicMac with QGIS, which is also an open source software, in order to create a new open source tool applied to photogrammetry/remote sensing. Python language was used to develop the application. This tool would be very useful in the manipulation and 3D modelling of a set of images. The main objective was to create a toolbar in QGIS with the basic functionalities with intuitive graphic interfaces. The toolbar is composed by three buttons: produce the points cloud, create the Digital Elevation Model (DEM) and produce the orthophoto of the study area. The application was tested considering 35 photos, a subset of images acquired by a RPAS in the Aguda beach area, Porto, Portugal. They were used in order to create a 3D terrain model and from this model obtain an orthophoto and the corresponding DEM. The code is open and can be modified according to the user requirements. This integration would be very useful in photogrammetry and remote sensing community combined with GIS capabilities.

YouGenMap: a web platform for dynamic multi-comparative mapping and visualization of genetic maps

Treesearch

Keith Batesole; Kokulapalan Wimalanathan; Lin Liu; Fan Zhang; Craig S. Echt; Chun Liang

2014-01-01

Comparative genetic maps are used in examination of genome organization, detection of conserved gene order, and exploration of marker order variations. YouGenMap is an open-source web tool that offers dynamic comparative mapping capability of users' own genetic mapping between 2 or more map sets. Users' genetic map data and optional gene annotations are...

A Model for an Open and Flexible E-Training Platform To Encourage Companies' Learning Culture and Meet Employees' Learning Needs.

ERIC Educational Resources Information Center

Bagnasco, Andrea; Chirico, Marco; Parodi, Giancarlo; Scapolla, A. Marina

2003-01-01

Distance education is an answer to the demand for flexibility in training. The aim is to build a virtual learning community on the basis of a knowledge model that meets different learning needs. This article analyzes possible innovations in corporate training, and proposes a framework that integrates all information sources and offers practice…

Cloud Computing for DoD

DTIC Science & Technology

2012-05-01

cloud computing 17 NASA Nebula Platform •  Cloud computing pilot program at NASA Ames •  Integrates open-source components into seamless, self...Mission support •  Education and public outreach (NASA Nebula , 2010) 18 NSF Supported Cloud Research •  Support for Cloud Computing in...Mell, P. & Grance, T. (2011). The NIST Definition of Cloud Computing. NIST Special Publication 800-145 •  NASA Nebula (2010). Retrieved from

Fall 2014 SEI Research Review Edge-Enabled Tactical Systems (EETS)

DTIC Science & Technology

2014-10-29

Effective communicate and reasoning despite connectivity issues • More generally, how to make programming distributed algorithms with extensible...distributed collaboration in VREP simulations for 5-12 quadcopters and ground robots • Open-source middleware and algorithms released to community...Integration into CMU Drone-RK quadcopter and Platypus autonomous boat platforms • Presentations at DARPA (CODE), AFRL C4I Workshop, and AFRL Eglin

Learning in an Introductory Physics MOOC: All Cohorts Learn Equally, Including an On-Campus Class

ERIC Educational Resources Information Center

Colvin, Kimberly F.; Champaign, John; Liu, Alwina; Zhou, Qian; Fredericks, Colin; Pritchard, David E.

2014-01-01

We studied student learning in the MOOC 8.MReV Mechanics ReView, run on the edX.org open source platform. We studied learning in two ways. We administered 13 conceptual questions both before and after instruction, analyzing the results using standard techniques for pre- and posttesting. We also analyzed each week's homework and test questions in…

Architecture and Implementation of OpenPET Firmware and Embedded Software

DOE PAGES

Abu-Nimeh, Faisal T.; Ito, Jennifer; Moses, William W.; ...

2016-01-11

OpenPET is an open source, modular, extendible, and high-performance platform suitable for multi-channel data acquisition and analysis. Due to the versatility of the hardware, firmware, and software architectures, the platform is capable of interfacing with a wide variety of detector modules not only in medical imaging but also in homeland security applications. Analog signals from radiation detectors share similar characteristics-a pulse whose area is proportional to the deposited energy and whose leading edge is used to extract a timing signal. As a result, a generic design method of the platform is adopted for the hardware, firmware, and software architectures andmore » implementations. The analog front-end is hosted on a module called a Detector Board, where each board can filter, combine, timestamp, and process multiple channels independently. The processed data is formatted and sent through a backplane bus to a module called Support Board, where 1 Support Board can host up to eight Detector Board modules. The data in the Support Board, coming from 8 Detector Board modules, can be aggregated or correlated (if needed) depending on the algorithm implemented or runtime mode selected. It is then sent out to a computer workstation for further processing. The number of channels (detector modules), to be processed, mandates the overall OpenPET System Configuration, which is designed to handle up to 1,024 channels using 16-channel Detector Boards in the Standard System Configuration and 16,384 channels using 32-channel Detector Boards in the Large System Configuration.« less

A Design of a Novel Airborne Aerosol Spectrometer for Remote Sensing Validation

NASA Astrophysics Data System (ADS)

Adler, G. A.; Brock, C. A.; Dube, W. P.; Erdesz, F.; Gordon, T.; Law, D. C.; Manfred, K.; Mason, B. J.; McLaughlin, R. J.; Richardson, M.; Wagner, N. L.; Washenfelder, R. A.; Murphy, D. M.

2016-12-01

Aerosols and their effect on the radiative properties of clouds contribute one of the largest sources of uncertainty to the Earth's energy budget. Many current global assessments, of atmospheric aerosol radiative forcing rely heavily on remote sensing observation; therefore, in situ aircraft and ground-based measurements are essential for validation of remote sensing measurements. Cavity ringdown spectrometers (CRD) measure aerosol extinction and are commonly used to validate remote sensing observations. These instruments have been deployed on aircraft based platforms over the years thus providing the opportunity to measure these properties over large areas in various conditions. However, deployment of the CRD on an aircraft platform has drawbacks. Typically, aircraft based CRDs draw sampled aerosol into a cabin based instrument through long lengths of tubing. This limits the ability of the instrument to measure: 1) Course mode aerosols (e.g. dust) 2) Aerosols at high relative humidity (above 90%) Here we describe the design of a novel aircraft based open path CRD. The open path CRD is intended to be mounted external to the cabin and has no sample tubing for aerosol delivery, thus measuring optical properties of all aerosol at the ambient conditions. However, the design of an open path CRD for operation on a wing-mounted aircraft platform has certain design complexities. The instrument's special design features include 2 CRD channels, 2 airfoils around the open Path CRD and a configuration which could be easily aligned and rigid at the same time. This novel implementation of cavity ringdown spectroscopy will provide a better assessment of the accuracy of remote sensing satellite measurements

Open source software and low cost sensors for teaching UAV science

NASA Astrophysics Data System (ADS)

Kefauver, S. C.; Sanchez-Bragado, R.; El-Haddad, G.; Araus, J. L.

2016-12-01

Drones, also known as UASs (unmanned aerial systems), UAVs (Unmanned Aerial Vehicles) or RPAS (Remotely piloted aircraft systems), are both useful advanced scientific platforms and recreational toys that are appealing to younger generations. As such, they can make for excellent education tools as well as low-cost scientific research project alternatives. However, the process of taking pretty pictures to remote sensing science can be daunting if one is presented with only expensive software and sensor options. There are a number of open-source tools and low cost platform and sensor options available that can provide excellent scientific research results, and, by often requiring more user-involvement than commercial software and sensors, provide even greater educational benefits. Scale-invariant feature transform (SIFT) algorithm implementations, such as the Microsoft Image Composite Editor (ICE), which can create quality 2D image mosaics with some motion and terrain adjustments and VisualSFM (Structure from Motion), which can provide full image mosaicking with movement and orthorectification capacities. RGB image quantification using alternate color space transforms, such as the BreedPix indices, can be calculated via plugins in the open-source software Fiji (http://fiji.sc/Fiji; http://github.com/george-haddad/CIMMYT). Recent analyses of aerial images from UAVs over different vegetation types and environments have shown RGB metrics can outperform more costly commercial sensors. Specifically, Hue-based pixel counts, the Triangle Greenness Index (TGI), and the Normalized Green Red Difference Index (NGRDI) consistently outperformed NDVI in estimating abiotic and biotic stress impacts on crop health. Also, simple kits are available for NDVI camera conversions. Furthermore, suggestions for multivariate analyses of the different RGB indices in the "R program for statistical computing", such as classification and regression trees can allow for a more approachable interpretation of results in the classroom.

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.

Collaboration-Centred Cities through Urban Apps Based on Open and User-Generated Data

PubMed Central

Aguilera, Unai; López-de-Ipiña, Diego; Pérez, Jorge

2016-01-01

This paper describes the IES Cities platform conceived to streamline the development of urban apps that combine heterogeneous datasets provided by diverse entities, namely, government, citizens, sensor infrastructure and other information data sources. This work pursues the challenge of achieving effective citizen collaboration by empowering them to prosume urban data across time. Particularly, this paper focuses on the query mapper; a key component of the IES Cities platform devised to democratize the development of open data-based mobile urban apps. This component allows developers not only to use available data, but also to contribute to existing datasets with the execution of SQL sentences. In addition, the component allows developers to create ad hoc storages for their applications, publishable as new datasets accessible by other consumers. As multiple users could be contributing and using a dataset, our solution also provides a data level permission mechanism to control how the platform manages the access to its datasets. We have evaluated the advantages brought forward by IES Cities from the developers’ perspective by describing an exemplary urban app created on top of it. In addition, we include an evaluation of the main functionalities of the query mapper. PMID:27376300

Collaboration-Centred Cities through Urban Apps Based on Open and User-Generated Data.

PubMed

Aguilera, Unai; López-de-Ipiña, Diego; Pérez, Jorge

2016-07-01

This paper describes the IES Cities platform conceived to streamline the development of urban apps that combine heterogeneous datasets provided by diverse entities, namely, government, citizens, sensor infrastructure and other information data sources. This work pursues the challenge of achieving effective citizen collaboration by empowering them to prosume urban data across time. Particularly, this paper focuses on the query mapper; a key component of the IES Cities platform devised to democratize the development of open data-based mobile urban apps. This component allows developers not only to use available data, but also to contribute to existing datasets with the execution of SQL sentences. In addition, the component allows developers to create ad hoc storages for their applications, publishable as new datasets accessible by other consumers. As multiple users could be contributing and using a dataset, our solution also provides a data level permission mechanism to control how the platform manages the access to its datasets. We have evaluated the advantages brought forward by IES Cities from the developers' perspective by describing an exemplary urban app created on top of it. In addition, we include an evaluation of the main functionalities of the query mapper.

Evaluation of the concentrations and distribution of carbonyl compounds in selected areas of a Brazilian bus terminal.

PubMed

de Mendonça Ochs, Soraya; de Almeida Furtado, Leonardo; Pereira Netto, Annibal Duarte

2015-06-01

This study describes the determination of 30 carbonyl compounds (CCs) in three areas (bus boarding platform, passenger circulation area, and a pastry shop) of the Presidente João Goulart Bus Terminal, located at Niterói City, RJ, Brazil, and in an open area 700 m distant from the terminal. Samples were collected using SEP-PAK cartridges impregnated with 2,4-dinitrophenylhydrazine, during May to July 2012. The hydrazones formed were analyzed using rapid resolution liquid chromatography with UV detection. The studied locations showed distinct profiles of distribution of CC. The circulation area, which is influenced by different pollution sources, presented an intermediate profile between that of the pastry shop and boarding platform. Formaldehyde and acetaldehyde were the most abundant CC, but acetaldehyde predominated in the pastry shop once it is a by-product of baking yeast fermentation. Samples taken in the pastry shop and circulation area showed significant concentrations of hexanaldehyde and nonanaldehyde emitted during cooking. The pastry shop showed the largest level of total CC among the studied areas followed by the circulation area, the boarding platform, and the open area.

An architecture for genomics analysis in a clinical setting using Galaxy and Docker

PubMed Central

Digan, W; Countouris, H; Barritault, M; Baudoin, D; Laurent-Puig, P; Blons, H; Burgun, A

2017-01-01

Abstract Next-generation sequencing is used on a daily basis to perform molecular analysis to determine subtypes of disease (e.g., in cancer) and to assist in the selection of the optimal treatment. Clinical bioinformatics handles the manipulation of the data generated by the sequencer, from the generation to the analysis and interpretation. Reproducibility and traceability are crucial issues in a clinical setting. We have designed an approach based on Docker container technology and Galaxy, the popular bioinformatics analysis support open-source software. Our solution simplifies the deployment of a small-size analytical platform and simplifies the process for the clinician. From the technical point of view, the tools embedded in the platform are isolated and versioned through Docker images. Along the Galaxy platform, we also introduce the AnalysisManager, a solution that allows single-click analysis for biologists and leverages standardized bioinformatics application programming interfaces. We added a Shiny/R interactive environment to ease the visualization of the outputs. The platform relies on containers and ensures the data traceability by recording analytical actions and by associating inputs and outputs of the tools to EDAM ontology through ReGaTe. The source code is freely available on Github at https://github.com/CARPEM/GalaxyDocker. PMID:29048555

An architecture for genomics analysis in a clinical setting using Galaxy and Docker.

PubMed

Digan, W; Countouris, H; Barritault, M; Baudoin, D; Laurent-Puig, P; Blons, H; Burgun, A; Rance, B

2017-11-01

Next-generation sequencing is used on a daily basis to perform molecular analysis to determine subtypes of disease (e.g., in cancer) and to assist in the selection of the optimal treatment. Clinical bioinformatics handles the manipulation of the data generated by the sequencer, from the generation to the analysis and interpretation. Reproducibility and traceability are crucial issues in a clinical setting. We have designed an approach based on Docker container technology and Galaxy, the popular bioinformatics analysis support open-source software. Our solution simplifies the deployment of a small-size analytical platform and simplifies the process for the clinician. From the technical point of view, the tools embedded in the platform are isolated and versioned through Docker images. Along the Galaxy platform, we also introduce the AnalysisManager, a solution that allows single-click analysis for biologists and leverages standardized bioinformatics application programming interfaces. We added a Shiny/R interactive environment to ease the visualization of the outputs. The platform relies on containers and ensures the data traceability by recording analytical actions and by associating inputs and outputs of the tools to EDAM ontology through ReGaTe. The source code is freely available on Github at https://github.com/CARPEM/GalaxyDocker. © The Author 2017. Published by Oxford University Press.

Galaxy Portal: interacting with the galaxy platform through mobile devices.

PubMed

Børnich, Claus; Grytten, Ivar; Hovig, Eivind; Paulsen, Jonas; Čech, Martin; Sandve, Geir Kjetil

2016-06-01

: We present Galaxy Portal app, an open source interface to the Galaxy system through smart phones and tablets. The Galaxy Portal provides convenient and efficient monitoring of job completion, as well as opportunities for inspection of results and execution history. In addition to being useful to the Galaxy community, we believe that the app also exemplifies a useful way of exploiting mobile interfaces for research/high-performance computing resources in general. The source is freely available under a GPL license on GitHub, along with user documentation and pre-compiled binaries and instructions for several platforms: https://github.com/Tarostar/QMLGalaxyPortal It is available for iOS version 7 (and newer) through the Apple App Store, and for Android through Google Play for version 4.1 (API 16) or newer. geirksa@ifi.uio.no. © The Author 2016. Published by Oxford University Press.

Electronic Health Record Application Support Service Enablers.

PubMed

Neofytou, M S; Neokleous, K; Aristodemou, A; Constantinou, I; Antoniou, Z; Schiza, E C; Pattichis, C S; Schizas, C N

2015-08-01

There is a huge need for open source software solutions in the healthcare domain, given the flexibility, interoperability and resource savings characteristics they offer. In this context, this paper presents the development of three open source libraries - Specific Enablers (SEs) for eHealth applications that were developed under the European project titled "Future Internet Social and Technological Alignment Research" (FI-STAR) funded under the "Future Internet Public Private Partnership" (FI-PPP) program. The three SEs developed under the Electronic Health Record Application Support Service Enablers (EHR-EN) correspond to: a) an Electronic Health Record enabler (EHR SE), b) a patient summary enabler based on the EU project "European patient Summary Open Source services" (epSOS SE) supporting patient mobility and the offering of interoperable services, and c) a Picture Archiving and Communications System (PACS) enabler (PACS SE) based on the dcm4che open source system for the support of medical imaging functionality. The EHR SE follows the HL7 Clinical Document Architecture (CDA) V2.0 and supports the Integrating the Healthcare Enterprise (IHE) profiles (recently awarded in Connectathon 2015). These three FI-STAR platform enablers are designed to facilitate the deployment of innovative applications and value added services in the health care sector. They can be downloaded from the FI-STAR cataloque website. Work in progress focuses in the validation and evaluation scenarios for the proving and demonstration of the usability, applicability and adaptability of the proposed enablers.

Encourage student learning of hydraulic matters by the use of Arduino platform

NASA Astrophysics Data System (ADS)

Rodriguez Sinobas, Leonor; Granja García, Javier; Sánchez Calvo, Raúl

2014-05-01

Arduino is an open-source electronics prototyping platform based on flexible, easy-to-use hardware and software. It's intended for several purposes to anyone interested in creating interactive objects or environments. The hydraulic matters teach at the Agricultural Engineering School at the Technical University of Madrid deal with practical issues regarding the measurement of variables such as pressure, discharge, temperature and soil water content. Most of the data loggers available in the market for these variables at expensive and not always affordable. On the other hand, current students are eager to manage new technological devices thus, their skills could be oriented not only to the application of an electronic platform as Arduino to build low cost data loggers for different purposes, but to encourage their learning in the hydraulic matters improving their self esteem

iAnn: an event sharing platform for the life sciences.

PubMed

Jimenez, Rafael C; Albar, Juan P; Bhak, Jong; Blatter, Marie-Claude; Blicher, Thomas; Brazas, Michelle D; Brooksbank, Cath; Budd, Aidan; De Las Rivas, Javier; Dreyer, Jacqueline; van Driel, Marc A; Dunn, Michael J; Fernandes, Pedro L; van Gelder, Celia W G; Hermjakob, Henning; Ioannidis, Vassilios; Judge, David P; Kahlem, Pascal; Korpelainen, Eija; Kraus, Hans-Joachim; Loveland, Jane; Mayer, Christine; McDowall, Jennifer; Moran, Federico; Mulder, Nicola; Nyronen, Tommi; Rother, Kristian; Salazar, Gustavo A; Schneider, Reinhard; Via, Allegra; Villaveces, Jose M; Yu, Ping; Schneider, Maria V; Attwood, Teresa K; Corpas, Manuel

2013-08-01

We present iAnn, an open source community-driven platform for dissemination of life science events, such as courses, conferences and workshops. iAnn allows automatic visualisation and integration of customised event reports. A central repository lies at the core of the platform: curators add submitted events, and these are subsequently accessed via web services. Thus, once an iAnn widget is incorporated into a website, it permanently shows timely relevant information as if it were native to the remote site. At the same time, announcements submitted to the repository are automatically disseminated to all portals that query the system. To facilitate the visualization of announcements, iAnn provides powerful filtering options and views, integrated in Google Maps and Google Calendar. All iAnn widgets are freely available. http://iann.pro/iannviewer manuel.corpas@tgac.ac.uk.

Genetic Constructor: An Online DNA Design Platform.

PubMed

Bates, Maxwell; Lachoff, Joe; Meech, Duncan; Zulkower, Valentin; Moisy, Anaïs; Luo, Yisha; Tekotte, Hille; Franziska Scheitz, Cornelia Johanna; Khilari, Rupal; Mazzoldi, Florencio; Chandran, Deepak; Groban, Eli

2017-12-15

Genetic Constructor is a cloud Computer Aided Design (CAD) application developed to support synthetic biologists from design intent through DNA fabrication and experiment iteration. The platform allows users to design, manage, and navigate complex DNA constructs and libraries, using a new visual language that focuses on functional parts abstracted from sequence. Features like combinatorial libraries and automated primer design allow the user to separate design from construction by focusing on functional intent, and design constraints aid iterative refinement of designs. A plugin architecture enables contributions from scientists and coders to leverage existing powerful software and connect to DNA foundries. The software is easily accessible and platform agnostic, free for academics, and available in an open-source community edition. Genetic Constructor seeks to democratize DNA design, manufacture, and access to tools and services from the synthetic biology community.

Numerical simulation of the SOFIA flowfield

NASA Technical Reports Server (NTRS)

Klotz, Stephen P.

1994-01-01

This report provides a concise summary of the contribution of computational fluid dynamics (CFD) to the SOFIA (Stratospheric Observatory for Infrared Astronomy) project at NASA Ames and presents results obtained from closed- and open-cavity SOFIA simulations. The aircraft platform is a Boeing 747SP and these are the first SOFIA simulations run with the aircraft empennage included in the geometry database. In the open-cavity run the telescope is mounted behind the wings. Results suggest that the cavity markedly influences the mean pressure distribution on empennage surfaces and that 110-140 decibel (db) sound pressure levels are typical in the cavity and on the horizontal and vertical stabilizers. A strong source of sound was found to exist on the rim of the open telescope cavity. The presence of this source suggests that additional design work needs to be performed in order to minimize the sound emanating from that location. A fluid dynamic analysis of the engine plumes is also contained in this report. The analysis was part of an effort to quantify the degradation of telescope performance resulting from the proximity of the port engine exhaust plumes to the open telescope bay.

Chemical effects in biological systems (CEBS) object model for toxicology data, SysTox-OM: design and application.

PubMed

Xirasagar, Sandhya; Gustafson, Scott F; Huang, Cheng-Cheng; Pan, Qinyan; Fostel, Jennifer; Boyer, Paul; Merrick, B Alex; Tomer, Kenneth B; Chan, Denny D; Yost, Kenneth J; Choi, Danielle; Xiao, Nianqing; Stasiewicz, Stanley; Bushel, Pierre; Waters, Michael D

2006-04-01

The CEBS data repository is being developed to promote a systems biology approach to understand the biological effects of environmental stressors. CEBS will house data from multiple gene expression platforms (transcriptomics), protein expression and protein-protein interaction (proteomics), and changes in low molecular weight metabolite levels (metabolomics) aligned by their detailed toxicological context. The system will accommodate extensive complex querying in a user-friendly manner. CEBS will store toxicological contexts including the study design details, treatment protocols, animal characteristics and conventional toxicological endpoints such as histopathology findings and clinical chemistry measures. All of these data types can be integrated in a seamless fashion to enable data query and analysis in a biologically meaningful manner. An object model, the SysBio-OM (Xirasagar et al., 2004) has been designed to facilitate the integration of microarray gene expression, proteomics and metabolomics data in the CEBS database system. We now report SysTox-OM as an open source systems toxicology model designed to integrate toxicological context into gene expression experiments. The SysTox-OM model is comprehensive and leverages other open source efforts, namely, the Standard for Exchange of Nonclinical Data (http://www.cdisc.org/models/send/v2/index.html) which is a data standard for capturing toxicological information for animal studies and Clinical Data Interchange Standards Consortium (http://www.cdisc.org/models/sdtm/index.html) that serves as a standard for the exchange of clinical data. Such standardization increases the accuracy of data mining, interpretation and exchange. The open source SysTox-OM model, which can be implemented on various software platforms, is presented here. A universal modeling language (UML) depiction of the entire SysTox-OM is available at http://cebs.niehs.nih.gov and the Rational Rose object model package is distributed under an open source license that permits unrestricted academic and commercial use and is available at http://cebs.niehs.nih.gov/cebsdownloads. Currently, the public toxicological data in CEBS can be queried via a web application based on the SysTox-OM at http://cebs.niehs.nih.gov xirasagars@saic.com Supplementary data are available at Bioinformatics online.

CellShape: A user-friendly image analysis tool for quantitative visualization of bacterial cell factories inside.

PubMed

Goñi-Moreno, Ángel; Kim, Juhyun; de Lorenzo, Víctor

2017-02-01

Visualization of the intracellular constituents of individual bacteria while performing as live biocatalysts is in principle doable through more or less sophisticated fluorescence microscopy. Unfortunately, rigorous quantitation of the wealth of data embodied in the resulting images requires bioinformatic tools that are not widely extended within the community-let alone that they are often subject to licensing that impedes software reuse. In this context we have developed CellShape, a user-friendly platform for image analysis with subpixel precision and double-threshold segmentation system for quantification of fluorescent signals stemming from single-cells. CellShape is entirely coded in Python, a free, open-source programming language with widespread community support. For a developer, CellShape enhances extensibility (ease of software improvements) by acting as an interface to access and use existing Python modules; for an end-user, CellShape presents standalone executable files ready to open without installation. We have adopted this platform to analyse with an unprecedented detail the tridimensional distribution of the constituents of the gene expression flow (DNA, RNA polymerase, mRNA and ribosomal proteins) in individual cells of the industrial platform strain Pseudomonas putida KT2440. While the CellShape first release version (v0.8) is readily operational, users and/or developers are enabled to expand the platform further. Copyright © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

An open and configurable embedded system for EMG pattern recognition implementation for artificial arms.

PubMed

Jun Liu; Fan Zhang; Huang, He Helen

2014-01-01

Pattern recognition (PR) based on electromyographic (EMG) signals has been developed for multifunctional artificial arms for decades. However, assessment of EMG PR control for daily prosthesis use is still limited. One of the major barriers is the lack of a portable and configurable embedded system to implement the EMG PR control. This paper aimed to design an open and configurable embedded system for EMG PR implementation so that researchers can easily modify and optimize the control algorithms upon our designed platform and test the EMG PR control outside of the lab environments. The open platform was built on an open source embedded Linux Operating System running a high-performance Gumstix board. Both the hardware and software system framework were openly designed. The system was highly flexible in terms of number of inputs/outputs and calibration interfaces used. Such flexibility enabled easy integration of our embedded system with different types of commercialized or prototypic artificial arms. Thus far, our system was portable for take-home use. Additionally, compared with previously reported embedded systems for EMG PR implementation, our system demonstrated improved processing efficiency and high system precision. Our long-term goals are (1) to develop a wearable and practical EMG PR-based control for multifunctional artificial arms, and (2) to quantify the benefits of EMG PR-based control over conventional myoelectric prosthesis control in a home setting.

The Water SWITCH-ON Spatial Information Platform (SIP)

NASA Astrophysics Data System (ADS)

Sala Calero, J., Sr.; Boot, G., Sr.; Dihé, P., Sr.; Arheimer, B.

2017-12-01

The amount of hydrological open data is continually growing and providing opportunities to the scientific community. Although the existing data portals (GEOSS Portal, INSPIRE community geoportal and others) enable access to open data, many users still find browsing through them difficult. Moreover, the time spent on gathering and preparing data usually is more significant than the time spent on the experiment itself. Thus, any improvement on searching, understanding, accessing or using open data is greatly beneficial. The Spatial Information Platform (SIP) has been developed to tackle these issues within the SWITCH-ON European Commission funded FP7 project. The SIP has been designed as a set of tools based on open standards that provide to the user all the necessary functionalities as described in the Publish-Find-Bind (PFB) pattern. In other words, this means that the SIP helps users to locate relevant and suitable data for their experiments analysis, to access and transform it (filtering, extraction, selection, conversion, aggregation). Moreover, the SIP can be used to provide descriptive information about the data and to publish it so others can find and use it. The SIP is based on existing open data protocols such as the OGC/CSW, OGC/WMS, OpenDAP and open-source components like PostgreSQL/PostGIS, GeoServer and pyCSW. The SIP is divided in three main user interfaces: the BYOD (Browse your open dataset) web interface, the Expert GUI tool and the Upload Data and Metadata web interface. The BYOD HTML5 client is the main entry point for users that want to browse through open data in the SIP. The BYOD has a map interface based on Leaflet JavaScript libraries so that the users can search more efficiently. The web-based Open Data Registration Tool is a user-friendly upload and metadata description interface (geographical extent, license, DOI generation). The Expert GUI is a desktop application that provides full metadata editing capabilities for the metadata moderators of the project. In conclusion, the Spatial Information Platform (SIP) provides to its community a set of tools for better understanding and ease of use of hydrological open-data. Moreover, the SIP has been based on well-known OGC standards that will allow the connection and data harvesting from popular open data portals such as the GEOSS system of systems.

The Reconstruction Toolkit (RTK), an open-source cone-beam CT reconstruction toolkit based on the Insight Toolkit (ITK)

NASA Astrophysics Data System (ADS)

Rit, S.; Vila Oliva, M.; Brousmiche, S.; Labarbe, R.; Sarrut, D.; Sharp, G. C.

2014-03-01

We propose the Reconstruction Toolkit (RTK, http://www.openrtk.org), an open-source toolkit for fast cone-beam CT reconstruction, based on the Insight Toolkit (ITK) and using GPU code extracted from Plastimatch. RTK is developed by an open consortium (see affiliations) under the non-contaminating Apache 2.0 license. The quality of the platform is daily checked with regression tests in partnership with Kitware, the company supporting ITK. Several features are already available: Elekta, Varian and IBA inputs, multi-threaded Feldkamp-David-Kress reconstruction on CPU and GPU, Parker short scan weighting, multi-threaded CPU and GPU forward projectors, etc. Each feature is either accessible through command line tools or C++ classes that can be included in independent software. A MIDAS community has been opened to share CatPhan datasets of several vendors (Elekta, Varian and IBA). RTK will be used in the upcoming cone-beam CT scanner developed by IBA for proton therapy rooms. Many features are under development: new input format support, iterative reconstruction, hybrid Monte Carlo / deterministic CBCT simulation, etc. RTK has been built to freely share tomographic reconstruction developments between researchers and is open for new contributions.

Characteristics of depositional environment and evolution of Upper Cretaceous Mishrif Formation, Halfaya Oil field, Iraq based on sedimentary microfacies analysis

NASA Astrophysics Data System (ADS)

Zhong, Yuan; Zhou, Lu; Tan, Xiucheng; Guo, Rui; Zhao, Limin; Li, Fei; Jin, Zhimin; Chen, Yantao

2018-04-01

As one of the most important carbonate targets in the Middle East, Upper Cretaceous Mishrif Formation has been highlighted for a long time. Although consensus has been reached on the overall sedimentary background, disputes still exist in understanding the sedimentary environment changes among sub-regions due to relatively limited research, rare outcrop, and incomplete drilled core, which hinders the analysis on sedimentary environment and thus the horizontal and vertical correlation. In this study, taking the Halfaya Oil Field as an example, the sedimentary microfacies analysis method was introduced to comprehensively characterize the cored interval of Mishrif Formation, including Single Layers MC1-1 to MA2. A total of 11 sedimentary microfacies are identified through system identification of sedimentary microfacies and environmental analysis, with reference to the standard microfacies classification in the rimmed carbonate platform. Then three kinds of environments are identified through microfacies assemblage analysis, namely restricted platform, open platform, and platform margin. Systematic analyses indicate that the deposits are mainly developed in the open platform and platform margin. Meanwhile, rock-electricity interpretation model is established according to the electricity response to cored intervals, and is then employed to interpret the uncored intervals, which finally helps build the sedimentary evolution pattern through horizontal and vertical correlation. It is proposed that the Single Layers MC1-1 to MB2-3 were deposited in the open platform featured by low water level, including sub-environments of low-energy shoal within platform and inter-shoal sea; Single Layers MB2-2 to MB1-2B were deposited in the open platform and platform margin, including sub-environments of high-energy shoal on the platform margin, low-energy shoal within platform, inter-shoal sea, and open sea; and Single Layers MB1-2A to MA2 were again deposited in the open platform with high water level, and the circumstance of open sea was dominant. The deposition of Single Layers MC1-1 to MA2 actually corresponded to a retrogradation-progradation process. Results of this study will not only provide significant guidance to the exploration and development of Mishrif Formation, Halfaya Oil Field, but also support that the theory of sedimentary environment correlation with adjacent areas is reliable.

SOCRAT Platform Design: A Web Architecture for Interactive Visual Analytics Applications

PubMed Central

Kalinin, Alexandr A.; Palanimalai, Selvam; Dinov, Ivo D.

2018-01-01

The modern web is a successful platform for large scale interactive web applications, including visualizations. However, there are no established design principles for building complex visual analytics (VA) web applications that could efficiently integrate visualizations with data management, computational transformation, hypothesis testing, and knowledge discovery. This imposes a time-consuming design and development process on many researchers and developers. To address these challenges, we consider the design requirements for the development of a module-based VA system architecture, adopting existing practices of large scale web application development. We present the preliminary design and implementation of an open-source platform for Statistics Online Computational Resource Analytical Toolbox (SOCRAT). This platform defines: (1) a specification for an architecture for building VA applications with multi-level modularity, and (2) methods for optimizing module interaction, re-usage, and extension. To demonstrate how this platform can be used to integrate a number of data management, interactive visualization, and analysis tools, we implement an example application for simple VA tasks including raw data input and representation, interactive visualization and analysis. PMID:29630069

SOCRAT Platform Design: A Web Architecture for Interactive Visual Analytics Applications.

PubMed

Kalinin, Alexandr A; Palanimalai, Selvam; Dinov, Ivo D

2017-04-01

The modern web is a successful platform for large scale interactive web applications, including visualizations. However, there are no established design principles for building complex visual analytics (VA) web applications that could efficiently integrate visualizations with data management, computational transformation, hypothesis testing, and knowledge discovery. This imposes a time-consuming design and development process on many researchers and developers. To address these challenges, we consider the design requirements for the development of a module-based VA system architecture, adopting existing practices of large scale web application development. We present the preliminary design and implementation of an open-source platform for Statistics Online Computational Resource Analytical Toolbox (SOCRAT). This platform defines: (1) a specification for an architecture for building VA applications with multi-level modularity, and (2) methods for optimizing module interaction, re-usage, and extension. To demonstrate how this platform can be used to integrate a number of data management, interactive visualization, and analysis tools, we implement an example application for simple VA tasks including raw data input and representation, interactive visualization and analysis.

Integrated Design and Implementation of Embedded Control Systems with Scilab

PubMed Central

Ma, Longhua; Xia, Feng; Peng, Zhe

2008-01-01

Embedded systems are playing an increasingly important role in control engineering. Despite their popularity, embedded systems are generally subject to resource constraints and it is therefore difficult to build complex control systems on embedded platforms. Traditionally, the design and implementation of control systems are often separated, which causes the development of embedded control systems to be highly time-consuming and costly. To address these problems, this paper presents a low-cost, reusable, reconfigurable platform that enables integrated design and implementation of embedded control systems. To minimize the cost, free and open source software packages such as Linux and Scilab are used. Scilab is ported to the embedded ARM-Linux system. The drivers for interfacing Scilab with several communication protocols including serial, Ethernet, and Modbus are developed. Experiments are conducted to test the developed embedded platform. The use of Scilab enables implementation of complex control algorithms on embedded platforms. With the developed platform, it is possible to perform all phases of the development cycle of embedded control systems in a unified environment, thus facilitating the reduction of development time and cost. PMID:27873827

Integrated Design and Implementation of Embedded Control Systems with Scilab.

PubMed

Ma, Longhua; Xia, Feng; Peng, Zhe

2008-09-05

Embedded systems are playing an increasingly important role in control engineering. Despite their popularity, embedded systems are generally subject to resource constraints and it is therefore difficult to build complex control systems on embedded platforms. Traditionally, the design and implementation of control systems are often separated, which causes the development of embedded control systems to be highly timeconsuming and costly. To address these problems, this paper presents a low-cost, reusable, reconfigurable platform that enables integrated design and implementation of embedded control systems. To minimize the cost, free and open source software packages such as Linux and Scilab are used. Scilab is ported to the embedded ARM-Linux system. The drivers for interfacing Scilab with several communication protocols including serial, Ethernet, and Modbus are developed. Experiments are conducted to test the developed embedded platform. The use of Scilab enables implementation of complex control algorithms on embedded platforms. With the developed platform, it is possible to perform all phases of the development cycle of embedded control systems in a unified environment, thus facilitating the reduction of development time and cost.

A Software Development Platform for Wearable Medical Applications.

PubMed

Zhang, Ruikai; Lin, Wei

2015-10-01

Wearable medical devices have become a leading trend in healthcare industry. Microcontrollers are computers on a chip with sufficient processing power and preferred embedded computing units in those devices. We have developed a software platform specifically for the design of the wearable medical applications with a small code footprint on the microcontrollers. It is supported by the open source real time operating system FreeRTOS and supplemented with a set of standard APIs for the architectural specific hardware interfaces on the microcontrollers for data acquisition and wireless communication. We modified the tick counter routine in FreeRTOS to include a real time soft clock. When combined with the multitasking features in the FreeRTOS, the platform offers the quick development of wearable applications and easy porting of the application code to different microprocessors. Test results have demonstrated that the application software developed using this platform are highly efficient in CPU usage while maintaining a small code foot print to accommodate the limited memory space in microcontrollers.

CILogon: An Integrated Identity and Access Management Platform for Science

NASA Astrophysics Data System (ADS)

Basney, J.

2016-12-01

When scientists work together, they use web sites and other software to share their ideas and data. To ensure the integrity of their work, these systems require the scientists to log in and verify that they are part of the team working on a particular science problem. Too often, the identity and access verification process is a stumbling block for the scientists. Scientific research projects are forced to invest time and effort into developing and supporting Identity and Access Management (IAM) services, distracting them from the core goals of their research collaboration. CILogon provides an IAM platform that enables scientists to work together to meet their IAM needs more effectively so they can allocate more time and effort to their core mission of scientific research. The CILogon platform enables federated identity management and collaborative organization management. Federated identity management enables researchers to use their home organization identities to access cyberinfrastructure, rather than requiring yet another username and password to log on. Collaborative organization management enables research projects to define user groups for authorization to collaboration platforms (e.g., wikis, mailing lists, and domain applications). CILogon's IAM platform serves the unique needs of research collaborations, namely the need to dynamically form collaboration groups across organizations and countries, sharing access to data, instruments, compute clusters, and other resources to enable scientific discovery. CILogon provides a software-as-a-service platform to ease integration with cyberinfrastructure, while making all software components publicly available under open source licenses to enable re-use. Figure 1 illustrates the components and interfaces of this platform. CILogon has been operational since 2010 and has been used by over 7,000 researchers from more than 170 identity providers to access cyberinfrastructure including Globus, LIGO, Open Science Grid, SeedMe, and XSEDE. The "CILogon 2.0" platform, launched in 2016, adds support for virtual organization (VO) membership management, identity linking, international collaborations, and standard integration protocols, through integration with the Internet2 COmanage collaboration software.

Interfacing HTCondor-CE with OpenStack

NASA Astrophysics Data System (ADS)

Bockelman, B.; Caballero Bejar, J.; Hover, J.

2017-10-01

Over the past few years, Grid Computing technologies have reached a high level of maturity. One key aspect of this success has been the development and adoption of newer Compute Elements to interface the external Grid users with local batch systems. These new Compute Elements allow for better handling of jobs requirements and a more precise management of diverse local resources. However, despite this level of maturity, the Grid Computing world is lacking diversity in local execution platforms. As Grid Computing technologies have historically been driven by the needs of the High Energy Physics community, most resource providers run the platform (operating system version and architecture) that best suits the needs of their particular users. In parallel, the development of virtualization and cloud technologies has accelerated recently, making available a variety of solutions, both commercial and academic, proprietary and open source. Virtualization facilitates performing computational tasks on platforms not available at most computing sites. This work attempts to join the technologies, allowing users to interact with computing sites through one of the standard Computing Elements, HTCondor-CE, but running their jobs within VMs on a local cloud platform, OpenStack, when needed. The system will re-route, in a transparent way, end user jobs into dynamically-launched VM worker nodes when they have requirements that cannot be satisfied by the static local batch system nodes. Also, once the automated mechanisms are in place, it becomes straightforward to allow an end user to invoke a custom Virtual Machine at the site. This will allow cloud resources to be used without requiring the user to establish a separate account. Both scenarios are described in this work.

Open-source algorithm for detecting sea ice surface features in high-resolution optical imagery

NASA Astrophysics Data System (ADS)

Wright, Nicholas C.; Polashenski, Chris M.

2018-04-01

Snow, ice, and melt ponds cover the surface of the Arctic Ocean in fractions that change throughout the seasons. These surfaces control albedo and exert tremendous influence over the energy balance in the Arctic. Increasingly available meter- to decimeter-scale resolution optical imagery captures the evolution of the ice and ocean surface state visually, but methods for quantifying coverage of key surface types from raw imagery are not yet well established. Here we present an open-source system designed to provide a standardized, automated, and reproducible technique for processing optical imagery of sea ice. The method classifies surface coverage into three main categories: snow and bare ice, melt ponds and submerged ice, and open water. The method is demonstrated on imagery from four sensor platforms and on imagery spanning from spring thaw to fall freeze-up. Tests show the classification accuracy of this method typically exceeds 96 %. To facilitate scientific use, we evaluate the minimum observation area required for reporting a representative sample of surface coverage. We provide an open-source distribution of this algorithm and associated training datasets and suggest the community consider this a step towards standardizing optical sea ice imagery processing. We hope to encourage future collaborative efforts to improve the code base and to analyze large datasets of optical sea ice imagery.

GABBs: Cyberinfrastructure for Self-Service Geospatial Data Exploration, Computation, and Sharing

NASA Astrophysics Data System (ADS)

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

2016-12-01

Geospatial data are present everywhere today with the proliferation of location-aware computing devices. 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. In addressing these needs, the Geospatial data Analysis Building Blocks (GABBs) project aims at building geospatial modeling, data analysis and visualization capabilities in an open source web platform, HUBzero. Funded by NSF's Data Infrastructure Building Blocks initiative, GABBs is creating a geospatial data architecture that integrates spatial data management, mapping and visualization, and interfaces in the HUBzero platform for scientific collaborations. The geo-rendering enabled Rappture toolkit, a generic Python mapping library, geospatial data exploration and publication tools, and an integrated online geospatial data management solution are among the software building blocks from the project. The GABBS software will be available through Amazon's AWS Marketplace VM images and open source. Hosting services are also available to the user community. The outcome of the project will enable researchers and educators to self-manage their scientific data, rapidly create GIS-enable tools, share geospatial data and tools on the web, and build dynamic workflows connecting data and tools, all without requiring significant software development skills, GIS expertise or IT administrative privileges. This presentation will describe the GABBs architecture, toolkits and libraries, and showcase the scientific use cases that utilize GABBs capabilities, as well as the challenges and solutions for GABBs to interoperate with other cyberinfrastructure platforms.

Open-Source Development of the Petascale Reactive Flow and Transport Code PFLOTRAN

NASA Astrophysics Data System (ADS)

Hammond, G. E.; Andre, B.; Bisht, G.; Johnson, T.; Karra, S.; Lichtner, P. C.; Mills, R. T.

2013-12-01

Open-source software development has become increasingly popular in recent years. Open-source encourages collaborative and transparent software development and promotes unlimited free redistribution of source code to the public. Open-source development is good for science as it reveals implementation details that are critical to scientific reproducibility, but generally excluded from journal publications. In addition, research funds that would have been spent on licensing fees can be redirected to code development that benefits more scientists. In 2006, the developers of PFLOTRAN open-sourced their code under the U.S. Department of Energy SciDAC-II program. Since that time, the code has gained popularity among code developers and users from around the world seeking to employ PFLOTRAN to simulate thermal, hydraulic, mechanical and biogeochemical processes in the Earth's surface/subsurface environment. PFLOTRAN is a massively-parallel subsurface reactive multiphase flow and transport simulator designed from the ground up to run efficiently on computing platforms ranging from the laptop to leadership-class supercomputers, all from a single code base. The code employs domain decomposition for parallelism and is founded upon the well-established and open-source parallel PETSc and HDF5 frameworks. PFLOTRAN leverages modern Fortran (i.e. Fortran 2003-2008) in its extensible object-oriented design. The use of this progressive, yet domain-friendly programming language has greatly facilitated collaboration in the code's software development. Over the past year, PFLOTRAN's top-level data structures were refactored as Fortran classes (i.e. extendible derived types) to improve the flexibility of the code, ease the addition of new process models, and enable coupling to external simulators. For instance, PFLOTRAN has been coupled to the parallel electrical resistivity tomography code E4D to enable hydrogeophysical inversion while the same code base can be used as a third-party library to provide hydrologic flow, energy transport, and biogeochemical capability to the community land model, CLM, part of the open-source community earth system model (CESM) for climate. In this presentation, the advantages and disadvantages of open source software development in support of geoscience research at government laboratories, universities, and the private sector are discussed. Since the code is open-source (i.e. it's transparent and readily available to competitors), the PFLOTRAN team's development strategy within a competitive research environment is presented. Finally, the developers discuss their approach to object-oriented programming and the leveraging of modern Fortran in support of collaborative geoscience research as the Fortran standard evolves among compiler vendors.

CAGE IIIA Distributed Simulation Design Methodology

DTIC Science & Technology

2014-05-01

2 VHF Very High Frequency VLC Video LAN Codec – an Open-source cross-platform multimedia player and framework VM Virtual Machine VOIP Voice Over...Implementing Defence Experimentation (GUIDEx). The key challenges for this methodology are with understanding how to: • design it o define the...operation and to be available in the other nation’s simulations. The challenge for the CAGE campaign of experiments is to continue to build upon this

The Virtual Collaboration Environment: New Media for Crisis Response

DTIC Science & Technology

2011-05-01

openvce.net/forum-alternative-platforms and http://openvce.net/more), the open-source Drupal ®-based Proceedings of the 8th International ISCRAM... Drupal is a widely used modular content management system, with an active development community of its own. It provides a user management system and...authoring text documents (a facility felt to be lacking at the time in Drupal ). This wiki feature has itself been supplemented with experimental

A Problem-Solving Environment for Biological Network Informatics: Bio-Spice

DTIC Science & Technology

2007-06-01

user an environment to access software tools. The Dashboard is built upon the NetBeans Integrated Development Environment (IDE), an open source Java...based integration platform was demonstrated. During the subsequent six month development cycle, the first version of the NetBeans based Bio-SPICE...frameworks (OAA, NetBeans , and Systems Biology Workbench (SBW)[15]), it becomes possible for Bio-SPICE tools to truly interoperate. This interoperation

Learning Management Platform for CyberCIEGE

DTIC Science & Technology

2011-12-01

developments were done using the NetBeans Integrated Development Environment (IDE) 7.0, which is a free and open source IDE. Some of these...developments could be implemented using the GUI design features of NetBeans . However, it was not done so because the existing Campaign Analyzer code base...directory through a dialog window. Also, the existing directory structures are not consistent with NetBeans project management assumptions and thus

Mobile Gaming and Student Interactions in a Science Center: The Future of Gaming in Science Education

ERIC Educational Resources Information Center

Atwood-Blaine, Dana; Huffman, Douglas

2017-01-01

This article explores the impact of an augmented reality iPad-based mobile game, called The Great STEM Caper, on students' interaction at a science center. An open-source, location-based game platform called ARIS (i.e. Augmented Reality and Interactive Storytelling) was used to create an iPad-based mobile game. The game used QR scan codes and a…

Harvest: a web-based biomedical data discovery and reporting application development platform.

PubMed

Italia, Michael J; Pennington, Jeffrey W; Ruth, Byron; Wrazien, Stacey; Loutrel, Jennifer G; Crenshaw, E Bryan; Miller, Jeffrey; White, Peter S

2013-01-01

Biomedical researchers share a common challenge of making complex data understandable and accessible. This need is increasingly acute as investigators seek opportunities for discovery amidst an exponential growth in the volume and complexity of laboratory and clinical data. To address this need, we developed Harvest, an open source framework that provides a set of modular components to aid the rapid development and deployment of custom data discovery software applications. Harvest incorporates visual representations of multidimensional data types in an intuitive, web-based interface that promotes a real-time, iterative approach to exploring complex clinical and experimental data. The Harvest architecture capitalizes on standards-based, open source technologies to address multiple functional needs critical to a research and development environment, including domain-specific data modeling, abstraction of complex data models, and a customizable web client.

Using Kepler for Tool Integration in Microarray Analysis Workflows.

PubMed

Gan, Zhuohui; Stowe, Jennifer C; Altintas, Ilkay; McCulloch, Andrew D; Zambon, Alexander C

Increasing numbers of genomic technologies are leading to massive amounts of genomic data, all of which requires complex analysis. More and more bioinformatics analysis tools are being developed by scientist to simplify these analyses. However, different pipelines have been developed using different software environments. This makes integrations of these diverse bioinformatics tools difficult. Kepler provides an open source environment to integrate these disparate packages. Using Kepler, we integrated several external tools including Bioconductor packages, AltAnalyze, a python-based open source tool, and R-based comparison tool to build an automated workflow to meta-analyze both online and local microarray data. The automated workflow connects the integrated tools seamlessly, delivers data flow between the tools smoothly, and hence improves efficiency and accuracy of complex data analyses. Our workflow exemplifies the usage of Kepler as a scientific workflow platform for bioinformatics pipelines.

PyGaze: an open-source, cross-platform toolbox for minimal-effort programming of eyetracking experiments.

PubMed

Dalmaijer, Edwin S; Mathôt, Sebastiaan; Van der Stigchel, Stefan

2014-12-01

The PyGaze toolbox is an open-source software package for Python, a high-level programming language. It is designed for creating eyetracking experiments in Python syntax with the least possible effort, and it offers programming ease and script readability without constraining functionality and flexibility. PyGaze can be used for visual and auditory stimulus presentation; for response collection via keyboard, mouse, joystick, and other external hardware; and for the online detection of eye movements using a custom algorithm. A wide range of eyetrackers of different brands (EyeLink, SMI, and Tobii systems) are supported. The novelty of PyGaze lies in providing an easy-to-use layer on top of the many different software libraries that are required for implementing eyetracking experiments. Essentially, PyGaze is a software bridge for eyetracking research.

Near-Field Characterization of Methane Emission Variability from a Compressor Station Using a Model Aircraft.

PubMed

Nathan, Brian J; Golston, Levi M; O'Brien, Anthony S; Ross, Kevin; Harrison, William A; Tao, Lei; Lary, David J; Johnson, Derek R; Covington, April N; Clark, Nigel N; Zondlo, Mark A

2015-07-07

A model aircraft equipped with a custom laser-based, open-path methane sensor was deployed around a natural gas compressor station to quantify the methane leak rate and its variability at a compressor station in the Barnett Shale. The open-path, laser-based sensor provides fast (10 Hz) and precise (0.1 ppmv) measurements of methane in a compact package while the remote control aircraft provides nimble and safe operation around a local source. Emission rates were measured from 22 flights over a one-week period. Mean emission rates of 14 ± 8 g CH4 s(-1) (7.4 ± 4.2 g CH4 s(-1) median) from the station were observed or approximately 0.02% of the station throughput. Significant variability in emission rates (0.3-73 g CH4 s(-1) range) was observed on time scales of hours to days, and plumes showed high spatial variability in the horizontal and vertical dimensions. Given the high spatiotemporal variability of emissions, individual measurements taken over short durations and from ground-based platforms should be used with caution when examining compressor station emissions. More generally, our results demonstrate the unique advantages and challenges of platforms like small unmanned aerial vehicles for quantifying local emission sources to the atmosphere.

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.

Efficient visualization of high-throughput targeted proteomics experiments: TAPIR.

PubMed

Röst, Hannes L; Rosenberger, George; Aebersold, Ruedi; Malmström, Lars

2015-07-15

Targeted mass spectrometry comprises a set of powerful methods to obtain accurate and consistent protein quantification in complex samples. To fully exploit these techniques, a cross-platform and open-source software stack based on standardized data exchange formats is required. We present TAPIR, a fast and efficient Python visualization software for chromatograms and peaks identified in targeted proteomics experiments. The input formats are open, community-driven standardized data formats (mzML for raw data storage and TraML encoding the hierarchical relationships between transitions, peptides and proteins). TAPIR is scalable to proteome-wide targeted proteomics studies (as enabled by SWATH-MS), allowing researchers to visualize high-throughput datasets. The framework integrates well with existing automated analysis pipelines and can be extended beyond targeted proteomics to other types of analyses. TAPIR is available for all computing platforms under the 3-clause BSD license at https://github.com/msproteomicstools/msproteomicstools. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

OpenStructure: a flexible software framework for computational structural biology.

PubMed

Biasini, Marco; Mariani, Valerio; Haas, Jürgen; Scheuber, Stefan; Schenk, Andreas D; Schwede, Torsten; Philippsen, Ansgar

2010-10-15

Developers of new methods in computational structural biology are often hampered in their research by incompatible software tools and non-standardized data formats. To address this problem, we have developed OpenStructure as a modular open source platform to provide a powerful, yet flexible general working environment for structural bioinformatics. OpenStructure consists primarily of a set of libraries written in C++ with a cleanly designed application programmer interface. All functionality can be accessed directly in C++ or in a Python layer, meeting both the requirements for high efficiency and ease of use. Powerful selection queries and the notion of entity views to represent these selections greatly facilitate the development and implementation of algorithms on structural data. The modular integration of computational core methods with powerful visualization tools makes OpenStructure an ideal working and development environment. Several applications, such as the latest versions of IPLT and QMean, have been implemented based on OpenStructure-demonstrating its value for the development of next-generation structural biology algorithms. Source code licensed under the GNU lesser general public license and binaries for MacOS X, Linux and Windows are available for download at http://www.openstructure.org. torsten.schwede@unibas.ch Supplementary data are available at Bioinformatics online.

OpenDA-WFLOW framework for improving hydrologic predictions using distributed hydrologic models

NASA Astrophysics Data System (ADS)

Weerts, Albrecht; Schellekens, Jaap; Kockx, Arno; Hummel, Stef

2017-04-01

Data assimilation (DA) holds considerable potential for improving hydrologic predictions (Liu et al., 2012) and increase the potential for early warning and/or smart water management. However, advances in hydrologic DA research have not yet been adequately or timely implemented in operational forecast systems to improve the skill of forecasts for better informed real-world decision making. The objective of this work is to highlight the development of a generic linkage of the open source OpenDA package and the open source community hydrologic modeling framework Openstreams/WFLOW and its application in operational hydrological forecasting on various spatial scales. The coupling between OpenDA and Openstreams/wflow framework is based on the emerging standard Basic Model Interface (BMI) as advocated by CSDMS using cross-platform webservices (i.e. Apache Thrift) developed by Hut et al. (2016). The potential application of the OpenDA-WFLOW for operational hydrologic forecasting including its integration with Delft-FEWS (used by more than 40 operational forecast centers around the world (Werner et al., 2013)) is demonstrated by the presented case studies. We will also highlight the possibility to give real-time insight into the working of the DA methods applied for supporting the forecaster as mentioned as one of the burning issues by Liu et al., (2012).

Heterogeneous compute in computer vision: OpenCL in OpenCV

NASA Astrophysics Data System (ADS)

Gasparakis, Harris

2014-02-01

We explore the relevance of Heterogeneous System Architecture (HSA) in Computer Vision, both as a long term vision, and as a near term emerging reality via the recently ratified OpenCL 2.0 Khronos standard. After a brief review of OpenCL 1.2 and 2.0, including HSA features such as Shared Virtual Memory (SVM) and platform atomics, we identify what genres of Computer Vision workloads stand to benefit by leveraging those features, and we suggest a new mental framework that replaces GPU compute with hybrid HSA APU compute. As a case in point, we discuss, in some detail, popular object recognition algorithms (part-based models), emphasizing the interplay and concurrent collaboration between the GPU and CPU. We conclude by describing how OpenCL has been incorporated in OpenCV, a popular open source computer vision library, emphasizing recent work on the Transparent API, to appear in OpenCV 3.0, which unifies the native CPU and OpenCL execution paths under a single API, allowing the same code to execute either on CPU or on a OpenCL enabled device, without even recompiling.

Land User and Land Cover Maps of Europe: a Webgis Platform

NASA Astrophysics Data System (ADS)

Brovelli, M. A.; Fahl, F. C.; Minghini, M.; Molinari, M. E.

2016-06-01

This paper presents the methods and implementation processes of a WebGIS platform designed to publish the available land use and land cover maps of Europe at continental scale. The system is built completely on open source infrastructure and open standards. The proposed architecture is based on a server-client model having GeoServer as the map server, Leaflet as the client-side mapping library and the Bootstrap framework at the core of the front-end user interface. The web user interface is designed to have typical features of a desktop GIS (e.g. activate/deactivate layers and order layers by drag and drop actions) and to show specific information on the activated layers (e.g. legend and simplified metadata). Users have the possibility to change the base map from a given list of map providers (e.g. OpenStreetMap and Microsoft Bing) and to control the opacity of each layer to facilitate the comparison with both other land cover layers and the underlying base map. In addition, users can add to the platform any custom layer available through a Web Map Service (WMS) and activate the visualization of photos from popular photo sharing services. This last functionality is provided in order to have a visual assessment of the available land coverages based on other user-generated contents available on the Internet. It is supposed to be a first step towards a calibration/validation service that will be made available in the future.

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.

Sensor Networks, Dataloggers, and Other Handy Gadgets Using Open-Source Electronics for the Christina River Basin CZO

NASA Astrophysics Data System (ADS)

Hicks, S. D.; Aufdenkampe, A. K.; Montgomery, D. S.

2011-12-01

The search for biogeochemical "hot spots" and "hot moments" that control ecosystem-level processes requires a rethinking of how we observe the environment. Extensive multi-sensor/measurement arrays are required to realize 2D, 3D, or 4D maps of environmental properties with sufficient spatial and temporal resolution to find and understand hot spots and hot moments. To date, the cost of the data logging and communication infrastructure has been a major limitation to large-scale sensor deployment, especially for near-real-time (NRT) wireless networks. A low-cost, user-friendly alternative is needed so that resources can be prioritized toward sensor hardware rather than data acquisition and communication hardware. A flexible development platform would also allow for easy creation of other useful devices in addition to the already apparent need for economical dataloggers. The recent proliferation of open-source electronics platforms offers an opportunity for environmental observatories to deploy sensors at large scales by reducing data logging and communications costs by more than an order of magnitude. Leading the open-source electronics revolution is the Arduino project, designed to make the process of using electronics in multidisciplinary projects more accessible to hobbyists and professionals alike. A large user community has developed and shared hundreds of practical applications for projects that interface with a variety of sensors and use embedded logic to control external hardware. Likewise, dozens of companies and individuals sell low-cost Arduino-compatible boards that can connect together in a modular framework, allowing the user to quickly create devices for a wide range of applications. Based on these open-source technologies and products, we are designing and building a variety of circuit devices for use in our research watersheds. One Arduino-based device is a multi-channel datalogger that can be used with a variety of analog and digital sensors, such as pressure transducers, conductivity sensors, soil moisture and temperature probes, and redox probes. Radio modules can be added to the loggers to create a self-meshing wireless network for streaming live sensor data. A variation of the logger circuit is a smaller handheld unit with a text display that can be used when testing sensors in the field. Another useful custom device is a remote streamwater sampling system, made up of an Arduino circuit and a prepaid cell phone, allowing a user to remotely control multiple pumps by following interactive voice menus and hearing live sensor value readouts. In the lab, an Arduino circuit is used in a multi-chamber CO2 respiration experiment where it is controlling dozens of solenoid valves and logging the data from the analytical instruments. One of the biggest benefits of open source hardware is the low cost of the components. Each of the devices we have built costs less than $100 and can be assembled in a few hours. These circuits could easily be adapted to other applications or interfaced with other sensors in a variety of configurations, making the Arduino platform an incredibly useful tool for researchers.

A Roadmap for using Agile Development in a Traditional System

NASA Technical Reports Server (NTRS)

Streiffert, Barbara; Starbird, Thomas

2006-01-01

I. Ensemble Development Group: a) Produces activity planning software for in spacecraft; b) Built on Eclipse Rich Client Platform (open source development and runtime software); c) Funded by multiple sources including the Mars Technology Program; d) Incorporated the use of Agile Development. II. Next Generation Uplink Planning System: a) Researches the Activity Planning and Sequencing Subsystem for Mars Science Laboratory (APSS); b) APSS includes Ensemble, Activity Modeling, Constraint Checking, Command Editing and Sequencing tools plus other uplink generation utilities; c) Funded by the Mars Technology Program; d) Integrates all of the tools for APSS.

Database Organisation in a Web-Enabled Free and Open-Source Software (foss) Environment for Spatio-Temporal Landslide Modelling

NASA Astrophysics Data System (ADS)

Das, I.; Oberai, K.; Sarathi Roy, P.

2012-07-01

Landslides exhibit themselves in different mass movement processes and are considered among the most complex natural hazards occurring on the earth surface. Making landslide database available online via WWW (World Wide Web) promotes the spreading and reaching out of the landslide information to all the stakeholders. The aim of this research is to present a comprehensive database for generating landslide hazard scenario with the help of available historic records of landslides and geo-environmental factors and make them available over the Web using geospatial Free & Open Source Software (FOSS). FOSS reduces the cost of the project drastically as proprietary software's are very costly. Landslide data generated for the period 1982 to 2009 were compiled along the national highway road corridor in Indian Himalayas. All the geo-environmental datasets along with the landslide susceptibility map were served through WEBGIS client interface. Open source University of Minnesota (UMN) mapserver was used as GIS server software for developing web enabled landslide geospatial database. PHP/Mapscript server-side application serve as a front-end application and PostgreSQL with PostGIS extension serve as a backend application for the web enabled landslide spatio-temporal databases. This dynamic virtual visualization process through a web platform brings an insight into the understanding of the landslides and the resulting damage closer to the affected people and user community. The landslide susceptibility dataset is also made available as an Open Geospatial Consortium (OGC) Web Feature Service (WFS) which can be accessed through any OGC compliant open source or proprietary GIS Software.

Cave Pearl Data Logger: A Flexible Arduino-Based Logging Platform for Long-Term Monitoring in Harsh Environments.

PubMed

Beddows, Patricia A; Mallon, Edward K

2018-02-09

A low-cost data logging platform is presented that provides long-term operation in remote or submerged environments. Three premade "breakout boards" from the open-source Arduino ecosystem are assembled into the core of the data logger. Power optimization techniques are presented which extend the operational life of this module-based design to >1 year on three alkaline AA batteries. Robust underwater housings are constructed for these loggers using PVC fittings. Both the logging platform and the enclosures, are easy to build and modify without specialized tools or a significant background in electronics. This combination turns the Cave Pearl data logger into a generalized prototyping system and this design flexibility is demonstrated with two field studies recording drip rates in a cave and water flow in a flooded cave system. This paper describes a complete DIY solution, suitable for a wide range of challenging deployment conditions.

Xi-cam: a versatile interface for data visualization and analysis

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

Pandolfi, Ronald J.; Allan, Daniel B.; Arenholz, Elke

Xi-cam is an extensible platform for data management, analysis and visualization.Xi-camaims to provide a flexible and extensible approach to synchrotron data treatment as a solution to rising demands for high-volume/high-throughput processing pipelines. The core ofXi-camis an extensible plugin-based graphical user interface platform which provides users with an interactive interface to processing algorithms. Plugins are available for SAXS/WAXS/GISAXS/GIWAXS, tomography and NEXAFS data. WithXi-cam's `advanced' mode, data processing steps are designed as a graph-based workflow, which can be executed live, locally or remotely. Remote execution utilizes high-performance computing or de-localized resources, allowing for the effective reduction of high-throughput data.Xi-cam's plugin-based architecture targetsmore » cross-facility and cross-technique collaborative development, in support of multi-modal analysis.Xi-camis open-source and cross-platform, and available for download on GitHub.« less

Xi-cam: a versatile interface for data visualization and analysis

DOE PAGES

Pandolfi, Ronald J.; Allan, Daniel B.; Arenholz, Elke; ...

2018-05-31

Xi-cam is an extensible platform for data management, analysis and visualization.Xi-camaims to provide a flexible and extensible approach to synchrotron data treatment as a solution to rising demands for high-volume/high-throughput processing pipelines. The core ofXi-camis an extensible plugin-based graphical user interface platform which provides users with an interactive interface to processing algorithms. Plugins are available for SAXS/WAXS/GISAXS/GIWAXS, tomography and NEXAFS data. WithXi-cam's `advanced' mode, data processing steps are designed as a graph-based workflow, which can be executed live, locally or remotely. Remote execution utilizes high-performance computing or de-localized resources, allowing for the effective reduction of high-throughput data.Xi-cam's plugin-based architecture targetsmore » cross-facility and cross-technique collaborative development, in support of multi-modal analysis.Xi-camis open-source and cross-platform, and available for download on GitHub.« less

Cave Pearl Data Logger: A Flexible Arduino-Based Logging Platform for Long-Term Monitoring in Harsh Environments

PubMed Central

Mallon, Edward K.

2018-01-01

A low-cost data logging platform is presented that provides long-term operation in remote or submerged environments. Three premade “breakout boards” from the open-source Arduino ecosystem are assembled into the core of the data logger. Power optimization techniques are presented which extend the operational life of this module-based design to >1 year on three alkaline AA batteries. Robust underwater housings are constructed for these loggers using PVC fittings. Both the logging platform and the enclosures, are easy to build and modify without specialized tools or a significant background in electronics. This combination turns the Cave Pearl data logger into a generalized prototyping system and this design flexibility is demonstrated with two field studies recording drip rates in a cave and water flow in a flooded cave system. This paper describes a complete DIY solution, suitable for a wide range of challenging deployment conditions. PMID:29425185

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).

PyFLOWGO: An open-source platform for simulation of channelized lava thermo-rheological properties

NASA Astrophysics Data System (ADS)

Chevrel, Magdalena Oryaëlle; Labroquère, Jérémie; Harris, Andrew J. L.; Rowland, Scott K.

2018-02-01

Lava flow advance can be modeled through tracking the evolution of the thermo-rheological properties of a control volume of lava as it cools and crystallizes. An example of such a model was conceived by Harris and Rowland (2001) who developed a 1-D model, FLOWGO, in which the velocity of a control volume flowing down a channel depends on rheological properties computed following the thermal path estimated via a heat balance box model. We provide here an updated version of FLOWGO written in Python that is an open-source, modern and flexible language. Our software, named PyFLOWGO, allows selection of heat fluxes and rheological models of the user's choice to simulate the thermo-rheological evolution of the lava control volume. We describe its architecture which offers more flexibility while reducing the risk of making error when changing models in comparison to the previous FLOWGO version. Three cases are tested using actual data from channel-fed lava flow systems and results are discussed in terms of model validation and convergence. PyFLOWGO is open-source and packaged in a Python library to be imported and reused in any Python program (https://github.com/pyflowgo/pyflowgo)

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

Is Multitask Deep Learning Practical for Pharma?

PubMed

Ramsundar, Bharath; Liu, Bowen; Wu, Zhenqin; Verras, Andreas; Tudor, Matthew; Sheridan, Robert P; Pande, Vijay

2017-08-28

Multitask deep learning has emerged as a powerful tool for computational drug discovery. However, despite a number of preliminary studies, multitask deep networks have yet to be widely deployed in the pharmaceutical and biotech industries. This lack of acceptance stems from both software difficulties and lack of understanding of the robustness of multitask deep networks. Our work aims to resolve both of these barriers to adoption. We introduce a high-quality open-source implementation of multitask deep networks as part of the DeepChem open-source platform. Our implementation enables simple python scripts to construct, fit, and evaluate sophisticated deep models. We use our implementation to analyze the performance of multitask deep networks and related deep models on four collections of pharmaceutical data (three of which have not previously been analyzed in the literature). We split these data sets into train/valid/test using time and neighbor splits to test multitask deep learning performance under challenging conditions. Our results demonstrate that multitask deep networks are surprisingly robust and can offer strong improvement over random forests. Our analysis and open-source implementation in DeepChem provide an argument that multitask deep networks are ready for widespread use in commercial drug discovery.

phylo-node: A molecular phylogenetic toolkit using Node.js.

PubMed

O'Halloran, Damien M

2017-01-01

Node.js is an open-source and cross-platform environment that provides a JavaScript codebase for back-end server-side applications. JavaScript has been used to develop very fast and user-friendly front-end tools for bioinformatic and phylogenetic analyses. However, no such toolkits are available using Node.js to conduct comprehensive molecular phylogenetic analysis. To address this problem, I have developed, phylo-node, which was developed using Node.js and provides a stable and scalable toolkit that allows the user to perform diverse molecular and phylogenetic tasks. phylo-node can execute the analysis and process the resulting outputs from a suite of software options that provides tools for read processing and genome alignment, sequence retrieval, multiple sequence alignment, primer design, evolutionary modeling, and phylogeny reconstruction. Furthermore, phylo-node enables the user to deploy server dependent applications, and also provides simple integration and interoperation with other Node modules and languages using Node inheritance patterns, and a customized piping module to support the production of diverse pipelines. phylo-node is open-source and freely available to all users without sign-up or login requirements. All source code and user guidelines are openly available at the GitHub repository: https://github.com/dohalloran/phylo-node.

CAMPAIGN: an open-source library of GPU-accelerated data clustering algorithms.

PubMed

Kohlhoff, Kai J; Sosnick, Marc H; Hsu, William T; Pande, Vijay S; Altman, Russ B

2011-08-15

Data clustering techniques are an essential component of a good data analysis toolbox. Many current bioinformatics applications are inherently compute-intense and work with very large datasets. Sequential algorithms are inadequate for providing the necessary performance. For this reason, we have created Clustering Algorithms for Massively Parallel Architectures, Including GPU Nodes (CAMPAIGN), a central resource for data clustering algorithms and tools that are implemented specifically for execution on massively parallel processing architectures. CAMPAIGN is a library of data clustering algorithms and tools, written in 'C for CUDA' for Nvidia GPUs. The library provides up to two orders of magnitude speed-up over respective CPU-based clustering algorithms and is intended as an open-source resource. New modules from the community will be accepted into the library and the layout of it is such that it can easily be extended to promising future platforms such as OpenCL. Releases of the CAMPAIGN library are freely available for download under the LGPL from https://simtk.org/home/campaign. Source code can also be obtained through anonymous subversion access as described on https://simtk.org/scm/?group_id=453. kjk33@cantab.net.