The US Response to China’s ASAT Test: An International Security Space Alliance for the Future (Drew Paper Number 8, August 2009)

DTIC Science & Technology

2009-08-01

per response, including the time for reviewing instructions, searching existing data sources , gathering and maintaining the data needed, and completing...Mastalir examines both that reevalu- ation and those intentions, relying on open- source material, particularly from Chinese strategic and military...identify the leading assumptions necessary to bound the problem. A forensic re- view of open- source Chinese literature—including the spoken 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 source EMR software: profiling, insights and hands-on analysis.

PubMed

Kiah, M L M; Haiqi, Ahmed; Zaidan, B B; Zaidan, A A

2014-11-01

The use of open source software in health informatics is increasingly advocated by authors in the literature. Although there is no clear evidence of the superiority of the current open source applications in the healthcare field, the number of available open source applications online is growing and they are gaining greater prominence. This repertoire of open source options is of a great value for any future-planner interested in adopting an electronic medical/health record system, whether selecting an existent application or building a new one. The following questions arise. How do the available open source options compare to each other with respect to functionality, usability and security? Can an implementer of an open source application find sufficient support both as a user and as a developer, and to what extent? Does the available literature provide adequate answers to such questions? This review attempts to shed some light on these aspects. The objective of this study is to provide more comprehensive guidance from an implementer perspective toward the available alternatives of open source healthcare software, particularly in the field of electronic medical/health records. The design of this study is twofold. In the first part, we profile the published literature on a sample of existent and active open source software in the healthcare area. The purpose of this part is to provide a summary of the available guides and studies relative to the sampled systems, and to identify any gaps in the published literature with respect to our research questions. In the second part, we investigate those alternative systems relative to a set of metrics, by actually installing the software and reporting a hands-on experience of the installation process, usability, as well as other factors. The literature covers many aspects of open source software implementation and utilization in healthcare practice. Roughly, those aspects could be distilled into a basic taxonomy, making the literature landscape more perceivable. Nevertheless, the surveyed articles fall short of fulfilling the targeted objective of providing clear reference to potential implementers. The hands-on study contributed a more detailed comparative guide relative to our set of assessment measures. Overall, no system seems to satisfy an industry-standard measure, particularly in security and interoperability. The systems, as software applications, feel similar from a usability perspective and share a common set of functionality, though they vary considerably in community support and activity. More detailed analysis of popular open source software can benefit the potential implementers of electronic health/medical records systems. The number of examined systems and the measures by which to compare them vary across studies, but still rewarding insights start to emerge. Our work is one step toward that goal. Our overall conclusion is that open source options in the medical field are still far behind the highly acknowledged open source products in other domains, e.g. operating systems market share. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

40 CFR 63.5810 - What are my options for meeting the standards for open molding and centrifugal casting operations...

Code of Federal Regulations, 2011 CFR

2011-07-01

... standards for open molding and centrifugal casting operations at new and existing sources? 63.5810 Section... § 63.5810 What are my options for meeting the standards for open molding and centrifugal casting... (d) of this section to meet the standards for open molding or centrifugal casting operations in Table...

40 CFR 63.5810 - What are my options for meeting the standards for open molding and centrifugal casting operations...

Code of Federal Regulations, 2010 CFR

2010-07-01

... standards for open molding and centrifugal casting operations at new and existing sources? 63.5810 Section... § 63.5810 What are my options for meeting the standards for open molding and centrifugal casting... (d) of this section to meet the standards for open molding or centrifugal casting operations in Table...

40 CFR 63.5810 - What are my options for meeting the standards for open molding and centrifugal casting operations...

Code of Federal Regulations, 2013 CFR

2013-07-01

... standards for open molding and centrifugal casting operations at new and existing sources? 63.5810 Section... Meeting Standards § 63.5810 What are my options for meeting the standards for open molding and centrifugal...) through (d) of this section to meet the standards for open molding or centrifugal casting operations in...

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

PubMed

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

2008-01-01

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

Evaluation of an open source tool for indexing and searching enterprise radiology and pathology reports

NASA Astrophysics Data System (ADS)

Kim, Woojin; Boonn, William

2010-03-01

Data mining of existing radiology and pathology reports within an enterprise health system can be used for clinical decision support, research, education, as well as operational analyses. In our health system, the database of radiology and pathology reports exceeds 13 million entries combined. We are building a web-based tool to allow search and data analysis of these combined databases using freely available and open source tools. This presentation will compare performance of an open source full-text indexing tool to MySQL's full-text indexing and searching and describe implementation procedures to incorporate these capabilities into a radiology-pathology search engine.

Computation in Classical Mechanics with Easy Java Simulations (EJS)

NASA Astrophysics Data System (ADS)

Cox, Anne J.

2006-12-01

Let your students enjoy creating animations and incorporating some computational physics into your Classical Mechanics course. This talk will demonstrate the use of an Open Source Physics package, Easy Java Simulations (EJS), in an already existing sophomore/junior level Classical Mechanics course. EJS allows for incremental introduction of computational physics into existing courses because it is easy to use (for instructors and students alike) and it is open source. Students can use this tool for numerical solutions to problems (as they can with commercial systems: Mathcad and Mathematica), but they can also generate their own animations. For example, students in Classical Mechanics use Lagrangian mechanics to solve a problem, and then use EJS not only to numerically solve the differential equations, but to show the associated motion (and check their answers). EJS, developed by Francisco Esquembre (http://fem.um.es/Ejs/), is built on the OpenSource Physics framework (http://www.opensourcephysics.org/) supported through NSF DUE0442581.

Open-source framework for power system transmission and distribution dynamics co-simulation

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

Huang, Renke; Fan, Rui; Daily, Jeff

The promise of the smart grid entails more interactions between the transmission and distribution networks, and there is an immediate need for tools to provide the comprehensive modelling and simulation required to integrate operations at both transmission and distribution levels. Existing electromagnetic transient simulators can perform simulations with integration of transmission and distribution systems, but the computational burden is high for large-scale system analysis. For transient stability analysis, currently there are only separate tools for simulating transient dynamics of the transmission and distribution systems. In this paper, we introduce an open source co-simulation framework “Framework for Network Co-Simulation” (FNCS), togethermore » with the decoupled simulation approach that links existing transmission and distribution dynamic simulators through FNCS. FNCS is a middleware interface and framework that manages the interaction and synchronization of the transmission and distribution simulators. Preliminary testing results show the validity and capability of the proposed open-source co-simulation framework and the decoupled co-simulation methodology.« less

4onse: four times open & non-conventional technology for sensing the environment

NASA Astrophysics Data System (ADS)

Cannata, Massimiliano; Ratnayake, Rangageewa; Antonovic, Milan; Strigaro, Daniele; Cardoso, Mirko; Hoffmann, Marcus

2017-04-01

The availability of complete, quality and dense monitoring hydro-meteorological data is essential to address a number of practical issues including, but not limited to, flood-water and urban drainage management, climate change impact assessment, early warning and risk management, now-casting and weather predictions. Thanks to the recent technological advances such as Internet Of Things, Big Data and Ubiquitous Internet, non-conventional monitoring systems based on open technologies and low cost sensors may represent a great opportunity either as a complement of authoritative monitoring network or as a vital source of information wherever existing monitoring networks are in decline or completely missing. Nevertheless, scientific literature on such a kind of open and non-conventional monitoring systems is still limited and often relates to prototype engineering and testing in rather limited case studies. For this reason the 4onse project aims at integrating existing open technologies in the field of Free & Open Source Software, Open Hardware, Open Data, and Open Standards and evaluate this kind of system in a real case (about 30 stations) for a medium period of 2 years to better scientifically understand strengths, criticalities and applicabilities in terms of data quality; system durability; management costs; performances; sustainability. The ultimate objective is to contribute in non-conventional monitoring systems adoption based on four open technologies.

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.

40 CFR 63.5716 - When must I conduct a performance test?

Code of Federal Regulations, 2010 CFR

2010-07-01

... PROGRAMS (CONTINUED) NATIONAL EMISSION STANDARDS FOR HAZARDOUS AIR POLLUTANTS FOR SOURCE CATEGORIES... for Open Molding Operations Controlled by Add-on Control Devices § 63.5716 When must I conduct a performance test? (a) If your source is an existing source, you must complete the add-on control device...

ImTK: an open source multi-center information management toolkit

NASA Astrophysics Data System (ADS)

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

2008-03-01

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

Embracing Open Source for NASA's Earth Science Data Systems

NASA Technical Reports Server (NTRS)

Baynes, Katie; Pilone, Dan; Boller, Ryan; Meyer, David; Murphy, Kevin

2017-01-01

The overarching purpose of NASAs Earth Science program is to develop a scientific understanding of Earth as a system. Scientific knowledge is most robust and actionable when resulting from transparent, traceable, and reproducible methods. Reproducibility includes open access to the data as well as the software used to arrive at results. Additionally, software that is custom-developed for NASA should be open to the greatest degree possible, to enable re-use across Federal agencies, reduce overall costs to the government, remove barriers to innovation, and promote consistency through the use of uniform standards. Finally, Open Source Software (OSS) practices facilitate collaboration between agencies and the private sector. To best meet these ends, NASAs Earth Science Division promotes the full and open sharing of not only all data, metadata, products, information, documentation, models, images, and research results but also the source code used to generate, manipulate and analyze them. This talk focuses on the challenges to open sourcing NASA developed software within ESD and the growing pains associated with establishing policies running the gamut of tracking issues, properly documenting build processes, engaging the open source community, maintaining internal compliance, and accepting contributions from external sources. This talk also covers the adoption of existing open source technologies and standards to enhance our custom solutions and our contributions back to the community. Finally, we will be introducing the most recent OSS contributions from NASA Earth Science program and promoting these projects for wider community review and adoption.

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.

Quantitative Image Feature Engine (QIFE): an Open-Source, Modular Engine for 3D Quantitative Feature Extraction from Volumetric Medical Images.

PubMed

Echegaray, Sebastian; Bakr, Shaimaa; Rubin, Daniel L; Napel, Sandy

2017-10-06

The aim of this study was to develop an open-source, modular, locally run or server-based system for 3D radiomics feature computation that can be used on any computer system and included in existing workflows for understanding associations and building predictive models between image features and clinical data, such as survival. The QIFE exploits various levels of parallelization for use on multiprocessor systems. It consists of a managing framework and four stages: input, pre-processing, feature computation, and output. Each stage contains one or more swappable components, allowing run-time customization. We benchmarked the engine using various levels of parallelization on a cohort of CT scans presenting 108 lung tumors. Two versions of the QIFE have been released: (1) the open-source MATLAB code posted to Github, (2) a compiled version loaded in a Docker container, posted to DockerHub, which can be easily deployed on any computer. The QIFE processed 108 objects (tumors) in 2:12 (h/mm) using 1 core, and 1:04 (h/mm) hours using four cores with object-level parallelization. We developed the Quantitative Image Feature Engine (QIFE), an open-source feature-extraction framework that focuses on modularity, standards, parallelism, provenance, and integration. Researchers can easily integrate it with their existing segmentation and imaging workflows by creating input and output components that implement their existing interfaces. Computational efficiency can be improved by parallelizing execution at the cost of memory usage. Different parallelization levels provide different trade-offs, and the optimal setting will depend on the size and composition of the dataset to be processed.

Eddylicious: A Python package for turbulent inflow generation

NASA Astrophysics Data System (ADS)

Mukha, Timofey; Liefvendahl, Mattias

2018-01-01

A Python package for generating inflow for scale-resolving computer simulations of turbulent flow is presented. The purpose of the package is to unite existing inflow generation methods in a single code-base and make them accessible to users of various Computational Fluid Dynamics (CFD) solvers. The currently existing functionality consists of an accurate inflow generation method suitable for flows with a turbulent boundary layer inflow and input/output routines for coupling with the open-source CFD solver OpenFOAM.

Scalar collapse in AdS with an OpenCL open source code

NASA Astrophysics Data System (ADS)

Liebling, Steven L.; Khanna, Gaurav

2017-10-01

We study the spherically symmetric collapse of a scalar field in anti-de Sitter spacetime using a newly constructed, open-source code which parallelizes over heterogeneous architectures using the open standard OpenCL. An open question for this scenario concerns how to tell, a priori, whether some form of initial data will be stable or will instead develop under the turbulent instability into a black hole in the limit of vanishing amplitude. Previous work suggested the existence of islands of stability around quasi-periodic solutions, and we use this new code to examine the stability properties of approximately quasi-periodic solutions which balance energy transfer to higher modes with energy transfer to lower modes. The evolutions provide some evidence, though not conclusively, for stability of initial data sufficiently close to quasiperiodic solutions.

Adopting Open Source Software to Address Software Risks during the Scientific Data Life Cycle

NASA Astrophysics Data System (ADS)

Vinay, S.; Downs, R. R.

2012-12-01

Software enables the creation, management, storage, distribution, discovery, and use of scientific data throughout the data lifecycle. However, the capabilities offered by software also present risks for the stewardship of scientific data, since future access to digital data is dependent on the use of software. From operating systems to applications for analyzing data, the dependence of data on software presents challenges for the stewardship of scientific data. Adopting open source software provides opportunities to address some of the proprietary risks of data dependence on software. For example, in some cases, open source software can be deployed to avoid licensing restrictions for using, modifying, and transferring proprietary software. The availability of the source code of open source software also enables the inclusion of modifications, which may be contributed by various community members who are addressing similar issues. Likewise, an active community that is maintaining open source software can be a valuable source of help, providing an opportunity to collaborate to address common issues facing adopters. As part of the effort to meet the challenges of software dependence for scientific data stewardship, risks from software dependence have been identified that exist during various times of the data lifecycle. The identification of these risks should enable the development of plans for mitigating software dependencies, where applicable, using open source software, and to improve understanding of software dependency risks for scientific data and how they can be reduced during the data life cycle.

Open-Source Programming for Automated Generation of Graphene Raman Spectral Maps

NASA Astrophysics Data System (ADS)

Vendola, P.; Blades, M.; Pierre, W.; Jedlicka, S.; Rotkin, S. V.

Raman microscopy is a useful tool for studying the structural characteristics of graphene deposited onto substrates. However, extracting useful information from the Raman spectra requires data processing and 2D map generation. An existing home-built confocal Raman microscope was optimized for graphene samples and programmed to automatically generate Raman spectral maps across a specified area. In particular, an open source data collection scheme was generated to allow the efficient collection and analysis of the Raman spectral data for future use. NSF ECCS-1509786.

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.

Disambiguate: An open-source application for disambiguating two species in next generation sequencing data from grafted samples.

PubMed

Ahdesmäki, Miika J; Gray, Simon R; Johnson, Justin H; Lai, Zhongwu

2016-01-01

Grafting of cell lines and primary tumours is a crucial step in the drug development process between cell line studies and clinical trials. Disambiguate is a program for computationally separating the sequencing reads of two species derived from grafted samples. Disambiguate operates on DNA or RNA-seq alignments to the two species and separates the components at very high sensitivity and specificity as illustrated in artificially mixed human-mouse samples. This allows for maximum recovery of data from target tumours for more accurate variant calling and gene expression quantification. Given that no general use open source algorithm accessible to the bioinformatics community exists for the purposes of separating the two species data, the proposed Disambiguate tool presents a novel approach and improvement to performing sequence analysis of grafted samples. Both Python and C++ implementations are available and they are integrated into several open and closed source pipelines. Disambiguate is open source and is freely available at https://github.com/AstraZeneca-NGS/disambiguate.

Combating Transnational Organized Crime: Strategies and Metrics for the Threat

DTIC Science & Technology

2012-05-01

TOC to facilitate weapons of mass destruction (WMD). 2. Use open source intelligence ( OSINT ) sources to develop profiles of individuals and...collection of information is estimated to average 1 hour per response, including the time for reviewing instructions, searching existing data sources ...Government. All information and sources for this paper were drawn from unclassified materials. Samuel Musa is a Senior Research Fellow at the Center

Oculomatic: High speed, reliable, and accurate open-source eye tracking for humans and non-human primates.

PubMed

Zimmermann, Jan; Vazquez, Yuriria; Glimcher, Paul W; Pesaran, Bijan; Louie, Kenway

2016-09-01

Video-based noninvasive eye trackers are an extremely useful tool for many areas of research. Many open-source eye trackers are available but current open-source systems are not designed to track eye movements with the temporal resolution required to investigate the mechanisms of oculomotor behavior. Commercial systems are available but employ closed source hardware and software and are relatively expensive, limiting wide-spread use. Here we present Oculomatic, an open-source software and modular hardware solution to eye tracking for use in humans and non-human primates. Oculomatic features high temporal resolution (up to 600Hz), real-time eye tracking with high spatial accuracy (<0.5°), and low system latency (∼1.8ms, 0.32ms STD) at a relatively low-cost. Oculomatic compares favorably to our existing scleral search-coil system while being fully non invasive. We propose that Oculomatic can support a wide range of research into the properties and neural mechanisms of oculomotor behavior. Copyright © 2016 Elsevier B.V. All rights reserved.

NOAA's Data Catalog and the Federal Open Data Policy

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

An open-source textbook for teaching climate-related risk analysis using the R computing environment

NASA Astrophysics Data System (ADS)

Applegate, P. J.; Keller, K.

2015-12-01

Greenhouse gas emissions lead to increased surface air temperatures and sea level rise. In turn, sea level rise increases the risks of flooding for people living near the world's coastlines. Our own research on assessing sea level rise-related risks emphasizes both Earth science and statistics. At the same time, the free, open-source computing environment R is growing in popularity among statisticians and scientists due to its flexibility and graphics capabilities, as well as its large library of existing functions. We have developed a set of laboratory exercises that introduce students to the Earth science and statistical concepts needed for assessing the risks presented by climate change, particularly sea-level rise. These exercises will be published as a free, open-source textbook on the Web. Each exercise begins with a description of the Earth science and/or statistical concepts that the exercise teaches, with references to key journal articles where appropriate. Next, students are asked to examine in detail a piece of existing R code, and the exercise text provides a clear explanation of how the code works. Finally, students are asked to modify the existing code to produce a well-defined outcome. We discuss our experiences in developing the exercises over two separate semesters at Penn State, plus using R Markdown to interweave explanatory text with sample code and figures in the textbook.

Close ISR Support: Re-organizing the Combined Forces Air Component Commander’s Intelligence, Surveillance and Reconnaissance Processes and Agencies

DTIC Science & Technology

2009-12-01

instruction, searching existing data sources , gathering and maintaining the data needed, and completing and reviewing the collection of information...146 1. Allocation vs. Apportionment .........................................................146 2. Collection Management Authority...290 D. MEASUREMENT AND SIGNATURE INTELLIGENCE .....................291 E. OPEN- SOURCE

Community-based Early Warning and Adaptive Response System (EWARS) for mosquito borne diseases: An open source/open community approach

NASA Astrophysics Data System (ADS)

Babu, A. N.; Soman, B.; Niehaus, E.; Shah, J.; Sarda, N. L.; Ramkumar, P. S.; Unnithan, C.

2014-11-01

A variety of studies around the world have evaluated the use of remote sensing with and without GIS in communicable diseases. The ongoing Ebola epidemic has highlighted the risks that can arise for the global community from rapidly spreading diseases which may outpace attempts at control and eradication. This paper presents an approach to the development, deployment, validation and wide-spread adoption of a GIS-based temporo-spatial decision support system which is being collaboratively developed in open source/open community mode by an international group that came together under UN auspices. The group believes in an open source/open community approach to make the fruits of knowledge as widely accessible as possible. A core initiative of the groups is the EWARS project. It proposes to strengthen existing public health systems by the development and validation a model for a community based surveillance and response system which will initially address mosquito borne diseases in the developing world. At present mathematical modeling to support EWARS is at an advanced state, and it planned to embark on a pilot project

Do Open Source LMSs Support Personalization? A Comparative Evaluation

NASA Astrophysics Data System (ADS)

Kerkiri, Tania; Paleologou, Angela-Maria

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

Learning Materials for Open Learning in Further Education. Coombe Lodge Working Paper. Information Bank Number 1606.

ERIC Educational Resources Information Center

Latcham, J.

Arguing that extensive efforts to produce open learning materials should not be undertaken until the possibility of using or adapting existing materials is considered, this paper identifies current sources of materials available in Great Britain for non-advanced further education. The first sections of the paper review common types of open…

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.

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

mdFoam+: Advanced molecular dynamics in OpenFOAM

NASA Astrophysics Data System (ADS)

Longshaw, S. M.; Borg, M. K.; Ramisetti, S. B.; Zhang, J.; Lockerby, D. A.; Emerson, D. R.; Reese, J. M.

2018-03-01

This paper introduces mdFoam+, which is an MPI parallelised molecular dynamics (MD) solver implemented entirely within the OpenFOAM software framework. It is open-source and released under the same GNU General Public License (GPL) as OpenFOAM. The source code is released as a publicly open software repository that includes detailed documentation and tutorial cases. Since mdFoam+ is designed entirely within the OpenFOAM C++ object-oriented framework, it inherits a number of key features. The code is designed for extensibility and flexibility, so it is aimed first and foremost as an MD research tool, in which new models and test cases can be developed and tested rapidly. Implementing mdFoam+ in OpenFOAM also enables easier development of hybrid methods that couple MD with continuum-based solvers. Setting up MD cases follows the standard OpenFOAM format, as mdFoam+ also relies upon the OpenFOAM dictionary-based directory structure. This ensures that useful pre- and post-processing capabilities provided by OpenFOAM remain available even though the fully Lagrangian nature of an MD simulation is not typical of most OpenFOAM applications. Results show that mdFoam+ compares well to another well-known MD code (e.g. LAMMPS) in terms of benchmark problems, although it also has additional functionality that does not exist in other open-source MD codes.

Turning a remotely controllable observatory into a fully autonomous system

NASA Astrophysics Data System (ADS)

Swindell, Scott; Johnson, Chris; Gabor, Paul; Zareba, Grzegorz; Kubánek, Petr; Prouza, Michael

2014-08-01

We describe a complex process needed to turn an existing, old, operational observatory - The Steward Observatory's 61" Kuiper Telescope - into a fully autonomous system, which observers without an observer. For this purpose, we employed RTS2,1 an open sourced, Linux based observatory control system, together with other open sourced programs and tools (GNU compilers, Python language for scripting, JQuery UI for Web user interface). This presentation provides a guide with time estimates needed for a newcomers to the field to handle such challenging tasks, as fully autonomous observatory operations.

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.

The effects of transistor source-to-gate bridging faults in complex CMOS gates

NASA Astrophysics Data System (ADS)

Visweswaran, G. S.; Ali, Akhtar-Uz-Zaman M.; Lala, Parag K.; Hartmann, Carlos R. P.

1991-06-01

A study of the effect of gate-to-source bridging faults in the pull-up section of a complex CMOS gate is presented. The manifestation of these faults depends on the resistance value of the connection causing the bridging. It is shown that such faults manifest themselves either as stuck-at or stuck-open faults and can be detected by tests for stuck-at and stuck-open faults generated for the equivalent logic current. It is observed that for transistor channel lengths larger than 1 microns there exists a range of values of the bridging resistance for which the fault behaves as a pseudo-stuck-open fault.

Databases and Networking for Development. The Organization of Information in Europe in the Field of Policy and Planning for Developing Countries.

ERIC Educational Resources Information Center

Lindsay, John

This work suggests that better organization of existing sources of information available in Europe and better application of these sources to training can result in improved understanding of how information systems work, and it provides an annotated list of some of these sources. The guide opens with an introduction to public policy and urban…

40 CFR 424.17 - Effluent limitations guidelines representing the degree of effluent reduction attainable by the...

Code of Federal Regulations, 2010 CFR

2010-07-01

... control technology. 424.17 Section 424.17 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS FERROALLOY MANUFACTURING POINT SOURCE CATEGORY Open Electric... control technology. Except as provided in §§ 125.30 through 125.32, any existing point source subject to...

40 CFR 424.17 - Effluent limitations guidelines representing the degree of effluent reduction attainable by the...

Code of Federal Regulations, 2013 CFR

2013-07-01

... control technology. 424.17 Section 424.17 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS FERROALLOY MANUFACTURING POINT SOURCE CATEGORY Open Electric... control technology. Except as provided in §§ 125.30 through 125.32, any existing point source subject to...

40 CFR 424.17 - Effluent limitations guidelines representing the degree of effluent reduction attainable by the...

Code of Federal Regulations, 2011 CFR

2011-07-01

... control technology. 424.17 Section 424.17 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS FERROALLOY MANUFACTURING POINT SOURCE CATEGORY Open Electric... control technology. Except as provided in §§ 125.30 through 125.32, any existing point source subject to...

40 CFR 424.17 - Effluent limitations guidelines representing the degree of effluent reduction attainable by the...

Code of Federal Regulations, 2012 CFR

2012-07-01

... control technology. 424.17 Section 424.17 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS FERROALLOY MANUFACTURING POINT SOURCE CATEGORY Open Electric... control technology. Except as provided in §§ 125.30 through 125.32, any existing point source subject to...

40 CFR 424.17 - Effluent limitations guidelines representing the degree of effluent reduction attainable by the...

Code of Federal Regulations, 2014 CFR

2014-07-01

... control technology. 424.17 Section 424.17 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS FERROALLOY MANUFACTURING POINT SOURCE CATEGORY Open Electric... control technology. Except as provided in §§ 125.30 through 125.32, any existing point source subject to...

Open-Source Integrated Design-Analysis Environment For Nuclear Energy Advanced Modeling & Simulation Final Scientific/Technical Report

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

O'Leary, Patrick

The framework created through the Open-Source Integrated Design-Analysis Environment (IDAE) for Nuclear Energy Advanced Modeling & Simulation grant has simplify and democratize advanced modeling and simulation in the nuclear energy industry that works on a range of nuclear engineering applications. It leverages millions of investment dollars from the Department of Energy's Office of Nuclear Energy for modeling and simulation of light water reactors and the Office of Nuclear Energy's research and development. The IDEA framework enhanced Kitware’s Computational Model Builder (CMB) while leveraging existing open-source toolkits and creating a graphical end-to-end umbrella guiding end-users and developers through the nuclear energymore » advanced modeling and simulation lifecycle. In addition, the work deliver strategic advancements in meshing and visualization for ensembles.« less

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.

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.

Autotune Calibrates Models to Building Use Data

ScienceCinema

None

2018-01-16

Models of existing buildings are currently unreliable unless calibrated manually by a skilled professional. Autotune, as the name implies, automates this process by calibrating the model of an existing building to measured data, and is now available as open source software. This enables private businesses to incorporate Autotune into their products so that their customers can more effectively estimate cost savings of reduced energy consumption measures in existing buildings.

a Framework for AN Open Source Geospatial Certification Model

NASA Astrophysics Data System (ADS)

Khan, T. U. R.; Davis, P.; Behr, F.-J.

2016-06-01

The geospatial industry is forecasted to have an enormous growth in the forthcoming years and an extended need for well-educated workforce. Hence ongoing education and training play an important role in the professional life. Parallel, in the geospatial and IT arena as well in the political discussion and legislation Open Source solutions, open data proliferation, and the use of open standards have an increasing significance. Based on the Memorandum of Understanding between International Cartographic Association, OSGeo Foundation, and ISPRS this development led to the implementation of the ICA-OSGeo-Lab imitative with its mission "Making geospatial education and opportunities accessible to all". Discussions in this initiative and the growth and maturity of geospatial Open Source software initiated the idea to develop a framework for a worldwide applicable Open Source certification approach. Generic and geospatial certification approaches are already offered by numerous organisations, i.e., GIS Certification Institute, GeoAcademy, ASPRS, and software vendors, i. e., Esri, Oracle, and RedHat. They focus different fields of expertise and have different levels and ways of examination which are offered for a wide range of fees. The development of the certification framework presented here is based on the analysis of diverse bodies of knowledge concepts, i.e., NCGIA Core Curriculum, URISA Body Of Knowledge, USGIF Essential Body Of Knowledge, the "Geographic Information: Need to Know", currently under development, and the Geospatial Technology Competency Model (GTCM). The latter provides a US American oriented list of the knowledge, skills, and abilities required of workers in the geospatial technology industry and influenced essentially the framework of certification. In addition to the theoretical analysis of existing resources the geospatial community was integrated twofold. An online survey about the relevance of Open Source was performed and evaluated with 105 respondents worldwide. 15 interviews (face-to-face or by telephone) with experts in different countries provided additional insights into Open Source usage and certification. The findings led to the development of a certification framework of three main categories with in total eleven sub-categories, i.e., "Certified Open Source Geospatial Data Associate / Professional", "Certified Open Source Geospatial Analyst Remote Sensing & GIS", "Certified Open Source Geospatial Cartographer", "Certified Open Source Geospatial Expert", "Certified Open Source Geospatial Associate Developer / Professional Developer", "Certified Open Source Geospatial Architect". Each certification is described by pre-conditions, scope and objectives, course content, recommended software packages, target group, expected benefits, and the methods of examination. Examinations can be flanked by proofs of professional career paths and achievements which need a peer qualification evaluation. After a couple of years a recertification is required. The concept seeks the accreditation by the OSGeo Foundation (and other bodies) and international support by a group of geospatial scientific institutions to achieve wide and international acceptance for this Open Source geospatial certification model. A business case for Open Source certification and a corresponding SWOT model is examined to support the goals of the Geo-For-All initiative of the ICA-OSGeo pact.

Loop-Mediated Isothermal Amplification (LAMP) Signature Identification Software

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

Torres, C.

2009-03-17

This is an extendable open-source Loop-mediated isothermal AMPlification (LAMP) signature design program called LAVA (LAMP Assay Versatile Analysis). LAVA was created in response to limitations of existing LAMP signature programs.

eMZed: an open source framework in Python for rapid and interactive development of LC/MS data analysis workflows.

PubMed

Kiefer, Patrick; Schmitt, Uwe; Vorholt, Julia A

2013-04-01

The Python-based, open-source eMZed framework was developed for mass spectrometry (MS) users to create tailored workflows for liquid chromatography (LC)/MS data analysis. The goal was to establish a unique framework with comprehensive basic functionalities that are easy to apply and allow for the extension and modification of the framework in a straightforward manner. eMZed supports the iterative development and prototyping of individual evaluation strategies by providing a computing environment and tools for inspecting and modifying underlying LC/MS data. The framework specifically addresses non-expert programmers, as it requires only basic knowledge of Python and relies largely on existing successful open-source software, e.g. OpenMS. The framework eMZed and its documentation are freely available at http://emzed.biol.ethz.ch/. eMZed is published under the GPL 3.0 license, and an online discussion group is available at https://groups.google.com/group/emzed-users. Supplementary data are available at Bioinformatics online.

Grade 1 to 6 Thai students' existing ideas about light: Across-age study

NASA Astrophysics Data System (ADS)

Horasirt, Yupaporn; Yuenyong, Chokchai

2018-01-01

This paper aimed to investigate Grade 1 to 6 Thai (6 - 12 years old) students' existing ideas about light, sight, vision, source of light. The participants included 36 Grade 1 to 6 students (6 students in each Grade) who studying at a primary school in Khon Kaen. The method of this study is a descriptive qualitative research design. The tools included the two-tiered test about light and open-ended question. Students' responses were categorized the students' existing ideas about light. Findings indicated that young students held various existing ideas about light that could be categorized into 6 different groups relating to sight, vision, and source of light. The paper discussed these students' existing ideas for developing constructivist learning about light in Thailand context.

Mobile Care (Moca) for Remote Diagnosis and Screening

PubMed Central

Celi, Leo Anthony; Sarmenta, Luis; Rotberg, Jhonathan; Marcelo, Alvin; Clifford, Gari

2010-01-01

Moca is a cell phone-facilitated clinical information system to improve diagnostic, screening and therapeutic capabilities in remote resource-poor settings. The software allows transmission of any medical file, whether a photo, x-ray, audio or video file, through a cell phone to (1) a central server for archiving and incorporation into an electronic medical record (to facilitate longitudinal care, quality control, and data mining), and (2) a remote specialist for real-time decision support (to leverage expertise). The open source software is designed as an end-to-end clinical information system that seamlessly connects health care workers to medical professionals. It is integrated with OpenMRS, an existing open source medical records system commonly used in developing countries. PMID:21822397

"Do-It-Yourself" reliable pH-stat device by using open-source software, inexpensive hardware and available laboratory equipment

PubMed Central

Kragic, Rastislav; Kostic, Mirjana

2018-01-01

In this paper, we present the construction of a reliable and inexpensive pH stat device, by using open-source “OpenPhControl” software, inexpensive hardware (a peristaltic and a syringe pump, Arduino, a step motor…), readily available laboratory devices: a pH meter, a computer, a webcam, and some 3D printed parts. We provide a methodology for the design, development and test results of each part of the device, as well as of the entire system. In addition to dosing reagents by means of a low-cost peristaltic pump, we also present carefully controlled dosing of reagents by an open-source syringe pump. The upgrading of the basic open-source syringe pump is given in terms of pump control and application of a larger syringe. In addition to the basic functions of pH stat, i.e. pH value measurement and maintenance, an improvement allowing the device to be used for potentiometric titration has been made as well. We have demonstrated the device’s utility when applied for cellulose fibers oxidation with 2,2,6,6-tetramethylpiperidine-1-oxyl radical, i.e. for TEMPO-mediated oxidation. In support of this, we present the results obtained for the oxidation kinetics, the consumption of added reagent and experimental repeatability. Considering that the open-source scientific tools are available to everyone, and that researchers can construct and adjust the device according to their needs, as well as, that the total cost of the open-source pH stat device, excluding the existing laboratory equipment (pH meter, computer and glossary) was less than 150 EUR, we believe that, at a small fraction of the cost of available commercial offers, our open-source pH stat can significantly improve experimental work where the use of pH stat is necessary. PMID:29509793

Free and Open Source Software for Geospatial in the field of planetary science

NASA Astrophysics Data System (ADS)

Frigeri, A.

2012-12-01

Information technology applied to geospatial analyses has spread quickly in the last ten years. The availability of OpenData and data from collaborative mapping projects increased the interest on tools, procedures and methods to handle spatially-related information. Free Open Source Software projects devoted to geospatial data handling are gaining a good success as the use of interoperable formats and protocols allow the user to choose what pipeline of tools and libraries is needed to solve a particular task, adapting the software scene to his specific problem. In particular, the Free Open Source model of development mimics the scientific method very well, and researchers should be naturally encouraged to take part to the development process of these software projects, as this represent a very agile way to interact among several institutions. When it comes to planetary sciences, geospatial Free Open Source Software is gaining a key role in projects that commonly involve different subjects in an international scenario. Very popular software suites for processing scientific mission data (for example, ISIS) and for navigation/planning (SPICE) are being distributed along with the source code and the interaction between user and developer is often very strict, creating a continuum between these two figures. A very widely spread library for handling geospatial data (GDAL) has started to support planetary data from the Planetary Data System, and recent contributions enabled the support to other popular data formats used in planetary science, as the Vicar one. The use of Geographic Information System in planetary science is now diffused, and Free Open Source GIS, open GIS formats and network protocols allow to extend existing tools and methods developed to solve Earth based problems, also to the case of the study of solar system bodies. A day in the working life of a researcher using Free Open Source Software for geospatial will be presented, as well as benefits and solutions to possible detriments coming from the effort required by using, supporting and contributing.

"Do-It-Yourself" reliable pH-stat device by using open-source software, inexpensive hardware and available laboratory equipment.

PubMed

Milanovic, Jovana Z; Milanovic, Predrag; Kragic, Rastislav; Kostic, Mirjana

2018-01-01

In this paper, we present the construction of a reliable and inexpensive pH stat device, by using open-source "OpenPhControl" software, inexpensive hardware (a peristaltic and a syringe pump, Arduino, a step motor…), readily available laboratory devices: a pH meter, a computer, a webcam, and some 3D printed parts. We provide a methodology for the design, development and test results of each part of the device, as well as of the entire system. In addition to dosing reagents by means of a low-cost peristaltic pump, we also present carefully controlled dosing of reagents by an open-source syringe pump. The upgrading of the basic open-source syringe pump is given in terms of pump control and application of a larger syringe. In addition to the basic functions of pH stat, i.e. pH value measurement and maintenance, an improvement allowing the device to be used for potentiometric titration has been made as well. We have demonstrated the device's utility when applied for cellulose fibers oxidation with 2,2,6,6-tetramethylpiperidine-1-oxyl radical, i.e. for TEMPO-mediated oxidation. In support of this, we present the results obtained for the oxidation kinetics, the consumption of added reagent and experimental repeatability. Considering that the open-source scientific tools are available to everyone, and that researchers can construct and adjust the device according to their needs, as well as, that the total cost of the open-source pH stat device, excluding the existing laboratory equipment (pH meter, computer and glossary) was less than 150 EUR, we believe that, at a small fraction of the cost of available commercial offers, our open-source pH stat can significantly improve experimental work where the use of pH stat is necessary.

40 CFR 52.1420 - Identification of Plan.

Code of Federal Regulations, 2011 CFR

2011-07-01

... (913) 551-7659; for material from a docket in EPA Headquarters Library, please call the Office of Air... Standards for Existing Stationary Sources 9/7/97 1/20/00, 65 FR 3130 129-30 Open Fires, Prohibited...

Multinational Experiment 7. Outcome 3 - Cyber Domain Objective 3.3. Guidelines for Decision Makers Version 2.0

DTIC Science & Technology

2012-10-03

depending on whether it is intrusive or not, may be regarded as either perfectly legitimate and lawful Open Source Intelligence ( OSINT ), or as...response, including the time for reviewing instructions, searching existing data sources , gathering and maintaining the data needed, and completing and...Context 2. Actor 3. Assessment of Activities 4. Source 5. Target/Objectives 6. Consequences 7. Extent 8. Breach of an International

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.

Sharing Lessons-Learned on Effective Open Data, Open-Source Practices from OpenAQ, a Global Open Air Quality Community.

NASA Astrophysics Data System (ADS)

Hasenkopf, C. A.

2017-12-01

Increasingly, open data, open-source projects are unearthing rich datasets and tools, previously impossible for more traditional avenues to generate. These projects are possible, in part, because of the emergence of online collaborative and code-sharing tools, decreasing costs of cloud-based services to fetch, store, and serve data, and increasing interest of individuals to contribute their time and skills to 'open projects.' While such projects have generated palpable enthusiasm from many sectors, many of these projects face uncharted paths for sustainability, visibility, and acceptance. Our project, OpenAQ, is an example of an open-source, open data community that is currently forging its own uncharted path. OpenAQ is an open air quality data platform that aggregates and universally formats government and research-grade air quality data from 50 countries across the world. To date, we make available more than 76 million air quality (PM2.5, PM10, SO2, NO2, O3, CO and black carbon) data points through an open Application Programming Interface (API) and a user-customizable download interface at https://openaq.org. The goal of the platform is to enable an ecosystem of users to advance air pollution efforts from science to policy to the private sector. The platform is also an open-source project (https://github.com/openaq) and has only been made possible through the coding and data contributions of individuals around the world. In our first two years of existence, we have seen requests for data to our API skyrocket to more than 6 million datapoints per month, and use-cases as varied as ingesting data aggregated from our system into real-time models of wildfires to building open-source statistical packages (e.g. ropenaq and py-openaq) on top of the platform to creating public-friendly apps and chatbots. We will share a whirl-wind trip through our evolution and the many lessons learned so far related to platform structure, community engagement, organizational model type and sustainability.

Dynamic robustness of knowledge collaboration network of open source product development community

NASA Astrophysics Data System (ADS)

Zhou, Hong-Li; Zhang, Xiao-Dong

2018-01-01

As an emergent innovative design style, open source product development communities are characterized by a self-organizing, mass collaborative, networked structure. The robustness of the community is critical to its performance. Using the complex network modeling method, the knowledge collaboration network of the community is formulated, and the robustness of the network is systematically and dynamically studied. The characteristics of the network along the development period determine that its robustness should be studied from three time stages: the start-up, development and mature stages of the network. Five kinds of user-loss pattern are designed, to assess the network's robustness under different situations in each of these three time stages. Two indexes - the largest connected component and the network efficiency - are used to evaluate the robustness of the community. The proposed approach is applied in an existing open source car design community. The results indicate that the knowledge collaboration networks show different levels of robustness in different stages and different user loss patterns. Such analysis can be applied to provide protection strategies for the key users involved in knowledge dissemination and knowledge contribution at different stages of the network, thereby promoting the sustainable and stable development of the open source community.

U.S. Tsunami Information technology (TIM) Modernization:Developing a Maintainable and Extensible Open Source Earthquake and Tsunami Warning System

NASA Astrophysics Data System (ADS)

Hellman, S. B.; Lisowski, S.; Baker, B.; Hagerty, M.; Lomax, A.; Leifer, J. M.; Thies, D. A.; Schnackenberg, A.; Barrows, J.

2015-12-01

Tsunami Information technology Modernization (TIM) is a National Oceanic and Atmospheric Administration (NOAA) project to update and standardize the earthquake and tsunami monitoring systems currently employed at the U.S. Tsunami Warning Centers in Ewa Beach, Hawaii (PTWC) and Palmer, Alaska (NTWC). While this project was funded by NOAA to solve a specific problem, the requirements that the delivered system be both open source and easily maintainable have resulted in the creation of a variety of open source (OS) software packages. The open source software is now complete and this is a presentation of the OS Software that has been funded by NOAA for benefit of the entire seismic community. The design architecture comprises three distinct components: (1) The user interface, (2) The real-time data acquisition and processing system and (3) The scientific algorithm library. The system follows a modular design with loose coupling between components. We now identify the major project constituents. The user interface, CAVE, is written in Java and is compatible with the existing National Weather Service (NWS) open source graphical system AWIPS. The selected real-time seismic acquisition and processing system is open source SeisComp3 (sc3). The seismic library (libseismic) contains numerous custom written and wrapped open source seismic algorithms (e.g., ML/mb/Ms/Mwp, mantle magnitude (Mm), w-phase moment tensor, bodywave moment tensor, finite-fault inversion, array processing). The seismic library is organized in a way (function naming and usage) that will be familiar to users of Matlab. The seismic library extends sc3 so that it can be called by the real-time system, but it can also be driven and tested outside of sc3, for example, by ObsPy or Earthworm. To unify the three principal components we have developed a flexible and lightweight communication layer called SeismoEdex.

pyLIMA : an open source microlensing software

NASA Astrophysics Data System (ADS)

Bachelet, Etienne

2017-01-01

Planetary microlensing is a unique tool to detect cold planets around low-mass stars which is approaching a watershed in discoveries as near-future missions incorporate dedicated surveys. NASA and ESA have decided to complement WFIRST-AFTA and Euclid with microlensing programs to enrich our statistics about this planetary population. Of the nany challenges in- herent in these missions, the data analysis is of primary importance, yet is often perceived as time consuming, complex and daunting barrier to participation in the field. We present the first open source modeling software to conduct a microlensing analysis. This software is written in Python and use as much as possible existing packages.

The Psychology Experiment Building Language (PEBL) and PEBL Test Battery

PubMed Central

Mueller, Shane T.; Piper, Brian J.

2014-01-01

Background We briefly describe the Psychology Experiment Building Language (PEBL), an open source software system for designing and running psychological experiments. New Method We describe the PEBL test battery, a set of approximately 70 behavioral tests which can be freely used, shared, and modified. Included is a comprehensive set of past research upon which tests in the battery are based. Results We report the results of benchmark tests that establish the timing precision of PEBL. Comparison with Existing Method We consider alternatives to the PEBL system and battery tests. Conclusions We conclude with a discussion of the ethical factors involved in the open source testing movement. PMID:24269254

Modeling Group Interactions via Open Data Sources

DTIC Science & Technology

2011-08-30

data. The state-of-art search engines are designed to help general query-specific search and not suitable for finding disconnected online groups. The...groups, (2) developing innovative mathematical and statistical models and efficient algorithms that leverage existing search engines and employ

Low-energy neutrinos

NASA Astrophysics Data System (ADS)

Ludhova, Livia

2016-05-01

There exist several kinds of sources emitting neutrinos in the MeV energy range. These low-energy neutrinos from different sources can be often detected by the same multipurpose detectors. The status-of-art of the field of solar neutrinos, geoneutrinos, and the search for sterile neutrino with artificial neutrino sources is provided here; other neutrino sources, as for example reactor or high-energy neutrinos, are described elsewhere. For each of these three fields, the present-day motivation and open questions, as well as the latest experimental results and future perspectives are discussed.

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

Design Science Methodology Applied to a Chemical Surveillance Tool

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

Huang, Zhuanyi; Han, Kyungsik; Charles-Smith, Lauren E.

Public health surveillance systems gain significant benefits from integrating existing early incident detection systems,supported by closed data sources, with open source data.However, identifying potential alerting incidents relies on finding accurate, reliable sources and presenting the high volume of data in a way that increases analysts work efficiency; a challenge for any system that leverages open source data. In this paper, we present the design concept and the applied design science research methodology of ChemVeillance, a chemical analyst surveillance system.Our work portrays a system design and approach that translates theoretical methodology into practice creating a powerful surveillance system built for specificmore » use cases.Researchers, designers, developers, and related professionals in the health surveillance community can build upon the principles and methodology described here to enhance and broaden current surveillance systems leading to improved situational awareness based on a robust integrated early warning system.« less

WriteSim TCExam - An open source text simulation environment for training novice researchers in scientific writing

PubMed Central

2010-01-01

Background The ability to write clearly and effectively is of central importance to the scientific enterprise. Encouraged by the success of simulation environments in other biomedical sciences, we developed WriteSim TCExam, an open-source, Web-based, textual simulation environment for teaching effective writing techniques to novice researchers. We shortlisted and modified an existing open source application - TCExam to serve as a textual simulation environment. After testing usability internally in our team, we conducted formal field usability studies with novice researchers. These were followed by formal surveys with researchers fitting the role of administrators and users (novice researchers) Results The development process was guided by feedback from usability tests within our research team. Online surveys and formal studies, involving members of the Research on Research group and selected novice researchers, show that the application is user-friendly. Additionally it has been used to train 25 novice researchers in scientific writing to date and has generated encouraging results. Conclusion WriteSim TCExam is the first Web-based, open-source textual simulation environment designed to complement traditional scientific writing instruction. While initial reviews by students and educators have been positive, a formal study is needed to measure its benefits in comparison to standard instructional methods. PMID:20509946

PMIX_Ring patch for SLURM

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

Moody, A. T.

2014-04-20

This code adds an implementation of PMIX_Ring to the existing PM12 Library in the SLURM open source software package (Simple Linux Utility for Resource Management). PMIX_Ring executes a particular communication pattern that is used to bootstrap connections between MPI processes in a parallel job.

SNPversity: A web-based tool for visualizing diversity

USDA-ARS?s Scientific Manuscript database

Background: Many stand-alone desktop software suites exist to visualize single nucleotide polymorphisms (SNP) diversity, but web-based software that can be easily implemented and used for biological databases is absent. SNPversity was created to answer this need by building an open-source visualizat...

Questions and Answers Regarding the 1997 State Plan Requirements for Hospital, Medical, and Infectious Waste Incinerators (HMIWI)

EPA Pesticide Factsheets

This November 1997 document contains questions and answers on the state plan requirements for HMIWI regulations. The questions cover topics such as re-opening existing sources, timelines for submission, consequences for failure to submit, and more.

PAPARA(ZZ)I: An open-source software interface for annotating photographs of the deep-sea

NASA Astrophysics Data System (ADS)

Marcon, Yann; Purser, Autun

PAPARA(ZZ)I is a lightweight and intuitive image annotation program developed for the study of benthic megafauna. It offers functionalities such as free, grid and random point annotation. Annotations may be made following existing classification schemes for marine biota and substrata or with the use of user defined, customised lists of keywords, which broadens the range of potential application of the software to other types of studies (e.g. marine litter distribution assessment). If Internet access is available, PAPARA(ZZ)I can also query and use standardised taxa names directly from the World Register of Marine Species (WoRMS). Program outputs include abundances, densities and size calculations per keyword (e.g. per taxon). These results are written into text files that can be imported into spreadsheet programs for further analyses. PAPARA(ZZ)I is open-source and is available at http://papara-zz-i.github.io. Compiled versions exist for most 64-bit operating systems: Windows, Mac OS X and Linux.

Anser EMT: the first open-source electromagnetic tracking platform for image-guided interventions.

PubMed

Jaeger, Herman Alexander; Franz, Alfred Michael; O'Donoghue, Kilian; Seitel, Alexander; Trauzettel, Fabian; Maier-Hein, Lena; Cantillon-Murphy, Pádraig

2017-06-01

Electromagnetic tracking is the gold standard for instrument tracking and navigation in the clinical setting without line of sight. Whilst clinical platforms exist for interventional bronchoscopy and neurosurgical navigation, the limited flexibility and high costs of electromagnetic tracking (EMT) systems for research investigations mitigate against a better understanding of the technology's characterisation and limitations. The Anser project provides an open-source implementation for EMT with particular application to image-guided interventions. This work provides implementation schematics for our previously reported EMT system which relies on low-cost acquisition and demodulation techniques using both National Instruments and Arduino hardware alongside MATLAB support code. The system performance is objectively compared to other commercial tracking platforms using the Hummel assessment protocol. Positional accuracy of 1.14 mm and angular rotation accuracy of [Formula: see text] are reported. Like other EMT platforms, Anser is susceptible to tracking errors due to eddy current and ferromagnetic distortion. The system is compatible with commercially available EMT sensors as well as the Open Network Interface for image-guided therapy (OpenIGTLink) for easy communication with visualisation and medical imaging toolkits such as MITK and 3D Slicer. By providing an open-source platform for research investigations, we believe that novel and collaborative approaches can overcome the limitations of current EMT technology.

SediFoam: A general-purpose, open-source CFD-DEM solver for particle-laden flow with emphasis on sediment transport

NASA Astrophysics Data System (ADS)

Sun, Rui; Xiao, Heng

2016-04-01

With the growth of available computational resource, CFD-DEM (computational fluid dynamics-discrete element method) becomes an increasingly promising and feasible approach for the study of sediment transport. Several existing CFD-DEM solvers are applied in chemical engineering and mining industry. However, a robust CFD-DEM solver for the simulation of sediment transport is still desirable. In this work, the development of a three-dimensional, massively parallel, and open-source CFD-DEM solver SediFoam is detailed. This solver is built based on open-source solvers OpenFOAM and LAMMPS. OpenFOAM is a CFD toolbox that can perform three-dimensional fluid flow simulations on unstructured meshes; LAMMPS is a massively parallel DEM solver for molecular dynamics. Several validation tests of SediFoam are performed using cases of a wide range of complexities. The results obtained in the present simulations are consistent with those in the literature, which demonstrates the capability of SediFoam for sediment transport applications. In addition to the validation test, the parallel efficiency of SediFoam is studied to test the performance of the code for large-scale and complex simulations. The parallel efficiency tests show that the scalability of SediFoam is satisfactory in the simulations using up to O(107) particles.

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.

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.

Support of Multidimensional Parallelism in the OpenMP Programming Model

NASA Technical Reports Server (NTRS)

Jin, Hao-Qiang; Jost, Gabriele

2003-01-01

OpenMP is the current standard for shared-memory programming. While providing ease of parallel programming, the OpenMP programming model also has limitations which often effect the scalability of applications. Examples for these limitations are work distribution and point-to-point synchronization among threads. We propose extensions to the OpenMP programming model which allow the user to easily distribute the work in multiple dimensions and synchronize the workflow among the threads. The proposed extensions include four new constructs and the associated runtime library. They do not require changes to the source code and can be implemented based on the existing OpenMP standard. We illustrate the concept in a prototype translator and test with benchmark codes and a cloud modeling code.

A New Architecture for Visualization: Open Mission Control Technologies

NASA Technical Reports Server (NTRS)

Trimble, Jay

2017-01-01

Open Mission Control Technologies (MCT) is a new architecture for visualisation of mission data. Driven by requirements for new mission capabilities, including distributed mission operations, access to data anywhere, customization by users, synthesis of multiple data sources, and flexibility for multi-mission adaptation, Open MCT provides users with an integrated customizable environment. Developed at NASAs Ames Research Center (ARC), in collaboration with NASAs Advanced Multimission Operations System (AMMOS) and NASAs Jet Propulsion Laboratory (JPL), Open MCT is getting its first mission use on the Jason 3 Mission, and is also available in the testbed for the Mars 2020 Rover and for development use for NASAs Resource Prospector Lunar Rover. The open source nature of the project provides for use outside of space missions, including open source contributions from a community of users. The defining features of Open MCT for mission users are data integration, end user composition and multiple views. Data integration provides access to mission data across domains in one place, making data such as activities, timelines, telemetry, imagery, event timers and procedures available in one place, without application switching. End user composition provides users with layouts, which act as a canvas to assemble visualisations. Multiple views provide the capability to view the same data in different ways, with live switching of data views in place. Open MCT is browser based, and works on the desktop as well as tablets and phones, providing access to data anywhere. An early use case for mobile data access took place on the Resource Prospector (RP) Mission Distributed Operations Test, in which rover engineers in the field were able to view telemetry on their phones. We envision this capability providing decision support to on console operators from off duty personnel. The plug-in architecture also allows for adaptation for different mission capabilities. Different data types and capabilities may be added or removed using plugins. An API provides a means to write new capabilities and to create data adaptors. Data plugins exist for mission data sources for NASA missions. Adaptors have been written by international and commercial users. Open MCT is open source. Open source enables collaborative development across organizations and also makes the product available outside of the space community, providing a potential source of usage and ideas to drive product design and development. The combination of open source with an Apache 2 license, and distribution on GitHub, has enabled an active community of users and contributors. The spectrum of users for Open MCT is, to our knowledge, unprecedented for mission software. In addition to our NASA users, we have, through open source, had users and inquires on projects ranging from Internet of Things, to radio hobbyists, to farming projects. We have an active community of contributors, enabling a flow of ideas inside and outside of the space community.

Elastic Cloud Computing Infrastructures in the Open Cirrus Testbed Implemented via Eucalyptus

NASA Astrophysics Data System (ADS)

Baun, Christian; Kunze, Marcel

Cloud computing realizes the advantages and overcomes some restrictionsof the grid computing paradigm. Elastic infrastructures can easily be createdand managed by cloud users. In order to accelerate the research ondata center management and cloud services the OpenCirrusTM researchtestbed has been started by HP, Intel and Yahoo!. Although commercialcloud offerings are proprietary, Open Source solutions exist in the field ofIaaS with Eucalyptus, PaaS with AppScale and at the applications layerwith Hadoop MapReduce. This paper examines the I/O performance ofcloud computing infrastructures implemented with Eucalyptus in contrastto Amazon S3.

Brokered virtual hubs for facilitating access and use of geospatial Open Data

NASA Astrophysics Data System (ADS)

Mazzetti, Paolo; Latre, Miguel; Kamali, Nargess; Brumana, Raffaella; Braumann, Stefan; Nativi, Stefano

2016-04-01

Open Data is a major trend in current information technology scenario and it is often publicised as one of the pillars of the information society in the near future. In particular, geospatial Open Data have a huge potential also for Earth Sciences, through the enablement of innovative applications and services integrating heterogeneous information. However, open does not mean usable. As it was recognized at the very beginning of the Web revolution, many different degrees of openness exist: from simple sharing in a proprietary format to advanced sharing in standard formats and including semantic information. Therefore, to fully unleash the potential of geospatial Open Data, advanced infrastructures are needed to increase the data openness degree, enhancing their usability. In October 2014, the ENERGIC OD (European NEtwork for Redistributing Geospatial Information to user Communities - Open Data) project, funded by the European Union under the Competitiveness and Innovation framework Programme (CIP), has started. In response to the EU call, the general objective of the project is to "facilitate the use of open (freely available) geographic data from different sources for the creation of innovative applications and services through the creation of Virtual Hubs". The ENERGIC OD Virtual Hubs aim to facilitate the use of geospatial Open Data by lowering and possibly removing the main barriers which hampers geo-information (GI) usage by end-users and application developers. Data and services heterogeneity is recognized as one of the major barriers to Open Data (re-)use. It imposes end-users and developers to spend a lot of effort in accessing different infrastructures and harmonizing datasets. Such heterogeneity cannot be completely removed through the adoption of standard specifications for service interfaces, metadata and data models, since different infrastructures adopt different standards to answer to specific challenges and to address specific use-cases. Thus, beyond a certain extent, heterogeneity is irreducible especially in interdisciplinary contexts. ENERGIC OD Virtual Hubs address heterogeneity adopting a mediation and brokering approach: specific components (brokers) are dedicated to harmonize service interfaces, metadata and data models, enabling seamless discovery and access to heterogeneous infrastructures and datasets. As an innovation project, ENERGIC OD integrates several existing technologies to implement Virtual Hubs as single points of access to geospatial datasets provided by new or existing platforms and infrastructures, including INSPIRE-compliant systems and Copernicus services. A first version of the ENERGIC OD brokers has been implemented based on the GI-Suite Brokering Framework developed by CNR-IIA, and complemented with other tools under integration and development. It already enables mediated discovery and harmonized access to different geospatial Open Data sources. It is accessible by users as Software-as-a-Service through a browser. Moreover, open APIs and a Javascript library are available for application developers. Six ENERGIC OD Virtual Hubs have been currently deployed: one at regional level (Berlin metropolitan area) and five at national-level (in France, Germany, Italy, Poland and Spain). Each Virtual Hub manager decided the deployment strategy (local infrastructure or commercial Infrastructure-as-a-Service cloud), and the list of connected Open Data sources. The ENERGIC OD Virtual Hubs are under test and validation through the development of ten different mobile and Web applications.

IQM: An Extensible and Portable Open Source Application for Image and Signal Analysis in Java

PubMed Central

Kainz, Philipp; Mayrhofer-Reinhartshuber, Michael; Ahammer, Helmut

2015-01-01

Image and signal analysis applications are substantial in scientific research. Both open source and commercial packages provide a wide range of functions for image and signal analysis, which are sometimes supported very well by the communities in the corresponding fields. Commercial software packages have the major drawback of being expensive and having undisclosed source code, which hampers extending the functionality if there is no plugin interface or similar option available. However, both variants cannot cover all possible use cases and sometimes custom developments are unavoidable, requiring open source applications. In this paper we describe IQM, a completely free, portable and open source (GNU GPLv3) image and signal analysis application written in pure Java. IQM does not depend on any natively installed libraries and is therefore runnable out-of-the-box. Currently, a continuously growing repertoire of 50 image and 16 signal analysis algorithms is provided. The modular functional architecture based on the three-tier model is described along the most important functionality. Extensibility is achieved using operator plugins, and the development of more complex workflows is provided by a Groovy script interface to the JVM. We demonstrate IQM’s image and signal processing capabilities in a proof-of-principle analysis and provide example implementations to illustrate the plugin framework and the scripting interface. IQM integrates with the popular ImageJ image processing software and is aiming at complementing functionality rather than competing with existing open source software. Machine learning can be integrated into more complex algorithms via the WEKA software package as well, enabling the development of transparent and robust methods for image and signal analysis. PMID:25612319

IQM: an extensible and portable open source application for image and signal analysis in Java.

PubMed

Kainz, Philipp; Mayrhofer-Reinhartshuber, Michael; Ahammer, Helmut

2015-01-01

Image and signal analysis applications are substantial in scientific research. Both open source and commercial packages provide a wide range of functions for image and signal analysis, which are sometimes supported very well by the communities in the corresponding fields. Commercial software packages have the major drawback of being expensive and having undisclosed source code, which hampers extending the functionality if there is no plugin interface or similar option available. However, both variants cannot cover all possible use cases and sometimes custom developments are unavoidable, requiring open source applications. In this paper we describe IQM, a completely free, portable and open source (GNU GPLv3) image and signal analysis application written in pure Java. IQM does not depend on any natively installed libraries and is therefore runnable out-of-the-box. Currently, a continuously growing repertoire of 50 image and 16 signal analysis algorithms is provided. The modular functional architecture based on the three-tier model is described along the most important functionality. Extensibility is achieved using operator plugins, and the development of more complex workflows is provided by a Groovy script interface to the JVM. We demonstrate IQM's image and signal processing capabilities in a proof-of-principle analysis and provide example implementations to illustrate the plugin framework and the scripting interface. IQM integrates with the popular ImageJ image processing software and is aiming at complementing functionality rather than competing with existing open source software. Machine learning can be integrated into more complex algorithms via the WEKA software package as well, enabling the development of transparent and robust methods for image and signal analysis.

HSE12 implementation in libxc

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

Moussa, Jonathan E.

2013-05-13

This piece of software is a new feature implemented inside an existing open-source library. Specifically, it is a new implementation of a density functional (HSE, short for Heyd-Scuseria-Ernzerhof) for a repository of density functionals, the libxc library. It fixes some numerical problems with existing implementations, as outlined in a scientific paper recently submitted for publication. Density functionals are components of electronic structure simulations, which model properties of electrons inside molecules and crystals.

Mayo clinical Text Analysis and Knowledge Extraction System (cTAKES): architecture, component evaluation and applications

PubMed Central

Masanz, James J; Ogren, Philip V; Zheng, Jiaping; Sohn, Sunghwan; Kipper-Schuler, Karin C; Chute, Christopher G

2010-01-01

We aim to build and evaluate an open-source natural language processing system for information extraction from electronic medical record clinical free-text. We describe and evaluate our system, the clinical Text Analysis and Knowledge Extraction System (cTAKES), released open-source at http://www.ohnlp.org. The cTAKES builds on existing open-source technologies—the Unstructured Information Management Architecture framework and OpenNLP natural language processing toolkit. Its components, specifically trained for the clinical domain, create rich linguistic and semantic annotations. Performance of individual components: sentence boundary detector accuracy=0.949; tokenizer accuracy=0.949; part-of-speech tagger accuracy=0.936; shallow parser F-score=0.924; named entity recognizer and system-level evaluation F-score=0.715 for exact and 0.824 for overlapping spans, and accuracy for concept mapping, negation, and status attributes for exact and overlapping spans of 0.957, 0.943, 0.859, and 0.580, 0.939, and 0.839, respectively. Overall performance is discussed against five applications. The cTAKES annotations are the foundation for methods and modules for higher-level semantic processing of clinical free-text. PMID:20819853

Flutrack.org: Open-source and linked data for epidemiology.

PubMed

Chorianopoulos, Konstantinos; Talvis, Karolos

2016-12-01

Epidemiology has made advances, thanks to the availability of real-time surveillance data and by leveraging the geographic analysis of incidents. There are many health information systems that visualize the symptoms of influenza-like illness on a digital map, which is suitable for end-users, but it does not afford further processing and analysis. Existing systems have emphasized the collection, analysis, and visualization of surveillance data, but they have neglected a modular and interoperable design that integrates high-resolution geo-location with real-time data. As a remedy, we have built an open-source project and we have been operating an open service that detects flu-related symptoms and shares the data in real-time with anyone who wants to built upon this system. An analysis of a small number of precisely geo-located status updates (e.g. Twitter) correlates closely with the Google Flu Trends and the Centers for Disease Control and Prevention flu-positive reports. We suggest that public health information systems should embrace an open-source approach and offer linked data, in order to facilitate the development of an ecosystem of applications and services, and in order to be transparent to the general public interest. © The Author(s) 2015.

77 FR 76040 - Government-wide Travel Advisory Committee (GTAC)

Federal Register 2010, 2011, 2012, 2013, 2014

2012-12-26

... the Administrator of General Services on a regular basis. There exists no other source within the... companies, airline companies, travel and lodging associations, convention and visitor bureaus, state and... are open to public observers, unless prior notice has been provided for a closed meeting. Nomination...

14 CFR 29.1357 - Circuit protective devices.

Code of Federal Regulations, 2013 CFR

2013-01-01

... devices in the generating system must be designed to de-energize and disconnect faulty power sources and power transmission equipment from their associated buses with sufficient rapidity to provide protection... be designed so that, when an overload or circuit fault exists, it will open the circuit regardless of...

14 CFR 29.1357 - Circuit protective devices.

Code of Federal Regulations, 2014 CFR

2014-01-01

... devices in the generating system must be designed to de-energize and disconnect faulty power sources and power transmission equipment from their associated buses with sufficient rapidity to provide protection... be designed so that, when an overload or circuit fault exists, it will open the circuit regardless of...

14 CFR 29.1357 - Circuit protective devices.

Code of Federal Regulations, 2011 CFR

2011-01-01

... devices in the generating system must be designed to de-energize and disconnect faulty power sources and power transmission equipment from their associated buses with sufficient rapidity to provide protection... be designed so that, when an overload or circuit fault exists, it will open the circuit regardless of...

14 CFR 29.1357 - Circuit protective devices.

Code of Federal Regulations, 2012 CFR

2012-01-01

... devices in the generating system must be designed to de-energize and disconnect faulty power sources and power transmission equipment from their associated buses with sufficient rapidity to provide protection... be designed so that, when an overload or circuit fault exists, it will open the circuit regardless of...

Integrating HCI Specialists into Open Source Software Development Projects

NASA Astrophysics Data System (ADS)

Hedberg, Henrik; Iivari, Netta

Typical open source software (OSS) development projects are organized around technically talented developers, whose communication is based on technical aspects and source code. Decision-making power is gained through proven competence and activity in the project, and non-technical end-user opinions are too many times neglected. In addition, also human-computer interaction (HCI) specialists have encountered difficulties in trying to participate in OSS projects, because there seems to be no clear authority and responsibility for them. In this paper, based on HCI and OSS literature, we introduce an extended OSS development project organization model that adds a new level of communication and roles for attending human aspects of software. The proposed model makes the existence of HCI specialists visible in the projects, and promotes interaction between developers and the HCI specialists in the course of a project.

Engineer. The Professional Bulletin of Army Engineers. Volume 42. May-August 2012

DTIC Science & Technology

2012-08-01

reviewing instructions, searching existing data sources , gathering and maintaining the data needed, and completing and reviewing the collection of...better than it is. I hope that you can see the intent to include good ideas from all sources in the contents of this profession- al bulletin; in the...openness displayed during visits around the world by the commandant, the regimental command ser- geant major, and regimental chief warrant officer; and

Multinational Experiment 7: Access to the Global Commons. Objective 3.3 Lexicon and Abbreviations. Version 1.1

DTIC Science & Technology

2012-05-28

operation in Europe OSINT Open Source Intelligence PDA Personal Digital Assistant SME Subject Matter Expert SWGCA Special Working Group on the...Form Approved Report Documentation Page OMB No. 0704-0/88 · 1 d’ the time for reviewing instructions, searching existing data sources , gathering and...illegal and covert activity of exploiting vulnerabilities and collecting protected information or intelligence in cyberspace (MNE 7 Outcome 3 Working

A Flexible Method for Producing F.E.M. Analysis of Bone Using Open-Source Software

NASA Technical Reports Server (NTRS)

Boppana, Abhishektha; Sefcik, Ryan; Meyers, Jerry G.; Lewandowski, Beth E.

2016-01-01

This project, performed in support of the NASA GRC Space Academy summer program, sought to develop an open-source workflow methodology that segmented medical image data, created a 3D model from the segmented data, and prepared the model for finite-element analysis. In an initial step, a technological survey evaluated the performance of various existing open-source software that claim to perform these tasks. However, the survey concluded that no single software exhibited the wide array of functionality required for the potential NASA application in the area of bone, muscle and bio fluidic studies. As a result, development of a series of Python scripts provided the bridging mechanism to address the shortcomings of the available open source tools. The implementation of the VTK library provided the most quick and effective means of segmenting regions of interest from the medical images; it allowed for the export of a 3D model by using the marching cubes algorithm to build a surface mesh. To facilitate the development of the model domain from this extracted information required a surface mesh to be processed in the open-source software packages Blender and Gmsh. The Preview program of the FEBio suite proved to be sufficient for volume filling the model with an unstructured mesh and preparing boundaries specifications for finite element analysis. To fully allow FEM modeling, an in house developed Python script allowed assignment of material properties on an element by element basis by performing a weighted interpolation of voxel intensity of the parent medical image correlated to published information of image intensity to material properties, such as ash density. A graphical user interface combined the Python scripts and other software into a user friendly interface. The work using Python scripts provides a potential alternative to expensive commercial software and inadequate, limited open-source freeware programs for the creation of 3D computational models. More work will be needed to validate this approach in creating finite-element models.

LMS Transitioning to "Moodle": A Surprising Case of Successful, Emergent Change Management

ERIC Educational Resources Information Center

Lawler, Alan

2011-01-01

During 2009-10 the University of Ballarat implemented the open-source learning management system (LMS) "Moodle" alongside its existing legacy LMS, "Blackboard". While previous IT implementations have been troublesome at the university, notably the student information and finance management systems in 2008-09, the…

GIMS—Software for asset market experiments

PubMed Central

Palan, Stefan

2015-01-01

In this article we lay out requirements for an experimental market software for financial and economic research. We then discuss existing solutions. Finally, we introduce GIMS, an open source market software which is characterized by extensibility and ease of use, while offering nearly all of the required functionality. PMID:26525085

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.

cp-R, an interface the R programming language for clinical laboratory method comparisons.

PubMed

Holmes, Daniel T

2015-02-01

Clinical scientists frequently need to compare two different bioanalytical methods as part of assay validation/monitoring. As a matter necessity, regression methods for quantitative comparison in clinical chemistry, hematology and other clinical laboratory disciplines must allow for error in both the x and y variables. Traditionally the methods popularized by 1) Deming and 2) Passing and Bablok have been recommended. While commercial tools exist, no simple open source tool is available. The purpose of this work was to develop and entirely open-source GUI-driven program for bioanalytical method comparisons capable of performing these regression methods and able to produce highly customized graphical output. The GUI is written in python and PyQt4 with R scripts performing regression and graphical functions. The program can be run from source code or as a pre-compiled binary executable. The software performs three forms of regression and offers weighting where applicable. Confidence bands of the regression are calculated using bootstrapping for Deming and Passing Bablok methods. Users can customize regression plots according to the tools available in R and can produced output in any of: jpg, png, tiff, bmp at any desired resolution or ps and pdf vector formats. Bland Altman plots and some regression diagnostic plots are also generated. Correctness of regression parameter estimates was confirmed against existing R packages. The program allows for rapid and highly customizable graphical output capable of conforming to the publication requirements of any clinical chemistry journal. Quick method comparisons can also be performed and cut and paste into spreadsheet or word processing applications. We present a simple and intuitive open source tool for quantitative method comparison in a clinical laboratory environment. Copyright © 2014 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials.

PubMed

Giannozzi, Paolo; Baroni, Stefano; Bonini, Nicola; Calandra, Matteo; Car, Roberto; Cavazzoni, Carlo; Ceresoli, Davide; Chiarotti, Guido L; Cococcioni, Matteo; Dabo, Ismaila; Dal Corso, Andrea; de Gironcoli, Stefano; Fabris, Stefano; Fratesi, Guido; Gebauer, Ralph; Gerstmann, Uwe; Gougoussis, Christos; Kokalj, Anton; Lazzeri, Michele; Martin-Samos, Layla; Marzari, Nicola; Mauri, Francesco; Mazzarello, Riccardo; Paolini, Stefano; Pasquarello, Alfredo; Paulatto, Lorenzo; Sbraccia, Carlo; Scandolo, Sandro; Sclauzero, Gabriele; Seitsonen, Ari P; Smogunov, Alexander; Umari, Paolo; Wentzcovitch, Renata M

2009-09-30

QUANTUM ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave). The acronym ESPRESSO stands for opEn Source Package for Research in Electronic Structure, Simulation, and Optimization. It is freely available to researchers around the world under the terms of the GNU General Public License. QUANTUM ESPRESSO builds upon newly-restructured electronic-structure codes that have been developed and tested by some of the original authors of novel electronic-structure algorithms and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency are still its main focus, with special attention paid to massively parallel architectures, and a great effort being devoted to user friendliness. QUANTUM ESPRESSO is evolving towards a distribution of independent and interoperable codes in the spirit of an open-source project, where researchers active in the field of electronic-structure calculations are encouraged to participate in the project by contributing their own codes or by implementing their own ideas into existing codes.

GeNeDA: An Open-Source Workflow for Design Automation of Gene Regulatory Networks Inspired from Microelectronics.

PubMed

Madec, Morgan; Pecheux, François; Gendrault, Yves; Rosati, Elise; Lallement, Christophe; Haiech, Jacques

2016-10-01

The topic of this article is the development of an open-source automated design framework for synthetic biology, specifically for the design of artificial gene regulatory networks based on a digital approach. In opposition to other tools, GeNeDA is an open-source online software based on existing tools used in microelectronics that have proven their efficiency over the last 30 years. The complete framework is composed of a computation core directly adapted from an Electronic Design Automation tool, input and output interfaces, a library of elementary parts that can be achieved with gene regulatory networks, and an interface with an electrical circuit simulator. Each of these modules is an extension of microelectronics tools and concepts: ODIN II, ABC, the Verilog language, SPICE simulator, and SystemC-AMS. GeNeDA is first validated on a benchmark of several combinatorial circuits. The results highlight the importance of the part library. Then, this framework is used for the design of a sequential circuit including a biological state machine.

On the seamless, harmonized use of ISO/IEEE11073 and openEHR.

PubMed

Trigo, Jesús D; Kohl, Christian D; Eguzkiza, Aitor; Martínez-Espronceda, Miguel; Alesanco, Álvaro; Serrano, Luis; García, José; Knaup, Petra

2014-05-01

Standardized exchange of clinical information is a key factor in the provision of high quality health care systems. In this context, the openEHR specification facilitates the management of health data in electronic health records (EHRs), while the ISO/IEEE11073 (also referred to as X73PHD) family of standards provides a reference framework for medical device interoperability. Hospitals and health care providers using openEHR require flawless integration of data coming from external sources, such as X73PHD. Hence, a harmonization process is crucial for achieving a seamless, coherent use of those specifications in real scenarios. Such harmonization is the aim of this paper. Thus, the classes and attributes of a representative number of X73PHD specializations for medical devices--weight, temperature, blood pressure, pulse and heart rate, oximetry, and electrocardiograph--along with the X73PHD core document--ISO/IEEE11073-20601--have been analyzed and mapped to openEHR archetypes. The proposed methodology reuses the existing archetypes when possible and suggests new ones--or appropriate modifications--otherwise. As a result, this paper analyzes the inconsistencies found and the implications thereof in the coordinated use of these two standards. The procedure has also shown how existing standards are able to influence the archetype development process, enhancing the existing archetype corpus.

Mass-losing red giants in open clusters

NASA Technical Reports Server (NTRS)

Jura, M.

1987-01-01

Mass-losing stars in open clusters with main-sequence turn-offs at intermediate mass have been searched for by using the IRAS data base. The absence of many strong 60 micron sources in open clusters implies that intermediate-mass stars lose much of their mass during an intense wind phase of rather short duration. For stars of about seven solar masses, this phase, if it exists at all, lasts for not much more than 100,000 yr. For stars of about four solar masses, the intense wind phase appears to last considerably less than 10 million yr; it may well last for less than a million yr.

Crawling The Web for Libre: Selecting, Integrating, Extending and Releasing Open Source Software

NASA Astrophysics Data System (ADS)

Truslove, I.; Duerr, R. E.; Wilcox, H.; Savoie, M.; Lopez, L.; Brandt, M.

2012-12-01

Libre is a project developed by the National Snow and Ice Data Center (NSIDC). Libre is devoted to liberating science data from its traditional constraints of publication, location, and findability. Libre embraces and builds on the notion of making knowledge freely available, and both Creative Commons licensed content and Open Source Software are crucial building blocks for, as well as required deliverable outcomes of the project. One important aspect of the Libre project is to discover cryospheric data published on the internet without prior knowledge of the location or even existence of that data. Inspired by well-known search engines and their underlying web crawling technologies, Libre has explored tools and technologies required to build a search engine tailored to allow users to easily discover geospatial data related to the polar regions. After careful consideration, the Libre team decided to base its web crawling work on the Apache Nutch project (http://nutch.apache.org). Nutch is "an open source web-search software project" written in Java, with good documentation, a significant user base, and an active development community. Nutch was installed and configured to search for the types of data of interest, and the team created plugins to customize the default Nutch behavior to better find and categorize these data feeds. This presentation recounts the Libre team's experiences selecting, using, and extending Nutch, and working with the Nutch user and developer community. We will outline the technical and organizational challenges faced in order to release the project's software as Open Source, and detail the steps actually taken. We distill these experiences into a set of heuristics and recommendations for using, contributing to, and releasing Open Source Software.

Interchange Reconnection Associated with a Confined Filament Eruption: Implications for the Source of Transient Cold-dense Plasma in Solar Winds

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

Zheng, Ruisheng; Chen, Yao; Wang, Bing

The cold-dense plasma is occasionally detected in the solar wind with in situ data, but the source of the cold-dense plasma remains illusive. Interchange reconnections (IRs) between closed fields and nearby open fields are known to contribute to the formation of solar winds. We present a confined filament eruption associated with a puff-like coronal mass ejection (CME) on 2014 December 24. The filament underwent successive activations and finally erupted, due to continuous magnetic flux cancelations and emergences. The confined erupting filament showed a clear untwist motion, and most of the filament material fell back. During the eruption, some tiny blobsmore » escaped from the confined filament body, along newly formed open field lines rooted around the south end of the filament, and some bright plasma flowed from the north end of the filament to remote sites at nearby open fields. The newly formed open field lines shifted southward with multiple branches. The puff-like CME also showed multiple bright fronts and a clear southward shift. All the results indicate an intermittent IR existed between closed fields of the confined erupting filament and nearby open fields, which released a portion of filament material (blobs) to form the puff-like CME. We suggest that the IR provides a possible source of cold-dense plasma in the solar wind.« less

Filling Terrorism Gaps: VEOs, Evaluating Databases, and Applying Risk Terrain Modeling to Terrorism

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

Hagan, Ross F.

2016-08-29

This paper aims to address three issues: the lack of literature differentiating terrorism and violent extremist organizations (VEOs), terrorism incident databases, and the applicability of Risk Terrain Modeling (RTM) to terrorism. Current open source literature and publicly available government sources do not differentiate between terrorism and VEOs; furthermore, they fail to define them. Addressing the lack of a comprehensive comparison of existing terrorism data sources, a matrix comparing a dozen terrorism databases is constructed, providing insight toward the array of data available. RTM, a method for spatial risk analysis at a micro level, has some applicability to terrorism research, particularlymore » for studies looking at risk indicators of terrorism. Leveraging attack data from multiple databases, combined with RTM, offers one avenue for closing existing research gaps in terrorism literature.« less

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.

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.

OnEarth: An Open Source Solution for Efficiently Serving High-Resolution Mapped Image Products

NASA Astrophysics Data System (ADS)

Thompson, C. K.; Plesea, L.; Hall, J. R.; Roberts, J. T.; Cechini, M. F.; Schmaltz, J. E.; Alarcon, C.; Huang, T.; McGann, J. M.; Chang, G.; Boller, R. A.; Ilavajhala, S.; Murphy, K. J.; Bingham, A. W.

2013-12-01

This presentation introduces OnEarth, a server side software package originally developed at the Jet Propulsion Laboratory (JPL), that facilitates network-based, minimum-latency geolocated image access independent of image size or spatial resolution. The key component in this package is the Meta Raster Format (MRF), a specialized raster file extension to the Geospatial Data Abstraction Library (GDAL) consisting of an internal indexed pyramid of image tiles. Imagery to be served is converted to the MRF format and made accessible online via an expandable set of server modules handling requests in several common protocols, including the Open Geospatial Consortium (OGC) compliant Web Map Tile Service (WMTS) as well as Tiled WMS and Keyhole Markup Language (KML). OnEarth has recently transitioned to open source status and is maintained and actively developed as part of GIBS (Global Imagery Browse Services), a collaborative project between JPL and Goddard Space Flight Center (GSFC). The primary function of GIBS is to enhance and streamline the data discovery process and to support near real-time (NRT) applications via the expeditious ingestion and serving of full-resolution imagery representing science products from across the NASA Earth Science spectrum. Open source software solutions are leveraged where possible in order to utilize existing available technologies, reduce development time, and enlist wider community participation. We will discuss some of the factors and decision points in transitioning OnEarth to a suitable open source paradigm, including repository and licensing agreement decision points, institutional hurdles, and perceived benefits. We will also provide examples illustrating how OnEarth is integrated within GIBS and other applications.

An Advanced, Interactive, High-Performance Liquid Chromatography Simulator and Instructor Resources

ERIC Educational Resources Information Center

Boswell, Paul G.; Stoll, Dwight R.; Carr, Peter W.; Nagel, Megan L.; Vitha, Mark F.; Mabbott, Gary A.

2013-01-01

High-performance liquid chromatography (HPLC) simulation software has long been recognized as an effective educational tool, yet many of the existing HPLC simulators are either too expensive, outdated, or lack many important features necessary to make them widely useful for educational purposes. Here, a free, open-source HPLC simulator is…

Open innovation for phenotypic drug discovery: The PD2 assay panel.

PubMed

Lee, Jonathan A; Chu, Shaoyou; Willard, Francis S; Cox, Karen L; Sells Galvin, Rachelle J; Peery, Robert B; Oliver, Sarah E; Oler, Jennifer; Meredith, Tamika D; Heidler, Steven A; Gough, Wendy H; Husain, Saba; Palkowitz, Alan D; Moxham, Christopher M

2011-07-01

Phenotypic lead generation strategies seek to identify compounds that modulate complex, physiologically relevant systems, an approach that is complementary to traditional, target-directed strategies. Unlike gene-specific assays, phenotypic assays interrogate multiple molecular targets and signaling pathways in a target "agnostic" fashion, which may reveal novel functions for well-studied proteins and discover new pathways of therapeutic value. Significantly, existing compound libraries may not have sufficient chemical diversity to fully leverage a phenotypic strategy. To address this issue, Eli Lilly and Company launched the Phenotypic Drug Discovery Initiative (PD(2)), a model of open innovation whereby external research groups can submit compounds for testing in a panel of Lilly phenotypic assays. This communication describes the statistical validation, operations, and initial screening results from the first PD(2) assay panel. Analysis of PD(2) submissions indicates that chemical diversity from open source collaborations complements internal sources. Screening results for the first 4691 compounds submitted to PD(2) have confirmed hit rates from 1.6% to 10%, with the majority of active compounds exhibiting acceptable potency and selectivity. Phenotypic lead generation strategies, in conjunction with novel chemical diversity obtained via open-source initiatives such as PD(2), may provide a means to identify compounds that modulate biology by novel mechanisms and expand the innovation potential of drug discovery.

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

PubMed Central

Zolfo, Maria; Diro, Ermias

2017-01-01

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

Closing gaps between open software and public data in a hackathon setting: User-centered software prototyping.

PubMed

Busby, Ben; Lesko, Matthew; Federer, Lisa

2016-01-01

In genomics, bioinformatics and other areas of data science, gaps exist between extant public datasets and the open-source software tools built by the community to analyze similar data types.  The purpose of biological data science hackathons is to assemble groups of genomics or bioinformatics professionals and software developers to rapidly prototype software to address these gaps.  The only two rules for the NCBI-assisted hackathons run so far are that 1) data either must be housed in public data repositories or be deposited to such repositories shortly after the hackathon's conclusion, and 2) all software comprising the final pipeline must be open-source or open-use.  Proposed topics, as well as suggested tools and approaches, are distributed to participants at the beginning of each hackathon and refined during the event.  Software, scripts, and pipelines are developed and published on GitHub, a web service providing publicly available, free-usage tiers for collaborative software development. The code resulting from each hackathon is published at https://github.com/NCBI-Hackathons/ with separate directories or repositories for each team.

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.

Refraction of sound by a shear layer - Experimental assessment

NASA Technical Reports Server (NTRS)

Schlinker, R. H.; Amiet, R. K.

1979-01-01

An experimental study was conducted to determine the refraction angle and amplitude changes associated with sound transmission through a circular, open jet shear layer. Both on-axis and off-axis acoustic source locations were used. Source frequency varied from 1 kHz to 10 kHz while freestream Mach number varied from 0.1 to 0.4. The experimental results were compared with an existing refraction theory which was extended to account for off-axis source positions. A simple experiment was also conducted to assess the importance of turbulence scattering between 1 kHz and 25 kHz.

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.

The RAVE/VERTIGO vertex reconstruction toolkit and framework

NASA Astrophysics Data System (ADS)

Waltenberger, W.; Mitaroff, W.; Moser, F.; Pflugfelder, B.; Riedel, H. V.

2008-07-01

A detector-independent toolkit for vertex reconstruction (RAVE1) is being developed, along with a standalone framework (VERTIGO2) for testing, analyzing and debugging. The core algorithms represent state-of-the-art for geometric vertex finding and fitting by both linear (Kalman filter) and robust estimation methods. Main design goals are ease of use, flexibility for embedding into existing software frameworks, extensibility, and openness. The implementation is based on modern object-oriented techniques, is coded in C++ with interfaces for Java and Python, and follows an open-source approach. A beta release is available.

Open source software to control Bioflo bioreactors.

PubMed

Burdge, David A; Libourel, Igor G L

2014-01-01

Bioreactors are designed to support highly controlled environments for growth of tissues, cell cultures or microbial cultures. A variety of bioreactors are commercially available, often including sophisticated software to enhance the functionality of the bioreactor. However, experiments that the bioreactor hardware can support, but that were not envisioned during the software design cannot be performed without developing custom software. In addition, support for third party or custom designed auxiliary hardware is often sparse or absent. This work presents flexible open source freeware for the control of bioreactors of the Bioflo product family. The functionality of the software includes setpoint control, data logging, and protocol execution. Auxiliary hardware can be easily integrated and controlled through an integrated plugin interface without altering existing software. Simple experimental protocols can be entered as a CSV scripting file, and a Python-based protocol execution model is included for more demanding conditional experimental control. The software was designed to be a more flexible and free open source alternative to the commercially available solution. The source code and various auxiliary hardware plugins are publicly available for download from https://github.com/LibourelLab/BiofloSoftware. In addition to the source code, the software was compiled and packaged as a self-installing file for 32 and 64 bit windows operating systems. The compiled software will be able to control a Bioflo system, and will not require the installation of LabVIEW.

Open Source Software to Control Bioflo Bioreactors

PubMed Central

Burdge, David A.; Libourel, Igor G. L.

2014-01-01

Bioreactors are designed to support highly controlled environments for growth of tissues, cell cultures or microbial cultures. A variety of bioreactors are commercially available, often including sophisticated software to enhance the functionality of the bioreactor. However, experiments that the bioreactor hardware can support, but that were not envisioned during the software design cannot be performed without developing custom software. In addition, support for third party or custom designed auxiliary hardware is often sparse or absent. This work presents flexible open source freeware for the control of bioreactors of the Bioflo product family. The functionality of the software includes setpoint control, data logging, and protocol execution. Auxiliary hardware can be easily integrated and controlled through an integrated plugin interface without altering existing software. Simple experimental protocols can be entered as a CSV scripting file, and a Python-based protocol execution model is included for more demanding conditional experimental control. The software was designed to be a more flexible and free open source alternative to the commercially available solution. The source code and various auxiliary hardware plugins are publicly available for download from https://github.com/LibourelLab/BiofloSoftware. In addition to the source code, the software was compiled and packaged as a self-installing file for 32 and 64 bit windows operating systems. The compiled software will be able to control a Bioflo system, and will not require the installation of LabVIEW. PMID:24667828

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

ROS Hexapod

NASA Technical Reports Server (NTRS)

Davis, Kirsch; Bankieris, Derek

2016-01-01

As an intern project for NASA Johnson Space Center (JSC), my job was to familiarize myself and operate a Robotics Operating System (ROS). The project outcome will convert existing software assets into ROS using nodes, enabling a robotic Hexapod to communicate and to be functional and controlled by an existing PlayStation 3 (PS3) controller. Existing control algorithms and current libraries have no ROS capabilities within the Hexapod C++ source code. Conversion of C++ codes to ROS will enable existing code to be compatible with ROS, and will be controlled using existing PS3 controller. Furthermore, my job description is to design ROS messages and script programs which will enable assets to participate in the ROS ecosystem. In addition, an open source software (IDE) Arduino board will be integrated in the ecosystem with designing circuitry on a breadboard to add additional behavior with push buttons, potentiometers and other simple elements in the electrical circuitry. Other projects with the Arduino will be a GPS module digital clock that will run off 22 satellites to show accurate real time using a GPS signal and internal patch antenna to communicate with satellites.

Urban Renewable Building And Neighborhood Optimization

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

URBANopt is a user interface for creating and running district and city scale building energy simulations. The framework is built around the OpenStudio Urban Measures which are part of the OpenStudio project. Building footprints, building height, building type, and other data can be imported from public records or other sources. Footprints and locations for new buildings and district systems can also be specified. OpenStudio Measures are used to create starting point energy models and to model energy design features and efficiency measures for each building. URBANopt allows a user to pose several scenarios such as “what if 30% of themore » commercial retail buildings added roof top solar” or “what if all elementary schools converted to ground source heat pumps” and then visualize the impacts at a district or city scale. URBANopt is capable of modeling existing buildings, new construction, and district energy systems. URBANopt can be used to explore options for achieving Zero Energy across a collection of buildings (e.g., Zero Energy Districts).« less

FASTQ quality control dashboard

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

2016-07-25

FQCDB builds up existing open source software, FastQC, implementing a modern web interface for across parsed output of FastQC. In addition, FQCDB is extensible as a web service to include additional plots of type line, boxplot, or heatmap, across data formatted according to guidelines. The interface is also configurable via more readable JSON format, enabling customization by non-web programmers.

Marrying Two Existing Software Packages into an Efficient Online Tutoring Tool

ERIC Educational Resources Information Center

Byrne, Timothy

2007-01-01

Many teachers today use Learning Management Systems (LMS), several of which are open-source. Specific examples are Claroline and Moodle. However, they are not specifically designed for language learning, and hence not entirely suitable. In this article, I will compare two uses of the Claroline LMS available at Louvain-la-Neuve within the framework…

40 CFR 440.33 - Effluent limitations representing the degree of effluent reduction attainable by the application...

Code of Federal Regulations, 2012 CFR

2012-07-01

...) The concentration of pollutants discharged in mine drainage from mines, either open-pit or underground, that produce uranium ore, including mines using in-situ leach methods, shall not exceed: Effluent...). Except as provided in subpart L of this part and 40 CFR 125.30 through 125.32, any existing point source...

40 CFR 440.33 - Effluent limitations representing the degree of effluent reduction attainable by the application...

Code of Federal Regulations, 2011 CFR

2011-07-01

... concentration of pollutants discharged in mine drainage from mines, either open-pit or underground, that produce uranium ore, including mines using in-situ leach methods, shall not exceed: Effluent characteristic... provided in subpart L of this part and 40 CFR 125.30 through 125.32, any existing point source subject to...

40 CFR 440.33 - Effluent limitations representing the degree of effluent reduction attainable by the application...

Code of Federal Regulations, 2014 CFR

2014-07-01

...) The concentration of pollutants discharged in mine drainage from mines, either open-pit or underground, that produce uranium ore, including mines using in-situ leach methods, shall not exceed: Effluent...). Except as provided in subpart L of this part and 40 CFR 125.30 through 125.32, any existing point source...

40 CFR 440.33 - Effluent limitations representing the degree of effluent reduction attainable by the application...

Code of Federal Regulations, 2010 CFR

2010-07-01

... concentration of pollutants discharged in mine drainage from mines, either open-pit or underground, that produce uranium ore, including mines using in-situ leach methods, shall not exceed: Effluent characteristic... provided in subpart L of this part and 40 CFR 125.30 through 125.32, any existing point source subject to...

CISUS: an integrated 3D ultrasound system for IGT using a modular tracking API

NASA Astrophysics Data System (ADS)

Boctor, Emad M.; Viswanathan, Anand; Pieper, Steve; Choti, Michael A.; Taylor, Russell H.; Kikinis, Ron; Fichtinger, Gabor

2004-05-01

Ultrasound has become popular in clinical/surgical applications, both as the primary image guidance modality and also in conjunction with other modalities like CT or MRI. Three dimensional ultrasound (3DUS) systems have also demonstrated usefulness in image-guided therapy (IGT). At the same time, however, current lack of open-source and open-architecture multi-modal medical visualization systems prevents 3DUS from fulfilling its potential. Several stand-alone 3DUS systems, like Stradx or In-Vivo exist today. Although these systems have been found to be useful in real clinical setting, it is difficult to augment their functionality and integrate them in versatile IGT systems. To address these limitations, a robotic/freehand 3DUS open environment (CISUS) is being integrated into the 3D Slicer, an open-source research tool developed for medical image analysis and surgical planning. In addition, the system capitalizes on generic application programming interfaces (APIs) for tracking devices and robotic control. The resulting platform-independent open-source system may serve as a valuable tool to the image guided surgery community. Other researchers could straightforwardly integrate the generic CISUS system along with other functionalities (i.e. dual view visualization, registration, real-time tracking, segmentation, etc) to rapidly create their medical/surgical applications. Our current driving clinical application is robotically assisted and freehand 3DUS-guided liver ablation, which is fully being integrated under the CISUS-3D Slicer. Initial functionality and pre-clinical feasibility are demonstrated on phantom and ex-vivo animal models.

Software Application Profile: Opal and Mica: open-source software solutions for epidemiological data management, harmonization and dissemination

PubMed Central

Doiron, Dany; Marcon, Yannick; Fortier, Isabel; Burton, Paul; Ferretti, Vincent

2017-01-01

Abstract Motivation Improving the dissemination of information on existing epidemiological studies and facilitating the interoperability of study databases are essential to maximizing the use of resources and accelerating improvements in health. To address this, Maelstrom Research proposes Opal and Mica, two inter-operable open-source software packages providing out-of-the-box solutions for epidemiological data management, harmonization and dissemination. Implementation Opal and Mica are two standalone but inter-operable web applications written in Java, JavaScript and PHP. They provide web services and modern user interfaces to access them. General features Opal allows users to import, manage, annotate and harmonize study data. Mica is used to build searchable web portals disseminating study and variable metadata. When used conjointly, Mica users can securely query and retrieve summary statistics on geographically dispersed Opal servers in real-time. Integration with the DataSHIELD approach allows conducting more complex federated analyses involving statistical models. Availability Opal and Mica are open-source and freely available at [www.obiba.org] under a General Public License (GPL) version 3, and the metadata models and taxonomies that accompany them are available under a Creative Commons licence. PMID:29025122

Open source libraries and frameworks for mass spectrometry based proteomics: A developer's perspective☆

PubMed Central

Perez-Riverol, Yasset; Wang, Rui; Hermjakob, Henning; Müller, Markus; Vesada, Vladimir; Vizcaíno, Juan Antonio

2014-01-01

Data processing, management and visualization are central and critical components of a state of the art high-throughput mass spectrometry (MS)-based proteomics experiment, and are often some of the most time-consuming steps, especially for labs without much bioinformatics support. The growing interest in the field of proteomics has triggered an increase in the development of new software libraries, including freely available and open-source software. From database search analysis to post-processing of the identification results, even though the objectives of these libraries and packages can vary significantly, they usually share a number of features. Common use cases include the handling of protein and peptide sequences, the parsing of results from various proteomics search engines output files, and the visualization of MS-related information (including mass spectra and chromatograms). In this review, we provide an overview of the existing software libraries, open-source frameworks and also, we give information on some of the freely available applications which make use of them. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan. PMID:23467006

Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective.

PubMed

Perez-Riverol, Yasset; Wang, Rui; Hermjakob, Henning; Müller, Markus; Vesada, Vladimir; Vizcaíno, Juan Antonio

2014-01-01

Data processing, management and visualization are central and critical components of a state of the art high-throughput mass spectrometry (MS)-based proteomics experiment, and are often some of the most time-consuming steps, especially for labs without much bioinformatics support. The growing interest in the field of proteomics has triggered an increase in the development of new software libraries, including freely available and open-source software. From database search analysis to post-processing of the identification results, even though the objectives of these libraries and packages can vary significantly, they usually share a number of features. Common use cases include the handling of protein and peptide sequences, the parsing of results from various proteomics search engines output files, and the visualization of MS-related information (including mass spectra and chromatograms). In this review, we provide an overview of the existing software libraries, open-source frameworks and also, we give information on some of the freely available applications which make use of them. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan. Copyright © 2013 Elsevier B.V. All rights reserved.

Pika: A snow science simulation tool built using the open-source framework MOOSE

NASA Astrophysics Data System (ADS)

Slaughter, A.; Johnson, M.

2017-12-01

The Department of Energy (DOE) is currently investing millions of dollars annually into various modeling and simulation tools for all aspects of nuclear energy. An important part of this effort includes developing applications based on the open-source Multiphysics Object Oriented Simulation Environment (MOOSE; mooseframework.org) from Idaho National Laboratory (INL).Thanks to the efforts of the DOE and outside collaborators, MOOSE currently contains a large set of physics modules, including phase-field, level set, heat conduction, tensor mechanics, Navier-Stokes, fracture and crack propagation (via the extended finite-element method), flow in porous media, and others. The heat conduction, tensor mechanics, and phase-field modules, in particular, are well-suited for snow science problems. Pika--an open-source MOOSE-based application--is capable of simulating both 3D, coupled nonlinear continuum heat transfer and large-deformation mechanics applications (such as settlement) and phase-field based micro-structure applications. Additionally, these types of problems may be coupled tightly in a single solve or across length and time scales using a loosely coupled Picard iteration approach. In addition to the wide range of physics capabilities, MOOSE-based applications also inherit an extensible testing framework, graphical user interface, and documentation system; tools that allow MOOSE and other applications to adhere to nuclear software quality standards. The snow science community can learn from the nuclear industry and harness the existing effort to build simulation tools that are open, modular, and share a common framework. In particular, MOOSE-based multiphysics solvers are inherently parallel, dimension agnostic, adaptive in time and space, fully coupled, and capable of interacting with other applications. The snow science community should build on existing tools to enable collaboration between researchers and practitioners throughout the world, and advance the state-of-the-art in line with other scientific research efforts.

Nmrglue: an open source Python package for the analysis of multidimensional NMR data.

PubMed

Helmus, Jonathan J; Jaroniec, Christopher P

2013-04-01

Nmrglue, an open source Python package for working with multidimensional NMR data, is described. When used in combination with other Python scientific libraries, nmrglue provides a highly flexible and robust environment for spectral processing, analysis and visualization and includes a number of common utilities such as linear prediction, peak picking and lineshape fitting. The package also enables existing NMR software programs to be readily tied together, currently facilitating the reading, writing and conversion of data stored in Bruker, Agilent/Varian, NMRPipe, Sparky, SIMPSON, and Rowland NMR Toolkit file formats. In addition to standard applications, the versatility offered by nmrglue makes the package particularly suitable for tasks that include manipulating raw spectrometer data files, automated quantitative analysis of multidimensional NMR spectra with irregular lineshapes such as those frequently encountered in the context of biomacromolecular solid-state NMR, and rapid implementation and development of unconventional data processing methods such as covariance NMR and other non-Fourier approaches. Detailed documentation, install files and source code for nmrglue are freely available at http://nmrglue.com. The source code can be redistributed and modified under the New BSD license.

Nmrglue: An Open Source Python Package for the Analysis of Multidimensional NMR Data

PubMed Central

Helmus, Jonathan J.; Jaroniec, Christopher P.

2013-01-01

Nmrglue, an open source Python package for working with multidimensional NMR data, is described. When used in combination with other Python scientific libraries, nmrglue provides a highly flexible and robust environment for spectral processing, analysis and visualization and includes a number of common utilities such as linear prediction, peak picking and lineshape fitting. The package also enables existing NMR software programs to be readily tied together, currently facilitating the reading, writing and conversion of data stored in Bruker, Agilent/Varian, NMRPipe, Sparky, SIMPSON, and Rowland NMR Toolkit file formats. In addition to standard applications, the versatility offered by nmrglue makes the package particularly suitable for tasks that include manipulating raw spectrometer data files, automated quantitative analysis of multidimensional NMR spectra with irregular lineshapes such as those frequently encountered in the context of biomacromolecular solid-state NMR, and rapid implementation and development of unconventional data processing methods such as covariance NMR and other non-Fourier approaches. Detailed documentation, install files and source code for nmrglue are freely available at http://nmrglue.com. The source code can be redistributed and modified under the New BSD license. PMID:23456039

Improving mapping for Ebola response through mobilising a local community with self-owned smartphones: Tonkolili District, Sierra Leone, January 2015.

PubMed

Nic Lochlainn, Laura M; Gayton, Ivan; Theocharopoulos, Georgios; Edwards, Robin; Danis, Kostas; Kremer, Ronald; Kleijer, Karline; Tejan, Sumaila M; Sankoh, Mohamed; Jimissa, Augustin; Greig, Jane; Caleo, Grazia

2018-01-01

During the 2014-16 Ebola virus disease (EVD) outbreak, the Magburaka Ebola Management Centre (EMC) operated by Médecins Sans Frontières (MSF) in Tonkolili District, Sierra Leone, identified that available district maps lacked up-to-date village information to facilitate timely implementation of EVD control strategies. In January 2015, we undertook a survey in chiefdoms within the MSF EMC catchment area to collect mapping and village data. We explore the feasibility and cost to mobilise a local community for this survey, describe validation against existing mapping sources and use of the data to prioritise areas for interventions, and lessons learned. We recruited local people with self-owned Android smartphones installed with open-source survey software (OpenDataKit (ODK)) and open-source navigation software (OpenStreetMap Automated Navigation Directions (OsmAnd)). Surveyors were paired with local motorbike drivers to travel to eligible villages. The collected mapping data were validated by checking for duplication and comparing the village names against a pre-existing village name and location list using a geographic distance and text string-matching algorithm. The survey teams gained sufficient familiarity with the ODK and OsmAnd software within 1-2 hours. Nine chiefdoms in Tonkolili District and three in Bombali District were surveyed within two weeks. Following de-duplication, the surveyors collected data from 891 villages with an estimated 127,021 households. The overall survey cost was €3,395; €3.80 per village surveyed. The MSF GIS team (MSF-OCG) created improved maps for the MSF Magburaka EMC team which were used to support surveillance, investigation of suspect EVD cases, hygiene-kit distribution and EVD survivor support. We shared the mapping data with OpenStreetMap, the local Ministry of Health and Sanitation and Sierra Leone District and National Ebola Response Centres. Involving local community and using accessible technology allowed rapid implementation, at moderate cost, of a survey to collect geographic and essential village information, and creation of updated maps. These methods could be used for future emergencies to facilitate response.

Improving mapping for Ebola response through mobilising a local community with self-owned smartphones: Tonkolili District, Sierra Leone, January 2015

PubMed Central

Gayton, Ivan; Theocharopoulos, Georgios; Edwards, Robin; Danis, Kostas; Kremer, Ronald; Kleijer, Karline; Tejan, Sumaila M.; Sankoh, Mohamed; Jimissa, Augustin; Greig, Jane; Caleo, Grazia

2018-01-01

Background During the 2014–16 Ebola virus disease (EVD) outbreak, the Magburaka Ebola Management Centre (EMC) operated by Médecins Sans Frontières (MSF) in Tonkolili District, Sierra Leone, identified that available district maps lacked up-to-date village information to facilitate timely implementation of EVD control strategies. In January 2015, we undertook a survey in chiefdoms within the MSF EMC catchment area to collect mapping and village data. We explore the feasibility and cost to mobilise a local community for this survey, describe validation against existing mapping sources and use of the data to prioritise areas for interventions, and lessons learned. Methods We recruited local people with self-owned Android smartphones installed with open-source survey software (OpenDataKit (ODK)) and open-source navigation software (OpenStreetMap Automated Navigation Directions (OsmAnd)). Surveyors were paired with local motorbike drivers to travel to eligible villages. The collected mapping data were validated by checking for duplication and comparing the village names against a pre-existing village name and location list using a geographic distance and text string-matching algorithm. Results The survey teams gained sufficient familiarity with the ODK and OsmAnd software within 1–2 hours. Nine chiefdoms in Tonkolili District and three in Bombali District were surveyed within two weeks. Following de-duplication, the surveyors collected data from 891 villages with an estimated 127,021 households. The overall survey cost was €3,395; €3.80 per village surveyed. The MSF GIS team (MSF-OCG) created improved maps for the MSF Magburaka EMC team which were used to support surveillance, investigation of suspect EVD cases, hygiene-kit distribution and EVD survivor support. We shared the mapping data with OpenStreetMap, the local Ministry of Health and Sanitation and Sierra Leone District and National Ebola Response Centres. Conclusions Involving local community and using accessible technology allowed rapid implementation, at moderate cost, of a survey to collect geographic and essential village information, and creation of updated maps. These methods could be used for future emergencies to facilitate response. PMID:29298314

Integrating new Storage Technologies into EOS

NASA Astrophysics Data System (ADS)

Peters, Andreas J.; van der Ster, Dan C.; Rocha, Joaquim; Lensing, Paul

2015-12-01

The EOS[1] storage software was designed to cover CERN disk-only storage use cases in the medium-term trading scalability against latency. To cover and prepare for long-term requirements the CERN IT data and storage services group (DSS) is actively conducting R&D and open source contributions to experiment with a next generation storage software based on CEPH[3] and ethernet enabled disk drives. CEPH provides a scale-out object storage system RADOS and additionally various optional high-level services like S3 gateway, RADOS block devices and a POSIX compliant file system CephFS. The acquisition of CEPH by Redhat underlines the promising role of CEPH as the open source storage platform of the future. CERN IT is running a CEPH service in the context of OpenStack on a moderate scale of 1 PB replicated storage. Building a 100+PB storage system based on CEPH will require software and hardware tuning. It is of capital importance to demonstrate the feasibility and possibly iron out bottlenecks and blocking issues beforehand. The main idea behind this R&D is to leverage and contribute to existing building blocks in the CEPH storage stack and implement a few CERN specific requirements in a thin, customisable storage layer. A second research topic is the integration of ethernet enabled disks. This paper introduces various ongoing open source developments, their status and applicability.

A Kernel for Open Source Drug Discovery in Tropical Diseases

PubMed Central

Ortí, Leticia; Carbajo, Rodrigo J.; Pieper, Ursula; Eswar, Narayanan; Maurer, Stephen M.; Rai, Arti K.; Taylor, Ginger; Todd, Matthew H.; Pineda-Lucena, Antonio; Sali, Andrej; Marti-Renom, Marc A.

2009-01-01

Background Conventional patent-based drug development incentives work badly for the developing world, where commercial markets are usually small to non-existent. For this reason, the past decade has seen extensive experimentation with alternative R&D institutions ranging from private–public partnerships to development prizes. Despite extensive discussion, however, one of the most promising avenues—open source drug discovery—has remained elusive. We argue that the stumbling block has been the absence of a critical mass of preexisting work that volunteers can improve through a series of granular contributions. Historically, open source software collaborations have almost never succeeded without such “kernels”. Methodology/Principal Findings Here, we use a computational pipeline for: (i) comparative structure modeling of target proteins, (ii) predicting the localization of ligand binding sites on their surfaces, and (iii) assessing the similarity of the predicted ligands to known drugs. Our kernel currently contains 143 and 297 protein targets from ten pathogen genomes that are predicted to bind a known drug or a molecule similar to a known drug, respectively. The kernel provides a source of potential drug targets and drug candidates around which an online open source community can nucleate. Using NMR spectroscopy, we have experimentally tested our predictions for two of these targets, confirming one and invalidating the other. Conclusions/Significance The TDI kernel, which is being offered under the Creative Commons attribution share-alike license for free and unrestricted use, can be accessed on the World Wide Web at http://www.tropicaldisease.org. We hope that the kernel will facilitate collaborative efforts towards the discovery of new drugs against parasites that cause tropical diseases. PMID:19381286

OPTiM: Optical projection tomography integrated microscope using open-source hardware and software

PubMed Central

Andrews, Natalie; Davis, Samuel; Bugeon, Laurence; Dallman, Margaret D.; McGinty, James

2017-01-01

We describe the implementation of an OPT plate to perform optical projection tomography (OPT) on a commercial wide-field inverted microscope, using our open-source hardware and software. The OPT plate includes a tilt adjustment for alignment and a stepper motor for sample rotation as required by standard projection tomography. Depending on magnification requirements, three methods of performing OPT are detailed using this adaptor plate: a conventional direct OPT method requiring only the addition of a limiting aperture behind the objective lens; an external optical-relay method allowing conventional OPT to be performed at magnifications >4x; a remote focal scanning and region-of-interest method for improved spatial resolution OPT (up to ~1.6 μm). All three methods use the microscope’s existing incoherent light source (i.e. arc-lamp) and all of its inherent functionality is maintained for day-to-day use. OPT acquisitions are performed on in vivo zebrafish embryos to demonstrate the implementations’ viability. PMID:28700724

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

PubMed

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

2017-11-13

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

An open source business model for malaria.

PubMed

Årdal, Christine; Røttingen, John-Arne

2015-01-01

Greater investment is required in developing new drugs and vaccines against malaria in order to eradicate malaria. These precious funds must be carefully managed to achieve the greatest impact. We evaluate existing efforts to discover and develop new drugs and vaccines for malaria to determine how best malaria R&D can benefit from an enhanced open source approach and how such a business model may operate. We assess research articles, patents, clinical trials and conducted a smaller survey among malaria researchers. Our results demonstrate that the public and philanthropic sectors are financing and performing the majority of malaria drug/vaccine discovery and development, but are then restricting access through patents, 'closed' publications and hidden away physical specimens. This makes little sense since it is also the public and philanthropic sector that purchases the drugs and vaccines. We recommend that a more "open source" approach is taken by making the entire value chain more efficient through greater transparency which may lead to more extensive collaborations. This can, for example, be achieved by empowering an existing organization like the Medicines for Malaria Venture (MMV) to act as a clearing house for malaria-related data. The malaria researchers that we surveyed indicated that they would utilize such registry data to increase collaboration. Finally, we question the utility of publicly or philanthropically funded patents for malaria medicines, where little to no profits are available. Malaria R&D benefits from a publicly and philanthropically funded architecture, which starts with academic research institutions, product development partnerships, commercialization assistance through UNITAID and finally procurement through mechanisms like The Global Fund to Fight AIDS, Tuberculosis and Malaria and the U.S.' President's Malaria Initiative. We believe that a fresh look should be taken at the cost/benefit of patents particularly related to new malaria medicines and consider alternative incentives, like WHO prequalification.

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.

Energy Sources and Systems Analysis: 40 South Lincoln Redevelopment District (Full Report)

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

Not Available

2011-08-01

This report presents the results of a case study to analyze district energy systems for their potential use in a project that involves redeveloping 270 units of existing public housing, along with other nearby sites. When complete, the redevelopment project will encompass more than 900 mixed-income residential units, commercial and retail properties, and open space. The analysis estimated the hourly heating, cooling, domestic hot water, and electric loads required by the community; investigated potential district system technologies to meet those needs; and researched available fuel sources to power such systems.

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

Opening up the Federal Employees Health Benefits Program.

PubMed

McArdle, F B

1995-01-01

The Federal Employees Health Benefits Program (FEHBP) can serve as a vehicle to extend access to private health insurance to nonfederal workers. Opening up the FEHBP may also be a politically feasible incremental change because it potentially appeals to those at both ends of the political spectrum. Each of the various ways of enabling nonfederal workers to participate in the FEHBP has its pros and cons. This paper looks at using the FEHBP as a voluntary buy-in opportunity to help those who lack health insurance--without displacing or disrupting existing sources of health coverage or creating an expensive federal program.

RAVE—a Detector-independent vertex reconstruction toolkit

NASA Astrophysics Data System (ADS)

Waltenberger, Wolfgang; Mitaroff, Winfried; Moser, Fabian

2007-10-01

A detector-independent toolkit for vertex reconstruction (RAVE ) is being developed, along with a standalone framework (VERTIGO ) for testing, analyzing and debugging. The core algorithms represent state of the art for geometric vertex finding and fitting by both linear (Kalman filter) and robust estimation methods. Main design goals are ease of use, flexibility for embedding into existing software frameworks, extensibility, and openness. The implementation is based on modern object-oriented techniques, is coded in C++ with interfaces for Java and Python, and follows an open-source approach. A beta release is available. VERTIGO = "vertex reconstruction toolkit and interface to generic objects".

A Quantitative Experimental Study of the Effectiveness of Systems to Identify Network Attackers

ERIC Educational Resources Information Center

Handorf, C. Russell

2016-01-01

This study analyzed the meta-data collected from a honeypot that was run by the Federal Bureau of Investigation for a period of 5 years. This analysis compared the use of existing industry methods and tools, such as Intrusion Detection System alerts, network traffic flow and system log traffic, within the Open Source Security Information Manager…

40 CFR 440.32 - Effluent limitations representing the degree of effluent reduction attainable by the application...

Code of Federal Regulations, 2010 CFR

2010-07-01

..., radium and vanadium including mill-mine facilities and mines using in-situ leach methods shall not exceed...). Except as provided in subpart L of this part and 40 CFR 125.30 through 125.32, any existing point source... available (BPT): (a) The concentration of pollutants discharged in mine drainage from mines, either open-pit...

40 CFR 440.32 - Effluent limitations representing the degree of effluent reduction attainable by the application...

Code of Federal Regulations, 2011 CFR

2011-07-01

..., radium and vanadium including mill-mine facilities and mines using in-situ leach methods shall not exceed...). Except as provided in subpart L of this part and 40 CFR 125.30 through 125.32, any existing point source... available (BPT): (a) The concentration of pollutants discharged in mine drainage from mines, either open-pit...

Enabling a systems biology knowledgebase with gaggle and firegoose

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

Baliga, Nitin S.

The overall goal of this project was to extend the existing Gaggle and Firegoose systems to develop an open-source technology that runs over the web and links desktop applications with many databases and software applications. This technology would enable researchers to incorporate workflows for data analysis that can be executed from this interface to other online applications. The four specific aims were to (1) provide one-click mapping of genes, proteins, and complexes across databases and species; (2) enable multiple simultaneous workflows; (3) expand sophisticated data analysis for online resources; and enhance open-source development of the Gaggle-Firegoose infrastructure. Gaggle is anmore » open-source Java software system that integrates existing bioinformatics programs and data sources into a user-friendly, extensible environment to allow interactive exploration, visualization, and analysis of systems biology data. Firegoose is an extension to the Mozilla Firefox web browser that enables data transfer between websites and desktop tools including Gaggle. In the last phase of this funding period, we have made substantial progress on development and application of the Gaggle integration framework. We implemented the workspace to the Network Portal. Users can capture data from Firegoose and save them to the workspace. Users can create workflows to start multiple software components programmatically and pass data between them. Results of analysis can be saved to the cloud so that they can be easily restored on any machine. We also developed the Gaggle Chrome Goose, a plugin for the Google Chrome browser in tandem with an opencpu server in the Amazon EC2 cloud. This allows users to interactively perform data analysis on a single web page using the R packages deployed on the opencpu server. The cloud-based framework facilitates collaboration between researchers from multiple organizations. We have made a number of enhancements to the cmonkey2 application to enable and improve the integration within different environments, and we have created a new tools pipeline for generating EGRIN2 models in a largely automated way.« less

MANTA--an open-source, high density electrophysiology recording suite for MATLAB.

PubMed

Englitz, B; David, S V; Sorenson, M D; Shamma, S A

2013-01-01

The distributed nature of nervous systems makes it necessary to record from a large number of sites in order to decipher the neural code, whether single cell, local field potential (LFP), micro-electrocorticograms (μECoG), electroencephalographic (EEG), magnetoencephalographic (MEG) or in vitro micro-electrode array (MEA) data are considered. High channel-count recordings also optimize the yield of a preparation and the efficiency of time invested by the researcher. Currently, data acquisition (DAQ) systems with high channel counts (>100) can be purchased from a limited number of companies at considerable prices. These systems are typically closed-source and thus prohibit custom extensions or improvements by end users. We have developed MANTA, an open-source MATLAB-based DAQ system, as an alternative to existing options. MANTA combines high channel counts (up to 1440 channels/PC), usage of analog or digital headstages, low per channel cost (<$90/channel), feature-rich display and filtering, a user-friendly interface, and a modular design permitting easy addition of new features. MANTA is licensed under the GPL and free of charge. The system has been tested by daily use in multiple setups for >1 year, recording reliably from 128 channels. It offers a growing list of features, including integrated spike sorting, PSTH and CSD display and fully customizable electrode array geometry (including 3D arrays), some of which are not available in commercial systems. MANTA runs on a typical PC and communicates via TCP/IP and can thus be easily integrated with existing stimulus generation/control systems in a lab at a fraction of the cost of commercial systems. With modern neuroscience developing rapidly, MANTA provides a flexible platform that can be rapidly adapted to the needs of new analyses and questions. Being open-source, the development of MANTA can outpace commercial solutions in functionality, while maintaining a low price-point.

MANTA—an open-source, high density electrophysiology recording suite for MATLAB

PubMed Central

Englitz, B.; David, S. V.; Sorenson, M. D.; Shamma, S. A.

2013-01-01

The distributed nature of nervous systems makes it necessary to record from a large number of sites in order to decipher the neural code, whether single cell, local field potential (LFP), micro-electrocorticograms (μECoG), electroencephalographic (EEG), magnetoencephalographic (MEG) or in vitro micro-electrode array (MEA) data are considered. High channel-count recordings also optimize the yield of a preparation and the efficiency of time invested by the researcher. Currently, data acquisition (DAQ) systems with high channel counts (>100) can be purchased from a limited number of companies at considerable prices. These systems are typically closed-source and thus prohibit custom extensions or improvements by end users. We have developed MANTA, an open-source MATLAB-based DAQ system, as an alternative to existing options. MANTA combines high channel counts (up to 1440 channels/PC), usage of analog or digital headstages, low per channel cost (<$90/channel), feature-rich display and filtering, a user-friendly interface, and a modular design permitting easy addition of new features. MANTA is licensed under the GPL and free of charge. The system has been tested by daily use in multiple setups for >1 year, recording reliably from 128 channels. It offers a growing list of features, including integrated spike sorting, PSTH and CSD display and fully customizable electrode array geometry (including 3D arrays), some of which are not available in commercial systems. MANTA runs on a typical PC and communicates via TCP/IP and can thus be easily integrated with existing stimulus generation/control systems in a lab at a fraction of the cost of commercial systems. With modern neuroscience developing rapidly, MANTA provides a flexible platform that can be rapidly adapted to the needs of new analyses and questions. Being open-source, the development of MANTA can outpace commercial solutions in functionality, while maintaining a low price-point. PMID:23653593

Open-source software platform for medical image segmentation applications

NASA Astrophysics Data System (ADS)

Namías, R.; D'Amato, J. P.; del Fresno, M.

2017-11-01

Segmenting 2D and 3D images is a crucial and challenging problem in medical image analysis. Although several image segmentation algorithms have been proposed for different applications, no universal method currently exists. Moreover, their use is usually limited when detection of complex and multiple adjacent objects of interest is needed. In addition, the continually increasing volumes of medical imaging scans require more efficient segmentation software design and highly usable applications. In this context, we present an extension of our previous segmentation framework which allows the combination of existing explicit deformable models in an efficient and transparent way, handling simultaneously different segmentation strategies and interacting with a graphic user interface (GUI). We present the object-oriented design and the general architecture which consist of two layers: the GUI at the top layer, and the processing core filters at the bottom layer. We apply the framework for segmenting different real-case medical image scenarios on public available datasets including bladder and prostate segmentation from 2D MRI, and heart segmentation in 3D CT. Our experiments on these concrete problems show that this framework facilitates complex and multi-object segmentation goals while providing a fast prototyping open-source segmentation tool.

Closing gaps between open software and public data in a hackathon setting: User-centered software prototyping

PubMed Central

Busby, Ben; Lesko, Matthew; Federer, Lisa

2016-01-01

In genomics, bioinformatics and other areas of data science, gaps exist between extant public datasets and the open-source software tools built by the community to analyze similar data types.  The purpose of biological data science hackathons is to assemble groups of genomics or bioinformatics professionals and software developers to rapidly prototype software to address these gaps.  The only two rules for the NCBI-assisted hackathons run so far are that 1) data either must be housed in public data repositories or be deposited to such repositories shortly after the hackathon’s conclusion, and 2) all software comprising the final pipeline must be open-source or open-use.  Proposed topics, as well as suggested tools and approaches, are distributed to participants at the beginning of each hackathon and refined during the event.  Software, scripts, and pipelines are developed and published on GitHub, a web service providing publicly available, free-usage tiers for collaborative software development. The code resulting from each hackathon is published at https://github.com/NCBI-Hackathons/ with separate directories or repositories for each team. PMID:27134733

Numerical simulation of the SOFIA flow field

NASA Technical Reports Server (NTRS)

Klotz, Stephen P.

1995-01-01

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 runs 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.

SWATH2stats: An R/Bioconductor Package to Process and Convert Quantitative SWATH-MS Proteomics Data for Downstream Analysis Tools.

PubMed

Blattmann, Peter; Heusel, Moritz; Aebersold, Ruedi

2016-01-01

SWATH-MS is an acquisition and analysis technique of targeted proteomics that enables measuring several thousand proteins with high reproducibility and accuracy across many samples. OpenSWATH is popular open-source software for peptide identification and quantification from SWATH-MS data. For downstream statistical and quantitative analysis there exist different tools such as MSstats, mapDIA and aLFQ. However, the transfer of data from OpenSWATH to the downstream statistical tools is currently technically challenging. Here we introduce the R/Bioconductor package SWATH2stats, which allows convenient processing of the data into a format directly readable by the downstream analysis tools. In addition, SWATH2stats allows annotation, analyzing the variation and the reproducibility of the measurements, FDR estimation, and advanced filtering before submitting the processed data to downstream tools. These functionalities are important to quickly analyze the quality of the SWATH-MS data. Hence, SWATH2stats is a new open-source tool that summarizes several practical functionalities for analyzing, processing, and converting SWATH-MS data and thus facilitates the efficient analysis of large-scale SWATH/DIA datasets.

Infrasonic wave accompanying a crack opening during the 2015 Hakone eruption

NASA Astrophysics Data System (ADS)

Yukutake, Yohei; Ichihara, Mie; Honda, Ryou

2018-03-01

To understand the initial process of the phreatic eruption of the Hakone volcano from June 29 to July 01, 2015, we analyzed infrasound data using the cross-correlation between infrasound and vertical ground velocity and compared the results of our analysis to the crustal deformation detected by tiltmeters and broadband seismometers. An infrasound signal and vertical ground motion due to an infrasound wave coupled to the ground were detected simultaneously with the opening of a crack source beneath the Owakudani geothermal region during the 2-min time period after 07:32 JST on June 29, 2015 (JST = UTC + 8 h). Given that the upper end of the open crack was approximately 150 m beneath the surface, the time for the direct emission of highly pressurized fluid from the upper end of the open crack to the surface should have exceeded the duration of the inflation owing to the hydraulic diffusivity in the porous media. Therefore, the infrasound signal coincident with the opening of the crack may reflect a sudden emission of volcanic gas resulting from the rapid vaporization of pre-existing groundwater beneath Owakudani because of the transfer of the volumetric strain change from the deformation source. We also noticed a correlation pattern corresponding to discrete impulsive infrasound signals during vent formation, which occurred several hours to 2 days after the opening of the crack. In particular, we noted that the sudden emission of vapor coincided with the inflation of the shallow pressure source, whereas the eruptive burst events accompanied by the largest vent formation were delayed by approximately 2 days. Furthermore, we demonstrated that the correlation method is a useful tool in detecting small infrasound signals and provides important information regarding the initial processes of the eruption.[Figure not available: see fulltext.

OpenTrials: towards a collaborative open database of all available information on all clinical trials.

PubMed

Goldacre, Ben; Gray, Jonathan

2016-04-08

OpenTrials is a collaborative and open database for all available structured data and documents on all clinical trials, threaded together by individual trial. With a versatile and expandable data schema, it is initially designed to host and match the following documents and data for each trial: registry entries; links, abstracts, or texts of academic journal papers; portions of regulatory documents describing individual trials; structured data on methods and results extracted by systematic reviewers or other researchers; clinical study reports; and additional documents such as blank consent forms, blank case report forms, and protocols. The intention is to create an open, freely re-usable index of all such information and to increase discoverability, facilitate research, identify inconsistent data, enable audits on the availability and completeness of this information, support advocacy for better data and drive up standards around open data in evidence-based medicine. The project has phase I funding. This will allow us to create a practical data schema and populate the database initially through web-scraping, basic record linkage techniques, crowd-sourced curation around selected drug areas, and import of existing sources of structured and documents. It will also allow us to create user-friendly web interfaces onto the data and conduct user engagement workshops to optimise the database and interface designs. Where other projects have set out to manually and perfectly curate a narrow range of information on a smaller number of trials, we aim to use a broader range of techniques and attempt to match a very large quantity of information on all trials. We are currently seeking feedback and additional sources of structured data.

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

The Open Global Glacier Model

NASA Astrophysics Data System (ADS)

Marzeion, B.; Maussion, F.

2017-12-01

Mountain glaciers are one of the few remaining sub-systems of the global climate system for which no globally applicable, open source, community-driven model exists. Notable examples from the ice sheet community include the Parallel Ice Sheet Model or Elmer/Ice. While the atmospheric modeling community has a long tradition of sharing models (e.g. the Weather Research and Forecasting model) or comparing them (e.g. the Coupled Model Intercomparison Project or CMIP), recent initiatives originating from the glaciological community show a new willingness to better coordinate global research efforts following the CMIP example (e.g. the Glacier Model Intercomparison Project or the Glacier Ice Thickness Estimation Working Group). In the recent past, great advances have been made in the global availability of data and methods relevant for glacier modeling, spanning glacier outlines, automatized glacier centerline identification, bed rock inversion methods, and global topographic data sets. Taken together, these advances now allow the ice dynamics of glaciers to be modeled on a global scale, provided that adequate modeling platforms are available. Here, we present the Open Global Glacier Model (OGGM), developed to provide a global scale, modular, and open source numerical model framework for consistently simulating past and future global scale glacier change. Global not only in the sense of leading to meaningful results for all glaciers combined, but also for any small ensemble of glaciers, e.g. at the headwater catchment scale. Modular to allow combinations of different approaches to the representation of ice flow and surface mass balance, enabling a new kind of model intercomparison. Open source so that the code can be read and used by anyone and so that new modules can be added and discussed by the community, following the principles of open governance. Consistent in order to provide uncertainty measures at all realizable scales.

GIS Technologies For The New Planetary Science Archive (PSA)

NASA Astrophysics Data System (ADS)

Docasal, R.; Barbarisi, I.; Rios, C.; Macfarlane, A. J.; Gonzalez, J.; Arviset, C.; De Marchi, G.; Martinez, S.; Grotheer, E.; Lim, T.; Besse, S.; Heather, D.; Fraga, D.; Barthelemy, M.

2015-12-01

Geographical information system (GIS) is becoming increasingly used for planetary science. GIS are computerised systems for the storage, retrieval, manipulation, analysis, and display of geographically referenced data. Some data stored in the Planetary Science Archive (PSA), for instance, a set of Mars Express/Venus Express data, have spatial metadata associated to them. To facilitate users in handling and visualising spatial data in GIS applications, the new PSA should support interoperability with interfaces implementing the standards approved by the Open Geospatial Consortium (OGC). These standards are followed in order to develop open interfaces and encodings that allow data to be exchanged with GIS Client Applications, well-known examples of which are Google Earth and NASA World Wind as well as open source tools such as Openlayers. The technology already exists within PostgreSQL databases to store searchable geometrical data in the form of the PostGIS extension. An existing open source maps server is GeoServer, an instance of which has been deployed for the new PSA, uses the OGC standards to allow, among others, the sharing, processing and editing of data and spatial data through the Web Feature Service (WFS) standard as well as serving georeferenced map images through the Web Map Service (WMS). The final goal of the new PSA, being developed by the European Space Astronomy Centre (ESAC) Science Data Centre (ESDC), is to create an archive which enables science exploitation of ESA's planetary missions datasets. This can be facilitated through the GIS framework, offering interfaces (both web GUI and scriptable APIs) that can be used more easily and scientifically by the community, and that will also enable the community to build added value services on top of the PSA.

The use and role of open source software applications in public and not-for-profit hospitals in the United States.

PubMed

Vest, Joshua R; Stephens, James H

2013-01-01

The potential cost savings and customizability of open source software (OSS) may be particularly attractive for hospitals. However, numerous health-care-specific OSS applications exist, the adoption of OSS health information technology (HIT) applications is not widespread in the United States. This disconnect between the availability of promising software and low adoption raises the basic question: If OSS HIT is so advantageous, why are more health care organizations not using it? We interviewed the chief information officer, or equivalent position, at 17 not-for-profit and public hospitals across the United States. Through targeted recruitment, our sample included nine hospitals using OSS HIT and eight hospitals not using OSS HIT. The open-ended interview questions were guided by domains included in the fit-viability theory, an organizational-level innovation adoption framework, and those suggested by a review of the literature. Transcripts were analyzed using an inductive and comparative approach, which involved an open coding for relevant themes. Interviews described the state of OSS use in hospitals. Specifically, general OSS applications were widely used by IT professionals. In addition, hospitals using OSS HIT still relied heavily on vendor support. In terms of why decisions arose to use OSS HIT, several hospitals using OSS HIT noted the cost advantages. In contrast, hospitals avoiding OSS HIT were clear, OSS as a class did not fit with clinical work and posed too much risk. Perceptions of OSS HIT ranged from enthusiastic embracement to resigned adoption, to refusal, to abandonment. Some organizations were achieving success with their OSS HIT choices, but they still relied on vendors for significant support. The decision to adopt OSS HIT was not uniform but contingent upon views of the risk posed by the technology, economic factors, and the hospital's existing capabilities.

Open Babel: An open chemical toolbox

PubMed Central

2011-01-01

Background A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de facto standards have arisen (for example, SMILES format), the need to interconvert formats is a continuing problem due to the multitude of different application areas for chemistry data, differences in the data stored by different formats (0D versus 3D, for example), and competition between software along with a lack of vendor-neutral formats. Results We discuss, for the first time, Open Babel, an open-source chemical toolbox that speaks the many languages of chemical data. Open Babel version 2.3 interconverts over 110 formats. The need to represent such a wide variety of chemical and molecular data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion. Conclusions Open Babel presents a solution to the proliferation of multiple chemical file formats. In addition, it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching. For developers, it can be used as a programming library to handle chemical data in areas such as organic chemistry, drug design, materials science, and computational chemistry. It is freely available under an open-source license from http://openbabel.org. PMID:21982300

Software Application Profile: Opal and Mica: open-source software solutions for epidemiological data management, harmonization and dissemination.

PubMed

Doiron, Dany; Marcon, Yannick; Fortier, Isabel; Burton, Paul; Ferretti, Vincent

2017-10-01

Improving the dissemination of information on existing epidemiological studies and facilitating the interoperability of study databases are essential to maximizing the use of resources and accelerating improvements in health. To address this, Maelstrom Research proposes Opal and Mica, two inter-operable open-source software packages providing out-of-the-box solutions for epidemiological data management, harmonization and dissemination. Opal and Mica are two standalone but inter-operable web applications written in Java, JavaScript and PHP. They provide web services and modern user interfaces to access them. Opal allows users to import, manage, annotate and harmonize study data. Mica is used to build searchable web portals disseminating study and variable metadata. When used conjointly, Mica users can securely query and retrieve summary statistics on geographically dispersed Opal servers in real-time. Integration with the DataSHIELD approach allows conducting more complex federated analyses involving statistical models. Opal and Mica are open-source and freely available at [www.obiba.org] under a General Public License (GPL) version 3, and the metadata models and taxonomies that accompany them are available under a Creative Commons licence. © The Author 2017; all rights reserved. Published by Oxford University Press on behalf of the International Epidemiological Association

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.

SCIFIO: an extensible framework to support scientific image formats.

PubMed

Hiner, Mark C; Rueden, Curtis T; Eliceiri, Kevin W

2016-12-07

No gold standard exists in the world of scientific image acquisition; a proliferation of instruments each with its own proprietary data format has made out-of-the-box sharing of that data nearly impossible. In the field of light microscopy, the Bio-Formats library was designed to translate such proprietary data formats to a common, open-source schema, enabling sharing and reproduction of scientific results. While Bio-Formats has proved successful for microscopy images, the greater scientific community was lacking a domain-independent framework for format translation. SCIFIO (SCientific Image Format Input and Output) is presented as a freely available, open-source library unifying the mechanisms of reading and writing image data. The core of SCIFIO is its modular definition of formats, the design of which clearly outlines the components of image I/O to encourage extensibility, facilitated by the dynamic discovery of the SciJava plugin framework. SCIFIO is structured to support coexistence of multiple domain-specific open exchange formats, such as Bio-Formats' OME-TIFF, within a unified environment. SCIFIO is a freely available software library developed to standardize the process of reading and writing scientific image formats.

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.

Adjusting to Social Change - A Multi-Level Analysis in Three Cultures

DTIC Science & Technology

2013-08-01

including the time for reviewing instructions, searching existing data sources, gathering and maintaining the data needed , and completing and reviewing the...presence is often associated with the large-scale movement of civilian populations, and who need to better understand the Distribution A: Approved for...valuing openness to change (self-direction, stimulation and sometimes hedonism values) with valuing conservation (conformity, tradition and security

Using leap motion to investigate the emergence of structure in speech and language.

PubMed

Eryilmaz, Kerem; Little, Hannah

2017-10-01

 In evolutionary linguistics, experiments using artificial signal spaces are being used to investigate the emergenceof speech structure. These signal spaces need to be continuous, non-discretized spaces from which discrete unitsand patterns can emerge. They need to be dissimilar from-but comparable with-the vocal tract, in order tominimize interference from pre-existing linguistic knowledge, while informing us about language. This is a hardbalance to strike. This article outlines a new approach that uses the Leap Motion, an infrared controller that canconvert manual movement in 3d space into sound. The signal space using this approach is more flexible than signalspaces in previous attempts. Further, output data using this approach is simpler to arrange and analyze. Theexperimental interface was built using free, and mostly open- source libraries in Python. We provide our sourcecode for other researchers as open source.

CONNJUR Workflow Builder: A software integration environment for spectral reconstruction

PubMed Central

Fenwick, Matthew; Weatherby, Gerard; Vyas, Jay; Sesanker, Colbert; Martyn, Timothy O.; Ellis, Heidi J.C.; Gryk, Michael R.

2015-01-01

CONNJUR Workflow Builder (WB) is an open-source software integration environment that leverages existing spectral reconstruction tools to create a synergistic, coherent platform for converting biomolecular NMR data from the time domain to the frequency domain. WB provides data integration of primary data and metadata using a relational database, and includes a library of pre-built workflows for processing time domain data. WB simplifies maximum entropy reconstruction, facilitating the processing of non-uniformly sampled time domain data. As will be shown in the paper, the unique features of WB provide it with novel abilities to enhance the quality, accuracy, and fidelity of the spectral reconstruction process. WB also provides features which promote collaboration, education, parameterization, and non-uniform data sets along with processing integrated with the Rowland NMR Toolkit (RNMRTK) and NMRPipe software packages. WB is available free of charge in perpetuity, dual-licensed under the MIT and GPL open source licenses. PMID:26066803

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.

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

NASA Astrophysics Data System (ADS)

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

2015-05-01

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

CONNJUR Workflow Builder: a software integration environment for spectral reconstruction.

PubMed

Fenwick, Matthew; Weatherby, Gerard; Vyas, Jay; Sesanker, Colbert; Martyn, Timothy O; Ellis, Heidi J C; Gryk, Michael R

2015-07-01

CONNJUR Workflow Builder (WB) is an open-source software integration environment that leverages existing spectral reconstruction tools to create a synergistic, coherent platform for converting biomolecular NMR data from the time domain to the frequency domain. WB provides data integration of primary data and metadata using a relational database, and includes a library of pre-built workflows for processing time domain data. WB simplifies maximum entropy reconstruction, facilitating the processing of non-uniformly sampled time domain data. As will be shown in the paper, the unique features of WB provide it with novel abilities to enhance the quality, accuracy, and fidelity of the spectral reconstruction process. WB also provides features which promote collaboration, education, parameterization, and non-uniform data sets along with processing integrated with the Rowland NMR Toolkit (RNMRTK) and NMRPipe software packages. WB is available free of charge in perpetuity, dual-licensed under the MIT and GPL open source licenses.

An open-source laser electronics suite

NASA Astrophysics Data System (ADS)

Pisenti, Neal C.; Reschovsky, Benjamin J.; Barker, Daniel S.; Restelli, Alessandro; Campbell, Gretchen K.

2016-05-01

We present an integrated set of open-source electronics for controlling external-cavity diode lasers and other instruments in the laboratory. The complete package includes a low-noise circuit for driving high-voltage piezoelectric actuators, an ultra-stable current controller based on the design of, and a high-performance, multi-channel temperature controller capable of driving thermo-electric coolers or resistive heaters. Each circuit (with the exception of the temperature controller) is designed to fit in a Eurocard rack equipped with a low-noise linear power supply capable of driving up to 5 A at +/- 15 V. A custom backplane allows signals to be shared between modules, and a digital communication bus makes the entire rack addressable by external control software over TCP/IP. The modular architecture makes it easy for additional circuits to be designed and integrated with existing electronics, providing a low-cost, customizable alternative to commercial systems without sacrificing performance.

Building Energy Management Open Source Software

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

Rahman, Saifur

Funded by the U.S. Department of Energy in November 2013, a Building Energy Management Open Source Software (BEMOSS) platform was engineered to improve sensing and control of equipment in small- and medium-sized commercial buildings. According to the Energy Information Administration (EIA), small- (5,000 square feet or smaller) and medium-sized (between 5,001 to 50,000 square feet) commercial buildings constitute about 95% of all commercial buildings in the U.S. These buildings typically do not have Building Automation Systems (BAS) to monitor and control building operation. While commercial BAS solutions exist, including those from Siemens, Honeywell, Johnsons Controls and many more, they aremore » not cost effective in the context of small- and medium-sized commercial buildings, and typically work with specific controller products from the same company. BEMOSS targets small and medium-sized commercial buildings to address this gap.« less

The Emergence of Open-Source Software in China

ERIC Educational Resources Information Center

Pan, Guohua; Bonk, Curtis J.

2007-01-01

The open-source software movement is gaining increasing momentum in China. Of the limited numbers of open-source software in China, "Red Flag Linux" stands out most strikingly, commanding 30 percent share of Chinese software market. Unlike the spontaneity of open-source movement in North America, open-source software development in…

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.

Open Access, Open Source and Digital Libraries: A Current Trend in University Libraries around the World

ERIC Educational Resources Information Center

Krishnamurthy, M.

2008-01-01

Purpose: The purpose of this paper is to describe the open access and open source movement in the digital library world. Design/methodology/approach: A review of key developments in the open access and open source movement is provided. Findings: Open source software and open access to research findings are of great use to scholars in developing…

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/ .

Description of the U.S. Geological Survey Geo Data Portal data integration framework

USGS Publications Warehouse

Blodgett, David L.; Booth, Nathaniel L.; Kunicki, Thomas C.; Walker, Jordan I.; Lucido, Jessica M.

2012-01-01

The U.S. Geological Survey has developed an open-standard data integration framework for working efficiently and effectively with large collections of climate and other geoscience data. A web interface accesses catalog datasets to find data services. Data resources can then be rendered for mapping and dataset metadata are derived directly from these web services. Algorithm configuration and information needed to retrieve data for processing are passed to a server where all large-volume data access and manipulation takes place. The data integration strategy described here was implemented by leveraging existing free and open source software. Details of the software used are omitted; rather, emphasis is placed on how open-standard web services and data encodings can be used in an architecture that integrates common geographic and atmospheric data.

New Open-Source Version of FLORIS Released | News | NREL

Science.gov Websites

New Open-Source Version of FLORIS Released New Open-Source Version of FLORIS Released January 26 , 2018 National Renewable Energy Laboratory (NREL) researchers recently released an updated open-source simplified and documented. Because of the living, open-source nature of the newly updated utility, NREL

Pharmer: efficient and exact pharmacophore search.

PubMed

Koes, David Ryan; Camacho, Carlos J

2011-06-27

Pharmacophore search is a key component of many drug discovery efforts. Pharmer is a new computational approach to pharmacophore search that scales with the breadth and complexity of the query, not the size of the compound library being screened. Two novel methods for organizing pharmacophore data, the Pharmer KDB-tree and Bloom fingerprints, enable Pharmer to perform an exact pharmacophore search of almost two million structures in less than a minute. In general, Pharmer is more than an order of magnitude faster than existing technologies. The complete source code is available under an open-source license at http://pharmer.sourceforge.net .

Automated extraction and semantic analysis of mutation impacts from the biomedical literature

PubMed Central

2012-01-01

Background Mutations as sources of evolution have long been the focus of attention in the biomedical literature. Accessing the mutational information and their impacts on protein properties facilitates research in various domains, such as enzymology and pharmacology. However, manually curating the rich and fast growing repository of biomedical literature is expensive and time-consuming. As a solution, text mining approaches have increasingly been deployed in the biomedical domain. While the detection of single-point mutations is well covered by existing systems, challenges still exist in grounding impacts to their respective mutations and recognizing the affected protein properties, in particular kinetic and stability properties together with physical quantities. Results We present an ontology model for mutation impacts, together with a comprehensive text mining system for extracting and analysing mutation impact information from full-text articles. Organisms, as sources of proteins, are extracted to help disambiguation of genes and proteins. Our system then detects mutation series to correctly ground detected impacts using novel heuristics. It also extracts the affected protein properties, in particular kinetic and stability properties, as well as the magnitude of the effects and validates these relations against the domain ontology. The output of our system can be provided in various formats, in particular by populating an OWL-DL ontology, which can then be queried to provide structured information. The performance of the system is evaluated on our manually annotated corpora. In the impact detection task, our system achieves a precision of 70.4%-71.1%, a recall of 71.3%-71.5%, and grounds the detected impacts with an accuracy of 76.5%-77%. The developed system, including resources, evaluation data and end-user and developer documentation is freely available under an open source license at http://www.semanticsoftware.info/open-mutation-miner. Conclusion We present Open Mutation Miner (OMM), the first comprehensive, fully open-source approach to automatically extract impacts and related relevant information from the biomedical literature. We assessed the performance of our work on manually annotated corpora and the results show the reliability of our approach. The representation of the extracted information into a structured format facilitates knowledge management and aids in database curation and correction. Furthermore, access to the analysis results is provided through multiple interfaces, including web services for automated data integration and desktop-based solutions for end user interactions. PMID:22759648

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.

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

Towards open collaborative health informatics - The Role of free/libre open source principles. Contribution of the IMIA Open Source Health Informatics Working Group.

PubMed

Karopka, T; Schmuhl, H; Marcelo, A; Molin, J Dal; Wright, G

2011-01-01

: To analyze the contribution of Free/Libre Open Source Software in health care (FLOSS-HC) and to give perspectives for future developments. The paper summarizes FLOSS-related trends in health care as anticipated by members of the IMIA Open Source Working Group. Data were obtained through literature review and personal experience and observations of the authors in the last two decades. A status quo is given by a frequency analysis of the database of Medfloss.org, one of the world's largest platforms dedicated to FLOSS-HC. The authors discuss current problems in the field of health care and finally give a prospective roadmap, a projection of the potential influences of FLOSS in health care. FLOSS-HC already exists for more than 2 decades. Several projects have shown that FLOSS may produce highly competitive alternatives to proprietary solutions that are at least equivalent in usability and have a better total cost of ownership ratio. The Medfloss.org database currently lists 221 projects of diverse application types. FLOSS principles hold a great potential for addressing several of the most critical problems in health care IT. The authors argue that an ecosystem perspective is relevant and that FLOSS principles are best suited to create health IT systems that are able to evolve over time as medical knowledge, technologies, insights, workflows etc. continuously change. All these factors that inherently influence the development of health IT systems are changing at an ever growing pace. Traditional models of software engineering are not able to follow these changes and provide up-to-date systems for an acceptable cost/value ratio. To allow FLOSS to positively influence Health IT in the future a "FLOSS-friendly" environment has to be provided. Policy makers should resolve uncertainties in the legal framework that disfavor FLOSS. Certification procedures should be specified in a way that they do not raise additional barriers for FLOSS.

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

PubMed

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

2012-08-01

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

Open Drug Discovery Teams: A Chemistry Mobile App for Collaboration

PubMed Central

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

2012-01-01

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

Issues of Food Chain Security and Case Studies in the Czech Army

NASA Astrophysics Data System (ADS)

Komar, Ales; Vasicka, Pavlina

Food supply system is fundamental extremely open complex. Global challenge is acknowledged and must be considered because food is important source of existence and can be used as a desirable terrorist vehicle. Raw material and food featured intentional versus accidental contamination. Manifestation of global challenges, aspiration for sustainable development and appearance of terrorism create the new paradigm for threats to food safety and defence management.

Combining Risk Analysis and Slicing for Test Reduction in Open Architecture

DTIC Science & Technology

2014-04-30

collection of information is estimated to average 1 hour per response, including the time for reviewing instructions, searching existing data sources...full-system testing, whose purpose is to check that all the parts work harmoniously together. This part of the effort cannot be reduced unless it is...that eliminates program statements irrelevant to a given slicing criterion. Slicing algorithms detect and follow dependencies of the kinds described

PAL: A Positional Astronomy Library

NASA Astrophysics Data System (ADS)

Jenness, T.; Berry, D. S.

2013-10-01

PAL is a new positional astronomy library written in C that attempts to retain the SLALIB API but is distributed with an open source GPL license. The library depends on the IAU SOFA library wherever a SOFA routine exists and uses the most recent nutation and precession models. Currently about 100 of the 200 SLALIB routines are available. Interfaces are also available from Perl and Python. PAL is freely available via github.

Mobile Computing Solutions for Effective and Efficient Generation and Dissemination of Tactical Operations Orders

DTIC Science & Technology

2017-06-01

and Joint doctrine, to establish a new paradigm for capturing, storing and transmitting the informational elements of an operations order. We...developed a working technology demonstrator that incorporates a new object-oriented data structure into existing open-source mobile technology to provide...instructor and practitioner in conjunction with Marine Corps and Joint doctrine, to establish a new paradigm for capturing, storing and transmitting the

A Descriptive Study of the Utilization of Behavioral Health Resources in the Fort Hood Catchment Area

DTIC Science & Technology

2008-07-15

therapy (CBT), eye movement desensitization and reprocessing ( EMDR ), and medications, particularly selective serotonin reuptake inhibitors (SSRI...Test. CAGE is an acronym created by taking the first letter of the words Cut Down, Annoyed, Guilty, and Eye Opener, which are words imbedded in the...hour per response, including the time for reviewing instructions, searching existing data sources gathering end maintaining the data needed, and

The Membership and Distance of the Open Cluster Collinder 419

DTIC Science & Technology

2010-09-01

distance based upon new spectral classifications of the brighter members, UBV photometry , and an analysis of astrometric and photometric data from the... photometry of the fainter cluster members in Section 4. Our results are summarized in Section 5. 2. SPECTROSCOPY AND REDDENING OF THE BRIGHTER STARS...including the time for reviewing instructions, searching existing data sources, gathering and maintaining the data needed, and completing and reviewing

Modeling the Galaxy-Halo Connection: An open-source approach with Halotools

NASA Astrophysics Data System (ADS)

Hearin, Andrew

2016-03-01

Although the modern form of galaxy-halo modeling has been in place for over ten years, there exists no common code base for carrying out large-scale structure calculations. Considering, for example, the advances in CMB science made possible by Boltzmann-solvers such as CMBFast, CAMB and CLASS, there are clear precedents for how theorists working in a well-defined subfield can mutually benefit from such a code base. Motivated by these and other examples, I present Halotools: an open-source, object-oriented python package for building and testing models of the galaxy-halo connection. Halotools is community-driven, and already includes contributions from over a dozen scientists spread across numerous universities. Designed with high-speed performance in mind, the package generates mock observations of synthetic galaxy populations with sufficient speed to conduct expansive MCMC likelihood analyses over a diverse and highly customizable set of models. The package includes an automated test suite and extensive web-hosted documentation and tutorials (halotools.readthedocs.org). I conclude the talk by describing how Halotools can be used to analyze existing datasets to obtain robust and novel constraints on galaxy evolution models, and by outlining the Halotools program to prepare the field of cosmology for the arrival of Stage IV dark energy experiments.

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

Open for Business

ERIC Educational Resources Information Center

Voyles, Bennett

2007-01-01

People know about the Sakai Project (open source course management system); they may even know about Kuali (open source financials). So, what is the next wave in open source software? This article discusses business intelligence (BI) systems. Though open source BI may still be only a rumor in most campus IT departments, some brave early adopters…

Open Access to research data - final perspectives from the RECODE project

NASA Astrophysics Data System (ADS)

Bigagli, Lorenzo; Sondervan, Jeroen

2015-04-01

Many networks, initiatives, and communities are addressing the key barriers to Open Access to data in scientific research. These organizations are typically heterogeneous and fragmented by discipline, location, sector (publishers, academics, data centers, etc.), as well as by other features. Besides, they often work in isolation, or with limited contacts with one another. The Policy RECommendations for Open Access to Research Data in Europe (RECODE) project, which will conclude in the first half of 2015, has scoped and addressed the challenges related to Open Access, dissemination and preservation of scientific data, leveraging the existing networks, initiatives, and communities. The overall objective of RECODE was to identify a series of targeted and over-arching policy recommendations for Open Access to European research data based on existing good practice. RECODE has undertaken a review of the existing state of the art and examined five case studies in different scientific disciplines: particle physics and astrophysics, clinical research, medicine and technical physiology (bioengineering), humanities (archaeology), and environmental sciences (Earth Observation). In particular for the latter discipline, GEOSS has been an optimal test bed for investigating the importance of technical and multidisciplinary interoperability, and what the challenges are in sharing and providing Open Access to research data from a variety of sources, and in a variety of formats. RECODE has identified five main technological and infrastructural challenges: • Heterogeneity - relates to interoperability, usability, accessibility, discoverability; • Sustainability - relates to obsolescence, curation, updates/upgrades, persistence, preservation; • Volume - also related to Big Data, which is somehow implied by Open Data; in our context, it relates to discoverability, accessibility (indexing), bandwidth, storage, scalability, energy footprint; • Quality - relates to completeness, description (metadata), usability, data (peer) review; • Security - relates to the technical aspects of policy enforcement, such the AAA-protocol for authentication, authorization and auditing/accounting, privacy issues, etc. RECODE has also focused on the identification of stakeholder values relevant to Open Access to research data, as well as on policy, legal, and institutional aspects. All these issues are of immediate relevance for the whole scientific ecosystem, including researchers, as data producers/users, as well as publishers and libraries, as means for data dissemination and management.

Criteria for Public Open Space Enhancement to Achieve Social Interaction: a Review Paper

NASA Astrophysics Data System (ADS)

Salih, S. A.; Ismail, S.

2017-12-01

A This paper presents a various literatures, studies, transcripts and papers aiming to provide an overview of some theories and existing research on the significance of natural environments and green open spaces to achieve social interaction and outdoor recreation. The main objective of the paper is to identify the factors that affecting social interaction in green open spaces, through proving that an appropriate open spaces is important to enhance social interaction and community. This study employs (qualitative) summarizing content analysis method which mainly focused on collect and summarizing of documentation such as transcripts, articles, papers, and books from more than 25 source, regarding the importance of public open spaces for the community. The summarizing content analysis of this paper is the fundament for a qualitative oriented procedure of text interpretation used to analyse the information gathered. Results of this study confirms that sound social interaction need an appropriate physical space including criteria of: design, activities, access and linkage, administration and maintenance, place attachment and users’ characteristics, also previous studies in this area have a health perspective with measures of physical activity of open spaces in general.

Development of Open source-based automatic shooting and processing UAV imagery for Orthoimage Using Smart Camera UAV

NASA Astrophysics Data System (ADS)

Park, J. W.; Jeong, H. H.; Kim, J. S.; Choi, C. U.

2016-06-01

Recently, aerial photography with unmanned aerial vehicle (UAV) system uses UAV and remote controls through connections of ground control system using bandwidth of about 430 MHz radio Frequency (RF) modem. However, as mentioned earlier, existing method of using RF modem has limitations in long distance communication. The Smart Camera equipments's LTE (long-term evolution), Bluetooth, and Wi-Fi to implement UAV that uses developed UAV communication module system carried out the close aerial photogrammetry with the automatic shooting. Automatic shooting system is an image capturing device for the drones in the area's that needs image capturing and software for loading a smart camera and managing it. This system is composed of automatic shooting using the sensor of smart camera and shooting catalog management which manages filmed images and information. Processing UAV imagery module used Open Drone Map. This study examined the feasibility of using the Smart Camera as the payload for a photogrammetric UAV system. The open soure tools used for generating Android, OpenCV (Open Computer Vision), RTKLIB, Open Drone Map.

The Commercial Open Source Business Model

NASA Astrophysics Data System (ADS)

Riehle, Dirk

Commercial open source software projects are open source software projects that are owned by a single firm that derives a direct and significant revenue stream from the software. Commercial open source at first glance represents an economic paradox: How can a firm earn money if it is making its product available for free as open source? This paper presents the core properties of com mercial open source business models and discusses how they work. Using a commercial open source approach, firms can get to market faster with a superior product at lower cost than possible for traditional competitors. The paper shows how these benefits accrue from an engaged and self-supporting user community. Lacking any prior comprehensive reference, this paper is based on an analysis of public statements by practitioners of commercial open source. It forges the various anecdotes into a coherent description of revenue generation strategies and relevant business functions.

Large-scale adverse effects related to treatment evidence standardization (LAERTES): an open scalable system for linking pharmacovigilance evidence sources with clinical data.

PubMed

2017-03-07

Integrating multiple sources of pharmacovigilance evidence has the potential to advance the science of safety signal detection and evaluation. In this regard, there is a need for more research on how to integrate multiple disparate evidence sources while making the evidence computable from a knowledge representation perspective (i.e., semantic enrichment). Existing frameworks suggest well-promising outcomes for such integration but employ a rather limited number of sources. In particular, none have been specifically designed to support both regulatory and clinical use cases, nor have any been designed to add new resources and use cases through an open architecture. This paper discusses the architecture and functionality of a system called Large-scale Adverse Effects Related to Treatment Evidence Standardization (LAERTES) that aims to address these shortcomings. LAERTES provides a standardized, open, and scalable architecture for linking evidence sources relevant to the association of drugs with health outcomes of interest (HOIs). Standard terminologies are used to represent different entities. For example, drugs and HOIs are represented in RxNorm and Systematized Nomenclature of Medicine -- Clinical Terms respectively. At the time of this writing, six evidence sources have been loaded into the LAERTES evidence base and are accessible through prototype evidence exploration user interface and a set of Web application programming interface services. This system operates within a larger software stack provided by the Observational Health Data Sciences and Informatics clinical research framework, including the relational Common Data Model for observational patient data created by the Observational Medical Outcomes Partnership. Elements of the Linked Data paradigm facilitate the systematic and scalable integration of relevant evidence sources. The prototype LAERTES system provides useful functionality while creating opportunities for further research. Future work will involve improving the method for normalizing drug and HOI concepts across the integrated sources, aggregated evidence at different levels of a hierarchy of HOI concepts, and developing more advanced user interface for drug-HOI investigations.

High performance geospatial and climate data visualization using GeoJS

NASA Astrophysics Data System (ADS)

Chaudhary, A.; Beezley, J. D.

2015-12-01

GeoJS (https://github.com/OpenGeoscience/geojs) is an open-source library developed to support interactive scientific and geospatial visualization of climate and earth science datasets in a web environment. GeoJS has a convenient application programming interface (API) that enables users to harness the fast performance of WebGL and Canvas 2D APIs with sophisticated Scalable Vector Graphics (SVG) features in a consistent and convenient manner. We started the project in response to the need for an open-source JavaScript library that can combine traditional geographic information systems (GIS) and scientific visualization on the web. Many libraries, some of which are open source, support mapping or other GIS capabilities, but lack the features required to visualize scientific and other geospatial datasets. For instance, such libraries are not be capable of rendering climate plots from NetCDF files, and some libraries are limited in regards to geoinformatics (infovis in a geospatial environment). While libraries such as d3.js are extremely powerful for these kinds of plots, in order to integrate them into other GIS libraries, the construction of geoinformatics visualizations must be completed manually and separately, or the code must somehow be mixed in an unintuitive way.We developed GeoJS with the following motivations:• To create an open-source geovisualization and GIS library that combines scientific visualization with GIS and informatics• To develop an extensible library that can combine data from multiple sources and render them using multiple backends• To build a library that works well with existing scientific visualizations tools such as VTKWe have successfully deployed GeoJS-based applications for multiple domains across various projects. The ClimatePipes project funded by the Department of Energy, for example, used GeoJS to visualize NetCDF datasets from climate data archives. Other projects built visualizations using GeoJS for interactively exploring data and analysis regarding 1) the human trafficking domain, 2) New York City taxi drop-offs and pick-ups, and 3) the Ebola outbreak. GeoJS supports advanced visualization features such as picking and selecting, as well as clustering. It also supports 2D contour plots, vector plots, heat maps, and geospatial graphs.

Openly Published Environmental Sensing (OPEnS) | Advancing Open-Source Research, Instrumentation, and Dissemination

NASA Astrophysics Data System (ADS)

Udell, C.; Selker, J. S.

2017-12-01

The increasing availability and functionality of Open-Source software and hardware along with 3D printing, low-cost electronics, and proliferation of open-access resources for learning rapid prototyping are contributing to fundamental transformations and new technologies in environmental sensing. These tools invite reevaluation of time-tested methodologies and devices toward more efficient, reusable, and inexpensive alternatives. Building upon Open-Source design facilitates community engagement and invites a Do-It-Together (DIT) collaborative framework for research where solutions to complex problems may be crowd-sourced. However, barriers persist that prevent researchers from taking advantage of the capabilities afforded by open-source software, hardware, and rapid prototyping. Some of these include: requisite technical skillsets, knowledge of equipment capabilities, identifying inexpensive sources for materials, money, space, and time. A university MAKER space staffed by engineering students to assist researchers is one proposed solution to overcome many of these obstacles. This presentation investigates the unique capabilities the USDA-funded Openly Published Environmental Sensing (OPEnS) Lab affords researchers, within Oregon State and internationally, and the unique functions these types of initiatives support at the intersection of MAKER spaces, Open-Source academic research, and open-access dissemination.

Ensembl 2004.

PubMed

Birney, E; Andrews, D; Bevan, P; Caccamo, M; Cameron, G; Chen, Y; Clarke, L; Coates, G; Cox, T; Cuff, J; Curwen, V; Cutts, T; Down, T; Durbin, R; Eyras, E; Fernandez-Suarez, X M; Gane, P; Gibbins, B; Gilbert, J; Hammond, M; Hotz, H; Iyer, V; Kahari, A; Jekosch, K; Kasprzyk, A; Keefe, D; Keenan, S; Lehvaslaiho, H; McVicker, G; Melsopp, C; Meidl, P; Mongin, E; Pettett, R; Potter, S; Proctor, G; Rae, M; Searle, S; Slater, G; Smedley, D; Smith, J; Spooner, W; Stabenau, A; Stalker, J; Storey, R; Ureta-Vidal, A; Woodwark, C; Clamp, M; Hubbard, T

2004-01-01

The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organize biology around the sequences of large genomes. It is a comprehensive and integrated source of annotation of large genome sequences, available via interactive website, web services or flat files. As well as being one of the leading sources of genome annotation, Ensembl is an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements. The facilities of the system range from sequence analysis to data storage and visualization and installations exist around the world both in companies and at academic sites. With a total of nine genome sequences available from Ensembl and more genomes to follow, recent developments have focused mainly on closer integration between genomes and external data.

Assessing biodiversity on the farm scale as basis for ecosystem service payments.

PubMed

von Haaren, Christina; Kempa, Daniela; Vogel, Katrin; Rüter, Stefan

2012-12-30

Ecosystem services payments must be based on a standardised transparent assessment of the goods and services provided. This is especially relevant in the context of EU agri-environmental programs, but also for organic-food companies that foster environmental services on their contractor farms. Addressing the farm scale is important because land users/owners are major recipients of payments and they could be more involved in data generation and conservation management. A standardised system for measuring on-farm biodiversity does not yet exist that concentrates on performance indicators and includes farmers in generating information. A method is required that produces ordinal or metric scaled assessment results as well as management measures. Another requirement is the ease of application, which includes the ease of gathering input data and understandability. In order to respond to this need, we developed a method which is designed for automated application in an open source farm assessment system named MANUELA. The method produces an ordinal scale assessment of biodiversity that includes biotopes, species, biotope connectivity and the influence of land use. In addition, specific measures for biotope types are proposed. The open source geographical information system OpenJump is used for the implementation of MANUELA. The results of the trial applications and robustness tests show that the assessment can be implemented, for the most part, using existing information as well as data available from farmers or advisors. The results are more sensitive for showing on-farm achievements and changes than existing biotope-type classifications. Such a differentiated classification is needed as a basis for ecosystem service payments and for designing effective measures. The robustness of the results with respect to biotope connectivity is comparable to that of complex models, but it should be further improved. Interviews with the test farmers substantiate that the assessment methods can be implemented on farms and they are understood by farmers. Copyright © 2012 Elsevier Ltd. All rights reserved.

Open-source software: not quite endsville.

PubMed

Stahl, Matthew T

2005-02-01

Open-source software will never achieve ubiquity. There are environments in which it simply does not flourish. By its nature, open-source development requires free exchange of ideas, community involvement, and the efforts of talented and dedicated individuals. However, pressures can come from several sources that prevent this from happening. In addition, openness and complex licensing issues invite misuse and abuse. Care must be taken to avoid the pitfalls of open-source software.

Developing an Open Source Option for NASA Software

NASA Technical Reports Server (NTRS)

Moran, Patrick J.; Parks, John W. (Technical Monitor)

2003-01-01

We present arguments in favor of developing an Open Source option for NASA software; in particular we discuss how Open Source is compatible with NASA's mission. We compare and contrast several of the leading Open Source licenses, and propose one - the Mozilla license - for use by NASA. We also address some of the related issues for NASA with respect to Open Source. In particular, we discuss some of the elements in the External Release of NASA Software document (NPG 2210.1A) that will likely have to be changed in order to make Open Source a reality withm the agency.

Federated Space-Time Query for Earth Science Data Using OpenSearch Conventions

NASA Astrophysics Data System (ADS)

Lynnes, C.; Beaumont, B.; Duerr, R. E.; Hua, H.

2009-12-01

The past decade has seen a burgeoning of remote sensing and Earth science data providers, as evidenced in the growth of the Earth Science Information Partner (ESIP) federation. At the same time, the need to combine diverse data sets to enable understanding of the Earth as a system has also grown. While the expansion of data providers is in general a boon to such studies, the diversity presents a challenge to finding useful data for a given study. Locating all the data files with aerosol information for a particular volcanic eruption, for example, may involve learning and using several different search tools to execute the requisite space-time queries. To address this issue, the ESIP federation is developing a federated space-time query framework, based on the OpenSearch convention (www.opensearch.org), with Geo and Time extensions. In this framework, data providers publish OpenSearch Description Documents that describe in a machine-readable form how to execute queries against the provider. The novelty of OpenSearch is that the space-time query interface becomes both machine callable and easy enough to integrate into the web browser's search box. This flexibility, together with a simple REST (HTTP-get) interface, should allow a variety of data providers to participate in the federated search framework, from large institutional data centers to individual scientists. The simple interface enables trivial querying of multiple data sources and participation in recursive-like federated searches--all using the same common OpenSearch interface. This simplicity also makes the construction of clients easy, as does existing OpenSearch client libraries in a variety of languages. Moreover, a number of clients and aggregation services already exist and OpenSearch is already supported by a number of web browsers such as Firefox and Internet Explorer.

The Earthquake Source Inversion Validation (SIV) - Project: Summary, Status, Outlook

NASA Astrophysics Data System (ADS)

Mai, P. M.

2017-12-01

Finite-fault earthquake source inversions infer the (time-dependent) displacement on the rupture surface from geophysical data. The resulting earthquake source models document the complexity of the rupture process. However, this kinematic source inversion is ill-posed and returns non-unique solutions, as seen for instance in multiple source models for the same earthquake, obtained by different research teams, that often exhibit remarkable dissimilarities. To address the uncertainties in earthquake-source inversions and to understand strengths and weaknesses of various methods, the Source Inversion Validation (SIV) project developed a set of forward-modeling exercises and inversion benchmarks. Several research teams then use these validation exercises to test their codes and methods, but also to develop and benchmark new approaches. In this presentation I will summarize the SIV strategy, the existing benchmark exercises and corresponding results. Using various waveform-misfit criteria and newly developed statistical comparison tools to quantify source-model (dis)similarities, the SIV platforms is able to rank solutions and identify particularly promising source inversion approaches. Existing SIV exercises (with related data and descriptions) and all computational tools remain available via the open online collaboration platform; additional exercises and benchmark tests will be uploaded once they are fully developed. I encourage source modelers to use the SIV benchmarks for developing and testing new methods. The SIV efforts have already led to several promising new techniques for tackling the earthquake-source imaging problem. I expect that future SIV benchmarks will provide further innovations and insights into earthquake source kinematics that will ultimately help to better understand the dynamics of the rupture process.

Evaluation of DICOM viewer software for workflow integration in clinical trials

NASA Astrophysics Data System (ADS)

Haak, Daniel; Page, Charles E.; Kabino, Klaus; Deserno, Thomas M.

2015-03-01

The digital imaging and communications in medicine (DICOM) protocol is nowadays the leading standard for capture, exchange and storage of image data in medical applications. A broad range of commercial, free, and open source software tools supporting a variety of DICOM functionality exists. However, different from patient's care in hospital, DICOM has not yet arrived in electronic data capture systems (EDCS) for clinical trials. Due to missing integration, even just the visualization of patient's image data in electronic case report forms (eCRFs) is impossible. Four increasing levels for integration of DICOM components into EDCS are conceivable, raising functionality but also demands on interfaces with each level. Hence, in this paper, a comprehensive evaluation of 27 DICOM viewer software projects is performed, investigating viewing functionality as well as interfaces for integration. Concerning general, integration, and viewing requirements the survey involves the criteria (i) license, (ii) support, (iii) platform, (iv) interfaces, (v) two-dimensional (2D) and (vi) three-dimensional (3D) image viewing functionality. Optimal viewers are suggested for applications in clinical trials for 3D imaging, hospital communication, and workflow. Focusing on open source solutions, the viewers ImageJ and MicroView are superior for 3D visualization, whereas GingkoCADx is advantageous for hospital integration. Concerning workflow optimization in multi-centered clinical trials, we suggest the open source viewer Weasis. Covering most use cases, an EDCS and PACS interconnection with Weasis is suggested.

An open source solution for an in-house built dynamic platform for the validation of stereotactic ablative body radiotherapy for VMAT and IMRT.

PubMed

Munoz, Luis; Ziebell, Amy; Morton, Jason; Bhat, Madhava

2016-12-01

An in-house solution for the verification of dose delivered to a moving phantom as required for the clinical implementation of lung stereotactic ablative body radiation therapy was developed. The superior-inferior movement required to simulate tumour motion during a normal breathing cycle was achieved via the novel use of an Arduino Uno™, a low-cost open-source microcontroller board connected to a high torque servo motor. Slow CT imaging was used to acquire the image set and a 4D cone beam CT (4D-CBCT) verified the efficacy of contoured margins before treatment on the moving phantom. Treatment fields were delivered to a section of a CIRS™ anthropomorphic phantom. Dose verification to the dynamic phantom with Gafchromic EBT3 film using 3 %-1 mm gamma analysis acceptance criteria registered an absolute dose pass rate for IMRT and VMAT of 98 and 96.6 %, respectively. It was verified that 100 % of the PTV received the prescribed dose of 12 Gy per fraction using the dynamic phantom, and no major discrepancy between planned and measured results due to interplay between multileaf collimator sequences and target motion was observed. This study confirmed that the use of an in-house solution using open source hardware and software with existing quality assurance equipment was appropriate in validating a new treatment technique.

compomics-utilities: an open-source Java library for computational proteomics.

PubMed

Barsnes, Harald; Vaudel, Marc; Colaert, Niklaas; Helsens, Kenny; Sickmann, Albert; Berven, Frode S; Martens, Lennart

2011-03-08

The growing interest in the field of proteomics has increased the demand for software tools and applications that process and analyze the resulting data. And even though the purpose of these tools can vary significantly, they usually share a basic set of features, including the handling of protein and peptide sequences, the visualization of (and interaction with) spectra and chromatograms, and the parsing of results from various proteomics search engines. Developers typically spend considerable time and effort implementing these support structures, which detracts from working on the novel aspects of their tool. In order to simplify the development of proteomics tools, we have implemented an open-source support library for computational proteomics, called compomics-utilities. The library contains a broad set of features required for reading, parsing, and analyzing proteomics data. compomics-utilities is already used by a long list of existing software, ensuring library stability and continued support and development. As a user-friendly, well-documented and open-source library, compomics-utilities greatly simplifies the implementation of the basic features needed in most proteomics tools. Implemented in 100% Java, compomics-utilities is fully portable across platforms and architectures. Our library thus allows the developers to focus on the novel aspects of their tools, rather than on the basic functions, which can contribute substantially to faster development, and better tools for proteomics.

Open-Source Data and the Study of Homicide.

PubMed

Parkin, William S; Gruenewald, Jeff

2015-07-20

To date, no discussion has taken place in the social sciences as to the appropriateness of using open-source data to augment, or replace, official data sources in homicide research. The purpose of this article is to examine whether open-source data have the potential to be used as a valid and reliable data source in testing theory and studying homicide. Official and open-source homicide data were collected as a case study in a single jurisdiction over a 1-year period. The data sets were compared to determine whether open-sources could recreate the population of homicides and variable responses collected in official data. Open-source data were able to replicate the population of homicides identified in the official data. Also, for every variable measured, the open-sources captured as much, or more, of the information presented in the official data. Also, variables not available in official data, but potentially useful for testing theory, were identified in open-sources. The results of the case study show that open-source data are potentially as effective as official data in identifying individual- and situational-level characteristics, provide access to variables not found in official homicide data, and offer geographic data that can be used to link macro-level characteristics to homicide events. © The Author(s) 2015.

A systematic literature review of open source software quality assessment models.

PubMed

Adewumi, Adewole; Misra, Sanjay; Omoregbe, Nicholas; Crawford, Broderick; Soto, Ricardo

2016-01-01

Many open source software (OSS) quality assessment models are proposed and available in the literature. However, there is little or no adoption of these models in practice. In order to guide the formulation of newer models so they can be acceptable by practitioners, there is need for clear discrimination of the existing models based on their specific properties. Based on this, the aim of this study is to perform a systematic literature review to investigate the properties of the existing OSS quality assessment models by classifying them with respect to their quality characteristics, the methodology they use for assessment, and their domain of application so as to guide the formulation and development of newer models. Searches in IEEE Xplore, ACM, Science Direct, Springer and Google Search is performed so as to retrieve all relevant primary studies in this regard. Journal and conference papers between the year 2003 and 2015 were considered since the first known OSS quality model emerged in 2003. A total of 19 OSS quality assessment model papers were selected. To select these models we have developed assessment criteria to evaluate the quality of the existing studies. Quality assessment models are classified into five categories based on the quality characteristics they possess namely: single-attribute, rounded category, community-only attribute, non-community attribute as well as the non-quality in use models. Our study reflects that software selection based on hierarchical structures is found to be the most popular selection method in the existing OSS quality assessment models. Furthermore, we found that majority (47%) of the existing models do not specify any domain of application. In conclusion, our study will be a valuable contribution to the community and helps the quality assessment model developers in formulating newer models and also to the practitioners (software evaluators) in selecting suitable OSS in the midst of alternatives.

PropeR revisited.

PubMed

van der Linden, Helma; Talmon, Jan; Tange, Huibert; Grimson, Jane; Hasman, Arie

2005-03-01

The PropeR EHR system (PropeRWeb) is a multidisciplinary electronic health record (EHR) system for multidisciplinary use in extramural patient care for stroke patients. The system is built using existing open source components and is based on open standards. It is implemented as a web application using servlets and Java Server Pages (JSP's) with a CORBA connection to the database servers, which are based on the OMG HDTF specifications. PropeRWeb is a generic system which can be readily customized for use in a variety of clinical domains. The system proved to be stable and flexible, although some aspects (a.o. user friendliness) could be improved. These improvements are currently under development in a second version.

A small, lightweight multipollutant sensor system for ground-mobile and aerial emission sampling from open area sources

NASA Astrophysics Data System (ADS)

Zhou, Xiaochi; Aurell, Johanna; Mitchell, William; Tabor, Dennis; Gullett, Brian

2017-04-01

Characterizing highly dynamic, transient, and vertically lofted emissions from open area sources poses unique measurement challenges. This study developed and applied a multipollutant sensor and time-integrated sampler system for use on mobile applications such as vehicles, tethered balloons (aerostats) and unmanned aerial vehicles (UAVs) to determine emission factors. The system is particularly applicable to open area sources, such as forest fires, due to its light weight (3.5 kg), compact size (6.75 L), and internal power supply. The sensor system, termed ;Kolibri;, consists of sensors measuring CO2 and CO, and samplers for particulate matter (PM) and volatile organic compounds (VOCs). The Kolibri is controlled by a microcontroller which can record and transfer data in real time through a radio module. Selection of the sensors was based on laboratory testing for accuracy, response delay and recovery, cross-sensitivity, and precision. The Kolibri was compared against rack-mounted continuous emissions monitoring system (CEMs) and another mobile sampling instrument (the ;Flyer;) that has been used in over ten open area pollutant sampling events. Our results showed that the time series of CO, CO2, and PM2.5 concentrations measured by the Kolibri agreed well with those from the CEMs and the Flyer, with a laboratory-tested percentage error of 4.9%, 3%, and 5.8%, respectively. The VOC emission factors obtained using the Kolibri were consistent with existing literature values that relate concentration to modified combustion efficiency. The potential effect of rotor downwash on particle sampling was investigated in an indoor laboratory and the preliminary results suggested that its influence is minimal. Field application of the Kolibri sampling open detonation plumes indicated that the CO and CO2 sensors responded dynamically and their concentrations co-varied with emission transients. The Kolibri system can be applied to various challenging open area scenarios such as fires, lagoons, flares, and landfills.

Autocorrel I: A Neural Network Based Network Event Correlation Approach

DTIC Science & Technology

2005-05-01

which concern any component of the network. 2.1.1 Existing Intrusion Detection Systems EMERALD [8] is a distributed, scalable, hierarchal, customizable...writing this paper, the updaters of this system had not released their correlation unit to the public. EMERALD ex- plicitly divides statistical analysis... EMERALD , NetSTAT is scalable and composi- ble. QuidSCOR [12] is an open-source IDS, though it requires a subscription from its publisher, Qualys Inc

Mousetrap: An integrated, open-source mouse-tracking package.

PubMed

Kieslich, Pascal J; Henninger, Felix

2017-10-01

Mouse-tracking - the analysis of mouse movements in computerized experiments - is becoming increasingly popular in the cognitive sciences. Mouse movements are taken as an indicator of commitment to or conflict between choice options during the decision process. Using mouse-tracking, researchers have gained insight into the temporal development of cognitive processes across a growing number of psychological domains. In the current article, we present software that offers easy and convenient means of recording and analyzing mouse movements in computerized laboratory experiments. In particular, we introduce and demonstrate the mousetrap plugin that adds mouse-tracking to OpenSesame, a popular general-purpose graphical experiment builder. By integrating with this existing experimental software, mousetrap allows for the creation of mouse-tracking studies through a graphical interface, without requiring programming skills. Thus, researchers can benefit from the core features of a validated software package and the many extensions available for it (e.g., the integration with auxiliary hardware such as eye-tracking, or the support of interactive experiments). In addition, the recorded data can be imported directly into the statistical programming language R using the mousetrap package, which greatly facilitates analysis. Mousetrap is cross-platform, open-source and available free of charge from https://github.com/pascalkieslich/mousetrap-os .

An open-source model and solution method to predict co-contraction in the finger.

PubMed

MacIntosh, Alexander R; Keir, Peter J

2017-10-01

A novel open-source biomechanical model of the index finger with an electromyography (EMG)-constrained static optimization solution method are developed with the goal of improving co-contraction estimates and providing means to assess tendon tension distribution through the finger. The Intrinsic model has four degrees of freedom and seven muscles (with a 14 component extensor mechanism). A novel plugin developed for the OpenSim modelling software applied the EMG-constrained static optimization solution method. Ten participants performed static pressing in three finger postures and five dynamic free motion tasks. Index finger 3D kinematics, force (5, 15, 30 N), and EMG (4 extrinsic muscles and first dorsal interosseous) were used in the analysis. The Intrinsic model predicted co-contraction increased by 29% during static pressing over the existing model. Further, tendon tension distribution patterns and forces, known to be essential to produce finger action, were determined by the model across all postures. The Intrinsic model and custom solution method improved co-contraction estimates to facilitate force propagation through the finger. These tools improve our interpretation of loads in the finger to develop better rehabilitation and workplace injury risk reduction strategies.

Google Sky as an Interactive Content Delivery System

NASA Astrophysics Data System (ADS)

Parrish, Michael

2009-05-01

In support of the International Year of Astronomy New Media Task Group's mission to create online astronomy content, several existing technologies are being leveraged. With this undertaking in mind, Google Sky provides an immersive contextual environment for both exploration and content presentation. As such, it affords opportunities for new methods of interactive media delivery. Traditional astronomy news sources and blogs are able to literally set a story at the location of their topic. Furthermore, audio based material can be complimented by a series of locations in the form of a guided tour. In order to provide automated generation and management of this content, an open source software suite has been developed.

Status of domestic wastewater management in relation to drinking-water supply in two states of India.

PubMed

Pandey, R A; Kaul, S N

2000-01-01

In India, supply of drinking water, treatment and disposal of domestic wastewater including faecal matter are managed by local bodies. The existing status of water supply, characteristics of domestic wastewater, modes of collection, treatment and disposal system for sewage and faecal matter in 82 municipalities and 4 municipal corporations were assessed in the States of Bihar and West Bengal in India. Domestic wastewater in the municipal areas is collected and discharged through open kachha (earthen), pucca (cement-concrete) and natural drains and discharged into water courses or disposed on land. Scavenger carriage system for night soil disposal is in-vogue at several places in the surveyed States. Open defecation by the inhabitants in some of the municipalities also occurs. The existing methods of collection, treatment and disposal of sewage impairs the water quality of different water sources. Techno-economically viable remedial measures for providing basic amenities, namely safe drinking-water supply and proper sanitation to the communities of these two States of India are suggested and discussed.

The state and profile of open source software projects in health and medical informatics.

PubMed

Janamanchi, Balaji; Katsamakas, Evangelos; Raghupathi, Wullianallur; Gao, Wei

2009-07-01

Little has been published about the application profiles and development patterns of open source software (OSS) in health and medical informatics. This study explores these issues with an analysis of health and medical informatics related OSS projects on SourceForge, a large repository of open source projects. A search was conducted on the SourceForge website during the period from May 1 to 15, 2007, to identify health and medical informatics OSS projects. This search resulted in a sample of 174 projects. A Java-based parser was written to extract data for several of the key variables of each project. Several visually descriptive statistics were generated to analyze the profiles of the OSS projects. Many of the projects have sponsors, implying a growing interest in OSS among organizations. Sponsorship, we discovered, has a significant impact on project success metrics. Nearly two-thirds of the projects have a restrictive license type. Restrictive licensing may indicate tighter control over the development process. Our sample includes a wide range of projects that are at various stages of development (status). Projects targeted towards the advanced end user are primarily focused on bio-informatics, data formats, database and medical science applications. We conclude that there exists an active and thriving OSS development community that is focusing on health and medical informatics. A wide range of OSS applications are in development, from bio-informatics to hospital information systems. A profile of OSS in health and medical informatics emerges that is distinct and unique to the health care field. Future research can focus on OSS acceptance and diffusion and impact on cost, efficiency and quality of health care.

How Is Open Source Special?

ERIC Educational Resources Information Center

Kapor, Mitchell

2005-01-01

Open source software projects involve the production of goods, but in software projects, the "goods" consist of information. The open source model is an alternative to the conventional centralized, command-and-control way in which things are usually made. In contrast, open source projects are genuinely decentralized and transparent. Transparent…

Common characteristics of open source software development and applicability for drug discovery: a systematic review.

PubMed

Ardal, Christine; Alstadsæter, Annette; Røttingen, John-Arne

2011-09-28

Innovation through an open source model has proven to be successful for software development. This success has led many to speculate if open source can be applied to other industries with similar success. We attempt to provide an understanding of open source software development characteristics for researchers, business leaders and government officials who may be interested in utilizing open source innovation in other contexts and with an emphasis on drug discovery. A systematic review was performed by searching relevant, multidisciplinary databases to extract empirical research regarding the common characteristics and barriers of initiating and maintaining an open source software development project. Common characteristics to open source software development pertinent to open source drug discovery were extracted. The characteristics were then grouped into the areas of participant attraction, management of volunteers, control mechanisms, legal framework and physical constraints. Lastly, their applicability to drug discovery was examined. We believe that the open source model is viable for drug discovery, although it is unlikely that it will exactly follow the form used in software development. Hybrids will likely develop that suit the unique characteristics of drug discovery. We suggest potential motivations for organizations to join an open source drug discovery project. We also examine specific differences between software and medicines, specifically how the need for laboratories and physical goods will impact the model as well as the effect of patents.

Open Source Paradigm: A Synopsis of The Cathedral and the Bazaar for Health and Social Care.

PubMed

Benson, Tim

2016-07-04

Open source software (OSS) is becoming more fashionable in health and social care, although the ideas are not new. However progress has been slower than many had expected. The purpose is to summarise the Free/Libre Open Source Software (FLOSS) paradigm in terms of what it is, how it impacts users and software engineers and how it can work as a business model in health and social care sectors. Much of this paper is a synopsis of Eric Raymond's seminal book The Cathedral and the Bazaar, which was the first comprehensive description of the open source ecosystem, set out in three long essays. Direct quotes from the book are used liberally, without reference to specific passages. The first part contrasts open and closed source approaches to software development and support. The second part describes the culture and practices of the open source movement. The third part considers business models. A key benefit of open source is that users can access and collaborate on improving the software if they wish. Closed source code may be regarded as a strategic business risk that that may be unacceptable if there is an open source alternative. The sharing culture of the open source movement fits well with that of health and social care.

Open Source Software Development

DTIC Science & Technology

2011-01-01

Software, 2002, 149(1), 3-17. 3. DiBona , C., Cooper, D., and Stone, M. (Eds.), Open Sources 2.0, 2005, O’Reilly Media, Sebastopol, CA. Also see, C... DiBona , S. Ockman, and M. Stone (Eds.). Open Sources: Vocides from the Open Source Revolution, 1999. O’Reilly Media, Sebastopol, CA. 4. Ducheneaut, N

Open-source chemogenomic data-driven algorithms for predicting drug-target interactions.

PubMed

Hao, Ming; Bryant, Stephen H; Wang, Yanli

2018-02-06

While novel technologies such as high-throughput screening have advanced together with significant investment by pharmaceutical companies during the past decades, the success rate for drug development has not yet been improved prompting researchers looking for new strategies of drug discovery. Drug repositioning is a potential approach to solve this dilemma. However, experimental identification and validation of potential drug targets encoded by the human genome is both costly and time-consuming. Therefore, effective computational approaches have been proposed to facilitate drug repositioning, which have proved to be successful in drug discovery. Doubtlessly, the availability of open-accessible data from basic chemical biology research and the success of human genome sequencing are crucial to develop effective in silico drug repositioning methods allowing the identification of potential targets for existing drugs. In this work, we review several chemogenomic data-driven computational algorithms with source codes publicly accessible for predicting drug-target interactions (DTIs). We organize these algorithms by model properties and model evolutionary relationships. We re-implemented five representative algorithms in R programming language, and compared these algorithms by means of mean percentile ranking, a new recall-based evaluation metric in the DTI prediction research field. We anticipate that this review will be objective and helpful to researchers who would like to further improve existing algorithms or need to choose appropriate algorithms to infer potential DTIs in the projects. The source codes for DTI predictions are available at: https://github.com/minghao2016/chemogenomicAlg4DTIpred. Published by Oxford University Press 2018. This work is written by US Government employees and is in the public domain in the US.

Using Support Vector Machines to Automatically Extract Open Water Signatures from POLDER Multi-Angle Data Over Boreal Regions

NASA Technical Reports Server (NTRS)

Pierce, J.; Diaz-Barrios, M.; Pinzon, J.; Ustin, S. L.; Shih, P.; Tournois, S.; Zarco-Tejada, P. J.; Vanderbilt, V. C.; Perry, G. L.; Brass, James A. (Technical Monitor)

2002-01-01

This study used Support Vector Machines to classify multiangle POLDER data. Boreal wetland ecosystems cover an estimated 90 x 10(exp 6) ha, about 36% of global wetlands, and are a major source of trace gases emissions to the atmosphere. Four to 20 percent of the global emission of methane to the atmosphere comes from wetlands north of 4 degrees N latitude. Large uncertainties in emissions exist because of large spatial and temporal variation in the production and consumption of methane. Accurate knowledge of the areal extent of open water and inundated vegetation is critical to estimating magnitudes of trace gas emissions. Improvements in land cover mapping have been sought using physical-modeling approaches, neural networks, and active microwave, examples that demonstrate the difficulties of separating open water, inundated vegetation and dry upland vegetation. Here we examine the feasibility of using a support vector machine to classify POLDER data representing open water, inundated vegetation and dry upland vegetation.

Open-source hardware for medical devices

PubMed Central

2016-01-01

Open-source hardware is hardware whose design is made publicly available so anyone can study, modify, distribute, make and sell the design or the hardware based on that design. Some open-source hardware projects can potentially be used as active medical devices. The open-source approach offers a unique combination of advantages, including reducing costs and faster innovation. This article compares 10 of open-source healthcare projects in terms of how easy it is to obtain the required components and build the device. PMID:27158528

Open-source hardware for medical devices.

PubMed

Niezen, Gerrit; Eslambolchilar, Parisa; Thimbleby, Harold

2016-04-01

Open-source hardware is hardware whose design is made publicly available so anyone can study, modify, distribute, make and sell the design or the hardware based on that design. Some open-source hardware projects can potentially be used as active medical devices. The open-source approach offers a unique combination of advantages, including reducing costs and faster innovation. This article compares 10 of open-source healthcare projects in terms of how easy it is to obtain the required components and build the device.

The case for open-source software in drug discovery.

PubMed

DeLano, Warren L

2005-02-01

Widespread adoption of open-source software for network infrastructure, web servers, code development, and operating systems leads one to ask how far it can go. Will "open source" spread broadly, or will it be restricted to niches frequented by hopeful hobbyists and midnight hackers? Here we identify reasons for the success of open-source software and predict how consumers in drug discovery will benefit from new open-source products that address their needs with increased flexibility and in ways complementary to proprietary options.

The discounting model selector: Statistical software for delay discounting applications.

PubMed

Gilroy, Shawn P; Franck, Christopher T; Hantula, Donald A

2017-05-01

Original, open-source computer software was developed and validated against established delay discounting methods in the literature. The software executed approximate Bayesian model selection methods from user-supplied temporal discounting data and computed the effective delay 50 (ED50) from the best performing model. Software was custom-designed to enable behavior analysts to conveniently apply recent statistical methods to temporal discounting data with the aid of a graphical user interface (GUI). The results of independent validation of the approximate Bayesian model selection methods indicated that the program provided results identical to that of the original source paper and its methods. Monte Carlo simulation (n = 50,000) confirmed that true model was selected most often in each setting. Simulation code and data for this study were posted to an online repository for use by other researchers. The model selection approach was applied to three existing delay discounting data sets from the literature in addition to the data from the source paper. Comparisons of model selected ED50 were consistent with traditional indices of discounting. Conceptual issues related to the development and use of computer software by behavior analysts and the opportunities afforded by free and open-sourced software are discussed and a review of possible expansions of this software are provided. © 2017 Society for the Experimental Analysis of Behavior.

PyPedia: using the wiki paradigm as crowd sourcing environment for bioinformatics protocols.

PubMed

Kanterakis, Alexandros; Kuiper, Joël; Potamias, George; Swertz, Morris A

2015-01-01

Today researchers can choose from many bioinformatics protocols for all types of life sciences research, computational environments and coding languages. Although the majority of these are open source, few of them possess all virtues to maximize reuse and promote reproducible science. Wikipedia has proven a great tool to disseminate information and enhance collaboration between users with varying expertise and background to author qualitative content via crowdsourcing. However, it remains an open question whether the wiki paradigm can be applied to bioinformatics protocols. We piloted PyPedia, a wiki where each article is both implementation and documentation of a bioinformatics computational protocol in the python language. Hyperlinks within the wiki can be used to compose complex workflows and induce reuse. A RESTful API enables code execution outside the wiki. Initial content of PyPedia contains articles for population statistics, bioinformatics format conversions and genotype imputation. Use of the easy to learn wiki syntax effectively lowers the barriers to bring expert programmers and less computer savvy researchers on the same page. PyPedia demonstrates how wiki can provide a collaborative development, sharing and even execution environment for biologists and bioinformaticians that complement existing resources, useful for local and multi-center research teams. PyPedia is available online at: http://www.pypedia.com. The source code and installation instructions are available at: https://github.com/kantale/PyPedia_server. The PyPedia python library is available at: https://github.com/kantale/pypedia. PyPedia is open-source, available under the BSD 2-Clause License.

Comparison of Point Cloud Registration Algorithms for Better Result Assessment - Towards AN Open-Source Solution

NASA Astrophysics Data System (ADS)

Lachat, E.; Landes, T.; Grussenmeyer, P.

2018-05-01

Terrestrial and airborne laser scanning, photogrammetry and more generally 3D recording techniques are used in a wide range of applications. After recording several individual 3D datasets known in local systems, one of the first crucial processing steps is the registration of these data into a common reference frame. To perform such a 3D transformation, commercial and open source software as well as programs from the academic community are available. Due to some lacks in terms of computation transparency and quality assessment in these solutions, it has been decided to develop an open source algorithm which is presented in this paper. It is dedicated to the simultaneous registration of multiple point clouds as well as their georeferencing. The idea is to use this algorithm as a start point for further implementations, involving the possibility of combining 3D data from different sources. Parallel to the presentation of the global registration methodology which has been employed, the aim of this paper is to confront the results achieved this way with the above-mentioned existing solutions. For this purpose, first results obtained with the proposed algorithm to perform the global registration of ten laser scanning point clouds are presented. An analysis of the quality criteria delivered by two selected software used in this study and a reflexion about these criteria is also performed to complete the comparison of the obtained results. The final aim of this paper is to validate the current efficiency of the proposed method through these comparisons.

Putting tools in the toolbox: Development of a free, open-source toolbox for quantitative image analysis of porous media.

NASA Astrophysics Data System (ADS)

Iltis, G.; Caswell, T. A.; Dill, E.; Wilkins, S.; Lee, W. K.

2014-12-01

X-ray tomographic imaging of porous media has proven to be a valuable tool for investigating and characterizing the physical structure and state of both natural and synthetic porous materials, including glass bead packs, ceramics, soil and rock. Given that most synchrotron facilities have user programs which grant academic researchers access to facilities and x-ray imaging equipment free of charge, a key limitation or hindrance for small research groups interested in conducting x-ray imaging experiments is the financial cost associated with post-experiment data analysis. While the cost of high performance computing hardware continues to decrease, expenses associated with licensing commercial software packages for quantitative image analysis continue to increase, with current prices being as high as $24,000 USD, for a single user license. As construction of the Nation's newest synchrotron accelerator nears completion, a significant effort is being made here at the National Synchrotron Light Source II (NSLS-II), Brookhaven National Laboratory (BNL), to provide an open-source, experiment-to-publication toolbox that reduces the financial and technical 'activation energy' required for performing sophisticated quantitative analysis of multidimensional porous media data sets, collected using cutting-edge x-ray imaging techniques. Implementation focuses on leveraging existing open-source projects and developing additional tools for quantitative analysis. We will present an overview of the software suite that is in development here at BNL including major design decisions, a demonstration of several test cases illustrating currently available quantitative tools for analysis and characterization of multidimensional porous media image data sets and plans for their future development.

Signatures of Slow Solar Wind Streams from Active Regions in the Inner Corona

NASA Astrophysics Data System (ADS)

Slemzin, V.; Harra, L.; Urnov, A.; Kuzin, S.; Goryaev, F.; Berghmans, D.

2013-08-01

The identification of solar-wind sources is an important question in solar physics. The existing solar-wind models ( e.g., the Wang-Sheeley-Arge model) provide the approximate locations of the solar wind sources based on magnetic field extrapolations. It has been suggested recently that plasma outflows observed at the edges of active regions may be a source of the slow solar wind. To explore this we analyze an isolated active region (AR) adjacent to small coronal hole (CH) in July/August 2009. On 1 August, Hinode/EUV Imaging Spectrometer observations showed two compact outflow regions in the corona. Coronal rays were observed above the active-region coronal hole (ARCH) region on the eastern limb on 31 July by STEREO-A/EUVI and at the western limb on 7 August by CORONAS- Photon/TESIS telescopes. In both cases the coronal rays were co-aligned with open magnetic-field lines given by the potential field source surface model, which expanded into the streamer. The solar-wind parameters measured by STEREO-B, ACE, Wind, and STEREO-A confirmed the identification of the ARCH as a source region of the slow solar wind. The results of the study support the suggestion that coronal rays can represent signatures of outflows from ARs propagating in the inner corona along open field lines into the heliosphere.

Special population planner 4 : an open source release.

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

Kuiper, J.; Metz, W.; Tanzman, E.

2008-01-01

Emergencies like Hurricane Katrina and the recent California wildfires underscore the critical need to meet the complex challenge of planning for individuals with special needs and for institutionalized special populations. People with special needs and special populations often have difficulty responding to emergencies or taking protective actions, and emergency responders may be unaware of their existence and situations during a crisis. Special Population Planner (SPP) is an ArcGIS-based emergency planning system released as an open source product. SPP provides for easy production of maps, reports, and analyses to develop and revise emergency response plans. It includes tools to manage amore » voluntary registry of data for people with special needs, integrated links to plans and documents, tools for response planning and analysis, preformatted reports and maps, and data on locations of special populations, facility and resource characteristics, and contacts. The system can be readily adapted for new settings without programming and is broadly applicable. Full documentation and a demonstration database are included in the release.« less

Localizer: fast, accurate, open-source, and modular software package for superresolution microscopy

PubMed Central

Duwé, Sam; Neely, Robert K.; Zhang, Jin

2012-01-01

Abstract. We present Localizer, a freely available and open source software package that implements the computational data processing inherent to several types of superresolution fluorescence imaging, such as localization (PALM/STORM/GSDIM) and fluctuation imaging (SOFI/pcSOFI). Localizer delivers high accuracy and performance and comes with a fully featured and easy-to-use graphical user interface but is also designed to be integrated in higher-level analysis environments. Due to its modular design, Localizer can be readily extended with new algorithms as they become available, while maintaining the same interface and performance. We provide front-ends for running Localizer from Igor Pro, Matlab, or as a stand-alone program. We show that Localizer performs favorably when compared with two existing superresolution packages, and to our knowledge is the only freely available implementation of SOFI/pcSOFI microscopy. By dramatically improving the analysis performance and ensuring the easy addition of current and future enhancements, Localizer strongly improves the usability of superresolution imaging in a variety of biomedical studies. PMID:23208219

CACTI: free, open-source software for the sequential coding of behavioral interactions.

PubMed

Glynn, Lisa H; Hallgren, Kevin A; Houck, Jon M; Moyers, Theresa B

2012-01-01

The sequential analysis of client and clinician speech in psychotherapy sessions can help to identify and characterize potential mechanisms of treatment and behavior change. Previous studies required coding systems that were time-consuming, expensive, and error-prone. Existing software can be expensive and inflexible, and furthermore, no single package allows for pre-parsing, sequential coding, and assignment of global ratings. We developed a free, open-source, and adaptable program to meet these needs: The CASAA Application for Coding Treatment Interactions (CACTI). Without transcripts, CACTI facilitates the real-time sequential coding of behavioral interactions using WAV-format audio files. Most elements of the interface are user-modifiable through a simple XML file, and can be further adapted using Java through the terms of the GNU Public License. Coding with this software yields interrater reliabilities comparable to previous methods, but at greatly reduced time and expense. CACTI is a flexible research tool that can simplify psychotherapy process research, and has the potential to contribute to the improvement of treatment content and delivery.

Uni10: an open-source library for tensor network algorithms

NASA Astrophysics Data System (ADS)

Kao, Ying-Jer; Hsieh, Yun-Da; Chen, Pochung

2015-09-01

We present an object-oriented open-source library for developing tensor network algorithms written in C++ called Uni10. With Uni10, users can build a symmetric tensor from a collection of bonds, while the bonds are constructed from a list of quantum numbers associated with different quantum states. It is easy to label and permute the indices of the tensors and access a block associated with a particular quantum number. Furthermore a network class is used to describe arbitrary tensor network structure and to perform network contractions efficiently. We give an overview of the basic structure of the library and the hierarchy of the classes. We present examples of the construction of a spin-1 Heisenberg Hamiltonian and the implementation of the tensor renormalization group algorithm to illustrate the basic usage of the library. The library described here is particularly well suited to explore and fast prototype novel tensor network algorithms and to implement highly efficient codes for existing algorithms.

A modular approach to disease registry design: successful adoption of an internet-based rare disease registry.

PubMed

Bellgard, Matthew I; Macgregor, Andrew; Janon, Fred; Harvey, Adam; O'Leary, Peter; Hunter, Adam; Dawkins, Hugh

2012-10-01

There is a need to develop Internet-based rare disease registries to support health care stakeholders to deliver improved quality patient outcomes. Such systems should be architected to enable multiple-level access by a range of user groups within a region or across regional/country borders in a secure and private way. However, this functionality is currently not available in many existing systems. A new approach to the design of an Internet-based architecture for disease registries has been developed for patients with clinical and genetic data in geographical disparate locations. The system addresses issues of multiple-level access by key stakeholders, security and privacy. The system has been successfully adopted for specific rare diseases in Australia and is open source. The results of this work demonstrate that it is feasible to design an open source Internet-based disease registry system in a scalable and customizable fashion and designed to facilitate interoperability with other systems. © 2012 Wiley Periodicals, Inc.

HERAFitter: Open source QCD fit project

DOE PAGES

Alekhin, S.; Behnke, O.; Belov, P.; ...

2015-07-01

HERAFitter is an open-source package that provides a framework for the determination of the parton distribution functions (PDFs) of the proton and for many different kinds of analyses in Quantum Chromodynamics (QCD). It encodes results from a wide range of experimental measurements in lepton-proton deep inelastic scattering and proton-proton (proton-antiproton) collisions at hadron colliders. These are complemented with a variety of theoretical options for calculating PDF-dependent cross section predictions corresponding to the measurements. The framework covers a large number of the existing methods and schemes used for PDF determination. The data and theoretical predictions are brought together through numerous methodologicalmore » options for carrying out PDF fits and plotting tools to help visualise the results. While primarily based on the approach of collinear factorisation, HERAFitter also provides facilities for fits of dipole models and transverse-momentum dependent PDFs. The package can be used to study the impact of new precise measurements from hadron colliders. This paper describes the general structure of HERAFitter and its wide choice of options.« less

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

Qi, Bing; Lougovski, Pavel; Pooser, Raphael C.

Continuous-variable quantum key distribution (CV-QKD) protocols based on coherent detection have been studied extensively in both theory and experiment. In all the existing implementations of CV-QKD, both the quantum signal and the local oscillator (LO) are generated from the same laser and propagate through the insecure quantum channel. This arrangement may open security loopholes and limit the potential applications of CV-QKD. In our paper, we propose and demonstrate a pilot-aided feedforward data recovery scheme that enables reliable coherent detection using a “locally” generated LO. Using two independent commercial laser sources and a spool of 25-km optical fiber, we construct amore » coherent communication system. The variance of the phase noise introduced by the proposed scheme is measured to be 0.04 (rad 2), which is small enough to enable secure key distribution. This technology opens the door for other quantum communication protocols, such as the recently proposed measurement-device-independent CV-QKD, where independent light sources are employed by different users.« less

BANNER: an executable survey of advances in biomedical named entity recognition.

PubMed

Leaman, Robert; Gonzalez, Graciela

2008-01-01

There has been an increasing amount of research on biomedical named entity recognition, the most basic text extraction problem, resulting in significant progress by different research teams around the world. This has created a need for a freely-available, open source system implementing the advances described in the literature. In this paper we present BANNER, an open-source, executable survey of advances in biomedical named entity recognition, intended to serve as a benchmark for the field. BANNER is implemented in Java as a machine-learning system based on conditional random fields and includes a wide survey of the best techniques recently described in the literature. It is designed to maximize domain independence by not employing brittle semantic features or rule-based processing steps, and achieves significantly better performance than existing baseline systems. It is therefore useful to developers as an extensible NER implementation, to researchers as a standard for comparing innovative techniques, and to biologists requiring the ability to find novel entities in large amounts of text.

Open-source LCA tool for estimating greenhouse gas emissions from crude oil production using field characteristics.

PubMed

El-Houjeiri, Hassan M; Brandt, Adam R; Duffy, James E

2013-06-04

Existing transportation fuel cycle emissions models are either general and calculate nonspecific values of greenhouse gas (GHG) emissions from crude oil production, or are not available for public review and auditing. We have developed the Oil Production Greenhouse Gas Emissions Estimator (OPGEE) to provide open-source, transparent, rigorous GHG assessments for use in scientific assessment, regulatory processes, and analysis of GHG mitigation options by producers. OPGEE uses petroleum engineering fundamentals to model emissions from oil and gas production operations. We introduce OPGEE and explain the methods and assumptions used in its construction. We run OPGEE on a small set of fictional oil fields and explore model sensitivity to selected input parameters. Results show that upstream emissions from petroleum production operations can vary from 3 gCO2/MJ to over 30 gCO2/MJ using realistic ranges of input parameters. Significant drivers of emissions variation are steam injection rates, water handling requirements, and rates of flaring of associated gas.

Generating the Local Oscillator "Locally" in Continuous-Variable Quantum Key Distribution Based on Coherent Detection

NASA Astrophysics Data System (ADS)

Qi, Bing; Lougovski, Pavel; Pooser, Raphael; Grice, Warren; Bobrek, Miljko

2015-10-01

Continuous-variable quantum key distribution (CV-QKD) protocols based on coherent detection have been studied extensively in both theory and experiment. In all the existing implementations of CV-QKD, both the quantum signal and the local oscillator (LO) are generated from the same laser and propagate through the insecure quantum channel. This arrangement may open security loopholes and limit the potential applications of CV-QKD. In this paper, we propose and demonstrate a pilot-aided feedforward data recovery scheme that enables reliable coherent detection using a "locally" generated LO. Using two independent commercial laser sources and a spool of 25-km optical fiber, we construct a coherent communication system. The variance of the phase noise introduced by the proposed scheme is measured to be 0.04 (rad2 ), which is small enough to enable secure key distribution. This technology also opens the door for other quantum communication protocols, such as the recently proposed measurement-device-independent CV-QKD, where independent light sources are employed by different users.

Measurements and Correlations of cis-1,3,3,3-Tetrafluoroprop-1-ene (R1234ze(Z)) Saturation Pressure

NASA Astrophysics Data System (ADS)

Fedele, Laura; Di Nicola, Giovanni; Brown, J. Steven; Bobbo, Sergio; Zilio, Claudio

2014-01-01

cis-1,3,3,3-Tetrafluoroprop-1-ene (R1234ze(Z)) is being investigated as a working fluid possessing a low global warming potential (GWP) for high-temperature heat pumping applications, organic Rankine cycles, and air-conditioning and refrigeration applications, and as a potential solvent, propellant, and foam blowing agent. Its GWP is less than one. The open literature contains a total of 79 vapor-pressure data from three sources and the critical state properties from a single source. The current paper provides 64 vapor-pressure data from two different laboratories over the temperature range from 238.13 K to 372.61 K. These data are regressed using Wagner and extended Antoine vapor-pressure correlations and then compared to the existing open literature data and correlations. The normal-boiling-point temperature and acentric factor for R1234ze(Z) are estimated to be 282.73 K and 0.3257, respectively.

Choosing Open Source ERP Systems: What Reasons Are There For Doing So?

NASA Astrophysics Data System (ADS)

Johansson, Björn; Sudzina, Frantisek

Enterprise resource planning (ERP) systems attract a high attention and open source software does it as well. The question is then if, and if so, when do open source ERP systems take off. The paper describes the status of open source ERP systems. Based on literature review of ERP system selection criteria based on Web of Science articles, it discusses reported reasons for choosing open source or proprietary ERP systems. Last but not least, the article presents some conclusions that could act as input for future research. The paper aims at building up a foundation for the basic question: What are the reasons for an organization to adopt open source ERP systems.

ENKI - An Open Source environmental modelling platfom

NASA Astrophysics Data System (ADS)

Kolberg, S.; Bruland, O.

2012-04-01

The ENKI software framework for implementing spatio-temporal models is now released under the LGPL license. Originally developed for evaluation and comparison of distributed hydrological model compositions, ENKI can be used for simulating any time-evolving process over a spatial domain. The core approach is to connect a set of user specified subroutines into a complete simulation model, and provide all administrative services needed to calibrate and run that model. This includes functionality for geographical region setup, all file I/O, calibration and uncertainty estimation etc. The approach makes it easy for students, researchers and other model developers to implement, exchange, and test single routines and various model compositions in a fixed framework. The open-source license and modular design of ENKI will also facilitate rapid dissemination of new methods to institutions engaged in operational water resource management. ENKI uses a plug-in structure to invoke separately compiled subroutines, separately built as dynamic-link libraries (dlls). The source code of an ENKI routine is highly compact, with a narrow framework-routine interface allowing the main program to recognise the number, types, and names of the routine's variables. The framework then exposes these variables to the user within the proper context, ensuring that distributed maps coincide spatially, time series exist for input variables, states are initialised, GIS data sets exist for static map data, manually or automatically calibrated values for parameters etc. By using function calls and memory data structures to invoke routines and facilitate information flow, ENKI provides good performance. For a typical distributed hydrological model setup in a spatial domain of 25000 grid cells, 3-4 time steps simulated per second should be expected. Future adaptation to parallel processing may further increase this speed. New modifications to ENKI include a full separation of API and user interface, making it possible to run ENKI from GIS programs and other software environments. ENKI currently compiles under Windows and Visual Studio only, but ambitions exist to remove the platform and compiler dependencies.

Developing open-source codes for electromagnetic geophysics using industry support

NASA Astrophysics Data System (ADS)

Key, K.

2017-12-01

Funding for open-source software development in academia often takes the form of grants and fellowships awarded by government bodies and foundations where there is no conflict-of-interest between the funding entity and the free dissemination of the open-source software products. Conversely, funding for open-source projects in the geophysics industry presents challenges to conventional business models where proprietary licensing offers value that is not present in open-source software. Such proprietary constraints make it easier to convince companies to fund academic software development under exclusive software distribution agreements. A major challenge for obtaining commercial funding for open-source projects is to offer a value proposition that overcomes the criticism that such funding is a give-away to the competition. This work draws upon a decade of experience developing open-source electromagnetic geophysics software for the oil, gas and minerals exploration industry, and examines various approaches that have been effective for sustaining industry sponsorship.

Behind Linus's Law: Investigating Peer Review Processes in Open Source

ERIC Educational Resources Information Center

Wang, Jing

2013-01-01

Open source software has revolutionized the way people develop software, organize collaborative work, and innovate. The numerous open source software systems that have been created and adopted over the past decade are influential and vital in all aspects of work and daily life. The understanding of open source software development can enhance its…

Implementing Open Source Platform for Education Quality Enhancement in Primary Education: Indonesia Experience

ERIC Educational Resources Information Center

Kisworo, Marsudi Wahyu

2016-01-01

Information and Communication Technology (ICT)-supported learning using free and open source platform draws little attention as open source initiatives were focused in secondary or tertiary educations. This study investigates possibilities of ICT-supported learning using open source platform for primary educations. The data of this study is taken…

An Analysis of Open Source Security Software Products Downloads

ERIC Educational Resources Information Center

Barta, Brian J.

2014-01-01

Despite the continued demand for open source security software, a gap in the identification of success factors related to the success of open source security software persists. There are no studies that accurately assess the extent of this persistent gap, particularly with respect to the strength of the relationships of open source software…

A Lifecycle Approach to Brokered Data Management for Hydrologic Modeling Data Using Open Standards.

NASA Astrophysics Data System (ADS)

Blodgett, D. L.; Booth, N.; Kunicki, T.; Walker, J.

2012-12-01

The U.S. Geological Survey Center for Integrated Data Analytics has formalized an information management-architecture to facilitate hydrologic modeling and subsequent decision support throughout a project's lifecycle. The architecture is based on open standards and open source software to decrease the adoption barrier and to build on existing, community supported software. The components of this system have been developed and evaluated to support data management activities of the interagency Great Lakes Restoration Initiative, Department of Interior's Climate Science Centers and WaterSmart National Water Census. Much of the research and development of this system has been in cooperation with international interoperability experiments conducted within the Open Geospatial Consortium. Community-developed standards and software, implemented to meet the unique requirements of specific disciplines, are used as a system of interoperable, discipline specific, data types and interfaces. This approach has allowed adoption of existing software that satisfies the majority of system requirements. Four major features of the system include: 1) assistance in model parameter and forcing creation from large enterprise data sources; 2) conversion of model results and calibrated parameters to standard formats, making them available via standard web services; 3) tracking a model's processes, inputs, and outputs as a cohesive metadata record, allowing provenance tracking via reference to web services; and 4) generalized decision support tools which rely on a suite of standard data types and interfaces, rather than particular manually curated model-derived datasets. Recent progress made in data and web service standards related to sensor and/or model derived station time series, dynamic web processing, and metadata management are central to this system's function and will be presented briefly along with a functional overview of the applications that make up the system. As the separate pieces of this system progress, they will be combined and generalized to form a sort of social network for nationally consistent hydrologic modeling.

Research on OpenStack of open source cloud computing in colleges and universities’ computer room

NASA Astrophysics Data System (ADS)

Wang, Lei; Zhang, Dandan

2017-06-01

In recent years, the cloud computing technology has a rapid development, especially open source cloud computing. Open source cloud computing has attracted a large number of user groups by the advantages of open source and low cost, have now become a large-scale promotion and application. In this paper, firstly we briefly introduced the main functions and architecture of the open source cloud computing OpenStack tools, and then discussed deeply the core problems of computer labs in colleges and universities. Combining with this research, it is not that the specific application and deployment of university computer rooms with OpenStack tool. The experimental results show that the application of OpenStack tool can efficiently and conveniently deploy cloud of university computer room, and its performance is stable and the functional value is good.

Common characteristics of open source software development and applicability for drug discovery: a systematic review

PubMed Central

2011-01-01

Background Innovation through an open source model has proven to be successful for software development. This success has led many to speculate if open source can be applied to other industries with similar success. We attempt to provide an understanding of open source software development characteristics for researchers, business leaders and government officials who may be interested in utilizing open source innovation in other contexts and with an emphasis on drug discovery. Methods A systematic review was performed by searching relevant, multidisciplinary databases to extract empirical research regarding the common characteristics and barriers of initiating and maintaining an open source software development project. Results Common characteristics to open source software development pertinent to open source drug discovery were extracted. The characteristics were then grouped into the areas of participant attraction, management of volunteers, control mechanisms, legal framework and physical constraints. Lastly, their applicability to drug discovery was examined. Conclusions We believe that the open source model is viable for drug discovery, although it is unlikely that it will exactly follow the form used in software development. Hybrids will likely develop that suit the unique characteristics of drug discovery. We suggest potential motivations for organizations to join an open source drug discovery project. We also examine specific differences between software and medicines, specifically how the need for laboratories and physical goods will impact the model as well as the effect of patents. PMID:21955914

The 2017 Bioinformatics Open Source Conference (BOSC)

PubMed Central

Harris, Nomi L.; Cock, Peter J.A.; Chapman, Brad; Fields, Christopher J.; Hokamp, Karsten; Lapp, Hilmar; Munoz-Torres, Monica; Tzovaras, Bastian Greshake; Wiencko, Heather

2017-01-01

The Bioinformatics Open Source Conference (BOSC) is a meeting organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. The 18th annual BOSC ( http://www.open-bio.org/wiki/BOSC_2017) took place in Prague, Czech Republic in July 2017. The conference brought together nearly 250 bioinformatics researchers, developers and users of open source software to interact and share ideas about standards, bioinformatics software development, open and reproducible science, and this year’s theme, open data. As in previous years, the conference was preceded by a two-day collaborative coding event open to the bioinformatics community, called the OBF Codefest. PMID:29118973

The 2017 Bioinformatics Open Source Conference (BOSC).

PubMed

Harris, Nomi L; Cock, Peter J A; Chapman, Brad; Fields, Christopher J; Hokamp, Karsten; Lapp, Hilmar; Munoz-Torres, Monica; Tzovaras, Bastian Greshake; Wiencko, Heather

2017-01-01

The Bioinformatics Open Source Conference (BOSC) is a meeting organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. The 18th annual BOSC ( http://www.open-bio.org/wiki/BOSC_2017) took place in Prague, Czech Republic in July 2017. The conference brought together nearly 250 bioinformatics researchers, developers and users of open source software to interact and share ideas about standards, bioinformatics software development, open and reproducible science, and this year's theme, open data. As in previous years, the conference was preceded by a two-day collaborative coding event open to the bioinformatics community, called the OBF Codefest.

The Efficient Utilization of Open Source Information

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

Baty, Samuel R.

These are a set of slides on the efficient utilization of open source information. Open source information consists of a vast set of information from a variety of sources. Not only does the quantity of open source information pose a problem, the quality of such information can hinder efforts. To show this, two case studies are mentioned: Iran and North Korea, in order to see how open source information can be utilized. The huge breadth and depth of open source information can complicate an analysis, especially because open information has no guarantee of accuracy. Open source information can provide keymore » insights either directly or indirectly: looking at supporting factors (flow of scientists, products and waste from mines, government budgets, etc.); direct factors (statements, tests, deployments). Fundamentally, it is the independent verification of information that allows for a more complete picture to be formed. Overlapping sources allow for more precise bounds on times, weights, temperatures, yields or other issues of interest in order to determine capability. Ultimately, a "good" answer almost never comes from an individual, but rather requires the utilization of a wide range of skill sets held by a team of people.« less

Two-step web-mining approach to study geology/geophysics-related open-source software projects

NASA Astrophysics Data System (ADS)

Behrends, Knut; Conze, Ronald

2013-04-01

Geology/geophysics is a highly interdisciplinary science, overlapping with, for instance, physics, biology and chemistry. In today's software-intensive work environments, geoscientists often encounter new open-source software from scientific fields that are only remotely related to the own field of expertise. We show how web-mining techniques can help to carry out systematic discovery and evaluation of such software. In a first step, we downloaded ~500 abstracts (each consisting of ~1 kb UTF-8 text) from agu-fm12.abstractcentral.com. This web site hosts the abstracts of all publications presented at AGU Fall Meeting 2012, the world's largest annual geology/geophysics conference. All abstracts belonged to the category "Earth and Space Science Informatics", an interdisciplinary label cross-cutting many disciplines such as "deep biosphere", "atmospheric research", and "mineral physics". Each publication was represented by a highly structured record with ~20 short data attributes, the largest authorship-record being the unstructured "abstract" field. We processed texts of the abstracts with the statistics software "R" to calculate a corpus and a term-document matrix. Using R package "tm", we applied text-mining techniques to filter data and develop hypotheses about software-development activities happening in various geology/geophysics fields. Analyzing the term-document matrix with basic techniques (e.g., word frequencies, co-occurences, weighting) as well as more complex methods (clustering, classification) several key pieces of information were extracted. For example, text-mining can be used to identify scientists who are also developers of open-source scientific software, and the names of their programming projects and codes can also be identified. In a second step, based on the intermediate results found by processing the conference-abstracts, any new hypotheses can be tested in another webmining subproject: by merging the dataset with open data from github.com and stackoverflow.com. These popular, developer-centric websites have powerful application-programmer interfaces, and follow an open-data policy. In this regard, these sites offer a web-accessible reservoir of information that can be tapped to study questions such as: which open source software projects are eminent in the various geoscience fields? What are the most popular programming languages? How are they trending? Are there any interesting temporal patterns in committer activities? How large are programming teams and how do they change over time? What free software packages exist in the vast realms of related fields? Does the software from these fields have capabilities that might still be useful to me as a researcher, or can help me perform my work better? Are there any open-source projects that might be commercially interesting? This evaluation strategy reveals programming projects that tend to be new. As many important legacy codes are not hosted on open-source code-repositories, the presented search method might overlook some older projects.

The 2015 Bioinformatics Open Source Conference (BOSC 2015).

PubMed

Harris, Nomi L; Cock, Peter J A; Lapp, Hilmar; Chapman, Brad; Davey, Rob; Fields, Christopher; Hokamp, Karsten; Munoz-Torres, Monica

2016-02-01

The Bioinformatics Open Source Conference (BOSC) is organized by the Open Bioinformatics Foundation (OBF), a nonprofit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community. Since its inception in 2000, BOSC has provided bioinformatics developers with a forum for communicating the results of their latest efforts to the wider research community. BOSC offers a focused environment for developers and users to interact and share ideas about standards; software development practices; practical techniques for solving bioinformatics problems; and approaches that promote open science and sharing of data, results, and software. BOSC is run as a two-day special interest group (SIG) before the annual Intelligent Systems in Molecular Biology (ISMB) conference. BOSC 2015 took place in Dublin, Ireland, and was attended by over 125 people, about half of whom were first-time attendees. Session topics included "Data Science;" "Standards and Interoperability;" "Open Science and Reproducibility;" "Translational Bioinformatics;" "Visualization;" and "Bioinformatics Open Source Project Updates". In addition to two keynote talks and dozens of shorter talks chosen from submitted abstracts, BOSC 2015 included a panel, titled "Open Source, Open Door: Increasing Diversity in the Bioinformatics Open Source Community," that provided an opportunity for open discussion about ways to increase the diversity of participants in BOSC in particular, and in open source bioinformatics in general. The complete program of BOSC 2015 is available online at http://www.open-bio.org/wiki/BOSC_2015_Schedule.

Gunshot identification system by integration of open source consumer electronics

NASA Astrophysics Data System (ADS)

López R., Juan Manuel; Marulanda B., Jose Ignacio

2014-05-01

This work presents a prototype of low-cost gunshots identification system that uses consumer electronics in order to ensure the existence of gunshots and then classify it according to a previously established database. The implementation of this tool in the urban areas is to set records that support the forensics, hence improving law enforcement also on developing countries. An analysis of its effectiveness is presented in comparison with theoretical results obtained with numerical simulations.

CVcat: An interactive database on cataclysmic variables

NASA Astrophysics Data System (ADS)

Kube, J.; Gänsicke, B. T.; Euchner, F.; Hoffmann, B.

2003-06-01

CVcat is a database that contains published data on cataclysmic variables and related objects. Unlike in the existing online sources, the users are allowed to add data to the catalogue. The concept of an ``open catalogue'' approach is reviewed together with the experience from one year of public usage of CVcat. New concepts to be included in the upcoming AstroCat framework and the next CVcat implementation are presented. CVcat can be found at http://www.cvcat.org.

FloWave.US: validated, open-source, and flexible software for ultrasound blood flow analysis.

PubMed

Coolbaugh, Crystal L; Bush, Emily C; Caskey, Charles F; Damon, Bruce M; Towse, Theodore F

2016-10-01

Automated software improves the accuracy and reliability of blood velocity, vessel diameter, blood flow, and shear rate ultrasound measurements, but existing software offers limited flexibility to customize and validate analyses. We developed FloWave.US-open-source software to automate ultrasound blood flow analysis-and demonstrated the validity of its blood velocity (aggregate relative error, 4.32%) and vessel diameter (0.31%) measures with a skeletal muscle ultrasound flow phantom. Compared with a commercial, manual analysis software program, FloWave.US produced equivalent in vivo cardiac cycle time-averaged mean (TAMean) velocities at rest and following a 10-s muscle contraction (mean bias <1 pixel for both conditions). Automated analysis of ultrasound blood flow data was 9.8 times faster than the manual method. Finally, a case study of a lower extremity muscle contraction experiment highlighted the ability of FloWave.US to measure small fluctuations in TAMean velocity, vessel diameter, and mean blood flow at specific time points in the cardiac cycle. In summary, the collective features of our newly designed software-accuracy, reliability, reduced processing time, cost-effectiveness, and flexibility-offer advantages over existing proprietary options. Further, public distribution of FloWave.US allows researchers to easily access and customize code to adapt ultrasound blood flow analysis to a variety of vascular physiology applications. Copyright © 2016 the American Physiological Society.

SANDS: A Service-Oriented Architecture for Clinical Decision Support in a National Health Information Network

PubMed Central

Wright, Adam; Sittig, Dean F.

2008-01-01

In this paper we describe and evaluate a new distributed architecture for clinical decision support called SANDS (Service-oriented Architecture for NHIN Decision Support), which leverages current health information exchange efforts and is based on the principles of a service-oriented architecture. The architecture allows disparate clinical information systems and clinical decision support systems to be seamlessly integrated over a network according to a set of interfaces and protocols described in this paper. The architecture described is fully defined and developed, and six use cases have been developed and tested using a prototype electronic health record which links to one of the existing prototype National Health Information Networks (NHIN): drug interaction checking, syndromic surveillance, diagnostic decision support, inappropriate prescribing in older adults, information at the point of care and a simple personal health record. Some of these use cases utilize existing decision support systems, which are either commercially or freely available at present, and developed outside of the SANDS project, while other use cases are based on decision support systems developed specifically for the project. Open source code for many of these components is available, and an open source reference parser is also available for comparison and testing of other clinical information systems and clinical decision support systems that wish to implement the SANDS architecture. PMID:18434256

Molpher: a software framework for systematic chemical space exploration

PubMed Central

2014-01-01

Background Chemical space is virtual space occupied by all chemically meaningful organic compounds. It is an important concept in contemporary chemoinformatics research, and its systematic exploration is vital to the discovery of either novel drugs or new tools for chemical biology. Results In this paper, we describe Molpher, an open-source framework for the systematic exploration of chemical space. Through a process we term ‘molecular morphing’, Molpher produces a path of structurally-related compounds. This path is generated by the iterative application of so-called ‘morphing operators’ that represent simple structural changes, such as the addition or removal of an atom or a bond. Molpher incorporates an optimized parallel exploration algorithm, compound logging and a two-dimensional visualization of the exploration process. Its feature set can be easily extended by implementing additional morphing operators, chemical fingerprints, similarity measures and visualization methods. Molpher not only offers an intuitive graphical user interface, but also can be run in batch mode. This enables users to easily incorporate molecular morphing into their existing drug discovery pipelines. Conclusions Molpher is an open-source software framework for the design of virtual chemical libraries focused on a particular mechanistic class of compounds. These libraries, represented by a morphing path and its surroundings, provide valuable starting data for future in silico and in vitro experiments. Molpher is highly extensible and can be easily incorporated into any existing computational drug design pipeline. PMID:24655571

Molpher: a software framework for systematic chemical space exploration.

PubMed

Hoksza, David; Skoda, Petr; Voršilák, Milan; Svozil, Daniel

2014-03-21

Chemical space is virtual space occupied by all chemically meaningful organic compounds. It is an important concept in contemporary chemoinformatics research, and its systematic exploration is vital to the discovery of either novel drugs or new tools for chemical biology. In this paper, we describe Molpher, an open-source framework for the systematic exploration of chemical space. Through a process we term 'molecular morphing', Molpher produces a path of structurally-related compounds. This path is generated by the iterative application of so-called 'morphing operators' that represent simple structural changes, such as the addition or removal of an atom or a bond. Molpher incorporates an optimized parallel exploration algorithm, compound logging and a two-dimensional visualization of the exploration process. Its feature set can be easily extended by implementing additional morphing operators, chemical fingerprints, similarity measures and visualization methods. Molpher not only offers an intuitive graphical user interface, but also can be run in batch mode. This enables users to easily incorporate molecular morphing into their existing drug discovery pipelines. Molpher is an open-source software framework for the design of virtual chemical libraries focused on a particular mechanistic class of compounds. These libraries, represented by a morphing path and its surroundings, provide valuable starting data for future in silico and in vitro experiments. Molpher is highly extensible and can be easily incorporated into any existing computational drug design pipeline.

Open Source, Openness, and Higher Education

ERIC Educational Resources Information Center

Wiley, David

2006-01-01

In this article David Wiley provides an overview of how the general expansion of open source software has affected the world of education in particular. In doing so, Wiley not only addresses the development of open source software applications for teachers and administrators, he also discusses how the fundamental philosophy of the open source…

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

None

Assessing the impact of energy efficiency technologies at a district or city scale is of great interest to local governments, real estate developers, utility companies, and policymakers. This paper describes a flexible framework that can be used to create and run district and city scale building energy simulations. The framework is built around the new OpenStudio City Database (CityDB). Building footprints, building height, building type, and other data can be imported from public records or other sources. Missing data can be inferred or assigned from a statistical sampling of other datasets. Once all required data is available, OpenStudio Measures aremore » used to create starting point energy models and to model energy efficiency measures for each building. Together this framework allows a user to pose several scenarios such as 'what if 30% of the commercial retail buildings added rooftop solar' or 'what if all elementary schools converted to ground source heat pumps' and then visualize the impacts at a district or city scale. This paper focuses on modeling existing building stock using public records. However, the framework is capable of supporting the evaluation of new construction, district systems, and the use of proprietary data sources.« less

The Emergence of Open-Source Software in North America

ERIC Educational Resources Information Center

Pan, Guohua; Bonk, Curtis J.

2007-01-01

Unlike conventional models of software development, the open source model is based on the collaborative efforts of users who are also co-developers of the software. Interest in open source software has grown exponentially in recent years. A "Google" search for the phrase open source in early 2005 returned 28.8 million webpage hits, while…

OpenComet: An automated tool for comet assay image analysis

PubMed Central

Gyori, Benjamin M.; Venkatachalam, Gireedhar; Thiagarajan, P.S.; Hsu, David; Clement, Marie-Veronique

2014-01-01

Reactive species such as free radicals are constantly generated in vivo and DNA is the most important target of oxidative stress. Oxidative DNA damage is used as a predictive biomarker to monitor the risk of development of many diseases. The comet assay is widely used for measuring oxidative DNA damage at a single cell level. The analysis of comet assay output images, however, poses considerable challenges. Commercial software is costly and restrictive, while free software generally requires laborious manual tagging of cells. This paper presents OpenComet, an open-source software tool providing automated analysis of comet assay images. It uses a novel and robust method for finding comets based on geometric shape attributes and segmenting the comet heads through image intensity profile analysis. Due to automation, OpenComet is more accurate, less prone to human bias, and faster than manual analysis. A live analysis functionality also allows users to analyze images captured directly from a microscope. We have validated OpenComet on both alkaline and neutral comet assay images as well as sample images from existing software packages. Our results show that OpenComet achieves high accuracy with significantly reduced analysis time. PMID:24624335

OpenComet: an automated tool for comet assay image analysis.

PubMed

Gyori, Benjamin M; Venkatachalam, Gireedhar; Thiagarajan, P S; Hsu, David; Clement, Marie-Veronique

2014-01-01

Reactive species such as free radicals are constantly generated in vivo and DNA is the most important target of oxidative stress. Oxidative DNA damage is used as a predictive biomarker to monitor the risk of development of many diseases. The comet assay is widely used for measuring oxidative DNA damage at a single cell level. The analysis of comet assay output images, however, poses considerable challenges. Commercial software is costly and restrictive, while free software generally requires laborious manual tagging of cells. This paper presents OpenComet, an open-source software tool providing automated analysis of comet assay images. It uses a novel and robust method for finding comets based on geometric shape attributes and segmenting the comet heads through image intensity profile analysis. Due to automation, OpenComet is more accurate, less prone to human bias, and faster than manual analysis. A live analysis functionality also allows users to analyze images captured directly from a microscope. We have validated OpenComet on both alkaline and neutral comet assay images as well as sample images from existing software packages. Our results show that OpenComet achieves high accuracy with significantly reduced analysis time.

Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on

PubMed Central

2011-01-01

Background The Blue Obelisk movement was established in 2005 as a response to the lack of Open Data, Open Standards and Open Source (ODOSOS) in chemistry. It aims to make it easier to carry out chemistry research by promoting interoperability between chemistry software, encouraging cooperation between Open Source developers, and developing community resources and Open Standards. Results This contribution looks back on the work carried out by the Blue Obelisk in the past 5 years and surveys progress and remaining challenges in the areas of Open Data, Open Standards, and Open Source in chemistry. Conclusions We show that the Blue Obelisk has been very successful in bringing together researchers and developers with common interests in ODOSOS, leading to development of many useful resources freely available to the chemistry community. PMID:21999342

A convolutional neural network approach to calibrating the rotation axis for X-ray computed tomography.

PubMed

Yang, Xiaogang; De Carlo, Francesco; Phatak, Charudatta; Gürsoy, Dogˇa

2017-03-01

This paper presents an algorithm to calibrate the center-of-rotation for X-ray tomography by using a machine learning approach, the Convolutional Neural Network (CNN). The algorithm shows excellent accuracy from the evaluation of synthetic data with various noise ratios. It is further validated with experimental data of four different shale samples measured at the Advanced Photon Source and at the Swiss Light Source. The results are as good as those determined by visual inspection and show better robustness than conventional methods. CNN has also great potential for reducing or removing other artifacts caused by instrument instability, detector non-linearity, etc. An open-source toolbox, which integrates the CNN methods described in this paper, is freely available through GitHub at tomography/xlearn and can be easily integrated into existing computational pipelines available at various synchrotron facilities. Source code, documentation and information on how to contribute are also provided.

Source Parameters for Moderate Earthquakes in the Zagros Mountains with Implications for the Depth Extent of Seismicity

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

Adams, A; Brazier, R; Nyblade, A

2009-02-23

Six earthquakes within the Zagros Mountains with magnitudes between 4.9 and 5.7 have been studied to determine their source parameters. These events were selected for study because they were reported in open catalogs to have lower crustal or upper mantle source depths and because they occurred within an area of the Zagros Mountains where crustal velocity structure has been constrained by previous studies. Moment tensor inversion of regional broadband waveforms have been combined with forward modeling of depth phases on short period teleseismic waveforms to constrain source depths and moment tensors. Our results show that all six events nucleated withinmore » the upper crust (<11 km depth) and have thrust mechanisms. This finding supports other studies that call into question the existence of lower crustal or mantle events beneath the Zagros Mountains.« less

Ensembl 2002: accommodating comparative genomics.

PubMed

Clamp, M; Andrews, D; Barker, D; Bevan, P; Cameron, G; Chen, Y; Clark, L; Cox, T; Cuff, J; Curwen, V; Down, T; Durbin, R; Eyras, E; Gilbert, J; Hammond, M; Hubbard, T; Kasprzyk, A; Keefe, D; Lehvaslaiho, H; Iyer, V; Melsopp, C; Mongin, E; Pettett, R; Potter, S; Rust, A; Schmidt, E; Searle, S; Slater, G; Smith, J; Spooner, W; Stabenau, A; Stalker, J; Stupka, E; Ureta-Vidal, A; Vastrik, I; Birney, E

2003-01-01

The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of human, mouse and other genome sequences, available as either an interactive web site or as flat files. Ensembl also integrates manually annotated gene structures from external sources where available. As well as being one of the leading sources of genome annotation, Ensembl is an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements. These range from sequence analysis to data storage and visualisation and installations exist around the world in both companies and at academic sites. With both human and mouse genome sequences available and more vertebrate sequences to follow, many of the recent developments in Ensembl have focusing on developing automatic comparative genome analysis and visualisation.

Alternative financing sources. ECRI. Emergency Care Research Institute.

PubMed

1987-01-01

A number of new capital sources have been developed and used by health care institutions unable to finance high-tech projects with equity or conventional tax-exempt debt instruments; these include REITs, MLPs, per-use rentals, venture capital, and banks as brokers. However, there are no magic capital acquisition solutions. Institutions with good credit will continue to find a number of doors open to them; poorer credit risks will have fewer options, and those available will carry greater risk, allow for less provider control over projects, and limit potential return on investment to some extent. It is essential to examine carefully the drawbacks inherent in each type of alternative financing source. Venture capital in particular requires specific analysis because of the wide variety of possible arrangements that exist. If you cannot find either traditional or alternative sources of funding for a proposed project, you should reexamine the project and its underlying utilization projections and reimbursement assumptions.

Open Genetic Code: on open source in the life sciences.

PubMed

Deibel, Eric

2014-01-01

The introduction of open source in the life sciences is increasingly being suggested as an alternative to patenting. This is an alternative, however, that takes its shape at the intersection of the life sciences and informatics. Numerous examples can be identified wherein open source in the life sciences refers to access, sharing and collaboration as informatic practices. This includes open source as an experimental model and as a more sophisticated approach of genetic engineering. The first section discusses the greater flexibly in regard of patenting and the relationship to the introduction of open source in the life sciences. The main argument is that the ownership of knowledge in the life sciences should be reconsidered in the context of the centrality of DNA in informatic formats. This is illustrated by discussing a range of examples of open source models. The second part focuses on open source in synthetic biology as exemplary for the re-materialization of information into food, energy, medicine and so forth. The paper ends by raising the question whether another kind of alternative might be possible: one that looks at open source as a model for an alternative to the commodification of life that is understood as an attempt to comprehensively remove the restrictions from the usage of DNA in any of its formats.

The Open Source Teaching Project (OSTP): Research Note.

ERIC Educational Resources Information Center

Hirst, Tony

The Open Source Teaching Project (OSTP) is an attempt to apply a variant of the successful open source software approach to the development of educational materials. Open source software is software licensed in such a way as to allow anyone the right to modify and use it. From such a simple premise, a whole industry has arisen, most notably in the…

Free for All: Open Source Software

ERIC Educational Resources Information Center

Schneider, Karen

2008-01-01

Open source software has become a catchword in libraryland. Yet many remain unclear about open source's benefits--or even what it is. So what is open source software (OSS)? It's software that is free in every sense of the word: free to download, free to use, and free to view or modify. Most OSS is distributed on the Web and one doesn't need to…

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

PubMed

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

2007-01-01

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

MIST: An Open Source Environmental Modelling Programming Language Incorporating Easy to Use Data Parallelism.

NASA Astrophysics Data System (ADS)

Bellerby, Tim

2014-05-01

Model Integration System (MIST) is open-source environmental modelling programming language that directly incorporates data parallelism. The language is designed to enable straightforward programming structures, such as nested loops and conditional statements to be directly translated into sequences of whole-array (or more generally whole data-structure) operations. MIST thus enables the programmer to use well-understood constructs, directly relating to the mathematical structure of the model, without having to explicitly vectorize code or worry about details of parallelization. A range of common modelling operations are supported by dedicated language structures operating on cell neighbourhoods rather than individual cells (e.g.: the 3x3 local neighbourhood needed to implement an averaging image filter can be simply accessed from within a simple loop traversing all image pixels). This facility hides details of inter-process communication behind more mathematically relevant descriptions of model dynamics. The MIST automatic vectorization/parallelization process serves both to distribute work among available nodes and separately to control storage requirements for intermediate expressions - enabling operations on very large domains for which memory availability may be an issue. MIST is designed to facilitate efficient interpreter based implementations. A prototype open source interpreter is available, coded in standard FORTRAN 95, with tools to rapidly integrate existing FORTRAN 77 or 95 code libraries. The language is formally specified and thus not limited to FORTRAN implementation or to an interpreter-based approach. A MIST to FORTRAN compiler is under development and volunteers are sought to create an ANSI-C implementation. Parallel processing is currently implemented using OpenMP. However, parallelization code is fully modularised and could be replaced with implementations using other libraries. GPU implementation is potentially possible.

VitaPad: visualization tools for the analysis of pathway data.

PubMed

Holford, Matthew; Li, Naixin; Nadkarni, Prakash; Zhao, Hongyu

2005-04-15

Packages that support the creation of pathway diagrams are limited by their inability to be readily extended to new classes of pathway-related data. VitaPad is a cross-platform application that enables users to create and modify biological pathway diagrams and incorporate microarray data with them. It improves on existing software in the following areas: (i) It can create diagrams dynamically through graph layout algorithms. (ii) It is open-source and uses an open XML format to store data, allowing for easy extension or integration with other tools. (iii) It features a cutting-edge user interface with intuitive controls, high-resolution graphics and fully customizable appearance. http://bioinformatics.med.yale.edu matthew.holford@yale.edu; hongyu.zhao@yale.edu.

Crossfostering in mice selectively bred for high and low levels of open-field thigmotaxis.

PubMed

Leppänen, Pia K; Ewalds-Kvist, S Béatrice M

2005-02-01

The main purpose of this research was to investigate whether the difference in open-field (OF) thigmotaxis between mice selectively bred for high and low levels of wall-seeking behavior originated from genetic or acquired sources. Unfostered, infostered, and crossfostered mice were compared in two experiments in which the effects of strain, sex, and fostering on ambulation, defecation, exploration, grooming, latency to move, radial latency, rearing, thigmotaxis, and urination were studied. These experiments revealed that OF thigmotaxis was unaffected by the foster condition and thus genetically determined. The selected strains of mice also diverged repeatedly with regard to exploration and rearing. The findings are in line with the previously described existence of an inverse relationship between emotionality and exploration.

Open Standards, Open Source, and Open Innovation: Harnessing the Benefits of Openness

ERIC Educational Resources Information Center

Committee for Economic Development, 2006

2006-01-01

Digitization of information and the Internet have profoundly expanded the capacity for openness. This report details the benefits of openness in three areas--open standards, open-source software, and open innovation--and examines the major issues in the debate over whether openness should be encouraged or not. The report explains each of these…

Automatic landslide detection from LiDAR DTM derivatives by geographic-object-based image analysis based on open-source software

NASA Astrophysics Data System (ADS)

Knevels, Raphael; Leopold, Philip; Petschko, Helene

2017-04-01

With high-resolution airborne Light Detection and Ranging (LiDAR) data more commonly available, many studies have been performed to facilitate the detailed information on the earth surface and to analyse its limitation. Specifically in the field of natural hazards, digital terrain models (DTM) have been used to map hazardous processes such as landslides mainly by visual interpretation of LiDAR DTM derivatives. However, new approaches are striving towards automatic detection of landslides to speed up the process of generating landslide inventories. These studies usually use a combination of optical imagery and terrain data, and are designed in commercial software packages such as ESRI ArcGIS, Definiens eCognition, or MathWorks MATLAB. The objective of this study was to investigate the potential of open-source software for automatic landslide detection based only on high-resolution LiDAR DTM derivatives in a study area within the federal state of Burgenland, Austria. The study area is very prone to landslides which have been mapped with different methodologies in recent years. The free development environment R was used to integrate open-source geographic information system (GIS) software, such as SAGA (System for Automated Geoscientific Analyses), GRASS (Geographic Resources Analysis Support System), or TauDEM (Terrain Analysis Using Digital Elevation Models). The implemented geographic-object-based image analysis (GEOBIA) consisted of (1) derivation of land surface parameters, such as slope, surface roughness, curvature, or flow direction, (2) finding optimal scale parameter by the use of an objective function, (3) multi-scale segmentation, (4) classification of landslide parts (main scarp, body, flanks) by k-mean thresholding, (5) assessment of the classification performance using a pre-existing landslide inventory, and (6) post-processing analysis for the further use in landslide inventories. The results of the developed open-source approach demonstrated good success rates to objectively detect landslides in high-resolution topography data by GEOBIA.

CMOST: an open-source framework for the microsimulation of colorectal cancer screening strategies.

PubMed

Prakash, Meher K; Lang, Brian; Heinrich, Henriette; Valli, Piero V; Bauerfeind, Peter; Sonnenberg, Amnon; Beerenwinkel, Niko; Misselwitz, Benjamin

2017-06-05

Colorectal cancer (CRC) is a leading cause of cancer-related mortality. CRC incidence and mortality can be reduced by several screening strategies, including colonoscopy, but randomized CRC prevention trials face significant obstacles such as the need for large study populations with long follow-up. Therefore, CRC screening strategies will likely be designed and optimized based on computer simulations. Several computational microsimulation tools have been reported for estimating efficiency and cost-effectiveness of CRC prevention. However, none of these tools is publicly available. There is a need for an open source framework to answer practical questions including testing of new screening interventions and adapting findings to local conditions. We developed and implemented a new microsimulation model, Colon Modeling Open Source Tool (CMOST), for modeling the natural history of CRC, simulating the effects of CRC screening interventions, and calculating the resulting costs. CMOST facilitates automated parameter calibration against epidemiological adenoma prevalence and CRC incidence data. Predictions of CMOST were highly similar compared to a large endoscopic CRC prevention study as well as predictions of existing microsimulation models. We applied CMOST to calculate the optimal timing of a screening colonoscopy. CRC incidence and mortality are reduced most efficiently by a colonoscopy between the ages of 56 and 59; while discounted life years gained (LYG) is maximal at 49-50 years. With a dwell time of 13 years, the most cost-effective screening is at 59 years, at $17,211 discounted USD per LYG. While cost-efficiency varied according to dwell time it did not influence the optimal time point of screening interventions within the tested range. Predictions of CMOST are highly similar compared to a randomized CRC prevention trial as well as those of other microsimulation tools. This open source tool will enable health-economics analyses in for various countries, health-care scenarios and CRC prevention strategies. CMOST is freely available under the GNU General Public License at https://gitlab.com/misselwb/CMOST.

A Web Portal-Based Time-Aware KML Animation Tool for Exploring Spatiotemporal Dynamics of Hydrological Events

NASA Astrophysics Data System (ADS)

Bao, X.; Cai, X.; Liu, Y.

2009-12-01

Understanding spatiotemporal dynamics of hydrological events such as storms and droughts is highly valuable for decision making on disaster mitigation and recovery. Virtual Globe-based technologies such as Google Earth and Open Geospatial Consortium KML standards show great promises for collaborative exploration of such events using visual analytical approaches. However, currently there are two barriers for wider usage of such approaches. First, there lacks an easy way to use open source tools to convert legacy or existing data formats such as shapefiles, geotiff, or web services-based data sources to KML and to produce time-aware KML files. Second, an integrated web portal-based time-aware animation tool is currently not available. Thus users usually share their files in the portal but have no means to visually explore them without leaving the portal environment which the users are familiar with. We develop a web portal-based time-aware KML animation tool for viewing extreme hydrologic events. The tool is based on Google Earth JavaScript API and Java Portlet standard 2.0 JSR-286, and it is currently deployable in one of the most popular open source portal frameworks, namely Liferay. We have also developed an open source toolkit kml-soc-ncsa (http://code.google.com/p/kml-soc-ncsa/) to facilitate the conversion of multiple formats into KML and the creation of time-aware KML files. We illustrate our tool using some example cases, in which drought and storm events with both time and space dimension can be explored in this web-based KML animation portlet. The tool provides an easy-to-use web browser-based portal environment for multiple users to collaboratively share and explore their time-aware KML files as well as improving the understanding of the spatiotemporal dynamics of the hydrological events.

The 2015 Bioinformatics Open Source Conference (BOSC 2015)

PubMed Central

Harris, Nomi L.; Cock, Peter J. A.; Lapp, Hilmar

2016-01-01

The Bioinformatics Open Source Conference (BOSC) is organized by the Open Bioinformatics Foundation (OBF), a nonprofit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community. Since its inception in 2000, BOSC has provided bioinformatics developers with a forum for communicating the results of their latest efforts to the wider research community. BOSC offers a focused environment for developers and users to interact and share ideas about standards; software development practices; practical techniques for solving bioinformatics problems; and approaches that promote open science and sharing of data, results, and software. BOSC is run as a two-day special interest group (SIG) before the annual Intelligent Systems in Molecular Biology (ISMB) conference. BOSC 2015 took place in Dublin, Ireland, and was attended by over 125 people, about half of whom were first-time attendees. Session topics included “Data Science;” “Standards and Interoperability;” “Open Science and Reproducibility;” “Translational Bioinformatics;” “Visualization;” and “Bioinformatics Open Source Project Updates”. In addition to two keynote talks and dozens of shorter talks chosen from submitted abstracts, BOSC 2015 included a panel, titled “Open Source, Open Door: Increasing Diversity in the Bioinformatics Open Source Community,” that provided an opportunity for open discussion about ways to increase the diversity of participants in BOSC in particular, and in open source bioinformatics in general. The complete program of BOSC 2015 is available online at http://www.open-bio.org/wiki/BOSC_2015_Schedule. PMID:26914653

quanTLC, an online open-source solution for videodensitometric quantification.

PubMed

Fichou, Dimitri; Morlock, Gertrud E

2018-07-27

The image is the key feature of planar chromatography. Videodensitometry by digital image conversion is the fastest way of its evaluation. Instead of scanning single sample tracks one after the other, only few clicks are needed to convert all tracks at one go. A minimalistic software was newly developed, termed quanTLC, that allowed the quantitative evaluation of samples in few minutes. quanTLC includes important assets such as open-source, online, free of charge, intuitive to use and tailored to planar chromatography, as none of the nine existent software for image evaluation covered these aspects altogether. quanTLC supports common image file formats for chromatogram upload. All necessary steps were included, i.e., videodensitogram extraction, preprocessing, automatic peak integration, calibration, statistical data analysis, reporting and data export. The default options for each step are suitable for most analyses while still being tunable, if needed. A one-minute video was recorded to serve as user manual. The software capabilities are shown on the example of a lipophilic dye mixture separation. The quantitative results were verified by comparison with those obtained by commercial videodensitometry software and opto-mechanical slit-scanning densitometry. The data can be exported at each step to be processed in further software, if required. The code was released open-source to be exploited even further. The software itself is online useable without installation and directly accessible at http://shinyapps.ernaehrung.uni-giessen.de/quanTLC. Copyright © 2018 Elsevier B.V. All rights reserved.

Energy Sources and Systems Analysis: 40 South Lincoln Redevelopment District (Short Report)

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

Not Available

2011-08-01

This report presents the a brief overview of the results of a case study to analyze district energy systems for their potential use in a project that involves redeveloping 270 units of existing public housing, along with other nearby sites. When complete, the redevelopment project will encompass more than 900 mixed-income residential units, commercial and retail properties, and open space. The analysis estimated the hourly heating, cooling, domestic hot water, and electric loads required by the community; investigated potential district system technologies to meet those needs; and researched available fuel sources to power such systems. A full report of thismore » case study is also available.« less

Manifestation of counteracting photovoltaic effect on IV characteristics in multi-junction solar cells

NASA Astrophysics Data System (ADS)

Mintairov, M. A.; Evstropov, V. V.; Mintairov, S. A.; Shvarts, M. Z.; Kozhukhovskaia, S. A.; Kalyuzhnyy, N. A.

2017-11-01

The existence within monolithic double- and triple-junction solar cells of a photoelectric source, which counteracts the basic photovoltaic p-n junctions, is proved. The paper presents a detailed analysis of the shape of the light IV-characteristics, as well as the dependence Voc-Jsc (open circuit voltage - short-circuit current). It is established that the counteracting source is tunnel p+-n+ junction. The photoelectric characteristics of samples with different tunnel diode peak current values were investigated, including the case of a zero value. When the tunnel p+-n+ junction is photoactive, the Voc-Jsc dependence has a dropping part, including a sharp jump. This undesirable effect decreases with increasing peak current.

The 2016 Bioinformatics Open Source Conference (BOSC).

PubMed

Harris, Nomi L; Cock, Peter J A; Chapman, Brad; Fields, Christopher J; Hokamp, Karsten; Lapp, Hilmar; Muñoz-Torres, Monica; Wiencko, Heather

2016-01-01

Message from the ISCB: The Bioinformatics Open Source Conference (BOSC) is a yearly meeting organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. BOSC has been run since 2000 as a two-day Special Interest Group (SIG) before the annual ISMB conference. The 17th annual BOSC ( http://www.open-bio.org/wiki/BOSC_2016) took place in Orlando, Florida in July 2016. As in previous years, the conference was preceded by a two-day collaborative coding event open to the bioinformatics community. The conference brought together nearly 100 bioinformatics researchers, developers and users of open source software to interact and share ideas about standards, bioinformatics software development, and open and reproducible science.

Beyond Open Source: According to Jim Hirsch, Open Technology, Not Open Source, Is the Wave of the Future

ERIC Educational Resources Information Center

Villano, Matt

2006-01-01

This article presents an interview with Jim Hirsch, an associate superintendent for technology at Piano Independent School District in Piano, Texas. Hirsch serves as a liaison for the open technologies committee of the Consortium for School Networking. In this interview, he shares his opinion on the significance of open source in K-12.

EMISSIONS OF ORGANIC AIR TOXICS FROM OPEN ...

EPA Pesticide Factsheets

A detailed literature search was performed to collect and collate available data reporting emissions of toxic organic substances into the air from open burning sources. Availability of data varied according to the source and the class of air toxics of interest. Volatile organic compound (VOC) and polycyclic aromatic hydrocarbon (PAH) data were available for many of the sources. Data on semivolatile organic compounds (SVOCs) that are not PAHs were available for several sources. Carbonyl and polychlorinated dibenzo-p-dioxins and polychlorinated dibenzofuran (PCDD/F) data were available for only a few sources. There were several sources for which no emissions data were available at all. Several observations were made including: 1) Biomass open burning sources typically emitted less VOCs than open burning sources with anthropogenic fuels on a mass emitted per mass burned basis, particularly those where polymers were concerned; 2) Biomass open burning sources typically emitted less SVOCs and PAHs than anthropogenic sources on a mass emitted per mass burned basis. Burning pools of crude oil and diesel fuel produced significant amounts of PAHs relative to other types of open burning. PAH emissions were highest when combustion of polymers was taking place; and 3) Based on very limited data, biomass open burning sources typically produced higher levels of carbonyls than anthropogenic sources on a mass emitted per mass burned basis, probably due to oxygenated structures r

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

From dark to bright: novel daylighting applications in solid state lighting

NASA Astrophysics Data System (ADS)

Adler, Helmar G.

2011-10-01

The term "daylighting" is used in various ways, on one hand in a more architectural sense, i.e. using existing daylight to illuminate spaces, and on the other, more recently, for using light sources to replicate daylight. The emergence of solid state lighting (SSL) opens up a large number of new avenues for daylighting. SSL allows innovative controllability of intensity and color for artificial light sources that can be advantageously applied to daylighting. With the assistance of these new technologies the combination of natural and artificial lighting could lead to improvements in energy savings and comfort of living beings. Thus it is imperative to revisit or even improve daylighting research so that building networks of the future with their sensor, energy (e.g. HVAC) and lighting requirements can benefit from the emerging capabilities. This paper will briefly review existing daylighting concepts and technology and discuss new ideas. An example of a tunable multi-color SSL system will be shown.

Nurturing reliable and robust open-source scientific software

NASA Astrophysics Data System (ADS)

Uieda, L.; Wessel, P.

2017-12-01

Scientific results are increasingly the product of software. The reproducibility and validity of published results cannot be ensured without access to the source code of the software used to produce them. Therefore, the code itself is a fundamental part of the methodology and must be published along with the results. With such a reliance on software, it is troubling that most scientists do not receive formal training in software development. Tools such as version control, continuous integration, and automated testing are routinely used in industry to ensure the correctness and robustness of software. However, many scientist do not even know of their existence (although efforts like Software Carpentry are having an impact on this issue; software-carpentry.org). Publishing the source code is only the first step in creating an open-source project. For a project to grow it must provide documentation, participation guidelines, and a welcoming environment for new contributors. Expanding the project community is often more challenging than the technical aspects of software development. Maintainers must invest time to enforce the rules of the project and to onboard new members, which can be difficult to justify in the context of the "publish or perish" mentality. This problem will continue as long as software contributions are not recognized as valid scholarship by hiring and tenure committees. Furthermore, there are still unsolved problems in providing attribution for software contributions. Many journals and metrics of academic productivity do not recognize citations to sources other than traditional publications. Thus, some authors choose to publish an article about the software and use it as a citation marker. One issue with this approach is that updating the reference to include new contributors involves writing and publishing a new article. A better approach would be to cite a permanent archive of individual versions of the source code in services such as Zenodo (zenodo.org). However, citations to these sources are not always recognized when computing citation metrics. In summary, the widespread development of reliable and robust open-source software relies on the creation of formal training programs in software development best practices and the recognition of software as a valid form of scholarship.

Cloud Based Metalearning System for Predictive Modeling of Biomedical Data

PubMed Central

Vukićević, Milan

2014-01-01

Rapid growth and storage of biomedical data enabled many opportunities for predictive modeling and improvement of healthcare processes. On the other side analysis of such large amounts of data is a difficult and computationally intensive task for most existing data mining algorithms. This problem is addressed by proposing a cloud based system that integrates metalearning framework for ranking and selection of best predictive algorithms for data at hand and open source big data technologies for analysis of biomedical data. PMID:24892101

THYME: Toolkit for Hybrid Modeling of Electric Power Systems

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

Nutaro Kalyan Perumalla, James Joseph

2011-01-01

THYME is an object oriented library for building models of wide area control and communications in electric power systems. This software is designed as a module to be used with existing open source simulators for discrete event systems in general and communication systems in particular. THYME consists of a typical model for simulating electro-mechanical transients (e.g., as are used in dynamic stability studies), data handling objects to work with CDF and PTI formatted power flow data, and sample models of discrete sensors and controllers.

An Analysis of a Video Game

NASA Astrophysics Data System (ADS)

Allain, Rhett; Williams, Richard

2009-02-01

Suppose we had a brand new world to study—a world that possibly works with a different set of principles, a non-Newtonian world. Maybe this world is Newtonian, maybe it isn't. This world exists in video games, and it is open for exploration. Most video games try to incorporate realistic physics, but sometimes this does not happen. The obvious approach is to look at the source code for the game, but this would not allow students to apply analysis techniques.

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.

Aerostat-Lofted Instrument Platform and Sampling Method for Determination of Emissions from Open Area Sources

EPA Science Inventory

Sampling emissions from open area sources, particularly sources of open burning, is difficult due to fast dilution of emissions and safety concerns for personnel. Representative emission samples can be difficult to obtain with flaming and explosive sources since personnel safety ...

Magnetic Topology of the Global MHD Configuration on 2010 August 1-2

NASA Astrophysics Data System (ADS)

Titov, V. S.; Mikic, Z.; Torok, T.; Linker, J.; Panasenco, O.

2014-12-01

It appears that the global magnetic topology of the solar corona predetermines to a large extent the magnetic flux transfer during solar eruptions. We have recently analyzed the global topology for a source-surface model of the background magnetic field at the time of the 2010 August 1-2 sympathetic CMEs (Titov et al. 2012). Now we extend this analysis to a more accurate thermodynamic MHD model of the solar corona. As for the source-surface model, we find a similar triplet of pseudo-streamers in the source regions of the eruptions. The new study confirms that all these pseudo-streamers contain separatrix curtains that fan out from a basic magnetic null point, individual for each of the pseudo-streamers. In combination with the associated separatrix domes, these separatrix curtains fully isolate adjacent coronal holes of the like polarity from each other. However, the size and shape of the coronal holes, as well as their open magnetic fluxes and the fluxes in the lobes of the separatrix domes, are very different for the two models. The definition of the open separator field lines, where the (interchange) reconnection between open and closed magnetic flux takes place, is also modified, since the structurally unstable source-surface null lines do not exist anymore in the MHD model. In spite of all these differences, we reassert our earlier hypothesis that magnetic reconnection at these nulls and the associated separators likely plays a key role in coupling the successive eruptions observed by SDO and STEREO. The results obtained provide further validation of our recent simplified MHD model of sympathetic eruptions (Török et al. 2011). Research supported by NASA's Heliophysics Theory and LWS Programs, and NSF/SHINE and NSF/FESD.

An Assessment of Some Design Constraints on Heat Production of a 3D Conceptual EGS Model Using an Open-Source Geothermal Reservoir Simulation Code

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

Yidong Xia; Mitch Plummer; Robert Podgorney

2016-02-01

Performance of heat production process over a 30-year period is assessed in a conceptual EGS model with a geothermal gradient of 65K per km depth in the reservoir. Water is circulated through a pair of parallel wells connected by a set of single large wing fractures. The results indicate that the desirable output electric power rate and lifespan could be obtained under suitable material properties and system parameters. A sensitivity analysis on some design constraints and operation parameters indicates that 1) the fracture horizontal spacing has profound effect on the long-term performance of heat production, 2) the downward deviation anglemore » for the parallel doublet wells may help overcome the difficulty of vertical drilling to reach a favorable production temperature, and 3) the thermal energy production rate and lifespan has close dependence on water mass flow rate. The results also indicate that the heat production can be improved when the horizontal fracture spacing, well deviation angle, and production flow rate are under reasonable conditions. To conduct the reservoir modeling and simulations, an open-source, finite element based, fully implicit, fully coupled hydrothermal code, namely FALCON, has been developed and used in this work. Compared with most other existing codes that are either closed-source or commercially available in this area, this new open-source code has demonstrated a code development strategy that aims to provide an unparalleled easiness for user-customization and multi-physics coupling. Test results have shown that the FALCON code is able to complete the long-term tests efficiently and accurately, thanks to the state-of-the-art nonlinear and linear solver algorithms implemented in the code.« less

The Visible Human Data Sets (VHD) and Insight Toolkit (ITk): Experiments in Open Source Software

PubMed Central

Ackerman, Michael J.; Yoo, Terry S.

2003-01-01

From its inception in 1989, the Visible Human Project was designed as an experiment in open source software. In 1994 and 1995 the male and female Visible Human data sets were released by the National Library of Medicine (NLM) as open source data sets. In 2002 the NLM released the first version of the Insight Toolkit (ITk) as open source software. PMID:14728278

A New Global Open Source Marine Hydrocarbon Emission Site Database

NASA Astrophysics Data System (ADS)

Onyia, E., Jr.; Wood, W. T.; Barnard, A.; Dada, T.; Qazzaz, M.; Lee, T. R.; Herrera, E.; Sager, W.

2017-12-01

Hydrocarbon emission sites (e.g. seeps) discharge large volumes of fluids and gases into the oceans that are not only important for biogeochemical budgets, but also support abundant chemosynthetic communities. Documenting the locations of modern emissions is a first step towards understanding and monitoring how they affect the global state of the seafloor and oceans. Currently, no global open source (i.e. non-proprietry) detailed maps of emissions sites are available. As a solution, we have created a database that is housed within an Excel spreadsheet and use the latest versions of Earthpoint and Google Earth for position coordinate conversions and data mapping, respectively. To date, approximately 1,000 data points have been collected from referenceable sources across the globe, and we are continualy expanding the dataset. Due to the variety of spatial extents encountered, to identify each site we used two different methods: 1) point (x, y, z) locations for individual sites and; 2) delineation of areas where sites are clustered. Certain well-known areas, such as the Gulf of Mexico and the Mediterranean Sea, have a greater abundance of information; whereas significantly less information is available in other regions due to the absence of emission sites, lack of data, or because the existing data is proprietary. Although the geographical extent of the data is currently restricted to regions where the most data is publicly available, as the database matures, we expect to have more complete coverage of the world's oceans. This database is an information resource that consolidates and organizes the existing literature on hydrocarbons released into the marine environment, thereby providing a comprehensive reference for future work. We expect that the availability of seafloor hydrocarbon emission maps will benefit scientific understanding of hydrocarbon rich areas as well as potentially aiding hydrocarbon exploration and environmental impact assessements.

Building Geospatial Web Services for Ecological Monitoring and Forecasting

NASA Astrophysics Data System (ADS)

Hiatt, S. H.; Hashimoto, H.; Melton, F. S.; Michaelis, A. R.; Milesi, C.; Nemani, R. R.; Wang, W.

2008-12-01

The Terrestrial Observation and Prediction System (TOPS) at NASA Ames Research Center is a modeling system that generates a suite of gridded data products in near real-time that are designed to enhance management decisions related to floods, droughts, forest fires, human health, as well as crop, range, and forest production. While these data products introduce great possibilities for assisting management decisions and informing further research, realization of their full potential is complicated by their shear volume and by the need for a necessary infrastructure for remotely browsing, visualizing, and analyzing the data. In order to address these difficulties we have built an OGC-compliant WMS and WCS server based on an open source software stack that provides standardized access to our archive of data. This server is built using the open source Java library GeoTools which achieves efficient I/O and image rendering through Java Advanced Imaging. We developed spatio-temporal raster management capabilities using the PostGrid raster indexation engine. We provide visualization and browsing capabilities through a customized Ajax web interface derived from the kaMap project. This interface allows resource managers to quickly assess ecosystem conditions and identify significant trends and anomalies from within their web browser without the need to download source data or install special software. Our standardized web services also expose TOPS data to a range of potential clients, from web mapping applications to virtual globes and desktop GIS packages. However, support for managing the temporal dimension of our data is currently limited in existing software systems. Future work will attempt to overcome this shortcoming by building time-series visualization and analysis tools that can be integrated with existing geospatial software.

The 2016 Bioinformatics Open Source Conference (BOSC)

PubMed Central

Harris, Nomi L.; Cock, Peter J.A.; Chapman, Brad; Fields, Christopher J.; Hokamp, Karsten; Lapp, Hilmar; Muñoz-Torres, Monica; Wiencko, Heather

2016-01-01

Message from the ISCB: The Bioinformatics Open Source Conference (BOSC) is a yearly meeting organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. BOSC has been run since 2000 as a two-day Special Interest Group (SIG) before the annual ISMB conference. The 17th annual BOSC ( http://www.open-bio.org/wiki/BOSC_2016) took place in Orlando, Florida in July 2016. As in previous years, the conference was preceded by a two-day collaborative coding event open to the bioinformatics community. The conference brought together nearly 100 bioinformatics researchers, developers and users of open source software to interact and share ideas about standards, bioinformatics software development, and open and reproducible science. PMID:27781083

Creating More Credible and Persuasive Recommender Systems: The Influence of Source Characteristics on Recommender System Evaluations

NASA Astrophysics Data System (ADS)

Yoo, Kyung-Hyan; Gretzel, Ulrike

Whether users are likely to accept the recommendations provided by a recommender system is of utmost importance to system designers and the marketers who implement them. By conceptualizing the advice seeking and giving relationship as a fundamentally social process, important avenues for understanding the persuasiveness of recommender systems open up. Specifically, research regarding the influence of source characteristics, which is abundant in the context of humanhuman relationships, can provide an important framework for identifying potential influence factors. This chapter reviews the existing literature on source characteristics in the context of human-human, human-computer, and human-recommender system interactions. It concludes that many social cues that have been identified as influential in other contexts have yet to be implemented and tested with respect to recommender systems. Implications for recommender system research and design are discussed.

Practical guide: Tools and methodologies for an oil and gas industry emission inventory

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

Thompson, C.C.; Killian, T.L.

1996-12-31

During the preparation of Title V Permit applications, the quantification and speciation of emission sources from oil and gas facilities were reevaluated to determine the {open_quotes}potential-to-emit.{close_quotes} The existing emissions were primarily based on EPA emission factors such as AP-42, for tanks, combustion sources, and fugitive emissions from component leaks. Emissions from insignificant activities and routine operations that are associated with maintenance, startups and shutdowns, and releases to control devices also required quantification. To reconcile EPA emission factors with test data, process knowledge, and manufacturer`s data, a careful review of other estimation options was performed. This paper represents the results ofmore » this analysis of emission sources at oil and gas facilities, including exploration and production, compressor stations and gas plants.« less

OpenMx: An Open Source Extended Structural Equation Modeling Framework

ERIC Educational Resources Information Center

Boker, Steven; Neale, Michael; Maes, Hermine; Wilde, Michael; Spiegel, Michael; Brick, Timothy; Spies, Jeffrey; Estabrook, Ryne; Kenny, Sarah; Bates, Timothy; Mehta, Paras; Fox, John

2011-01-01

OpenMx is free, full-featured, open source, structural equation modeling (SEM) software. OpenMx runs within the "R" statistical programming environment on Windows, Mac OS-X, and Linux computers. The rationale for developing OpenMx is discussed along with the philosophy behind the user interface. The OpenMx data structures are…

Specifications for updating USGS land use and land cover maps

USGS Publications Warehouse

Milazzo, Valerie A.

1983-01-01

To meet the increasing demands for up-to-date land use and land cover information, a primary goal of the U.S. Geological Survey's (USGS) national land use and land cover mapping program is to provide for periodic updating of maps and data in a timely and uniform manner. The technical specifications for updating existing USGS land use and land cover maps that are presented here cover both the interpretive aspects of detecting and identifying land use and land cover changes and the cartographic aspects of mapping and presenting the change data in conventional map format. They provide the map compiler with the procedures and techniques necessary to then use these change data to update existing land use and land cover maps in a manner that is both standardized and repeatable. Included are specifications for the acquisition of remotely sensed source materials, selection of compilation map bases, handling of data base corrections, editing and quality control operations, generation of map update products for USGS open file, and the reproduction and distribution of open file materials. These specifications are planned to become part of the National Mapping Division's Technical Instructions.

Mapping Atmospheric Ammonia Emissions Using a Mobile Quantum Cascade Laser-based Open-path Sensor

NASA Astrophysics Data System (ADS)

Sun, K.; Tao, L.; Miller, D. J.; Khan, M. A.; Zondlo, M. A.

2012-12-01

Ammonia (NH3) is a key precursor to atmospheric fine particulate matter, with strong implications for regional air quality and global climate change. Despite the importance of atmospheric ammonia, its spatial/temporal variation is poorly characterized, and the knowledge of its sources, sinks, and transport is severely limited. Existing measurements suggest that traffic exhaust may provide significant amounts of ammonia in urban areas, which cause greater impacts on particulate matter formation and urban air quality. To capture the spatial and temporal variation of ammonia emissions, a portable, low power sensor with high time resolution is necessary. We have developed a portable open-path ammonia sensor with a detection limit of 0.5 ppbv ammonia for 1 s measurements. The sensor has a power consumption of about 60 W and is capable of running on a car battery continuously for 24 hours. An additional laser has been coupled to the sensor to yield concurrent N2O and CO measurements as tracers for determining various sources. The overall sensor prototype fits on a 60 cm × 20 cm aluminum breadboard. Roadside measurements indicated NH3/CO emission ratios of 4.1±5.4 ppbv/ppmv from a fleet of 320 vehicles, which agree with existing on-ramp measurements. Urban measurements in the Baltimore and Washington, DC metropolitan areas have shown significant ammonia mixing ratios concurrent with carbon monoxide levels from the morning and evening rush hours. On-road measurements of our open-path sensor have also been performed continuously from the Midwest to Princeton, NJ including urban areas such as Pittsburgh, tunnels, and relatively clean conditions. The emission ratios of ammonia against CO and/or CO2 help identify the sources and amounts of both urban and agricultural ammonia emissions. Preliminary data from both spatial mapping, monitoring, and vehicle exhaust measurements suggest that urban ammonia emissions from fossil fuel combustion are significant and may provide an unrecognized source in the atmospheric ammonia budget. Ongoing efforts include spatial mapping of ammonia and other tracers in the New York City and Philadelphia metropolitan areas. Further comparison with TES satellite ammonia retrieval will help to put the measurements into a larger geographical and temporal context.

Strengthened IAEA Safeguards-Imagery Analysis: Geospatial Tools for Nonproliferation Analysis

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

Pabian, Frank V

2012-08-14

This slide presentation focuses on the growing role and importance of imagery analysis for IAEA safeguards applications and how commercial satellite imagery, together with the newly available geospatial tools, can be used to promote 'all-source synergy.' As additional sources of openly available information, satellite imagery in conjunction with the geospatial tools can be used to significantly augment and enhance existing information gathering techniques, procedures, and analyses in the remote detection and assessment of nonproliferation relevant activities, facilities, and programs. Foremost of the geospatial tools are the 'Digital Virtual Globes' (i.e., GoogleEarth, Virtual Earth, etc.) that are far better than previouslymore » used simple 2-D plan-view line drawings for visualization of known and suspected facilities of interest which can be critical to: (1) Site familiarization and true geospatial context awareness; (2) Pre-inspection planning; (3) Onsite orientation and navigation; (4) Post-inspection reporting; (5) Site monitoring over time for changes; (6) Verification of states site declarations and for input to State Evaluation reports; and (7) A common basis for discussions among all interested parties (Member States). Additionally, as an 'open-source', such virtual globes can also provide a new, essentially free, means to conduct broad area search for undeclared nuclear sites and activities - either alleged through open source leads; identified on internet BLOGS and WIKI Layers, with input from a 'free' cadre of global browsers and/or by knowledgeable local citizens (a.k.a.: 'crowdsourcing'), that can include ground photos and maps; or by other initiatives based on existing information and in-house country knowledge. They also provide a means to acquire ground photography taken by locals, hobbyists, and tourists of the surrounding locales that can be useful in identifying and discriminating between relevant and non-relevant facilities and their associated infrastructure. The digital globes also provide highly accurate terrain mapping for better geospatial context and allow detailed 3-D perspectives of all sites or areas of interest. 3-D modeling software (i.e., Google's SketchUp6 newly available in 2007) when used in conjunction with these digital globes can significantly enhance individual building characterization and visualization (including interiors), allowing for better assessments including walk-arounds or fly-arounds and perhaps better decision making on multiple levels (e.g., the best placement for International Atomic Energy Agency (IAEA) video monitoring cameras).« less

The Case for Open Source: Open Source Has Made Significant Leaps in Recent Years. What Does It Have to Offer Education?

ERIC Educational Resources Information Center

Guhlin, Miguel

2007-01-01

Open source has continued to evolve and in the past three years the development of a graphical user interface has made it increasingly accessible and viable for end users without special training. Open source relies to a great extent on the free software movement. In this context, the term free refers not to cost, but to the freedom users have to…

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.

SolTrace | Concentrating Solar Power | NREL

Science.gov Websites

NREL packaged distribution or from source code at the SolTrace open source project website. NREL Publications Support FAQs SolTrace open source project The code uses Monte-Carlo ray-tracing methodology. The -tracing capabilities. With the release of the SolTrace open source project, the software has adopted

A national upgrade of the climate monitoring grid in Sri Lanka. The place of Open Design, OSHW and FOSS.

NASA Astrophysics Data System (ADS)

Chemin, Yann; Bandara, Niroshan; Eriyagama, Nishadi

2015-04-01

The National Climate Observatory of Sri lanka is a proposition designed for the Government of Sri Lanka in September and discussed with private and public stakeholders in November 2014. The idea was initially to install a networked grid of weather instruments from locally-made open source hardware technology, on land and seas, that report live the state of climate. After initial stakeholder meetings, it was agreed to first try to connect any existing weather stations from different governmental and private sector agencies. This would bring existing information to a common ground through the Internet. At this point, it was realized that extracting information from various vendors set up would take a large amount of efforts, that is still the best and fastest anyway, as considerations from ownership and maintenance are the most important issues in a tropical humid country as Sri Lanka. Thus, the question of Open Design, open source hardware (OSHW) and free and open source software (FOSS) became a pivotal element in considering operationalization of any future elements of a national grid. Reasons range from ownership, to low-cost and customization, but prominently it is about technology ownership, royalty-free and local availability. Building on previous work from (Chemin and Bandara, 2014) we proposed to open design specifications and prototypes for weather monitoring for various kinds of needs, the Meteorological Department clearly specified that the highest variability observed spatially in Sri Lanka is rainfall, and their willingness to investigate OSHW electronics using their new team of electronics and sensors specialists. A local manufacturer is providing an OSHW micro-controller product, a start up is providing additional sensor boards under OSHW specifications and local manufacture of the sensors (tipping-bucket and other wind sensors) is under development and blueprints have been made available in the Public Domain for CNC machine, 3D printing or Plastic Molding. The Lanka Rainwater Harvesting Forum was in need of volumetric estimation of rainfall-runoff contributed to recharge of the aquifers. Regular reporting of high quality rainfall events and intensity is still a challenge to be addressed in Sri Lanka. A combination of OSHW and FOSS is being used to created a royalty-free, cheap raingauge design, with full control of on-board data collection and statistics. Development of an initial 15 raingauges include capacity-building, joint set up from the ground to scouting and installation, and full ownership of all aspects (hardware sourcing locally, software modification, communication troubleshooting, etc.). The Irrigation Department in Malwatu Oya had a requirement for real time rainfall information to manage reservoirs in cascade ("daisy chain") and mitigate flooding consequences downstream. 5 generic prototypes are now reporting to reservoir managers, and the reservoir management model is now rerun as often as needed to re-assess decision-requirements from any new rainfall about certain, already-known, dangerous intensity. The irrigation department capacity-building was provided in two trainings, one for engineers (decision-making support) and technicians (reporting and maintenance). Interest for further level of control in the system is low. Reporting online is following several potential routes, and an open design GPRS protocol is being developed, to simplify future weather stations design specifications in Sri Lanka.

When Free Isn't Free: The Realities of Running Open Source in School

ERIC Educational Resources Information Center

Derringer, Pam

2009-01-01

Despite the last few years' growth in awareness of open-source software in schools and the potential savings it represents, its widespread adoption is still hampered. Randy Orwin, technology director of the Bainbridge Island School District in Washington State and a strong open-source advocate, cautions that installing an open-source…

GlobiPack v. 1.0

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

Bartlett, Roscoe

2010-03-31

GlobiPack contains a small collection of optimization globalization algorithms. These algorithms are used by optimization and various nonlinear equation solver algorithms.Used as the line-search procedure with Newton and Quasi-Newton optimization and nonlinear equation solver methods. These are standard published 1-D line search algorithms such as are described in the book Nocedal and Wright Numerical Optimization: 2nd edition, 2006. One set of algorithms were copied and refactored from the existing open-source Trilinos package MOOCHO where the linear search code is used to globalize SQP methods. This software is generic to any mathematical optimization problem where smooth derivatives exist. There is nomore » specific connection or mention whatsoever to any specific application, period. You cannot find more general mathematical software.« less

A Conformance Test Suite for Arden Syntax Compilers and Interpreters.

PubMed

Wolf, Klaus-Hendrik; Klimek, Mike

2016-01-01

The Arden Syntax for Medical Logic Modules is a standardized and well-established programming language to represent medical knowledge. To test the compliance level of existing compilers and interpreters no public test suite exists. This paper presents the research to transform the specification into a set of unit tests, represented in JUnit. It further reports on the utilization of the test suite testing four different Arden Syntax processors. The presented and compared results reveal the status conformance of the tested processors. How test driven development of Arden Syntax processors can help increasing the compliance with the standard is described with two examples. In the end some considerations how an open source test suite can improve the development and distribution of the Arden Syntax are presented.

Convex Accelerated Maximum Entropy Reconstruction

PubMed Central

Worley, Bradley

2016-01-01

Maximum entropy (MaxEnt) spectral reconstruction methods provide a powerful framework for spectral estimation of nonuniformly sampled datasets. Many methods exist within this framework, usually defined based on the magnitude of a Lagrange multiplier in the MaxEnt objective function. An algorithm is presented here that utilizes accelerated first-order convex optimization techniques to rapidly and reliably reconstruct nonuniformly sampled NMR datasets using the principle of maximum entropy. This algorithm – called CAMERA for Convex Accelerated Maximum Entropy Reconstruction Algorithm – is a new approach to spectral reconstruction that exhibits fast, tunable convergence in both constant-aim and constant-lambda modes. A high-performance, open source NMR data processing tool is described that implements CAMERA, and brief comparisons to existing reconstruction methods are made on several example spectra. PMID:26894476

Implementing an Open Source Electronic Health Record System in Kenyan Health Care Facilities: Case Study

PubMed Central

Magare, Steve; Monda, Jonathan; Kamau, Onesmus; Houston, Stuart; Fraser, Hamish; Powell, John; English, Mike; Paton, Chris

2018-01-01

Background The Kenyan government, working with international partners and local organizations, has developed an eHealth strategy, specified standards, and guidelines for electronic health record adoption in public hospitals and implemented two major health information technology projects: District Health Information Software Version 2, for collating national health care indicators and a rollout of the KenyaEMR and International Quality Care Health Management Information Systems, for managing 600 HIV clinics across the country. Following these projects, a modified version of the Open Medical Record System electronic health record was specified and developed to fulfill the clinical and administrative requirements of health care facilities operated by devolved counties in Kenya and to automate the process of collating health care indicators and entering them into the District Health Information Software Version 2 system. Objective We aimed to present a descriptive case study of the implementation of an open source electronic health record system in public health care facilities in Kenya. Methods We conducted a landscape review of existing literature concerning eHealth policies and electronic health record development in Kenya. Following initial discussions with the Ministry of Health, the World Health Organization, and implementing partners, we conducted a series of visits to implementing sites to conduct semistructured individual interviews and group discussions with stakeholders to produce a historical case study of the implementation. Results This case study describes how consultants based in Kenya, working with developers in India and project stakeholders, implemented the new system into several public hospitals in a county in rural Kenya. The implementation process included upgrading the hospital information technology infrastructure, training users, and attempting to garner administrative and clinical buy-in for adoption of the system. The initial deployment was ultimately scaled back due to a complex mix of sociotechnical and administrative issues. Learning from these early challenges, the system is now being redesigned and prepared for deployment in 6 new counties across Kenya. Conclusions Implementing electronic health record systems is a challenging process in high-income settings. In low-income settings, such as Kenya, open source software may offer some respite from the high costs of software licensing, but the familiar challenges of clinical and administration buy-in, the need to adequately train users, and the need for the provision of ongoing technical support are common across the North-South divide. Strategies such as creating local support teams, using local development resources, ensuring end user buy-in, and rolling out in smaller facilities before larger hospitals are being incorporated into the project. These are positive developments to help maintain momentum as the project continues. Further integration with existing open source communities could help ongoing development and implementations of the project. We hope this case study will provide some lessons and guidance for other challenging implementations of electronic health record systems as they continue across Africa. PMID:29669709

A study of the effects of degraded imagery on tactical 3D model generation using structure-from-motion

NASA Astrophysics Data System (ADS)

Bolick, Leslie; Harguess, Josh

2016-05-01

An emerging technology in the realm of airborne intelligence, surveillance, and reconnaissance (ISR) systems is structure-from-motion (SfM), which enables the creation of three-dimensional (3D) point clouds and 3D models from two-dimensional (2D) imagery. There are several existing tools, such as VisualSFM and open source project OpenSfM, to assist in this process, however, it is well-known that pristine imagery is usually required to create meaningful 3D data from the imagery. In military applications, such as the use of unmanned aerial vehicles (UAV) for surveillance operations, imagery is rarely pristine. Therefore, we present an analysis of structure-from-motion packages on imagery that has been degraded in a controlled manner.

A Generic Software Architecture For Prognostics

NASA Technical Reports Server (NTRS)

Teubert, Christopher; Daigle, Matthew J.; Sankararaman, Shankar; Goebel, Kai; Watkins, Jason

2017-01-01

Prognostics is a systems engineering discipline focused on predicting end-of-life of components and systems. As a relatively new and emerging technology, there are few fielded implementations of prognostics, due in part to practitioners perceiving a large hurdle in developing the models, algorithms, architecture, and integration pieces. As a result, no open software frameworks for applying prognostics currently exist. This paper introduces the Generic Software Architecture for Prognostics (GSAP), an open-source, cross-platform, object-oriented software framework and support library for creating prognostics applications. GSAP was designed to make prognostics more accessible and enable faster adoption and implementation by industry, by reducing the effort and investment required to develop, test, and deploy prognostics. This paper describes the requirements, design, and testing of GSAP. Additionally, a detailed case study involving battery prognostics demonstrates its use.

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.

Mocking the weak lensing universe: The LensTools Python computing package

NASA Astrophysics Data System (ADS)

Petri, A.

2016-10-01

We present a newly developed software package which implements a wide range of routines frequently used in Weak Gravitational Lensing (WL). With the continuously increasing size of the WL scientific community we feel that easy to use Application Program Interfaces (APIs) for common calculations are a necessity to ensure efficiency and coordination across different working groups. Coupled with existing open source codes, such as CAMB (Lewis et al., 2000) and Gadget2 (Springel, 2005), LensTools brings together a cosmic shear simulation pipeline which, complemented with a variety of WL feature measurement tools and parameter sampling routines, provides easy access to the numerics for theoretical studies of WL as well as for experiment forecasts. Being implemented in PYTHON (Rossum, 1995), LensTools takes full advantage of a range of state-of-the art techniques developed by the large and growing open-source software community (Jones et al., 2001; McKinney, 2010; Astrophy Collaboration, 2013; Pedregosa et al., 2011; Foreman-Mackey et al., 2013). We made the LensTools code available on the Python Package Index and published its documentation on http://lenstools.readthedocs.io.

SIproc: an open-source biomedical data processing platform for large hyperspectral images.

PubMed

Berisha, Sebastian; Chang, Shengyuan; Saki, Sam; Daeinejad, Davar; He, Ziqi; Mankar, Rupali; Mayerich, David

2017-04-10

There has recently been significant interest within the vibrational spectroscopy community to apply quantitative spectroscopic imaging techniques to histology and clinical diagnosis. However, many of the proposed methods require collecting spectroscopic images that have a similar region size and resolution to the corresponding histological images. Since spectroscopic images contain significantly more spectral samples than traditional histology, the resulting data sets can approach hundreds of gigabytes to terabytes in size. This makes them difficult to store and process, and the tools available to researchers for handling large spectroscopic data sets are limited. Fundamental mathematical tools, such as MATLAB, Octave, and SciPy, are extremely powerful but require that the data be stored in fast memory. This memory limitation becomes impractical for even modestly sized histological images, which can be hundreds of gigabytes in size. In this paper, we propose an open-source toolkit designed to perform out-of-core processing of hyperspectral images. By taking advantage of graphical processing unit (GPU) computing combined with adaptive data streaming, our software alleviates common workstation memory limitations while achieving better performance than existing applications.

Tessera: Open source software for accelerated data science

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

Sego, Landon H.; Hafen, Ryan P.; Director, Hannah M.

2014-06-30

Extracting useful, actionable information from data can be a formidable challenge for the safeguards, nonproliferation, and arms control verification communities. Data scientists are often on the “front-lines” of making sense of complex and large datasets. They require flexible tools that make it easy to rapidly reformat large datasets, interactively explore and visualize data, develop statistical algorithms, and validate their approaches—and they need to perform these activities with minimal lines of code. Existing commercial software solutions often lack extensibility and the flexibility required to address the nuances of the demanding and dynamic environments where data scientists work. To address this need,more » Pacific Northwest National Laboratory developed Tessera, an open source software suite designed to enable data scientists to interactively perform their craft at the terabyte scale. Tessera automatically manages the complicated tasks of distributed storage and computation, empowering data scientists to do what they do best: tackling critical research and mission objectives by deriving insight from data. We illustrate the use of Tessera with an example analysis of computer network data.« less

Rethinking the outpatient medication list: increasing patient activation and education while architecting for centralization and improved medication reconciliation.

PubMed

Pandolfe, Frank; Wright, Adam; Slack, Warner V; Safran, Charles

2018-05-17

Identify barriers impacting the time consuming and error fraught process of medication reconciliation. Design and implement an electronic medication management system where patient and trusted healthcare proxies can participate in establishing and maintaining an inclusive and up-to-date list of medications. A patient-facing electronic medication manager was deployed within an existing research project focused on elder care management funded by the AHRQ, InfoSAGE, allowing patients and patients' proxies the ability to build and maintain an accurate and up-to-date medication list. Free and open-source tools available from the U.S. government were used to embed the tenets of centralization, interoperability, data federation, and patient activation into the design. Using patient-centered design and free, open-source tools, we implemented a web and mobile enabled patient-facing medication manager for complex medication management. Patient and caregiver participation are essential to improve medication safety. Our medication manager is an early step towards a patient-facing medication manager that has been designed with data federation and interoperability in mind.

Generating the local oscillator "locally" in continuous-variable quantum key distribution based on coherent detection

DOE PAGES

Qi, Bing; Lougovski, Pavel; Pooser, Raphael C.; ...

2015-10-21

Continuous-variable quantum key distribution (CV-QKD) protocols based on coherent detection have been studied extensively in both theory and experiment. In all the existing implementations of CV-QKD, both the quantum signal and the local oscillator (LO) are generated from the same laser and propagate through the insecure quantum channel. This arrangement may open security loopholes and limit the potential applications of CV-QKD. In our paper, we propose and demonstrate a pilot-aided feedforward data recovery scheme that enables reliable coherent detection using a “locally” generated LO. Using two independent commercial laser sources and a spool of 25-km optical fiber, we construct amore » coherent communication system. The variance of the phase noise introduced by the proposed scheme is measured to be 0.04 (rad 2), which is small enough to enable secure key distribution. This technology opens the door for other quantum communication protocols, such as the recently proposed measurement-device-independent CV-QKD, where independent light sources are employed by different users.« less

The risk factors for avian influenza on poultry farms: a meta-analysis.

PubMed

Wang, Youming; Li, Peng; Wu, Yangli; Sun, Xiangdong; Yu, Kangzhen; Yu, Chuanhua; Qin, Aijian

2014-11-01

Avian influenza is a severe threat both to humans and poultry, but so far, no systematic review on the identification and evaluation of the risk factors of avian influenza infection has been published. The objective of this meta-analysis is to provide evidence for decision-making and further research on AI prevention through identifying the risk factors associated with AI infection on poultry farms. The results from 15 selected studies on risk factors for AI infections on poultry farms were analyzed quantitatively by meta-analysis. Open water source (OR=2.89), infections on nearby farms (OR=4.54), other livestock (OR=1.90) and disinfection of farm (OR=0.54) have significant association with AI infection on poultry farms. The subgroup analysis results indicate that there exist different risk factors for AI infections in different types of farms. The main risk factors for AI infection in poultry farms are environmental conditions (open water source, infections on nearby farms), keeping other livestock on the same farm and no disinfection of the farm. Copyright © 2014 Elsevier B.V. All rights reserved.

CACTI: Free, Open-Source Software for the Sequential Coding of Behavioral Interactions

PubMed Central

Glynn, Lisa H.; Hallgren, Kevin A.; Houck, Jon M.; Moyers, Theresa B.

2012-01-01

The sequential analysis of client and clinician speech in psychotherapy sessions can help to identify and characterize potential mechanisms of treatment and behavior change. Previous studies required coding systems that were time-consuming, expensive, and error-prone. Existing software can be expensive and inflexible, and furthermore, no single package allows for pre-parsing, sequential coding, and assignment of global ratings. We developed a free, open-source, and adaptable program to meet these needs: The CASAA Application for Coding Treatment Interactions (CACTI). Without transcripts, CACTI facilitates the real-time sequential coding of behavioral interactions using WAV-format audio files. Most elements of the interface are user-modifiable through a simple XML file, and can be further adapted using Java through the terms of the GNU Public License. Coding with this software yields interrater reliabilities comparable to previous methods, but at greatly reduced time and expense. CACTI is a flexible research tool that can simplify psychotherapy process research, and has the potential to contribute to the improvement of treatment content and delivery. PMID:22815713

CONNJUR spectrum translator: an open source application for reformatting NMR spectral data.

PubMed

Nowling, Ronald J; Vyas, Jay; Weatherby, Gerard; Fenwick, Matthew W; Ellis, Heidi J C; Gryk, Michael R

2011-05-01

NMR spectroscopists are hindered by the lack of standardization for spectral data among the file formats for various NMR data processing tools. This lack of standardization is cumbersome as researchers must perform their own file conversion in order to switch between processing tools and also restricts the combination of tools employed if no conversion option is available. The CONNJUR Spectrum Translator introduces a new, extensible architecture for spectrum translation and introduces two key algorithmic improvements. This first is translation of NMR spectral data (time and frequency domain) to a single in-memory data model to allow addition of new file formats with two converter modules, a reader and a writer, instead of writing a separate converter to each existing format. Secondly, the use of layout descriptors allows a single fid data translation engine to be used for all formats. For the end user, sophisticated metadata readers allow conversion of the majority of files with minimum user configuration. The open source code is freely available at http://connjur.sourceforge.net for inspection and extension.

Open Source Vision

ERIC Educational Resources Information Center

Villano, Matt

2006-01-01

Increasingly, colleges and universities are turning to open source as a way to meet their technology infrastructure and application needs. Open source has changed life for visionary CIOs and their campus communities nationwide. The author discusses what these technologists see as the benefits--and the considerations.

An open source hydroeconomic model for California's water supply system: PyVIN

NASA Astrophysics Data System (ADS)

Dogan, M. S.; White, E.; Herman, J. D.; Hart, Q.; Merz, J.; Medellin-Azuara, J.; Lund, J. R.

2016-12-01

Models help operators and decision makers explore and compare different management and policy alternatives, better allocate scarce resources, and predict the future behavior of existing or proposed water systems. Hydroeconomic models are useful tools to increase benefits or decrease costs of managing water. Bringing hydrology and economics together, these models provide a framework for different disciplines that share similar objectives. This work proposes a new model to evaluate operation and adaptation strategies under existing and future hydrologic conditions for California's interconnected water system. This model combines the network structure of CALVIN, a statewide optimization model for California's water infrastructure, along with an open source solver written in the Python programming language. With the flexibilities of the model, reservoir operations, including water supply and hydropower, groundwater pumping, and the Delta water operations and requirements can now be better represented. Given time series of hydrologic inputs to the model, typical outputs include urban, agricultural and wildlife refuge water deliveries and shortage costs, conjunctive use of surface and groundwater systems, and insights into policy and management decisions, such as capacity expansion and groundwater management policies. Water market operations also represented in the model, allocating water from lower-valued users to higher-valued users. PyVIN serves as a cross-platform, extensible model to evaluate systemwide water operations. PyVIN separates data from the model structure, enabling model to be easily applied to other parts of the world where water is a scarce resource.

SANDS: a service-oriented architecture for clinical decision support in a National Health Information Network.

PubMed

Wright, Adam; Sittig, Dean F

2008-12-01

In this paper, we describe and evaluate a new distributed architecture for clinical decision support called SANDS (Service-oriented Architecture for NHIN Decision Support), which leverages current health information exchange efforts and is based on the principles of a service-oriented architecture. The architecture allows disparate clinical information systems and clinical decision support systems to be seamlessly integrated over a network according to a set of interfaces and protocols described in this paper. The architecture described is fully defined and developed, and six use cases have been developed and tested using a prototype electronic health record which links to one of the existing prototype National Health Information Networks (NHIN): drug interaction checking, syndromic surveillance, diagnostic decision support, inappropriate prescribing in older adults, information at the point of care and a simple personal health record. Some of these use cases utilize existing decision support systems, which are either commercially or freely available at present, and developed outside of the SANDS project, while other use cases are based on decision support systems developed specifically for the project. Open source code for many of these components is available, and an open source reference parser is also available for comparison and testing of other clinical information systems and clinical decision support systems that wish to implement the SANDS architecture. The SANDS architecture for decision support has several significant advantages over other architectures for clinical decision support. The most salient of these are:

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.

GALARIO: a GPU accelerated library for analysing radio interferometer observations

NASA Astrophysics Data System (ADS)

Tazzari, Marco; Beaujean, Frederik; Testi, Leonardo

2018-06-01

We present GALARIO, a computational library that exploits the power of modern graphical processing units (GPUs) to accelerate the analysis of observations from radio interferometers like Atacama Large Millimeter and sub-millimeter Array or the Karl G. Jansky Very Large Array. GALARIO speeds up the computation of synthetic visibilities from a generic 2D model image or a radial brightness profile (for axisymmetric sources). On a GPU, GALARIO is 150 faster than standard PYTHON and 10 times faster than serial C++ code on a CPU. Highly modular, easy to use, and to adopt in existing code, GALARIO comes as two compiled libraries, one for Nvidia GPUs and one for multicore CPUs, where both have the same functions with identical interfaces. GALARIO comes with PYTHON bindings but can also be directly used in C or C++. The versatility and the speed of GALARIO open new analysis pathways that otherwise would be prohibitively time consuming, e.g. fitting high-resolution observations of large number of objects, or entire spectral cubes of molecular gas emission. It is a general tool that can be applied to any field that uses radio interferometer observations. The source code is available online at http://github.com/mtazzari/galario under the open source GNU Lesser General Public License v3.

76 FR 34634 - Federal Acquisition Regulation; Prioritizing Sources of Supplies and Services for Use by the...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-14

... contracts before commercial sources in the open market. The proposed rule amends FAR 8.002 as follows: The... requirements for supplies and services from commercial sources in the open market. The proposed FAR 8.004 would... subpart 8.6). (b) Commercial sources (including educational and non-profit institutions) in the open...

Four simple recommendations to encourage best practices in research software

PubMed Central

Jiménez, Rafael C.; Kuzak, Mateusz; Alhamdoosh, Monther; Barker, Michelle; Batut, Bérénice; Borg, Mikael; Capella-Gutierrez, Salvador; Chue Hong, Neil; Cook, Martin; Corpas, Manuel; Flannery, Madison; Garcia, Leyla; Gelpí, Josep Ll.; Gladman, Simon; Goble, Carole; González Ferreiro, Montserrat; Gonzalez-Beltran, Alejandra; Griffin, Philippa C.; Grüning, Björn; Hagberg, Jonas; Holub, Petr; Hooft, Rob; Ison, Jon; Katz, Daniel S.; Leskošek, Brane; López Gómez, Federico; Oliveira, Luis J.; Mellor, David; Mosbergen, Rowland; Mulder, Nicola; Perez-Riverol, Yasset; Pergl, Robert; Pichler, Horst; Pope, Bernard; Sanz, Ferran; Schneider, Maria V.; Stodden, Victoria; Suchecki, Radosław; Svobodová Vařeková, Radka; Talvik, Harry-Anton; Todorov, Ilian; Treloar, Andrew; Tyagi, Sonika; van Gompel, Maarten; Vaughan, Daniel; Via, Allegra; Wang, Xiaochuan; Watson-Haigh, Nathan S.; Crouch, Steve

2017-01-01

Scientific research relies on computer software, yet software is not always developed following practices that ensure its quality and sustainability. This manuscript does not aim to propose new software development best practices, but rather to provide simple recommendations that encourage the adoption of existing best practices. Software development best practices promote better quality software, and better quality software improves the reproducibility and reusability of research. These recommendations are designed around Open Source values, and provide practical suggestions that contribute to making research software and its source code more discoverable, reusable and transparent. This manuscript is aimed at developers, but also at organisations, projects, journals and funders that can increase the quality and sustainability of research software by encouraging the adoption of these recommendations. PMID:28751965

Four simple recommendations to encourage best practices in research software.

PubMed

Jiménez, Rafael C; Kuzak, Mateusz; Alhamdoosh, Monther; Barker, Michelle; Batut, Bérénice; Borg, Mikael; Capella-Gutierrez, Salvador; Chue Hong, Neil; Cook, Martin; Corpas, Manuel; Flannery, Madison; Garcia, Leyla; Gelpí, Josep Ll; Gladman, Simon; Goble, Carole; González Ferreiro, Montserrat; Gonzalez-Beltran, Alejandra; Griffin, Philippa C; Grüning, Björn; Hagberg, Jonas; Holub, Petr; Hooft, Rob; Ison, Jon; Katz, Daniel S; Leskošek, Brane; López Gómez, Federico; Oliveira, Luis J; Mellor, David; Mosbergen, Rowland; Mulder, Nicola; Perez-Riverol, Yasset; Pergl, Robert; Pichler, Horst; Pope, Bernard; Sanz, Ferran; Schneider, Maria V; Stodden, Victoria; Suchecki, Radosław; Svobodová Vařeková, Radka; Talvik, Harry-Anton; Todorov, Ilian; Treloar, Andrew; Tyagi, Sonika; van Gompel, Maarten; Vaughan, Daniel; Via, Allegra; Wang, Xiaochuan; Watson-Haigh, Nathan S; Crouch, Steve

2017-01-01

Scientific research relies on computer software, yet software is not always developed following practices that ensure its quality and sustainability. This manuscript does not aim to propose new software development best practices, but rather to provide simple recommendations that encourage the adoption of existing best practices. Software development best practices promote better quality software, and better quality software improves the reproducibility and reusability of research. These recommendations are designed around Open Source values, and provide practical suggestions that contribute to making research software and its source code more discoverable, reusable and transparent. This manuscript is aimed at developers, but also at organisations, projects, journals and funders that can increase the quality and sustainability of research software by encouraging the adoption of these recommendations.

AMIDE: a free software tool for multimodality medical image analysis.

PubMed

Loening, Andreas Markus; Gambhir, Sanjiv Sam

2003-07-01

Amide's a Medical Image Data Examiner (AMIDE) has been developed as a user-friendly, open-source software tool for displaying and analyzing multimodality volumetric medical images. Central to the package's abilities to simultaneously display multiple data sets (e.g., PET, CT, MRI) and regions of interest is the on-demand data reslicing implemented within the program. Data sets can be freely shifted, rotated, viewed, and analyzed with the program automatically handling interpolation as needed from the original data. Validation has been performed by comparing the output of AMIDE with that of several existing software packages. AMIDE runs on UNIX, Macintosh OS X, and Microsoft Windows platforms, and it is freely available with source code under the terms of the GNU General Public License.

Biosecurity and Open-Source Biology: The Promise and Peril of Distributed Synthetic Biological Technologies.

PubMed

Evans, Nicholas G; Selgelid, Michael J

2015-08-01

In this article, we raise ethical concerns about the potential misuse of open-source biology (OSB): biological research and development that progresses through an organisational model of radical openness, deskilling, and innovation. We compare this organisational structure to that of the open-source software model, and detail salient ethical implications of this model. We demonstrate that OSB, in virtue of its commitment to openness, may be resistant to governance attempts.

Using R to implement spatial analysis in open source environment

NASA Astrophysics Data System (ADS)

Shao, Yixi; Chen, Dong; Zhao, Bo

2007-06-01

R is an open source (GPL) language and environment for spatial analysis, statistical computing and graphics which provides a wide variety of statistical and graphical techniques, and is highly extensible. In the Open Source environment it plays an important role in doing spatial analysis. So, to implement spatial analysis in the Open Source environment which we called the Open Source geocomputation is using the R data analysis language integrated with GRASS GIS and MySQL or PostgreSQL. This paper explains the architecture of the Open Source GIS environment and emphasizes the role R plays in the aspect of spatial analysis. Furthermore, one apt illustration of the functions of R is given in this paper through the project of constructing CZPGIS (Cheng Zhou Population GIS) supported by Changzhou Government, China. In this project we use R to implement the geostatistics in the Open Source GIS environment to evaluate the spatial correlation of land price and estimate it by Kriging Interpolation. We also use R integrated with MapServer and php to show how R and other Open Source software cooperate with each other in WebGIS environment, which represents the advantages of using R to implement spatial analysis in Open Source GIS environment. And in the end, we points out that the packages for spatial analysis in R is still scattered and the limited memory is still a bottleneck when large sum of clients connect at the same time. Therefore further work is to group the extensive packages in order or design normative packages and make R cooperate better with other commercial software such as ArcIMS. Also we look forward to developing packages for land price evaluation.

The world’s user-generated road map is more than 80% complete

PubMed Central

2017-01-01

OpenStreetMap, a crowdsourced geographic database, provides the only global-level, openly licensed source of geospatial road data, and the only national-level source in many countries. However, researchers, policy makers, and citizens who want to make use of OpenStreetMap (OSM) have little information about whether it can be relied upon in a particular geographic setting. In this paper, we use two complementary, independent methods to assess the completeness of OSM road data in each country in the world. First, we undertake a visual assessment of OSM data against satellite imagery, which provides the input for estimates based on a multilevel regression and poststratification model. Second, we fit sigmoid curves to the cumulative length of contributions, and use them to estimate the saturation level for each country. Both techniques may have more general use for assessing the development and saturation of crowd-sourced data. Our results show that in many places, researchers and policymakers can rely on the completeness of OSM, or will soon be able to do so. We find (i) that globally, OSM is ∼83% complete, and more than 40% of countries—including several in the developing world—have a fully mapped street network; (ii) that well-governed countries with good Internet access tend to be more complete, and that completeness has a U-shaped relationship with population density—both sparsely populated areas and dense cities are the best mapped; and (iii) that existing global datasets used by the World Bank undercount roads by more than 30%. PMID:28797037

Meta-image navigation augmenters for unmanned aircraft systems (MINA for UAS)

NASA Astrophysics Data System (ADS)

Òªelik, Koray; Somani, Arun K.; Schnaufer, Bernard; Hwang, Patrick Y.; McGraw, Gary A.; Nadke, Jeremy

2013-05-01

GPS is a critical sensor for Unmanned Aircraft Systems (UASs) due to its accuracy, global coverage and small hardware footprint, but is subject to denial due to signal blockage or RF interference. When GPS is unavailable, position, velocity and attitude (PVA) performance from other inertial and air data sensors is not sufficient, especially for small UASs. Recently, image-based navigation algorithms have been developed to address GPS outages for UASs, since most of these platforms already include a camera as standard equipage. Performing absolute navigation with real-time aerial images requires georeferenced data, either images or landmarks, as a reference. Georeferenced imagery is readily available today, but requires a large amount of storage, whereas collections of discrete landmarks are compact but must be generated by pre-processing. An alternative, compact source of georeferenced data having large coverage area is open source vector maps from which meta-objects can be extracted for matching against real-time acquired imagery. We have developed a novel, automated approach called MINA (Meta Image Navigation Augmenters), which is a synergy of machine-vision and machine-learning algorithms for map aided navigation. As opposed to existing image map matching algorithms, MINA utilizes publicly available open-source geo-referenced vector map data, such as OpenStreetMap, in conjunction with real-time optical imagery from an on-board, monocular camera to augment the UAS navigation computer when GPS is not available. The MINA approach has been experimentally validated with both actual flight data and flight simulation data and results are presented in the paper.

Duke Surgery Patient Safety: an open-source application for anonymous reporting of adverse and near-miss surgical events

PubMed Central

Pietrobon, Ricardo; Lima, Raquel; Shah, Anand; Jacobs, Danny O; Harker, Matthew; McCready, Mariana; Martins, Henrique; Richardson, William

2007-01-01

Background Studies have shown that 4% of hospitalized patients suffer from an adverse event caused by the medical treatment administered. Some institutions have created systems to encourage medical workers to report these adverse events. However, these systems often prove to be inadequate and/or ineffective for reviewing the data collected and improving the outcomes in patient safety. Objective To describe the Web-application Duke Surgery Patient Safety, designed for the anonymous reporting of adverse and near-miss events as well as scheduled reporting to surgeons and hospital administration. Software architecture DSPS was developed primarily using Java language running on a Tomcat server and with MySQL database as its backend. Results Formal and field usability tests were used to aid in development of DSPS. Extensive experience with DSPS at our institution indicate that DSPS is easy to learn and use, has good speed, provides needed functionality, and is well received by both adverse-event reporters and administrators. Discussion This is the first description of an open-source application for reporting patient safety, which allows the distribution of the application to other institutions in addition for its ability to adapt to the needs of different departments. DSPS provides a mechanism for anonymous reporting of adverse events and helps to administer Patient Safety initiatives. Conclusion The modifiable framework of DSPS allows adherence to evolving national data standards. The open-source design of DSPS permits surgical departments with existing reporting mechanisms to integrate them with DSPS. The DSPS application is distributed under the GNU General Public License. PMID:17472749

nSTAT: Open-Source Neural Spike Train Analysis Toolbox for Matlab

PubMed Central

Cajigas, I.; Malik, W.Q.; Brown, E.N.

2012-01-01

Over the last decade there has been a tremendous advance in the analytical tools available to neuroscientists to understand and model neural function. In particular, the point process - Generalized Linear Model (PPGLM) framework has been applied successfully to problems ranging from neuro-endocrine physiology to neural decoding. However, the lack of freely distributed software implementations of published PP-GLM algorithms together with problem-specific modifications required for their use, limit wide application of these techniques. In an effort to make existing PP-GLM methods more accessible to the neuroscience community, we have developed nSTAT – an open source neural spike train analysis toolbox for Matlab®. By adopting an Object-Oriented Programming (OOP) approach, nSTAT allows users to easily manipulate data by performing operations on objects that have an intuitive connection to the experiment (spike trains, covariates, etc.), rather than by dealing with data in vector/matrix form. The algorithms implemented within nSTAT address a number of common problems including computation of peri-stimulus time histograms, quantification of the temporal response properties of neurons, and characterization of neural plasticity within and across trials. nSTAT provides a starting point for exploratory data analysis, allows for simple and systematic building and testing of point process models, and for decoding of stimulus variables based on point process models of neural function. By providing an open-source toolbox, we hope to establish a platform that can be easily used, modified, and extended by the scientific community to address limitations of current techniques and to extend available techniques to more complex problems. PMID:22981419

Duke Surgery Patient Safety: an open-source application for anonymous reporting of adverse and near-miss surgical events.

PubMed

Pietrobon, Ricardo; Lima, Raquel; Shah, Anand; Jacobs, Danny O; Harker, Matthew; McCready, Mariana; Martins, Henrique; Richardson, William

2007-05-01

Studies have shown that 4% of hospitalized patients suffer from an adverse event caused by the medical treatment administered. Some institutions have created systems to encourage medical workers to report these adverse events. However, these systems often prove to be inadequate and/or ineffective for reviewing the data collected and improving the outcomes in patient safety. To describe the Web-application Duke Surgery Patient Safety, designed for the anonymous reporting of adverse and near-miss events as well as scheduled reporting to surgeons and hospital administration. SOFTWARE ARCHITECTURE: DSPS was developed primarily using Java language running on a Tomcat server and with MySQL database as its backend. Formal and field usability tests were used to aid in development of DSPS. Extensive experience with DSPS at our institution indicate that DSPS is easy to learn and use, has good speed, provides needed functionality, and is well received by both adverse-event reporters and administrators. This is the first description of an open-source application for reporting patient safety, which allows the distribution of the application to other institutions in addition for its ability to adapt to the needs of different departments. DSPS provides a mechanism for anonymous reporting of adverse events and helps to administer Patient Safety initiatives. The modifiable framework of DSPS allows adherence to evolving national data standards. The open-source design of DSPS permits surgical departments with existing reporting mechanisms to integrate them with DSPS. The DSPS application is distributed under the GNU General Public License.

Gimli: open source and high-performance biomedical name recognition

PubMed Central

2013-01-01

Background Automatic recognition of biomedical names is an essential task in biomedical information extraction, presenting several complex and unsolved challenges. In recent years, various solutions have been implemented to tackle this problem. However, limitations regarding system characteristics, customization and usability still hinder their wider application outside text mining research. Results We present Gimli, an open-source, state-of-the-art tool for automatic recognition of biomedical names. Gimli includes an extended set of implemented and user-selectable features, such as orthographic, morphological, linguistic-based, conjunctions and dictionary-based. A simple and fast method to combine different trained models is also provided. Gimli achieves an F-measure of 87.17% on GENETAG and 72.23% on JNLPBA corpus, significantly outperforming existing open-source solutions. Conclusions Gimli is an off-the-shelf, ready to use tool for named-entity recognition, providing trained and optimized models for recognition of biomedical entities from scientific text. It can be used as a command line tool, offering full functionality, including training of new models and customization of the feature set and model parameters through a configuration file. Advanced users can integrate Gimli in their text mining workflows through the provided library, and extend or adapt its functionalities. Based on the underlying system characteristics and functionality, both for final users and developers, and on the reported performance results, we believe that Gimli is a state-of-the-art solution for biomedical NER, contributing to faster and better research in the field. Gimli is freely available at http://bioinformatics.ua.pt/gimli. PMID:23413997

The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching.

PubMed

Willighagen, Egon L; Mayfield, John W; Alvarsson, Jonathan; Berg, Arvid; Carlsson, Lars; Jeliazkova, Nina; Kuhn, Stefan; Pluskal, Tomáš; Rojas-Chertó, Miquel; Spjuth, Ola; Torrance, Gilleain; Evelo, Chris T; Guha, Rajarshi; Steinbeck, Christoph

2017-06-06

The Chemistry Development Kit (CDK) is a widely used open source cheminformatics toolkit, providing data structures to represent chemical concepts along with methods to manipulate such structures and perform computations on them. The library implements a wide variety of cheminformatics algorithms ranging from chemical structure canonicalization to molecular descriptor calculations and pharmacophore perception. It is used in drug discovery, metabolomics, and toxicology. Over the last 10 years, the code base has grown significantly, however, resulting in many complex interdependencies among components and poor performance of many algorithms. We report improvements to the CDK v2.0 since the v1.2 release series, specifically addressing the increased functional complexity and poor performance. We first summarize the addition of new functionality, such atom typing and molecular formula handling, and improvement to existing functionality that has led to significantly better performance for substructure searching, molecular fingerprints, and rendering of molecules. Second, we outline how the CDK has evolved with respect to quality control and the approaches we have adopted to ensure stability, including a code review mechanism. This paper highlights our continued efforts to provide a community driven, open source cheminformatics library, and shows that such collaborative projects can thrive over extended periods of time, resulting in a high-quality and performant library. By taking advantage of community support and contributions, we show that an open source cheminformatics project can act as a peer reviewed publishing platform for scientific computing software. Graphical abstract CDK 2.0 provides new features and improved performance.

[The use of open source software in graphic anatomic reconstructions and in biomechanic simulations].

PubMed

Ciobanu, O

2009-01-01

The objective of this study was to obtain three-dimensional (3D) images and to perform biomechanical simulations starting from DICOM images obtained by computed tomography (CT). Open source software were used to prepare digitized 2D images of tissue sections and to create 3D reconstruction from the segmented structures. Finally, 3D images were used in open source software in order to perform biomechanic simulations. This study demonstrates the applicability and feasibility of open source software developed in our days for the 3D reconstruction and biomechanic simulation. The use of open source software may improve the efficiency of investments in imaging technologies and in CAD/CAM technologies for implants and prosthesis fabrication which need expensive specialized software.

76 FR 76180 - Notice of Realty Action: Termination of Segregation, Opening of Public Lands; Montana

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-06

...] Notice of Realty Action: Termination of Segregation, Opening of Public Lands; Montana AGENCY: Bureau of... generally, subject to valid existing rights, the provisions of existing withdrawals, other segregations of..., subject to valid existing rights, the provision of existing withdrawals, other segregations of record, and...

Planetary-scale surface water detection from space

NASA Astrophysics Data System (ADS)

Donchyts, G.; Baart, F.; Winsemius, H.; Gorelick, N.

2017-12-01

Accurate, efficient and high-resolution methods of surface water detection are needed for a better water management. Datasets on surface water extent and dynamics are crucial for a better understanding of natural and human-made processes, and as an input data for hydrological and hydraulic models. In spite of considerable progress in the harmonization of freely available satellite data, producing accurate and efficient higher-level surface water data products remains very challenging. This presentation will provide an overview of existing methods for surface water extent and change detection from multitemporal and multi-sensor satellite imagery. An algorithm to detect surface water changes from multi-temporal satellite imagery will be demonstrated as well as its open-source implementation (http://aqua-monitor.deltares.nl). This algorithm was used to estimate global surface water changes at high spatial resolution. These changes include climate change, land reclamation, reservoir construction/decommissioning, erosion/accretion, and many other. This presentation will demonstrate how open satellite data and open platforms such as Google Earth Engine have helped with this research.

Web GIS in practice IV: publishing your health maps and connecting to remote WMS sources using the Open Source UMN MapServer and DM Solutions MapLab

PubMed Central

Boulos, Maged N Kamel; Honda, Kiyoshi

2006-01-01

Open Source Web GIS software systems have reached a stage of maturity, sophistication, robustness and stability, and usability and user friendliness rivalling that of commercial, proprietary GIS and Web GIS server products. The Open Source Web GIS community is also actively embracing OGC (Open Geospatial Consortium) standards, including WMS (Web Map Service). WMS enables the creation of Web maps that have layers coming from multiple different remote servers/sources. In this article we present one easy to implement Web GIS server solution that is based on the Open Source University of Minnesota (UMN) MapServer. By following the accompanying step-by-step tutorial instructions, interested readers running mainstream Microsoft® Windows machines and with no prior technical experience in Web GIS or Internet map servers will be able to publish their own health maps on the Web and add to those maps additional layers retrieved from remote WMS servers. The 'digital Asia' and 2004 Indian Ocean tsunami experiences in using free Open Source Web GIS software are also briefly described. PMID:16420699

Rapid development of medical imaging tools with open-source libraries.

PubMed

Caban, Jesus J; Joshi, Alark; Nagy, Paul

2007-11-01

Rapid prototyping is an important element in researching new imaging analysis techniques and developing custom medical applications. In the last ten years, the open source community and the number of open source libraries and freely available frameworks for biomedical research have grown significantly. What they offer are now considered standards in medical image analysis, computer-aided diagnosis, and medical visualization. A cursory review of the peer-reviewed literature in imaging informatics (indeed, in almost any information technology-dependent scientific discipline) indicates the current reliance on open source libraries to accelerate development and validation of processes and techniques. In this survey paper, we review and compare a few of the most successful open source libraries and frameworks for medical application development. Our dual intentions are to provide evidence that these approaches already constitute a vital and essential part of medical image analysis, diagnosis, and visualization and to motivate the reader to use open source libraries and software for rapid prototyping of medical applications and tools.

Open-Source RTOS Space Qualification: An RTEMS Case Study

NASA Technical Reports Server (NTRS)

Zemerick, Scott

2017-01-01

NASA space-qualification of reusable off-the-shelf real-time operating systems (RTOSs) remains elusive due to several factors notably (1) The diverse nature of RTOSs utilized across NASA, (2) No single NASA space-qualification criteria, lack of verification and validation (V&V) analysis, or test beds, and (3) different RTOS heritages, specifically open-source RTOSs and closed vendor-provided RTOSs. As a leader in simulation test beds, the NASA IV&V Program is poised to help jump-start and lead the space-qualification effort of the open source Real-Time Executive for Multiprocessor Systems (RTEMS) RTOS. RTEMS, as a case-study, can be utilized as an example of how to qualify all RTOSs, particularly the reusable non-commercial (open-source) ones that are gaining usage and popularity across NASA. Qualification will improve the overall safety and mission assurance of RTOSs for NASA-agency wide usage. NASA's involvement in space-qualification of an open-source RTOS such as RTEMS will drive the RTOS industry toward a more qualified and mature open-source RTOS product.

Geochemical Trends and Natural Attenuation of RDX, Nitrate, and Perchlorate in the Hazardous Test Area Fractured-Granite Aquifer, White Sands Missile Range, New Mexico, 1996-2006

USGS Publications Warehouse

Langman, Jeff B.; Robertson, Andrew J.; Bynum, Jamar; Gebhardt, Fredrick E.

2008-01-01

A fractured-granite aquifer at White Sands Missile Range is contaminated with the explosive compound RDX, nitrate, and perchlorate (oxidizer associated with rocket propellant) from the previous use of the Open Burn/Open Detonation site at the Hazardous Test Area. RDX, nitrate, and perchlorate ground-water concentrations were analyzed to examine source characteristics, spatial and temporal variability, and the influence of the natural attenuation processes of dilution and degradation in the Hazardous Test Area fractured-granite aquifer. Two transects of ground-water wells from the existing monitoring-site network - one perpendicular to ground-water flow (transect A-A') and another parallel to ground-water flow (transect B-B') - were selected to examine source characteristics and the spatial and temporal variability of the contaminant concentrations. Ground-water samples collected in 2005 from a larger sampling of monitoring sites than the two transects were analyzed for various tracers including major ions, trace elements, RDX degradates, dissolved gases, water isotopes, nitrate isotopes, and sulfate isotopes to examine the natural attenuation processes of dilution and degradation. Recharge entrains contaminants at the site and transports them downgradient towards the Tularosa Basin floor through a poorly connected fracture system(s). From 1996 to 2006, RDX, nitrate, and perchlorate concentrations in ground water downgradient from the Open Burn/Open Detonation site have been relatively stable. RDX, nitrate, and perchlorate in ground water from wells near the site indicate dispersed contaminant sources in and near the Open Burn/Open Detonation pits. The sources of RDX and nitrate in the pit area have shifted with time, and the shift correlates with the regrading of the south and east berms of each pit in 2002 and 2003 following closure of the site. The largest RDX concentrations were in ground water about 0.1 mile downgradient from the pits, the largest perchlorate concentrations were in ground water about 0.15 mile downgradient from the pits, and the largest nitrate concentrations were in ground water about 0.25 mile down-gradient from the pits. Strong and moderate correlation of water level and the contaminant concentrations near the source areas and low correlation outside and downgradient from the source areas indicates a diminishing of the water level/contaminant relation with downgradient flow. Ground water was not progressively older at all locations downgradient from the Open Burn/Open Detonation site indicating multiple recharge areas. Major ion and strontium concentrations and d2H and d18O values identified similar sources of recharge waters comprising the aquifer except along the basin periphery where recharge water may be influenced by dissolution of mineral assemblages associated with ore deposits that are present along the basin margins. Ground-water ages, dissolved-solids concentrations, and calcium-strontium concentrations indicate limited or partial connectivity between fractures and contributions of uncontaminated recharge water downgradient from the site that dilutes contaminant concentrations. Changes in RDX and nitrate concentration patterns, the presence of methane, changes in carbon dioxide concentrations and d15N and d34S values, and variable reduction-oxidation conditions suggest degradation of contaminants in the downgradient direction. Estimated values of electron potential were assigned to ground water collected in October 2005 from all monitoring sites at the Hazardous Test Area. Moderate to strong reducing conditions were present upgradient from the Open Burn/Open Detonation site, at the site, and at various locations downgradient from the site, but the aquifer contained well-oxygenated water between many of the reducing areas. The spatial variability of reduction-oxidation conditions in the aquifer exemplifies the partial connectivity of the fracture system(s). Dilution of the contaminants i

Learning from hackers: open-source clinical trials.

PubMed

Dunn, Adam G; Day, Richard O; Mandl, Kenneth D; Coiera, Enrico

2012-05-02

Open sharing of clinical trial data has been proposed as a way to address the gap between the production of clinical evidence and the decision-making of physicians. A similar gap was addressed in the software industry by their open-source software movement. Here, we examine how the social and technical principles of the movement can guide the growth of an open-source clinical trial community.

Real-time GPS integration for prototype earthquake early warning and near-field imaging of the earthquake rupture process

NASA Astrophysics Data System (ADS)

Hudnut, K. W.; Given, D.; King, N. E.; Lisowski, M.; Langbein, J. O.; Murray-Moraleda, J. R.; Gomberg, J. S.

2011-12-01

Over the past several years, USGS has developed the infrastructure for integrating real-time GPS with seismic data in order to improve our ability to respond to earthquakes and volcanic activity. As part of this effort, we have tested real-time GPS processing software components , and identified the most robust and scalable options. Simultaneously, additional near-field monitoring stations have been built using a new station design that combines dual-frequency GPS with high quality strong-motion sensors and dataloggers. Several existing stations have been upgraded in this way, using USGS Multi-Hazards Demonstration Project and American Recovery and Reinvestment Act funds in southern California. In particular, existing seismic stations have been augmented by the addition of GPS and vice versa. The focus of new instrumentation as well as datalogger and telemetry upgrades to date has been along the southern San Andreas fault in hopes of 1) capturing a large and potentially damaging rupture in progress and augmenting inputs to earthquake early warning systems, and 2) recovering high quality recordings on scale of large dynamic displacement waveforms, static displacements and immediate and long-term post-seismic transient deformation. Obtaining definitive records of large ground motions close to a large San Andreas or Cascadia rupture (or volcanic activity) would be a fundamentally important contribution to understanding near-source large ground motions and the physics of earthquakes, including the rupture process and friction associated with crack propagation and healing. Soon, telemetry upgrades will be completed in Cascadia and throughout the Plate Boundary Observatory as well. By collaborating with other groups on open-source automation system development, we will be ready to process the newly available real-time GPS data streams and to fold these data in with existing strong-motion and other seismic data. Data from these same stations will also serve the very practical purpose of enabling earthquake early warning and greatly improving rapid finite-fault source modeling. Multiple uses of the effectively very broad-band data obtained by these stations, for operational and research purposes, are bound to occur especially because all data will be freely, openly and instantly available.

Evaluation and selection of open-source EMR software packages based on integrated AHP and TOPSIS.

PubMed

Zaidan, A A; Zaidan, B B; Al-Haiqi, Ahmed; Kiah, M L M; Hussain, Muzammil; Abdulnabi, Mohamed

2015-02-01

Evaluating and selecting software packages that meet the requirements of an organization are difficult aspects of software engineering process. Selecting the wrong open-source EMR software package can be costly and may adversely affect business processes and functioning of the organization. This study aims to evaluate and select open-source EMR software packages based on multi-criteria decision-making. A hands-on study was performed and a set of open-source EMR software packages were implemented locally on separate virtual machines to examine the systems more closely. Several measures as evaluation basis were specified, and the systems were selected based a set of metric outcomes using Integrated Analytic Hierarchy Process (AHP) and TOPSIS. The experimental results showed that GNUmed and OpenEMR software can provide better basis on ranking score records than other open-source EMR software packages. Copyright © 2014 Elsevier Inc. All rights reserved.

A Rule-Based Spatial Reasoning Approach for OpenStreetMap Data Quality Enrichment; Case Study of Routing and Navigation

PubMed Central

2017-01-01

Finding relevant geospatial information is increasingly critical because of the growing volume of geospatial data available within the emerging “Big Data” era. Users are expecting that the availability of massive datasets will create more opportunities to uncover hidden information and answer more complex queries. This is especially the case with routing and navigation services where the ability to retrieve points of interest and landmarks make the routing service personalized, precise, and relevant. In this paper, we propose a new geospatial information approach that enables the retrieval of implicit information, i.e., geospatial entities that do not exist explicitly in the available source. We present an information broker that uses a rule-based spatial reasoning algorithm to detect topological relations. The information broker is embedded into a framework where annotations and mappings between OpenStreetMap data attributes and external resources, such as taxonomies, support the enrichment of queries to improve the ability of the system to retrieve information. Our method is tested with two case studies that leads to enriching the completeness of OpenStreetMap data with footway crossing points-of-interests as well as building entrances for routing and navigation purposes. It is concluded that the proposed approach can uncover implicit entities and contribute to extract required information from the existing datasets. PMID:29088125

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

Zhang, Quanhao; Wang, Yuming; Hu, Youqiu

Since only the magnetic conditions at the photosphere can be routinely observed in current observations, it is of great significance to determine the influences of photospheric magnetic conditions on solar eruptive activities. Previous studies about catastrophe indicated that the magnetic system consisting of a flux rope in a partially open bipolar field is subject to catastrophe, but not if the bipolar field is completely closed under the same specified photospheric conditions. In order to investigate the influence of the photospheric magnetic conditions on the catastrophic behavior of this system, we expand upon the 2.5-dimensional ideal magnetohydrodynamic model in Cartesian coordinatesmore » to simulate the evolution of the equilibrium states of the system under different photospheric flux distributions. Our simulation results reveal that a catastrophe occurs only when the photospheric flux is not concentrated too much toward the polarity inversion line and the source regions of the bipolar field are not too weak; otherwise no catastrophe occurs. As a result, under certain photospheric conditions, a catastrophe could take place in a completely closed configuration, whereas it ceases to exist in a partially open configuration. This indicates that whether the background field is completely closed or partially open is not the only necessary condition for the existence of catastrophe, and that the photospheric conditions also play a crucial role in the catastrophic behavior of the flux rope system.« less

BioMart: a data federation framework for large collaborative projects.

PubMed

Zhang, Junjun; Haider, Syed; Baran, Joachim; Cros, Anthony; Guberman, Jonathan M; Hsu, Jack; Liang, Yong; Yao, Long; Kasprzyk, Arek

2011-01-01

BioMart is a freely available, open source, federated database system that provides a unified access to disparate, geographically distributed data sources. It is designed to be data agnostic and platform independent, such that existing databases can easily be incorporated into the BioMart framework. BioMart allows databases hosted on different servers to be presented seamlessly to users, facilitating collaborative projects between different research groups. BioMart contains several levels of query optimization to efficiently manage large data sets and offers a diverse selection of graphical user interfaces and application programming interfaces to ensure that queries can be performed in whatever manner is most convenient for the user. The software has now been adopted by a large number of different biological databases spanning a wide range of data types and providing a rich source of annotation available to bioinformaticians and biologists alike.

Scoping Study of Machine Learning Techniques for Visualization and Analysis of Multi-source Data in Nuclear Safeguards

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

Cui, Yonggang

In implementation of nuclear safeguards, many different techniques are being used to monitor operation of nuclear facilities and safeguard nuclear materials, ranging from radiation detectors, flow monitors, video surveillance, satellite imagers, digital seals to open source search and reports of onsite inspections/verifications. Each technique measures one or more unique properties related to nuclear materials or operation processes. Because these data sets have no or loose correlations, it could be beneficial to analyze the data sets together to improve the effectiveness and efficiency of safeguards processes. Advanced visualization techniques and machine-learning based multi-modality analysis could be effective tools in such integratedmore » analysis. In this project, we will conduct a survey of existing visualization and analysis techniques for multi-source data and assess their potential values in nuclear safeguards.« less

The riddle of Tasmanian languages

PubMed Central

Bowern, Claire

2012-01-01

Recent work which combines methods from linguistics and evolutionary biology has been fruitful in discovering the history of major language families because of similarities in evolutionary processes. Such work opens up new possibilities for language research on previously unsolvable problems, especially in areas where information from other sources may be lacking. I use phylogenetic methods to investigate Tasmanian languages. Existing materials are so fragmentary that scholars have been unable to discover how many languages are represented in the sources. Using a clustering algorithm which identifies admixture, source materials representing more than one language are identified. Using the Neighbor-Net algorithm, 12 languages are identified in five clusters. Bayesian phylogenetic methods reveal that the families are not demonstrably related; an important result, given the importance of Tasmanian Aborigines for information about how societies have responded to population collapse in prehistory. This work provides insight into the societies of prehistoric Tasmania and illustrates a new utility of phylogenetics in reconstructing linguistic history. PMID:23015621

CosmoQuest Transient Tracker: Opensource Photometry & Astrometry software

NASA Astrophysics Data System (ADS)

Myers, Joseph L.; Lehan, Cory; Gay, Pamela; Richardson, Matthew; CosmoQuest Team

2018-01-01

CosmoQuest is moving from online citizen science, to observational astronomy with the creation of Transient Trackers. This open source software is designed to identify asteroids and other transient/variable objects in image sets. Transient Tracker’s features in final form will include: astrometric and photometric solutions, identification of moving/transient objects, identification of variable objects, and lightcurve analysis. In this poster we present our initial, v0.1 release and seek community input.This software builds on the existing NIH funded ImageJ libraries. Creation of this suite of opensource image manipulation routines is lead by Wayne Rasband and is released primarily under the MIT license. In this release, we are building on these libraries to add source identification for point / point-like sources, and to do astrometry. Our materials released under the Apache 2.0 license on github (http://github.com/CosmoQuestTeam) and documentation can be found at http://cosmoquest.org/TransientTracker.

The validity of open-source data when assessing jail suicides.

PubMed

Thomas, Amanda L; Scott, Jacqueline; Mellow, Jeff

2018-05-09

The Bureau of Justice Statistics' Deaths in Custody Reporting Program is the primary source for jail suicide research, though the data is restricted from general dissemination. This study is the first to examine whether jail suicide data obtained from publicly available sources can help inform our understanding of this serious public health problem. Of the 304 suicides that were reported through the DCRP in 2009, roughly 56 percent (N = 170) of those suicides were identified through the open-source search protocol. Each of the sources was assessed based on how much information was collected on the incident and the types of variables available. A descriptive analysis was then conducted on the variables that were present in both data sources. The four variables present in each data source were: (1) demographic characteristics of the victim, (2) the location of occurrence within the facility, (3) the location of occurrence by state, and (4) the size of the facility. Findings demonstrate that the prevalence and correlates of jail suicides are extremely similar in both open-source and official data. However, for almost every variable measured, open-source data captured as much information as official data did, if not more. Further, variables not found in official data were identified in the open-source database, thus allowing researchers to have a more nuanced understanding of the situational characteristics of the event. This research provides support for the argument in favor of including open-source data in jail suicide research as it illustrates how open-source data can be used to provide additional information not originally found in official data. In sum, this research is vital in terms of possible suicide prevention, which may be directly linked to being able to manipulate environmental factors.

A convolutional neural network approach to calibrating the rotation axis for X-ray computed tomography

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

Yang, Xiaogang; De Carlo, Francesco; Phatak, Charudatta

This paper presents an algorithm to calibrate the center-of-rotation for X-ray tomography by using a machine learning approach, the Convolutional Neural Network (CNN). The algorithm shows excellent accuracy from the evaluation of synthetic data with various noise ratios. It is further validated with experimental data of four different shale samples measured at the Advanced Photon Source and at the Swiss Light Source. The results are as good as those determined by visual inspection and show better robustness than conventional methods. CNN has also great potential forreducing or removingother artifacts caused by instrument instability, detector non-linearity,etc. An open-source toolbox, which integratesmore » the CNN methods described in this paper, is freely available through GitHub at tomography/xlearn and can be easily integrated into existing computational pipelines available at various synchrotron facilities. Source code, documentation and information on how to contribute are also provided.« less

Scientific Software - the role of best practices and recommendations

NASA Astrophysics Data System (ADS)

Fritzsch, Bernadette; Bernstein, Erik; Castell, Wolfgang zu; Diesmann, Markus; Haas, Holger; Hammitzsch, Martin; Konrad, Uwe; Lähnemann, David; McHardy, Alice; Pampel, Heinz; Scheliga, Kaja; Schreiber, Andreas; Steglich, Dirk

2017-04-01

In Geosciences - like in most other communities - scientific work strongly depends on software. For big data analysis, existing (closed or open source) program packages are often mixed with newly developed codes. Different versions of software components and varying configurations can influence the result of data analysis. This often makes reproducibility of results and reuse of codes very difficult. Policies for publication and documentation of used and newly developed software, along with best practices, can help tackle this problem. Within the Helmholtz Association a Task Group "Access to and Re-use of scientific software" was implemented by the Open Science Working Group in 2016. The aim of the Task Group is to foster the discussion about scientific software in the Open Science context and to formulate recommendations for the production and publication of scientific software, ensuring open access to it. As a first step, a workshop gathered interested scientists from institutions across Germany. The workshop brought together various existing initiatives from different scientific communities to analyse current problems, share established best practices and come up with possible solutions. The subjects in the working groups covered a broad range of themes, including technical infrastructures, standards and quality assurance, citation of software and reproducibility. Initial recommendations are presented and discussed in the talk. They are the foundation for further discussions in the Helmholtz Association and the Priority Initiative "Digital Information" of the Alliance of Science Organisations in Germany. The talk aims to inform about the activities and to link with other initiatives on the national or international level.

Open source tools and toolkits for bioinformatics: significance, and where are we?

PubMed

Stajich, Jason E; Lapp, Hilmar

2006-09-01

This review summarizes important work in open-source bioinformatics software that has occurred over the past couple of years. The survey is intended to illustrate how programs and toolkits whose source code has been developed or released under an Open Source license have changed informatics-heavy areas of life science research. Rather than creating a comprehensive list of all tools developed over the last 2-3 years, we use a few selected projects encompassing toolkit libraries, analysis tools, data analysis environments and interoperability standards to show how freely available and modifiable open-source software can serve as the foundation for building important applications, analysis workflows and resources.

Open Source 2010: Reflections on 2007

ERIC Educational Resources Information Center

Wheeler, Brad

2007-01-01

Colleges and universities and commercial firms have demonstrated great progress in realizing the vision proffered for "Open Source 2007," and 2010 will mark even greater progress. Although much work remains in refining open source for higher education applications, the signals are now clear: the collaborative development of software can provide…

Development and Use of an Open-Source, User-Friendly Package to Simulate Voltammetry Experiments

ERIC Educational Resources Information Center

Wang, Shuo; Wang, Jing; Gao, Yanjing

2017-01-01

An open-source electrochemistry simulation package has been developed that simulates the electrode processes of four reaction mechanisms and two typical electroanalysis techniques: cyclic voltammetry and chronoamperometry. Unlike other open-source simulation software, this package balances the features with ease of learning and implementation and…

Creating Open Source Conversation

ERIC Educational Resources Information Center

Sheehan, Kate

2009-01-01

Darien Library, where the author serves as head of knowledge and learning services, launched a new website on September 1, 2008. The website is built with Drupal, an open source content management system (CMS). In this article, the author describes how she and her colleagues overhauled the library's website to provide an open source content…

Integrating an Automatic Judge into an Open Source LMS

ERIC Educational Resources Information Center

Georgouli, Katerina; Guerreiro, Pedro

2011-01-01

This paper presents the successful integration of the evaluation engine of Mooshak into the open source learning management system Claroline. Mooshak is an open source online automatic judge that has been used for international and national programming competitions. although it was originally designed for programming competitions, Mooshak has also…

76 FR 75875 - Defense Federal Acquisition Regulation Supplement; Open Source Software Public Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-05

... Regulation Supplement; Open Source Software Public Meeting AGENCY: Defense Acquisition Regulations System... initiate a dialogue with industry regarding the use of open source software in DoD contracts. DATES: Public... be held in the General Services Administration (GSA), Central Office Auditorium, 1800 F Street NW...

The open-source movement: an introduction for forestry professionals

Treesearch

Patrick Proctor; Paul C. Van Deusen; Linda S. Heath; Jeffrey H. Gove

2005-01-01

In recent years, the open-source movement has yielded a generous and powerful suite of software and utilities that rivals those developed by many commercial software companies. Open-source programs are available for many scientific needs: operating systems, databases, statistical analysis, Geographic Information System applications, and object-oriented programming....

Open Source Software Development and Lotka's Law: Bibliometric Patterns in Programming.

ERIC Educational Resources Information Center

Newby, Gregory B.; Greenberg, Jane; Jones, Paul

2003-01-01

Applies Lotka's Law to metadata on open source software development. Authoring patterns found in software development productivity are found to be comparable to prior studies of Lotka's Law for scientific and scholarly publishing, and offer promise in predicting aggregate behavior of open source developers. (Author/LRW)

XDesign: an open-source software package for designing X-ray imaging phantoms and experiments.

PubMed

Ching, Daniel J; Gürsoy, Dogˇa

2017-03-01

The development of new methods or utilization of current X-ray computed tomography methods is impeded by the substantial amount of expertise required to design an X-ray computed tomography experiment from beginning to end. In an attempt to make material models, data acquisition schemes and reconstruction algorithms more accessible to researchers lacking expertise in some of these areas, a software package is described here which can generate complex simulated phantoms and quantitatively evaluate new or existing data acquisition schemes and image reconstruction algorithms for targeted applications.

PedVizApi: a Java API for the interactive, visual analysis of extended pedigrees.

PubMed

Fuchsberger, Christian; Falchi, Mario; Forer, Lukas; Pramstaller, Peter P

2008-01-15

PedVizApi is a Java API (application program interface) for the visual analysis of large and complex pedigrees. It provides all the necessary functionality for the interactive exploration of extended genealogies. While available packages are mostly focused on a static representation or cannot be added to an existing application, PedVizApi is a highly flexible open source library for the efficient construction of visual-based applications for the analysis of family data. An extensive demo application and a R interface is provided. http://www.pedvizapi.org

XDesign: An open-source software package for designing X-ray imaging phantoms and experiments

DOE PAGES

Ching, Daniel J.; Gursoy, Dogˇa

2017-02-21

Here, the development of new methods or utilization of current X-ray computed tomography methods is impeded by the substantial amount of expertise required to design an X-ray computed tomography experiment from beginning to end. In an attempt to make material models, data acquisition schemes and reconstruction algorithms more accessible to researchers lacking expertise in some of these areas, a software package is described here which can generate complex simulated phantoms and quantitatively evaluate new or existing data acquisition schemes and image reconstruction algorithms for targeted applications.

It’s an app. It’s a hypervisor. It’s a hypapp. : Design and Implementation of an eXtensible and Modular Hypervisor Framework

DTIC Science & Technology

2012-06-26

existing commercial-grade virtualization solutions (e.g., Xen, Linux KVM, VMware, or L4 ), but generally do not require such rich functional- ity [9...ports multiprocessor configuration on both AMD and Intel x86 platforms. Xen [8], KVM [27], VMware [39], NOVA [33], Virtual- box‡‡ and L4 are some...popular general purpose (open-source) hypervisors and microkernels which have been used for var- ious hypervisor based research [9,15,26,30,32,34,45

Conceptualization and validation of an open-source closed-loop deep brain stimulation system in rat.

PubMed

Wu, Hemmings; Ghekiere, Hartwin; Beeckmans, Dorien; Tambuyzer, Tim; van Kuyck, Kris; Aerts, Jean-Marie; Nuttin, Bart

2015-04-21

Conventional deep brain stimulation (DBS) applies constant electrical stimulation to specific brain regions to treat neurological disorders. Closed-loop DBS with real-time feedback is gaining attention in recent years, after proved more effective than conventional DBS in terms of pathological symptom control clinically. Here we demonstrate the conceptualization and validation of a closed-loop DBS system using open-source hardware. We used hippocampal theta oscillations as system input, and electrical stimulation in the mesencephalic reticular formation (mRt) as controller output. It is well documented that hippocampal theta oscillations are highly related to locomotion, while electrical stimulation in the mRt induces freezing. We used an Arduino open-source microcontroller between input and output sources. This allowed us to use hippocampal local field potentials (LFPs) to steer electrical stimulation in the mRt. Our results showed that closed-loop DBS significantly suppressed locomotion compared to no stimulation, and required on average only 56% of the stimulation used in open-loop DBS to reach similar effects. The main advantages of open-source hardware include wide selection and availability, high customizability, and affordability. Our open-source closed-loop DBS system is effective, and warrants further research using open-source hardware for closed-loop neuromodulation.

Conceptualization and validation of an open-source closed-loop deep brain stimulation system in rat

PubMed Central

Wu, Hemmings; Ghekiere, Hartwin; Beeckmans, Dorien; Tambuyzer, Tim; van Kuyck, Kris; Aerts, Jean-Marie; Nuttin, Bart

2015-01-01

Conventional deep brain stimulation (DBS) applies constant electrical stimulation to specific brain regions to treat neurological disorders. Closed-loop DBS with real-time feedback is gaining attention in recent years, after proved more effective than conventional DBS in terms of pathological symptom control clinically. Here we demonstrate the conceptualization and validation of a closed-loop DBS system using open-source hardware. We used hippocampal theta oscillations as system input, and electrical stimulation in the mesencephalic reticular formation (mRt) as controller output. It is well documented that hippocampal theta oscillations are highly related to locomotion, while electrical stimulation in the mRt induces freezing. We used an Arduino open-source microcontroller between input and output sources. This allowed us to use hippocampal local field potentials (LFPs) to steer electrical stimulation in the mRt. Our results showed that closed-loop DBS significantly suppressed locomotion compared to no stimulation, and required on average only 56% of the stimulation used in open-loop DBS to reach similar effects. The main advantages of open-source hardware include wide selection and availability, high customizability, and affordability. Our open-source closed-loop DBS system is effective, and warrants further research using open-source hardware for closed-loop neuromodulation. PMID:25897892

Open Source and ROI: Open Source Has Made Significant Leaps in Recent Years. What Does It Have to Offer Education?

ERIC Educational Resources Information Center

Guhlin, Miguel

2007-01-01

A switch to free open source software can minimize cost and allow funding to be diverted to equipment and other programs. For instance, the OpenOffice suite is an alternative to expensive basic application programs offered by major vendors. Many such programs on the market offer features seldom used in education but for which educators must pay.…

Open source drug discovery--a new paradigm of collaborative research in tuberculosis drug development.

PubMed

Bhardwaj, Anshu; Scaria, Vinod; Raghava, Gajendra Pal Singh; Lynn, Andrew Michael; Chandra, Nagasuma; Banerjee, Sulagna; Raghunandanan, Muthukurussi V; Pandey, Vikas; Taneja, Bhupesh; Yadav, Jyoti; Dash, Debasis; Bhattacharya, Jaijit; Misra, Amit; Kumar, Anil; Ramachandran, Srinivasan; Thomas, Zakir; Brahmachari, Samir K

2011-09-01

It is being realized that the traditional closed-door and market driven approaches for drug discovery may not be the best suited model for the diseases of the developing world such as tuberculosis and malaria, because most patients suffering from these diseases have poor paying capacity. To ensure that new drugs are created for patients suffering from these diseases, it is necessary to formulate an alternate paradigm of drug discovery process. The current model constrained by limitations for collaboration and for sharing of resources with confidentiality hampers the opportunities for bringing expertise from diverse fields. These limitations hinder the possibilities of lowering the cost of drug discovery. The Open Source Drug Discovery project initiated by Council of Scientific and Industrial Research, India has adopted an open source model to power wide participation across geographical borders. Open Source Drug Discovery emphasizes integrative science through collaboration, open-sharing, taking up multi-faceted approaches and accruing benefits from advances on different fronts of new drug discovery. Because the open source model is based on community participation, it has the potential to self-sustain continuous development by generating a storehouse of alternatives towards continued pursuit for new drug discovery. Since the inventions are community generated, the new chemical entities developed by Open Source Drug Discovery will be taken up for clinical trial in a non-exclusive manner by participation of multiple companies with majority funding from Open Source Drug Discovery. This will ensure availability of drugs through a lower cost community driven drug discovery process for diseases afflicting people with poor paying capacity. Hopefully what LINUX the World Wide Web have done for the information technology, Open Source Drug Discovery will do for drug discovery. Copyright © 2011 Elsevier Ltd. All rights reserved.

State-of-the-practice and lessons learned on implementing open data and open source policies.

DOT National Transportation Integrated Search

2012-05-01

This report describes the current government, academic, and private sector practices associated with open data and open source application development. These practices are identified; and the potential uses with the ITS Programs Data Capture and M...

Your Personal Analysis Toolkit - An Open Source Solution

NASA Astrophysics Data System (ADS)

Mitchell, T.

2009-12-01

Open source software is commonly known for its web browsers, word processors and programming languages. However, there is a vast array of open source software focused on geographic information management and geospatial application building in general. As geo-professionals, having easy access to tools for our jobs is crucial. Open source software provides the opportunity to add a tool to your tool belt and carry it with you for your entire career - with no license fees, a supportive community and the opportunity to test, adopt and upgrade at your own pace. OSGeo is a US registered non-profit representing more than a dozen mature geospatial data management applications and programming resources. Tools cover areas such as desktop GIS, web-based mapping frameworks, metadata cataloging, spatial database analysis, image processing and more. Learn about some of these tools as they apply to AGU members, as well as how you can join OSGeo and its members in getting the job done with powerful open source tools. If you haven't heard of OSSIM, MapServer, OpenLayers, PostGIS, GRASS GIS or the many other projects under our umbrella - then you need to hear this talk. Invest in yourself - use open source!

All-source Information Management and Integration for Improved Collective Intelligence Production

DTIC Science & Technology

2011-06-01

Intelligence (ELINT) • Open Source Intelligence ( OSINT ) • Technical Intelligence (TECHINT) These intelligence disciplines produce... intelligence , measurement and signature intelligence , signals intelligence , and open - source data, in the production of intelligence . All- source intelligence ...All- Source Information Integration and Management) R&D Project 3 All- Source Intelligence

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.

pvsR: An Open Source Interface to Big Data on the American Political Sphere.

PubMed

Matter, Ulrich; Stutzer, Alois

2015-01-01

Digital data from the political sphere is abundant, omnipresent, and more and more directly accessible through the Internet. Project Vote Smart (PVS) is a prominent example of this big public data and covers various aspects of U.S. politics in astonishing detail. Despite the vast potential of PVS' data for political science, economics, and sociology, it is hardly used in empirical research. The systematic compilation of semi-structured data can be complicated and time consuming as the data format is not designed for conventional scientific research. This paper presents a new tool that makes the data easily accessible to a broad scientific community. We provide the software called pvsR as an add-on to the R programming environment for statistical computing. This open source interface (OSI) serves as a direct link between a statistical analysis and the large PVS database. The free and open code is expected to substantially reduce the cost of research with PVS' new big public data in a vast variety of possible applications. We discuss its advantages vis-à-vis traditional methods of data generation as well as already existing interfaces. The validity of the library is documented based on an illustration involving female representation in local politics. In addition, pvsR facilitates the replication of research with PVS data at low costs, including the pre-processing of data. Similar OSIs are recommended for other big public databases.

The eGo grid model: An open-source and open-data based synthetic medium-voltage grid model for distribution power supply systems

NASA Astrophysics Data System (ADS)

Amme, J.; Pleßmann, G.; Bühler, J.; Hülk, L.; Kötter, E.; Schwaegerl, P.

2018-02-01

The increasing integration of renewable energy into the electricity supply system creates new challenges for distribution grids. The planning and operation of distribution systems requires appropriate grid models that consider the heterogeneity of existing grids. In this paper, we describe a novel method to generate synthetic medium-voltage (MV) grids, which we applied in our DIstribution Network GeneratOr (DINGO). DINGO is open-source software and uses freely available data. Medium-voltage grid topologies are synthesized based on location and electricity demand in defined demand areas. For this purpose, we use GIS data containing demand areas with high-resolution spatial data on physical properties, land use, energy, and demography. The grid topology is treated as a capacitated vehicle routing problem (CVRP) combined with a local search metaheuristics. We also consider the current planning principles for MV distribution networks, paying special attention to line congestion and voltage limit violations. In the modelling process, we included power flow calculations for validation. The resulting grid model datasets contain 3608 synthetic MV grids in high resolution, covering all of Germany and taking local characteristics into account. We compared the modelled networks with real network data. In terms of number of transformers and total cable length, we conclude that the method presented in this paper generates realistic grids that could be used to implement a cost-optimised electrical energy system.

SUPRA: open-source software-defined ultrasound processing for real-time applications : A 2D and 3D pipeline from beamforming to B-mode.

PubMed

Göbl, Rüdiger; Navab, Nassir; Hennersperger, Christoph

2018-06-01

Research in ultrasound imaging is limited in reproducibility by two factors: First, many existing ultrasound pipelines are protected by intellectual property, rendering exchange of code difficult. Second, most pipelines are implemented in special hardware, resulting in limited flexibility of implemented processing steps on such platforms. With SUPRA, we propose an open-source pipeline for fully software-defined ultrasound processing for real-time applications to alleviate these problems. Covering all steps from beamforming to output of B-mode images, SUPRA can help improve the reproducibility of results and make modifications to the image acquisition mode accessible to the research community. We evaluate the pipeline qualitatively, quantitatively, and regarding its run time. The pipeline shows image quality comparable to a clinical system and backed by point spread function measurements a comparable resolution. Including all processing stages of a usual ultrasound pipeline, the run-time analysis shows that it can be executed in 2D and 3D on consumer GPUs in real time. Our software ultrasound pipeline opens up the research in image acquisition. Given access to ultrasound data from early stages (raw channel data, radiofrequency data), it simplifies the development in imaging. Furthermore, it tackles the reproducibility of research results, as code can be shared easily and even be executed without dedicated ultrasound hardware.

A small, lightweight multipollutant sensor system for ground ...

EPA Pesticide Factsheets

Characterizing highly dynamic, transient, and vertically lofted emissions from open area sources poses unique measurement challenges. This study developed and applied a multipollutant sensor and integrated sampler system for use on mobile applications including tethered balloons (aerostats) and unmanned aerial vehicles (UAVs). The system is particularly applicable to open area sources, such as forest fires, due to its light weight (3.5 kg), compact size (6.75 L), and internal power supply. The sensor system, termed “Kolibri”, consists of sensors measuring CO2 and CO, and samplers for particulate matter (PM) and volatile organic compounds (VOCs). The Kolibri is controlled by a microcontroller which can record and transfer data in real time through a radio module. Selection of the sensors was based on laboratory testing for accuracy, response delay and recovery, cross-sensitivity, and precision. The Kolibri was compared against rack-mounted continuous emissions monitoring system (CEMs) and another mobile sampling instrument (the “Flyer”) that has been used in over ten open area pollutant sampling events. Our results showed that the time series of CO, CO2, and PM2.5 concentrations measured by the Kolibri agreed well with those from the CEMs and the Flyer, with a laboratory-tested percentage error of 4.9%, 3%, and 5.8%, respectively. The VOC emission factors obtained using the Kolibri were consistent with existing literature values that relate concentration

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.

AxonPacking: An Open-Source Software to Simulate Arrangements of Axons in White Matter

PubMed Central

Mingasson, Tom; Duval, Tanguy; Stikov, Nikola; Cohen-Adad, Julien

2017-01-01

HIGHLIGHTS AxonPacking: Open-source software for simulating white matter microstructure.Validation on a theoretical disk packing problem.Reproducible and stable for various densities and diameter distributions.Can be used to study interplay between myelin/fiber density and restricted fraction. Quantitative Magnetic Resonance Imaging (MRI) can provide parameters that describe white matter microstructure, such as the fiber volume fraction (FVF), the myelin volume fraction (MVF) or the axon volume fraction (AVF) via the fraction of restricted water (fr). While already being used for clinical application, the complex interplay between these parameters requires thorough validation via simulations. These simulations required a realistic, controlled and adaptable model of the white matter axons with the surrounding myelin sheath. While there already exist useful algorithms to perform this task, none of them combine optimisation of axon packing, presence of myelin sheath and availability as free and open source software. Here, we introduce a novel disk packing algorithm that addresses these issues. The performance of the algorithm is tested in term of reproducibility over 50 runs, resulting density, and stability over iterations. This tool was then used to derive multiple values of FVF and to study the impact of this parameter on fr and MVF in light of the known microstructure based on histology sample. The standard deviation of the axon density over runs was lower than 10−3 and the expected hexagonal packing for monodisperse disks was obtained with a density close to the optimal density (obtained: 0.892, theoretical: 0.907). Using an FVF ranging within [0.58, 0.82] and a mean inter-axon gap ranging within [0.1, 1.1] μm, MVF ranged within [0.32, 0.44] and fr ranged within [0.39, 0.71], which is consistent with the histology. The proposed algorithm is implemented in the open-source software AxonPacking (https://github.com/neuropoly/axonpacking) and can be useful for validating diffusion models as well as for enabling researchers to study the interplay between microstructure parameters when evaluating qMRI methods. PMID:28197091

Global Dynamic Exposure and the OpenBuildingMap

NASA Astrophysics Data System (ADS)

Schorlemmer, D.; Beutin, T.; Hirata, N.; Hao, K. X.; Wyss, M.; Cotton, F.; Prehn, K.

2015-12-01

Detailed understanding of local risk factors regarding natural catastrophes requires in-depth characterization of the local exposure. Current exposure capture techniques have to find the balance between resolution and coverage. We aim at bridging this gap by employing a crowd-sourced approach to exposure capturing focusing on risk related to earthquake hazard. OpenStreetMap (OSM), the rich and constantly growing geographical database, is an ideal foundation for us. More than 2.5 billion geographical nodes, more than 150 million building footprints (growing by ~100'000 per day), and a plethora of information about school, hospital, and other critical facility locations allow us to exploit this dataset for risk-related computations. We will harvest this dataset by collecting exposure and vulnerability indicators from explicitly provided data (e.g. hospital locations), implicitly provided data (e.g. building shapes and positions), and semantically derived data, i.e. interpretation applying expert knowledge. With this approach, we can increase the resolution of existing exposure models from fragility classes distribution via block-by-block specifications to building-by-building vulnerability. To increase coverage, we will provide a framework for collecting building data by any person or community. We will implement a double crowd-sourced approach to bring together the interest and enthusiasm of communities with the knowledge of earthquake and engineering experts. The first crowd-sourced approach aims at collecting building properties in a community by local people and activists. This will be supported by tailored building capture tools for mobile devices for simple and fast building property capturing. The second crowd-sourced approach involves local experts in estimating building vulnerability that will provide building classification rules that translate building properties into vulnerability and exposure indicators as defined in the Building Taxonomy 2.0 developed by the Global Earthquake Model (GEM). These indicators will then be combined with a hazard model using the GEM OpenQuake engine to compute a risk model. The free/open framework we will provide can be used on commodity hardware for local to regional exposure capturing and for communities to understand their earthquake risk.

A fast template periodogram

NASA Astrophysics Data System (ADS)

Hoffman, John; VanderPlas, Jake; Hartman, Joel; Bakos, Gáspár

2017-09-01

This proceedings contribution presents a novel, non-linear extension to the Lomb-Scargle periodogram that allows periodograms to be generated for arbitrary signal shapes. Such periodograms are already known as "template periodograms" or "periodic matched filters," but current implementations are computationally inefficient. The "fast template periodogram" presented here improves existing techniques by a factor of ˜a few for small test cases (O(10) observations), and over three orders of magnitude for lightcurves containing O(104) observations. The fast template periodogram scales asymptotically as O(HNf log HNf + H4Nf), where H denotes the number of harmonics required to adequately approximate the template and Nf is the number of trial frequencies. Existing implementations scale as O(NobsNf), where Nobs is the number of observations in the lightcurve. An open source Python implementation is available on GitHub.

The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes.

PubMed

Treangen, Todd J; Ondov, Brian D; Koren, Sergey; Phillippy, Adam M

2014-01-01

Whole-genome sequences are now available for many microbial species and clades, however existing whole-genome alignment methods are limited in their ability to perform sequence comparisons of multiple sequences simultaneously. Here we present the Harvest suite of core-genome alignment and visualization tools for the rapid and simultaneous analysis of thousands of intraspecific microbial strains. Harvest includes Parsnp, a fast core-genome multi-aligner, and Gingr, a dynamic visual platform. Together they provide interactive core-genome alignments, variant calls, recombination detection, and phylogenetic trees. Using simulated and real data we demonstrate that our approach exhibits unrivaled speed while maintaining the accuracy of existing methods. The Harvest suite is open-source and freely available from: http://github.com/marbl/harvest.

detectIR: a novel program for detecting perfect and imperfect inverted repeats using complex numbers and vector calculation.

PubMed

Ye, Congting; Ji, Guoli; Li, Lei; Liang, Chun

2014-01-01

Inverted repeats are present in abundance in both prokaryotic and eukaryotic genomes and can form DNA secondary structures--hairpins and cruciforms that are involved in many important biological processes. Bioinformatics tools for efficient and accurate detection of inverted repeats are desirable, because existing tools are often less accurate and time consuming, sometimes incapable of dealing with genome-scale input data. Here, we present a MATLAB-based program called detectIR for the perfect and imperfect inverted repeat detection that utilizes complex numbers and vector calculation and allows genome-scale data inputs. A novel algorithm is adopted in detectIR to convert the conventional sequence string comparison in inverted repeat detection into vector calculation of complex numbers, allowing non-complementary pairs (mismatches) in the pairing stem and a non-palindromic spacer (loop or gaps) in the middle of inverted repeats. Compared with existing popular tools, our program performs with significantly higher accuracy and efficiency. Using genome sequence data from HIV-1, Arabidopsis thaliana, Homo sapiens and Zea mays for comparison, detectIR can find lots of inverted repeats missed by existing tools whose outputs often contain many invalid cases. detectIR is open source and its source code is freely available at: https://sourceforge.net/projects/detectir.

MOSFiT: Modular Open Source Fitter for Transients

NASA Astrophysics Data System (ADS)

Guillochon, James; Nicholl, Matt; Villar, V. Ashley; Mockler, Brenna; Narayan, Gautham; Mandel, Kaisey S.; Berger, Edo; Williams, Peter K. G.

2018-05-01

Much of the progress made in time-domain astronomy is accomplished by relating observational multiwavelength time-series data to models derived from our understanding of physical laws. This goal is typically accomplished by dividing the task in two: collecting data (observing), and constructing models to represent that data (theorizing). Owing to the natural tendency for specialization, a disconnect can develop between the best available theories and the best available data, potentially delaying advances in our understanding new classes of transients. We introduce MOSFiT: the Modular Open Source Fitter for Transients, a Python-based package that downloads transient data sets from open online catalogs (e.g., the Open Supernova Catalog), generates Monte Carlo ensembles of semi-analytical light-curve fits to those data sets and their associated Bayesian parameter posteriors, and optionally delivers the fitting results back to those same catalogs to make them available to the rest of the community. MOSFiT is designed to help bridge the gap between observations and theory in time-domain astronomy; in addition to making the application of existing models and creation of new models as simple as possible, MOSFiT yields statistically robust predictions for transient characteristics, with a standard output format that includes all the setup information necessary to reproduce a given result. As large-scale surveys such as that conducted with the Large Synoptic Survey Telescope (LSST), discover entirely new classes of transients, tools such as MOSFiT will be critical for enabling rapid comparison of models against data in statistically consistent, reproducible, and scientifically beneficial ways.

An Open-Source Toolbox for Surrogate Modeling of Joint Contact Mechanics

PubMed Central

Eskinazi, Ilan

2016-01-01

Goal Incorporation of elastic joint contact models into simulations of human movement could facilitate studying the interactions between muscles, ligaments, and bones. Unfortunately, elastic joint contact models are often too expensive computationally to be used within iterative simulation frameworks. This limitation can be overcome by using fast and accurate surrogate contact models that fit or interpolate input-output data sampled from existing elastic contact models. However, construction of surrogate contact models remains an arduous task. The aim of this paper is to introduce an open-source program called Surrogate Contact Modeling Toolbox (SCMT) that facilitates surrogate contact model creation, evaluation, and use. Methods SCMT interacts with the third party software FEBio to perform elastic contact analyses of finite element models and uses Matlab to train neural networks that fit the input-output contact data. SCMT features sample point generation for multiple domains, automated sampling, sample point filtering, and surrogate model training and testing. Results An overview of the software is presented along with two example applications. The first example demonstrates creation of surrogate contact models of artificial tibiofemoral and patellofemoral joints and evaluates their computational speed and accuracy, while the second demonstrates the use of surrogate contact models in a forward dynamic simulation of an open-chain leg extension-flexion motion. Conclusion SCMT facilitates the creation of computationally fast and accurate surrogate contact models. Additionally, it serves as a bridge between FEBio and OpenSim musculoskeletal modeling software. Significance Researchers may now create and deploy surrogate models of elastic joint contact with minimal effort. PMID:26186761

pyJac: Analytical Jacobian generator for chemical kinetics

NASA Astrophysics Data System (ADS)

Niemeyer, Kyle E.; Curtis, Nicholas J.; Sung, Chih-Jen

2017-06-01

Accurate simulations of combustion phenomena require the use of detailed chemical kinetics in order to capture limit phenomena such as ignition and extinction as well as predict pollutant formation. However, the chemical kinetic models for hydrocarbon fuels of practical interest typically have large numbers of species and reactions and exhibit high levels of mathematical stiffness in the governing differential equations, particularly for larger fuel molecules. In order to integrate the stiff equations governing chemical kinetics, generally reactive-flow simulations rely on implicit algorithms that require frequent Jacobian matrix evaluations. Some in situ and a posteriori computational diagnostics methods also require accurate Jacobian matrices, including computational singular perturbation and chemical explosive mode analysis. Typically, finite differences numerically approximate these, but for larger chemical kinetic models this poses significant computational demands since the number of chemical source term evaluations scales with the square of species count. Furthermore, existing analytical Jacobian tools do not optimize evaluations or support emerging SIMD processors such as GPUs. Here we introduce pyJac, a Python-based open-source program that generates analytical Jacobian matrices for use in chemical kinetics modeling and analysis. In addition to producing the necessary customized source code for evaluating reaction rates (including all modern reaction rate formulations), the chemical source terms, and the Jacobian matrix, pyJac uses an optimized evaluation order to minimize computational and memory operations. As a demonstration, we first establish the correctness of the Jacobian matrices for kinetic models of hydrogen, methane, ethylene, and isopentanol oxidation (number of species ranging 13-360) by showing agreement within 0.001% of matrices obtained via automatic differentiation. We then demonstrate the performance achievable on CPUs and GPUs using pyJac via matrix evaluation timing comparisons; the routines produced by pyJac outperformed first-order finite differences by 3-7.5 times and the existing analytical Jacobian software TChem by 1.1-2.2 times on a single-threaded basis. It is noted that TChem is not thread-safe, while pyJac is easily parallelized, and hence can greatly outperform TChem on multicore CPUs. The Jacobian matrix generator we describe here will be useful for reducing the cost of integrating chemical source terms with implicit algorithms in particular and algorithms that require an accurate Jacobian matrix in general. Furthermore, the open-source release of the program and Python-based implementation will enable wide adoption.

Tentacle: distributed quantification of genes in metagenomes.

PubMed

Boulund, Fredrik; Sjögren, Anders; Kristiansson, Erik

2015-01-01

In metagenomics, microbial communities are sequenced at increasingly high resolution, generating datasets with billions of DNA fragments. Novel methods that can efficiently process the growing volumes of sequence data are necessary for the accurate analysis and interpretation of existing and upcoming metagenomes. Here we present Tentacle, which is a novel framework that uses distributed computational resources for gene quantification in metagenomes. Tentacle is implemented using a dynamic master-worker approach in which DNA fragments are streamed via a network and processed in parallel on worker nodes. Tentacle is modular, extensible, and comes with support for six commonly used sequence aligners. It is easy to adapt Tentacle to different applications in metagenomics and easy to integrate into existing workflows. Evaluations show that Tentacle scales very well with increasing computing resources. We illustrate the versatility of Tentacle on three different use cases. Tentacle is written for Linux in Python 2.7 and is published as open source under the GNU General Public License (v3). Documentation, tutorials, installation instructions, and the source code are freely available online at: http://bioinformatics.math.chalmers.se/tentacle.

CILogon-HA. Higher Assurance Federated Identities for DOE Science

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

Basney, James

The CILogon-HA project extended the existing open source CILogon service (initially developed with funding from the National Science Foundation) to provide credentials at multiple levels of assurance to users of DOE facilities for collaborative science. CILogon translates mechanism and policy across higher education and grid trust federations, bridging from the InCommon identity federation (which federates university and DOE lab identities) to the Interoperable Global Trust Federation (which defines standards across the Worldwide LHC Computing Grid, the Open Science Grid, and other cyberinfrastructure). The CILogon-HA project expanded the CILogon service to support over 160 identity providers (including 6 DOE facilities) andmore » 3 internationally accredited certification authorities. To provide continuity of operations upon the end of the CILogon-HA project period, project staff transitioned the CILogon service to operation by XSEDE.« less

Getting Open Source Software into Schools: Strategies and Challenges

ERIC Educational Resources Information Center

Hepburn, Gary; Buley, Jan

2006-01-01

In this article Gary Hepburn and Jan Buley outline different approaches to implementing open source software (OSS) in schools; they also address the challenges that open source advocates should anticipate as they try to convince educational leaders to adopt OSS. With regard to OSS implementation, they note that schools have a flexible range of…

Open Source Library Management Systems: A Multidimensional Evaluation

ERIC Educational Resources Information Center

Balnaves, Edmund

2008-01-01

Open source library management systems have improved steadily in the last five years. They now present a credible option for small to medium libraries and library networks. An approach to their evaluation is proposed that takes account of three additional dimensions that only open source can offer: the developer and support community, the source…

Open Source as Appropriate Technology for Global Education

ERIC Educational Resources Information Center

Carmichael, Patrick; Honour, Leslie

2002-01-01

Economic arguments for the adoption of "open source" software in business have been widely discussed. In this paper we draw on personal experience in the UK, South Africa and Southeast Asia to forward compelling reasons why open source software should be considered as an appropriate and affordable alternative to the currently prevailing…

Government Technology Acquisition Policy: The Case of Proprietary versus Open Source Software

ERIC Educational Resources Information Center

Hemphill, Thomas A.

2005-01-01

This article begins by explaining the concepts of proprietary and open source software technology, which are now competing in the marketplace. A review of recent individual and cooperative technology development and public policy advocacy efforts, by both proponents of open source software and advocates of proprietary software, subsequently…

Open Source Communities in Technical Writing: Local Exigence, Global Extensibility

ERIC Educational Resources Information Center

Conner, Trey; Gresham, Morgan; McCracken, Jill

2011-01-01

By offering open-source software (OSS)-based networks as an affordable technology alternative, we partnered with a nonprofit community organization. In this article, we narrate the client-based experiences of this partnership, highlighting the ways in which OSS and open-source culture (OSC) transformed our students' and our own expectations of…

Personal Electronic Devices and the ISR Data Explosion: The Impact of Cyber Cameras on the Intelligence Community

DTIC Science & Technology

2015-06-01

ground.aspx?p=1 Texas Tech Security Group, “Automated Open Source Intelligence ( OSINT ) Using APIs.” RaiderSec, Sunday 30 December 2012, http...Open Source Intelligence ( OSINT ) Using APIs,” RaiderSec, Sunday 30 December 2012, http://raidersec.blogspot.com/2012/12/automated-open- source

Open-Source Unionism: New Workers, New Strategies

ERIC Educational Resources Information Center

Schmid, Julie M.

2004-01-01

In "Open-Source Unionism: Beyond Exclusive Collective Bargaining," published in fall 2002 in the journal Working USA, labor scholars Richard B. Freeman and Joel Rogers use the term "open-source unionism" to describe a form of unionization that uses Web technology to organize in hard-to-unionize workplaces. Rather than depend on the traditional…

Perceptions of Open Source versus Commercial Software: Is Higher Education Still on the Fence?

ERIC Educational Resources Information Center

van Rooij, Shahron Williams

2007-01-01

This exploratory study investigated the perceptions of technology and academic decision-makers about open source benefits and risks versus commercial software applications. The study also explored reactions to a concept for outsourcing campus-wide deployment and maintenance of open source. Data collected from telephone interviews were analyzed,…

Open Source for Knowledge and Learning Management: Strategies beyond Tools

ERIC Educational Resources Information Center

Lytras, Miltiadis, Ed.; Naeve, Ambjorn, Ed.

2007-01-01

In the last years, knowledge and learning management have made a significant impact on the IT research community. "Open Source for Knowledge and Learning Management: Strategies Beyond Tools" presents learning and knowledge management from a point of view where the basic tools and applications are provided by open source technologies.…

Open-Source Learning Management Systems: A Predictive Model for Higher Education

ERIC Educational Resources Information Center

van Rooij, S. Williams

2012-01-01

The present study investigated the role of pedagogical, technical, and institutional profile factors in an institution of higher education's decision to select an open-source learning management system (LMS). Drawing on the results of previous research that measured patterns of deployment of open-source software (OSS) in US higher education and…

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…

Technology collaboration by means of an open source government

NASA Astrophysics Data System (ADS)

Berardi, Steven M.

2009-05-01

The idea of open source software originally began in the early 1980s, but it never gained widespread support until recently, largely due to the explosive growth of the Internet. Only the Internet has made this kind of concept possible, bringing together millions of software developers from around the world to pool their knowledge. The tremendous success of open source software has prompted many corporations to adopt the culture of open source and thus share information they previously held secret. The government, and specifically the Department of Defense (DoD), could also benefit from adopting an open source culture. In acquiring satellite systems, the DoD often builds walls between program offices, but installing doors between programs can promote collaboration and information sharing. This paper addresses the challenges and consequences of adopting an open source culture to facilitate technology collaboration for DoD space acquisitions. DISCLAIMER: The views presented here are the views of the author, and do not represent the views of the United States Government, United States Air Force, or the Missile Defense Agency.

An Open Source Business Model for Malaria

PubMed Central

Årdal, Christine; Røttingen, John-Arne

2015-01-01

Greater investment is required in developing new drugs and vaccines against malaria in order to eradicate malaria. These precious funds must be carefully managed to achieve the greatest impact. We evaluate existing efforts to discover and develop new drugs and vaccines for malaria to determine how best malaria R&D can benefit from an enhanced open source approach and how such a business model may operate. We assess research articles, patents, clinical trials and conducted a smaller survey among malaria researchers. Our results demonstrate that the public and philanthropic sectors are financing and performing the majority of malaria drug/vaccine discovery and development, but are then restricting access through patents, ‘closed’ publications and hidden away physical specimens. This makes little sense since it is also the public and philanthropic sector that purchases the drugs and vaccines. We recommend that a more “open source” approach is taken by making the entire value chain more efficient through greater transparency which may lead to more extensive collaborations. This can, for example, be achieved by empowering an existing organization like the Medicines for Malaria Venture (MMV) to act as a clearing house for malaria-related data. The malaria researchers that we surveyed indicated that they would utilize such registry data to increase collaboration. Finally, we question the utility of publicly or philanthropically funded patents for malaria medicines, where little to no profits are available. Malaria R&D benefits from a publicly and philanthropically funded architecture, which starts with academic research institutions, product development partnerships, commercialization assistance through UNITAID and finally procurement through mechanisms like The Global Fund to Fight AIDS, Tuberculosis and Malaria and the U.S.’ President’s Malaria Initiative. We believe that a fresh look should be taken at the cost/benefit of patents particularly related to new malaria medicines and consider alternative incentives, like WHO prequalification. PMID:25658590

Long-term Science Data Curation Using a Digital Object Model and Open-Source Frameworks

NASA Astrophysics Data System (ADS)

Pan, J.; Lenhardt, W.; Wilson, B. E.; Palanisamy, G.; Cook, R. B.

2010-12-01

Scientific digital content, including Earth Science observations and model output, has become more heterogeneous in format and more distributed across the Internet. In addition, data and metadata are becoming necessarily linked internally and externally on the Web. As a result, such content has become more difficult for providers to manage and preserve and for users to locate, understand, and consume. Specifically, it is increasingly harder to deliver relevant metadata and data processing lineage information along with the actual content consistently. Readme files, data quality information, production provenance, and other descriptive metadata are often separated in the storage level as well as in the data search and retrieval interfaces available to a user. Critical archival metadata, such as auditing trails and integrity checks, are often even more difficult for users to access, if they exist at all. We investigate the use of several open-source software frameworks to address these challenges. We use Fedora Commons Framework and its digital object abstraction as the repository, Drupal CMS as the user-interface, and the Islandora module as the connector from Drupal to Fedora Repository. With the digital object model, metadata of data description and data provenance can be associated with data content in a formal manner, so are external references and other arbitrary auxiliary information. Changes are formally audited on an object, and digital contents are versioned and have checksums automatically computed. Further, relationships among objects are formally expressed with RDF triples. Data replication, recovery, metadata export are supported with standard protocols, such as OAI-PMH. We provide a tentative comparative analysis of the chosen software stack with the Open Archival Information System (OAIS) reference model, along with our initial results with the existing terrestrial ecology data collections at NASA’s ORNL Distributed Active Archive Center for Biogeochemical Dynamics (ORNL DAAC).

Scientific Platform as a Service - Tools and solutions for efficient access to and analysis of oceanographic data

NASA Astrophysics Data System (ADS)

Vines, Aleksander; Hansen, Morten W.; Korosov, Anton

2017-04-01

Existing infrastructure international and Norwegian projects, e.g., NorDataNet, NMDC and NORMAP, provide open data access through the OPeNDAP protocol following the conventions for CF (Climate and Forecast) metadata, designed to promote the processing and sharing of files created with the NetCDF application programming interface (API). This approach is now also being implemented in the Norwegian Sentinel Data Hub (satellittdata.no) to provide satellite EO data to the user community. Simultaneously with providing simplified and unified data access, these projects also seek to use and establish common standards for use and discovery metadata. This then allows development of standardized tools for data search and (subset) streaming over the internet to perform actual scientific analysis. A combinnation of software tools, which we call a Scientific Platform as a Service (SPaaS), will take advantage of these opportunities to harmonize and streamline the search, retrieval and analysis of integrated satellite and auxiliary observations of the oceans in a seamless system. The SPaaS is a cloud solution for integration of analysis tools with scientific datasets via an API. The core part of the SPaaS is a distributed metadata catalog to store granular metadata describing the structure, location and content of available satellite, model, and in situ datasets. The analysis tools include software for visualization (also online), interactive in-depth analysis, and server-based processing chains. The API conveys search requests between system nodes (i.e., interactive and server tools) and provides easy access to the metadata catalog, data repositories, and the tools. The SPaaS components are integrated in virtual machines, of which provisioning and deployment are automatized using existing state-of-the-art open-source tools (e.g., Vagrant, Ansible, Docker). The open-source code for scientific tools and virtual machine configurations is under version control at https://github.com/nansencenter/, and is coupled to an online continuous integration system (e.g., Travis CI).

Open source software integrated into data services of Japanese planetary explorations

NASA Astrophysics Data System (ADS)

Yamamoto, Y.; Ishihara, Y.; Otake, H.; Imai, K.; Masuda, K.

2015-12-01

Scientific data obtained by Japanese scientific satellites and lunar and planetary explorations are archived in DARTS (Data ARchives and Transmission System). DARTS provides the data with a simple method such as HTTP directory listing for long-term preservation while DARTS tries to provide rich web applications for ease of access with modern web technologies based on open source software. This presentation showcases availability of open source software through our services. KADIAS is a web-based application to search, analyze, and obtain scientific data measured by SELENE(Kaguya), a Japanese lunar orbiter. KADIAS uses OpenLayers to display maps distributed from Web Map Service (WMS). As a WMS server, open source software MapServer is adopted. KAGUYA 3D GIS (KAGUYA 3D Moon NAVI) provides a virtual globe for the SELENE's data. The main purpose of this application is public outreach. NASA World Wind Java SDK is used to develop. C3 (Cross-Cutting Comparisons) is a tool to compare data from various observations and simulations. It uses Highcharts to draw graphs on web browsers. Flow is a tool to simulate a Field-Of-View of an instrument onboard a spacecraft. This tool itself is open source software developed by JAXA/ISAS, and the license is BSD 3-Caluse License. SPICE Toolkit is essential to compile FLOW. SPICE Toolkit is also open source software developed by NASA/JPL, and the website distributes many spacecrafts' data. Nowadays, open source software is an indispensable tool to integrate DARTS services.

Managing and Integrating Open Environmental Data - Technological Requirements and Challenges

NASA Astrophysics Data System (ADS)

Devaraju, Anusuriya; Kunkel, Ralf; Jirka, Simon

2014-05-01

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

Limitations of Phased Array Beamforming in Open Rotor Noise Source Imaging

NASA Technical Reports Server (NTRS)

Horvath, Csaba; Envia, Edmane; Podboy, Gary G.

2013-01-01

Phased array beamforming results of the F31/A31 historical baseline counter-rotating open rotor blade set were investigated for measurement data taken on the NASA Counter-Rotating Open Rotor Propulsion Rig in the 9- by 15-Foot Low-Speed Wind Tunnel of NASA Glenn Research Center as well as data produced using the LINPROP open rotor tone noise code. The planar microphone array was positioned broadside and parallel to the axis of the open rotor, roughly 2.3 rotor diameters away. The results provide insight as to why the apparent noise sources of the blade passing frequency tones and interaction tones appear at their nominal Mach radii instead of at the actual noise sources, even if those locations are not on the blades. Contour maps corresponding to the sound fields produced by the radiating sound waves, taken from the simulations, are used to illustrate how the interaction patterns of circumferential spinning modes of rotating coherent noise sources interact with the phased array, often giving misleading results, as the apparent sources do not always show where the actual noise sources are located. This suggests that a more sophisticated source model would be required to accurately locate the sources of each tone. The results of this study also have implications with regard to the shielding of open rotor sources by airframe empennages.

Implementation of highly parallel and large scale GW calculations within the OpenAtom software

NASA Astrophysics Data System (ADS)

Ismail-Beigi, Sohrab

The need to describe electronic excitations with better accuracy than provided by band structures produced by Density Functional Theory (DFT) has been a long-term enterprise for the computational condensed matter and materials theory communities. In some cases, appropriate theoretical frameworks have existed for some time but have been difficult to apply widely due to computational cost. For example, the GW approximation incorporates a great deal of important non-local and dynamical electronic interaction effects but has been too computationally expensive for routine use in large materials simulations. OpenAtom is an open source massively parallel ab initiodensity functional software package based on plane waves and pseudopotentials (http://charm.cs.uiuc.edu/OpenAtom/) that takes advantage of the Charm + + parallel framework. At present, it is developed via a three-way collaboration, funded by an NSF SI2-SSI grant (ACI-1339804), between Yale (Ismail-Beigi), IBM T. J. Watson (Glenn Martyna) and the University of Illinois at Urbana Champaign (Laxmikant Kale). We will describe the project and our current approach towards implementing large scale GW calculations with OpenAtom. Potential applications of large scale parallel GW software for problems involving electronic excitations in semiconductor and/or metal oxide systems will be also be pointed out.

A robust scientific workflow for assessing fire danger levels using open-source software

NASA Astrophysics Data System (ADS)

Vitolo, Claudia; Di Giuseppe, Francesca; Smith, Paul

2017-04-01

Modelling forest fires is theoretically and computationally challenging because it involves the use of a wide variety of information, in large volumes and affected by high uncertainties. In-situ observations of wildfire, for instance, are highly sparse and need to be complemented by remotely sensed data measuring biomass burning to achieve homogeneous coverage at global scale. Fire models use weather reanalysis products to measure energy release and rate of spread but can only assess the potential predictability of fire danger as the actual ignition is due to human behaviour and, therefore, very unpredictable. Lastly, fire forecasting systems rely on weather forecasts to extend the advance warning but are currently calibrated using fire danger thresholds that are defined at global scale and do not take into account the spatial variability of fuel availability. As a consequence, uncertainties sharply increase cascading from the observational to the modelling stage and they might be further inflated by non-reproducible analyses. Although uncertainties in observations will only decrease with technological advances over the next decades, the other uncertainties (i.e. generated during modelling and post-processing) can already be addressed by developing transparent and reproducible analysis workflows, even more if implemented within open-source initiatives. This is because reproducible workflows aim to streamline the processing task as they present ready-made solutions to handle and manipulate complex and heterogeneous datasets. Also, opening the code to the scrutiny of other experts increases the chances to implement more robust solutions and avoids duplication of efforts. In this work we present our contribution to the forest fire modelling community: an open-source tool called "caliver" for the calibration and verification of forest fire model results. This tool is developed in the R programming language and publicly available under an open license. We will present the caliver R package, illustrate the main functionalities and show the results of our preliminary experiments calculating fire danger thresholds for various regions on Earth. We will compare these with the existing global thresholds and, lastly, demonstrate how these newly-calculated regional thresholds can lead to improved calibration of fire forecast models in an operational setting.

Kinota: An Open-Source NoSQL implementation of OGC SensorThings for large-scale high-resolution real-time environmental monitoring

NASA Astrophysics Data System (ADS)

Miles, B.; Chepudira, K.; LaBar, W.

2017-12-01

The Open Geospatial Consortium (OGC) SensorThings API (STA) specification, ratified in 2016, is a next-generation open standard for enabling real-time communication of sensor data. Building on over a decade of OGC Sensor Web Enablement (SWE) Standards, STA offers a rich data model that can represent a range of sensor and phenomena types (e.g. fixed sensors sensing fixed phenomena, fixed sensors sensing moving phenomena, mobile sensors sensing fixed phenomena, and mobile sensors sensing moving phenomena) and is data agnostic. Additionally, and in contrast to previous SWE standards, STA is developer-friendly, as is evident from its convenient JSON serialization, and expressive OData-based query language (with support for geospatial queries); with its Message Queue Telemetry Transport (MQTT), STA is also well-suited to efficient real-time data publishing and discovery. All these attributes make STA potentially useful for use in environmental monitoring sensor networks. Here we present Kinota(TM), an Open-Source NoSQL implementation of OGC SensorThings for large-scale high-resolution real-time environmental monitoring. Kinota, which roughly stands for Knowledge from Internet of Things Analyses, relies on Cassandra its underlying data store, which is a horizontally scalable, fault-tolerant open-source database that is often used to store time-series data for Big Data applications (though integration with other NoSQL or rational databases is possible). With this foundation, Kinota can scale to store data from an arbitrary number of sensors collecting data every 500 milliseconds. Additionally, Kinota architecture is very modular allowing for customization by adopters who can choose to replace parts of the existing implementation when desirable. The architecture is also highly portable providing the flexibility to choose between cloud providers like azure, amazon, google etc. The scalable, flexible and cloud friendly architecture of Kinota makes it ideal for use in next-generation large-scale and high-resolution real-time environmental monitoring networks used in domains such as hydrology, geomorphology, and geophysics, as well as management applications such as flood early warning, and regulatory enforcement.

Develop Direct Geo-referencing System Based on Open Source Software and Hardware Platform

NASA Astrophysics Data System (ADS)

Liu, H. S.; Liao, H. M.

2015-08-01

Direct geo-referencing system uses the technology of remote sensing to quickly grasp images, GPS tracks, and camera position. These data allows the construction of large volumes of images with geographic coordinates. So that users can be measured directly on the images. In order to properly calculate positioning, all the sensor signals must be synchronized. Traditional aerial photography use Position and Orientation System (POS) to integrate image, coordinates and camera position. However, it is very expensive. And users could not use the result immediately because the position information does not embed into image. To considerations of economy and efficiency, this study aims to develop a direct geo-referencing system based on open source software and hardware platform. After using Arduino microcontroller board to integrate the signals, we then can calculate positioning with open source software OpenCV. In the end, we use open source panorama browser, panini, and integrate all these to open source GIS software, Quantum GIS. A wholesome collection of data - a data processing system could be constructed.

77 FR 16863 - Proposed Extension of Existing Information Collection; Mine Mapping and Records of Opening...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-22

... DEPARTMENT OF LABOR Mine Safety and Health Administration Proposed Extension of Existing Information Collection; Mine Mapping and Records of Opening, Closing, and Reopening of Mines (Formerly, Record of Mine Closures, Opening & Reopening of Mines) AGENCY: Mine Safety and Health Administration, Labor...

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.

Software for Real-Time Analysis of Subsonic Test Shot Accuracy

DTIC Science & Technology

2014-03-01

used the C++ programming language, the Open Source Computer Vision ( OpenCV ®) software library, and Microsoft Windows® Application Programming...video for comparison through OpenCV image analysis tools. Based on the comparison, the software then computed the coordinates of each shot relative to...DWB researchers wanted to use the Open Source Computer Vision ( OpenCV ) software library for capturing and analyzing frames of video. OpenCV contains

Open source electronic health records and chronic disease management.

PubMed

Goldwater, Jason C; Kwon, Nancy J; Nathanson, Ashley; Muckle, Alison E; Brown, Alexa; Cornejo, Kerri

2014-02-01

To study and report on the use of open source electronic health records (EHR) to assist with chronic care management within safety net medical settings, such as community health centers (CHC). The study was conducted by NORC at the University of Chicago from April to September 2010. The NORC team undertook a comprehensive environmental scan, including a literature review, a dozen key informant interviews using a semistructured protocol, and a series of site visits to CHC that currently use an open source EHR. Two of the sites chosen by NORC were actively using an open source EHR to assist in the redesign of their care delivery system to support more effective chronic disease management. This included incorporating the chronic care model into an CHC and using the EHR to help facilitate its elements, such as care teams for patients, in addition to maintaining health records on indigent populations, such as tuberculosis status on homeless patients. The ability to modify the open-source EHR to adapt to the CHC environment and leverage the ecosystem of providers and users to assist in this process provided significant advantages in chronic care management. Improvements in diabetes management, controlled hypertension and increases in tuberculosis vaccinations were assisted through the use of these open source systems. The flexibility and adaptability of open source EHR demonstrated its utility and viability in the provision of necessary and needed chronic disease care among populations served by CHC.

What an open source clinical trial community can learn from hackers

PubMed Central

Dunn, Adam G.; Day, Richard O.; Mandl, Kenneth D.; Coiera, Enrico

2014-01-01

Summary Open sharing of clinical trial data has been proposed as a way to address the gap between the production of clinical evidence and the decision-making of physicians. Since a similar gap has already been addressed in the software industry by the open source software movement, we examine how the social and technical principles of the movement can be used to guide the growth of an open source clinical trial community. PMID:22553248

Outflow structure of the quiet sun corona probed by spacecraft radio scintillations in strong scattering

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

Imamura, Takeshi; Ando, Hiroki; Toda, Tomoaki

Radio scintillation observations have been unable to probe flow speeds in the low corona where the scattering of radio waves is exceedingly strong. Here we estimate outflow speeds continuously from the vicinity of the Sun to the outer corona (heliocentric distances of 1.5-20.5 solar radii) by applying the strong scattering theory to radio scintillations for the first time, using the Akatsuki spacecraft as the radio source. Small, nonzero outflow speeds were observed over a wide latitudinal range in the quiet-Sun low corona, suggesting that the supply of plasma from closed loops to the solar wind occurs over an extended area.more » The existence of power-law density fluctuations down to the scale of 100 m was suggested, which is indicative of well-developed turbulence which can play a key role in heating the corona. At higher altitudes, a rapid acceleration typical of radial open fields is observed, and the temperatures derived from the speed profile show a distinct maximum in the outer corona. This study opened up a possibility of observing detailed flow structures near the Sun from a vast amount of existing interplanetary scintillation data.« less

Photon-HDF5: An Open File Format for Timestamp-Based Single-Molecule Fluorescence Experiments.

PubMed

Ingargiola, Antonino; Laurence, Ted; Boutelle, Robert; Weiss, Shimon; Michalet, Xavier

2016-01-05

We introduce Photon-HDF5, an open and efficient file format to simplify exchange and long-term accessibility of data from single-molecule fluorescence experiments based on photon-counting detectors such as single-photon avalanche diode, photomultiplier tube, or arrays of such detectors. The format is based on HDF5, a widely used platform- and language-independent hierarchical file format for which user-friendly viewers are available. Photon-HDF5 can store raw photon data (timestamp, channel number, etc.) from any acquisition hardware, but also setup and sample description, information on provenance, authorship and other metadata, and is flexible enough to include any kind of custom data. The format specifications are hosted on a public website, which is open to contributions by the biophysics community. As an initial resource, the website provides code examples to read Photon-HDF5 files in several programming languages and a reference Python library (phconvert), to create new Photon-HDF5 files and convert several existing file formats into Photon-HDF5. To encourage adoption by the academic and commercial communities, all software is released under the MIT open source license. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Photon-HDF5: An Open File Format for Timestamp-Based Single-Molecule Fluorescence Experiments

PubMed Central

Ingargiola, Antonino; Laurence, Ted; Boutelle, Robert; Weiss, Shimon; Michalet, Xavier

2016-01-01

We introduce Photon-HDF5, an open and efficient file format to simplify exchange and long-term accessibility of data from single-molecule fluorescence experiments based on photon-counting detectors such as single-photon avalanche diode, photomultiplier tube, or arrays of such detectors. The format is based on HDF5, a widely used platform- and language-independent hierarchical file format for which user-friendly viewers are available. Photon-HDF5 can store raw photon data (timestamp, channel number, etc.) from any acquisition hardware, but also setup and sample description, information on provenance, authorship and other metadata, and is flexible enough to include any kind of custom data. The format specifications are hosted on a public website, which is open to contributions by the biophysics community. As an initial resource, the website provides code examples to read Photon-HDF5 files in several programming languages and a reference Python library (phconvert), to create new Photon-HDF5 files and convert several existing file formats into Photon-HDF5. To encourage adoption by the academic and commercial communities, all software is released under the MIT open source license. PMID:26745406

Photon-HDF5: an open file format for single-molecule fluorescence experiments using photon-counting detectors

DOE PAGES

Ingargiola, A.; Laurence, T. A.; Boutelle, R.; ...

2015-12-23

We introduce Photon-HDF5, an open and efficient file format to simplify exchange and long term accessibility of data from single-molecule fluorescence experiments based on photon-counting detectors such as single-photon avalanche diode (SPAD), photomultiplier tube (PMT) or arrays of such detectors. The format is based on HDF5, a widely used platform- and language-independent hierarchical file format for which user-friendly viewers are available. Photon-HDF5 can store raw photon data (timestamp, channel number, etc) from any acquisition hardware, but also setup and sample description, information on provenance, authorship and other metadata, and is flexible enough to include any kind of custom data. Themore » format specifications are hosted on a public website, which is open to contributions by the biophysics community. As an initial resource, the website provides code examples to read Photon-HDF5 files in several programming languages and a reference python library (phconvert), to create new Photon-HDF5 files and convert several existing file formats into Photon-HDF5. As a result, to encourage adoption by the academic and commercial communities, all software is released under the MIT open source license.« less

Evaluating Open Source Software for Use in Library Initiatives: A Case Study Involving Electronic Publishing

ERIC Educational Resources Information Center

Samuels, Ruth Gallegos; Griffy, Henry

2012-01-01

This article discusses best practices for evaluating open source software for use in library projects, based on the authors' experience evaluating electronic publishing solutions. First, it presents a brief review of the literature, emphasizing the need to evaluate open source solutions carefully in order to minimize Total Cost of Ownership. Next,…

A Requirements-Based Exploration of Open-Source Software Development Projects--Towards a Natural Language Processing Software Analysis Framework

ERIC Educational Resources Information Center

Vlas, Radu Eduard

2012-01-01

Open source projects do have requirements; they are, however, mostly informal, text descriptions found in requests, forums, and other correspondence. Understanding such requirements provides insight into the nature of open source projects. Unfortunately, manual analysis of natural language requirements is time-consuming, and for large projects,…

Open Source Meets Virtual Reality--An Instructor's Journey Unearths New Opportunities for Learning, Community, and Academia

ERIC Educational Resources Information Center

O'Connor, Eileen A.

2015-01-01

Opening with the history, recent advances, and emerging ways to use avatar-based virtual reality, an instructor who has used virtual environments since 2007 shares how these environments bring more options to community building, teaching, and education. With the open-source movement, where the source code for virtual environments was made…

Migrations of the Mind: The Emergence of Open Source Education

ERIC Educational Resources Information Center

Glassman, Michael; Bartholomew, Mitchell; Jones, Travis

2011-01-01

The authors describe an Open Source approach to education. They define Open Source Education (OSE) as a teaching and learning framework where the use and presentation of information is non-hierarchical, malleable, and subject to the needs and contributions of students as they become "co-owners" of the course. The course transforms itself into an…

Prepare for Impact

ERIC Educational Resources Information Center

Waters, John K.

2010-01-01

Open source software is poised to make a profound impact on K-12 education. For years industry experts have been predicting the widespread adoption of open source tools by K-12 school districts. They're about to be proved right. The impact may not yet have been profound, but it's fair to say that some open source systems and non-proprietary…

7 Questions to Ask Open Source Vendors

ERIC Educational Resources Information Center

Raths, David

2012-01-01

With their budgets under increasing pressure, many campus IT directors are considering open source projects for the first time. On the face of it, the savings can be significant. Commercial emergency-planning software can cost upward of six figures, for example, whereas the open source Kuali Ready might run as little as $15,000 per year when…

Cognitive Readiness Assessment and Reporting: An Open Source Mobile Framework for Operational Decision Support and Performance Improvement

ERIC Educational Resources Information Center

Heric, Matthew; Carter, Jenn

2011-01-01

Cognitive readiness (CR) and performance for operational time-critical environments are continuing points of focus for military and academic communities. In response to this need, we designed an open source interactive CR assessment application as a highly adaptive and efficient open source testing administration and analysis tool. It is capable…

A mesh generation and machine learning framework for Drosophila gene expression pattern image analysis

PubMed Central

2013-01-01

Background Multicellular organisms consist of cells of many different types that are established during development. Each type of cell is characterized by the unique combination of expressed gene products as a result of spatiotemporal gene regulation. Currently, a fundamental challenge in regulatory biology is to elucidate the gene expression controls that generate the complex body plans during development. Recent advances in high-throughput biotechnologies have generated spatiotemporal expression patterns for thousands of genes in the model organism fruit fly Drosophila melanogaster. Existing qualitative methods enhanced by a quantitative analysis based on computational tools we present in this paper would provide promising ways for addressing key scientific questions. Results We develop a set of computational methods and open source tools for identifying co-expressed embryonic domains and the associated genes simultaneously. To map the expression patterns of many genes into the same coordinate space and account for the embryonic shape variations, we develop a mesh generation method to deform a meshed generic ellipse to each individual embryo. We then develop a co-clustering formulation to cluster the genes and the mesh elements, thereby identifying co-expressed embryonic domains and the associated genes simultaneously. Experimental results indicate that the gene and mesh co-clusters can be correlated to key developmental events during the stages of embryogenesis we study. The open source software tool has been made available at http://compbio.cs.odu.edu/fly/. Conclusions Our mesh generation and machine learning methods and tools improve upon the flexibility, ease-of-use and accuracy of existing methods. PMID:24373308

Implementing an Open Source Electronic Health Record System in Kenyan Health Care Facilities: Case Study.

PubMed

Muinga, Naomi; Magare, Steve; Monda, Jonathan; Kamau, Onesmus; Houston, Stuart; Fraser, Hamish; Powell, John; English, Mike; Paton, Chris

2018-04-18

The Kenyan government, working with international partners and local organizations, has developed an eHealth strategy, specified standards, and guidelines for electronic health record adoption in public hospitals and implemented two major health information technology projects: District Health Information Software Version 2, for collating national health care indicators and a rollout of the KenyaEMR and International Quality Care Health Management Information Systems, for managing 600 HIV clinics across the country. Following these projects, a modified version of the Open Medical Record System electronic health record was specified and developed to fulfill the clinical and administrative requirements of health care facilities operated by devolved counties in Kenya and to automate the process of collating health care indicators and entering them into the District Health Information Software Version 2 system. We aimed to present a descriptive case study of the implementation of an open source electronic health record system in public health care facilities in Kenya. We conducted a landscape review of existing literature concerning eHealth policies and electronic health record development in Kenya. Following initial discussions with the Ministry of Health, the World Health Organization, and implementing partners, we conducted a series of visits to implementing sites to conduct semistructured individual interviews and group discussions with stakeholders to produce a historical case study of the implementation. This case study describes how consultants based in Kenya, working with developers in India and project stakeholders, implemented the new system into several public hospitals in a county in rural Kenya. The implementation process included upgrading the hospital information technology infrastructure, training users, and attempting to garner administrative and clinical buy-in for adoption of the system. The initial deployment was ultimately scaled back due to a complex mix of sociotechnical and administrative issues. Learning from these early challenges, the system is now being redesigned and prepared for deployment in 6 new counties across Kenya. Implementing electronic health record systems is a challenging process in high-income settings. In low-income settings, such as Kenya, open source software may offer some respite from the high costs of software licensing, but the familiar challenges of clinical and administration buy-in, the need to adequately train users, and the need for the provision of ongoing technical support are common across the North-South divide. Strategies such as creating local support teams, using local development resources, ensuring end user buy-in, and rolling out in smaller facilities before larger hospitals are being incorporated into the project. These are positive developments to help maintain momentum as the project continues. Further integration with existing open source communities could help ongoing development and implementations of the project. We hope this case study will provide some lessons and guidance for other challenging implementations of electronic health record systems as they continue across Africa. ©Naomi Muinga, Steve Magare, Jonathan Monda, Onesmus Kamau, Stuart Houston, Hamish Fraser, John Powell, Mike English, Chris Paton. Originally published in JMIR Medical Informatics (http://medinform.jmir.org), 18.04.2018.

Open source IPSEC software in manned and unmanned space missions

NASA Astrophysics Data System (ADS)

Edwards, Jacob

Network security is a major topic of research because cyber attackers pose a threat to national security. Securing ground-space communications for NASA missions is important because attackers could endanger mission success and human lives. This thesis describes how an open source IPsec software package was used to create a secure and reliable channel for ground-space communications. A cost efficient, reproducible hardware testbed was also created to simulate ground-space communications. The testbed enables simulation of low-bandwidth and high latency communications links to experiment how the open source IPsec software reacts to these network constraints. Test cases were built that allowed for validation of the testbed and the open source IPsec software. The test cases also simulate using an IPsec connection from mission control ground routers to points of interest in outer space. Tested open source IPsec software did not meet all the requirements. Software changes were suggested to meet requirements.

Upon the Shoulders of Giants: Open-Source Hardware and Software in Analytical Chemistry.

PubMed

Dryden, Michael D M; Fobel, Ryan; Fobel, Christian; Wheeler, Aaron R

2017-04-18

Isaac Newton famously observed that "if I have seen further it is by standing on the shoulders of giants." We propose that this sentiment is a powerful motivation for the "open-source" movement in scientific research, in which creators provide everything needed to replicate a given project online, as well as providing explicit permission for users to use, improve, and share it with others. Here, we write to introduce analytical chemists who are new to the open-source movement to best practices and concepts in this area and to survey the state of open-source research in analytical chemistry. We conclude by considering two examples of open-source projects from our own research group, with the hope that a description of the process, motivations, and results will provide a convincing argument about the benefits that this movement brings to both creators and users.

Open-Source 3-D Platform for Low-Cost Scientific Instrument Ecosystem.

PubMed

Zhang, C; Wijnen, B; Pearce, J M

2016-08-01

The combination of open-source software and hardware provides technically feasible methods to create low-cost, highly customized scientific research equipment. Open-source 3-D printers have proven useful for fabricating scientific tools. Here the capabilities of an open-source 3-D printer are expanded to become a highly flexible scientific platform. An automated low-cost 3-D motion control platform is presented that has the capacity to perform scientific applications, including (1) 3-D printing of scientific hardware; (2) laboratory auto-stirring, measuring, and probing; (3) automated fluid handling; and (4) shaking and mixing. The open-source 3-D platform not only facilities routine research while radically reducing the cost, but also inspires the creation of a diverse array of custom instruments that can be shared and replicated digitally throughout the world to drive down the cost of research and education further. © 2016 Society for Laboratory Automation and Screening.

Inexpensive, Low Power, Open-Source Data Logging hardware development

NASA Astrophysics Data System (ADS)

Sandell, C. T.; Schulz, B.; Wickert, A. D.

2017-12-01

Over the past six years, we have developed a suite of open-source, low-cost, and lightweight data loggers for scientific research. These loggers employ the popular and easy-to-use Arduino programming environment, but consist of custom hardware optimized for field research. They may be connected to a broad and expanding range of off-the-shelf sensors, with software support built in directly to the "ALog" library. Three main models exist: The ALog (for Autonomous or Arduino Logger) is the extreme low-power model for years-long deployments with only primary AA or D batteries. The ALog shield is a stripped-down ALog that nests with a standard Arduino board for prototyping or education. The TLog (for Telemetering Logger) contains an embedded radio with 500 m range and a GPS for communications and precision timekeeping. This enables meshed networks of loggers that can send their data back to an internet-connected "home base" logger for near-real-time field data retrieval. All boards feature feature a high-precision clock, full size SD card slot for high-volume data storage, large screw terminals to connect sensors, interrupts, SPI and I2C communication capability, and 3.3V/5V power outputs. The ALog and TLog have fourteen 16-bit analog inputs with a precision voltage reference for precise analog measurements. Their components are rated -40 to +85 degrees C, and they have been tested in harsh field conditions. These low-cost and open-source data loggers have enabled our research group to collect field data across North and South America on a limited budget, support student projects, and build toward better future scientific data systems.

FOODIE: Farm-Oriented Open Data in Europe

NASA Astrophysics Data System (ADS)

Ángel Esbri Palomares, Miguel; Charvat, Karel; Campos, Antonio Manuel; Palma, Raúl

2014-05-01

The agriculture sector is a unique sector due to its strategic importance for both European citizens (consumers) and European economy (regional and global) which, ideally, should make the whole sector a network of interacting organizations. Rural areas are of particular importance with respect to the agro-food sector and should be specifically addressed within this scope. The different groups of stakeholders involved in the agricultural activities have to manage many different and heterogeneous sources of information that need to be combined in order to make economically and environmentally sound decisions, which include (among others) the definition of policies (subsidies, standardisation and regulation, national strategies for rural development, climate change), valuation of ecological performances, development of sustainable agriculture, crop recollection timing and pricing, plagues detection, etc. Such processes are very labour intensive because most parts have to be executed manually and the necessary information is not always available or easily accessible. In this context, future agriculture knowledge management systems have to support not only direct profitability of agriculture or environment protection, but also activities of individuals and groups allowing effective collaboration among groups in agri-food industry, consumers, public administrations and wider stakeholders communities, especially in rural domain. To that end FOODIE project aims at building an open and interoperable agricultural specialized platform hub on the cloud for the management of spatial and non-spatial data relevant for farming production; for discovery of spatial and non-spatial agriculture related data from heterogeneous sources; integration of existing and valuable European open datasets related to agriculture; data publication and data linking of external agriculture data sources contributed by different public and private stakeholders allowing to provide specific and high-value applications and services for the support in the planning and decision-making processes of different stakeholders groups related to the agricultural and environmental domains.

SubductionGenerator: A program to build three-dimensional plate configurations

NASA Astrophysics Data System (ADS)

Jadamec, M. A.; Kreylos, O.; Billen, M. I.; Turcotte, D. L.; Knepley, M.

2016-12-01

Geologic, geochemical, and geophysical data from subduction zones indicate that a two-dimensional paradigm for plate tectonic boundaries is no longer adequate to explain the observations. Many open source software packages exist to simulate the viscous flow of the Earth, such as the dynamics of subduction. However, there are few open source programs that generate the three-dimensional model input. We present an open source software program, SubductionGenerator, that constructs the three-dimensional initial thermal structure and plate boundary structure. A 3D model mesh and tectonic configuration are constructed based on a user specified model domain, slab surface, seafloor age grid file, and shear zone surface. The initial 3D thermal structure for the plates and mantle within the model domain is then constructed using a series of libraries within the code that use a half-space cooling model, plate cooling model, and smoothing functions. The code maps the initial 3D thermal structure and the 3D plate interface onto the mesh nodes using a series of libraries including a k-d tree to increase efficiency. In this way, complicated geometries and multiple plates with variable thickness can be built onto a multi-resolution finite element mesh with a 3D thermal structure and 3D isotropic shear zones oriented at any angle with respect to the grid. SubductionGenerator is aimed at model set-ups more representative of the earth, which can be particularly challenging to construct. Examples include subduction zones where the physical attributes vary in space, such as slab dip and temperature, and overriding plate temperature and thickness. Thus, the program can been used to construct initial tectonic configurations for triple junctions and plate boundary corners.

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.

Information-Theoretical Analysis of EEG Microstate Sequences in Python.

PubMed

von Wegner, Frederic; Laufs, Helmut

2018-01-01

We present an open-source Python package to compute information-theoretical quantities for electroencephalographic data. Electroencephalography (EEG) measures the electrical potential generated by the cerebral cortex and the set of spatial patterns projected by the brain's electrical potential on the scalp surface can be clustered into a set of representative maps called EEG microstates. Microstate time series are obtained by competitively fitting the microstate maps back into the EEG data set, i.e., by substituting the EEG data at a given time with the label of the microstate that has the highest similarity with the actual EEG topography. As microstate sequences consist of non-metric random variables, e.g., the letters A-D, we recently introduced information-theoretical measures to quantify these time series. In wakeful resting state EEG recordings, we found new characteristics of microstate sequences such as periodicities related to EEG frequency bands. The algorithms used are here provided as an open-source package and their use is explained in a tutorial style. The package is self-contained and the programming style is procedural, focusing on code intelligibility and easy portability. Using a sample EEG file, we demonstrate how to perform EEG microstate segmentation using the modified K-means approach, and how to compute and visualize the recently introduced information-theoretical tests and quantities. The time-lagged mutual information function is derived as a discrete symbolic alternative to the autocorrelation function for metric time series and confidence intervals are computed from Markov chain surrogate data. The software package provides an open-source extension to the existing implementations of the microstate transform and is specifically designed to analyze resting state EEG recordings.

The Privacy and Security Implications of Open Data in Healthcare.

PubMed

Kobayashi, Shinji; Kane, Thomas B; Paton, Chris

2018-04-22

 The International Medical Informatics Association (IMIA) Open Source Working Group (OSWG) initiated a group discussion to discuss current privacy and security issues in the open data movement in the healthcare domain from the perspective of the OSWG membership.  Working group members independently reviewed the recent academic and grey literature and sampled a number of current large-scale open data projects to inform the working group discussion.  This paper presents an overview of open data repositories and a series of short case reports to highlight relevant issues present in the recent literature concerning the adoption of open approaches to sharing healthcare datasets. Important themes that emerged included data standardisation, the inter-connected nature of the open source and open data movements, and how publishing open data can impact on the ethics, security, and privacy of informatics projects.  The open data and open source movements in healthcare share many common philosophies and approaches including developing international collaborations across multiple organisations and domains of expertise. Both movements aim to reduce the costs of advancing scientific research and improving healthcare provision for people around the world by adopting open intellectual property licence agreements and codes of practice. Implications of the increased adoption of open data in healthcare include the need to balance the security and privacy challenges of opening data sources with the potential benefits of open data for improving research and healthcare delivery. Georg Thieme Verlag KG Stuttgart.

75 FR 36756 - Self-Regulatory Organizations; Financial Industry Regulatory Authority, Inc.; Notice of Filing of...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-28

... existing paragraph (b)(4) of the Rule, entitled ``Numerical Guidelines Applicable to Volatile Market Opens... existing paragraph (b)(2), which provides flexibility to FINRA to use different Numerical Guidelines or... of paragraph (b)(4) (``Numerical Guidelines Applicable to Volatile Market Opens'') of the existing...

Simulation of partially coherent light propagation using parallel computing devices

NASA Astrophysics Data System (ADS)

Magalhães, Tiago C.; Rebordão, José M.

2017-08-01

Light acquires or loses coherence and coherence is one of the few optical observables. Spectra can be derived from coherence functions and understanding any interferometric experiment is also relying upon coherence functions. Beyond the two limiting cases (full coherence or incoherence) the coherence of light is always partial and it changes with propagation. We have implemented a code to compute the propagation of partially coherent light from the source plane to the observation plane using parallel computing devices (PCDs). In this paper, we restrict the propagation in free space only. To this end, we used the Open Computing Language (OpenCL) and the open-source toolkit PyOpenCL, which gives access to OpenCL parallel computation through Python. To test our code, we chose two coherence source models: an incoherent source and a Gaussian Schell-model source. In the former case, we divided into two different source shapes: circular and rectangular. The results were compared to the theoretical values. Our implemented code allows one to choose between the PyOpenCL implementation and a standard one, i.e using the CPU only. To test the computation time for each implementation (PyOpenCL and standard), we used several computer systems with different CPUs and GPUs. We used powers of two for the dimensions of the cross-spectral density matrix (e.g. 324, 644) and a significant speed increase is observed in the PyOpenCL implementation when compared to the standard one. This can be an important tool for studying new source models.

An Open Source Simulation System

NASA Technical Reports Server (NTRS)

Slack, Thomas

2005-01-01

An investigation into the current state of the art of open source real time programming practices. This document includes what technologies are available, how easy is it to obtain, configure, and use them, and some performance measures done on the different systems. A matrix of vendors and their products is included as part of this investigation, but this is not an exhaustive list, and represents only a snapshot of time in a field that is changing rapidly. Specifically, there are three approaches investigated: 1. Completely open source on generic hardware, downloaded from the net. 2. Open source packaged by a vender and provided as free evaluation copy. 3. Proprietary hardware with pre-loaded proprietary source available software provided by the vender as for our evaluation.

Zephyr: Open-source Parallel Seismic Waveform Inversion in an Integrated Python-based Framework

NASA Astrophysics Data System (ADS)

Smithyman, B. R.; Pratt, R. G.; Hadden, S. M.

2015-12-01

Seismic Full-Waveform Inversion (FWI) is an advanced method to reconstruct wave properties of materials in the Earth from a series of seismic measurements. These methods have been developed by researchers since the late 1980s, and now see significant interest from the seismic exploration industry. As researchers move towards implementing advanced numerical modelling (e.g., 3D, multi-component, anisotropic and visco-elastic physics), it is desirable to make use of a modular approach, minimizing the effort developing a new set of tools for each new numerical problem. SimPEG (http://simpeg.xyz) is an open source project aimed at constructing a general framework to enable geophysical inversion in various domains. In this abstract we describe Zephyr (https://github.com/bsmithyman/zephyr), which is a coupled research project focused on parallel FWI in the seismic context. The software is built on top of Python, Numpy and IPython, which enables very flexible testing and implementation of new features. Zephyr is an open source project, and is released freely to enable reproducible research. We currently implement a parallel, distributed seismic forward modelling approach that solves the 2.5D (two-and-one-half dimensional) viscoacoustic Helmholtz equation at a range modelling frequencies, generating forward solutions for a given source behaviour, and gradient solutions for a given set of observed data. Solutions are computed in a distributed manner on a set of heterogeneous workers. The researcher's frontend computer may be separated from the worker cluster by a network link to enable full support for computation on remote clusters from individual workstations or laptops. The present codebase introduces a numerical discretization equivalent to that used by FULLWV, a well-known seismic FWI research codebase. This makes it straightforward to compare results from Zephyr directly with FULLWV. The flexibility introduced by the use of a Python programming environment makes extension of the codebase with new methods much more straightforward. This enables comparison and integration of new efforts with existing results.

TMSEEG: A MATLAB-Based Graphical User Interface for Processing Electrophysiological Signals during Transcranial Magnetic Stimulation.

PubMed

Atluri, Sravya; Frehlich, Matthew; Mei, Ye; Garcia Dominguez, Luis; Rogasch, Nigel C; Wong, Willy; Daskalakis, Zafiris J; Farzan, Faranak

2016-01-01

Concurrent recording of electroencephalography (EEG) during transcranial magnetic stimulation (TMS) is an emerging and powerful tool for studying brain health and function. Despite a growing interest in adaptation of TMS-EEG across neuroscience disciplines, its widespread utility is limited by signal processing challenges. These challenges arise due to the nature of TMS and the sensitivity of EEG to artifacts that often mask TMS-evoked potentials (TEP)s. With an increase in the complexity of data processing methods and a growing interest in multi-site data integration, analysis of TMS-EEG data requires the development of a standardized method to recover TEPs from various sources of artifacts. This article introduces TMSEEG, an open-source MATLAB application comprised of multiple algorithms organized to facilitate a step-by-step procedure for TMS-EEG signal processing. Using a modular design and interactive graphical user interface (GUI), this toolbox aims to streamline TMS-EEG signal processing for both novice and experienced users. Specifically, TMSEEG provides: (i) targeted removal of TMS-induced and general EEG artifacts; (ii) a step-by-step modular workflow with flexibility to modify existing algorithms and add customized algorithms; (iii) a comprehensive display and quantification of artifacts; (iv) quality control check points with visual feedback of TEPs throughout the data processing workflow; and (v) capability to label and store a database of artifacts. In addition to these features, the software architecture of TMSEEG ensures minimal user effort in initial setup and configuration of parameters for each processing step. This is partly accomplished through a close integration with EEGLAB, a widely used open-source toolbox for EEG signal processing. In this article, we introduce TMSEEG, validate its features and demonstrate its application in extracting TEPs across several single- and multi-pulse TMS protocols. As the first open-source GUI-based pipeline for TMS-EEG signal processing, this toolbox intends to promote the widespread utility and standardization of an emerging technology in brain research.

TMSEEG: A MATLAB-Based Graphical User Interface for Processing Electrophysiological Signals during Transcranial Magnetic Stimulation

PubMed Central

Atluri, Sravya; Frehlich, Matthew; Mei, Ye; Garcia Dominguez, Luis; Rogasch, Nigel C.; Wong, Willy; Daskalakis, Zafiris J.; Farzan, Faranak

2016-01-01

Concurrent recording of electroencephalography (EEG) during transcranial magnetic stimulation (TMS) is an emerging and powerful tool for studying brain health and function. Despite a growing interest in adaptation of TMS-EEG across neuroscience disciplines, its widespread utility is limited by signal processing challenges. These challenges arise due to the nature of TMS and the sensitivity of EEG to artifacts that often mask TMS-evoked potentials (TEP)s. With an increase in the complexity of data processing methods and a growing interest in multi-site data integration, analysis of TMS-EEG data requires the development of a standardized method to recover TEPs from various sources of artifacts. This article introduces TMSEEG, an open-source MATLAB application comprised of multiple algorithms organized to facilitate a step-by-step procedure for TMS-EEG signal processing. Using a modular design and interactive graphical user interface (GUI), this toolbox aims to streamline TMS-EEG signal processing for both novice and experienced users. Specifically, TMSEEG provides: (i) targeted removal of TMS-induced and general EEG artifacts; (ii) a step-by-step modular workflow with flexibility to modify existing algorithms and add customized algorithms; (iii) a comprehensive display and quantification of artifacts; (iv) quality control check points with visual feedback of TEPs throughout the data processing workflow; and (v) capability to label and store a database of artifacts. In addition to these features, the software architecture of TMSEEG ensures minimal user effort in initial setup and configuration of parameters for each processing step. This is partly accomplished through a close integration with EEGLAB, a widely used open-source toolbox for EEG signal processing. In this article, we introduce TMSEEG, validate its features and demonstrate its application in extracting TEPs across several single- and multi-pulse TMS protocols. As the first open-source GUI-based pipeline for TMS-EEG signal processing, this toolbox intends to promote the widespread utility and standardization of an emerging technology in brain research. PMID:27774054

Applying an Archetype-Based Approach to Electroencephalography/Event-Related Potential Experiments in the EEGBase Resource.

PubMed

Papež, Václav; Mouček, Roman

2017-01-01

The purpose of this study is to investigate the feasibility of applying openEHR (an archetype-based approach for electronic health records representation) to modeling data stored in EEGBase, a portal for experimental electroencephalography/event-related potential (EEG/ERP) data management. The study evaluates re-usage of existing openEHR archetypes and proposes a set of new archetypes together with the openEHR templates covering the domain. The main goals of the study are to (i) link existing EEGBase data/metadata and openEHR archetype structures and (ii) propose a new openEHR archetype set describing the EEG/ERP domain since this set of archetypes currently does not exist in public repositories. The main methodology is based on the determination of the concepts obtained from EEGBase experimental data and metadata that are expressible structurally by the openEHR reference model and semantically by openEHR archetypes. In addition, templates as the third openEHR resource allow us to define constraints over archetypes. Clinical Knowledge Manager (CKM), a public openEHR archetype repository, was searched for the archetypes matching the determined concepts. According to the search results, the archetypes already existing in CKM were applied and the archetypes not existing in the CKM were newly developed. openEHR archetypes support linkage to external terminologies. To increase semantic interoperability of the new archetypes, binding with the existing odML electrophysiological terminology was assured. Further, to increase structural interoperability, also other current solutions besides EEGBase were considered during the development phase. Finally, a set of templates using the selected archetypes was created to meet EEGBase requirements. A set of eleven archetypes that encompassed the domain of experimental EEG/ERP measurements were identified. Of these, six were reused without changes, one was extended, and four were newly created. All archetypes were arranged in the templates reflecting the EEGBase metadata structure. A mechanism of odML terminology referencing was proposed to assure semantic interoperability of the archetypes. The openEHR approach was found to be useful not only for clinical purposes but also for experimental data modeling.

Municipal solid waste management in Kolkata, India - A review

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

Chattopadhyay, Subhasish; Dutta, Amit; Ray, Subhabrata

2009-04-15

Kolkata is one of four metropolitan cities in India. With an area of 187.33 sq km and a population of about 8 million, it generates around 3,000 t d{sup -1} of municipal solid waste (MSW) at a rate of 450-500 g per capita per day. With rapid urbanization as a result of planned and unplanned growth and industrialization, the problems associated with handling MSW have increased at an alarming rate over the past few years. No source segregation arrangement exists; there is only limited (60%) house-to-house collection; and 50-55% open vats are used in the present collection system. The operationalmore » efficiency of the Kolkata Municipal Corporation (KMC) transport system is about 50%, with a fleet composed of about 30-35% old vehicles. The majority (80%) of these, particularly the hired vehicles, are more than 20 years old. The newly added areas covered by KMC have even lower collection efficiencies, and only an informal recycling system exists. The waste collected has a low energy value (3,350-4,200 kJ kg{sup -1}) with high moisture and inert content. A 700 t d{sup -1} compost plant set up in 2000 has not been functioning effectively since 2003. Open dumping (without liners and without a leachate management facility) and the threat of groundwater pollution, as well as saturation of an existing landfill site (Dhapa) are the most pressing problems for the city today. KMC spends 70-75% of its total expenditures on collection of solid waste, 25-30% on transportation, and less than 5% on final disposal arrangements. The Kolkata Environmental Improvement Project, funded by the Asian Development Bank, is seen as only a partial solution to the problem. A detailed plan should emphasize segregation at the source, investment in disposal arrangements (including the use of liners and leachate collection), and an optimized transport arrangement, among improvements.« less

A clinic compatible, open source electrophysiology system.

PubMed

Hermiz, John; Rogers, Nick; Kaestner, Erik; Ganji, Mehran; Cleary, Dan; Snider, Joseph; Barba, David; Dayeh, Shadi; Halgren, Eric; Gilja, Vikash

2016-08-01

Open source electrophysiology (ephys) recording systems have several advantages over commercial systems such as customization and affordability enabling more researchers to conduct ephys experiments. Notable open source ephys systems include Open-Ephys, NeuroRighter and more recently Willow, all of which have high channel count (64+), scalability, and advanced software to develop on top of. However, little work has been done to build an open source ephys system that is clinic compatible, particularly in the operating room where acute human electrocorticography (ECoG) research is performed. We developed an affordable (<; $10,000) and open system for research purposes that features power isolation for patient safety, compact and water resistant enclosures and 256 recording channels sampled up to 20ksam/sec, 16-bit. The system was validated by recording ECoG with a high density, thin film device for an acute, awake craniotomy study at UC San Diego, Thornton Hospital Operating Room.

Freeing Worldview's development process: Open source everything!

NASA Astrophysics Data System (ADS)

Gunnoe, T.

2016-12-01

Freeing your code and your project are important steps for creating an inviting environment for collaboration, with the added side effect of keeping a good relationship with your users. NASA Worldview's codebase was released with the open source NOSA (NASA Open Source Agreement) license in 2014, but this is only the first step. We also have to free our ideas, empower our users by involving them in the development process, and open channels that lead to the creation of a community project. There are many highly successful examples of Free and Open Source Software (FOSS) projects of which we can take note: the Linux kernel, Debian, GNOME, etc. These projects owe much of their success to having a passionate mix of developers/users with a great community and a common goal in mind. This presentation will describe the scope of this openness and how Worldview plans to move forward with a more community-inclusive approach.

Digital data collection in paleoanthropology.

PubMed

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

2015-01-01

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

The connectome viewer toolkit: an open source framework to manage, analyze, and visualize connectomes.

PubMed

Gerhard, Stephan; Daducci, Alessandro; Lemkaddem, Alia; Meuli, Reto; Thiran, Jean-Philippe; Hagmann, Patric

2011-01-01

Advanced neuroinformatics tools are required for methods of connectome mapping, analysis, and visualization. The inherent multi-modality of connectome datasets poses new challenges for data organization, integration, and sharing. We have designed and implemented the Connectome Viewer Toolkit - a set of free and extensible open source neuroimaging tools written in Python. The key components of the toolkit are as follows: (1) The Connectome File Format is an XML-based container format to standardize multi-modal data integration and structured metadata annotation. (2) The Connectome File Format Library enables management and sharing of connectome files. (3) The Connectome Viewer is an integrated research and development environment for visualization and analysis of multi-modal connectome data. The Connectome Viewer's plugin architecture supports extensions with network analysis packages and an interactive scripting shell, to enable easy development and community contributions. Integration with tools from the scientific Python community allows the leveraging of numerous existing libraries for powerful connectome data mining, exploration, and comparison. We demonstrate the applicability of the Connectome Viewer Toolkit using Diffusion MRI datasets processed by the Connectome Mapper. The Connectome Viewer Toolkit is available from http://www.cmtk.org/

Introducing GHOST: The Geospace/Heliosphere Observation & Simulation Tool-kit

NASA Astrophysics Data System (ADS)

Murphy, J. J.; Elkington, S. R.; Schmitt, P.; Wiltberger, M. J.; Baker, D. N.

2013-12-01

Simulation models of the heliospheric and geospace environments can provide key insights into the geoeffective potential of solar disturbances such as Coronal Mass Ejections and High Speed Solar Wind Streams. Advanced post processing of the results of these simulations greatly enhances the utility of these models for scientists and other researchers. Currently, no supported centralized tool exists for performing these processing tasks. With GHOST, we introduce a toolkit for the ParaView visualization environment that provides a centralized suite of tools suited for Space Physics post processing. Building on the work from the Center For Integrated Space Weather Modeling (CISM) Knowledge Transfer group, GHOST is an open-source tool suite for ParaView. The tool-kit plugin currently provides tools for reading LFM and Enlil data sets, and provides automated tools for data comparison with NASA's CDAweb database. As work progresses, many additional tools will be added and through open-source collaboration, we hope to add readers for additional model types, as well as any additional tools deemed necessary by the scientific public. The ultimate end goal of this work is to provide a complete Sun-to-Earth model analysis toolset.

Executing SPARQL Queries over the Web of Linked Data

NASA Astrophysics Data System (ADS)

Hartig, Olaf; Bizer, Christian; Freytag, Johann-Christoph

The Web of Linked Data forms a single, globally distributed dataspace. Due to the openness of this dataspace, it is not possible to know in advance all data sources that might be relevant for query answering. This openness poses a new challenge that is not addressed by traditional research on federated query processing. In this paper we present an approach to execute SPARQL queries over the Web of Linked Data. The main idea of our approach is to discover data that might be relevant for answering a query during the query execution itself. This discovery is driven by following RDF links between data sources based on URIs in the query and in partial results. The URIs are resolved over the HTTP protocol into RDF data which is continuously added to the queried dataset. This paper describes concepts and algorithms to implement our approach using an iterator-based pipeline. We introduce a formalization of the pipelining approach and show that classical iterators may cause blocking due to the latency of HTTP requests. To avoid blocking, we propose an extension of the iterator paradigm. The evaluation of our approach shows its strengths as well as the still existing challenges.

pyomo.dae: a modeling and automatic discretization framework for optimization with differential and algebraic equations

DOE PAGES

Nicholson, Bethany; Siirola, John D.; Watson, Jean-Paul; ...

2017-12-20

We describe pyomo.dae, an open source Python-based modeling framework that enables high-level abstract specification of optimization problems with differential and algebraic equations. The pyomo.dae framework is integrated with the Pyomo open source algebraic modeling language, and is available at http://www.pyomo.org. One key feature of pyomo.dae is that it does not restrict users to standard, predefined forms of differential equations, providing a high degree of modeling flexibility and the ability to express constraints that cannot be easily specified in other modeling frameworks. Other key features of pyomo.dae are the ability to specify optimization problems with high-order differential equations and partial differentialmore » equations, defined on restricted domain types, and the ability to automatically transform high-level abstract models into finite-dimensional algebraic problems that can be solved with off-the-shelf solvers. Moreover, pyomo.dae users can leverage existing capabilities of Pyomo to embed differential equation models within stochastic and integer programming models and mathematical programs with equilibrium constraint formulations. Collectively, these features enable the exploration of new modeling concepts, discretization schemes, and the benchmarking of state-of-the-art optimization solvers.« less

The TimeStudio Project: An open source scientific workflow system for the behavioral and brain sciences.

PubMed

Nyström, Pär; Falck-Ytter, Terje; Gredebäck, Gustaf

2016-06-01

This article describes a new open source scientific workflow system, the TimeStudio Project, dedicated to the behavioral and brain sciences. The program is written in MATLAB and features a graphical user interface for the dynamic pipelining of computer algorithms developed as TimeStudio plugins. TimeStudio includes both a set of general plugins (for reading data files, modifying data structures, visualizing data structures, etc.) and a set of plugins specifically developed for the analysis of event-related eyetracking data as a proof of concept. It is possible to create custom plugins to integrate new or existing MATLAB code anywhere in a workflow, making TimeStudio a flexible workbench for organizing and performing a wide range of analyses. The system also features an integrated sharing and archiving tool for TimeStudio workflows, which can be used to share workflows both during the data analysis phase and after scientific publication. TimeStudio thus facilitates the reproduction and replication of scientific studies, increases the transparency of analyses, and reduces individual researchers' analysis workload. The project website ( http://timestudioproject.com ) contains the latest releases of TimeStudio, together with documentation and user forums.

The Connectome Viewer Toolkit: An Open Source Framework to Manage, Analyze, and Visualize Connectomes

PubMed Central

Gerhard, Stephan; Daducci, Alessandro; Lemkaddem, Alia; Meuli, Reto; Thiran, Jean-Philippe; Hagmann, Patric

2011-01-01

Advanced neuroinformatics tools are required for methods of connectome mapping, analysis, and visualization. The inherent multi-modality of connectome datasets poses new challenges for data organization, integration, and sharing. We have designed and implemented the Connectome Viewer Toolkit – a set of free and extensible open source neuroimaging tools written in Python. The key components of the toolkit are as follows: (1) The Connectome File Format is an XML-based container format to standardize multi-modal data integration and structured metadata annotation. (2) The Connectome File Format Library enables management and sharing of connectome files. (3) The Connectome Viewer is an integrated research and development environment for visualization and analysis of multi-modal connectome data. The Connectome Viewer's plugin architecture supports extensions with network analysis packages and an interactive scripting shell, to enable easy development and community contributions. Integration with tools from the scientific Python community allows the leveraging of numerous existing libraries for powerful connectome data mining, exploration, and comparison. We demonstrate the applicability of the Connectome Viewer Toolkit using Diffusion MRI datasets processed by the Connectome Mapper. The Connectome Viewer Toolkit is available from http://www.cmtk.org/ PMID:21713110

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.

The development of experimental techniques for the study of helicopter rotor noise

NASA Technical Reports Server (NTRS)

Widnall, S. E.; Harris, W. L.; Lee, Y. C. A.; Drees, H. M.

1974-01-01

The features of existing wind tunnels involved in noise studies are discussed. The acoustic characteristics of the MIT low noise open jet wind tunnel are obtained by employing calibration techniques: one technique is to measure the decay of sound pressure with distance in the far field; the other technique is to utilize a speaker, which was calibrated, as a sound source. The sound pressure level versus frequency was obtained in the wind tunnel chamber and compared with the corresponding calibrated values. Fiberglas board-block units were installed on the chamber interior. The free field was increased significantly after this treatment and the chamber cut-off frequency was reduced to 160 Hz from the original designed 250 Hz. The flow field characteristics of the rotor-tunnel configuration were studied by using flow visualization techniques. The influence of open-jet shear layer on the sound transmission was studied by using an Aeolian tone as the sound source. A dynamometer system was designed to measure the steady and low harmonics of the rotor thrust. A theoretical Mach number scaling formula was developed to scale the rotational noise and blade slap noise data of model rotors to full scale helicopter rotors.