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.

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

NASA Astrophysics Data System (ADS)

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

2017-06-01

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

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

PubMed

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

2017-06-01

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

The Role of Free/Libre and Open Source Software in Learning Health Systems.

PubMed

Paton, C; Karopka, T

2017-08-01

Objective: To give an overview of the role of Free/Libre and Open Source Software (FLOSS) in the context of secondary use of patient data to enable Learning Health Systems (LHSs). Methods: We conducted an environmental scan of the academic and grey literature utilising the MedFLOSS database of open source systems in healthcare to inform a discussion of the role of open source in developing LHSs that reuse patient data for research and quality improvement. Results: A wide range of FLOSS is identified that contributes to the information technology (IT) infrastructure of LHSs including operating systems, databases, frameworks, interoperability software, and mobile and web apps. The recent literature around the development and use of key clinical data management tools is also reviewed. Conclusions: FLOSS already plays a critical role in modern health IT infrastructure for the collection, storage, and analysis of patient data. The nature of FLOSS systems to be collaborative, modular, and modifiable may make open source approaches appropriate for building the digital infrastructure for a LHS. Georg Thieme Verlag KG Stuttgart.

Ontology-Based Data Integration of Open Source Electronic Medical Record and Data Capture Systems

ERIC Educational Resources Information Center

Guidry, Alicia F.

2013-01-01

In low-resource settings, the prioritization of clinical care funding is often determined by immediate health priorities. As a result, investment directed towards the development of standards for clinical data representation and exchange are rare and accordingly, data management systems are often redundant. Open-source systems such as OpenMRS and…

Open Source Clinical NLP – More than Any Single System

PubMed Central

Masanz, James; Pakhomov, Serguei V.; Xu, Hua; Wu, Stephen T.; Chute, Christopher G.; Liu, Hongfang

2014-01-01

The number of Natural Language Processing (NLP) tools and systems for processing clinical free-text has grown as interest and processing capability have surged. Unfortunately any two systems typically cannot simply interoperate, even when both are built upon a framework designed to facilitate the creation of pluggable components. We present two ongoing activities promoting open source clinical NLP. The Open Health Natural Language Processing (OHNLP) Consortium was originally founded to foster a collaborative community around clinical NLP, releasing UIMA-based open source software. OHNLP’s mission currently includes maintaining a catalog of clinical NLP software and providing interfaces to simplify the interaction of NLP systems. Meanwhile, Apache cTAKES aims to integrate best-of-breed annotators, providing a world-class NLP system for accessing clinical information within free-text. These two activities are complementary. OHNLP promotes open source clinical NLP activities in the research community and Apache cTAKES bridges research to the health information technology (HIT) practice. PMID:25954581

Passive rejection of heat from an isotope heat source through an open door

NASA Technical Reports Server (NTRS)

Burns, R. K.

1971-01-01

The isotope heat-source design for a Brayton power system includes a door in the thermal insulation through which the heat can be passively rejected to space when the power system is not operating. The results of an analysis to predict the heat-source surface temperature and the heat-source heat-exchanger temperature during passive heat rejection as a function of insulation door opening angle are presented. They show that for a door opening angle greater than 20 deg, the temperatures are less than the steady-state temperatures during power system operation.

Open Source, Open Standards, and Health Care Information Systems

PubMed Central

2011-01-01

Recognition of the improvements in patient safety, quality of patient care, and efficiency that health care information systems have the potential to bring has led to significant investment. Globally the sale of health care information systems now represents a multibillion dollar industry. As policy makers, health care professionals, and patients, we have a responsibility to maximize the return on this investment. To this end we analyze alternative licensing and software development models, as well as the role of standards. We describe how licensing affects development. We argue for the superiority of open source licensing to promote safer, more effective health care information systems. We claim that open source licensing in health care information systems is essential to rational procurement strategy. PMID:21447469

Open source, open standards, and health care information systems.

PubMed

Reynolds, Carl J; Wyatt, Jeremy C

2011-02-17

Recognition of the improvements in patient safety, quality of patient care, and efficiency that health care information systems have the potential to bring has led to significant investment. Globally the sale of health care information systems now represents a multibillion dollar industry. As policy makers, health care professionals, and patients, we have a responsibility to maximize the return on this investment. To this end we analyze alternative licensing and software development models, as well as the role of standards. We describe how licensing affects development. We argue for the superiority of open source licensing to promote safer, more effective health care information systems. We claim that open source licensing in health care information systems is essential to rational procurement strategy.

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.

Dynamic mobility applications open source application development portal : Task 4 : system requirements specifications : final report.

DOT National Transportation Integrated Search

2016-10-12

This document describes the System Requirements Specifications (SyRS) of the Dynamic Mobility Applications (DMA) Open Source Application Development Portal (OSADP) system in details according to IEEE-Std. 1233-1998. The requirement statements discuss...

Utilization of open source electronic health record around the world: A systematic review.

PubMed

Aminpour, Farzaneh; Sadoughi, Farahnaz; Ahamdi, Maryam

2014-01-01

Many projects on developing Electronic Health Record (EHR) systems have been carried out in many countries. The current study was conducted to review the published data on the utilization of open source EHR systems in different countries all over the world. Using free text and keyword search techniques, six bibliographic databases were searched for related articles. The identified papers were screened and reviewed during a string of stages for the irrelevancy and validity. The findings showed that open source EHRs have been wildly used by source limited regions in all continents, especially in Sub-Saharan Africa and South America. It would create opportunities to improve national healthcare level especially in developing countries with minimal financial resources. Open source technology is a solution to overcome the problems of high-costs and inflexibility associated with the proprietary health information systems.

Models for Deploying Open Source and Commercial Software to Support Earth Science Data Processing and Distribution

NASA Astrophysics Data System (ADS)

Yetman, G.; Downs, R. R.

2011-12-01

Software deployment is needed to process and distribute scientific data throughout the data lifecycle. Developing software in-house can take software development teams away from other software development projects and can require efforts to maintain the software over time. Adopting and reusing software and system modules that have been previously developed by others can reduce in-house software development and maintenance costs and can contribute to the quality of the system being developed. A variety of models are available for reusing and deploying software and systems that have been developed by others. These deployment models include open source software, vendor-supported open source software, commercial software, and combinations of these approaches. Deployment in Earth science data processing and distribution has demonstrated the advantages and drawbacks of each model. Deploying open source software offers advantages for developing and maintaining scientific data processing systems and applications. By joining an open source community that is developing a particular system module or application, a scientific data processing team can contribute to aspects of the software development without having to commit to developing the software alone. Communities of interested developers can share the work while focusing on activities that utilize in-house expertise and addresses internal requirements. Maintenance is also shared by members of the community. Deploying vendor-supported open source software offers similar advantages to open source software. However, by procuring the services of a vendor, the in-house team can rely on the vendor to provide, install, and maintain the software over time. Vendor-supported open source software may be ideal for teams that recognize the value of an open source software component or application and would like to contribute to the effort, but do not have the time or expertise to contribute extensively. Vendor-supported software may also have the additional benefits of guaranteed up-time, bug fixes, and vendor-added enhancements. Deploying commercial software can be advantageous for obtaining system or software components offered by a vendor that meet in-house requirements. The vendor can be contracted to provide installation, support and maintenance services as needed. Combining these options offers a menu of choices, enabling selection of system components or software modules that meet the evolving requirements encountered throughout the scientific data lifecycle.

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.

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.

Preparing a scientific manuscript in Linux: Today's possibilities and limitations.

PubMed

Tchantchaleishvili, Vakhtang; Schmitto, Jan D

2011-10-22

Increasing number of scientists are enthusiastic about using free, open source software for their research purposes. Authors' specific goal was to examine whether a Linux-based operating system with open source software packages would allow to prepare a submission-ready scientific manuscript without the need to use the proprietary software. Preparation and editing of scientific manuscripts is possible using Linux and open source software. This letter to the editor describes key steps for preparation of a publication-ready scientific manuscript in a Linux-based operating system, as well as discusses the necessary software components. This manuscript was created using Linux and open source programs for Linux.

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.

Managing multicentre clinical trials with open source.

PubMed

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

2014-03-01

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

Utilization of open source electronic health record around the world: A systematic review

PubMed Central

Aminpour, Farzaneh; Sadoughi, Farahnaz; Ahamdi, Maryam

2014-01-01

Many projects on developing Electronic Health Record (EHR) systems have been carried out in many countries. The current study was conducted to review the published data on the utilization of open source EHR systems in different countries all over the world. Using free text and keyword search techniques, six bibliographic databases were searched for related articles. The identified papers were screened and reviewed during a string of stages for the irrelevancy and validity. The findings showed that open source EHRs have been wildly used by source limited regions in all continents, especially in Sub-Saharan Africa and South America. It would create opportunities to improve national healthcare level especially in developing countries with minimal financial resources. Open source technology is a solution to overcome the problems of high-costs and inflexibility associated with the proprietary health information systems. PMID:24672566

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...

Open-Source web-based geographical information system for health exposure assessment

PubMed Central

2012-01-01

This paper presents the design and development of an open source web-based Geographical Information System allowing users to visualise, customise and interact with spatial data within their web browser. The developed application shows that by using solely Open Source software it was possible to develop a customisable web based GIS application that provides functions necessary to convey health and environmental data to experts and non-experts alike without the requirement of proprietary software. PMID:22233606

Implementing an Open Source Learning Management System: A Critical Analysis of Change Strategies

ERIC Educational Resources Information Center

Uys, Philip M.

2010-01-01

This paper analyses the change and innovation strategies that Charles Sturt University (CSU) used from 2007 to 2009 during the implementation and mainstreaming of an open source learning management system (LMS), Sakai, named locally as "CSU Interact". CSU was in January 2008 the first Australian University to implement an open source…

Preparing a scientific manuscript in Linux: Today's possibilities and limitations

PubMed Central

2011-01-01

Background Increasing number of scientists are enthusiastic about using free, open source software for their research purposes. Authors' specific goal was to examine whether a Linux-based operating system with open source software packages would allow to prepare a submission-ready scientific manuscript without the need to use the proprietary software. Findings Preparation and editing of scientific manuscripts is possible using Linux and open source software. This letter to the editor describes key steps for preparation of a publication-ready scientific manuscript in a Linux-based operating system, as well as discusses the necessary software components. This manuscript was created using Linux and open source programs for Linux. PMID:22018246

Open source Matrix Product States: Opening ways to simulate entangled many-body quantum systems in one dimension

NASA Astrophysics Data System (ADS)

Jaschke, Daniel; Wall, Michael L.; Carr, Lincoln D.

2018-04-01

Numerical simulations are a powerful tool to study quantum systems beyond exactly solvable systems lacking an analytic expression. For one-dimensional entangled quantum systems, tensor network methods, amongst them Matrix Product States (MPSs), have attracted interest from different fields of quantum physics ranging from solid state systems to quantum simulators and quantum computing. Our open source MPS code provides the community with a toolset to analyze the statics and dynamics of one-dimensional quantum systems. Here, we present our open source library, Open Source Matrix Product States (OSMPS), of MPS methods implemented in Python and Fortran2003. The library includes tools for ground state calculation and excited states via the variational ansatz. We also support ground states for infinite systems with translational invariance. Dynamics are simulated with different algorithms, including three algorithms with support for long-range interactions. Convenient features include built-in support for fermionic systems and number conservation with rotational U(1) and discrete Z2 symmetries for finite systems, as well as data parallelism with MPI. We explain the principles and techniques used in this library along with examples of how to efficiently use the general interfaces to analyze the Ising and Bose-Hubbard models. This description includes the preparation of simulations as well as dispatching and post-processing of them.

Completeness and overlap in open access systems: Search engines, aggregate institutional repositories and physics-related open sources.

PubMed

Tsay, Ming-Yueh; Wu, Tai-Luan; Tseng, Ling-Li

2017-01-01

This study examines the completeness and overlap of coverage in physics of six open access scholarly communication systems, including two search engines (Google Scholar and Microsoft Academic), two aggregate institutional repositories (OAIster and OpenDOAR), and two physics-related open sources (arXiv.org and Astrophysics Data System). The 2001-2013 Nobel Laureates in Physics served as the sample. Bibliographic records of their publications were retrieved and downloaded from each system, and a computer program was developed to perform the analytical tasks of sorting, comparison, elimination, aggregation and statistical calculations. Quantitative analyses and cross-referencing were performed to determine the completeness and overlap of the system coverage of the six open access systems. The results may enable scholars to select an appropriate open access system as an efficient scholarly communication channel, and academic institutions may build institutional repositories or independently create citation index systems in the future. Suggestions on indicators and tools for academic assessment are presented based on the comprehensiveness assessment of each system.

A Framework for the Systematic Collection of Open Source Intelligence

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

Pouchard, Line Catherine; Trien, Joseph P; Dobson, Jonathan D

2009-01-01

Following legislative directions, the Intelligence Community has been mandated to make greater use of Open Source Intelligence (OSINT). Efforts are underway to increase the use of OSINT but there are many obstacles. One of these obstacles is the lack of tools helping to manage the volume of available data and ascertain its credibility. We propose a unique system for selecting, collecting and storing Open Source data from the Web and the Open Source Center. Some data management tasks are automated, document source is retained, and metadata containing geographical coordinates are added to the documents. Analysts are thus empowered to search,more » view, store, and analyze Web data within a single tool. We present ORCAT I and ORCAT II, two implementations of the system.« less

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…

Facilitating Constructive Alignment in Power Systems Engineering Education Using Free and Open-Source Software

ERIC Educational Resources Information Center

Vanfretti, L.; Milano, F.

2012-01-01

This paper describes how the use of free and open-source software (FOSS) can facilitate the application of constructive alignment theory in power systems engineering education by enabling the deep learning approach in power system analysis courses. With this aim, this paper describes the authors' approach in using the Power System Analysis Toolbox…

Weather forecasting with open source software

NASA Astrophysics Data System (ADS)

Rautenhaus, Marc; Dörnbrack, Andreas

2013-04-01

To forecast the weather situation during aircraft-based atmospheric field campaigns, we employ a tool chain of existing and self-developed open source software tools and open standards. Of particular value are the Python programming language with its extension libraries NumPy, SciPy, PyQt4, Matplotlib and the basemap toolkit, the NetCDF standard with the Climate and Forecast (CF) Metadata conventions, and the Open Geospatial Consortium Web Map Service standard. These open source libraries and open standards helped to implement the "Mission Support System", a Web Map Service based tool to support weather forecasting and flight planning during field campaigns. The tool has been implemented in Python and has also been released as open source (Rautenhaus et al., Geosci. Model Dev., 5, 55-71, 2012). In this presentation we discuss the usage of free and open source software for weather forecasting in the context of research flight planning, and highlight how the field campaign work benefits from using open source tools and open standards.

Cooking up an open source EMR for developing countries: OpenMRS - a recipe for successful collaboration.

PubMed

Mamlin, Burke W; Biondich, Paul G; Wolfe, Ben A; Fraser, Hamish; Jazayeri, Darius; Allen, Christian; Miranda, Justin; Tierney, William M

2006-01-01

Millions of people are continue to die each year from HIV/AIDS. The majority of infected persons (>95%) live in the developing world. A worthy response to this pandemic will require coordinated, scalable, and flexible information systems. We describe the OpenMRS system, an open source, collaborative effort that can serve as a foundation for EMR development in developing countries. We report our progress to date, lessons learned, and future directions.

Open source hardware and software platform for robotics and artificial intelligence applications

NASA Astrophysics Data System (ADS)

Liang, S. Ng; Tan, K. O.; Lai Clement, T. H.; Ng, S. K.; Mohammed, A. H. Ali; Mailah, Musa; Azhar Yussof, Wan; Hamedon, Zamzuri; Yussof, Zulkifli

2016-02-01

Recent developments in open source hardware and software platforms (Android, Arduino, Linux, OpenCV etc.) have enabled rapid development of previously expensive and sophisticated system within a lower budget and flatter learning curves for developers. Using these platform, we designed and developed a Java-based 3D robotic simulation system, with graph database, which is integrated in online and offline modes with an Android-Arduino based rubbish picking remote control car. The combination of the open source hardware and software system created a flexible and expandable platform for further developments in the future, both in the software and hardware areas, in particular in combination with graph database for artificial intelligence, as well as more sophisticated hardware, such as legged or humanoid robots.

Development and evaluation of a lightweight sensor system for aerial emission sampling from open area sources

EPA Science Inventory

A new sensor system for mobile and aerial emission sampling was developed for open area pollutant sources, such as prescribed forest burns. The sensor system, termed “Kolibri”, consists of multiple low-cost air quality sensors measuring CO2, CO, samplers for particulate matter wi...

Development and evaluation of a lightweight sensor system for aerial emission sampling from open area sources (Abstract)

EPA Science Inventory

A new sensor system for mobile and aerial emission sampling was developed for open area pollutant sources, such as prescribed forest burns. The sensor system, termed “Kolibri”, consists of multiple low-cost air quality sensors measuring CO2, CO, samplers for particulate matter wi...

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…

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.

Integrating open-source software applications to build molecular dynamics systems.

PubMed

Allen, Bruce M; Predecki, Paul K; Kumosa, Maciej

2014-04-05

Three open-source applications, NanoEngineer-1, packmol, and mis2lmp are integrated using an open-source file format to quickly create molecular dynamics (MD) cells for simulation. The three software applications collectively make up the open-source software (OSS) suite known as MD Studio (MDS). The software is validated through software engineering practices and is verified through simulation of the diglycidyl ether of bisphenol-a and isophorone diamine (DGEBA/IPD) system. Multiple simulations are run using the MDS software to create MD cells, and the data generated are used to calculate density, bulk modulus, and glass transition temperature of the DGEBA/IPD system. Simulation results compare well with published experimental and numerical results. The MDS software prototype confirms that OSS applications can be analyzed against real-world research requirements and integrated to create a new capability. Copyright © 2014 Wiley Periodicals, Inc.

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

EPA Science Inventory

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 ...

Completeness and overlap in open access systems: Search engines, aggregate institutional repositories and physics-related open sources

PubMed Central

Wu, Tai-luan; Tseng, Ling-li

2017-01-01

This study examines the completeness and overlap of coverage in physics of six open access scholarly communication systems, including two search engines (Google Scholar and Microsoft Academic), two aggregate institutional repositories (OAIster and OpenDOAR), and two physics-related open sources (arXiv.org and Astrophysics Data System). The 2001–2013 Nobel Laureates in Physics served as the sample. Bibliographic records of their publications were retrieved and downloaded from each system, and a computer program was developed to perform the analytical tasks of sorting, comparison, elimination, aggregation and statistical calculations. Quantitative analyses and cross-referencing were performed to determine the completeness and overlap of the system coverage of the six open access systems. The results may enable scholars to select an appropriate open access system as an efficient scholarly communication channel, and academic institutions may build institutional repositories or independently create citation index systems in the future. Suggestions on indicators and tools for academic assessment are presented based on the comprehensiveness assessment of each system. PMID:29267327

Building CHAOS: An Operating System for Livermore Linux Clusters

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

Garlick, J E; Dunlap, C M

2003-02-21

The Livermore Computing (LC) Linux Integration and Development Project (the Linux Project) produces and supports the Clustered High Availability Operating System (CHAOS), a cluster operating environment based on Red Hat Linux. Each CHAOS release begins with a set of requirements and ends with a formally tested, packaged, and documented release suitable for use on LC's production Linux clusters. One characteristic of CHAOS is that component software packages come from different sources under varying degrees of project control. Some are developed by the Linux Project, some are developed by other LC projects, some are external open source projects, and some aremore » commercial software packages. A challenge to the Linux Project is to adhere to release schedules and testing disciplines in a diverse, highly decentralized development environment. Communication channels are maintained for externally developed packages in order to obtain support, influence development decisions, and coordinate/understand release schedules. The Linux Project embraces open source by releasing locally developed packages under open source license, by collaborating with open source projects where mutually beneficial, and by preferring open source over proprietary software. Project members generally use open source development tools. The Linux Project requires system administrators and developers to work together to resolve problems that arise in production. This tight coupling of production and development is a key strategy for making a product that directly addresses LC's production requirements. It is another challenge to balance support and development activities in such a way that one does not overwhelm the other.« less

Koha@ESO Reloaded

NASA Astrophysics Data System (ADS)

Meakins, S.; Grothkopf, U.

2015-04-01

What happened to the ESO library's plan to use the open source software Koha as their new library system? After an intensive migration process, we finally went online in June 2012. We want to share some of our experiences, point out advantages and disadvantages of an open source system and show some highlights of Koha, especially the flexibility the system offers.

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

OpenFLUID: an open-source software environment for modelling fluxes in landscapes

NASA Astrophysics Data System (ADS)

Fabre, Jean-Christophe; Rabotin, Michaël; Crevoisier, David; Libres, Aline; Dagès, Cécile; Moussa, Roger; Lagacherie, Philippe; Raclot, Damien; Voltz, Marc

2013-04-01

Integrative landscape functioning has become a common concept in environmental management. Landscapes are complex systems where many processes interact in time and space. In agro-ecosystems, these processes are mainly physical processes, including hydrological-processes, biological processes and human activities. Modelling such systems requires an interdisciplinary approach, coupling models coming from different disciplines, developed by different teams. In order to support collaborative works, involving many models coupled in time and space for integrative simulations, an open software modelling platform is a relevant answer. OpenFLUID is an open source software platform for modelling landscape functioning, mainly focused on spatial fluxes. It provides an advanced object-oriented architecture allowing to i) couple models developed de novo or from existing source code, and which are dynamically plugged to the platform, ii) represent landscapes as hierarchical graphs, taking into account multi-scale, spatial heterogeneities and landscape objects connectivity, iii) run and explore simulations in many ways : using the OpenFLUID software interfaces for users (command line interface, graphical user interface), or using external applications such as GNU R through the provided ROpenFLUID package. OpenFLUID is developed in C++ and relies on open source libraries only (Boost, libXML2, GLib/GTK, OGR/GDAL, …). For modelers and developers, OpenFLUID provides a dedicated environment for model development, which is based on an open source toolchain, including the Eclipse editor, the GCC compiler and the CMake build system. OpenFLUID is distributed under the GPLv3 open source license, with a special exception allowing to plug existing models licensed under any license. It is clearly in the spirit of sharing knowledge and favouring collaboration in a community of modelers. OpenFLUID has been involved in many research applications, such as modelling of hydrological network transfer, diagnosis and prediction of water quality taking into account human activities, study of the effect of spatial organization on hydrological fluxes, modelling of surface-subsurface water exchanges, … At LISAH research unit, OpenFLUID is the supporting development platform of the MHYDAS model, which is a distributed model for agrosystems (Moussa et al., 2002, Hydrological Processes, 16, 393-412). OpenFLUID web site : http://www.openfluid-project.org

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.

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.

Chinese Localisation of Evergreen: An Open Source Integrated Library System

ERIC Educational Resources Information Center

Zou, Qing; Liu, Guoying

2009-01-01

Purpose: The purpose of this paper is to investigate various issues related to Chinese language localisation in Evergreen, an open source integrated library system (ILS). Design/methodology/approach: A Simplified Chinese version of Evergreen was implemented and tested and various issues such as encoding, indexing, searching, and sorting…

Online Textbooks Deliver Timely, Real-World Content

ERIC Educational Resources Information Center

Seidel, Kim

2009-01-01

Faced with the challenge of keeping up with the rapidly changing field of information systems, author and teacher John Gallaugher opted to write an open source textbook with a new online company, Flat World Knowledge (FWK). Gallaugher's open source textbook, "Information Systems: A Manager's Guide to Harnessing Technology", has an expected…

Of Birkenstocks and Wingtips: Open Source Licenses

ERIC Educational Resources Information Center

Gandel, Paul B.; Wheeler, Brad

2005-01-01

The notion of collaborating to create open source applications for higher education is rapidly gaining momentum. From course management systems to ERP financial systems, higher education institutions are working together to explore whether they can in fact build a better mousetrap. As Lois Brooks, of Stanford University, recently observed, the…

Open Source Cloud-Based Technologies for Bim

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

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

PubMed

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

2016-02-15

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

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

PubMed

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

2015-06-01

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

Open-Source Intelligence in the Czech Military: Knowledge System and Process Design

DTIC Science & Technology

2002-06-01

in Open-Source Intelligence OSINT, as one of the intelligence disciplines, bears some of the general problems of intelligence " business " OSINT...ADAPTING KNOWLEDGE MANAGEMENT THEORY TO THE CZECH MILITARY INTELLIGENCE Knowledge work is the core business of the military intelligence . As...NAVAL POSTGRADUATE SCHOOL Monterey, California THESIS Approved for public release; distribution is unlimited OPEN-SOURCE INTELLIGENCE IN THE

The State of Open Source Electronic Health Record Projects: A Software Anthropology Study

PubMed Central

2017-01-01

Background Electronic health records (EHR) are a key tool in managing and storing patients’ information. Currently, there are over 50 open source EHR systems available. Functionality and usability are important factors for determining the success of any system. These factors are often a direct reflection of the domain knowledge and developers’ motivations. However, few published studies have focused on the characteristics of free and open source software (F/OSS) EHR systems and none to date have discussed the motivation, knowledge background, and demographic characteristics of the developers involved in open source EHR projects. Objective This study analyzed the characteristics of prevailing F/OSS EHR systems and aimed to provide an understanding of the motivation, knowledge background, and characteristics of the developers. Methods This study identified F/OSS EHR projects on SourceForge and other websites from May to July 2014. Projects were classified and characterized by license type, downloads, programming languages, spoken languages, project age, development status, supporting materials, top downloads by country, and whether they were “certified” EHRs. Health care F/OSS developers were also surveyed using an online survey. Results At the time of the assessment, we uncovered 54 open source EHR projects, but only four of them had been successfully certified under the Office of the National Coordinator for Health Information Technology (ONC Health IT) Certification Program. In the majority of cases, the open source EHR software was downloaded by users in the United States (64.07%, 148,666/232,034), underscoring that there is a significant interest in EHR open source applications in the United States. A survey of EHR open source developers was conducted and a total of 103 developers responded to the online questionnaire. The majority of EHR F/OSS developers (65.3%, 66/101) are participating in F/OSS projects as part of a paid activity and only 25.7% (26/101) of EHR F/OSS developers are, or have been, health care providers in their careers. In addition, 45% (45/99) of developers do not work in the health care field. Conclusion The research presented in this study highlights some challenges that may be hindering the future of health care F/OSS. A minority of developers have been health care professionals, and only 55% (54/99) work in the health care field. This undoubtedly limits the ability of functional design of F/OSS EHR systems from being a competitive advantage over prevailing commercial EHR systems. Open source software seems to be a significant interest to many; however, given that only four F/OSS EHR systems are ONC-certified, this interest is unlikely to yield significant adoption of these systems in the United States. Although the Health Information Technology for Economic and Clinical Health (HITECH) act was responsible for a substantial infusion of capital into the EHR marketplace, the lack of a corporate entity in most F/OSS EHR projects translates to a marginal capacity to market the respective F/OSS system and to navigate certification. This likely has further disadvantaged F/OSS EHR adoption in the United States. PMID:28235750

Low Cost and Flexible UAV Deployment of Sensors

PubMed Central

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

2017-01-01

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

Low Cost and Flexible UAV Deployment of Sensors.

PubMed

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

2017-01-14

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

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

NASA Astrophysics Data System (ADS)

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

2011-12-01

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

The use of open source electronic health records within the federal safety net.

PubMed

Goldwater, Jason C; Kwon, Nancy J; Nathanson, Ashley; Muckle, Alison E; Brown, Alexa; Cornejo, Kerri

2014-01-01

To conduct a federally funded study that examines the acquisition, implementation and operation of open source electronic health records (EHR) within safety net medical settings, such as federally qualified health centers (FQHC). The study was conducted by the National Opinion Research Center (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 West Virginia, California and Arizona FQHC that were currently using an open source EHR. Five of the six sites that were chosen as part of the study found a number of advantages in the use of their open source EHR system, such as utilizing a large community of users and developers to modify their EHR to fit the needs of their provider and patient communities, and lower acquisition and implementation costs as compared to a commercial system. Despite these advantages, many of the informants and site visit participants felt that widespread dissemination and use of open source was restrained due to a negative connotation regarding this type of software. In addition, a number of participants stated that there is a necessary level of technical acumen needed within the FQHC to make an open source EHR effective. An open source EHR provides advantages for FQHC that have limited resources to acquire and implement an EHR, but additional study is needed to evaluate its overall effectiveness.

Open source electronic health records and chronic disease management

PubMed Central

Goldwater, Jason C; Kwon, Nancy J; Nathanson, Ashley; Muckle, Alison E; Brown, Alexa; Cornejo, Kerri

2014-01-01

Objective 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). Methods and Materials 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. Results 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. Discussion 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. Conclusions 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. PMID:23813566

Open Energy Info (OpenEI) (Fact Sheet)

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

Not Available

2010-12-01

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

Open source data assimilation framework for hydrological modeling

NASA Astrophysics Data System (ADS)

Ridler, Marc; Hummel, Stef; van Velzen, Nils; Katrine Falk, Anne; Madsen, Henrik

2013-04-01

An open-source data assimilation framework is proposed for hydrological modeling. Data assimilation (DA) in hydrodynamic and hydrological forecasting systems has great potential to improve predictions and improve model result. The basic principle is to incorporate measurement information into a model with the aim to improve model results by error minimization. Great strides have been made to assimilate traditional in-situ measurements such as discharge, soil moisture, hydraulic head and snowpack into hydrologic models. More recently, remotely sensed data retrievals of soil moisture, snow water equivalent or snow cover area, surface water elevation, terrestrial water storage and land surface temperature have been successfully assimilated in hydrological models. The assimilation algorithms have become increasingly sophisticated to manage measurement and model bias, non-linear systems, data sparsity (time & space) and undetermined system uncertainty. It is therefore useful to use a pre-existing DA toolbox such as OpenDA. OpenDA is an open interface standard for (and free implementation of) a set of tools to quickly implement DA and calibration for arbitrary numerical models. The basic design philosophy of OpenDA is to breakdown DA into a set of building blocks programmed in object oriented languages. To implement DA, a model must interact with OpenDA to create model instances, propagate the model, get/set variables (or parameters) and free the model once DA is completed. An open-source interface for hydrological models exists capable of all these tasks: OpenMI. OpenMI is an open source standard interface already adopted by key hydrological model providers. It defines a universal approach to interact with hydrological models during simulation to exchange data during runtime, thus facilitating the interactions between models and data sources. The interface is flexible enough so that models can interact even if the model is coded in a different language, represent processes from a different domain or have different spatial and temporal resolutions. An open source framework that bridges OpenMI and OpenDA is presented. The framework provides a generic and easy means for any OpenMI compliant model to assimilate observation measurements. An example test case will be presented using MikeSHE, and OpenMI compliant fully coupled integrated hydrological model that can accurately simulate the feedback dynamics of overland flow, unsaturated zone and saturated zone.

Applying Open Source Game Engine for Building Visual Simulation Training System of Fire Fighting

NASA Astrophysics Data System (ADS)

Yuan, Diping; Jin, Xuesheng; Zhang, Jin; Han, Dong

There's a growing need for fire departments to adopt a safe and fair method of training to ensure that the firefighting commander is in a position to manage a fire incident. Visual simulation training systems, with their ability to replicate and interact with virtual fire scenarios through the use of computer graphics or VR, become an effective and efficient method for fire ground education. This paper describes the system architecture and functions of a visual simulated training system of fire fighting on oil storage, which adopting Delat3D, a open source game and simulation engine, to provide realistic 3D views. It presents that using open source technology provides not only the commercial-level 3D effects but also a great reduction of cost.

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

PubMed Central

Zolfo, Maria; Diro, Ermias

2017-01-01

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

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

NASA Astrophysics Data System (ADS)

Melton, R.; Thomas, J.

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

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

PubMed

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

2007-11-01

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

Open Source Solutions for Libraries: ABCD vs Koha

ERIC Educational Resources Information Center

Macan, Bojan; Fernandez, Gladys Vanesa; Stojanovski, Jadranka

2013-01-01

Purpose: The purpose of this study is to present an overview of the two open source (OS) integrated library systems (ILS)--Koha and ABCD (ISIS family), to compare their "next-generation library catalog" functionalities, and to give comparison of other important features available through ILS modules. Design/methodology/approach: Two open source…

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.

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.

Application of Open-Source Enterprise Information System Modules: An Empirical Study

ERIC Educational Resources Information Center

Lee, Sang-Heui

2010-01-01

Although there have been a number of studies on large scale implementation of proprietary enterprise information systems (EIS), open-source software (OSS) for EIS has received limited attention in spite of its potential as a disruptive innovation. Cost saving is the main driver for adopting OSS among the other possible benefits including security…

Fac-Back-OPAC: An Open Source Interface to Your Library System

ERIC Educational Resources Information Center

Beccaria, Mike; Scott, Dan

2007-01-01

The new Fac-Back-OPAC (a faceted backup OPAC) is built on code that was originally developed by Casey Durfee in February 2007. It represents the convergence of two prominent trends in library tools: the decoupling of discovery tools from the traditional integrated library system (ILS) and the use of readily available open source components to…

The State of Open Source Electronic Health Record Projects: A Software Anthropology Study.

PubMed

Alsaffar, Mona; Yellowlees, Peter; Odor, Alberto; Hogarth, Michael

2017-02-24

Electronic health records (EHR) are a key tool in managing and storing patients' information. Currently, there are over 50 open source EHR systems available. Functionality and usability are important factors for determining the success of any system. These factors are often a direct reflection of the domain knowledge and developers' motivations. However, few published studies have focused on the characteristics of free and open source software (F/OSS) EHR systems and none to date have discussed the motivation, knowledge background, and demographic characteristics of the developers involved in open source EHR projects. This study analyzed the characteristics of prevailing F/OSS EHR systems and aimed to provide an understanding of the motivation, knowledge background, and characteristics of the developers. This study identified F/OSS EHR projects on SourceForge and other websites from May to July 2014. Projects were classified and characterized by license type, downloads, programming languages, spoken languages, project age, development status, supporting materials, top downloads by country, and whether they were "certified" EHRs. Health care F/OSS developers were also surveyed using an online survey. At the time of the assessment, we uncovered 54 open source EHR projects, but only four of them had been successfully certified under the Office of the National Coordinator for Health Information Technology (ONC Health IT) Certification Program. In the majority of cases, the open source EHR software was downloaded by users in the United States (64.07%, 148,666/232,034), underscoring that there is a significant interest in EHR open source applications in the United States. A survey of EHR open source developers was conducted and a total of 103 developers responded to the online questionnaire. The majority of EHR F/OSS developers (65.3%, 66/101) are participating in F/OSS projects as part of a paid activity and only 25.7% (26/101) of EHR F/OSS developers are, or have been, health care providers in their careers. In addition, 45% (45/99) of developers do not work in the health care field. The research presented in this study highlights some challenges that may be hindering the future of health care F/OSS. A minority of developers have been health care professionals, and only 55% (54/99) work in the health care field. This undoubtedly limits the ability of functional design of F/OSS EHR systems from being a competitive advantage over prevailing commercial EHR systems. Open source software seems to be a significant interest to many; however, given that only four F/OSS EHR systems are ONC-certified, this interest is unlikely to yield significant adoption of these systems in the United States. Although the Health Information Technology for Economic and Clinical Health (HITECH) act was responsible for a substantial infusion of capital into the EHR marketplace, the lack of a corporate entity in most F/OSS EHR projects translates to a marginal capacity to market the respective F/OSS system and to navigate certification. This likely has further disadvantaged F/OSS EHR adoption in the United States. ©Mona Alsaffar, Peter Yellowlees, Alberto Odor, Michael Hogarth. Originally published in JMIR Medical Informatics (http://medinform.jmir.org), 24.02.2017.

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.

Projector-Camera Systems for Immersive Training

DTIC Science & Technology

2006-01-01

average to a sequence of 100 captured distortion corrected images. The OpenCV library [ OpenCV ] was used for camera calibration. To correct for...rendering application [Treskunov, Pair, and Swartout, 2004]. It was transposed to take into account different matrix conventions between OpenCV and...Screen Imperfections. Proc. Workshop on Projector-Camera Systems (PROCAMS), Nice, France, IEEE. OpenCV : Open Source Computer Vision. [Available

The open-source neutral-mass spectrometer on Atmosphere Explorer-C, -D, and -E.

NASA Technical Reports Server (NTRS)

Nier, A. O.; Potter, W. E.; Hickman, D. R.; Mauersberger, K.

1973-01-01

The open-source mass spectrometer will be used to obtain the number densities of the neutral atmospheric gases in the mass range 1 to 48 amu at the satellite location. The ion source has been designed to allow gas particles to enter the ionizing region with the minimum practicable number of prior collisions with surfaces. This design minimizes the loss of atomic oxygen and other reactive species due to reactions with the walls of the ion source. The principal features of the open-source spectrometer and the laboratory calibration system are discussed.

NASA's Core Trajectory Sub-System Project: Using JBoss Enterprise Middleware for Building Software Systems Used to Support Spacecraft Trajectory Operations

NASA Technical Reports Server (NTRS)

Stensrud, Kjell C.; Hamm, Dustin

2007-01-01

NASA's Johnson Space Center (JSC) / Flight Design and Dynamics Division (DM) has prototyped the use of Open Source middleware technology for building its next generation spacecraft mission support system. This is part of a larger initiative to use open standards and open source software as building blocks for future mission and safety critical systems. JSC is hoping to leverage standardized enterprise architectures, such as Java EE, so that its internal software development efforts can be focused on the core aspects of their problem domain. This presentation will outline the design and implementation of the Trajectory system and the lessons learned during the exercise.

Low cost and open source multi-fluorescence imaging system for teaching and research in biology and bioengineering.

PubMed

Nuñez, Isaac; Matute, Tamara; Herrera, Roberto; Keymer, Juan; Marzullo, Timothy; Rudge, Timothy; Federici, Fernán

2017-01-01

The advent of easy-to-use open source microcontrollers, off-the-shelf electronics and customizable manufacturing technologies has facilitated the development of inexpensive scientific devices and laboratory equipment. In this study, we describe an imaging system that integrates low-cost and open-source hardware, software and genetic resources. The multi-fluorescence imaging system consists of readily available 470 nm LEDs, a Raspberry Pi camera and a set of filters made with low cost acrylics. This device allows imaging in scales ranging from single colonies to entire plates. We developed a set of genetic components (e.g. promoters, coding sequences, terminators) and vectors following the standard framework of Golden Gate, which allowed the fabrication of genetic constructs in a combinatorial, low cost and robust manner. In order to provide simultaneous imaging of multiple wavelength signals, we screened a series of long stokes shift fluorescent proteins that could be combined with cyan/green fluorescent proteins. We found CyOFP1, mBeRFP and sfGFP to be the most compatible set for 3-channel fluorescent imaging. We developed open source Python code to operate the hardware to run time-lapse experiments with automated control of illumination and camera and a Python module to analyze data and extract meaningful biological information. To demonstrate the potential application of this integral system, we tested its performance on a diverse range of imaging assays often used in disciplines such as microbial ecology, microbiology and synthetic biology. We also assessed its potential use in a high school environment to teach biology, hardware design, optics, and programming. Together, these results demonstrate the successful integration of open source hardware, software, genetic resources and customizable manufacturing to obtain a powerful, low cost and robust system for education, scientific research and bioengineering. All the resources developed here are available under open source licenses.

Low cost and open source multi-fluorescence imaging system for teaching and research in biology and bioengineering

PubMed Central

Herrera, Roberto; Keymer, Juan; Marzullo, Timothy; Rudge, Timothy

2017-01-01

The advent of easy-to-use open source microcontrollers, off-the-shelf electronics and customizable manufacturing technologies has facilitated the development of inexpensive scientific devices and laboratory equipment. In this study, we describe an imaging system that integrates low-cost and open-source hardware, software and genetic resources. The multi-fluorescence imaging system consists of readily available 470 nm LEDs, a Raspberry Pi camera and a set of filters made with low cost acrylics. This device allows imaging in scales ranging from single colonies to entire plates. We developed a set of genetic components (e.g. promoters, coding sequences, terminators) and vectors following the standard framework of Golden Gate, which allowed the fabrication of genetic constructs in a combinatorial, low cost and robust manner. In order to provide simultaneous imaging of multiple wavelength signals, we screened a series of long stokes shift fluorescent proteins that could be combined with cyan/green fluorescent proteins. We found CyOFP1, mBeRFP and sfGFP to be the most compatible set for 3-channel fluorescent imaging. We developed open source Python code to operate the hardware to run time-lapse experiments with automated control of illumination and camera and a Python module to analyze data and extract meaningful biological information. To demonstrate the potential application of this integral system, we tested its performance on a diverse range of imaging assays often used in disciplines such as microbial ecology, microbiology and synthetic biology. We also assessed its potential use in a high school environment to teach biology, hardware design, optics, and programming. Together, these results demonstrate the successful integration of open source hardware, software, genetic resources and customizable manufacturing to obtain a powerful, low cost and robust system for education, scientific research and bioengineering. All the resources developed here are available under open source licenses. PMID:29140977

Note: Tormenta: An open source Python-powered control software for camera based optical microscopy.

PubMed

Barabas, Federico M; Masullo, Luciano A; Stefani, Fernando D

2016-12-01

Until recently, PC control and synchronization of scientific instruments was only possible through closed-source expensive frameworks like National Instruments' LabVIEW. Nowadays, efficient cost-free alternatives are available in the context of a continuously growing community of open-source software developers. Here, we report on Tormenta, a modular open-source software for the control of camera-based optical microscopes. Tormenta is built on Python, works on multiple operating systems, and includes some key features for fluorescence nanoscopy based on single molecule localization.

Note: Tormenta: An open source Python-powered control software for camera based optical microscopy

NASA Astrophysics Data System (ADS)

Barabas, Federico M.; Masullo, Luciano A.; Stefani, Fernando D.

2016-12-01

Until recently, PC control and synchronization of scientific instruments was only possible through closed-source expensive frameworks like National Instruments' LabVIEW. Nowadays, efficient cost-free alternatives are available in the context of a continuously growing community of open-source software developers. Here, we report on Tormenta, a modular open-source software for the control of camera-based optical microscopes. Tormenta is built on Python, works on multiple operating systems, and includes some key features for fluorescence nanoscopy based on single molecule localization.

Impacts and Viability of Open Source Software on Earth Science Metadata Clearing House and Service Registry Applications

NASA Astrophysics Data System (ADS)

Pilone, D.; Cechini, M. F.; Mitchell, A.

2011-12-01

Earth Science applications typically deal with large amounts of data and high throughput rates, if not also high transaction rates. While Open Source is frequently used for smaller scientific applications, large scale, highly available systems frequently fall back to "enterprise" class solutions like Oracle RAC or commercial grade JEE Application Servers. NASA's Earth Observing System Data and Information System (EOSDIS) provides end-to-end capabilities for managing NASA's Earth science data from multiple sources - satellites, aircraft, field measurements, and various other programs. A core capability of EOSDIS, the Earth Observing System (EOS) Clearinghouse (ECHO), is a highly available search and order clearinghouse of over 100 million pieces of science data that has evolved from its early R&D days to a fully operational system. Over the course of this maturity ECHO has largely transitioned from commercial frameworks, databases, and operating systems to Open Source solutions...and in some cases, back. In this talk we discuss the progression of our technological solutions and our lessons learned in the areas of: ? High performance, large scale searching solutions ? GeoSpatial search capabilities and dealing with multiple coordinate systems ? Search and storage of variable format source (science) data ? Highly available deployment solutions ? Scalable (elastic) solutions to visual searching and image handling Throughout the evolution of the ECHO system we have had to evaluate solutions with respect to performance, cost, developer productivity, reliability, and maintainability in the context of supporting global science users. Open Source solutions have played a significant role in our architecture and development but several critical commercial components remain (or have been reinserted) to meet our operational demands.

Open-source point-of-care electronic medical records for use in resource-limited settings: systematic review and questionnaire surveys

PubMed Central

Bru, Juan; Berger, Christopher A

2012-01-01

Background Point-of-care electronic medical records (EMRs) are a key tool to manage chronic illness. Several EMRs have been developed for use in treating HIV and tuberculosis, but their applicability to primary care, technical requirements and clinical functionalities are largely unknown. Objectives This study aimed to address the needs of clinicians from resource-limited settings without reliable internet access who are considering adopting an open-source EMR. Study eligibility criteria Open-source point-of-care EMRs suitable for use in areas without reliable internet access. Study appraisal and synthesis methods The authors conducted a comprehensive search of all open-source EMRs suitable for sites without reliable internet access. The authors surveyed clinician users and technical implementers from a single site and technical developers of each software product. The authors evaluated availability, cost and technical requirements. Results The hardware and software for all six systems is easily available, but they vary considerably in proprietary components, installation requirements and customisability. Limitations This study relied solely on self-report from informants who developed and who actively use the included products. Conclusions and implications of key findings Clinical functionalities vary greatly among the systems, and none of the systems yet meet minimum requirements for effective implementation in a primary care resource-limited setting. The safe prescribing of medications is a particular concern with current tools. The dearth of fully functional EMR systems indicates a need for a greater emphasis by global funding agencies to move beyond disease-specific EMR systems and develop a universal open-source health informatics platform. PMID:22763661

The use of open source electronic health records within the federal safety net

PubMed Central

Goldwater, Jason C; Kwon, Nancy J; Nathanson, Ashley; Muckle, Alison E; Brown, Alexa; Cornejo, Kerri

2014-01-01

Objective To conduct a federally funded study that examines the acquisition, implementation and operation of open source electronic health records (EHR) within safety net medical settings, such as federally qualified health centers (FQHC). Methods and materials The study was conducted by the National Opinion Research Center (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 West Virginia, California and Arizona FQHC that were currently using an open source EHR. Results Five of the six sites that were chosen as part of the study found a number of advantages in the use of their open source EHR system, such as utilizing a large community of users and developers to modify their EHR to fit the needs of their provider and patient communities, and lower acquisition and implementation costs as compared to a commercial system. Discussion Despite these advantages, many of the informants and site visit participants felt that widespread dissemination and use of open source was restrained due to a negative connotation regarding this type of software. In addition, a number of participants stated that there is a necessary level of technical acumen needed within the FQHC to make an open source EHR effective. Conclusions An open source EHR provides advantages for FQHC that have limited resources to acquire and implement an EHR, but additional study is needed to evaluate its overall effectiveness. PMID:23744787

Charting a Course through CORAL: Texas A&M University Libraries' Experience Implementing an Open-Source Electronic Resources Management System

ERIC Educational Resources Information Center

Hartnett, Eric; Beh, Eugenia; Resnick, Taryn; Ugaz, Ana; Tabacaru, Simona

2013-01-01

In 2010, after two previous unsuccessful attempts at electronic resources management system (ERMS) implementation, Texas A&M University (TAMU) Libraries set out once again to find an ERMS that would fit its needs. After surveying the field, TAMU Libraries selected the University of Notre Dame Hesburgh Libraries-developed, open-source ERMS,…

Cultural Geography Model Validation

DTIC Science & Technology

2010-03-01

the Cultural Geography Model (CGM), a government owned, open source multi - agent system utilizing Bayesian networks, queuing systems, the Theory of...referent determined either from theory or SME opinion. 4. CGM Overview The CGM is a government-owned, open source, data driven multi - agent social...HSCB, validation, social network analysis ABSTRACT: In the current warfighting environment , the military needs robust modeling and simulation (M&S

Tank Information System (tis): a Case Study in Migrating Web Mapping Application from Flex to Dojo for Arcgis Server and then to Open Source

NASA Astrophysics Data System (ADS)

Pulsani, B. R.

2017-11-01

Tank Information System is a web application which provides comprehensive information about minor irrigation tanks of Telangana State. As part of the program, a web mapping application using Flex and ArcGIS server was developed to make the data available to the public. In course of time as Flex be-came outdated, a migration of the client interface to the latest JavaScript based technologies was carried out. Initially, the Flex based application was migrated to ArcGIS JavaScript API using Dojo Toolkit. Both the client applications used published services from ArcGIS server. To check the migration pattern from proprietary to open source, the JavaScript based ArcGIS application was later migrated to OpenLayers and Dojo Toolkit which used published service from GeoServer. The migration pattern noticed in the study especially emphasizes upon the use of Dojo Toolkit and PostgreSQL database for ArcGIS server so that migration to open source could be performed effortlessly. The current ap-plication provides a case in study which could assist organizations in migrating their proprietary based ArcGIS web applications to open source. Furthermore, the study reveals cost benefits of adopting open source against commercial software's.

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

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

An Open-source Meteorological Operational System and its Installation in Portuguese- speaking Countries

NASA Astrophysics Data System (ADS)

Almeida, W. G.; Ferreira, A. L.; Mendes, M. V.; Ribeiro, A.; Yoksas, T.

2007-05-01

CPTEC, a division of Brazil’s INPE, has been using several open-source software packages for a variety of tasks in its Data Division. Among these tools are ones traditionally used in research and educational communities such as GrADs (Grid Analysis and Display System from the Center for Ocean-Land-Atmosphere Studies (COLA)), the Local Data Manager (LDM) and GEMPAK (from Unidata), andl operational tools such the Automatic File Distributor (AFD) that are popular among National Meteorological Services. In addition, some tools developed locally at CPTEC are also being made available as open-source packages. One package is being used to manage the data from Automatic Weather Stations that INPE operates. This system uses only open- source tools such as MySQL database, PERL scripts and Java programs for web access, and Unidata’s Internet Data Distribution (IDD) system and AFD for data delivery. All of these packages are get bundled into a low-cost and easy to install and package called the Meteorological Data Operational System. Recently, in a cooperation with the SICLIMAD project, this system has been modified for use by Portuguese- speaking countries in Africa to manage data from many Automatic Weather Stations that are being installed in these countries under SICLIMAD sponsorship. In this presentation we describe the tools included-in and and architecture-of the Meteorological Data Operational System.

Open-Source Automated Mapping Four-Point Probe.

PubMed

Chandra, Handy; Allen, Spencer W; Oberloier, Shane W; Bihari, Nupur; Gwamuri, Jephias; Pearce, Joshua M

2017-01-26

Scientists have begun using self-replicating rapid prototyper (RepRap) 3-D printers to manufacture open source digital designs of scientific equipment. This approach is refined here to develop a novel instrument capable of performing automated large-area four-point probe measurements. The designs for conversion of a RepRap 3-D printer to a 2-D open source four-point probe (OS4PP) measurement device are detailed for the mechanical and electrical systems. Free and open source software and firmware are developed to operate the tool. The OS4PP was validated against a wide range of discrete resistors and indium tin oxide (ITO) samples of different thicknesses both pre- and post-annealing. The OS4PP was then compared to two commercial proprietary systems. Results of resistors from 10 to 1 MΩ show errors of less than 1% for the OS4PP. The 3-D mapping of sheet resistance of ITO samples successfully demonstrated the automated capability to measure non-uniformities in large-area samples. The results indicate that all measured values are within the same order of magnitude when compared to two proprietary measurement systems. In conclusion, the OS4PP system, which costs less than 70% of manual proprietary systems, is comparable electrically while offering automated 100 micron positional accuracy for measuring sheet resistance over larger areas.

Finding Resolution for the Responsible Transparency of Economic Models in Health and Medicine.

PubMed

Padula, William V; McQueen, Robert Brett; Pronovost, Peter J

2017-11-01

The Second Panel on Cost-Effectiveness in Health and Medicine recommendations for conduct, methodological practices, and reporting of cost-effectiveness analyses has a number of questions unanswered with respect to the implementation of transparent, open source code interface for economic models. The possibility of making economic model source code could be positive and progressive for the field; however, several unintended consequences of this system should be first considered before complete implementation of this model. First, there is the concern regarding intellectual property rights that modelers have to their analyses. Second, the open source code could make analyses more accessible to inexperienced modelers, leading to inaccurate or misinterpreted results. We propose several resolutions to these concerns. The field should establish a licensing system of open source code such that the model originators maintain control of the code use and grant permissions to other investigators who wish to use it. The field should also be more forthcoming towards the teaching of cost-effectiveness analysis in medical and health services education so that providers and other professionals are familiar with economic modeling and able to conduct analyses with open source code. These types of unintended consequences need to be fully considered before the field's preparedness to move forward into an era of model transparency with open source code.

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 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 Rapid Computer Aided Control System Design Toolchain Using Scilab, Scicos and RTAI Linux

NASA Astrophysics Data System (ADS)

Bouchpan-Lerust-Juéry, L.

2007-08-01

Current and next generation on-board computer systems tend to implement real-time embedded control applications (e.g. Attitude and Orbit Control Subsystem (AOCS), Packet Utililization Standard (PUS), spacecraft autonomy . . . ) which must meet high standards of Reliability and Predictability as well as Safety. All these requirements require a considerable amount of effort and cost for Space Sofware Industry. This paper, in a first part, presents a free Open Source integrated solution to develop RTAI applications from analysis, design, simulation and direct implementation using code generation based on Open Source and in its second part summarises this suggested approach, its results and the conclusion for further work.

OSIRIX: open source multimodality image navigation software

NASA Astrophysics Data System (ADS)

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

2005-04-01

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

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

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

PubMed

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

2016-10-01

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

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.

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.

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.

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

OOSTethys - Open Source Software for the Global Earth Observing Systems of Systems

NASA Astrophysics Data System (ADS)

Bridger, E.; Bermudez, L. E.; Maskey, M.; Rueda, C.; Babin, B. L.; Blair, R.

2009-12-01

An open source software project is much more than just picking the right license, hosting modular code and providing effective documentation. Success in advancing in an open collaborative way requires that the process match the expected code functionality to the developer's personal expertise and organizational needs as well as having an enthusiastic and responsive core lead group. We will present the lessons learned fromOOSTethys , which is a community of software developers and marine scientists who develop open source tools, in multiple languages, to integrate ocean observing systems into an Integrated Ocean Observing System (IOOS). OOSTethys' goal is to dramatically reduce the time it takes to install, adopt and update standards-compliant web services. OOSTethys has developed servers, clients and a registry. Open source PERL, PYTHON, JAVA and ASP tool kits and reference implementations are helping the marine community publish near real-time observation data in interoperable standard formats. In some cases publishing an OpenGeospatial Consortium (OGC), Sensor Observation Service (SOS) from NetCDF files or a database or even CSV text files could take only minutes depending on the skills of the developer. OOSTethys is also developing an OGC standard registry, Catalog Service for Web (CSW). This open source CSW registry was implemented to easily register and discover SOSs using ISO 19139 service metadata. A web interface layer over the CSW registry simplifies the registration process by harvesting metadata describing the observations and sensors from the “GetCapabilities” response of SOS. OPENIOOS is the web client, developed in PERL to visualize the sensors in the SOS services. While the number of OOSTethys software developers is small, currently about 10 around the world, the number of OOSTethys toolkit implementers is larger and growing and the ease of use has played a large role in spreading the use of interoperable standards compliant web services widely in the marine community.

40 CFR Table 7 to Subpart Ffff of... - Requirements for Wastewater Streams and Liquid Streams in Open Systems Within an MCPU

Code of Federal Regulations, 2010 CFR

2010-07-01

... Liquid Streams in Open Systems Within an MCPU 7 Table 7 to Subpart FFFF of Part 63 Protection of... FOR HAZARDOUS AIR POLLUTANTS FOR SOURCE CATEGORIES National Emission Standards for Hazardous Air... of Part 63—Requirements for Wastewater Streams and Liquid Streams in Open Systems Within an MCPU As...

EPRI and Schneider Electric Demonstrate Distributed Resource Communications

Science.gov Websites

Electric Power Research Institute (EPRI) is designing, building, and testing a flexible, open-source Schneider Electric ADMS, open software platforms, an open-platform home energy management system

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

Meurer, Aaron; Smith, Christopher P.; Paprocki, Mateusz

Here, SymPy is a full featured computer algebra system (CAS) written in the Python programming language. It is open source, being licensed under the extremely permissive 3-clause BSD license. SymPy was started by Ondrej Certik in 2005, and it has since grown into a large open source project, with over 500 contributors.

Efficient radiologic reading environment by using an open-source macro program as connection software.

PubMed

Lee, Young Han

2012-01-01

The objectives are (1) to introduce an easy open-source macro program as connection software and (2) to illustrate the practical usages in radiologic reading environment by simulating the radiologic reading process. The simulation is a set of radiologic reading process to do a practical task in the radiologic reading room. The principal processes are: (1) to view radiologic images on the Picture Archiving and Communicating System (PACS), (2) to connect the HIS/EMR (Hospital Information System/Electronic Medical Record) system, (3) to make an automatic radiologic reporting system, and (4) to record and recall information of interesting cases. This simulation environment was designed by using open-source macro program as connection software. The simulation performed well on the Window-based PACS workstation. Radiologists practiced the steps of the simulation comfortably by utilizing the macro-powered radiologic environment. This macro program could automate several manual cumbersome steps in the radiologic reading process. This program successfully acts as connection software for the PACS software, EMR/HIS, spreadsheet, and other various input devices in the radiologic reading environment. A user-friendly efficient radiologic reading environment could be established by utilizing open-source macro program as connection software. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

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

Review on open source operating systems for internet of things

NASA Astrophysics Data System (ADS)

Wang, Zhengmin; Li, Wei; Dong, Huiliang

2017-08-01

Internet of Things (IoT) is an environment in which everywhere and every device became smart in a smart world. Internet of Things is growing vastly; it is an integrated system of uniquely identifiable communicating devices which exchange information in a connected network to provide extensive services. IoT devices have very limited memory, computational power, and power supply. Traditional operating systems (OS) have no way to meet the needs of IoT systems. In this paper, we thus analyze the challenges of IoT OS and survey applicable open source OSs.

General Mission Analysis Tool (GMAT)

NASA Technical Reports Server (NTRS)

Hughes, Steven P.

2007-01-01

The General Mission Analysis Tool (GMAT) is a space trajectory optimization and mission analysis system developed by NASA and private industry in the spirit of the NASA Mission. GMAT contains new technology and is a testbed for future technology development. The goal of the GMAT project is to develop new space trajectory optimization and mission design technology by working inclusively with ordinary people, universities, businesses, and other government organizations, and to share that technology in an open and unhindered way. GMAT is a free and open source software system licensed under the NASA Open Source Agreement: free for anyone to use in development of new mission concepts or to improve current missions, freely available in source code form for enhancement or further technology development.

Developing a GIS for CO2 analysis using lightweight, open source components

NASA Astrophysics Data System (ADS)

Verma, R.; Goodale, C. E.; Hart, A. F.; Kulawik, S. S.; Law, E.; Osterman, G. B.; Braverman, A.; Nguyen, H. M.; Mattmann, C. A.; Crichton, D. J.; Eldering, A.; Castano, R.; Gunson, M. R.

2012-12-01

There are advantages to approaching the realm of geographic information systems (GIS) using lightweight, open source components in place of a more traditional web map service (WMS) solution. Rapid prototyping, schema-less data storage, the flexible interchange of components, and open source community support are just some of the benefits. In our effort to develop an application supporting the geospatial and temporal rendering of remote sensing carbon-dioxide (CO2) data for the CO2 Virtual Science Data Environment project, we have connected heterogeneous open source components together to form a GIS. Utilizing widely popular open source components including the schema-less database MongoDB, Leaflet interactive maps, the HighCharts JavaScript graphing library, and Python Bottle web-services, we have constructed a system for rapidly visualizing CO2 data with reduced up-front development costs. These components can be aggregated together, resulting in a configurable stack capable of replicating features provided by more standard GIS technologies. The approach we have taken is not meant to replace the more established GIS solutions, but to instead offer a rapid way to provide GIS features early in the development of an application and to offer a path towards utilizing more capable GIS technology in the future.

Open-Source Automated Mapping Four-Point Probe

PubMed Central

Chandra, Handy; Allen, Spencer W.; Oberloier, Shane W.; Bihari, Nupur; Gwamuri, Jephias; Pearce, Joshua M.

2017-01-01

Scientists have begun using self-replicating rapid prototyper (RepRap) 3-D printers to manufacture open source digital designs of scientific equipment. This approach is refined here to develop a novel instrument capable of performing automated large-area four-point probe measurements. The designs for conversion of a RepRap 3-D printer to a 2-D open source four-point probe (OS4PP) measurement device are detailed for the mechanical and electrical systems. Free and open source software and firmware are developed to operate the tool. The OS4PP was validated against a wide range of discrete resistors and indium tin oxide (ITO) samples of different thicknesses both pre- and post-annealing. The OS4PP was then compared to two commercial proprietary systems. Results of resistors from 10 to 1 MΩ show errors of less than 1% for the OS4PP. The 3-D mapping of sheet resistance of ITO samples successfully demonstrated the automated capability to measure non-uniformities in large-area samples. The results indicate that all measured values are within the same order of magnitude when compared to two proprietary measurement systems. In conclusion, the OS4PP system, which costs less than 70% of manual proprietary systems, is comparable electrically while offering automated 100 micron positional accuracy for measuring sheet resistance over larger areas. PMID:28772471

Opening up Architectures of Software-Intensive Systems: A Functional Decomposition to Support System Comprehension

DTIC Science & Technology

2007-10-01

Architecture ................................................................................ 14 Figure 2. Eclipse Java Model...16 Figure 3. Eclipse Java Model at the Source Code Level...24 Figure 9. Java Source Code

XtalOpt  version r9: An open-source evolutionary algorithm for crystal structure prediction

DOE PAGES

Falls, Zackary; Lonie, David C.; Avery, Patrick; ...

2015-10-23

This is a new version of XtalOpt, an evolutionary algorithm for crystal structure prediction available for download from the CPC library or the XtalOpt website, http://xtalopt.github.io. XtalOpt is published under the Gnu Public License (GPL), which is an open source license that is recognized by the Open Source Initiative. We have detailed the new version incorporates many bug-fixes and new features here and predict the crystal structure of a system from its stoichiometry alone, using evolutionary algorithms.

Aerostat-lofted instrument and sampling method for determination of emissions from open area sources

EPA Science Inventory

An aerostat-borne instrument and sampling method was developed to characterize air samples from area sources, such as emissions from open burning. The 10 kg battery-powered instrument system, termed "the Flyer," is lofted with a helium-filled aerostat of 4 m nominal diameter and ...

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.

Distributed GIS Systems, Open Specifications and Interoperability: How do They Relate to the Sustainable Management of Natural Resources?

Treesearch

Rafael Moreno-Sanchez

2006-01-01

The aim of this is paper is to provide a conceptual framework for the session: “The role of web-based Geographic Information Systems in supporting sustainable management.” The concepts of sustainability, sustainable forest management, Web Services, Distributed Geographic Information Systems, interoperability, Open Specifications, and Open Source Software are defined...

Geowall: Investigations into low-cost stereo display technologies

USGS Publications Warehouse

Steinwand, Daniel R.; Davis, Brian; Weeks, Nathan

2003-01-01

Recently, the combination of new projection technology, fast, low-cost graphics cards, and Linux-powered personal computers has made it possible to provide a stereoprojection and stereoviewing system that is much more affordable than previous commercial solutions. These Geowall systems are low-cost visualization systems built with commodity off-the-shelf components, run on open-source (and other) operating systems, and using open-source applications software. In short, they are ?Beowulf-class? visualization systems that provide a cost-effective way for the U. S. Geological Survey to broaden participation in the visualization community and view stereoimagery and three-dimensional models2.

A Tale of Two Observing Systems: Interoperability in the World of Microsoft Windows

NASA Astrophysics Data System (ADS)

Babin, B. L.; Hu, L.

2008-12-01

Louisiana Universities Marine Consortium's (LUMCON) and Dauphin Island Sea Lab's (DISL) Environmental Monitoring System provide a unified coastal ocean observing system. These two systems are mirrored to maintain autonomy while offering an integrated data sharing environment. Both systems collect data via Campbell Scientific Data loggers, store the data in Microsoft SQL servers, and disseminate the data in real- time on the World Wide Web via Microsoft Internet Information Servers and Active Server Pages (ASP). The utilization of Microsoft Windows technologies presented many challenges to these observing systems as open source tools for interoperability grow. The current open source tools often require the installation of additional software. In order to make data available through common standards formats, "home grown" software has been developed. One example of this is the development of software to generate xml files for transmission to the National Data Buoy Center (NDBC). OOSTethys partners develop, test and implement easy-to-use, open-source, OGC-compliant software., and have created a working prototype of networked, semantically interoperable, real-time data systems. Partnering with OOSTethys, we are developing a cookbook to implement OGC web services. The implementation will be written in ASP, will run in a Microsoft operating system environment, and will serve data via Sensor Observation Services (SOS). This cookbook will give observing systems running Microsoft Windows the tools to easily participate in the Open Geospatial Consortium (OGC) Oceans Interoperability Experiment (OCEANS IE).

Emission Measurements of Open Area Combustion Sources with an Unmanned Aerial System

EPA Science Inventory

miniaturized sensor/sampler system (“Kolibri”) on a six-motor, unmanned aerial system (UAS) was used to quantify emissions from open burning of obsolete military propellants. The UAS afforded the ability to sample plume emissions at altitude and from a safe distance ...

77 FR 21808 - Privacy Act of 1974; System of Records

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-11

... and open source records and commercial database. EXEMPTIONS CLAIMED FOR THE SYSTEM: The Attorney... notification procedures, the record access procedures, the contesting record procedures, the record source..., confidential sources, and victims of crimes. The offenses and alleged offenses associated with the individuals...

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

Gearhart, Jared Lee; Adair, Kristin Lynn; Durfee, Justin David.

When developing linear programming models, issues such as budget limitations, customer requirements, or licensing may preclude the use of commercial linear programming solvers. In such cases, one option is to use an open-source linear programming solver. A survey of linear programming tools was conducted to identify potential open-source solvers. From this survey, four open-source solvers were tested using a collection of linear programming test problems and the results were compared to IBM ILOG CPLEX Optimizer (CPLEX) [1], an industry standard. The solvers considered were: COIN-OR Linear Programming (CLP) [2], [3], GNU Linear Programming Kit (GLPK) [4], lp_solve [5] and Modularmore » In-core Nonlinear Optimization System (MINOS) [6]. As no open-source solver outperforms CPLEX, this study demonstrates the power of commercial linear programming software. CLP was found to be the top performing open-source solver considered in terms of capability and speed. GLPK also performed well but cannot match the speed of CLP or CPLEX. lp_solve and MINOS were considerably slower and encountered issues when solving several test problems.« less

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.

openECA Platform and Analytics Alpha Test Results

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

Robertson, Russell

The objective of the Open and Extensible Control and Analytics (openECA) Platform for Phasor Data project is to develop an open source software platform that significantly accelerates the production, use, and ongoing development of real-time decision support tools, automated control systems, and off-line planning systems that (1) incorporate high-fidelity synchrophasor data and (2) enhance system reliability while enabling the North American Electric Reliability Corporation (NERC) operating functions of reliability coordinator, transmission operator, and/or balancing authority to be executed more effectively.

openECA Platform and Analytics Beta Demonstration Results

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

Robertson, Russell

The objective of the Open and Extensible Control and Analytics (openECA) Platform for Phasor Data project is to develop an open source software platform that significantly accelerates the production, use, and ongoing development of real-time decision support tools, automated control systems, and off-line planning systems that (1) incorporate high-fidelity synchrophasor data and (2) enhance system reliability while enabling the North American Electric Reliability Corporation (NERC) operating functions of reliability coordinator, transmission operator, and/or balancing authority to be executed more effectively.

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

PubMed

Barre, Arnaud; Armand, Stéphane

2014-04-01

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

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

Introduction to an Open Source Internet-Based Testing Program for Medical Student Examinations

PubMed Central

2009-01-01

The author developed a freely available open source internet-based testing program for medical examination. PHP and Java script were used as the programming language and postgreSQL as the database management system on an Apache web server and Linux operating system. The system approach was that a super user inputs the items, each school administrator inputs the examinees' information, and examinees access the system. The examinee's score is displayed immediately after examination with item analysis. The set-up of the system beginning with installation is described. This may help medical professors to easily adopt an internet-based testing system for medical education. PMID:20046457

Introduction to an open source internet-based testing program for medical student examinations.

PubMed

Lee, Yoon-Hwan

2009-12-20

The author developed a freely available open source internet-based testing program for medical examination. PHP and Java script were used as the programming language and postgreSQL as the database management system on an Apache web server and Linux operating system. The system approach was that a super user inputs the items, each school administrator inputs the examinees' information, and examinees access the system. The examinee's score is displayed immediately after examination with item analysis. The set-up of the system beginning with installation is described. This may help medical professors to easily adopt an internet-based testing system for medical education.

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

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

Open Source and These United States

DTIC Science & Technology

1999-04-01

the ability of all participants to freely access the source code and keep abreast of progress. There can be no information hoarding on an open source... developed in this way depends upon ready and reliable communications. Just as the internet has increased the ability of people to exchange information...investment is maximized through long use and reuse. This process results in systems which harnesses the collaborative abilities of its user developers

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.

Tracking Clouds with low cost GNSS chips aided by the Arduino platform

NASA Astrophysics Data System (ADS)

Hameed, Saji; Realini, Eugenio; Ishida, Shinya

2016-04-01

The Global Navigation Satellite System (GNSS) is a constellation of satellites that is used to provide geo-positioning services. Besides this application, the GNSS system is important for a wide range of scientific and civilian applications. For example, GNSS systems are routinely used in civilian applications such as surveying and scientific applications such as the study of crustal deformation. Another important scientific application of GNSS system is in meteorological research. Here it is mainly used to determine the total water vapour content of the troposphere, hereafter Precipitable Water Vapor (PWV). However, both GNSS receivers and software have prohibitively high price due to a variety of reasons. To overcome this somewhat artificial barrier we are exploring the use of low-cost GNSS receivers along with open source GNSS software for scientific research, in particular for GNSS meteorology research. To achieve this aim, we have developed a custom Arduino compatible data logging board that is able to operate together with a specific low-cost single frequency GNSS receiver chip from NVS Technologies AG. We have also developed an open-source software bundle that includes a new Arduino core for the Atmel324p chip, which is the main processor used in our custom logger. We have also developed software code that enables data collection, logging and parsing of the GNSS data stream. Additionally we have comprehensively evaluated the low power characteristics of the GNSS receiver and logger boards. Currently we are exploring the use of several openly source or free to use for research software to map GNSS delays to PWV. These include the open source goGPS (http://www.gogps-project.org/) and gLAB (http://gage.upc.edu/gLAB) and the openly available GAMIT software from Massachusetts Institute of Technology (MIT). We note that all the firmware and software developed as part of this project is available on an open source license.

SymPy: Symbolic computing in python

DOE PAGES

Meurer, Aaron; Smith, Christopher P.; Paprocki, Mateusz; ...

2017-01-02

Here, SymPy is a full featured computer algebra system (CAS) written in the Python programming language. It is open source, being licensed under the extremely permissive 3-clause BSD license. SymPy was started by Ondrej Certik in 2005, and it has since grown into a large open source project, with over 500 contributors.

Critical Analysis on Open Source LMSs Using FCA

ERIC Educational Resources Information Center

Sumangali, K.; Kumar, Ch. Aswani

2013-01-01

The objective of this paper is to apply Formal Concept Analysis (FCA) to identify the best open source Learning Management System (LMS) for an E-learning environment. FCA is a mathematical framework that represents knowledge derived from a formal context. In constructing the formal context, LMSs are treated as objects and their features as…

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

PubMed Central

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

2014-01-01

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

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.

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.

Low Power Switching for Antenna Reconfiguration

NASA Technical Reports Server (NTRS)

Bauhahn, Paul E. (Inventor); Becker, Robert C. (Inventor); Meyers, David W. (Inventor); Muldoon, Kelly P. (Inventor)

2008-01-01

Methods and systems for low power switching are provided. In one embodiment, an optical switching system is provided. The system comprises at least one optically controlled switch adapted to maintain one of an open state and a closed state based on an associated light signal; and at least one light source adapted to output the associated light signal to the at least one switch, wherein the at least one light source cycles the light signal on and off, wherein the at least one light source is cycled on for a sufficient duration of time and with a sufficient periodicity to maintain the optically controlled switch in one of an open state and a closed state.

OpenClimateGIS - A Web Service Providing Climate Model Data in Commonly Used Geospatial Formats

NASA Astrophysics Data System (ADS)

Erickson, T. A.; Koziol, B. W.; Rood, R. B.

2011-12-01

The goal of the OpenClimateGIS project is to make climate model datasets readily available in commonly used, modern geospatial formats used by GIS software, browser-based mapping tools, and virtual globes.The climate modeling community typically stores climate data in multidimensional gridded formats capable of efficiently storing large volumes of data (such as netCDF, grib) while the geospatial community typically uses flexible vector and raster formats that are capable of storing small volumes of data (relative to the multidimensional gridded formats). OpenClimateGIS seeks to address this difference in data formats by clipping climate data to user-specified vector geometries (i.e. areas of interest) and translating the gridded data on-the-fly into multiple vector formats. The OpenClimateGIS system does not store climate data archives locally, but rather works in conjunction with external climate archives that expose climate data via the OPeNDAP protocol. OpenClimateGIS provides a RESTful API web service for accessing climate data resources via HTTP, allowing a wide range of applications to access the climate data.The OpenClimateGIS system has been developed using open source development practices and the source code is publicly available. The project integrates libraries from several other open source projects (including Django, PostGIS, numpy, Shapely, and netcdf4-python).OpenClimateGIS development is supported by a grant from NOAA's Climate Program Office.

Towards open-source, low-cost haptics for surgery simulation.

PubMed

Suwelack, Stefan; Sander, Christian; Schill, Julian; Serf, Manuel; Danz, Marcel; Asfour, Tamim; Burger, Wolfgang; Dillmann, Rüdiger; Speidel, Stefanie

2014-01-01

In minimally invasive surgery (MIS), virtual reality (VR) training systems have become a promising education tool. However, the adoption of these systems in research and clinical settings is still limited by the high costs of dedicated haptics hardware for MIS. In this paper, we present ongoing research towards an open-source, low-cost haptic interface for MIS simulation. We demonstrate the basic mechanical design of the device, the sensor setup as well as its software integration.

The openEHR Java reference implementation project.

PubMed

Chen, Rong; Klein, Gunnar

2007-01-01

The openEHR foundation has developed an innovative design for interoperable and future-proof Electronic Health Record (EHR) systems based on a dual model approach with a stable reference information model complemented by archetypes for specific clinical purposes.A team from Sweden has implemented all the stable specifications in the Java programming language and donated the source code to the openEHR foundation. It was adopted as the openEHR Java Reference Implementation in March 2005 and released under open source licenses. This encourages early EHR implementation projects around the world and a number of groups have already started to use this code. The early Java implementation experience has also led to the publication of the openEHR Java Implementation Technology Specification. A number of design changes to the specifications and important minor corrections have been directly initiated by the implementation project over the last two years. The Java Implementation has been important for the validation and improvement of the openEHR design specifications and provides building blocks for future EHR systems.

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

Open Source Seismic Software in NOAA's Next Generation Tsunami Warning System

NASA Astrophysics Data System (ADS)

Hellman, S. B.; Baker, B. I.; Hagerty, M. T.; Leifer, J. M.; Lisowski, S.; Thies, D. A.; Donnelly, B. K.; Griffith, F. P.

2014-12-01

The Tsunami Information technology Modernization (TIM) is a project spearheaded by National Oceanic and Atmospheric Administration to update the United States' Tsunami Warning System software currently employed at the Pacific Tsunami Warning Center (Eva Beach, Hawaii) and the National Tsunami Warning Center (Palmer, Alaska). This entirely open source software project will integrate various seismic processing utilities with the National Weather Service Weather Forecast Office's core software, AWIPS2. For the real-time and near real-time seismic processing aspect of this project, NOAA has elected to integrate the open source portions of GFZ's SeisComP 3 (SC3) processing system into AWIPS2. To provide for better tsunami threat assessments we are developing open source tools for magnitude estimations (e.g., moment magnitude, energy magnitude, surface wave magnitude), detection of slow earthquakes with the Theta discriminant, moment tensor inversions (e.g. W-phase and teleseismic body waves), finite fault inversions, and array processing. With our reliance on common data formats such as QuakeML and seismic community standard messaging systems, all new facilities introduced into AWIPS2 and SC3 will be available as stand-alone tools or could be easily integrated into other real time seismic monitoring systems such as Earthworm, Antelope, etc. Additionally, we have developed a template based design paradigm so that the developer or scientist can efficiently create upgrades, replacements, and/or new metrics to the seismic data processing with only a cursory knowledge of the underlying SC3.

Exploring the Role of Value Networks for Software Innovation

NASA Astrophysics Data System (ADS)

Morgan, Lorraine; Conboy, Kieran

This paper describes a research-in-progress that aims to explore the applicability and implications of open innovation practices in two firms - one that employs agile development methods and another that utilizes open source software. The open innovation paradigm has a lot in common with open source and agile development methodologies. A particular strength of agile approaches is that they move away from 'introverted' development, involving only the development personnel, and intimately involves the customer in all areas of software creation, supposedly leading to the development of a more innovative and hence more valuable information system. Open source software (OSS) development also shares two key elements of the open innovation model, namely the collaborative development of the technology and shared rights to the use of the technology. However, one shortfall with agile development in particular is the narrow focus on a single customer representative. In response to this, we argue that current thinking regarding innovation needs to be extended to include multiple stakeholders both across and outside the organization. Additionally, for firms utilizing open source, it has been found that their position in a network of potential complementors determines the amount of superior value they create for their customers. Thus, this paper aims to get a better understanding of the applicability and implications of open innovation practices in firms that employ open source and agile development methodologies. In particular, a conceptual framework is derived for further testing.

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

PubMed

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

2012-11-15

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

The Open Source DataTurbine Initiative: Streaming Data Middleware for Environmental Observing Systems

NASA Technical Reports Server (NTRS)

Fountain T.; Tilak, S.; Shin, P.; Hubbard, P.; Freudinger, L.

2009-01-01

The Open Source DataTurbine Initiative is an international community of scientists and engineers sharing a common interest in real-time streaming data middleware and applications. The technology base of the OSDT Initiative is the DataTurbine open source middleware. Key applications of DataTurbine include coral reef monitoring, lake monitoring and limnology, biodiversity and animal tracking, structural health monitoring and earthquake engineering, airborne environmental monitoring, and environmental sustainability. DataTurbine software emerged as a commercial product in the 1990 s from collaborations between NASA and private industry. In October 2007, a grant from the USA National Science Foundation (NSF) Office of Cyberinfrastructure allowed us to transition DataTurbine from a proprietary software product into an open source software initiative. This paper describes the DataTurbine software and highlights key applications in environmental monitoring.

Developing open source, self-contained disease surveillance software applications for use in resource-limited settings

PubMed Central

2012-01-01

Background Emerging public health threats often originate in resource-limited countries. In recognition of this fact, the World Health Organization issued revised International Health Regulations in 2005, which call for significantly increased reporting and response capabilities for all signatory nations. Electronic biosurveillance systems can improve the timeliness of public health data collection, aid in the early detection of and response to disease outbreaks, and enhance situational awareness. Methods As components of its Suite for Automated Global bioSurveillance (SAGES) program, The Johns Hopkins University Applied Physics Laboratory developed two open-source, electronic biosurveillance systems for use in resource-limited settings. OpenESSENCE provides web-based data entry, analysis, and reporting. ESSENCE Desktop Edition provides similar capabilities for settings without internet access. Both systems may be configured to collect data using locally available cell phone technologies. Results ESSENCE Desktop Edition has been deployed for two years in the Republic of the Philippines. Local health clinics have rapidly adopted the new technology to provide daily reporting, thus eliminating the two-to-three week data lag of the previous paper-based system. Conclusions OpenESSENCE and ESSENCE Desktop Edition are two open-source software products with the capability of significantly improving disease surveillance in a wide range of resource-limited settings. These products, and other emerging surveillance technologies, can assist resource-limited countries compliance with the revised International Health Regulations. PMID:22950686

Digital time stamping system based on open source technologies.

PubMed

Miskinis, Rimantas; Smirnov, Dmitrij; Urba, Emilis; Burokas, Andrius; Malysko, Bogdan; Laud, Peeter; Zuliani, Francesco

2010-03-01

A digital time stamping system based on open source technologies (LINUX-UBUNTU, OpenTSA, OpenSSL, MySQL) is described in detail, including all important testing results. The system, called BALTICTIME, was developed under a project sponsored by the European Commission under the Program FP 6. It was designed to meet the requirements posed to the systems of legal and accountable time stamping and to be applicable to the hardware commonly used by the national time metrology laboratories. The BALTICTIME system is intended for the use of governmental and other institutions as well as personal bodies. Testing results demonstrate that the time stamps issued to the user by BALTICTIME and saved in BALTICTIME's archives (which implies that the time stamps are accountable) meet all the regulatory requirements. Moreover, the BALTICTIME in its present implementation is able to issue more than 10 digital time stamps per second. The system can be enhanced if needed. The test version of the BALTICTIME service is free and available at http://baltictime. pfi.lt:8080/btws/ and http://baltictime.lnmc.lv:8080/btws/.

Lighting system with thermal management system

DOEpatents

Arik, Mehmet; Weaver, Stanton Earl; Stecher, Thomas Elliot; Seeley, Charles Erklin; Kuenzler, Glenn Howard; Wolfe, Jr., Charles Franklin; Utturkar, Yogen Vishwas; Sharma, Rajdeep; Prabhakaran, Satish; Icoz, Tunc

2015-02-24

Lighting systems having unique configurations are provided. For instance, the lighting system may include a light source, a thermal management system and driver electronics, each contained within a housing structure. The light source is configured to provide illumination visible through an opening in the housing structure. The thermal management system is configured to provide an air flow, such as a unidirectional air flow, through the housing structure in order to cool the light source. The driver electronics are configured to provide power to each of the light source and the thermal management system.

Lighting system with thermal management system

DOEpatents

Arik, Mehmet; Weaver, Stanton Earl; Stecher, Thomas Elliot; Seeley, Charles Erklin; Kuenzler, Glenn Howard; Wolfe, Jr., Charles Franklin; Utturkar, Yogen Vishwas; Sharma, Rajdeep; Prabhakaran, Satish; Icoz, Tunc

2015-08-25

Lighting systems having unique configurations are provided. For instance, the lighting system may include a light source, a thermal management system and driver electronics, each contained within a housing structure. The light source is configured to provide illumination visible through an opening in the housing structure. The thermal management system is configured to provide an air flow, such as a unidirectional air flow, through the housing structure in order to cool the light source. The driver electronics are configured to provide power to each of the light source and the thermal management system.

Lighting system with thermal management system

DOEpatents

Arik, Mehmet; Weaver, Stanton; Stecher, Thomas; Seeley, Charles; Kuenzler, Glenn; Wolfe, Jr., Charles; Utturkar, Yogen; Sharma, Rajdeep; Prabhakaran, Satish; Icoz, Tunc

2013-05-07

Lighting systems having unique configurations are provided. For instance, the lighting system may include a light source, a thermal management system and driver electronics, each contained within a housing structure. The light source is configured to provide illumination visible through an opening in the housing structure. The thermal management system is configured to provide an air flow, such as a unidirectional air flow, through the housing structure in order to cool the light source. The driver electronics are configured to provide power to each of the light source and the thermal management system.

Lighting system with thermal management system

DOEpatents

Arik, Mehmet; Weaver, Stanton Earl; Stecher, Thomas Elliot; Seeley, Charles Erklin; Kuenzler, Glenn Howard; Wolfe, Jr, Charles Franklin; Utturkar, Yogen Vishwas; Sharma, Rajdeep; Prabhakaran, Satish; Icoz, Tunc

2016-10-11

Lighting systems having unique configurations are provided. For instance, the lighting system may include a light source, a thermal management system and driver electronics, each contained within a housing structure. The light source is configured to provide illumination visible through an opening in the housing structure. The thermal management system is configured to provide an air flow, such as a unidirectional air flow, through the housing structure in order to cool the light source. The driver electronics are configured to provide power to each of the light source and the thermal management system.

Phased Migration to Koha: Our Library's Experience

ERIC Educational Resources Information Center

Kohn, Karen; McCloy, Eric

2010-01-01

Landman Library is two-thirds of the way through a three-stage process of migrating to the Koha open-source integrated library system (http://koha-community.org). We are an academic library with roughly 143,000 volumes, six professional librarians, and three support staff. The migration to open source was driven by the desire to access our own…

Users' Acceptance and Use of Moodle: The Community Influence

ERIC Educational Resources Information Center

Baytiyeh, Hoda

2013-01-01

The open source course management system Moodle, which a great number of organizations worldwide have adopted, is designed to help instructors deliver course materials to their students from a social constructivist perspective. The aim of this research is evaluate the acceptance and use of Moodle as an open source application from the viewpoint of…

Modular and Spatially Explicit: A Novel Approach to System Dynamics

EPA Science Inventory

The Open Modeling Environment (OME) is an open-source System Dynamics (SD) simulation engine which has been created as a joint project between Oregon State University and the US Environmental Protection Agency. It is designed around a modular implementation, and provides a standa...

Status, upgrades, and advances of RTS2: the open source astronomical observatory manager

NASA Astrophysics Data System (ADS)

Kubánek, Petr

2016-07-01

RTS2 is an open source observatory control system. Being developed from early 2000, it continue to receive new features in last two years. RTS2 is a modulat, network-based distributed control system, featuring telescope drivers with advanced tracking and pointing capabilities, fast camera drivers and high level modules for "business logic" of the observatory, connected to a SQL database. Running on all continents of the planet, it accumulated a lot to control parts or full observatory setups.

Empirical tests of Zipf's law mechanism in open source Linux distribution.

PubMed

Maillart, T; Sornette, D; Spaeth, S; von Krogh, G

2008-11-21

Zipf's power law is a ubiquitous empirical regularity found in many systems, thought to result from proportional growth. Here, we establish empirically the usually assumed ingredients of stochastic growth models that have been previously conjectured to be at the origin of Zipf's law. We use exceptionally detailed data on the evolution of open source software projects in Linux distributions, which offer a remarkable example of a growing complex self-organizing adaptive system, exhibiting Zipf's law over four full decades.

ms_lims, a simple yet powerful open source laboratory information management system for MS-driven proteomics.

PubMed

Helsens, Kenny; Colaert, Niklaas; Barsnes, Harald; Muth, Thilo; Flikka, Kristian; Staes, An; Timmerman, Evy; Wortelkamp, Steffi; Sickmann, Albert; Vandekerckhove, Joël; Gevaert, Kris; Martens, Lennart

2010-03-01

MS-based proteomics produces large amounts of mass spectra that require processing, identification and possibly quantification before interpretation can be undertaken. High-throughput studies require automation of these various steps, and management of the data in association with the results obtained. We here present ms_lims (http://genesis.UGent.be/ms_lims), a freely available, open-source system based on a central database to automate data management and processing in MS-driven proteomics analyses.

48 CFR 206.202 - Establishing or maintaining alternative sources.

Code of Federal Regulations, 2010 CFR

2010-10-01

... Open Competition After Exclusion of Sources 206.202 Establishing or maintaining alternative sources. (a) Agencies may use this authority to totally or partially exclude a particular source from a contract action... maintaining alternative sources. 206.202 Section 206.202 Federal Acquisition Regulations System DEFENSE...

Greenhouse gas and ammonia emissions from an open-freestall dairy in southern idaho.

PubMed

Leytem, April B; Dungan, Robert S; Bjorneberg, David L; Koehn, Anita C

2013-01-01

Concentrated dairy operations emit trace gases such as ammonia (NH), methane (CH), and nitrous oxide (NO) to the atmosphere. The implementation of air quality regulations in livestock-producing states increases the need for accurate on-farm determination of emission rates. Our objective was to determine the emission rates of NH, CH, and NO from the open-freestall and wastewater pond source areas on a commercial dairy in southern Idaho using a flush system with anaerobic digestion. Gas concentrations and wind statistics were measured and used with an inverse dispersion model to calculate emission rates. Average emissions per cow per day from the open-freestall source area were 0.08 kg NH, 0.41 kg CH, and 0.02 kg NO. Average emissions from the wastewater ponds (g m d) were 6.8 NH, 22 CH, and 0.2 NO. The combined emissions on a per cow per day basis from the open-freestall and wastewater pond areas averaged 0.20 kg NH and 0.75 kg CH. Combined NO emissions were not calculated due to limited available data. The wastewater ponds were the greatest source of total farm NH emissions (67%) in spring and summer. The emissions of CH were approximately equal from the two source areas in spring and summer. During the late fall and winter months, the open-freestall area constituted the greatest source area of NH and CH emissions. Data from this study can be used to develop trace gas emissions factors from open-freestall dairies in southern Idaho and other open-freestall production systems in similar climatic regions. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

Open Source Hbim for Cultural Heritage: a Project Proposal

NASA Astrophysics Data System (ADS)

Diara, F.; Rinaudo, F.

2018-05-01

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

Efficiency analysis of semi-open sorption heat pump systems

DOE PAGES

Gluesenkamp, Kyle R.; Chugh, Devesh; Abdelaziz, Omar; ...

2016-08-10

Sorption systems traditionally fall into two categories: closed (heat pumps and chillers) and open (dehumidification). Recent work has explored the possibility of semi-open systems, which can perform heat pumping or chilling while utilizing ambient humidity as the working fluid of the cycle, and are still capable of being driven by solar, waste, or combustion heat sources. The efficiencies of closed and open systems are well characterized, and can typically be determined from four temperature s. In this work, the performance potential of semi-open systems is explored by adapting expressions for the efficiency of closed and open systems to the novelmore » semi-open systems. A key new parameter is introduced, which involves five temperatures, since both the ambient dry bulb and ambient dew point are used. Furthermore, this additional temperature is necessary to capture the open absorber performance in terms of both the absorption of humidity and sensible heat transfer with surrounding air.« less

Efficiency analysis of semi-open sorption heat pump systems

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

Gluesenkamp, Kyle R.; Chugh, Devesh; Abdelaziz, Omar

Sorption systems traditionally fall into two categories: closed (heat pumps and chillers) and open (dehumidification). Recent work has explored the possibility of semi-open systems, which can perform heat pumping or chilling while utilizing ambient humidity as the working fluid of the cycle, and are still capable of being driven by solar, waste, or combustion heat sources. The efficiencies of closed and open systems are well characterized, and can typically be determined from four temperature s. In this work, the performance potential of semi-open systems is explored by adapting expressions for the efficiency of closed and open systems to the novelmore » semi-open systems. A key new parameter is introduced, which involves five temperatures, since both the ambient dry bulb and ambient dew point are used. Furthermore, this additional temperature is necessary to capture the open absorber performance in terms of both the absorption of humidity and sensible heat transfer with surrounding air.« less

48 CFR 906.202 - Establishing or maintaining alternative sources.

Code of Federal Regulations, 2010 CFR

2010-10-01

... maintaining alternative sources. 906.202 Section 906.202 Federal Acquisition Regulations System DEPARTMENT OF ENERGY COMPETITION ACQUISITION PLANNING COMPETITION REQUIREMENTS Full and Open Competition After Exclusion of Sources 906.202 Establishing or maintaining alternative sources. (b)(1) Every proposed contract...

48 CFR 406.202 - Establishing or maintaining alternative sources.

Code of Federal Regulations, 2010 CFR

2010-10-01

... maintaining alternative sources. 406.202 Section 406.202 Federal Acquisition Regulations System DEPARTMENT OF AGRICULTURE COMPETITION AND ACQUISITION PLANNING COMPETITION REQUIREMENTS Full and Open Competition After Exclusion of Sources 406.202 Establishing or maintaining alternative sources. The Senior Procurement...

48 CFR 1406.202 - Establishing or maintaining alternative sources.

Code of Federal Regulations, 2010 CFR

2010-10-01

... maintaining alternative sources. 1406.202 Section 1406.202 Federal Acquisition Regulations System DEPARTMENT OF THE INTERIOR COMPETITION AND ACQUISITION PLANNING COMPETITION REQUIREMENTS Full and Open Competition After Exclusion of Sources 1406.202 Establishing or maintaining alternative sources. HCAs are...

48 CFR 1306.202 - Establishing or maintaining alternative sources.

Code of Federal Regulations, 2010 CFR

2010-10-01

... maintaining alternative sources. 1306.202 Section 1306.202 Federal Acquisition Regulations System DEPARTMENT OF COMMERCE COMPETITION AND ACQUISITION PLANNING COMPETITION REQUIREMENTS Full and Open Competition After Exclusion of Sources 1306.202 Establishing or maintaining alternative sources. The authority to...

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.

Open-Source Syringe Pump Library

PubMed Central

Wijnen, Bas; Hunt, Emily J.; Anzalone, Gerald C.; Pearce, Joshua M.

2014-01-01

This article explores a new open-source method for developing and manufacturing high-quality scientific equipment suitable for use in virtually any laboratory. A syringe pump was designed using freely available open-source computer aided design (CAD) software and manufactured using an open-source RepRap 3-D printer and readily available parts. The design, bill of materials and assembly instructions are globally available to anyone wishing to use them. Details are provided covering the use of the CAD software and the RepRap 3-D printer. The use of an open-source Rasberry Pi computer as a wireless control device is also illustrated. Performance of the syringe pump was assessed and the methods used for assessment are detailed. The cost of the entire system, including the controller and web-based control interface, is on the order of 5% or less than one would expect to pay for a commercial syringe pump having similar performance. The design should suit the needs of a given research activity requiring a syringe pump including carefully controlled dosing of reagents, pharmaceuticals, and delivery of viscous 3-D printer media among other applications. PMID:25229451

Data Shaping in the Cultural Simulation Modeler Integrated Behavioral Assessment Capability. Phase I

DTIC Science & Technology

2007-07-01

articles that appeared in global media in the years 1999-2006. The articles were all open source information and were obtained in part through an...agreement between Factiva Dow Jones and the NRL for this project, and in part collected by IndaSea from the Open Source Center database and a variety of...This view implied that a system geared to assist analysts should be open and completely dynamic. It is IndaSea’s perspective that there are advantages

Implementation and performance evaluation open-source controller for precision control of gripper

NASA Astrophysics Data System (ADS)

Lee, Seung-Yong; Ham, Un-Hyeong; Park, Young-Woo; Jung, Hak-Sang; Jung, Il-Kyun; Lim, Sun

2017-12-01

This paper proposes integrating gripper embedded operating system, which consist of external interface structure for sophisticated gripper control. This system has multiple functions that control the gripping module and measure the pose of the gripper body with respect to contact environment. A controller based on open source only for the gripper is developed and an external communication interface between robot controller and gripper controller is designed. An experimental environment for the fixed-cycle test consists of integrating magic gripper software system and hardware on commercial business. As a result, a deviation is measured approximately 2% and the system were verified for gripper control.

UAV using the open-source flight-control-system in the application of aerial survey

NASA Astrophysics Data System (ADS)

Huang, Ji-chen; Ru, Chen

2015-12-01

The aerial survey as one of the branches of the Space Information Technology system, has an important application in data acquisition of the earth's surface. In recent years, the trend of UVA (unmanned aerial vehicle) to replace traditional survey aircraft has become increasingly obvious with the progress of science and technology. At present, the price of the commercial UAV Flight Control System is higher, limiting the application of UVA. This paper mainly discusses the possibility that the open-source's flight-control-system take the place of the commercial one. Result is that the costs of UVA are reduced, and make the application more widely.

Utilization of Open Source Technology to Create Cost-Effective Microscope Camera Systems for Teaching.

PubMed

Konduru, Anil Reddy; Yelikar, Balasaheb R; Sathyashree, K V; Kumar, Ankur

2018-01-01

Open source technologies and mobile innovations have radically changed the way people interact with technology. These innovations and advancements have been used across various disciplines and already have a significant impact. Microscopy, with focus on visually appealing contrasting colors for better appreciation of morphology, forms the core of the disciplines such as Pathology, microbiology, and anatomy. Here, learning happens with the aid of multi-head microscopes and digital camera systems for teaching larger groups and in organizing interactive sessions for students or faculty of other departments. The cost of the original equipment manufacturer (OEM) camera systems in bringing this useful technology at all the locations is a limiting factor. To avoid this, we have used the low-cost technologies like Raspberry Pi, Mobile high definition link and 3D printing for adapters to create portable camera systems. Adopting these open source technologies enabled us to convert any binocular or trinocular microscope be connected to a projector or HD television at a fraction of the cost of the OEM camera systems with comparable quality. These systems, in addition to being cost-effective, have also provided the added advantage of portability, thus providing the much-needed flexibility at various teaching locations.

OpenDMAP: An open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression

PubMed Central

Hunter, Lawrence; Lu, Zhiyong; Firby, James; Baumgartner, William A; Johnson, Helen L; Ogren, Philip V; Cohen, K Bretonnel

2008-01-01

Background Information extraction (IE) efforts are widely acknowledged to be important in harnessing the rapid advance of biomedical knowledge, particularly in areas where important factual information is published in a diverse literature. Here we report on the design, implementation and several evaluations of OpenDMAP, an ontology-driven, integrated concept analysis system. It significantly advances the state of the art in information extraction by leveraging knowledge in ontological resources, integrating diverse text processing applications, and using an expanded pattern language that allows the mixing of syntactic and semantic elements and variable ordering. Results OpenDMAP information extraction systems were produced for extracting protein transport assertions (transport), protein-protein interaction assertions (interaction) and assertions that a gene is expressed in a cell type (expression). Evaluations were performed on each system, resulting in F-scores ranging from .26 – .72 (precision .39 – .85, recall .16 – .85). Additionally, each of these systems was run over all abstracts in MEDLINE, producing a total of 72,460 transport instances, 265,795 interaction instances and 176,153 expression instances. Conclusion OpenDMAP advances the performance standards for extracting protein-protein interaction predications from the full texts of biomedical research articles. Furthermore, this level of performance appears to generalize to other information extraction tasks, including extracting information about predicates of more than two arguments. The output of the information extraction system is always constructed from elements of an ontology, ensuring that the knowledge representation is grounded with respect to a carefully constructed model of reality. The results of these efforts can be used to increase the efficiency of manual curation efforts and to provide additional features in systems that integrate multiple sources for information extraction. The open source OpenDMAP code library is freely available at PMID:18237434

Mobile service for open data visualization on geo-based images

NASA Astrophysics Data System (ADS)

Lee, Kiwon; Kim, Kwangseob; Kang, Sanggoo

2015-12-01

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

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

NASA Astrophysics Data System (ADS)

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

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

OpenDA Open Source Generic Data Assimilation Environment and its Application in Process Models

NASA Astrophysics Data System (ADS)

El Serafy, Ghada; Verlaan, Martin; Hummel, Stef; Weerts, Albrecht; Dhondia, Juzer

2010-05-01

Data Assimilation techniques are essential elements in state-of-the-art development of models and their optimization with data in the field of groundwater, surface water and soil systems. They are essential tools in calibration of complex modelling systems and improvement of model forecasts. The OpenDA is a new and generic open source data assimilation environment for application to a choice of physical process models, applied to case dependent domains. OpenDA was introduced recently when the developers of Costa, an open-source TU Delft project [http://www.costapse.org; Van Velzen and Verlaan; 2007] and those of the DATools from the former WL|Delft Hydraulics [El Serafy et al 2007; Weerts et al. 2009] decided to join forces. OpenDA makes use of a set of interfaces that describe the interaction between models, observations and data assimilation algorithms. It focuses on flexible applications in portable systems for modelling geophysical processes. It provides a generic interfacing protocol that allows combination of the implemented data assimilation techniques with, in principle, any time-stepping model duscribing a process(atmospheric processes, 3D circulation, 2D water level, sea surface temperature, soil systems, groundwater etc.). Presently, OpenDA features filtering techniques and calibration techniques. The presentation will give an overview of the OpenDA and the results of some of its practical applications. Application of data assimilation in portable operational forecasting systems—the DATools assimilation environment, El Serafy G.Y., H. Gerritsen, S. Hummel, A. H. Weerts, A.E. Mynett and M. Tanaka (2007), Journal of Ocean Dynamics, DOI 10.1007/s10236-007-0124-3, pp.485-499. COSTA a problem solving environment for data assimilation applied for hydrodynamical modelling, Van Velzen and Verlaan (2007), Meteorologische Zeitschrift, Volume 16, Number 6, December 2007 , pp. 777-793(17). Application of generic data assimilation tools (DATools) for flood forecasting purposes, A.H. Weerts, G.Y.H. El Serafy, S. Hummel, J. Dhondia, and H. Gerritsen (2009), accepted by Geoscience & Computers.

A new chapter in environmental sensing: The Open-Source Published Environmental Sensing (OPENS) laboratory

NASA Astrophysics Data System (ADS)

Selker, J. S.; Roques, C.; Higgins, C. W.; Good, S. P.; Hut, R.; Selker, A.

2015-12-01

The confluence of 3-Dimensional printing, low-cost solid-state-sensors, low-cost, low-power digital controllers (e.g., Arduinos); and open-source publishing (e.g., Github) is poised to transform environmental sensing. The Open-Source Published Environmental Sensing (OPENS) laboratory has launched and is available for all to use. OPENS combines cutting edge technologies and makes them available to the global environmental sensing community. OPENS includes a Maker lab space where people may collaborate in person or virtually via on-line forum for the publication and discussion of environmental sensing technology (Corvallis, Oregon, USA, please feel free to request a free reservation for space and equipment use). The physical lab houses a test-bed for sensors, as well as a complete classical machine shop, 3-D printers, electronics development benches, and workstations for code development. OPENS will provide a web-based formal publishing framework wherein global students and scientists can peer-review publish (with DOI) novel and evolutionary advancements in environmental sensor systems. This curated and peer-reviewed digital collection will include complete sets of "printable" parts and operating computer code for sensing systems. The physical lab will include all of the machines required to produce these sensing systems. These tools can be addressed in person or virtually, creating a truly global venue for advancement in monitoring earth's environment and agricultural systems. In this talk we will present an example of the process of design and publication the design and data from the OPENS-Permeameter. The publication includes 3-D printing code, Arduino (or other control/logging platform) operational code; sample data sets, and a full discussion of the design set in the scientific context of previous related devices. Editors for the peer-review process are currently sought - contact John.Selker@Oregonstate.edu or Clement.Roques@Oregonstate.edu.

Building an Open Source Framework for Integrated Catchment Modeling

NASA Astrophysics Data System (ADS)

Jagers, B.; Meijers, E.; Villars, M.

2015-12-01

In order to develop effective strategies and associated policies for environmental management, we need to understand the dynamics of the natural system as a whole and the human role therein. This understanding is gained by comparing our mental model of the world with observations from the field. However, to properly understand the system we should look at dynamics of water, sediments, water quality, and ecology throughout the whole system from catchment to coast both at the surface and in the subsurface. Numerical models are indispensable in helping us understand the interactions of the overall system, but we need to be able to update and adjust them to improve our understanding and test our hypotheses. To support researchers around the world with this challenging task we started a few years ago with the development of a new open source modeling environment DeltaShell that integrates distributed hydrological models with 1D, 2D, and 3D hydraulic models including generic components for the tracking of sediment, water quality, and ecological quantities throughout the hydrological cycle composed of the aforementioned components. The open source approach combined with a modular approach based on open standards, which allow for easy adjustment and expansion as demands and knowledge grow, provides an ideal starting point for addressing challenging integrated environmental questions.

48 CFR 2406.202 - Establishing or maintaining alternative sources.

Code of Federal Regulations, 2010 CFR

2010-10-01

... alternative sources. 2406.202 Section 2406.202 Federal Acquisition Regulations System DEPARTMENT OF HOUSING AND URBAN DEVELOPMENT COMPETITION AND ACQUISITION PLANNING COMPETITION REQUIREMENTS Full and Open Competition After Exclusion of Sources 2406.202 Establishing or maintaining alternative sources. (b)(1) The...

48 CFR 606.202 - Establishing or maintaining alternate sources.

Code of Federal Regulations, 2010 CFR

2010-10-01

... maintaining alternate sources. 606.202 Section 606.202 Federal Acquisition Regulations System DEPARTMENT OF STATE COMPETITION AND ACQUISITION PLANNING COMPETITION REQUIREMENTS Full and Open Competition After Exclusion of Sources 606.202 Establishing or maintaining alternate sources. The Procurement Executive is the...

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 Platform Application to Groundwater Characterization and Monitoring

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

JBoss Middleware for Spacecraft Trajectory Operations

NASA Technical Reports Server (NTRS)

Stensrud, Kjell; Srinivasan, Ravi; Hamm, Dustin

2008-01-01

This viewgraph presentation reviews the use of middleware for spacecraft trajectory planning. It reviews the following areas and questions: 1. Project Background - What is the environment where we are considering Open Source Middleware? 2. System Architecture - What technologies and design did we apply? 3. Testing overview - What are the quality scenarios and test points? 4. Project Conclusion - What did we learn about Open Source Middleware?

Open source cardiology electronic health record development for DIGICARDIAC implementation

NASA Astrophysics Data System (ADS)

Dugarte, Nelson; Medina, Rubén.; Huiracocha, Lourdes; Rojas, Rubén.

2015-12-01

This article presents the development of a Cardiology Electronic Health Record (CEHR) system. Software consists of a structured algorithm designed under Health Level-7 (HL7) international standards. Novelty of the system is the integration of high resolution ECG (HRECG) signal acquisition and processing tools, patient information management tools and telecardiology tools. Acquisition tools are for management and control of the DIGICARDIAC electrocardiograph functions. Processing tools allow management of HRECG signal analysis searching for indicative patterns of cardiovascular pathologies. Telecardiology tools incorporation allows system communication with other health care centers decreasing access time to the patient information. CEHR system was completely developed using open source software. Preliminary results of process validation showed the system efficiency.

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 computed tomography (QCT) as a radiology reporting tool by using optical character recognition (OCR) and macro program.

PubMed

Lee, Young Han; Song, Ho-Taek; Suh, Jin-Suck

2012-12-01

The objectives are (1) to introduce a new concept of making a quantitative computed tomography (QCT) reporting system by using optical character recognition (OCR) and macro program and (2) to illustrate the practical usages of the QCT reporting system in radiology reading environment. This reporting system was created as a development tool by using an open-source OCR software and an open-source macro program. The main module was designed for OCR to report QCT images in radiology reading process. The principal processes are as follows: (1) to save a QCT report as a graphic file, (2) to recognize the characters from an image as a text, (3) to extract the T scores from the text, (4) to perform error correction, (5) to reformat the values into QCT radiology reporting template, and (6) to paste the reports into the electronic medical record (EMR) or picture archiving and communicating system (PACS). The accuracy test of OCR was performed on randomly selected QCTs. QCT as a radiology reporting tool successfully acted as OCR of QCT. The diagnosis of normal, osteopenia, or osteoporosis is also determined. Error correction of OCR is done with AutoHotkey-coded module. The results of T scores of femoral neck and lumbar vertebrae had an accuracy of 100 and 95.4 %, respectively. A convenient QCT reporting system could be established by utilizing open-source OCR software and open-source macro program. This method can be easily adapted for other QCT applications and PACS/EMR.

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

PubMed

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

2014-10-01

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

Creating system engineering products with executable models in a model-based engineering environment

NASA Astrophysics Data System (ADS)

Karban, Robert; Dekens, Frank G.; Herzig, Sebastian; Elaasar, Maged; Jankevičius, Nerijus

2016-08-01

Applying systems engineering across the life-cycle results in a number of products built from interdependent sources of information using different kinds of system level analysis. This paper focuses on leveraging the Executable System Engineering Method (ESEM) [1] [2], which automates requirements verification (e.g. power and mass budget margins and duration analysis of operational modes) using executable SysML [3] models. The particular value proposition is to integrate requirements, and executable behavior and performance models for certain types of system level analysis. The models are created with modeling patterns that involve structural, behavioral and parametric diagrams, and are managed by an open source Model Based Engineering Environment (named OpenMBEE [4]). This paper demonstrates how the ESEM is applied in conjunction with OpenMBEE to create key engineering products (e.g. operational concept document) for the Alignment and Phasing System (APS) within the Thirty Meter Telescope (TMT) project [5], which is under development by the TMT International Observatory (TIO) [5].

Model-Based Reinforcement of Kinect Depth Data for Human Motion Capture Applications

PubMed Central

Calderita, Luis Vicente; Bandera, Juan Pedro; Bustos, Pablo; Skiadopoulos, Andreas

2013-01-01

Motion capture systems have recently experienced a strong evolution. New cheap depth sensors and open source frameworks, such as OpenNI, allow for perceiving human motion on-line without using invasive systems. However, these proposals do not evaluate the validity of the obtained poses. This paper addresses this issue using a model-based pose generator to complement the OpenNI human tracker. The proposed system enforces kinematics constraints, eliminates odd poses and filters sensor noise, while learning the real dimensions of the performer's body. The system is composed by a PrimeSense sensor, an OpenNI tracker and a kinematics-based filter and has been extensively tested. Experiments show that the proposed system improves pure OpenNI results at a very low computational cost. PMID:23845933

48 CFR 2406.202 - Establishing or maintaining alternative sources.

Code of Federal Regulations, 2011 CFR

2011-10-01

... maintaining alternative sources. 2406.202 Section 2406.202 Federal Acquisition Regulations System DEPARTMENT OF HOUSING AND URBAN DEVELOPMENT COMPETITION AND ACQUISITION PLANNING COMPETITION REQUIREMENTS Full and Open Competition After Exclusion of Sources 2406.202 Establishing or maintaining alternative...

Open source system OpenVPN in a function of Virtual Private Network

NASA Astrophysics Data System (ADS)

Skendzic, A.; Kovacic, B.

2017-05-01

Using of Virtual Private Networks (VPN) can establish high security level in network communication. VPN technology enables high security networking using distributed or public network infrastructure. VPN uses different security and managing rules inside networks. It can be set up using different communication channels like Internet or separate ISP communication infrastructure. VPN private network makes security communication channel over public network between two endpoints (computers). OpenVPN is an open source software product under GNU General Public License (GPL) that can be used to establish VPN communication between two computers inside business local network over public communication infrastructure. It uses special security protocols and 256-bit Encryption and it is capable of traversing network address translators (NATs) and firewalls. It allows computers to authenticate each other using a pre-shared secret key, certificates or username and password. This work gives review of VPN technology with a special accent on OpenVPN. This paper will also give comparison and financial benefits of using open source VPN software in business environment.

Using OpenOffice as a Portable Interface to JAVA-Based Applications

NASA Astrophysics Data System (ADS)

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

2004-07-01

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

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

NASA Technical Reports Server (NTRS)

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

1989-01-01

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

Opendf - An Implementation of the Dual Fermion Method for Strongly Correlated Systems

NASA Astrophysics Data System (ADS)

Antipov, Andrey E.; LeBlanc, James P. F.; Gull, Emanuel

The dual fermion method is a multiscale approach for solving lattice problems of interacting strongly correlated systems. In this paper, we present the opendfcode, an open-source implementation of the dual fermion method applicable to fermionic single- orbital lattice models in dimensions D = 1, 2, 3 and 4. The method is built on a dynamical mean field starting point, which neglects all local correlations, and perturbatively adds spatial correlations. Our code is distributed as an open-source package under the GNU public license version 2.

Open-Source Learning Management System and Web 2.0 Online Social Software Applications as Learning Platforms for an Elementary School in Singapore

ERIC Educational Resources Information Center

Tay, Lee Yong; Lim, Cher Ping; Lye, Sze Yee; Ng, Kay Joo; Lim, Siew Khiaw

2011-01-01

This paper analyses how an elementary-level future school in Singapore implements and uses various open-source online platforms, which are easily available online and could be implemented with minimal software cost, for the purpose of teaching and learning. Online platforms have the potential to facilitate students' engagement for independent and…

48 CFR 3006.202 - Establishing or maintaining alternative sources.

Code of Federal Regulations, 2010 CFR

2010-10-01

... COMPETITION REQUIREMENTS Full and Open Competition After Exclusion of Sources 3006.202 Establishing or maintaining alternative sources. (b)(1) The HCA is delegated authority to approve a D&F in support of a... maintaining alternative sources. 3006.202 Section 3006.202 Federal Acquisition Regulations System DEPARTMENT...

High School Open On-Line Courses (HOOC): A Case Study from Italy

ERIC Educational Resources Information Center

Canessa, Enrique; Pisani, Armando

2013-01-01

The first implementation of complete high school, open on-line courses (HOOC) aiming to support the training and basic scientific knowledge of young students from the Liceo Ginnasio Dante Alighieri in Gorizia, Italy, is discussed. Using the open source and automated recording system openEyA, HOOC give a student the opportunity to watch on-line, at…

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

Field determination of multipollutant, open area combustion source emission factors with a hexacopter unmanned aerial vehicle

EPA Science Inventory

An emission sensor/sampler system was coupled to a NASA hexacopter unmanned aerial system (UAS) to characterize gases and particles in the plume emitted from open burning of military ordnance. The UAS/sampler was tested at two field sites resulting in 33 flights at Radford, VA a...

A Customizable and Expandable Electroencephalography (EEG) Data Collection System

DTIC Science & Technology

2016-03-01

devices, including Emotiv Systems3 and Advanced Brain Monitoring,4 as well as open source alternatives such as OpenBCI.5 These products generally...Analysis, Inc and ACI Society; 2006. p. 91–101. 3. Emotiv . San Francisco (CA): Emotiv , Inc; c2011 – 2015 [accessed 2015 Mar 6]. http://emotiv.com/. 4

Open Source Next Generation Visualization Software for Interplanetary Missions

NASA Technical Reports Server (NTRS)

Trimble, Jay; Rinker, George

2016-01-01

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

Numerical Simulation of Dispersion from Urban Greenhouse Gas Sources

NASA Astrophysics Data System (ADS)

Nottrott, Anders; Tan, Sze; He, Yonggang; Winkler, Renato

2017-04-01

Cities are characterized by complex topography, inhomogeneous turbulence, and variable pollutant source distributions. These features create a scale separation between local sources and urban scale emissions estimates known as the Grey-Zone. Modern computational fluid dynamics (CFD) techniques provide a quasi-deterministic, physically based toolset to bridge the scale separation gap between source level dynamics, local measurements, and urban scale emissions inventories. CFD has the capability to represent complex building topography and capture detailed 3D turbulence fields in the urban boundary layer. This presentation discusses the application of OpenFOAM to urban CFD simulations of natural gas leaks in cities. OpenFOAM is an open source software for advanced numerical simulation of engineering and environmental fluid flows. When combined with free or low cost computer aided drawing and GIS, OpenFOAM generates a detailed, 3D representation of urban wind fields. OpenFOAM was applied to model scalar emissions from various components of the natural gas distribution system, to study the impact of urban meteorology on mobile greenhouse gas measurements. The numerical experiments demonstrate that CH4 concentration profiles are highly sensitive to the relative location of emission sources and buildings. Sources separated by distances of 5-10 meters showed significant differences in vertical dispersion of plumes, due to building wake effects. The OpenFOAM flow fields were combined with an inverse, stochastic dispersion model to quantify and visualize the sensitivity of point sensors to upwind sources in various built environments. The Boussinesq approximation was applied to investigate the effects of canopy layer temperature gradients and convection on sensor footprints.

The use of an active controlled enclosure to attenuate sound radiation from a heavy radiator

NASA Astrophysics Data System (ADS)

Sun, Yao; Yang, Tiejun; Zhu, Minggang; Pan, Jie

2017-03-01

Active structural acoustical control usually experiences difficulty in the control of heavy sources or sources where direct applications of control forces are not practical. To overcome this difficulty, an active controlled enclosure, which forms a cavity with both flexible and open boundary, is employed. This configuration permits indirect implementation of active control in which the control inputs can be applied to subsidiary structures other than the sources. To determine the control effectiveness of the configuration, the vibro-acoustic behavior of the system, which consists of a top plate with an open, a sound cavity and a source panel, is investigated in this paper. A complete mathematical model of the system is formulated involving modified Fourier series formulations and the governing equations are solved using the Rayleigh-Ritz method. The coupling mechanisms of a partly opened cavity and a plate are analysed in terms of modal responses and directivity patterns. Furthermore, to attenuate sound power radiated from both the top panel and the open, two strategies are studied: minimizing the total radiated power and the cancellation of volume velocity. Moreover, three control configurations are compared, using a point force on the control panel (structural control), using a sound source in the cavity (acoustical control) and applying hybrid structural-acoustical control. In addition, the effects of boundary condition of the control panel on the sound radiation and control performance are discussed.

GIS-MODFLOW: Ein kleines OpenSource-Werkzeug zur Anbindung von GIS-Daten an MODFLOW

NASA Astrophysics Data System (ADS)

Gossel, Wolfgang

2013-06-01

The numerical model MODFLOW (Harbaugh 2005) is an efficient and up-to-date tool for groundwater flow modelling. On the other hand, Geo-Information-Systems (GIS) provide useful tools for data preparation and visualization that can also be incorporated in numerical groundwater modelling. An interface between both would therefore be useful for many hydrogeological investigations. To date, several integrated stand-alone tools have been developed that rely on MODFLOW, MODPATH and transport modelling tools. Simultaneously, several open source-GIS codes were developed to improve functionality and ease of use. These GIS tools can be used as pre- and post-processors of the numerical model MODFLOW via a suitable interface. Here we present GIS-MODFLOW as an open-source tool that provides a new universal interface by using the ESRI ASCII GRID data format that can be converted into MODFLOW input data. This tool can also treat MODFLOW results. Such a combination of MODFLOW and open-source GIS opens new possibilities to render groundwater flow modelling, and simulation results, available to larger circles of hydrogeologists.

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.

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

PubMed Central

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

2017-01-01

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

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

PubMed

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

2017-04-01

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

STORMSeq: an open-source, user-friendly pipeline for processing personal genomics data in the cloud.

PubMed

Karczewski, Konrad J; Fernald, Guy Haskin; Martin, Alicia R; Snyder, Michael; Tatonetti, Nicholas P; Dudley, Joel T

2014-01-01

The increasing public availability of personal complete genome sequencing data has ushered in an era of democratized genomics. However, read mapping and variant calling software is constantly improving and individuals with personal genomic data may prefer to customize and update their variant calls. Here, we describe STORMSeq (Scalable Tools for Open-Source Read Mapping), a graphical interface cloud computing solution that does not require a parallel computing environment or extensive technical experience. This customizable and modular system performs read mapping, read cleaning, and variant calling and annotation. At present, STORMSeq costs approximately $2 and 5-10 hours to process a full exome sequence and $30 and 3-8 days to process a whole genome sequence. We provide this open-access and open-source resource as a user-friendly interface in Amazon EC2.

Massive stereo-based DTM production for Mars on cloud computers

NASA Astrophysics Data System (ADS)

Tao, Y.; Muller, J.-P.; Sidiropoulos, P.; Xiong, Si-Ting; Putri, A. R. D.; Walter, S. H. G.; Veitch-Michaelis, J.; Yershov, V.

2018-05-01

Digital Terrain Model (DTM) creation is essential to improving our understanding of the formation processes of the Martian surface. Although there have been previous demonstrations of open-source or commercial planetary 3D reconstruction software, planetary scientists are still struggling with creating good quality DTMs that meet their science needs, especially when there is a requirement to produce a large number of high quality DTMs using "free" software. In this paper, we describe a new open source system to overcome many of these obstacles by demonstrating results in the context of issues found from experience with several planetary DTM pipelines. We introduce a new fully automated multi-resolution DTM processing chain for NASA Mars Reconnaissance Orbiter (MRO) Context Camera (CTX) and High Resolution Imaging Science Experiment (HiRISE) stereo processing, called the Co-registration Ames Stereo Pipeline (ASP) Gotcha Optimised (CASP-GO), based on the open source NASA ASP. CASP-GO employs tie-point based multi-resolution image co-registration, and Gotcha sub-pixel refinement and densification. CASP-GO pipeline is used to produce planet-wide CTX and HiRISE DTMs that guarantee global geo-referencing compliance with respect to High Resolution Stereo Colour imaging (HRSC), and thence to the Mars Orbiter Laser Altimeter (MOLA); providing refined stereo matching completeness and accuracy. All software and good quality products introduced in this paper are being made open-source to the planetary science community through collaboration with NASA Ames, United States Geological Survey (USGS) and the Jet Propulsion Laboratory (JPL), Advanced Multi-Mission Operations System (AMMOS) Planetary Data System (PDS) Pipeline Service (APPS-PDS4), as well as browseable and visualisable through the iMars web based Geographic Information System (webGIS) system.

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

PubMed

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

2004-09-24

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

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

ERIC Educational Resources Information Center

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

2012-01-01

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

Open Data, Open Specifications and Free and Open Source Software: A powerful mix to create distributed Web-based water information systems

NASA Astrophysics Data System (ADS)

Arias, Carolina; Brovelli, Maria Antonia; Moreno, Rafael

2015-04-01

We are in an age when water resources are increasingly scarce and the impacts of human activities on them are ubiquitous. These problems don't respect administrative or political boundaries and they must be addressed integrating information from multiple sources at multiple spatial and temporal scales. Communication, coordination and data sharing are critical for addressing the water conservation and management issues of the 21st century. However, different countries, provinces, local authorities and agencies dealing with water resources have diverse organizational, socio-cultural, economic, environmental and information technology (IT) contexts that raise challenges to the creation of information systems capable of integrating and distributing information across their areas of responsibility in an efficient and timely manner. Tight and disparate financial resources, and dissimilar IT infrastructures (data, hardware, software and personnel expertise) further complicate the creation of these systems. There is a pressing need for distributed interoperable water information systems that are user friendly, easily accessible and capable of managing and sharing large volumes of spatial and non-spatial data. In a distributed system, data and processes are created and maintained in different locations each with competitive advantages to carry out specific activities. Open Data (data that can be freely distributed) is available in the water domain, and it should be further promoted across countries and organizations. Compliance with Open Specifications for data collection, storage and distribution is the first step toward the creation of systems that are capable of interacting and exchanging data in a seamlessly (interoperable) way. The features of Free and Open Source Software (FOSS) offer low access cost that facilitate scalability and long-term viability of information systems. The World Wide Web (the Web) will be the platform of choice to deploy and access these systems. Geospatial capabilities for mapping, visualization, and spatial analysis will be important components of these new generation of Web-based interoperable information systems in the water domain. The purpose of this presentation is to increase the awareness of scientists, IT personnel and agency managers about the advantages offered by the combined use of Open Data, Open Specifications for geospatial and water-related data collection, storage and sharing, as well as mature FOSS projects for the creation of interoperable Web-based information systems in the water domain. A case study is used to illustrate how these principles and technologies can be integrated to create a system with the previously mentioned characteristics for managing and responding to flood events.

Open source clinical portals: a model for healthcare information systems to support care processes and feed clinical research. An Italian case of design, development, reuse, and exploitation.

PubMed

Locatelli, Paolo; Baj, Emanuele; Restifo, Nicola; Origgi, Gianni; Bragagia, Silvia

2011-01-01

Open source is a still unexploited chance for healthcare organizations and technology providers to answer to a growing demand for innovation and to join economical benefits with a new way of managing hospital information systems. This chapter will present the case of the web enterprise clinical portal developed in Italy by Niguarda Hospital in Milan with the support of Fondazione Politecnico di Milano, to enable a paperless environment for clinical and administrative activities in the ward. This represents also one rare case of open source technology and reuse in the healthcare sector, as the system's porting is now taking place at Besta Neurological Institute in Milan. This institute is customizing the portal to feed researchers with structured clinical data collected in its portal's patient records, so that they can be analyzed, e.g., through business intelligence tools. Both organizational and clinical advantages are investigated, from process monitoring, to semantic data structuring, to recognition of common patterns in care processes.

Clinical records anonymisation and text extraction (CRATE): an open-source software system.

PubMed

Cardinal, Rudolf N

2017-04-26

Electronic medical records contain information of value for research, but contain identifiable and often highly sensitive confidential information. Patient-identifiable information cannot in general be shared outside clinical care teams without explicit consent, but anonymisation/de-identification allows research uses of clinical data without explicit consent. This article presents CRATE (Clinical Records Anonymisation and Text Extraction), an open-source software system with separable functions: (1) it anonymises or de-identifies arbitrary relational databases, with sensitivity and precision similar to previous comparable systems; (2) it uses public secure cryptographic methods to map patient identifiers to research identifiers (pseudonyms); (3) it connects relational databases to external tools for natural language processing; (4) it provides a web front end for research and administrative functions; and (5) it supports a specific model through which patients may consent to be contacted about research. Creation and management of a research database from sensitive clinical records with secure pseudonym generation, full-text indexing, and a consent-to-contact process is possible and practical using entirely free and open-source software.

Unclassified Information Sharing and Coordination in Security, Stabilization, Transition and Reconstruction Efforts

DTIC Science & Technology

2008-03-01

is implemented using the Drupal (2007) content management system (CMS) and many of the baseline information sharing and collaboration tools have...been contributed through the Dru- pal open source community. Drupal is a very modular open source software written in PHP hypertext processor...needed to suit the particular problem domain. While other frameworks have the potential to provide similar advantages (“Ruby,” 2007), Drupal was

Improving the All-Hazards Homeland Security Enterprise Through the Use of an Emergency Management Intelligence Model

DTIC Science & Technology

2013-09-01

Office of the Inspector General OSINT Open Source Intelligence PPD Presidential Policy Directive SIGINT Signals Intelligence SLFC State/Local Fusion...Geospatial Intelligence (GEOINT) from Geographic Information Systems (GIS), and Open Source Intelligence ( OSINT ) from Social Media. GIS is widely...and monitor make it a feasible tool to capitalize on for OSINT . A formalized EM intelligence process would help expedite the processing of such

Development of an open source laboratory information management system for 2-D gel electrophoresis-based proteomics workflow

PubMed Central

Morisawa, Hiraku; Hirota, Mikako; Toda, Tosifusa

2006-01-01

Background In the post-genome era, most research scientists working in the field of proteomics are confronted with difficulties in management of large volumes of data, which they are required to keep in formats suitable for subsequent data mining. Therefore, a well-developed open source laboratory information management system (LIMS) should be available for their proteomics research studies. Results We developed an open source LIMS appropriately customized for 2-D gel electrophoresis-based proteomics workflow. The main features of its design are compactness, flexibility and connectivity to public databases. It supports the handling of data imported from mass spectrometry software and 2-D gel image analysis software. The LIMS is equipped with the same input interface for 2-D gel information as a clickable map on public 2DPAGE databases. The LIMS allows researchers to follow their own experimental procedures by reviewing the illustrations of 2-D gel maps and well layouts on the digestion plates and MS sample plates. Conclusion Our new open source LIMS is now available as a basic model for proteome informatics, and is accessible for further improvement. We hope that many research scientists working in the field of proteomics will evaluate our LIMS and suggest ways in which it can be improved. PMID:17018156

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

NASA Astrophysics Data System (ADS)

Ames, D. P.

2013-12-01

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

National Geothermal Data System: Open Access to Geoscience Data, Maps, and Documents

NASA Astrophysics Data System (ADS)

Caudill, C. M.; Richard, S. M.; Musil, L.; Sonnenschein, A.; Good, J.

2014-12-01

The U.S. National Geothermal Data System (NGDS) provides free open access to millions of geoscience data records, publications, maps, and reports via distributed web services to propel geothermal research, development, and production. NGDS is built on the US Geoscience Information Network (USGIN) data integration framework, which is a joint undertaking of the USGS and the Association of American State Geologists (AASG), and is compliant with international standards and protocols. NGDS currently serves geoscience information from 60+ data providers in all 50 states. Free and open source software is used in this federated system where data owners maintain control of their data. This interactive online system makes geoscience data easily discoverable, accessible, and interoperable at no cost to users. The dynamic project site http://geothermaldata.org serves as the information source and gateway to the system, allowing data and applications discovery and availability of the system's data feed. It also provides access to NGDS specifications and the free and open source code base (on GitHub), a map-centric and library style search interface, other software applications utilizing NGDS services, NGDS tutorials (via YouTube and USGIN site), and user-created tools and scripts. The user-friendly map-centric web-based application has been created to support finding, visualizing, mapping, and acquisition of data based on topic, location, time, provider, or key words. Geographic datasets visualized through the map interface also allow users to inspect the details of individual GIS data points (e.g. wells, geologic units, etc.). In addition, the interface provides the information necessary for users to access the GIS data from third party software applications such as GoogleEarth, UDig, and ArcGIS. A redistributable, free and open source software package called GINstack (USGIN software stack) was also created to give data providers a simple way to release data using interoperable and shareable standards, upload data and documents, and expose those data as a node in the NGDS or any larger data system through a CSW endpoint. The easy-to-use interface is supported by back-end software including Postgres, GeoServer, and custom CKAN extensions among others.

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

PubMed

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

2017-08-01

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

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

NASA Astrophysics Data System (ADS)

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

2017-08-01

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

14 CFR 25.1325 - Static pressure systems.

Code of Federal Regulations, 2010 CFR

2010-01-01

... installation of the static pressure system must be such that— (1) Positive drainage of moisture is provided..., the other is blocked off; and (2) Both sources cannot be blocked off simultaneously. (h) For... other static pressure source being open or blocked. [Doc. No. 5066, 29 FR 18291, Dec. 24, 1964, as...

77 FR 32142 - Privacy Act of 1974, as Amended; System of Records Notices

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-31

... contains, the sources of information in the records, and the proposed ``routine uses'' of the system of... are found in 36 CFR part 1202. RECORDS SOURCE CATEGORIES: Information in these contestant application..., MD 20740-6001. FOR FURTHER INFORMATION CONTACT: Pamela Wright, Open Government Office, Room 3200...

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

ERIC Educational Resources Information Center

Cripps, Michael J.

2011-01-01

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

Security of patient data when decommissioning ultrasound systems.

PubMed

Moggridge, James

2017-02-01

Although ultrasound systems generally archive to Picture Archiving and Communication Systems (PACS), their archiving workflow typically involves storage to an internal hard disk before data are transferred onwards. Deleting records from the local system will delete entries in the database and from the file allocation table or equivalent but, as with a PC, files can be recovered. Great care is taken with disposal of media from a healthcare organisation to prevent data breaches, but ultrasound systems are routinely returned to lease companies, sold on or donated to third parties without such controls. In this project, five methods of hard disk erasure were tested on nine ultrasound systems being decommissioned: the system's own delete function; full reinstallation of system software; the manufacturer's own disk wiping service; open source disk wiping software for full and just blank space erasure. Attempts were then made to recover data using open source recovery tools. All methods deleted patient data as viewable from the ultrasound system and from browsing the disk from a PC. However, patient identifiable data (PID) could be recovered following the system's own deletion and the reinstallation methods. No PID could be recovered after using the manufacturer's wiping service or the open source wiping software. The typical method of reinstalling an ultrasound system's software may not prevent PID from being recovered. When transferring ownership, care should be taken that an ultrasound system's hard disk has been wiped to a sufficient level, particularly if the scanner is to be returned with approved parts and in a fully working state.

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

PubMed

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

2007-02-22

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

Achieving Better Buying Power through Acquisition of Open Architecture Software Systems. Volume 2 Understanding Open Architecture Software Systems: Licensing and Security Research and Recommendations

DTIC Science & Technology

2016-01-06

of- breed software components and software products lines (SPLs) that are subject to different IP license and cybersecurity requirements. The... commercially priced closed source software components, to be used in the design, implementation, deployment, and evolution of open architecture (OA... breed software components and software products lines (SPLs) that are subject to different IP license and cybersecurity requirements. The Department

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

NASA Technical Reports Server (NTRS)

Conway, Darrel J.; Hughes, Steven P.

2010-01-01

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

The Pixhawk Open-Source Computer Vision Framework for Mavs

NASA Astrophysics Data System (ADS)

Meier, L.; Tanskanen, P.; Fraundorfer, F.; Pollefeys, M.

2011-09-01

Unmanned aerial vehicles (UAV) and micro air vehicles (MAV) are already intensively used in geodetic applications. State of the art autonomous systems are however geared towards the application area in safe and obstacle-free altitudes greater than 30 meters. Applications at lower altitudes still require a human pilot. A new application field will be the reconstruction of structures and buildings, including the facades and roofs, with semi-autonomous MAVs. Ongoing research in the MAV robotics field is focusing on enabling this system class to operate at lower altitudes in proximity to nearby obstacles and humans. PIXHAWK is an open source and open hardware toolkit for this purpose. The quadrotor design is optimized for onboard computer vision and can connect up to four cameras to its onboard computer. The validity of the system design is shown with a fully autonomous capture flight along a building.

Linking Primary Care Information Systems and Public Health Vertical Programs in the Philippines: An Open-source Experience

PubMed Central

Tolentino, Herman; Marcelo, Alvin; Marcelo, Portia; Maramba, Inocencio

2005-01-01

Community-based primary care information systems are one of the building blocks for national health information systems. In the Philippines, after the devolution of health care to local governments, we observed “health information system islands” connected to national vertical programs being implemented in devolved health units. These structures lead to a huge amount of “information work” in the transformation of health information at the community level. This paper describes work done to develop and implement the open-source Community Based Health Information Tracking System (CHITS) Project, which was implemented to address this information management problem and its outcomes. Several lessons learned from the field as well as software development strategies are highlighted in building community level information systems that link to national level health information systems. PMID:16779052

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

DasPy – Open Source Multivariate Land Data Assimilation Framework with High Performance Computing

NASA Astrophysics Data System (ADS)

Han, Xujun; Li, Xin; Montzka, Carsten; Kollet, Stefan; Vereecken, Harry; Hendricks Franssen, Harrie-Jan

2015-04-01

Data assimilation has become a popular method to integrate observations from multiple sources with land surface models to improve predictions of the water and energy cycles of the soil-vegetation-atmosphere continuum. In recent years, several land data assimilation systems have been developed in different research agencies. Because of the software availability or adaptability, these systems are not easy to apply for the purpose of multivariate land data assimilation research. Multivariate data assimilation refers to the simultaneous assimilation of observation data for multiple model state variables into a simulation model. Our main motivation was to develop an open source multivariate land data assimilation framework (DasPy) which is implemented using the Python script language mixed with C++ and Fortran language. This system has been evaluated in several soil moisture, L-band brightness temperature and land surface temperature assimilation studies. The implementation allows also parameter estimation (soil properties and/or leaf area index) on the basis of the joint state and parameter estimation approach. LETKF (Local Ensemble Transform Kalman Filter) is implemented as the main data assimilation algorithm, and uncertainties in the data assimilation can be represented by perturbed atmospheric forcings, perturbed soil and vegetation properties and model initial conditions. The CLM4.5 (Community Land Model) was integrated as the model operator. The CMEM (Community Microwave Emission Modelling Platform), COSMIC (COsmic-ray Soil Moisture Interaction Code) and the two source formulation were integrated as observation operators for assimilation of L-band passive microwave, cosmic-ray soil moisture probe and land surface temperature measurements, respectively. DasPy is parallelized using the hybrid MPI (Message Passing Interface) and OpenMP (Open Multi-Processing) techniques. All the input and output data flow is organized efficiently using the commonly used NetCDF file format. Online 1D and 2D visualization of data assimilation results is also implemented to facilitate the post simulation analysis. In summary, DasPy is a ready to use open source parallel multivariate land data assimilation framework.

Instrumentino: An Open-Source Software for Scientific Instruments.

PubMed

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

2015-01-01

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

CoSN K12 Open Technologies Implementation Study #3. Moodle: An Open Learning Content Management System for Schools

ERIC Educational Resources Information Center

Consortium for School Networking (NJ1), 2008

2008-01-01

This report introduces educators to Moodle, an open-source software program for managing courses online. It briefly defines what Moodle is, what it can do, and gives specific examples of how it is being implemented. An appendix contains brief profiles of five school organizations that are using Moodle.

STORMSeq: An Open-Source, User-Friendly Pipeline for Processing Personal Genomics Data in the Cloud

PubMed Central

Karczewski, Konrad J.; Fernald, Guy Haskin; Martin, Alicia R.; Snyder, Michael; Tatonetti, Nicholas P.; Dudley, Joel T.

2014-01-01

The increasing public availability of personal complete genome sequencing data has ushered in an era of democratized genomics. However, read mapping and variant calling software is constantly improving and individuals with personal genomic data may prefer to customize and update their variant calls. Here, we describe STORMSeq (Scalable Tools for Open-Source Read Mapping), a graphical interface cloud computing solution that does not require a parallel computing environment or extensive technical experience. This customizable and modular system performs read mapping, read cleaning, and variant calling and annotation. At present, STORMSeq costs approximately $2 and 5–10 hours to process a full exome sequence and $30 and 3–8 days to process a whole genome sequence. We provide this open-access and open-source resource as a user-friendly interface in Amazon EC2. PMID:24454756

Comparison of petroleum generation kinetics by isothermal hydrous and nonisothermal open-system pyrolysis

USGS Publications Warehouse

Lewan, M.D.; Ruble, T.E.

2002-01-01

This study compares kinetic parameters determined by open-system pyrolysis and hydrous pyrolysis using aliquots of source rocks containing different kerogen types. Kinetic parameters derived from these two pyrolysis methods not only differ in the conditions employed and products generated, but also in the derivation of the kinetic parameters (i.e., isothermal linear regression and non-isothermal nonlinear regression). Results of this comparative study show that there is no correlation between kinetic parameters derived from hydrous pyrolysis and open-system pyrolysis. Hydrous-pyrolysis kinetic parameters determine narrow oil windows that occur over a wide range of temperatures and depths depending in part on the organic-sulfur content of the original kerogen. Conversely, open-system kinetic parameters determine broad oil windows that show no significant differences with kerogen types or their organic-sulfur contents. Comparisons of the kinetic parameters in a hypothetical thermal-burial history (2.5 ??C/my) show open-system kinetic parameters significantly underestimate the extent and timing of oil generation for Type-US kerogen and significantly overestimate the extent and timing of petroleum formation for Type-I kerogen compared to hydrous pyrolysis kinetic parameters. These hypothetical differences determined by the kinetic parameters are supported by natural thermal-burial histories for the Naokelekan source rock (Type-IIS kerogen) in the Zagros basin of Iraq and for the Green River Formation (Type-I kerogen) in the Uinta basin of Utah. Differences in extent and timing of oil generation determined by open-system pyrolysis and hydrous pyrolysis can be attributed to the former not adequately simulating natural oil generation conditions, products, and mechanisms.

OpCost: an open-source system for estimating costs of stand-level forest operations

Treesearch

Conor K. Bell; Robert F. Keefe; Jeremy S. Fried

2017-01-01

This report describes and documents the OpCost forest operations cost model, a key component of the BioSum analysis framework. OpCost is available in two editions: as a callable module for use with BioSum, and in a stand-alone edition that can be run directly from R. OpCost model logic and assumptions for this open-source tool are explained, references to the...

Open source tools for large-scale neuroscience.

PubMed

Freeman, Jeremy

2015-06-01

New technologies for monitoring and manipulating the nervous system promise exciting biology but pose challenges for analysis and computation. Solutions can be found in the form of modern approaches to distributed computing, machine learning, and interactive visualization. But embracing these new technologies will require a cultural shift: away from independent efforts and proprietary methods and toward an open source and collaborative neuroscience. Copyright © 2015 The Author. Published by Elsevier Ltd.. All rights reserved.

Method and apparatus for enhanced sensitivity filmless medical x-ray imaging, including three-dimensional imaging

DOEpatents

Parker, S.

1995-10-24

A filmless X-ray imaging system includes at least one X-ray source, upper and lower collimators, and a solid-state detector array, and can provide three-dimensional imaging capability. The X-ray source plane is distance z{sub 1} above upper collimator plane, distance z{sub 2} above the lower collimator plane, and distance z{sub 3} above the plane of the detector array. The object to be X-rayed is located between the upper and lower collimator planes. The upper and lower collimators and the detector array are moved horizontally with scanning velocities v{sub 1}, v{sub 2}, v{sub 3} proportional to z{sub 1}, z{sub 2} and z{sub 3}, respectively. The pattern and size of openings in the collimators, and between detector positions is proportional such that similar triangles are always defined relative to the location of the X-ray source. X-rays that pass through openings in the upper collimator will always pass through corresponding and similar openings in the lower collimator, and thence to a corresponding detector in the underlying detector array. Substantially 100% of the X-rays irradiating the object (and neither absorbed nor scattered) pass through the lower collimator openings and are detected, which promotes enhanced sensitivity. A computer system coordinates repositioning of the collimators and detector array, and X-ray source locations. The computer system can store detector array output, and can associate a known X-ray source location with detector array output data, to provide three-dimensional imaging. Detector output may be viewed instantly, stored digitally, and/or transmitted electronically for image viewing at a remote site. 5 figs.

Method and apparatus for enhanced sensitivity filmless medical x-ray imaging, including three-dimensional imaging

DOEpatents

Parker, Sherwood

1995-01-01

A filmless X-ray imaging system includes at least one X-ray source, upper and lower collimators, and a solid-state detector array, and can provide three-dimensional imaging capability. The X-ray source plane is distance z.sub.1 above upper collimator plane, distance z.sub.2 above the lower collimator plane, and distance z.sub.3 above the plane of the detector array. The object to be X-rayed is located between the upper and lower collimator planes. The upper and lower collimators and the detector array are moved horizontally with scanning velocities v.sub.1, v.sub.2, v.sub.3 proportional to z.sub.1, z.sub.2 and z.sub.3, respectively. The pattern and size of openings in the collimators, and between detector positions is proportional such that similar triangles are always defined relative to the location of the X-ray source. X-rays that pass through openings in the upper collimator will always pass through corresponding and similar openings in the lower collimator, and thence to a corresponding detector in the underlying detector array. Substantially 100% of the X-rays irradiating the object (and neither absorbed nor scattered) pass through the lower collimator openings and are detected, which promotes enhanced sensitivity. A computer system coordinates repositioning of the collimators and detector array, and X-ray source locations. The computer system can store detector array output, and can associate a known X-ray source location with detector array output data, to provide three-dimensional imaging. Detector output may be viewed instantly, stored digitally, and/or transmitted electronically for image viewing at a remote site.

Open-tube diffusion techniques for InP/LnGaAs heterojunctior bipolar transistors

NASA Astrophysics Data System (ADS)

Schuitemaker, P.; Houston, P. A.

1986-11-01

Open-tube diffusion techniques used between 450 and 600° C are described which involve the supply of diffusant from a vapour source (via a solution) and a solid evaporated metal source. Investigations of Zn into InP and InGaAs(P) have been undertaken using both sources. SIMS profile analyses show that in the case of the vapour source the profiles indicate a concentration-dependent diffusion coefficient while the solid source diffusions can be well described by a Gaussian-type profile. The usefulness of the vapour source method has been demonstrated in the fabrication of bipolar transistors which exhibit good d.c. characteristics. The solid source method is limited by the slow diffusion velocity and more gradual profile. The InGaAs(P)/InP materials system has important applications in optical communications and future high speed microwave and switching devices. Useful technologies allied to the introduction of impurities into Si by diffusion, have gradually been emerging for use in the III-V semiconductor family. Closed tube systems1 have been used in order to contain the volatile group V species and prevent surface erosion. In addition, simpler open tube systems2,3 have been developed that maintain a sufficient overpressure of the group V element. Zn and Cd p-dopants have been studied extensively because of the volatility and relatively large diffusion rates in III-V semiconductors. Opentube diffusion into both InP and InGaAs2-6 has been studied but little detail has appeared concerning InGaAs and InGaAsP. In this paper we describe a comprehensive study of the diffusion of Zn into InP and InGaAs(P) using both open-tube vapour source and a Au/Zn/Au evaporated solid source with SiNx acting both as a mask and also an encapsulant to prevent loss of Zn and decomposition of the substrate material. The techniques have been successfully applied to the fabrication of InP/lnGaAs heterojunction bipolar transistors which show good dc characteristics. Reference to InGaAs in the text implies the InP lattice-matched composition In0.53Ga0.47As.

SU-G-IeP4-04: DD-Neutron Source Collimation for Neutron Stimulated Emission Computed Tomography: A Monte Carlo Simulation Study

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

Fong, G; Kapadia, A

Purpose: To optimize collimation and shielding for a deuterium-deuterium (DD) neutron generator for an inexpensive and compact clinical neutron imaging system. The envisioned application is cancer diagnosis through Neutron Stimulated Emission Computed Tomography (NSECT). Methods: Collimator designs were tested with an isotropic 2.5 MeV neutron source through GEANT4 simulations. The collimator is a 52×52×52 cm{sup 3} polyethylene block coupled with a 1 cm lead sheet in sequence. Composite opening was modeled into the collimator to permit passage of neutrons. The opening varied in shape (cylindrical vs. tapered), size (1–5 cm source-side and target-side openings) and aperture placements (13–39 cm frommore » source-side). Spatial and energy distribution of neutrons and gammas were tracked from each collimator design. Parameters analyzed were primary beam width (FWHM), divergence, and efficiency (percent transmission) for different configurations of the collimator. Select resultant outputs were then used for simulated NSECT imaging of a virtual breast phantom containing a 2.5 cm diameter tumor to assess the effect of the collimator on spatial resolution, noise, and scan time. Finally, composite shielding enclosure made of polyethylene and lead was designed and evaluated to block 99.99% of neutron and gamma radiation generated in the system. Results: Analysis of primary beam indicated the beam-width is linear to the aperture size. Increasing source-side opening allowed at least 20% more neutron throughput for all designs relative to the cylindrical openings. Maximum throughput for all designs was 364% relative to cylindrical openings. Conclusion: The work indicates potential for collimating and shielding a DD neutron generator for use in a clinical NSECT system. The proposed collimator designs produced a well-defined collimated neutron beam that can be used to image samples of interest with millimeter resolution. Balance in output efficiency, noise reduction, and scan time should be considered to determine the optimal design for specific NSECT applications.« less

"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

"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.

Lighting system with thermal management system having point contact synthetic jets

DOEpatents

Arik, Mehmet; Weaver, Stanton Earl; Kuenzler, Glenn Howard; Wolfe, Jr., Charles Franklin; Sharma, Rajdeep

2013-12-10

Lighting system having unique configurations are provided. For instance, the lighting system may include a light source, a thermal management system and driver electronics, each contained within a housing structure. The light source is configured to provide illumination visible through an opening in the housing structure. The thermal management system includes a plurality of synthetic jets. The synthetic jets are arranged within the lighting system such that they are secured at contact points.

Lighting system with thermal management system having point contact synthetic jets

DOEpatents

Arik, Mehmet; Weaver, Stanton Earl; Kuenzler, Glenn Howard; Wolfe, Jr, Charles Franklin; Sharma, Rajdeep

2016-08-30

Lighting systems having unique configurations are provided. For instance, the lighting system may include a light source, a thermal management system and driver electronics, each contained within a housing structure. The light source is configured to provide illumination visible through an opening in the housing structure. The thermal management system includes a plurality of synthetic jets. The synthetic jets are arranged within the lighting system such that they are secured at contact points.

Lighting system with thermal management system having point contact synthetic jets

DOEpatents

Arik, Mehmet; Weaver, Stanton Earl; Kuenzler, Glenn Howard; Wolfe, Jr., Charles Franklin; Sharma, Rajdeep

2016-08-23

Lighting systems having unique configurations are provided. For instance, the lighting system may include a light source, a thermal management system and driver electronics, each contained within a housing structure. The light source is configured to provide illumination visible through an opening in the housing structure. The thermal management system includes a plurality of synthetic jets. The synthetic jets are arranged within the lighting system such that they are secured at contact points.

GOC-TX: A Reliable Ticket Synchronization Application for the Open Science Grid

NASA Astrophysics Data System (ADS)

Hayashi, Soichi; Gopu, Arvind; Quick, Robert

2011-12-01

One of the major operational issues faced by large multi-institutional collaborations is permitting its users and support staff to use their native ticket tracking environment while also exchanging these tickets with collaborators. After several failed attempts at email-parser based ticket exchanges, the OSG Operations Group has designed a comprehensive ticket synchronizing application. The GOC-TX application uses web-service interfaces offered by various commercial, open source and other homegrown ticketing systems, to synchronize tickets between two or more of these systems. GOC-TX operates independently from any ticketing system. It can be triggered by one ticketing system via email, active messaging, or a web-services call to check for current sync-status, pull applicable recent updates since prior synchronizations to the source ticket, and apply the updates to a destination ticket. The currently deployed production version of GOC-TX is able to synchronize tickets between the Numara Footprints ticketing system used by the OSG and the following systems: European Grid Initiative's system Global Grid User Support (GGUS) and the Request Tracker (RT) system used by Brookhaven. Additional interfaces to the BMC Remedy system used by Fermilab, and to other instances of RT used by other OSG partners, are expected to be completed in summer 2010. A fully configurable open source version is expected to be made available by early autumn 2010. This paper will cover the structure of the GOC-TX application, its evolution, and the problems encountered by OSG Operations group with ticket exchange within the OSG Collaboration.

NASA's Earth Imagery Service as Open Source Software

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

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.

PASSIM--an open source software system for managing information in biomedical studies.

PubMed

Viksna, Juris; Celms, Edgars; Opmanis, Martins; Podnieks, Karlis; Rucevskis, Peteris; Zarins, Andris; Barrett, Amy; Neogi, Sudeshna Guha; Krestyaninova, Maria; McCarthy, Mark I; Brazma, Alvis; Sarkans, Ugis

2007-02-09

One of the crucial aspects of day-to-day laboratory information management is collection, storage and retrieval of information about research subjects and biomedical samples. An efficient link between sample data and experiment results is absolutely imperative for a successful outcome of a biomedical study. Currently available software solutions are largely limited to large-scale, expensive commercial Laboratory Information Management Systems (LIMS). Acquiring such LIMS indeed can bring laboratory information management to a higher level, but often implies sufficient investment of time, effort and funds, which are not always available. There is a clear need for lightweight open source systems for patient and sample information management. We present a web-based tool for submission, management and retrieval of sample and research subject data. The system secures confidentiality by separating anonymized sample information from individuals' records. It is simple and generic, and can be customised for various biomedical studies. Information can be both entered and accessed using the same web interface. User groups and their privileges can be defined. The system is open-source and is supplied with an on-line tutorial and necessary documentation. It has proven to be successful in a large international collaborative project. The presented system closes the gap between the need and the availability of lightweight software solutions for managing information in biomedical studies involving human research subjects.

Exploring the potential of open big data from ticketing websites to characterize travel patterns within the Chinese high-speed rail system

PubMed Central

Luan, Xiali; Han, Shanrui; Zhou, Wen

2017-01-01

Big data have contributed to deepen our understanding in regards to many human systems, particularly human mobility patterns and the structure and functioning of transportation systems. Resonating the recent call for ‘open big data,’ big data from various sources on a range of scales have become increasingly accessible to the public. However, open big data relevant to travelers within public transit tools remain scarce, hindering any further in-depth study on human mobility patterns. Here, we explore ticketing-website derived data that are publically available but have been largely neglected. We demonstrate the power, potential and limitations of this open big data, using the Chinese high-speed rail (HSR) system as an example. Using an application programming interface, we automatically collected the data on the remaining tickets (RTD) for scheduled trains at the last second before departure in order to retrieve information on unused transit capacity, occupancy rate of trains, and passenger flux at stations. We show that this information is highly useful in characterizing the spatiotemporal patterns of traveling behaviors on the Chinese HSR, such as weekend traveling behavior, imbalanced commuting behavior, and station functionality. Our work facilitates the understanding of human traveling patterns along the Chinese HSR, and the functionality of the largest HSR system in the world. We expect our work to attract attention regarding this unique open big data source for the study of analogous transportation systems. PMID:28574991

Exploring the potential of open big data from ticketing websites to characterize travel patterns within the Chinese high-speed rail system.

PubMed

Wei, Sheng; Yuan, Jinfu; Qiu, Yanning; Luan, Xiali; Han, Shanrui; Zhou, Wen; Xu, Chi

2017-01-01

Big data have contributed to deepen our understanding in regards to many human systems, particularly human mobility patterns and the structure and functioning of transportation systems. Resonating the recent call for 'open big data,' big data from various sources on a range of scales have become increasingly accessible to the public. However, open big data relevant to travelers within public transit tools remain scarce, hindering any further in-depth study on human mobility patterns. Here, we explore ticketing-website derived data that are publically available but have been largely neglected. We demonstrate the power, potential and limitations of this open big data, using the Chinese high-speed rail (HSR) system as an example. Using an application programming interface, we automatically collected the data on the remaining tickets (RTD) for scheduled trains at the last second before departure in order to retrieve information on unused transit capacity, occupancy rate of trains, and passenger flux at stations. We show that this information is highly useful in characterizing the spatiotemporal patterns of traveling behaviors on the Chinese HSR, such as weekend traveling behavior, imbalanced commuting behavior, and station functionality. Our work facilitates the understanding of human traveling patterns along the Chinese HSR, and the functionality of the largest HSR system in the world. We expect our work to attract attention regarding this unique open big data source for the study of analogous transportation systems.

Opening Pandora's Box: The impact of open system modeling on interpretations of anoxia

NASA Astrophysics Data System (ADS)

Hotinski, Roberta M.; Kump, Lee R.; Najjar, Raymond G.

2000-06-01

The geologic record preserves evidence that vast regions of ancient oceans were once anoxic, with oxygen levels too low to sustain animal life. Because anoxic conditions have been postulated to foster deposition of petroleum source rocks and have been implicated as a kill mechanism in extinction events, the genesis of such anoxia has been an area of intense study. Most previous models of ocean oxygen cycling proposed, however, have either been qualitative or used closed-system approaches. We reexamine the question of anoxia in open-system box models in order to test the applicability of closed-system results over long timescales and find that open and closed-system modeling results may differ significantly on both short and long timescales. We also compare a scenario with basinwide diffuse upwelling (a three-box model) to a model with upwelling concentrated in the Southern Ocean (a four-box model). While a three-box modeling approach shows that only changes in high-latitude convective mixing rate and character of deepwater sources are likely to cause anoxia, four-box model experiments indicate that slowing of thermohaline circulation, a reduction in wind-driven upwelling, and changes in high-latitude export production may also cause dysoxia or anoxia in part of the deep ocean on long timescales. These results suggest that box models must capture the open-system and vertically stratified nature of the ocean to allow meaningful interpretations of long-lived episodes of anoxia.

Building a Snow Data Management System using Open Source Software (and IDL)

NASA Astrophysics Data System (ADS)

Goodale, C. E.; Mattmann, C. A.; Ramirez, P.; Hart, A. F.; Painter, T.; Zimdars, P. A.; Bryant, A.; Brodzik, M.; Skiles, M.; Seidel, F. C.; Rittger, K. E.

2012-12-01

At NASA's Jet Propulsion Laboratory free and open source software is used everyday to support a wide range of projects, from planetary to climate to research and development. In this abstract I will discuss the key role that open source software has played in building a robust science data processing pipeline for snow hydrology research, and how the system is also able to leverage programs written in IDL, making JPL's Snow Data System a hybrid of open source and proprietary software. Main Points: - The Design of the Snow Data System (illustrate how the collection of sub-systems are combined to create a complete data processing pipeline) - Discuss the Challenges of moving from a single algorithm on a laptop, to running 100's of parallel algorithms on a cluster of servers (lesson's learned) - Code changes - Software license related challenges - Storage Requirements - System Evolution (from data archiving, to data processing, to data on a map, to near-real-time products and maps) - Road map for the next 6 months (including how easily we re-used the snowDS code base to support the Airborne Snow Observatory Mission) Software in Use and their Software Licenses: IDL - Used for pre and post processing of data. Licensed under a proprietary software license held by Excelis. Apache OODT - Used for data management and workflow processing. Licensed under the Apache License Version 2. GDAL - Geospatial Data processing library used for data re-projection currently. Licensed under the X/MIT license. GeoServer - WMS Server. Licensed under the General Public License Version 2.0 Leaflet.js - Javascript web mapping library. Licensed under the Berkeley Software Distribution License. Python - Glue code and miscellaneous data processing support. Licensed under the Python Software Foundation License. Perl - Script wrapper for running the SCAG algorithm. Licensed under the General Public License Version 3. PHP - Front-end web application programming. Licensed under the PHP License Version 3.01

46 CFR 112.05-3 - Main-emergency bus-tie.

Code of Federal Regulations, 2010 CFR

2010-10-01

... emergency switchboard; (b) Be arranged to prevent parallel operation of an emergency power source with any other source of electric power, except for interlock systems for momentary transfer of loads; and (c) If arranged for feedback operation, open automatically upon overload of the emergency power source before the...

An Open Port Sampling Interface for Liquid Introduction Atmospheric Pressure Ionization Mass Spectrometry

DOE PAGES

Van Berkel, Gary J.; Kertesz, Vilmos

2015-08-25

RATIONALE: A simple method to introduce unprocessed samples into a solvent for rapid characterization by liquid introduction atmospheric pressure ionization mass spectrometry has been lacking. The continuous flow, self-cleaning open port sampling interface introduced here fills this void. METHODS: The open port sampling interface used a vertically aligned, co-axial tube arrangement enabling solvent delivery to the sampling end of the device through the tubing annulus and solvent aspiration down the center tube and into the mass spectrometer ionization source via the commercial APCI emitter probe. The solvent delivery rate to the interface was set to exceed the aspiration rate creatingmore » a continuous sampling interface along with a constant, self-cleaning spillover of solvent from the top of the probe. RESULTS: Using the open port sampling interface with positive ion mode APCI and a hybrid quadrupole time of flight mass spectrometer, rapid, direct sampling and analysis possibilities are exemplified with plastics, ballpoint and felt tip ink pens, skin, and vegetable oils. These results demonstrated that the open port sampling interface could be used as a simple, versatile and self-cleaning system to rapidly introduce multiple types of unprocessed, sometimes highly concentrated and complex, samples into a solvent flow stream for subsequent ionization and analysis by mass spectrometry. The basic setup presented here could be incorporated with any self-aspirating liquid introduction ionization source (e.g., ESI, APCI, APPI, ICP, etc.) or any type of atmospheric pressure sampling ready mass spectrometer system. CONCLUSIONS: The open port sampling interface provides a means to introduce and quickly analyze unprocessed solid or liquid samples with liquid introduction atmospheric pressure ionization source without fear of sampling interface or ionization source contamination.« 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.

40 CFR Table 3 to Subpart Wwww of... - Organic HAP Emissions Limits for Existing Open Molding Sources, New Open Molding Sources Emitting...

Code of Federal Regulations, 2010 CFR

2010-07-01

... Existing Open Molding Sources, New Open Molding Sources Emitting Less Than 100 TPY of HAP, and New and... CATEGORIES National Emissions Standards for Hazardous Air Pollutants: Reinforced Plastic Composites... Existing Open Molding Sources, New Open Molding Sources Emitting Less Than 100 TPY of HAP, and New and...

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.

An integrated and open source GIS environmental management system for a protected area in the south of Portugal

NASA Astrophysics Data System (ADS)

Teodoro, A.; Duarte, L.; Sillero, N.; Gonçalves, J. A.; Fonte, J.; Gonçalves-Seco, L.; Pinheiro da Luz, L. M.; dos Santos Beja, N. M. R.

2015-10-01

Herdade da Contenda (HC), located in Moura municipality, Beja district (Alentejo province) in the south of Portugal (southwestern Iberia Peninsula), is a national hunting area with 5270ha. The development of an integrated system that aims to make the management of the natural and cultural heritage resources will be very useful for an effective management of this area. This integrated system should include the physical characterization of the territory, natural conservation, land use and land management themes, as well the cultural heritage resources. This paper presents a new tool for an integrated environmental management system of the HC, which aims to produce maps under a GIS open source environment (QGIS). The application is composed by a single button which opens a window. The window is composed by twelve menus (File, DRASTIC, Forest Fire Risk, Revised Universal Soil Loss Equation (RUSLE), Bioclimatic Index, Cultural Heritage, Fauna and Flora, Ortofoto, Normalizes Difference Vegetation Index (NDVI), Digital Elevation Model (DEM), Land Use Land Cover Cover (LULC) and Help. Several inputs are requires to generate these maps, e.g. DEM, geologic information, soil map, hydraulic conductivity information, LULC map, vulnerability and economic information, NDVI. Six buttons were added to the toolbar which allows to manipulate the information in the map canvas: Zoom in, Zoom out, Pan, Print/Layout and Clear. This integrated and open source GIS environment management system was developed for the HC area, but could be easily adapted to other natural or protected area. Despite the lack of data, the methodology presented fulfills the objectives.

A reliable, low-cost picture archiving and communications system for small and medium veterinary practices built using open-source technology.

PubMed

Iotti, Bryan; Valazza, Alberto

2014-10-01

Picture Archiving and Communications Systems (PACS) are the most needed system in a modern hospital. As an integral part of the Digital Imaging and Communications in Medicine (DICOM) standard, they are charged with the responsibility for secure storage and accessibility of the diagnostic imaging data. These machines need to offer high performance, stability, and security while proving reliable and ergonomic in the day-to-day and long-term storage and retrieval of the data they safeguard. This paper reports the experience of the authors in developing and installing a compact and low-cost solution based on open-source technologies in the Veterinary Teaching Hospital for the University of Torino, Italy, during the course of the summer of 2012. The PACS server was built on low-cost x86-based hardware and uses an open source operating system derived from Oracle OpenSolaris (Oracle Corporation, Redwood City, CA, USA) to host the DCM4CHEE PACS DICOM server (DCM4CHEE, http://www.dcm4che.org ). This solution features very high data security and an ergonomic interface to provide easy access to a large amount of imaging data. The system has been in active use for almost 2 years now and has proven to be a scalable, cost-effective solution for practices ranging from small to very large, where the use of different hardware combinations allows scaling to the different deployments, while the use of paravirtualization allows increased security and easy migrations and upgrades.

Terra Harvest Open Source Environment (THOSE): a universal unattended ground sensor controller

NASA Astrophysics Data System (ADS)

Gold, Joshua; Klawon, Kevin; Humeniuk, David; Landoll, Darren

2011-06-01

Under the Terra Harvest Program, the Defense Intelligence Agency (DIA) has the objective of developing a universal Controller for the Unattended Ground Sensor (UGS) community. The mission is to define, implement, and thoroughly document an open architecture that universally supports UGS missions, integrating disparate systems, peripherals, etc. The Controller's inherent interoperability with numerous systems enables the integration of both legacy and future Unattended Ground Sensor System (UGSS) components, while the design's open architecture supports rapid third-party development to ensure operational readiness. The successful accomplishment of these objectives by the program's Phase 3b contractors is demonstrated via integration of the companies' respective plug-'n-play contributions that include various peripherals, such as sensors, cameras, etc., and their associated software drivers. In order to independently validate the Terra Harvest architecture, L-3 Nova Engineering, along with its partner, the University of Dayton Research Institute (UDRI), is developing the Terra Harvest Open Source Environment (THOSE), a Java based system running on an embedded Linux Operating System (OS). The Use Cases on which the software is developed support the full range of UGS operational scenarios such as remote sensor triggering, image capture, and data exfiltration. The Team is additionally developing an ARM microprocessor evaluation platform that is both energyefficient and operationally flexible. The paper describes the overall THOSE architecture, as well as the implementation strategy for some of the key software components. Preliminary integration/test results and the Team's approach for transitioning the THOSE design and source code to the Government are also presented.

Building a Billion Spatio-Temporal Object Search and Visualization Platform

NASA Astrophysics Data System (ADS)

Kakkar, D.; Lewis, B.

2017-10-01

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

An Open Avionics and Software Architecture to Support Future NASA Exploration Missions

NASA Technical Reports Server (NTRS)

Schlesinger, Adam

2017-01-01

The presentation describes an avionics and software architecture that has been developed through NASAs Advanced Exploration Systems (AES) division. The architecture is open-source, highly reliable with fault tolerance, and utilizes standard capabilities and interfaces, which are scalable and customizable to support future exploration missions. Specific focus areas of discussion will include command and data handling, software, human interfaces, communication and wireless systems, and systems engineering and integration.

General Mission Analysis Tool (GMAT): Mission, Vision, and Business Case

NASA Technical Reports Server (NTRS)

Hughes, Steven P.

2007-01-01

The Goal of the GMAT project is to develop new space trajectory optimization and mission design technology by working inclusively with ordinary people, universities businesses and other government organizations; and to share that technology in an open and unhindered way. GMAT's a free and open source software system; free for anyone to use in development of new mission concepts or to improve current missions, freely available in source code form for enhancement or future technology development.

Electronic Health Record Application Support Service Enablers.

PubMed

Neofytou, M S; Neokleous, K; Aristodemou, A; Constantinou, I; Antoniou, Z; Schiza, E C; Pattichis, C S; Schizas, C N

2015-08-01

There is a huge need for open source software solutions in the healthcare domain, given the flexibility, interoperability and resource savings characteristics they offer. In this context, this paper presents the development of three open source libraries - Specific Enablers (SEs) for eHealth applications that were developed under the European project titled "Future Internet Social and Technological Alignment Research" (FI-STAR) funded under the "Future Internet Public Private Partnership" (FI-PPP) program. The three SEs developed under the Electronic Health Record Application Support Service Enablers (EHR-EN) correspond to: a) an Electronic Health Record enabler (EHR SE), b) a patient summary enabler based on the EU project "European patient Summary Open Source services" (epSOS SE) supporting patient mobility and the offering of interoperable services, and c) a Picture Archiving and Communications System (PACS) enabler (PACS SE) based on the dcm4che open source system for the support of medical imaging functionality. The EHR SE follows the HL7 Clinical Document Architecture (CDA) V2.0 and supports the Integrating the Healthcare Enterprise (IHE) profiles (recently awarded in Connectathon 2015). These three FI-STAR platform enablers are designed to facilitate the deployment of innovative applications and value added services in the health care sector. They can be downloaded from the FI-STAR cataloque website. Work in progress focuses in the validation and evaluation scenarios for the proving and demonstration of the usability, applicability and adaptability of the proposed enablers.

Evaluation of Teacher Perceptions and Potential of OpenOffice in a K-12 School District

ERIC Educational Resources Information Center

Vajda, James; Abbitt, Jason T.

2011-01-01

Through this mixed-method evaluation study the authors investigated a pilot implementation of an open-source productivity suite for teachers in a K-12 public school district. The authors evaluated OpenOffice version 3.0 using measures identified by the technology acceptance model as predictors of acceptance and use of technology systems. During a…

OOPS, Turning MIT Opencourseware into Chinese: An Analysis of a Community of Practice of Global Translators

ERIC Educational Resources Information Center

Lee, Mimi Miyoung; Lin, Meng-Fen Grace; Bonk, Curtis J.

2007-01-01

An all-volunteer organization called the Opensource Opencourseware Prototype System (OOPS), headquartered in Taiwan, was initially designed to translate open source materials from MIT OpenCourseWare (OCW) site into Chinese. Given the recent plethora of open educational resources (OER), such as the OCW, the growing use of such resources by the…

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.

Web-based spatial analysis with the ILWIS open source GIS software and satellite images from GEONETCast

NASA Astrophysics Data System (ADS)

Lemmens, R.; Maathuis, B.; Mannaerts, C.; Foerster, T.; Schaeffer, B.; Wytzisk, A.

2009-12-01

This paper involves easy accessible integrated web-based analysis of satellite images with a plug-in based open source software. The paper is targeted to both users and developers of geospatial software. Guided by a use case scenario, we describe the ILWIS software and its toolbox to access satellite images through the GEONETCast broadcasting system. The last two decades have shown a major shift from stand-alone software systems to networked ones, often client/server applications using distributed geo-(web-)services. This allows organisations to combine without much effort their own data with remotely available data and processing functionality. Key to this integrated spatial data analysis is a low-cost access to data from within a user-friendly and flexible software. Web-based open source software solutions are more often a powerful option for developing countries. The Integrated Land and Water Information System (ILWIS) is a PC-based GIS & Remote Sensing software, comprising a complete package of image processing, spatial analysis and digital mapping and was developed as commercial software from the early nineties onwards. Recent project efforts have migrated ILWIS into a modular, plug-in-based open source software, and provide web-service support for OGC-based web mapping and processing. The core objective of the ILWIS Open source project is to provide a maintainable framework for researchers and software developers to implement training components, scientific toolboxes and (web-) services. The latest plug-ins have been developed for multi-criteria decision making, water resources analysis and spatial statistics analysis. The development of this framework is done since 2007 in the context of 52°North, which is an open initiative that advances the development of cutting edge open source geospatial software, using the GPL license. GEONETCast, as part of the emerging Global Earth Observation System of Systems (GEOSS), puts essential environmental data at the fingertips of users around the globe. This user-friendly and low-cost information dissemination provides global information as a basis for decision-making in a number of critical areas, including public health, energy, agriculture, weather, water, climate, natural disasters and ecosystems. GEONETCast makes available satellite images via Digital Video Broadcast (DVB) technology. An OGC WMS interface and plug-ins which convert GEONETCast data streams allow an ILWIS user to integrate various distributed data sources with data locally stored on his machine. Our paper describes a use case in which ILWIS is used with GEONETCast satellite imagery for decision making processes in Ghana. We also explain how the ILWIS software can be extended with additional functionality by means of building plug-ins and unfold our plans to implement other OGC standards, such as WCS and WPS in the same context. Especially, the latter one can be seen as a major step forward in terms of moving well-proven desktop based processing functionality to the web. This enables the embedding of ILWIS functionality in Spatial Data Infrastructures or even the execution in scalable and on-demand cloud computing environments.

Automated Transformation of CDISC ODM to OpenClinica.

PubMed

Gessner, Sophia; Storck, Michael; Hegselmann, Stefan; Dugas, Martin; Soto-Rey, Iñaki

2017-01-01

Due to the increasing use of electronic data capture systems for clinical research, the interest in saving resources by automatically generating and reusing case report forms in clinical studies is growing. OpenClinica, an open-source electronic data capture system enables the reuse of metadata in its own Excel import template, hampering the reuse of metadata defined in other standard formats. One of these standard formats is the Operational Data Model for metadata, administrative and clinical data in clinical studies. This work suggests a mapping from Operational Data Model to OpenClinica and describes the implementation of a converter to automatically generate OpenClinica conform case report forms based upon metadata in the Operational Data Model.

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

PubMed

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

2010-04-16

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

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

PubMed Central

2010-01-01

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

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

PubMed Central

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

2013-01-01

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

Open Source 3D Multipurpose Measurement System with Submillimetre Fidelity and First Application in Magnetic Resonance.

PubMed

Han, Haopeng; Moritz, Raphael; Oberacker, Eva; Waiczies, Helmar; Niendorf, Thoralf; Winter, Lukas

2017-10-18

Magnetic resonance imaging (MRI) is the mainstay of diagnostic imaging, a versatile instrument for clinical science and the subject of intense research interest. Advancing clinical science, research and technology of MRI requires high fidelity measurements in quantity, location and time of the given physical property. To meet this goal a broad spectrum of commercial measurement systems has been made available. These instruments frequently share in common that they are costly and typically employ closed proprietary hardware and software. This shortcoming makes any adjustment for a specified application difficult if not prohibitive. Recognizing this limitation this work presents COSI Measure, an automated open source measurement system that provides submillimetre resolution, robust configuration and a large working volume to support a versatile range of applications. The submillimetre fidelity and reproducibility/backlash performance were evaluated experimentally. Magnetic field mapping of a single ring Halbach magnet, a 3.0 T and a 7.0 T MR scanner as well as temperature mapping of a radio frequency coil were successfully conducted. Due to its open source nature and versatile construction, the system can be easily modified for other applications. In a resource limited research setting, COSI Measure makes efficient use of laboratory space, financial resources and collaborative efforts.

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

PubMed

Mueller, Shane T; Piper, Brian J

2014-01-30

We briefly describe the Psychology Experiment Building Language (PEBL), an open source software system for designing and running psychological experiments. 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. We report the results of benchmark tests that establish the timing precision of PEBL. We consider alternatives to the PEBL system and battery tests. We conclude with a discussion of the ethical factors involved in the open source testing movement. Copyright © 2013 Elsevier B.V. All rights reserved.

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

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

PubMed

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

2016-01-01

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

Open-source three-dimensional printing of biodegradable polymer scaffolds for tissue engineering.

PubMed

Trachtenberg, Jordan E; Mountziaris, Paschalia M; Miller, Jordan S; Wettergreen, Matthew; Kasper, Fred K; Mikos, Antonios G

2014-12-01

The fabrication of scaffolds for tissue engineering requires elements of customization depending on the application and is often limited due to the flexibility of the processing technique. This investigation seeks to address this obstacle by utilizing an open-source three-dimensional printing (3DP) system that allows vast customizability and facilitates reproduction of experiments. The effects of processing parameters on printed poly(ε-caprolactone) scaffolds with uniform and gradient pore architectures have been characterized with respect to fiber and pore morphology and mechanical properties. The results demonstrate the ability to tailor the fiber diameter, pore size, and porosity through modification of pressure, printing speed, and programmed fiber spacing. A model was also used to predict the compressive mechanical properties of uniform and gradient scaffolds, and it was found that modulus and yield strength declined with increasing porosity. The use of open-source 3DP technologies for printing tissue-engineering scaffolds provides a flexible system that can be readily modified at a low cost and is supported by community documentation. In this manner, the 3DP system is more accessible to the scientific community, which further facilitates the translation of these technologies toward successful tissue-engineering strategies.

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.

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

PubMed Central

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

2016-01-01

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

Vision Based Autonomous Robotic Control for Advanced Inspection and Repair

NASA Technical Reports Server (NTRS)

Wehner, Walter S.

2014-01-01

The advanced inspection system is an autonomous control and analysis system that improves the inspection and remediation operations for ground and surface systems. It uses optical imaging technology with intelligent computer vision algorithms to analyze physical features of the real-world environment to make decisions and learn from experience. The advanced inspection system plans to control a robotic manipulator arm, an unmanned ground vehicle and cameras remotely, automatically and autonomously. There are many computer vision, image processing and machine learning techniques available as open source for using vision as a sensory feedback in decision-making and autonomous robotic movement. My responsibilities for the advanced inspection system are to create a software architecture that integrates and provides a framework for all the different subsystem components; identify open-source algorithms and techniques; and integrate robot hardware.

OpenDanubia - An integrated, modular simulation system to support regional water resource management

NASA Astrophysics Data System (ADS)

Muerth, M.; Waldmann, D.; Heinzeller, C.; Hennicker, R.; Mauser, W.

2012-04-01

The already completed, multi-disciplinary research project GLOWA-Danube has developed a regional scale, integrated modeling system, which was successfully applied on the 77,000 km2 Upper Danube basin to investigate the impact of Global Change on both the natural and anthropogenic water cycle. At the end of the last project phase, the integrated modeling system was transferred into the open source project OpenDanubia, which now provides both the core system as well as all major model components to the general public. First, this will enable decision makers from government, business and management to use OpenDanubia as a tool for proactive management of water resources in the context of global change. Secondly, the model framework to support integrated simulations and all simulation models developed for OpenDanubia in the scope of GLOWA-Danube are further available for future developments and research questions. OpenDanubia allows for the investigation of water-related scenarios considering different ecological and economic aspects to support both scientists and policy makers to design policies for sustainable environmental management. OpenDanubia is designed as a framework-based, distributed system. The model system couples spatially distributed physical and socio-economic process during run-time, taking into account their mutual influence. To simulate the potential future impacts of Global Change on agriculture, industrial production, water supply, households and tourism businesses, so-called deep actor models are implemented in OpenDanubia. All important water-related fluxes and storages in the natural environment are implemented in OpenDanubia as spatially explicit, process-based modules. This includes the land surface water and energy balance, dynamic plant water uptake, ground water recharge and flow as well as river routing and reservoirs. Although the complete system is relatively demanding on data requirements and hardware requirements, the modular structure and the generic core system (Core Framework, Actor Framework) allows the application in new regions and the selection of a reduced number of modules for simulation. As part of the Open Source Initiative in GLOWA-Danube (opendanubia.glowa-danube.de) a comprehensive documentation for the system installation was created and both the program code of the framework and of all major components is licensed under the GNU General Public License. In addition, some helpful programs and scripts necessary for the operation and processing of input and result data sets are provided.

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

PubMed

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

2017-10-10

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

33 CFR 127.607 - Fire main systems.

Code of Federal Regulations, 2010 CFR

2010-07-01

... meter (75 p.s.i.), the two outlets having the greatest pressure drop between the source of water and the hose or monitor nozzle, when only those two outlets are open. (d) If the source of water for the fire... marine transfer area for LNG must have a fire main system that provides at least two water streams to...

Integration of Ground-Based Solar FT-IR Absorption Spectroscopy and Open-Path Systems for Atmospheric Analysis

NASA Astrophysics Data System (ADS)

Steill, J. D.; Hager, J. S.; Compton, R. N.

2006-05-01

Air quality issues in the Knoxville and East Tennessee region are of great concern, particularly as regards the nearby Great Smoky Mountains National Park. Infrared absorption spectroscopy of the atmosphere provides a unique opportunity to analyze the local chemical composition, since many trace atmospheric constituents are open to this analysis, such as O3, CO, CH4, and N2O. Integration of a Bomem DA8 FT-IR spectrometer with rooftop sun-tracking optics and an open-path system provide solar-sourced and boundary- layer atmospheric infrared spectra of these and other relevant atmospheric components. Boundary layer concentrations as well as total column abundances and vertical concentration profiles are derived. Vertical concentration profiles are determined by fitting solar-sourced absorbance lines with the SFIT2 algorithm. Improved fitting of solar spectra has been demonstrated by incorporating the tropospheric concentrations as determined by open-path measurements. A record of solar-sourced atmospheric spectra of greater than two years duration is under analysis to characterize experimental error and thus the limit of precision in the concentration determinations. Initial efforts using atmospheric O2 as a calibration indicate the solar- sourced spectra may not yet meet the precision required for accurate atmospheric CO2 quantification by such efforts as the OCO and NDSC. However, this variability is also indicative of local concentration fluxes pertinent to the regional atmospheric chemistry. In addition to providing a means to improve the analysis of solar spectra, the open-path data is useful for elucidation of seasonal and diurnal trends in the local trace gas concentrations.

Open-source software for collision detection in external beam radiation therapy

NASA Astrophysics Data System (ADS)

Suriyakumar, Vinith M.; Xu, Renee; Pinter, Csaba; Fichtinger, Gabor

2017-03-01

PURPOSE: Collision detection for external beam radiation therapy (RT) is important for eliminating the need for dryruns that aim to ensure patient safety. Commercial treatment planning systems (TPS) offer this feature but they are expensive and proprietary. Cobalt-60 RT machines are a viable solution to RT practice in low-budget scenarios. However, such clinics are hesitant to invest in these machines due to a lack of affordable treatment planning software. We propose the creation of an open-source room's eye view visualization module with automated collision detection as part of the development of an open-source TPS. METHODS: An openly accessible linac 3D geometry model is sliced into the different components of the treatment machine. The model's movements are based on the International Electrotechnical Commission standard. Automated collision detection is implemented between the treatment machine's components. RESULTS: The room's eye view module was built in C++ as part of SlicerRT, an RT research toolkit built on 3D Slicer. The module was tested using head and neck and prostate RT plans. These tests verified that the module accurately modeled the movements of the treatment machine and radiation beam. Automated collision detection was verified using tests where geometric parameters of the machine's components were changed, demonstrating accurate collision detection. CONCLUSION: Room's eye view visualization and automated collision detection are essential in a Cobalt-60 treatment planning system. Development of these features will advance the creation of an open-source TPS that will potentially help increase the feasibility of adopting Cobalt-60 RT.

An Open Source Graphical User Interface Surrogate C2 System for Battle Management Language Experimentation

DTIC Science & Technology

2011-06-01

file –  Open source at http://c4i.gmu.edu/BML 10 BMLC2GUI ICCRTS’11-175 BML C2 GUI Scripted BML Web Service v2 09F- SIW -015 11 ! BML C2...BMLC2GUI ICCRTS’11-175 17 Publish/Subscribe Architecture BMLC2GUI ICCRTS’11-175 SBML in NATO MSG-048 •  Paper 10S- SIW -049 describes a significant...from C2LG GUI: –  Open resource –  Quick response to changes –  Ease of use –  Low development cost Scripted BML Web Service v2 09F- SIW -015

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.

Multicriteria analysis using open-source data and software for the implementation of a centralized biomedical waste management system in a developing country (Guinea, Conakry).

NASA Astrophysics Data System (ADS)

Pérez Peña, José Vicente; Baldó, Mane; Acosta, Yarci; Verschueren, Laurent; Thibaud, Kenmognie; Bilivogui, Pépé; Jean-Paul Ngandu, Alain; Beavogui, Maoro

2017-04-01

In the last decade the increasing interest for public health has promoted specific regulations for the transport, storage, transformation and/or elimination of potentially toxic waste. A special concern should focus on the effective management of biomedical waste, due to the environmental and health risk associated with them. The first stage for the effective management these waste includes the selection of the best sites for the location of facilities for its storage and/or elimination. Best-site selection is accomplished by means of multi-criteria decision analyses (MCDA) that aim to minimize the social and environmental impact, and to maximize management efficiency. In this work we presented a methodology that uses open-source software and data to analyze the best location for the implantation of a centralized waste management system in a developing country (Guinea, Conakry). We applied an analytical hierarchy process (AHP) using different thematic layers such as land use (derived from up-to-date Sentinel 2 remote sensing images), soil type, distance and type of roads, hydrography, distance to dense populated areas, etc. Land-use data were derived from up-to-date Sentinel 2 remote sensing images, whereas roads and hydrography were obtained from the Open Street Map database and latter validated with administrative data. We performed the AHP analysis with the aid of QGIS open-software Geospatial Information System. This methodology is very effective for developing countries as it uses open-source software and data for the MCDA analysis, thus reducing costs in these first stages of the integrated analysis.

QuTiP: An open-source Python framework for the dynamics of open quantum systems

NASA Astrophysics Data System (ADS)

Johansson, J. R.; Nation, P. D.; Nori, Franco

2012-08-01

We present an object-oriented open-source framework for solving the dynamics of open quantum systems written in Python. Arbitrary Hamiltonians, including time-dependent systems, may be built up from operators and states defined by a quantum object class, and then passed on to a choice of master equation or Monte Carlo solvers. We give an overview of the basic structure for the framework before detailing the numerical simulation of open system dynamics. Several examples are given to illustrate the build up to a complete calculation. Finally, we measure the performance of our library against that of current implementations. The framework described here is particularly well suited to the fields of quantum optics, superconducting circuit devices, nanomechanics, and trapped ions, while also being ideal for use in classroom instruction. Catalogue identifier: AEMB_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEMB_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 16 482 No. of bytes in distributed program, including test data, etc.: 213 438 Distribution format: tar.gz Programming language: Python Computer: i386, x86-64 Operating system: Linux, Mac OSX, Windows RAM: 2+ Gigabytes Classification: 7 External routines: NumPy (http://numpy.scipy.org/), SciPy (http://www.scipy.org/), Matplotlib (http://matplotlib.sourceforge.net/) Nature of problem: Dynamics of open quantum systems. Solution method: Numerical solutions to Lindblad master equation or Monte Carlo wave function method. Restrictions: Problems must meet the criteria for using the master equation in Lindblad form. Running time: A few seconds up to several tens of minutes, depending on size of underlying Hilbert space.

Curriculum-Guided Crowd Sourcing of Assessments in a Developing Country

ERIC Educational Resources Information Center

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

2012-01-01

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

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…

A Study of Clinically Related Open Source Software Projects

PubMed Central

Hogarth, Michael A.; Turner, Stuart

2005-01-01

Open source software development has recently gained significant interest due to several successful mainstream open source projects. This methodology has been proposed as being similarly viable and beneficial in the clinical application domain as well. However, the clinical software development venue differs significantly from the mainstream software venue. Existing clinical open source projects have not been well characterized nor formally studied so the ‘fit’ of open source in this domain is largely unknown. In order to better understand the open source movement in the clinical application domain, we undertook a study of existing open source clinical projects. In this study we sought to characterize and classify existing clinical open source projects and to determine metrics for their viability. This study revealed several findings which we believe could guide the healthcare community in its quest for successful open source clinical software projects. PMID:16779056

Structure for common access and support of fuel cell stacks

DOEpatents

Walsh, Michael M.

2000-01-01

A structure provides common support and access to multiple fuel cells externally mounted thereto. The structure has openings leading to passages defined therein for providing the access. Various other fuel cell power system components are connected at the openings, such as reactant and coolant sources.

Ricardo Oliveira | NREL

Science.gov Websites

the System Modeling & Geospatial Data Science Group in the Strategic Energy Analysis Center. Areas Publications Oliveira, R and Moreno, R. 2016. Harvesting, Integrating and Distributing Large Open Geospatial Datasets Using Free and Open-Source Software. Int. Arch. Photogramm. Remote Sens. Spatial Inf. Sci., XLI-B7

GridAPPS-D

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

2017-03-28

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

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

PubMed

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

2012-06-28

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

Mushu, a free- and open source BCI signal acquisition, written in Python.

PubMed

Venthur, Bastian; Blankertz, Benjamin

2012-01-01

The following paper describes Mushu, a signal acquisition software for retrieval and online streaming of Electroencephalography (EEG) data. It is written, but not limited, to the needs of Brain Computer Interfacing (BCI). It's main goal is to provide a unified interface to EEG data regardless of the amplifiers used. It runs under all major operating systems, like Windows, Mac OS and Linux, is written in Python and is free- and open source software licensed under the terms of the GNU General Public License.

The MyHealthService approach for chronic disease management based on free open source software and low cost components.

PubMed

Vognild, Lars K; Burkow, Tatjana M; Luque, Luis Fernandez

2009-01-01

In this paper we present an approach to building personal health services, supporting following-up, physical exercising, health education, and psychosocial support for the chronically ill, based on free open source software and low-cost computers, mobile devices, and consumer health and fitness devices. We argue that this will lower the cost of the systems, which is important given the increasing number of people with chronicle diseases and limited healthcare budgets.

QuantumOptics.jl: A Julia framework for simulating open quantum systems

NASA Astrophysics Data System (ADS)

Krämer, Sebastian; Plankensteiner, David; Ostermann, Laurin; Ritsch, Helmut

2018-06-01

We present an open source computational framework geared towards the efficient numerical investigation of open quantum systems written in the Julia programming language. Built exclusively in Julia and based on standard quantum optics notation, the toolbox offers speed comparable to low-level statically typed languages, without compromising on the accessibility and code readability found in dynamic languages. After introducing the framework, we highlight its features and showcase implementations of generic quantum models. Finally, we compare its usability and performance to two well-established and widely used numerical quantum libraries.

Technical Note: FreeCT_ICD: An Open Source Implementation of a Model-Based Iterative Reconstruction Method using Coordinate Descent Optimization for CT Imaging Investigations.

PubMed

Hoffman, John M; Noo, Frédéric; Young, Stefano; Hsieh, Scott S; McNitt-Gray, Michael

2018-06-01

To facilitate investigations into the impacts of acquisition and reconstruction parameters on quantitative imaging, radiomics and CAD using CT imaging, we previously released an open source implementation of a conventional weighted filtered backprojection reconstruction called FreeCT_wFBP. Our purpose was to extend that work by providing an open-source implementation of a model-based iterative reconstruction method using coordinate descent optimization, called FreeCT_ICD. Model-based iterative reconstruction offers the potential for substantial radiation dose reduction, but can impose substantial computational processing and storage requirements. FreeCT_ICD is an open source implementation of a model-based iterative reconstruction method that provides a reasonable tradeoff between these requirements. This was accomplished by adapting a previously proposed method that allows the system matrix to be stored with a reasonable memory requirement. The method amounts to describing the attenuation coefficient using rotating slices that follow the helical geometry. In the initially-proposed version, the rotating slices are themselves described using blobs. We have replaced this description by a unique model that relies on tri-linear interpolation together with the principles of Joseph's method. This model offers an improvement in memory requirement while still allowing highly accurate reconstruction for conventional CT geometries. The system matrix is stored column-wise and combined with an iterative coordinate descent (ICD) optimization. The result is FreeCT_ICD, which is a reconstruction program developed on the Linux platform using C++ libraries and the open source GNU GPL v2.0 license. The software is capable of reconstructing raw projection data of helical CT scans. In this work, the software has been described and evaluated by reconstructing datasets exported from a clinical scanner which consisted of an ACR accreditation phantom dataset and a clinical pediatric thoracic scan. For the ACR phantom, image quality was comparable to clinical reconstructions as well as reconstructions using open-source FreeCT_wFBP software. The pediatric thoracic scan also yielded acceptable results. In addition, we did not observe any deleterious impact in image quality associated with the utilization of rotating slices. These evaluations also demonstrated reasonable tradeoffs in storage requirements and computational demands. FreeCT_ICD is an open-source implementation of a model-based iterative reconstruction method that extends the capabilities of previously released open source reconstruction software and provides the ability to perform vendor-independent reconstructions of clinically acquired raw projection data. This implementation represents a reasonable tradeoff between storage and computational requirements and has demonstrated acceptable image quality in both simulated and clinical image datasets. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

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…

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.

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.

Brunn: an open source laboratory information system for microplates with a graphical plate layout design process.

PubMed

Alvarsson, Jonathan; Andersson, Claes; Spjuth, Ola; Larsson, Rolf; Wikberg, Jarl E S

2011-05-20

Compound profiling and drug screening generates large amounts of data and is generally based on microplate assays. Current information systems used for handling this are mainly commercial, closed source, expensive, and heavyweight and there is a need for a flexible lightweight open system for handling plate design, and validation and preparation of data. A Bioclipse plugin consisting of a client part and a relational database was constructed. A multiple-step plate layout point-and-click interface was implemented inside Bioclipse. The system contains a data validation step, where outliers can be removed, and finally a plate report with all relevant calculated data, including dose-response curves. Brunn is capable of handling the data from microplate assays. It can create dose-response curves and calculate IC50 values. Using a system of this sort facilitates work in the laboratory. Being able to reuse already constructed plates and plate layouts by starting out from an earlier step in the plate layout design process saves time and cuts down on error sources.

OpenSHMEM-UCX : Evaluation of UCX for implementing OpenSHMEM Programming Model

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

Baker, Matthew B; Gorentla Venkata, Manjunath; Aderholdt, William Ferrol

2016-01-01

The OpenSHMEM reference implementation was developed towards the goal of developing an open source and high-performing Open- SHMEM implementation. To achieve portability and performance across various networks, the OpenSHMEM reference implementation uses GAS- Net and UCCS for network operations. Recently, new network layers have emerged with the promise of providing high-performance, scalabil- ity, and portability for HPC applications. In this paper, we implement the OpenSHMEM reference implementation to use the UCX framework for network operations. Then, we evaluate its performance and scalabil- ity on Cray XK systems to understand UCX s suitability for developing the OpenSHMEM programming model. Further, wemore » develop a bench- mark called SHOMS for evaluating the OpenSHMEM implementation. Our experimental results show that OpenSHMEM-UCX outperforms the vendor supplied OpenSHMEM implementation in most cases on the Cray XK system by up to 40% with respect to message rate and up to 70% for the execution of application kernels.« less

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

Open-Source Development of the Petascale Reactive Flow and Transport Code PFLOTRAN

NASA Astrophysics Data System (ADS)

Hammond, G. E.; Andre, B.; Bisht, G.; Johnson, T.; Karra, S.; Lichtner, P. C.; Mills, R. T.

2013-12-01

Open-source software development has become increasingly popular in recent years. Open-source encourages collaborative and transparent software development and promotes unlimited free redistribution of source code to the public. Open-source development is good for science as it reveals implementation details that are critical to scientific reproducibility, but generally excluded from journal publications. In addition, research funds that would have been spent on licensing fees can be redirected to code development that benefits more scientists. In 2006, the developers of PFLOTRAN open-sourced their code under the U.S. Department of Energy SciDAC-II program. Since that time, the code has gained popularity among code developers and users from around the world seeking to employ PFLOTRAN to simulate thermal, hydraulic, mechanical and biogeochemical processes in the Earth's surface/subsurface environment. PFLOTRAN is a massively-parallel subsurface reactive multiphase flow and transport simulator designed from the ground up to run efficiently on computing platforms ranging from the laptop to leadership-class supercomputers, all from a single code base. The code employs domain decomposition for parallelism and is founded upon the well-established and open-source parallel PETSc and HDF5 frameworks. PFLOTRAN leverages modern Fortran (i.e. Fortran 2003-2008) in its extensible object-oriented design. The use of this progressive, yet domain-friendly programming language has greatly facilitated collaboration in the code's software development. Over the past year, PFLOTRAN's top-level data structures were refactored as Fortran classes (i.e. extendible derived types) to improve the flexibility of the code, ease the addition of new process models, and enable coupling to external simulators. For instance, PFLOTRAN has been coupled to the parallel electrical resistivity tomography code E4D to enable hydrogeophysical inversion while the same code base can be used as a third-party library to provide hydrologic flow, energy transport, and biogeochemical capability to the community land model, CLM, part of the open-source community earth system model (CESM) for climate. In this presentation, the advantages and disadvantages of open source software development in support of geoscience research at government laboratories, universities, and the private sector are discussed. Since the code is open-source (i.e. it's transparent and readily available to competitors), the PFLOTRAN team's development strategy within a competitive research environment is presented. Finally, the developers discuss their approach to object-oriented programming and the leveraging of modern Fortran in support of collaborative geoscience research as the Fortran standard evolves among compiler vendors.

Building Energy Management Open Source Software

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

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

Datacube Services in Action, Using Open Source and Open Standards

NASA Astrophysics Data System (ADS)

Baumann, P.; Misev, D.

2016-12-01

Array Databases comprise novel, promising technology for massive spatio-temporal datacubes, extending the SQL paradigm of "any query, anytime" to n-D arrays. On server side, such queries can be optimized, parallelized, and distributed based on partitioned array storage. The rasdaman ("raster data manager") system, which has pioneered Array Databases, is available in open source on www.rasdaman.org. Its declarative query language extends SQL with array operators which are optimized and parallelized on server side. The rasdaman engine, which is part of OSGeo Live, is mature and in operational use databases individually holding dozens of Terabytes. Further, the rasdaman concepts have strongly impacted international Big Data standards in the field, including the forthcoming MDA ("Multi-Dimensional Array") extension to ISO SQL, the OGC Web Coverage Service (WCS) and Web Coverage Processing Service (WCPS) standards, and the forthcoming INSPIRE WCS/WCPS; in both OGC and INSPIRE, OGC is WCS Core Reference Implementation. In our talk we present concepts, architecture, operational services, and standardization impact of open-source rasdaman, as well as experiences made.

High-performance semiconductor quantum-dot single-photon sources

NASA Astrophysics Data System (ADS)

Senellart, Pascale; Solomon, Glenn; White, Andrew

2017-11-01

Single photons are a fundamental element of most quantum optical technologies. The ideal single-photon source is an on-demand, deterministic, single-photon source delivering light pulses in a well-defined polarization and spatiotemporal mode, and containing exactly one photon. In addition, for many applications, there is a quantum advantage if the single photons are indistinguishable in all their degrees of freedom. Single-photon sources based on parametric down-conversion are currently used, and while excellent in many ways, scaling to large quantum optical systems remains challenging. In 2000, semiconductor quantum dots were shown to emit single photons, opening a path towards integrated single-photon sources. Here, we review the progress achieved in the past few years, and discuss remaining challenges. The latest quantum dot-based single-photon sources are edging closer to the ideal single-photon source, and have opened new possibilities for quantum technologies.

Development of Simulated Disturbing Source for Isolation Switch

NASA Astrophysics Data System (ADS)

Cheng, Lin; Liu, Xiang; Deng, Xiaoping; Pan, Zhezhe; Zhou, Hang; Zhu, Yong

2018-01-01

In order to simulate the substation in the actual scene of the harsh electromagnetic environment, and then research on electromagnetic compatibility testing of electronic instrument transformer, On the basis of the original isolation switch as a harassment source of the electronic instrument transformer electromagnetic compatibility test system, an isolated switch simulation source system was developed, to promote the standardization of the original test. In this paper, the circuit breaker is used to control the opening and closing of the gap arc to simulate the operating of isolating switch, and the isolation switch simulation harassment source system is designed accordingly. Comparison with the actual test results of the isolating switch, it is proved that the system can meet the test requirements, and the simulation harassment source system has good stability and high reliability.

BioSig: The Free and Open Source Software Library for Biomedical Signal Processing

PubMed Central

Vidaurre, Carmen; Sander, Tilmann H.; Schlögl, Alois

2011-01-01

BioSig is an open source software library for biomedical signal processing. The aim of the BioSig project is to foster research in biomedical signal processing by providing free and open source software tools for many different application areas. Some of the areas where BioSig can be employed are neuroinformatics, brain-computer interfaces, neurophysiology, psychology, cardiovascular systems, and sleep research. Moreover, the analysis of biosignals such as the electroencephalogram (EEG), electrocorticogram (ECoG), electrocardiogram (ECG), electrooculogram (EOG), electromyogram (EMG), or respiration signals is a very relevant element of the BioSig project. Specifically, BioSig provides solutions for data acquisition, artifact processing, quality control, feature extraction, classification, modeling, and data visualization, to name a few. In this paper, we highlight several methods to help students and researchers to work more efficiently with biomedical signals. PMID:21437227

BioSig: the free and open source software library for biomedical signal processing.

PubMed

Vidaurre, Carmen; Sander, Tilmann H; Schlögl, Alois

2011-01-01

BioSig is an open source software library for biomedical signal processing. The aim of the BioSig project is to foster research in biomedical signal processing by providing free and open source software tools for many different application areas. Some of the areas where BioSig can be employed are neuroinformatics, brain-computer interfaces, neurophysiology, psychology, cardiovascular systems, and sleep research. Moreover, the analysis of biosignals such as the electroencephalogram (EEG), electrocorticogram (ECoG), electrocardiogram (ECG), electrooculogram (EOG), electromyogram (EMG), or respiration signals is a very relevant element of the BioSig project. Specifically, BioSig provides solutions for data acquisition, artifact processing, quality control, feature extraction, classification, modeling, and data visualization, to name a few. In this paper, we highlight several methods to help students and researchers to work more efficiently with biomedical signals.

Current interruption in inductive storage systems with inertial current source

NASA Astrophysics Data System (ADS)

Vitkovitsky, I. M.; Conte, D.; Ford, R. D.; Lupton, W. H.

1980-03-01

Utilization of inertial current source inductive storage with high power output requires a switch with short opening time. This switch must operate as a circuit breaker, i.e., be capable to carry the current for a time period characteristic of inertial systems, such as homopolar generators. For reasonable efficiency, its opening time must be fast to minimize the energy dissipated in downstream fuse stages required for any additional pulse compression. A switch that satisfies these criteria, as well as other requirements such as that for high voltage operation associated with high power output, is an explosively driven switch consisting of large number of gaps arranged in series. The performance of this switch in limiting and/or interrupting currents produced by large generators has been studied. Single switch modules were designed and tested for limiting the commutating current output of 1 MW, 60 Hz, generator and 500 KJ capacitor banks. Current limiting and commutation were evaluated, using these sources, for currents ranging up to 0.4 MA. The explosive opening of the switch was found to provide an effective first stage for further pulse compression. It opens in tens of microseconds, commutates current at high efficiency ( = 905) recovers very rapidly over a wide range of operating conditions.

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

PubMed Central

Akrivopoulos, Orestis

2017-01-01

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

Breaking Away

ERIC Educational Resources Information Center

Panettieri, Joseph C.

2007-01-01

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

77 FR 40630 - Privacy Act of 1974; System of Records

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-10

... the United States against terrorist and foreign intelligence threats and to enforce U.S. criminal laws..., informants, sources, bystanders, law enforcement personnel, intelligence personnel, other responders... intelligence operation; individuals who are identified in open source information or commercial databases, or...

48 CFR 2901.603-70 - Responsibility of other government personnel.

Code of Federal Regulations, 2011 CFR

2011-10-01

... and open competition are satisfied to the maximum extent practicable. Sole source purchases may only... LABOR GENERAL DEPARTMENT OF LABOR ACQUISITION REGULATION SYSTEM Career Development, Contracting... being overly restrictive in accordance with FAR 11.002; (2) Competitive sources are solicited, evaluated...

Spectral-element Seismic Wave Propagation on CUDA/OpenCL Hardware Accelerators

NASA Astrophysics Data System (ADS)

Peter, D. B.; Videau, B.; Pouget, K.; Komatitsch, D.

2015-12-01

Seismic wave propagation codes are essential tools to investigate a variety of wave phenomena in the Earth. Furthermore, they can now be used for seismic full-waveform inversions in regional- and global-scale adjoint tomography. Although these seismic wave propagation solvers are crucial ingredients to improve the resolution of tomographic images to answer important questions about the nature of Earth's internal processes and subsurface structure, their practical application is often limited due to high computational costs. They thus need high-performance computing (HPC) facilities to improving the current state of knowledge. At present, numerous large HPC systems embed many-core architectures such as graphics processing units (GPUs) to enhance numerical performance. Such hardware accelerators can be programmed using either the CUDA programming environment or the OpenCL language standard. CUDA software development targets NVIDIA graphic cards while OpenCL was adopted by additional hardware accelerators, like e.g. AMD graphic cards, ARM-based processors as well as Intel Xeon Phi coprocessors. For seismic wave propagation simulations using the open-source spectral-element code package SPECFEM3D_GLOBE, we incorporated an automatic source-to-source code generation tool (BOAST) which allows us to use meta-programming of all computational kernels for forward and adjoint runs. Using our BOAST kernels, we generate optimized source code for both CUDA and OpenCL languages within the source code package. Thus, seismic wave simulations are able now to fully utilize CUDA and OpenCL hardware accelerators. We show benchmarks of forward seismic wave propagation simulations using SPECFEM3D_GLOBE on CUDA/OpenCL GPUs, validating results and comparing performances for different simulations and hardware usages.

General Mission Analysis Tool (GMAT) Architectural Specification. Draft

NASA Technical Reports Server (NTRS)

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

2007-01-01

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

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.

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

NASA Astrophysics Data System (ADS)

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

2011-12-01

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

Modular Open System Architecture for Reducing Contamination Risk in the Space and Missile Defense Supply Chain

NASA Technical Reports Server (NTRS)

Seasly, Elaine

2015-01-01

To combat contamination of physical assets and provide reliable data to decision makers in the space and missile defense community, a modular open system architecture for creation of contamination models and standards is proposed. Predictive tools for quantifying the effects of contamination can be calibrated from NASA data of long-term orbiting assets. This data can then be extrapolated to missile defense predictive models. By utilizing a modular open system architecture, sensitive data can be de-coupled and protected while benefitting from open source data of calibrated models. This system architecture will include modules that will allow the designer to trade the effects of baseline performance against the lifecycle degradation due to contamination while modeling the lifecycle costs of alternative designs. In this way, each member of the supply chain becomes an informed and active participant in managing contamination risk early in the system lifecycle.

Open source electronic health record and patient data management system for intensive care.

PubMed

Massaut, Jacques; Reper, Pascal

2008-01-01

In Intensive Care Units, the amount of data to be processed for patients care, the turn over of the patients, the necessity for reliability and for review processes indicate the use of Patient Data Management Systems (PDMS) and electronic health records (EHR). To respond to the needs of an Intensive Care Unit and not to be locked with proprietary software, we developed a PDMS and EHR based on open source software and components. The software was designed as a client-server architecture running on the Linux operating system and powered by the PostgreSQL data base system. The client software was developed in C using GTK interface library. The application offers to the users the following functions: medical notes captures, observations and treatments, nursing charts with administration of medications, scoring systems for classification, and possibilities to encode medical activities for billing processes. Since his deployment in February 2004, the PDMS was used to care more than three thousands patients with the expected software reliability and facilitated data management and review processes. Communications with other medical software were not developed from the start, and are realized by the use of the Mirth HL7 communication engine. Further upgrade of the system will include multi-platform support, use of typed language with static analysis, and configurable interface. The developed system based on open source software components was able to respond to the medical needs of the local ICU environment. The use of OSS for development allowed us to customize the software to the preexisting organization and contributed to the acceptability of the whole system.

Security of patient data when decommissioning ultrasound systems

PubMed Central

2017-01-01

Background Although ultrasound systems generally archive to Picture Archiving and Communication Systems (PACS), their archiving workflow typically involves storage to an internal hard disk before data are transferred onwards. Deleting records from the local system will delete entries in the database and from the file allocation table or equivalent but, as with a PC, files can be recovered. Great care is taken with disposal of media from a healthcare organisation to prevent data breaches, but ultrasound systems are routinely returned to lease companies, sold on or donated to third parties without such controls. Methods In this project, five methods of hard disk erasure were tested on nine ultrasound systems being decommissioned: the system’s own delete function; full reinstallation of system software; the manufacturer’s own disk wiping service; open source disk wiping software for full and just blank space erasure. Attempts were then made to recover data using open source recovery tools. Results All methods deleted patient data as viewable from the ultrasound system and from browsing the disk from a PC. However, patient identifiable data (PID) could be recovered following the system’s own deletion and the reinstallation methods. No PID could be recovered after using the manufacturer’s wiping service or the open source wiping software. Conclusion The typical method of reinstalling an ultrasound system’s software may not prevent PID from being recovered. When transferring ownership, care should be taken that an ultrasound system’s hard disk has been wiped to a sufficient level, particularly if the scanner is to be returned with approved parts and in a fully working state. PMID:28228821

MetaLIMS, a simple open-source laboratory information management system for small metagenomic labs

PubMed Central

Gaultier, Nicolas Paul Eugène; Miller, Dana; Purbojati, Rikky Wenang; Lauro, Federico M.

2017-01-01

Abstract Background: As the cost of sequencing continues to fall, smaller groups increasingly initiate and manage larger sequencing projects and take on the complexity of data storage for high volumes of samples. This has created a need for low-cost laboratory information management systems (LIMS) that contain flexible fields to accommodate the unique nature of individual labs. Many labs do not have a dedicated information technology position, so LIMS must also be easy to setup and maintain with minimal technical proficiency. Findings: MetaLIMS is a free and open-source web-based application available via GitHub. The focus of MetaLIMS is to store sample metadata prior to sequencing and analysis pipelines. Initially designed for environmental metagenomics labs, in addition to storing generic sample collection information and DNA/RNA processing information, the user can also add fields specific to the user's lab. MetaLIMS can also produce a basic sequencing submission form compatible with the proprietary Clarity LIMS system used by some sequencing facilities. To help ease the technical burden associated with web deployment, MetaLIMS options the use of commercial web hosting combined with MetaLIMS bash scripts for ease of setup. Conclusions: MetaLIMS overcomes key challenges common in LIMS by giving labs access to a low-cost and open-source tool that also has the flexibility to meet individual lab needs and an option for easy deployment. By making the web application open source and hosting it on GitHub, we hope to encourage the community to build upon MetaLIMS, making it more robust and tailored to the needs of more researchers. PMID:28430964

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.

MetaLIMS, a simple open-source laboratory information management system for small metagenomic labs.

PubMed

Heinle, Cassie Elizabeth; Gaultier, Nicolas Paul Eugène; Miller, Dana; Purbojati, Rikky Wenang; Lauro, Federico M

2017-06-01

As the cost of sequencing continues to fall, smaller groups increasingly initiate and manage larger sequencing projects and take on the complexity of data storage for high volumes of samples. This has created a need for low-cost laboratory information management systems (LIMS) that contain flexible fields to accommodate the unique nature of individual labs. Many labs do not have a dedicated information technology position, so LIMS must also be easy to setup and maintain with minimal technical proficiency. MetaLIMS is a free and open-source web-based application available via GitHub. The focus of MetaLIMS is to store sample metadata prior to sequencing and analysis pipelines. Initially designed for environmental metagenomics labs, in addition to storing generic sample collection information and DNA/RNA processing information, the user can also add fields specific to the user's lab. MetaLIMS can also produce a basic sequencing submission form compatible with the proprietary Clarity LIMS system used by some sequencing facilities. To help ease the technical burden associated with web deployment, MetaLIMS options the use of commercial web hosting combined with MetaLIMS bash scripts for ease of setup. MetaLIMS overcomes key challenges common in LIMS by giving labs access to a low-cost and open-source tool that also has the flexibility to meet individual lab needs and an option for easy deployment. By making the web application open source and hosting it on GitHub, we hope to encourage the community to build upon MetaLIMS, making it more robust and tailored to the needs of more researchers. © The Authors 2017. Published by Oxford University Press.

MITK-OpenIGTLink for combining open-source toolkits in real-time computer-assisted interventions.

PubMed

Klemm, Martin; Kirchner, Thomas; Gröhl, Janek; Cheray, Dominique; Nolden, Marco; Seitel, Alexander; Hoppe, Harald; Maier-Hein, Lena; Franz, Alfred M

2017-03-01

Due to rapid developments in the research areas of medical imaging, medical image processing and robotics, computer-assisted interventions (CAI) are becoming an integral part of modern patient care. From a software engineering point of view, these systems are highly complex and research can benefit greatly from reusing software components. This is supported by a number of open-source toolkits for medical imaging and CAI such as the medical imaging interaction toolkit (MITK), the public software library for ultrasound imaging research (PLUS) and 3D Slicer. An independent inter-toolkit communication such as the open image-guided therapy link (OpenIGTLink) can be used to combine the advantages of these toolkits and enable an easier realization of a clinical CAI workflow. MITK-OpenIGTLink is presented as a network interface within MITK that allows easy to use, asynchronous two-way messaging between MITK and clinical devices or other toolkits. Performance and interoperability tests with MITK-OpenIGTLink were carried out considering the whole CAI workflow from data acquisition over processing to visualization. We present how MITK-OpenIGTLink can be applied in different usage scenarios. In performance tests, tracking data were transmitted with a frame rate of up to 1000 Hz and a latency of 2.81 ms. Transmission of images with typical ultrasound (US) and greyscale high-definition (HD) resolutions of [Formula: see text] and [Formula: see text] is possible at up to 512 and 128 Hz, respectively. With the integration of OpenIGTLink into MITK, this protocol is now supported by all established open-source toolkits in the field. This eases interoperability between MITK and toolkits such as PLUS or 3D Slicer and facilitates cross-toolkit research collaborations. MITK and its submodule MITK-OpenIGTLink are provided open source under a BSD-style licence ( http://mitk.org ).

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.

Open Source Virtual Worlds and Low Cost Sensors for Physical Rehab of Patients with Chronic Diseases

NASA Astrophysics Data System (ADS)

Romero, Salvador J.; Fernandez-Luque, Luis; Sevillano, José L.; Vognild, Lars

For patients with chronic diseases, exercise is a key part of rehab to deal better with their illness. Some of them do rehabilitation at home with telemedicine systems. However, keeping to their exercising program is challenging and many abandon the rehabilitation. We postulate that information technologies for socializing and serious games can encourage patients to keep doing physical exercise and rehab. In this paper we present Virtual Valley, a low cost telemedicine system for home exercising, based on open source virtual worlds and utilizing popular low cost motion controllers (e.g. Wii Remote) and medical sensors. Virtual Valley allows patient to socialize, learn, and play group based serious games while exercising.

Spatial Dmbs Architecture for a Free and Open Source Bim

NASA Astrophysics Data System (ADS)

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

2017-08-01

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

Quantum theory of open systems based on stochastic differential equations of generalized Langevin (non-Wiener) type

NASA Astrophysics Data System (ADS)

Basharov, A. M.

2012-09-01

It is shown that the effective Hamiltonian representation, as it is formulated in author's papers, serves as a basis for distinguishing, in a broadband environment of an open quantum system, independent noise sources that determine, in terms of the stationary quantum Wiener and Poisson processes in the Markov approximation, the effective Hamiltonian and the equation for the evolution operator of the open system and its environment. General stochastic differential equations of generalized Langevin (non-Wiener) type for the evolution operator and the kinetic equation for the density matrix of an open system are obtained, which allow one to analyze the dynamics of a wide class of localized open systems in the Markov approximation. The main distinctive features of the dynamics of open quantum systems described in this way are the stabilization of excited states with respect to collective processes and an additional frequency shift of the spectrum of the open system. As an illustration of the general approach developed, the photon dynamics in a single-mode cavity without losses on the mirrors is considered, which contains identical intracavity atoms coupled to the external vacuum electromagnetic field. For some atomic densities, the photons of the cavity mode are "locked" inside the cavity, thus exhibiting a new phenomenon of radiation trapping and non-Wiener dynamics.

42: An Open-Source Simulation Tool for Study and Design of Spacecraft Attitude Control Systems

NASA Technical Reports Server (NTRS)

Stoneking, Eric

2018-01-01

Simulation is an important tool in the analysis and design of spacecraft attitude control systems. The speaker will discuss the simulation tool, called simply 42, that he has developed over the years to support his own work as an engineer in the Attitude Control Systems Engineering Branch at NASA Goddard Space Flight Center. 42 was intended from the outset to be high-fidelity and powerful, but also fast and easy to use. 42 is publicly available as open source since 2014. The speaker will describe some of 42's models and features, and discuss its applicability to studies ranging from early concept studies through the design cycle, integration, and operations. He will outline 42's architecture and share some thoughts on simulation development as a long-term project.

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

Hierarchical Testing with Automated Document Generation for Amanzi, ASCEM's Subsurface Flow and Reactive Transport Simulator

NASA Astrophysics Data System (ADS)

Moulton, J. D.; Steefel, C. I.; Yabusaki, S.; Castleton, K.; Scheibe, T. D.; Keating, E. H.; Freedman, V. L.

2013-12-01

The Advanced Simulation Capabililty for Environmental Management (ASCEM) program is developing an approach and open-source tool suite for standardized risk and performance assessments at legacy nuclear waste sites. These assessments use a graded and iterative approach, beginning with simplified highly abstracted models, and adding geometric and geologic complexity as understanding is gained. To build confidence in this assessment capability, extensive testing of the underlying tools is needed. Since the tools themselves, such as the subsurface flow and reactive-transport simulator, Amanzi, are under active development, testing must be both hierarchical and highly automated. In this presentation we show how we have met these requirements, by leveraging the python-based open-source documentation system called Sphinx with several other open-source tools. Sphinx builds on the reStructured text tool docutils, with important extensions that include high-quality formatting of equations, and integrated plotting through matplotlib. This allows the documentation, as well as the input files for tests, benchmark and tutorial problems, to be maintained with the source code under a version control system. In addition, it enables developers to build documentation in several different formats (e.g., html and pdf) from a single source. We will highlight these features, and discuss important benefits of this approach for Amanzi. In addition, we'll show that some of ASCEM's other tools, such as the sampling provided by the Uncertainty Quantification toolset, are naturally leveraged to enable more comprehensive testing. Finally, we will highlight the integration of this hiearchical testing and documentation framework with our build system and tools (CMake, CTest, and CDash).

Open Source Tools for Numerical Simulation of Urban Greenhouse Gas Emissions

NASA Astrophysics Data System (ADS)

Nottrott, A.; Tan, S. M.; He, Y.

2016-12-01

There is a global movement toward urbanization. Approximately 7% of the global population lives in just 28 megacities, occupying less than 0.1% of the total land area used by human activity worldwide. These cities contribute a significant fraction of the global budget of anthropogenic primary pollutants and greenhouse gasses. The 27 largest cities consume 9.9%, 9.3%, 6.7% and 3.0% of global gasoline, electricity, energy and water use, respectively. This impact motivates novel approaches to quantify and mitigate the growing contribution of megacity emissions to global climate change. Cities are characterized by complex topography, inhomogeneous turbulence, and variable pollutant source distributions. These features create a scale separation between local sources and urban scale emissions estimates known as the Grey-Zone. Modern computational fluid dynamics (CFD) techniques provide a quasi-deterministic, physically based toolset to bridge the scale separation gap between source level dynamics, local measurements, and urban scale emissions inventories. CFD has the capability to represent complex building topography and capture detailed 3D turbulence fields in the urban boundary layer. This presentation discusses the application of OpenFOAM to urban CFD simulations of natural gas leaks in cities. OpenFOAM is an open source software for advanced numerical simulation of engineering and environmental fluid flows. When combined with free or low cost computer aided drawing and GIS, OpenFOAM generates a detailed, 3D representation of urban wind fields. OpenFOAM was applied to model methane (CH4) emissions from various components of the natural gas distribution system, to investigate the impact of urban meteorology on mobile CH4 measurements. The numerical experiments demonstrate that CH4 concentration profiles are highly sensitive to the relative location of emission sources and buildings. Sources separated by distances of 5-10 meters showed significant differences in vertical dispersion of the plume due to building wake effects. The OpenFOAM flow fields were combined with an inverse, stochastic dispersion model to quantify and visualize the sensitivity of point sensors to upwind sources in various built environments.

Open-path spectroscopic methane detection using a broadband monolithic distributed feedback-quantum cascade laser array.

PubMed

Michel, Anna P M; Kapit, Jason; Witinski, Mark F; Blanchard, Romain

2017-04-10

Methane is a powerful greenhouse gas that has both natural and anthropogenic sources. The ability to measure methane using an integrated path length approach such as an open/long-path length sensor would be beneficial in several environments for examining anthropogenic and natural sources, including tundra landscapes, rivers, lakes, landfills, estuaries, fracking sites, pipelines, and agricultural sites. Here a broadband monolithic distributed feedback-quantum cascade laser array was utilized as the source for an open-path methane sensor. Two telescopes were utilized for the launch (laser source) and receiver (detector) in a bistatic configuration for methane sensing across a 50 m path length. Direct-absorption spectroscopy was utilized with intrapulse tuning. Ambient methane levels were detectable, and an instrument precision of 70 ppb with 100 s averaging and 90 ppb with 10 s averaging was achieved. The sensor system was designed to work "off the grid" and utilizes batteries that are rechargeable with solar panels and wind turbines.

Tip Vortex and Wake Characteristics of a Counterrotating Open Rotor

NASA Technical Reports Server (NTRS)

VanZante, Dale E.; Wernet, Mark P.

2012-01-01

One of the primary noise sources for Open Rotor systems is the interaction of the forward rotor tip vortex and blade wake with the aft rotor. NASA has collaborated with General Electric on the testing of a new generation of low noise, counterrotating Open Rotor systems. Three-dimensional particle image velocimetry measurements were acquired in the intra-rotor gap of the Historical Baseline blade set. The velocity measurements are of sufficient resolution to characterize the tip vortex size and trajectory as well as the rotor wake decay and turbulence character. The tip clearance vortex trajectory is compared to results from previously developed models. Forward rotor wake velocity profiles are shown. Results are presented in a form as to assist numerical modeling of Open Rotor system aerodynamics and acoustics.

The Development of an Open Hardware and Software System Onboard Unmanned Aerial Vehicles to Monitor Concentrated Solar Power Plants

PubMed Central

Mesas-Carrascosa, Francisco Javier; Verdú Santano, Daniel; Pérez Porras, Fernando; Meroño-Larriva, José Emilio; García-Ferrer, Alfonso

2017-01-01

Concentrated solar power (CSP) plants are increasingly gaining interest as a source of renewable energy. These plants face several technical problems and the inspection of components such as absorber tubes in parabolic trough concentrators (PTC), which are widely deployed, is necessary to guarantee plant efficiency. This article presents a system for real-time industrial inspection of CSP plants using low-cost, open-source components in conjunction with a thermographic sensor and an unmanned aerial vehicle (UAV). The system, available in open-source hardware and software, is designed to be employed independently of the type of device used for inspection (laptop, smartphone, tablet or smartglasses) and its operating system. Several UAV flight missions were programmed as follows: flight altitudes at 20, 40, 60, 80, 100 and 120 m above ground level; and three cruising speeds: 5, 7 and 10 m/s. These settings were chosen and analyzed in order to optimize inspection time. The results indicate that it is possible to perform inspections by an UAV in real time at CSP plants as a means of detecting anomalous absorber tubes and improving the effectiveness of methodologies currently being utilized. Moreover, aside from thermographic sensors, this contribution can be applied to other sensors and can be used in a broad range of applications where real-time georeferenced data visualization is necessary. PMID:28594353

The Development of an Open Hardware and Software System Onboard Unmanned Aerial Vehicles to Monitor Concentrated Solar Power Plants.

PubMed

Mesas-Carrascosa, Francisco Javier; Verdú Santano, Daniel; Pérez Porras, Fernando; Meroño-Larriva, José Emilio; García-Ferrer, Alfonso

2017-06-08

Concentrated solar power (CSP) plants are increasingly gaining interest as a source of renewable energy. These plants face several technical problems and the inspection of components such as absorber tubes in parabolic trough concentrators (PTC), which are widely deployed, is necessary to guarantee plant efficiency. This article presents a system for real-time industrial inspection of CSP plants using low-cost, open-source components in conjunction with a thermographic sensor and an unmanned aerial vehicle (UAV). The system, available in open-source hardware and software, is designed to be employed independently of the type of device used for inspection (laptop, smartphone, tablet or smartglasses) and its operating system. Several UAV flight missions were programmed as follows: flight altitudes at 20, 40, 60, 80, 100 and 120 m above ground level; and three cruising speeds: 5, 7 and 10 m/s. These settings were chosen and analyzed in order to optimize inspection time. The results indicate that it is possible to perform inspections by an UAV in real time at CSP plants as a means of detecting anomalous absorber tubes and improving the effectiveness of methodologies currently being utilized. Moreover, aside from thermographic sensors, this contribution can be applied to other sensors and can be used in a broad range of applications where real-time georeferenced data visualization is necessary.

The 'PhenoBox', a flexible, automated, open-source plant phenotyping solution.

PubMed

Czedik-Eysenberg, Angelika; Seitner, Sebastian; Güldener, Ulrich; Koemeda, Stefanie; Jez, Jakub; Colombini, Martin; Djamei, Armin

2018-04-05

There is a need for flexible and affordable plant phenotyping solutions for basic research and plant breeding. We demonstrate our open source plant imaging and processing solution ('PhenoBox'/'PhenoPipe') and provide construction plans, source code and documentation to rebuild the system. Use of the PhenoBox is exemplified by studying infection of the model grass Brachypodium distachyon by the head smut fungus Ustilago bromivora, comparing phenotypic responses of maize to infection with a solopathogenic Ustilago maydis (corn smut) strain and effector deletion strains, and studying salt stress response in Nicotiana benthamiana. In U. bromivora-infected grass, phenotypic differences between infected and uninfected plants were detectable weeks before qualitative head smut symptoms. Based on this, we could predict the infection outcome for individual plants with high accuracy. Using a PhenoPipe module for calculation of multi-dimensional distances from phenotyping data, we observe a time after infection-dependent impact of U. maydis effector deletion strains on phenotypic response in maize. The PhenoBox/PhenoPipe system is able to detect established salt stress responses in N. benthamiana. We have developed an affordable, automated, open source imaging and data processing solution that can be adapted to various phenotyping applications in plant biology and beyond. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

Apache Open Climate Workbench: Building Open Source Climate Science Tools and Community at the Apache Software Foundation

NASA Astrophysics Data System (ADS)

Joyce, M.; Ramirez, P.; Boustani, M.; Mattmann, C. A.; Khudikyan, S.; McGibbney, L. J.; Whitehall, K. D.

2014-12-01

Apache Open Climate Workbench (OCW; https://climate.apache.org/) is a Top-Level Project at the Apache Software Foundation that aims to provide a suite of tools for performing climate science evaluations using model outputs from a multitude of different sources (ESGF, CORDEX, U.S. NCA, NARCCAP) with remote sensing data from NASA, NOAA, and other agencies. Apache OCW is the second NASA project to become a Top-Level Project at the Apache Software Foundation. It grew out of the Jet Propulsion Laboratory's (JPL) Regional Climate Model Evaluation System (RCMES) project, a collaboration between JPL and the University of California, Los Angeles' Joint Institute for Regional Earth System Science and Engineering (JIFRESSE). Apache OCW provides scientists and developers with tools for data manipulation, metrics for dataset comparisons, and a visualization suite. In addition to a powerful low-level API, Apache OCW also supports a web application for quick, browser-controlled evaluations, a command line application for local evaluations, and a virtual machine for isolated experimentation with minimal setup. This talk will look at the difficulties and successes of moving a closed community research project out into the wild world of open source. We'll explore the growing pains Apache OCW went through to become a Top-Level Project at the Apache Software Foundation as well as the benefits gained by opening up development to the broader climate and computer science communities.

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.

A simple object-oriented and open-source model for scientific and policy analyses of the global climate system – Hector v1.0

DOE PAGES

Hartin, Corinne A.; Patel, Pralit L.; Schwarber, Adria; ...

2015-04-01

Simple climate models play an integral role in the policy and scientific communities. They are used for climate mitigation scenarios within integrated assessment models, complex climate model emulation, and uncertainty analyses. Here we describe Hector v1.0, an open source, object-oriented, simple global climate carbon-cycle model. This model runs essentially instantaneously while still representing the most critical global-scale earth system processes. Hector has a three-part main carbon cycle: a one-pool atmosphere, land, and ocean. The model's terrestrial carbon cycle includes primary production and respiration fluxes, accommodating arbitrary geographic divisions into, e.g., ecological biomes or political units. Hector actively solves the inorganicmore » carbon system in the surface ocean, directly calculating air–sea fluxes of carbon and ocean pH. Hector reproduces the global historical trends of atmospheric [CO 2], radiative forcing, and surface temperatures. The model simulates all four Representative Concentration Pathways (RCPs) with equivalent rates of change of key variables over time compared to current observations, MAGICC (a well-known simple climate model), and models from the 5th Coupled Model Intercomparison Project. Hector's flexibility, open-source nature, and modular design will facilitate a broad range of research in various areas.« less

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

PubMed

Suhanic, West; Crandall, Ian; Pennefather, Peter

2009-07-17

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

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.

Open Source and Open Standard based decision support system: the example of lake Verbano floods management.

NASA Astrophysics Data System (ADS)

Cannata, Massimiliano; Antonovic, Milan; Pozzoni, Maurizio; Graf, Andrea

2015-04-01

The Locarno area (Switzerland, Canton Ticino) is exposed to lacual floods with a return period of about 7-8 years. The risk is of particular concern because the area is located in a floodplain that registered in the last decades a great increase in settlement and values of the real estates. Moreover small differences in lake altitude may produce a significant increase in flooded area due to the very low average slope of the terrain. While fatalities are not generally registered, several important economic costs are associated, e.g.: damages to real estates, interruption of activities, evacuation and relocation and environmental damages. While important events were registered in 1978, 1993, 2000, 2002 and 2014 the local stakeholder invested time and money in the set-up of an up-to-date decision support system that allows for the reduction of risks. Thanks to impressive technological advances the visionary concept of the Digital Earth (Gore 1992, 1998) is being realizing: geospatial coverages and monitoring systems data are increasingly available on the Web, and more importantly, in a standard format. As a result, today is possible to develop innovative decision support systems (Molinari et al. 2013) which mesh-up several information sources and offers special features for risk scenarios evaluation. In agreement with the exposed view, the authors have recently developed a new Web system whose design is based on the Service Oriented Architecture pattern. Open source software (e.g.: Geoserver, PostGIS, OpenLayers) has been used throughout the whole system and geospatial Open Standards (e.g.: SOS, WMS, WFS) are the pillars it rely on. SITGAP 2.0, implemented in collaboration with the Civil protection of Locarno e Vallemaggia, combines a number of data sources such as the Federal Register of Buildings and Dwellings, the Cantonal Register of residents, the Cadastral Surveying, the Cantonal Hydro-meteorological monitoring observations, the Meteoswiss weather forecasts, and others. As a result of this orchestration of data, SITGAP 2.0 serves features that allows, for example, to be informed on active alarms, to visualize lake level forecasts and associated flooding areas, to evaluate and map exposed elements and people, to plan and manage evacuation by searching for people living in particular areas or buildings, by registering evacuation actions and by searching for evacuated people. System architecture and functionalities, and consideration on the integration and accessibility of the beneath information together with the lesson learnt during the usage of the system during the last floods of November 2014, provides interesting discussion points for the identification of current and future needs.

osni.info-Using free/libre/open source software to build a virtual international community for open source nursing informatics.

PubMed

Oyri, Karl; Murray, Peter J

2005-12-01

Many health informatics organizations seem to be slow to take up the advantages of dynamic, web-based technologies for providing services to, and interaction with, their members; these are often the very technologies they promote for use within healthcare environments. This paper aims to introduce some of the many free/libre/open source (FLOSS) applications that are now available to develop interactive websites and dynamic online communities as part of the structure of health informatics organizations, and to show how the Open Source Nursing Informatics Working Group (OSNI) of the special interest group in nursing informatics of the International Medical Informatics Association (IMIA-NI) is using some of these tools to develop an online community of nurse informaticians through their website, at . Some background introduction to FLOSS applications is used for the benefit of those less familiar with such tools, and examples of some of the FLOSS content management systems (CMS) being used by OSNI are described. The experiences of the OSNI will facilitate a knowledgeable nursing contribution to the wider discussions on the applications of FLOSS within health and healthcare, and provides a model that many other groups could adopt.

Open-Source GIS

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

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

2012-01-01

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

Investigating Advances in the Acquisition of Systems Based on Open Architecture and Open Source Software

DTIC Science & Technology

2011-08-01

dominates the global mobile application market and mobile computing software ecosystems. But overall, OA systems are not necessarily excluded from...License 3.0 (OSL)  Corel Transactional License ( CTL ) The licenses were chosen to represent a variety of kinds of licenses, and include one...proprietary ( CTL ), three academic (Apache, BSD, MIT), and six reciprocal licenses (CPL, EPL, GPL, LGPL, MPL, OSL) that take varying approaches in

TriBITS (Tribal Build, Integrate, and Test System)

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

2013-05-16

TriBITS is a configuration, build, test, and reporting system that uses the Kitware open-source CMake/CTest/CDash system. TriBITS contains a number of custom CMake/CTest scripts and python scripts that extend the functionality of the out-of-the-box CMake/CTest/CDash system.

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

Review assessment support in Open Journal System using TextRank

NASA Astrophysics Data System (ADS)

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

2017-01-01

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

Mantle to surface degassing of alkalic magmas at Erebus volcano, Antarctica

USGS Publications Warehouse

Oppenheimer, C.; Moretti, R.; Kyle, P.R.; Eschenbacher, A.; Lowenstern, J. B.; Hervig, R.L.; Dunbar, N.W.

2011-01-01

Continental intraplate volcanoes, such as Erebus volcano, Antarctica, are associated with extensional tectonics, mantle upwelling and high heat flow. Typically, erupted magmas are alkaline and rich in volatiles (especially CO2), inherited from low degrees of partial melting of mantle sources. We examine the degassing of the magmatic system at Erebus volcano using melt inclusion data and high temporal resolution open-path Fourier transform infrared (FTIR) spectroscopic measurements of gas emissions from the active lava lake. Remarkably different gas signatures are associated with passive and explosive gas emissions, representative of volatile contents and redox conditions that reveal contrasting shallow and deep degassing sources. We show that this unexpected degassing signature provides a unique probe for magma differentiation and transfer of CO2-rich oxidised fluids from the mantle to the surface, and evaluate how these processes operate in time and space. Extensive crystallisation driven by CO2 fluxing is responsible for isobaric fractionation of parental basanite magmas close to their source depth. Magma deeper than 4kbar equilibrates under vapour-buffered conditions. At shallower depths, CO2-rich fluids accumulate and are then released either via convection-driven, open-system gas loss or as closed-system slugs that ascend and result in Strombolian eruptions in the lava lake. The open-system gases have a reduced state (below the QFM buffer) whereas the closed-system gases preserve their deep oxidised signatures (close to the NNO buffer). ?? 2011 Elsevier B.V.

Open source GIS for HIV/AIDS management

PubMed Central

Vanmeulebrouk, Bas; Rivett, Ulrike; Ricketts, Adam; Loudon, Melissa

2008-01-01

Background Reliable access to basic services can improve a community's resilience to HIV/AIDS. Accordingly, work is being done to upgrade the physical infrastructure in affected areas, often employing a strategy of decentralised service provision. Spatial characteristics are one of the major determinants in implementing services, even in the smaller municipal areas, and good quality spatial information is needed to inform decision making processes. However, limited funds, technical infrastructure and human resource capacity result in little or no access to spatial information for crucial infrastructure development decisions at local level. This research investigated whether it would be possible to develop a GIS for basic infrastructure planning and management at local level. Given the resource constraints of the local government context, particularly in small municipalities, it was decided that open source software should be used for the prototype system. Results The design and development of a prototype system illustrated that it is possible to develop an open source GIS system that can be used within the context of local information management. Usability tests show a high degree of usability for the system, which is important considering the heavy workload and high staff turnover that characterises local government in South Africa. Local infrastructure management stakeholders interviewed in a case study of a South African municipality see the potential for the use of GIS as a communication tool and are generally positive about the use of GIS for these purposes. They note security issues that may arise through the sharing of information, lack of skills and resource constraints as the major barriers to adoption. Conclusion The case study shows that spatial information is an identified need at local level. Open source GIS software can be used to develop a system to provide local-level stakeholders with spatial information. However, the suitability of the technology is only a part of the system – there are wider information and management issues which need to be addressed before the implementation of a local-level GIS for infrastructure management can be successful. PMID:18945338

Characterization of Site for Installing Open Loop Ground Source Heat Pump System

NASA Astrophysics Data System (ADS)

Yun, S. W.; Park, Y.; Lee, J. Y.; Yi, M. J.; Cha, J. H.

2014-12-01

This study was conducted to understand hydrogeological properties of site where open loop ground source heat pump system will be installed and operated. Groundwater level and water temperature were hourly measured at the well developed for usage of open loop ground source heat pump system from 11 October 2013 to 8 January 2014. Groundwater was sampled in January and August 2013 and its chemical and isotopic compositions were analyzed. The bedrock of study area is the Jurassic granodiorite that mainly consists of quartz (27.9 to 46.8%), plagioclase (26.0 to 45.5%), and alkali feldspar (9.5 to 18.7%). The groundwater level ranged from 68.30 to 68.94 m (above mean sea level). Recharge rate was estimated using modified watertable fluctuation method and the recharge ratios was 9.1%. The water temperature ranged from 14.8 to 15.0oC. The vertical Increase rates of water temperature were 1.91 to 1.94/100 m. The water temperature showed the significant seasonal variation above 50 m depth, but had constant value below 50 m depth. Therefore, heat energy of the groundwater can be used securely in open loop ground source heat pump system. Electrical conductivity ranged from 120 to 320 µS/cm in dry season and from 133 to 310 µS/cm in wet season. The electrical conductivity gradually decreased with depth. In particular, electrical conductivity in approximately 30 m depth decreased dramatically (287 to 249 µS/cm) in wet season. The groundwater was Ca-HCO3 type. The concentrations of dissolved components did not show the vertically significant variations from 0 to 250 m depth. The δ18O and δD ranged from -9.5 to -9.4‰ and from -69 to -68‰. This work is supported by the New and Renewable Energy of the Korea Institute of Energy Technology Evaluation and Planning (KETEP) grant funded by the Korea government Ministry of Knowledge Economy (No.20123040110010).

Open Source GIS based integrated watershed management

NASA Astrophysics Data System (ADS)

Byrne, J. M.; Lindsay, J.; Berg, A. A.

2013-12-01

Optimal land and water management to address future and current resource stresses and allocation challenges requires the development of state-of-the-art geomatics and hydrological modelling tools. Future hydrological modelling tools should be of high resolution, process based with real-time capability to assess changing resource issues critical to short, medium and long-term enviromental management. The objective here is to merge two renowned, well published resource modeling programs to create an source toolbox for integrated land and water management applications. This work will facilitate a much increased efficiency in land and water resource security, management and planning. Following an 'open-source' philosophy, the tools will be computer platform independent with source code freely available, maximizing knowledge transfer and the global value of the proposed research. The envisioned set of water resource management tools will be housed within 'Whitebox Geospatial Analysis Tools'. Whitebox, is an open-source geographical information system (GIS) developed by Dr. John Lindsay at the University of Guelph. The emphasis of the Whitebox project has been to develop a user-friendly interface for advanced spatial analysis in environmental applications. The plugin architecture of the software is ideal for the tight-integration of spatially distributed models and spatial analysis algorithms such as those contained within the GENESYS suite. Open-source development extends knowledge and technology transfer to a broad range of end-users and builds Canadian capability to address complex resource management problems with better tools and expertise for managers in Canada and around the world. GENESYS (Generate Earth Systems Science input) is an innovative, efficient, high-resolution hydro- and agro-meteorological model for complex terrain watersheds developed under the direction of Dr. James Byrne. GENESYS is an outstanding research and applications tool to address challenging resource management issues in industry, government and nongovernmental agencies. Current research and analysis tools were developed to manage meteorological, climatological, and land and water resource data efficiently at high resolution in space and time. The deliverable for this work is a Whitebox-GENESYS open-source resource management capacity with routines for GIS based watershed management including water in agriculture and food production. We are adding urban water management routines through GENESYS in 2013-15 with an engineering PhD candidate. Both Whitebox-GAT and GENESYS are already well-established tools. The proposed research will combine these products to create an open-source geomatics based water resource management tool that is revolutionary in both capacity and availability to a wide array of Canadian and global users

Delay Tolerant Networking on NASA's Space Communication and Navigation Testbed

NASA Technical Reports Server (NTRS)

Johnson, Sandra; Eddy, Wesley

2016-01-01

This presentation covers the status of the implementation of an open source software that implements the specifications developed by the CCSDS Working Group. Interplanetary Overlay Network (ION) is open source software and it implements specifications that have been developed by two international working groups through IETF and CCSDS. ION was implemented on the SCaN Testbed, a testbed located on an external pallet on ISS, by the GRC team. The presentation will cover the architecture of the system, high level implementation details, and issues porting ION to VxWorks.

Open source approaches to health information systems in Kenya.

PubMed

Drury, Peter; Dahlman, Bruce

2005-01-01

This paper focuses on the experience to date of an installation of a Free Open Source Software (FOSS) product, Care2X, at a church hospital in Kenya. The FOSS movement has been maturing rapidly. In developed countries, its benefits relative to proprietary software have been extensively discussed and ways of quantifying the total costs of the development have been developed. Nevertheless, empirical data on the impact of FOSS, particularly in the developing world, concerning its use and development is still quite limited, although the possibilities of FOSS are becoming increasingly attractive.

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

Evaluating Open-Source Full-Text Search Engines for Matching ICD-10 Codes.

PubMed

Jurcău, Daniel-Alexandru; Stoicu-Tivadar, Vasile

2016-01-01

This research presents the results of evaluating multiple free, open-source engines on matching ICD-10 diagnostic codes via full-text searches. The study investigates what it takes to get an accurate match when searching for a specific diagnostic code. For each code the evaluation starts by extracting the words that make up its text and continues with building full-text search queries from the combinations of these words. The queries are then run against all the ICD-10 codes until a match indicates the code in question as a match with the highest relative score. This method identifies the minimum number of words that must be provided in order for the search engines choose the desired entry. The engines analyzed include a popular Java-based full-text search engine, a lightweight engine written in JavaScript which can even execute on the user's browser, and two popular open-source relational database management systems.

Long distance education for croatian nurses with open source software.

PubMed

Radenovic, Aleksandar; Kalauz, Sonja

2006-01-01

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

CymeR: cytometry analysis using KNIME, docker and R

PubMed Central

Muchmore, B.; Alarcón-Riquelme, M.E.

2017-01-01

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

CymeR: cytometry analysis using KNIME, docker and R.

PubMed

Muchmore, B; Alarcón-Riquelme, M E

2017-03-01

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

astroplan: An Open Source Observation Planning Package in Python

NASA Astrophysics Data System (ADS)

Morris, Brett M.; Tollerud, Erik; Sipőcz, Brigitta; Deil, Christoph; Douglas, Stephanie T.; Berlanga Medina, Jazmin; Vyhmeister, Karl; Smith, Toby R.; Littlefair, Stuart; Price-Whelan, Adrian M.; Gee, Wilfred T.; Jeschke, Eric

2018-03-01

We present astroplan—an open source, open development, Astropy affiliated package for ground-based observation planning and scheduling in Python. astroplan is designed to provide efficient access to common observational quantities such as celestial rise, set, and meridian transit times and simple transformations from sky coordinates to altitude-azimuth coordinates without requiring a detailed understanding of astropy’s implementation of coordinate systems. astroplan provides convenience functions to generate common observational plots such as airmass and parallactic angle as a function of time, along with basic sky (finder) charts. Users can determine whether or not a target is observable given a variety of observing constraints, such as airmass limits, time ranges, Moon illumination/separation ranges, and more. A selection of observation schedulers are included that divide observing time among a list of targets, given observing constraints on those targets. Contributions to the source code from the community are welcome.

Implementation and Testing of Low Cost Uav Platform for Orthophoto Imaging

NASA Astrophysics Data System (ADS)

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

2013-08-01

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

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.

Towards Standardized Patient Data Exchange: Integrating a FHIR Based API for the Open Medical Record System.

PubMed

Kasthurirathne, Suranga N; Mamlin, Burke; Grieve, Grahame; Biondich, Paul

2015-01-01

Interoperability is essential to address limitations caused by the ad hoc implementation of clinical information systems and the distributed nature of modern medical care. The HL7 V2 and V3 standards have played a significant role in ensuring interoperability for healthcare. FHIR is a next generation standard created to address fundamental limitations in HL7 V2 and V3. FHIR is particularly relevant to OpenMRS, an Open Source Medical Record System widely used across emerging economies. FHIR has the potential to allow OpenMRS to move away from a bespoke, application specific API to a standards based API. We describe efforts to design and implement a FHIR based API for the OpenMRS platform. Lessons learned from this effort were used to define long term plans to transition from the legacy OpenMRS API to a FHIR based API that greatly reduces the learning curve for developers and helps enhance adhernce to standards.

Software licensing policy for the Open Source Application Development Portal (OSADP).

DOT National Transportation Integrated Search

1998-07-01

The purpose of the Commercial Vehicle Information Systems and Networks Model Deployment Initiative (CVISN MDI) is to demonstrate the technical and institutional feasibility, costs, and benefits of the primary Intelligent Transportation Systems (ITS) ...

Testing of Cerex Open Path Ultraviolet Differential Optical Absorption Spectroscopy Systems for Fenceline Monitoring Applications

EPA Science Inventory

Industrial facilities, energy production, and refining operations can be significant sources of gas-phase air pollutants. Some industrial emissions originate from fugitive sources (leaks) or process malfunctions and can be mitigated if identified. In recent amendments to the Nati...

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.

Integration of a clinical trial database with a PACS

NASA Astrophysics Data System (ADS)

van Herk, M.

2014-03-01

Many clinical trials use Electronic Case Report Forms (ECRF), e.g., from OpenClinica. Trial data is augmented if DICOM scans, dose cubes, etc. from the Picture Archiving and Communication System (PACS) are included for data mining. Unfortunately, there is as yet no structured way to collect DICOM objects in trial databases. In this paper, we obtain a tight integration of ECRF and PACS using open source software. Methods: DICOM identifiers for selected images/series/studies are stored in associated ECRF events (e.g., baseline) as follows: 1) JavaScript added to OpenClinica communicates using HTML with a gateway server inside the hospitals firewall; 2) On this gateway, an open source DICOM server runs scripts to query and select the data, returning anonymized identifiers; 3) The scripts then collects, anonymizes, zips and transmits selected data to a central trial server; 4) Here data is stored in a DICOM archive which allows authorized ECRF users to view and download the anonymous images associated with each event. Results: All integration scripts are open source. The PACS administrator configures the anonymization script and decides to use the gateway in passive (receiving) mode or in an active mode going out to the PACS to gather data. Our ECRF centric approach supports automatic data mining by iterating over the cases in the ECRF database, providing the identifiers to load images and the clinical data to correlate with image analysis results. Conclusions: Using open source software and web technology, a tight integration has been achieved between PACS and ECRF.

A Proof-Carrying File System

DTIC Science & Technology

2009-06-06

written in Standard ML, and comprises nearly 7,000 lines of code. OpenSSL is used for all cryptographic operations. Because the front end tools are used...be managed. Macrobenchmarks. To understand the performance of PCFS in practice, we also ran two simple macrobenchmarks. The first (called OpenSSL in...the table below), untars the OpenSSL source code, compiles it and deletes it. The other (called Fuse in the table below), performs similar operations

48 CFR 1406.302-1 - Only one responsible source and no other supplies or services will satisfy agency requirements.

Code of Federal Regulations, 2010 CFR

2010-10-01

... COMPETITION REQUIREMENTS Other Than Full and Open Competition 1406.302-1 Only one responsible source and no... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false Only one responsible source and no other supplies or services will satisfy agency requirements. 1406.302-1 Section 1406.302-1...

48 CFR 606.302-1 - Only one responsible source and no other supplies or services will satisfy agency requirements.

Code of Federal Regulations, 2010 CFR

2010-10-01

... COMPETITION REQUIREMENTS Other Than Full and Open Competition 606.302-1 Only one responsible source and no... 48 Federal Acquisition Regulations System 4 2010-10-01 2010-10-01 false Only one responsible source and no other supplies or services will satisfy agency requirements. 606.302-1 Section 606.302-1...

A Flexible, Extensible Online Testing System for Mathematics

ERIC Educational Resources Information Center

Passmore, Tim; Brookshaw, Leigh; Butler, Harry

2011-01-01

An online testing system developed for entry-skills testing of first-year university students in algebra and calculus is described. The system combines the open-source computer algebra system "Maxima" with computer scripts to parse student answers, which are entered using standard mathematical notation and conventions. The answers can…

Quality Test of Flexible Flat Cable (FFC) With Short Open Test Using Law Ohm Approach through Embedded Fuzzy Logic Based On Open Source Arduino Data Logger

NASA Astrophysics Data System (ADS)

Rohmanu, Ajar; Everhard, Yan

2017-04-01

A technological development, especially in the field of electronics is very fast. One of the developments in the electronics hardware device is Flexible Flat Cable (FFC), which serves as a media liaison between the main boards with other hardware parts. The production of Flexible Flat Cable (FFC) will go through the process of testing and measuring of the quality Flexible Flat Cable (FFC). Currently, the testing and measurement is still done manually by observing the Light Emitting Diode (LED) by the operator, so there were many problems. This study will be made of test quality Flexible Flat Cable (FFC) computationally utilize Open Source Embedded System. The method used is the measurement with Short Open Test method using Ohm’s Law approach to 4-wire (Kelvin) and fuzzy logic as a decision maker measurement results based on Open Source Arduino Data Logger. This system uses a sensor current INA219 as a sensor to read the voltage value thus obtained resistance value Flexible Flat Cable (FFC). To get a good system we will do the Black-box testing as well as testing the accuracy and precision with the standard deviation method. In testing the system using three models samples were obtained the test results in the form of standard deviation for the first model of 1.921 second model of 4.567 and 6.300 for the third model. While the value of the Standard Error of Mean (SEM) for the first model of the model 0.304 second at 0.736 and 0.996 of the third model. In testing this system, we will also obtain the average value of the measurement tolerance resistance values for the first model of - 3.50% 4.45% second model and the third model of 5.18% with the standard measurement of prisoners and improve productivity becomes 118.33%. From the results of the testing system is expected to improve the quality and productivity in the process of testing Flexible Flat Cable (FFC).

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.

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

PubMed

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

2016-09-01

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

Resource sharing of online teaching materials: The lon-capa project

NASA Astrophysics Data System (ADS)

Bauer, Wolfgang

2004-03-01

The use of information technology resources in conventional lecture-based courses, in distance-learning offerings, as well as hybrid courses, is increasing. But this may put additional burden on faculty, who are now asked to deliver this new content. Additionally, it may require the installation of commercial courseware systems, putting the colleges and universities in new financial licensing dependencies. To address exactly these two problems, the lon-capa system was invented to provide an open-source, gnu public license based, courseware system that allows for sharing of educational resources across institutional and disciplinary boundaries. This presentation will focus on both aspects of the system, the courseware capabilities that allow for customized environments for individual students, and the educational resources library that enables teachers to take full advantages of the work of their colleagues. Research results on learning effectiveness, resource and system usage patterns, and customization for different learning styles will be shown. Institutional perceptions of and responses to open source courseware systems will be discussed.

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.

Automated population of an i2b2 clinical data warehouse from an openEHR-based data repository.

PubMed

Haarbrandt, Birger; Tute, Erik; Marschollek, Michael

2016-10-01

Detailed Clinical Model (DCM) approaches have recently seen wider adoption. More specifically, openEHR-based application systems are now used in production in several countries, serving diverse fields of application such as health information exchange, clinical registries and electronic medical record systems. However, approaches to efficiently provide openEHR data to researchers for secondary use have not yet been investigated or established. We developed an approach to automatically load openEHR data instances into the open source clinical data warehouse i2b2. We evaluated query capabilities and the performance of this approach in the context of the Hanover Medical School Translational Research Framework (HaMSTR), an openEHR-based data repository. Automated creation of i2b2 ontologies from archetypes and templates and the integration of openEHR data instances from 903 patients of a paediatric intensive care unit has been achieved. In total, it took an average of ∼2527s to create 2.311.624 facts from 141.917 XML documents. Using the imported data, we conducted sample queries to compare the performance with two openEHR systems and to investigate if this representation of data is feasible to support cohort identification and record level data extraction. We found the automated population of an i2b2 clinical data warehouse to be a feasible approach to make openEHR data instances available for secondary use. Such an approach can facilitate timely provision of clinical data to researchers. It complements analytics based on the Archetype Query Language by allowing querying on both, legacy clinical data sources and openEHR data instances at the same time and by providing an easy-to-use query interface. However, due to different levels of expressiveness in the data models, not all semantics could be preserved during the ETL process. Copyright © 2016 Elsevier Inc. All rights reserved.

A low-cost, computer-controlled robotic flower system for behavioral experiments.

PubMed

Kuusela, Erno; Lämsä, Juho

2016-04-01

Human observations during behavioral studies are expensive, time-consuming, and error prone. For this reason, automatization of experiments is highly desirable, as it reduces the risk of human errors and workload. The robotic system we developed is simple and cheap to build and handles feeding and data collection automatically. The system was built using mostly off-the-shelf components and has a novel feeding mechanism that uses servos to perform refill operations. We used the robotic system in two separate behavioral studies with bumblebees (Bombus terrestris): The system was used both for training of the bees and for the experimental data collection. The robotic system was reliable, with no flight in our studies failing due to a technical malfunction. The data recorded were easy to apply for further analysis. The software and the hardware design are open source. The development of cheap open-source prototyping platforms during the recent years has opened up many possibilities in designing of experiments. Automatization not only reduces workload, but also potentially allows experimental designs never done before, such as dynamic experiments, where the system responds to, for example, learning of the animal. We present a complete system with hardware and software, and it can be used as such in various experiments requiring feeders and collection of visitation data. Use of the system is not limited to any particular experimental setup or even species.

OpenID Connect as a security service in cloud-based medical imaging systems.

PubMed

Ma, Weina; Sartipi, Kamran; Sharghigoorabi, Hassan; Koff, David; Bak, Peter

2016-04-01

The evolution of cloud computing is driving the next generation of medical imaging systems. However, privacy and security concerns have been consistently regarded as the major obstacles for adoption of cloud computing by healthcare domains. OpenID Connect, combining OpenID and OAuth together, is an emerging representational state transfer-based federated identity solution. It is one of the most adopted open standards to potentially become the de facto standard for securing cloud computing and mobile applications, which is also regarded as "Kerberos of cloud." We introduce OpenID Connect as an authentication and authorization service in cloud-based diagnostic imaging (DI) systems, and propose enhancements that allow for incorporating this technology within distributed enterprise environments. The objective of this study is to offer solutions for secure sharing of medical images among diagnostic imaging repository (DI-r) and heterogeneous picture archiving and communication systems (PACS) as well as Web-based and mobile clients in the cloud ecosystem. The main objective is to use OpenID Connect open-source single sign-on and authorization service and in a user-centric manner, while deploying DI-r and PACS to private or community clouds should provide equivalent security levels to traditional computing model.

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.

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

PubMed Central

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

2017-01-01

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

Creating a Clinical Video-Conferencing Facility in a Security-Constrained Environment Using Open-Source AccessGrid Software and Consumer Hardware

PubMed Central

Terrazas, Enrique; Hamill, Timothy R.; Wang, Ye; Channing Rodgers, R. P.

2007-01-01

The Department of Laboratory Medicine at the University of California, San Francisco (UCSF) has been split into widely separated facilities, leading to much time being spent traveling between facilities for meetings. We installed an open-source AccessGrid multi-media-conferencing system using (largely) consumer-grade equipment, connecting 6 sites at 5 separate facilities. The system was accepted rapidly and enthusiastically, and was inexpensive compared to alternative approaches. Security was addressed by aspects of the AG software and by local network administrative practices. The chief obstacles to deployment arose from security restrictions imposed by multiple independent network administration regimes, requiring a drastically reduced list of network ports employed by AG components. PMID:18693930

Creating a clinical video-conferencing facility in a security-constrained environment using open-source AccessGrid software and consumer hardware.

PubMed

Terrazas, Enrique; Hamill, Timothy R; Wang, Ye; Channing Rodgers, R P

2007-10-11

The Department of Laboratory Medicine at the University of California, San Francisco (UCSF) has been split into widely separated facilities, leading to much time being spent traveling between facilities for meetings. We installed an open-source AccessGrid multi-media-conferencing system using (largely) consumer-grade equipment, connecting 6 sites at 5 separate facilities. The system was accepted rapidly and enthusiastically, and was inexpensive compared to alternative approaches. Security was addressed by aspects of the AG software and by local network administrative practices. The chief obstacles to deployment arose from security restrictions imposed by multiple independent network administration regimes, requiring a drastically reduced list of network ports employed by AG components.

[Construction of DICOM-WWW gateway by open source, and application to PDAs using the high-speed mobile communications network].

PubMed

Yokohama, Noriya

2003-09-01

The author constructed a medical image network system using open source software that took security into consideration. This system was enabled for search and browse with a WWW browser, and images were stored in a DICOM server. In order to realize this function, software was developed to fill in the gap between the DICOM protocol and HTTP using PHP language. The transmission speed was evaluated by the difference in protocols between DICOM and HTTP. Furthermore, an attempt was made to evaluate the convenience of medical image access with a personal information terminal via the Internet through the high-speed mobile communication terminal. Results suggested the feasibility of remote diagnosis and application to emergency care.

Effects Of Nutrient Source And Supply On Crude Oil Biodegradation In Continuous-Flow Beach Microcosms

EPA Science Inventory

Ammonium and nitrate were used as nitrogen sources to support microbial biodegradation of crude oil in continuous-flow beach microcosms to determine whether either nutrient was more effective in open systems, such as intertidal shorelines. No differences in the rate or the exten...

Investigating the Acquisition of Software Systems that Rely on Open Architecture and Open Source Software

DTIC Science & Technology

2010-03-01

associated with certain software systems [Breaux and Anton 2008]. With this basis to build on, it is now possible to analyze the alignment of...Kazman, R., (2003). Software Architecture in Practice, 2nd Edition, Addison-Wesley Pro- fessional, New York.. Breaux, T.D. and Anton , A.I. (2008... calculus for license rights and obligations in license and context models. Using them, we calculate rights and obligations for specific sys- tems, identify

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.

A Standard Platform for Testing and Comparison of MDAO Architectures

NASA Technical Reports Server (NTRS)

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

2012-01-01

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

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…

Implementation of Open-Source Web Mapping Technologies to Support Monitoring of Governmental Schemes

NASA Astrophysics Data System (ADS)

Pulsani, B. R.

2015-10-01

Several schemes are undertaken by the government to uplift social and economic condition of people. The monitoring of these schemes is done through information technology where involvement of Geographic Information System (GIS) is lacking. To demonstrate the benefits of thematic mapping as a tool for assisting the officials in making decisions, a web mapping application for three government programs such as Mother and Child Tracking system (MCTS), Telangana State Housing Corporation Limited (TSHCL) and Ground Water Quality Mapping (GWQM) has been built. Indeed the three applications depicted the distribution of various parameters thematically and helped in identifying the areas with higher and weaker distributions. Based on the three applications, the study tends to find similarities of many government schemes reflecting the nature of thematic mapping and hence deduces to implement this kind of approach for other schemes as well. These applications have been developed using SharpMap Csharp library which is a free and open source mapping library for developing geospatial applications. The study highlights upon the cost benefits of SharpMap and brings out the advantage of this library over proprietary vendors and further discusses its advantages over other open source libraries as well.

Development of AN Open-Source Automatic Deformation Monitoring System for Geodetical and Geotechnical Measurements

NASA Astrophysics Data System (ADS)

Engel, P.; Schweimler, B.

2016-04-01

The deformation monitoring of structures and buildings is an important task field of modern engineering surveying, ensuring the standing and reliability of supervised objects over a long period. Several commercial hardware and software solutions for the realization of such monitoring measurements are available on the market. In addition to them, a research team at the Neubrandenburg University of Applied Sciences (NUAS) is actively developing a software package for monitoring purposes in geodesy and geotechnics, which is distributed under an open source licence and free of charge. The task of managing an open source project is well-known in computer science, but it is fairly new in a geodetic context. This paper contributes to that issue by detailing applications, frameworks, and interfaces for the design and implementation of open hardware and software solutions for sensor control, sensor networks, and data management in automatic deformation monitoring. It will be discussed how the development effort of networked applications can be reduced by using free programming tools, cloud computing technologies, and rapid prototyping methods.

Web Mapping Architectures Based on Open Specifications and Free and Open Source Software in the Water Domain

NASA Astrophysics Data System (ADS)

Arias Muñoz, C.; Brovelli, M. A.; Kilsedar, C. E.; Moreno-Sanchez, R.; Oxoli, D.

2017-09-01

The availability of water-related data and information across different geographical and jurisdictional scales is of critical importance for the conservation and management of water resources in the 21st century. Today information assets are often found fragmented across multiple agencies that use incompatible data formats and procedures for data collection, storage, maintenance, analysis, and distribution. The growing adoption of Web mapping systems in the water domain is reducing the gap between data availability and its practical use and accessibility. Nevertheless, more attention must be given to the design and development of these systems to achieve high levels of interoperability and usability while fulfilling different end user informational needs. This paper first presents a brief overview of technologies used in the water domain, and then presents three examples of Web mapping architectures based on free and open source software (FOSS) and the use of open specifications (OS) that address different users' needs for data sharing, visualization, manipulation, scenario simulations, and map production. The purpose of the paper is to illustrate how the latest developments in OS for geospatial and water-related data collection, storage, and sharing, combined with the use of mature FOSS projects facilitate the creation of sophisticated interoperable Web-based information systems in the water domain.

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.

Colloquium: Non-Markovian dynamics in open quantum systems

NASA Astrophysics Data System (ADS)

Breuer, Heinz-Peter; Laine, Elsi-Mari; Piilo, Jyrki; Vacchini, Bassano

2016-04-01

The dynamical behavior of open quantum systems plays a key role in many applications of quantum mechanics, examples ranging from fundamental problems, such as the environment-induced decay of quantum coherence and relaxation in many-body systems, to applications in condensed matter theory, quantum transport, quantum chemistry, and quantum information. In close analogy to a classical Markovian stochastic process, the interaction of an open quantum system with a noisy environment is often modeled phenomenologically by means of a dynamical semigroup with a corresponding time-independent generator in Lindblad form, which describes a memoryless dynamics of the open system typically leading to an irreversible loss of characteristic quantum features. However, in many applications open systems exhibit pronounced memory effects and a revival of genuine quantum properties such as quantum coherence, correlations, and entanglement. Here recent theoretical results on the rich non-Markovian quantum dynamics of open systems are discussed, paying particular attention to the rigorous mathematical definition, to the physical interpretation and classification, as well as to the quantification of quantum memory effects. The general theory is illustrated by a series of physical examples. The analysis reveals that memory effects of the open system dynamics reflect characteristic features of the environment which opens a new perspective for applications, namely, to exploit a small open system as a quantum probe signifying nontrivial features of the environment it is interacting with. This Colloquium further explores the various physical sources of non-Markovian quantum dynamics, such as structured environmental spectral densities, nonlocal correlations between environmental degrees of freedom, and correlations in the initial system-environment state, in addition to developing schemes for their local detection. Recent experiments addressing the detection, quantification, and control of non-Markovian quantum dynamics are also briefly discussed.

Ted Kwasnik | NREL

Science.gov Websites

Architecture/Implementation of GIS Applications Open Source Programming and Web Development Spatial Analysis and Cartography Research Interests Transportation Systems and Urban Mobility Wind and Solar Resource

Teaching Introductory GIS Programming to Geographers Using an Open Source Python Approach

ERIC Educational Resources Information Center

Etherington, Thomas R.

2016-01-01

Computer programming is not commonly taught to geographers as a part of geographic information system (GIS) courses, but the advent of NeoGeography, big data and open GIS means that programming skills are becoming more important. To encourage the teaching of programming to geographers, this paper outlines a course based around a series of…

The Open University in the Third World.

ERIC Educational Resources Information Center

Hawkridge, David G.

The British Open University is described in the first section of this paper as a multi-media system for teaching at a distance. Details are provided on the texts and other materials mailed to the students, the radio and television broadcasts provided by the British Broadcasting Company, and on the auxiliary sources of assistance offered to the…

Common Approach to Geoprocessing of Uav Data across Application Domains

NASA Astrophysics Data System (ADS)

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

2015-08-01

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

Open Source 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

Collaboration using open standards and open source software (examples of DIAS/CEOS Water Portal)

NASA Astrophysics Data System (ADS)

Miura, S.; Sekioka, S.; Kuroiwa, K.; Kudo, Y.

2015-12-01

The DIAS/CEOS Water Portal is a part of the DIAS (Data Integration and Analysis System, http://www.editoria.u-tokyo.ac.jp/projects/dias/?locale=en_US) systems for data distribution for users including, but not limited to, scientists, decision makers and officers like river administrators. One of the functions of this portal is to enable one-stop search and access variable water related data archived multiple data centers located all over the world. This portal itself does not store data. Instead, according to requests made by users on the web page, it retrieves data from distributed data centers on-the-fly and lets them download and see rendered images/plots. Our system mainly relies on the open source software GI-cat (http://essi-lab.eu/do/view/GIcat) and open standards such as OGC-CSW, Opensearch and OPeNDAP protocol to enable the above functions. Details on how it works will be introduced during the presentation. Although some data centers have unique meta data format and/or data search protocols, our portal's brokering function enables users to search across various data centers at one time. And this portal is also connected to other data brokering systems, including GEOSS DAB (Discovery and Access Broker). As a result, users can search over thousands of datasets, millions of files at one time. Users can access the DIAS/CEOS Water Portal system at http://waterportal.ceos.org/.

Chemical effects in biological systems (CEBS) object model for toxicology data, SysTox-OM: design and application.

PubMed

Xirasagar, Sandhya; Gustafson, Scott F; Huang, Cheng-Cheng; Pan, Qinyan; Fostel, Jennifer; Boyer, Paul; Merrick, B Alex; Tomer, Kenneth B; Chan, Denny D; Yost, Kenneth J; Choi, Danielle; Xiao, Nianqing; Stasiewicz, Stanley; Bushel, Pierre; Waters, Michael D

2006-04-01

The CEBS data repository is being developed to promote a systems biology approach to understand the biological effects of environmental stressors. CEBS will house data from multiple gene expression platforms (transcriptomics), protein expression and protein-protein interaction (proteomics), and changes in low molecular weight metabolite levels (metabolomics) aligned by their detailed toxicological context. The system will accommodate extensive complex querying in a user-friendly manner. CEBS will store toxicological contexts including the study design details, treatment protocols, animal characteristics and conventional toxicological endpoints such as histopathology findings and clinical chemistry measures. All of these data types can be integrated in a seamless fashion to enable data query and analysis in a biologically meaningful manner. An object model, the SysBio-OM (Xirasagar et al., 2004) has been designed to facilitate the integration of microarray gene expression, proteomics and metabolomics data in the CEBS database system. We now report SysTox-OM as an open source systems toxicology model designed to integrate toxicological context into gene expression experiments. The SysTox-OM model is comprehensive and leverages other open source efforts, namely, the Standard for Exchange of Nonclinical Data (http://www.cdisc.org/models/send/v2/index.html) which is a data standard for capturing toxicological information for animal studies and Clinical Data Interchange Standards Consortium (http://www.cdisc.org/models/sdtm/index.html) that serves as a standard for the exchange of clinical data. Such standardization increases the accuracy of data mining, interpretation and exchange. The open source SysTox-OM model, which can be implemented on various software platforms, is presented here. A universal modeling language (UML) depiction of the entire SysTox-OM is available at http://cebs.niehs.nih.gov and the Rational Rose object model package is distributed under an open source license that permits unrestricted academic and commercial use and is available at http://cebs.niehs.nih.gov/cebsdownloads. Currently, the public toxicological data in CEBS can be queried via a web application based on the SysTox-OM at http://cebs.niehs.nih.gov xirasagars@saic.com Supplementary data are available at Bioinformatics online.

National Geothermal Data System (USA): an Exemplar of Open Access to Data

NASA Astrophysics Data System (ADS)

Allison, M. Lee; Richard, Stephen; Blackman, Harold; Anderson, Arlene; Patten, Kim

2014-05-01

The National Geothermal Data System's (NGDS - www.geothermaldata.org) formal launch in April, 2014 will provide open access to millions of data records, sharing -relevant geoscience and longer term to land use data to propel geothermal development and production. NGDS serves information from all of the U.S. Department of Energy's sponsored development and research projects and geologic data from all 50 states, using free and open source software. This interactive online system is opening new exploration opportunities and potentially shortening project development by making data easily discoverable, accessible, and interoperable. We continue to populate our prototype functional data system with multiple data nodes and nationwide data online and available to the public. Data from state geological surveys and partners includes more than 6 million records online, including 1.72 million well headers (oil and gas, water, geothermal), 670,000 well logs, and 497,000 borehole temperatures and is growing rapidly. There are over 312 interoperable Web services and another 106 WMS (Web Map Services) registered in the system as of January, 2014. Companion projects run by Southern Methodist University and U.S. Geological Survey (USGS) are adding millions of additional data records. The DOE Geothermal Data Repository, currently hosted on OpenEI, is a system node and clearinghouse for data from hundreds of U.S. DOE-funded geothermal projects. NGDS is built on the US Geoscience Information Network (USGIN) data integration framework, which is a joint undertaking of the USGS and the Association of American State Geologists (AASG). NGDS complies with the White House Executive Order of May 2013, requiring all federal agencies to make their data holdings publicly accessible online in open source, interoperable formats with common core and extensible metadata. The National Geothermal Data System is being designed, built, deployed, and populated primarily with support from the US Department of Energy, Geothermal Technologies Office. To keep this system operational after the original implementation will require four core elements: continued serving of data and applications by providers; maintenance of system operations; a governance structure; and an effective business model. Each of these presents a number of challenges currently under consideration.

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.

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…

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

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

Liao, C; Quinlan, D; Panas, T

2010-01-25

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

Can ICTs contribute to the efficiency and provide equitable access to the health care system in Sub-Saharan Africa? The Mali experience.

PubMed

Bagayoko, C O; Anne, A; Fieschi, M; Geissbuhler, A

2011-01-01

The aim of this study is to demonstrate from actual projects that ICT can contribute to the balance of health systems in developing countries and to equitable access to human resources and quality health care service. Our study is focused on two essential elements which are: i) Capacity building and support of health professionals, especially those in isolated areas using telemedicine tools; ii) Strengthening of hospital information systems by taking advantage of full potential offered by open-source software. Our research was performed on the activities carried out in Mali and in part through the RAFT (Réseau en Afrique Francophone pour la Télémédecine) Network. We focused mainly on the activities of e-learning, telemedicine, and hospital information systems. These include the use of platforms that work with low Internet connection bandwidth. With regard to information systems, our strategy is mainly focused on the improvement and implementation of open-source tools. Several telemedicine application projects were reviewed including continuing online medical education and the support of isolated health professionals through the usage of innovative tools. This review covers the RAFT project for continuing medical education in French-speaking Africa, the tele-radiology project in Mali, the "EQUI-ResHuS" project for equal access to health over ICT in Mali, The "Pact-e.Santé" project for community health workers in Mali. We also detailed a large-scale experience of an open-source hospital information system implemented in Mali: "Cinz@n". We report on successful experiences in the field of telemedicine and on the evaluation by the end-users of the Cinz@n project, a pilot hospital information system in Mali. These reflect the potential of healthcare-ICT for Sub-Saharan African countries.

48 CFR 6.201 - Policy.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 48 Federal Acquisition Regulations System 1 2011-10-01 2011-10-01 false Policy. 6.201 Section 6.201 Federal Acquisition Regulations System FEDERAL ACQUISITION REGULATION ACQUISITION PLANNING COMPETITION REQUIREMENTS Full and Open Competition After Exclusion of Sources 6.201 Policy. Acquisitions made...

48 CFR 6.201 - Policy.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 48 Federal Acquisition Regulations System 1 2013-10-01 2013-10-01 false Policy. 6.201 Section 6.201 Federal Acquisition Regulations System FEDERAL ACQUISITION REGULATION ACQUISITION PLANNING COMPETITION REQUIREMENTS Full and Open Competition After Exclusion of Sources 6.201 Policy. Acquisitions made...

48 CFR 6.201 - Policy.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 48 Federal Acquisition Regulations System 1 2010-10-01 2010-10-01 false Policy. 6.201 Section 6.201 Federal Acquisition Regulations System FEDERAL ACQUISITION REGULATION ACQUISITION PLANNING COMPETITION REQUIREMENTS Full and Open Competition After Exclusion of Sources 6.201 Policy. Acquisitions made...

GET SMARTE: A DECISION SUPPORT SYSTEM TO REVITALIZE COMMUNITIES - CABERNET 2007

EPA Science Inventory

Sustainable Management Approaches and Revitalization Tools - electronic (SMARTe), is an open-source, web-based, decision support system for developing and evaluating future reuse scenarios for potentially contaminated land. SMARTe contains information and analysis tools for all a...

VideoHacking: Automated Tracking and Quantification of Locomotor Behavior with Open Source Software and Off-the-Shelf Video Equipment.

PubMed

Conklin, Emily E; Lee, Kathyann L; Schlabach, Sadie A; Woods, Ian G

2015-01-01

Differences in nervous system function can result in differences in behavioral output. Measurements of animal locomotion enable the quantification of these differences. Automated tracking of animal movement is less labor-intensive and bias-prone than direct observation, and allows for simultaneous analysis of multiple animals, high spatial and temporal resolution, and data collection over extended periods of time. Here, we present a new video-tracking system built on Python-based software that is free, open source, and cross-platform, and that can analyze video input from widely available video capture devices such as smartphone cameras and webcams. We validated this software through four tests on a variety of animal species, including larval and adult zebrafish (Danio rerio), Siberian dwarf hamsters (Phodopus sungorus), and wild birds. These tests highlight the capacity of our software for long-term data acquisition, parallel analysis of multiple animals, and application to animal species of different sizes and movement patterns. We applied the software to an analysis of the effects of ethanol on thigmotaxis (wall-hugging) behavior on adult zebrafish, and found that acute ethanol treatment decreased thigmotaxis behaviors without affecting overall amounts of motion. The open source nature of our software enables flexibility, customization, and scalability in behavioral analyses. Moreover, our system presents a free alternative to commercial video-tracking systems and is thus broadly applicable to a wide variety of educational settings and research programs.

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

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.

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.

Growth and Properties of Lattice Matched GaAsSbN Epilayer on GaAs for Solar Cell Applications

NASA Technical Reports Server (NTRS)

Bharatan, Sudhakar; Iyer, Shanthi; Matney, Kevin; Collis, Ward J.; Nunna Kalyan; Li, Jia; Wu, Liangjin; McGuire, Kristopher; McNeil, Laurie E.

2006-01-01

The growth and properties of GaAsSbN single quantum wells (SQWs) are investigated in this work. The heterostructures were grown on GaAs substrates in an elemental solid source molecular beam epitaxy (MBE) system assisted with a RF plasma nitrogen source. A systematic study has been carried out to determine the influence of various growth conditions, such as the growth temperature and the source shutter-opening sequence, on the quality of the grown layers and the incorporation of N and Sb. The effects of ex situ and in situ annealing under As overpressure on the optical properties of the layers have also been investigated. Substrate temperature in the range of 450-470 C was found to be optimum. Simultaneous opening of the source shutters was found to yield sharper QW interfaces. N and Sb incorporations were found to depend strongly upon substrate temperatures and source shutter opening sequences. A significant increase in PL intensity with a narrowing of PL line shape and blue shift in emission energy were observed on annealing the GaAsSbN/GaAs SQW, with in situ annealing under As overpressure providing better results, compared to ex situ annealing.

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…

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

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.

76 FR 13994 - Privacy Act of 1974; System of Records

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-15

... received which result in a contrary determination. ADDRESSES: You may submit comments, identified by dock... of Defense. Deletion: K700.03 Manpower and Personnel System (MAPS) (February 22, 1993, 58 FR 10562). Reason: Manpower and Personnel System (MAPS) has been replaced with Open Source Corporate Management...

48 CFR 34.002 - Policy.

Code of Federal Regulations, 2011 CFR

2011-10-01

... acquiring major systems shall— (a) Promote innovation and full and open competition as required by part 6 in the development of major system concepts by (1) expressing agency needs and major system acquisition... and sources for as long as it is beneficial. [48 FR 42351, Sept. 19, 1983, as amended at 50 FR 52434...

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

NASA Technical Reports Server (NTRS)

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

The Bern Simple Climate Model (BernSCM) v1.0: an extensible and fully documented open-source re-implementation of the Bern reduced-form model for global carbon cycle-climate simulations

NASA Astrophysics Data System (ADS)

Strassmann, Kuno M.; Joos, Fortunat

2018-05-01

The Bern Simple Climate Model (BernSCM) is a free open-source re-implementation of a reduced-form carbon cycle-climate model which has been used widely in previous scientific work and IPCC assessments. BernSCM represents the carbon cycle and climate system with a small set of equations for the heat and carbon budget, the parametrization of major nonlinearities, and the substitution of complex component systems with impulse response functions (IRFs). The IRF approach allows cost-efficient yet accurate substitution of detailed parent models of climate system components with near-linear behavior. Illustrative simulations of scenarios from previous multimodel studies show that BernSCM is broadly representative of the range of the climate-carbon cycle response simulated by more complex and detailed models. Model code (in Fortran) was written from scratch with transparency and extensibility in mind, and is provided open source. BernSCM makes scientifically sound carbon cycle-climate modeling available for many applications. Supporting up to decadal time steps with high accuracy, it is suitable for studies with high computational load and for coupling with integrated assessment models (IAMs), for example. Further applications include climate risk assessment in a business, public, or educational context and the estimation of CO2 and climate benefits of emission mitigation options.

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

Recent Developments of Versatile Photoinitiating Systems for Cationic Ring Opening Polymerization Operating at Any Wavelengths and under Low Light Intensity Sources.

PubMed

Lalevée, Jacques; Mokbel, Haifaa; Fouassier, Jean-Pierre

2015-04-20

Photoinitiators (PI) or photoinitiating systems (PIS) usable in light induced cationic polymerization (CP) and free radical promoted cationic polymerization (FRPCP) reactions (more specifically for cationic ring opening polymerization (ROP)) together with the involved mechanisms are briefly reviewed. The recent developments of novel two- and three-component PISs for CP and FRPCP upon exposure to low intensity blue to red lights is emphasized in details. Examples of such reactions under various experimental conditions are provided.

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

NASA Astrophysics Data System (ADS)

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

2009-02-01

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

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.

Analyzing huge pathology images with open source software.

PubMed

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

2013-06-06

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

Analyzing huge pathology images with open source software

PubMed Central

2013-01-01

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

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

Medical imaging systems

DOEpatents

Frangioni, John V

2013-06-25

A medical imaging system provides simultaneous rendering of visible light and diagnostic or functional images. The system may be portable, and may include adapters for connecting various light sources and cameras in open surgical environments or laparascopic or endoscopic environments. A user interface provides control over the functionality of the integrated imaging system. In one embodiment, the system provides a tool for surgical pathology.

A Versatile and Reproducible Multi-Frequency Electrical Impedance Tomography System

PubMed Central

Avery, James; Dowrick, Thomas; Faulkner, Mayo; Goren, Nir; Holder, David

2017-01-01

A highly versatile Electrical Impedance Tomography (EIT) system, nicknamed the ScouseTom, has been developed. The system allows control over current amplitude, frequency, number of electrodes, injection protocol and data processing. Current is injected using a Keithley 6221 current source, and voltages are recorded with a 24-bit EEG system with minimum bandwidth of 3.2 kHz. Custom PCBs interface with a PC to control the measurement process, electrode addressing and triggering of external stimuli. The performance of the system was characterised using resistor phantoms to represent human scalp recordings, with an SNR of 77.5 dB, stable across a four hour recording and 20 Hz to 20 kHz. In studies of both haeomorrhage using scalp electrodes, and evoked activity using epicortical electrode mats in rats, it was possible to reconstruct images matching established literature at known areas of onset. Data collected using scalp electrode in humans matched known tissue impedance spectra and was stable over frequency. The experimental procedure is software controlled and is readily adaptable to new paradigms. Where possible, commercial or open-source components were used, to minimise the complexity in reproduction. The hardware designs and software for the system have been released under an open source licence, encouraging contributions and allowing for rapid replication. PMID:28146122

Enhanced terahertz magnetic dipole response by subwavelength fiber

NASA Astrophysics Data System (ADS)

Atakaramians, Shaghik; Shadrivov, Ilya V.; Miroshnichenko, Andrey E.; Stefani, Alessio; Ebendorff-Heidepriem, Heike; Monro, Tanya M.; Afshar V., Shahraam

2018-05-01

Dielectric sub-wavelength particles have opened up a new platform for realization of magnetic light. Recently, we have demonstrated that a dipole emitter by a sub-wavelength fiber leads to an enhanced magnetic response. Here, we experimentally demonstrate an enhanced magnetic dipole source in the terahertz frequency range. By placing the fiber next to the hole in a metal screen, we find that the radiation power can be enhanced more than one order of magnitude. The enhancement is due to the excitation of the Mie-type resonances in the fiber. We demonstrate that such a system is equivalent to a double-fiber system excited by a magnetic source. This coupled magnetic dipole and optical fiber system can be considered a unit cell of metasurfaces for manipulation of terahertz radiation and is a proof-of-concept of a possibility to achieve enhanced radiation of a dipole source in proximity of a sub-wavelength fiber. It can also be scaled down to optical frequencies opening up promising avenues for developing integrated nanophotonic devices such as nanoantennas or lasers on fibers.

Advanced penning ion source

DOEpatents

Schenkel, Thomas; Ji, Qing; Persaud, Arun; Sy, Amy V.

2016-11-01

This disclosure provides systems, methods, and apparatus for ion generation. In one aspect, an apparatus includes an anode, a first cathode, a second cathode, and a plurality of cusp magnets. The anode has a first open end and a second open end. The first cathode is associated with the first open end of the anode. The second cathode is associated with the second open end of the anode. The anode, the first cathode, and the second cathode define a chamber. The second cathode has an open region configured for the passage of ions from the chamber. Each cusp magnet of the plurality of cusp magnets is disposed along a length of the anode.

Nonimaging Optical Illumination System

DOEpatents

Winston, Roland

1994-02-22

A nonimaging illumination or concentration optical device. An optical device is provided having a light source, a light reflecting surface with an opening and positioned partially around the light source which is opposite the opening of the light reflecting surface. The light reflecting surface is disposed to produce a substantially uniform intensity output with the reflecting surface defined in terms of a radius vector R.sub.i in conjunction with an angle .phi..sub.i between R.sub.i, a direction from the source and an angle .theta..sub.i between direct forward illumination and the light ray reflected once from the reflecting surface. R.sub.i varies as the exponential of tan (.phi..sub.i -.theta..sub.i)/2 integrated over .phi..sub.i.

Configurations and implementation of payroll system using open source erp: a case study of Koperasi PT Sri

NASA Astrophysics Data System (ADS)

Terminanto, A.; Swantoro, H. A.; Hidayanto, A. N.

2017-12-01

Enterprise Resource Planning (ERP) is an integrated information system to manage business processes of companies of various business scales. Because of the high cost of ERP investment, ERP implementation is usually done in large-scale enterprises, Due to the complexity of implementation problems, the success rate of ERP implementation is still low. Open Source System ERP becomes an alternative choice of ERP application to SME companies in terms of cost and customization. This study aims to identify characteristics and configure the implementation of OSS ERP Payroll module in KKPS (Employee Cooperative PT SRI) using OSS ERP Odoo and using ASAP method. This study is classified into case study research and action research. Implementation of OSS ERP Payroll module is done because the HR section of KKPS has not been integrated with other parts. The results of this study are the characteristics and configuration of OSS ERP payroll module in KKPS.

Potentiometric surfaces of the intermediate aquifer system, west-central Florida, September 2000

USGS Publications Warehouse

Duerr, A.D.

2001-01-01

The intermediate aquifer system underlies a 5,000-square-mile area within the Southwest Florida Water Management District including De Soto, Sarasota, Hardee, Manatee, and parts of Charlotte, Hillsborough, Highlands, Polk, and Lee Counties.  The intermediate aquifer system is overlain by the surficial aquifer system and is underlain by the Floridan aquifer system.  The intermediate aquifer system consists of layers of sand, shell, clay, calcareous clay, limestone, and dolomite of the Tamiami Formation and Hawthorn Group of Oligocene to Pleistocene age (Wingard and others, 1995).  The intermediate aquifer system contains one or more water-bearing units separated by discontinuous confining units.  The intermediate aquifer system is the principal source of potable water in the southwestern part of the study area and is widely used as a source of water where wells are open to the intermediate aquifer system or to both the intermediate and Floridan aquifer systems.  Yields of individual wells open to the intermediate aquifer system vary from a few gallons to several hundred gallons per minute.  The volume of water withdrawn from the intermediate aquifer system is considerably less than that withdrawn from the Floridan aquifer system in the study area (Duerr and others, 1988).

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…

Issues in Brazilian School Finance.

ERIC Educational Resources Information Center

Plank, David N.

1990-01-01

The Brazilian educational finance system faces three principal problems: the persistence of large regional and intrastate inequalities on all wealth and development indices; the federal government's predominance in controlling revenue sources; and the education system's openness to political abuses. Disparities can only be rectified by…

48 CFR 6.204 - Section 8(a) competition.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 48 Federal Acquisition Regulations System 1 2010-10-01 2010-10-01 false Section 8(a) competition. 6.204 Section 6.204 Federal Acquisition Regulations System FEDERAL ACQUISITION REGULATION ACQUISITION PLANNING COMPETITION REQUIREMENTS Full and Open Competition After Exclusion of Sources 6.204...

Methods, Knowledge Support, and Experimental Tools for Modeling

DTIC Science & Technology

2006-10-01

open source software entities: the PostgreSQL relational database management system (http://www.postgres.org), the Apache web server (http...past. The revision control system allows the program to capture disagreements, and allows users to explore the history of such disagreements by

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…

Case study of open-source enterprise resource planning implementation in a small business

NASA Astrophysics Data System (ADS)

Olson, David L.; Staley, Jesse

2012-02-01

Enterprise resource planning (ERP) systems have been recognised as offering great benefit to some organisations, although they are expensive and problematic to implement. The cost and risk make well-developed proprietorial systems unaffordable to small businesses. Open-source software (OSS) has become a viable means of producing ERP system products. The question this paper addresses is the feasibility of OSS ERP systems for small businesses. A case is reported involving two efforts to implement freely distributed ERP software products in a small US make-to-order engineering firm. The case emphasises the potential of freely distributed ERP systems, as well as some of the hurdles involved in their implementation. The paper briefly reviews highlights of OSS ERP systems, with the primary focus on reporting the case experiences for efforts to implement ERPLite software and xTuple software. While both systems worked from a technical perspective, both failed due to economic factors. While these economic conditions led to imperfect results, the case demonstrates the feasibility of OSS ERP for small businesses. Both experiences are evaluated in terms of risk dimension.

Emission from open burning of municipal solid waste in India.

PubMed

Kumari, Kanchan; Kumar, Sunil; Rajagopal, Vineel; Khare, Ankur; Kumar, Rakesh

2017-07-27

Open burning of Municipal Solid Waste (MSW) is a potential non-point source of emission, which causes greater concern especially in developing countries such as India. Lack of awareness about environmental impact of open burning, and ignorance of the fact, i.e. 'Open burning is a source of emission of carcinogenic substances' are major hindrances towards an appropriate municipal solid waste management system in India. The paper highlights the open burning of MSW practices in India, and the current and projected emission of 10 major pollutants (dioxin, furans, particulate matter, carbon monoxide, sulphur oxides, nitrogen oxides, benzene, toluene, ethyl benzene and 1-hexene) emitted due to the open burning of MSW. Waste to Energy potential of MSW was also estimated adopting effective biological and thermal techniques. Statistical techniques were applied to analyse the data and current and projected emission of various pollutants were estimated. Data pertaining to population, MSW generation and its collection efficiency were compiled for 29 States and 7 Union Territories. Thereafter, emission of 10 pollutants was measured following methodology prescribed in Intergovernmental Panel on Climate Change guideline for National Greenhouse Gas Inventories, 2006. The study revealed that people living in Metropolitan cities are more affected by emissions from open burning.

Fast and Efficient XML Data Access for Next-Generation Mass Spectrometry.

PubMed

Röst, Hannes L; Schmitt, Uwe; Aebersold, Ruedi; Malmström, Lars

2015-01-01

In mass spectrometry-based proteomics, XML formats such as mzML and mzXML provide an open and standardized way to store and exchange the raw data (spectra and chromatograms) of mass spectrometric experiments. These file formats are being used by a multitude of open-source and cross-platform tools which allow the proteomics community to access algorithms in a vendor-independent fashion and perform transparent and reproducible data analysis. Recent improvements in mass spectrometry instrumentation have increased the data size produced in a single LC-MS/MS measurement and put substantial strain on open-source tools, particularly those that are not equipped to deal with XML data files that reach dozens of gigabytes in size. Here we present a fast and versatile parsing library for mass spectrometric XML formats available in C++ and Python, based on the mature OpenMS software framework. Our library implements an API for obtaining spectra and chromatograms under memory constraints using random access or sequential access functions, allowing users to process datasets that are much larger than system memory. For fast access to the raw data structures, small XML files can also be completely loaded into memory. In addition, we have improved the parsing speed of the core mzML module by over 4-fold (compared to OpenMS 1.11), making our library suitable for a wide variety of algorithms that need fast access to dozens of gigabytes of raw mass spectrometric data. Our C++ and Python implementations are available for the Linux, Mac, and Windows operating systems. All proposed modifications to the OpenMS code have been merged into the OpenMS mainline codebase and are available to the community at https://github.com/OpenMS/OpenMS.

Fast and Efficient XML Data Access for Next-Generation Mass Spectrometry

PubMed Central

Röst, Hannes L.; Schmitt, Uwe; Aebersold, Ruedi; Malmström, Lars

2015-01-01

Motivation In mass spectrometry-based proteomics, XML formats such as mzML and mzXML provide an open and standardized way to store and exchange the raw data (spectra and chromatograms) of mass spectrometric experiments. These file formats are being used by a multitude of open-source and cross-platform tools which allow the proteomics community to access algorithms in a vendor-independent fashion and perform transparent and reproducible data analysis. Recent improvements in mass spectrometry instrumentation have increased the data size produced in a single LC-MS/MS measurement and put substantial strain on open-source tools, particularly those that are not equipped to deal with XML data files that reach dozens of gigabytes in size. Results Here we present a fast and versatile parsing library for mass spectrometric XML formats available in C++ and Python, based on the mature OpenMS software framework. Our library implements an API for obtaining spectra and chromatograms under memory constraints using random access or sequential access functions, allowing users to process datasets that are much larger than system memory. For fast access to the raw data structures, small XML files can also be completely loaded into memory. In addition, we have improved the parsing speed of the core mzML module by over 4-fold (compared to OpenMS 1.11), making our library suitable for a wide variety of algorithms that need fast access to dozens of gigabytes of raw mass spectrometric data. Availability Our C++ and Python implementations are available for the Linux, Mac, and Windows operating systems. All proposed modifications to the OpenMS code have been merged into the OpenMS mainline codebase and are available to the community at https://github.com/OpenMS/OpenMS. PMID:25927999

The impact of in-canopy wind attenuation formulations onheat flux estimation using the remote sensing-based two-source model for an open orchard canopy in southern Italy

USDA-ARS?s Scientific Manuscript database

For open orchard and vineyard canopies containing significant fractions of exposed soil (>50%), typical of Mediterranean agricultural regions, the energy balance of the vegetation elements is strongly influenced by heat exchange with the bare soil/substrate. For these agricultural systems a “two-sou...

Combining data from multiple sources using the CUAHSI Hydrologic Information System

NASA Astrophysics Data System (ADS)

Tarboton, D. G.; Ames, D. P.; Horsburgh, J. S.; Goodall, J. L.

2012-12-01

The Consortium of Universities for the Advancement of Hydrologic Science, Inc. (CUAHSI) has developed a Hydrologic Information System (HIS) to provide better access to data by enabling the publication, cataloging, discovery, retrieval, and analysis of hydrologic data using web services. The CUAHSI HIS is an Internet based system comprised of hydrologic databases and servers connected through web services as well as software for data publication, discovery and access. The HIS metadata catalog lists close to 100 web services registered to provide data through this system, ranging from large federal agency data sets to experimental watersheds managed by University investigators. The system's flexibility in storing and enabling public access to similarly formatted data and metadata has created a community data resource from governmental and academic data that might otherwise remain private or analyzed only in isolation. Comprehensive understanding of hydrology requires integration of this information from multiple sources. HydroDesktop is the client application developed as part of HIS to support data discovery and access through this system. HydroDesktop is founded on an open source GIS client and has a plug-in architecture that has enabled the integration of modeling and analysis capability with the functionality for data discovery and access. Model integration is possible through a plug-in built on the OpenMI standard and data visualization and analysis is supported by an R plug-in. This presentation will demonstrate HydroDesktop, showing how it provides an analysis environment within which data from multiple sources can be discovered, accessed and integrated.

MARVIN: a medical research application framework based on open source software.

PubMed

Rudolph, Tobias; Puls, Marc; Anderegg, Christoph; Ebert, Lars; Broehan, Martina; Rudin, Adrian; Kowal, Jens

2008-08-01

This paper describes the open source framework MARVIN for rapid application development in the field of biomedical and clinical research. MARVIN applications consist of modules that can be plugged together in order to provide the functionality required for a specific experimental scenario. Application modules work on a common patient database that is used to store and organize medical data as well as derived data. MARVIN provides a flexible input/output system with support for many file formats including DICOM, various 2D image formats and surface mesh data. Furthermore, it implements an advanced visualization system and interfaces to a wide range of 3D tracking hardware. Since it uses only highly portable libraries, MARVIN applications run on Unix/Linux, Mac OS X and Microsoft Windows.

Open-source products for a lighting experiment device.

PubMed

Gildea, Kevin M; Milburn, Nelda

2014-12-01

The capabilities of open-source software and microcontrollers were used to construct a device for controlled lighting experiments. The device was designed to ascertain whether individuals with certain color vision deficiencies were able to discriminate between the red and white lights in fielded systems on the basis of luminous intensity. The device provided the ability to control the timing and duration of light-emitting diode (LED) and incandescent light stimulus presentations, to present the experimental sequence and verbal instructions automatically, to adjust LED and incandescent luminous intensity, and to display LED and incandescent lights with various spectral emissions. The lighting device could easily be adapted for experiments involving flashing or timed presentations of colored lights, or the components could be expanded to study areas such as threshold light perception and visual alerting systems.

Enhancing Learning Outcomes through Experiential Learning: Using Open-Source Systems to Teach Enterprise Systems and Business Process Management

ERIC Educational Resources Information Center

Jewer, Jennifer; Evermann, Joerg

2015-01-01

Enterprise systems and business process management are the two key information technologies to integrate the functions of a modern business into a coherent and efficient system. While the benefits of these systems are easy to describe, students, especially those without business experience, have difficulty appreciating how these systems are used…

A 868MHz-based wireless sensor network for ground truthing of soil moisture for a hyperspectral remote sensing campaign - design and preliminary results

NASA Astrophysics Data System (ADS)

Näthe, Paul; Becker, Rolf

2014-05-01

Soil moisture and plant available water are important environmental parameters that affect plant growth and crop yield. Hence, they are significant parameters for vegetation monitoring and precision agriculture. However, validation through ground-based soil moisture measurements is necessary for accessing soil moisture, plant canopy temperature, soil temperature and soil roughness with airborne hyperspectral imaging systems in a corresponding hyperspectral imaging campaign as a part of the INTERREG IV A-Project SMART INSPECTORS. At this point, commercially available sensors for matric potential, plant available water and volumetric water content are utilized for automated measurements with smart sensor nodes which are developed on the basis of open-source 868MHz radio modules, featuring a full-scale microcontroller unit that allows an autarkic operation of the sensor nodes on batteries in the field. The generated data from each of these sensor nodes is transferred wirelessly with an open-source protocol to a central node, the so-called "gateway". This gateway collects, interprets and buffers the sensor readings and, eventually, pushes the data-time series onto a server-based database. The entire data processing chain from the sensor reading to the final storage of data-time series on a server is realized with open-source hardware and software in such a way that the recorded data can be accessed from anywhere through the internet. It will be presented how this open-source based wireless sensor network is developed and specified for the application of ground truthing. In addition, the system's perspectives and potentials with respect to usability and applicability for vegetation monitoring and precision agriculture shall be pointed out. Regarding the corresponding hyperspectral imaging campaign, results from ground measurements will be discussed in terms of their contributing aspects to the remote sensing system. Finally, the significance of the wireless sensor network for the application of ground truthing shall be determined.

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.

VIVO Open Source Software: Connecting Facilities to Promote Discovery and Further Research.

NASA Astrophysics Data System (ADS)

Gross, M. B.; Rowan, L. R.; Mayernik, M. S.; Daniels, M. D.; Stott, D.; Allison, J.; Maull, K. E.; Krafft, D. B.; Khan, H.

2016-12-01

EarthCollab (http://earthcube.org/group/earthcollab), a National Science Foundation (NSF) EarthCube Building Block project, has adapted an open source semantic web application, VIVO, for use within the earth science domain. EarthCollab is a partnership between UNAVCO, an NSF facility supporting research through geodetic services, the Earth Observing Laboratory (EOL) at the National Center for Atmospheric Research (NCAR), and Cornell University, where VIVO was created to highlight the scholarly output of researchers at universities. Two public sites have been released: Connect UNAVCO (connect.unavco.org) and Arctic Data Connects (vivo.eol.ucar.edu). The core VIVO software and ontology have been extended to work better with concepts necessary for capturing work within UNAVCO's and EOL's province such as principal investigators for continuous GPS/GNSS stations at UNAVCO and keywords describing cruise datasets at EOL. The sites increase discoverability of large and diverse data archives by linking data with people, research, and field projects. Disambiguation is a major challenge when using VIVO and open data when "anyone can say anything about anything." Concepts and controlled vocabularies help to build consistent and easily searchable connections within VIVO. We use aspects of subject heading services such as FAST and LOC, as well as AGU and GSA fields of research and subject areas to reveal connections, especially with VIVO instances at other institutions. VIVO works effectively with persistent IDs and the projects strive to utilize publication and data DOIs, ORCIDs for people, and ISNI and GRID for organizations. ORCID, an open source project, is very useful for disambiguation and unlike other identifier systems for people developed by publishers, makes public data available via an API. VIVO utilizes Solr and Freemarker, which are open source search engine and templating technologies, respectively. Additionally, a handful of popular open source libraries and applications are being used in the project such as D3.js, jQuery, Leaflet, and Elasticsearch. Our implementation of these open source projects within VIVO is available for adaptation by other institutions using VIVO via GitHub (git.io/vG9AJ).

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

MicMac GIS application: free open source

NASA Astrophysics Data System (ADS)

Duarte, L.; Moutinho, O.; Teodoro, A.

2016-10-01

The use of Remotely Piloted Aerial System (RPAS) for remote sensing applications is becoming more frequent as the technologies on on-board cameras and the platform itself are becoming a serious contender to satellite and airplane imagery. MicMac is a photogrammetric tool for image matching that can be used in different contexts. It is an open source software and it can be used as a command line or with a graphic interface (for each command). The main objective of this work was the integration of MicMac with QGIS, which is also an open source software, in order to create a new open source tool applied to photogrammetry/remote sensing. Python language was used to develop the application. This tool would be very useful in the manipulation and 3D modelling of a set of images. The main objective was to create a toolbar in QGIS with the basic functionalities with intuitive graphic interfaces. The toolbar is composed by three buttons: produce the points cloud, create the Digital Elevation Model (DEM) and produce the orthophoto of the study area. The application was tested considering 35 photos, a subset of images acquired by a RPAS in the Aguda beach area, Porto, Portugal. They were used in order to create a 3D terrain model and from this model obtain an orthophoto and the corresponding DEM. The code is open and can be modified according to the user requirements. This integration would be very useful in photogrammetry and remote sensing community combined with GIS capabilities.

OpenID Connect as a security service in cloud-based medical imaging systems

PubMed Central

Ma, Weina; Sartipi, Kamran; Sharghigoorabi, Hassan; Koff, David; Bak, Peter

2016-01-01

Abstract. The evolution of cloud computing is driving the next generation of medical imaging systems. However, privacy and security concerns have been consistently regarded as the major obstacles for adoption of cloud computing by healthcare domains. OpenID Connect, combining OpenID and OAuth together, is an emerging representational state transfer-based federated identity solution. It is one of the most adopted open standards to potentially become the de facto standard for securing cloud computing and mobile applications, which is also regarded as “Kerberos of cloud.” We introduce OpenID Connect as an authentication and authorization service in cloud-based diagnostic imaging (DI) systems, and propose enhancements that allow for incorporating this technology within distributed enterprise environments. The objective of this study is to offer solutions for secure sharing of medical images among diagnostic imaging repository (DI-r) and heterogeneous picture archiving and communication systems (PACS) as well as Web-based and mobile clients in the cloud ecosystem. The main objective is to use OpenID Connect open-source single sign-on and authorization service and in a user-centric manner, while deploying DI-r and PACS to private or community clouds should provide equivalent security levels to traditional computing model. PMID:27340682

Potentiometric surface of the intermediate aquifer system, west- central Florida, May 1987

USGS Publications Warehouse

Lewelling, B.R.

1988-01-01

The intermediate aquifer system within the Southwest Florida Water Management District underlies a 5,000 sq mi area of De Soto, Sarasota, Hardee, Manatee, and parts of Charlotte, Hillsborough, Highlands, and Polk Counties. The intermediate aquifer system occurs between the overlying surficial aquifer system and the underlying Floridan aquifer system, and consists of layers of sand, shell, clay, marl, limestone, and dolom of the Tamiami, Hawthorn, and Tampa Formations of late Tertiary age. The intermediate aquifer system contains one or more water-bearing units separated by discontinuous confining units. This aquifer system is the principal source of potable water in the southwestern part of the study area and is widely used as a source of water in other parts where wells are open to the intermediate aquifer system or to both the intermediate and Floridan aquifer systems. Yields of individual wells open to the intermediate aquifer system range from a few gallons to several hundred gallons per minute. The volume of water withdrawn from the intermediate aquifer system is considerably less than that withdrawn from the Floridan aquifer system in the study area. The surface was mapped by determining the altitude of water levels in a network of wells and is represented on maps by contours that connect points of equal altitude. The compos potentiometric surface of all water-bearing units within the intermediate aquifer system is shown. In areas where multiple aquifers exist, wells open to all aquifers were selected for water level measurements whenever possible. In the southwestern and lower coastal region of the study area, two aquifers and confining units are described for the intermediate aquifer system: the Tamiami-upper Hawthorn aquifer and the underlying lower Hawthorn-upper Tampa aquifer. The potentiometric surface of the Tamiami-upper Hawthorn aquifer is also shown. Water levels are from wells drilled and open exclusively to that aquifer. The exact boundary for the Tamiami-upper Hawthorn aquifer is undetermined because of limd geohydrologic data available from wells. (Lantz-PTT)

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.

Online characterization of planetary surfaces: PlanetServer, an open-source analysis and visualization tool

NASA Astrophysics Data System (ADS)

Marco Figuera, R.; Pham Huu, B.; Rossi, A. P.; Minin, M.; Flahaut, J.; Halder, A.

2018-01-01

The lack of open-source tools for hyperspectral data visualization and analysis creates a demand for new tools. In this paper we present the new PlanetServer, a set of tools comprising a web Geographic Information System (GIS) and a recently developed Python Application Programming Interface (API) capable of visualizing and analyzing a wide variety of hyperspectral data from different planetary bodies. Current WebGIS open-source tools are evaluated in order to give an overview and contextualize how PlanetServer can help in this matters. The web client is thoroughly described as well as the datasets available in PlanetServer. Also, the Python API is described and exposed the reason of its development. Two different examples of mineral characterization of different hydrosilicates such as chlorites, prehnites and kaolinites in the Nili Fossae area on Mars are presented. As the obtained results show positive outcome in hyperspectral analysis and visualization compared to previous literature, we suggest using the PlanetServer approach for such investigations.

Clarity: An Open Source Manager for Laboratory Automation

PubMed Central

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

2013-01-01

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

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.

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…