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

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

NASA Astrophysics Data System (ADS)

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

2015-02-01

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

ProteoWizard: open source software for rapid proteomics tools development.

PubMed

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

2008-11-01

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

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

PubMed

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

2014-02-01

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

Integrated Environment for Development and Assurance

DTIC Science & Technology

2015-01-26

Jan 26, 2015 © 2015 Carnegie Mellon University We Rely on Software for Safe Aircraft Operation Embedded software systems introduce a new class of...eveloper Compute Platform Runtime Architecture Application Software Embedded SW System Engineer Data Stream Characteristics Latency jitter affects...Why do system level failures still occur despite fault tolerance techniques being deployed in systems ? Embedded software system as major source of

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

NASA Astrophysics Data System (ADS)

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

2014-03-01

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

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

PubMed

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

2014-01-01

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

Distributed and Collaborative Software Analysis

NASA Astrophysics Data System (ADS)

Ghezzi, Giacomo; Gall, Harald C.

Throughout the years software engineers have come up with a myriad of specialized tools and techniques that focus on a certain type of software analysissoftware analysis such as source code analysis, co-change analysis or bug prediction. However, easy and straight forward synergies between these analyses and tools rarely exist because of their stand-alone nature, their platform dependence, their different input and output formats and the variety of data to analyze. As a consequence, distributed and collaborative software analysiscollaborative software analysis scenarios and in particular interoperability are severely limited. We describe a distributed and collaborative software analysis platform that allows for a seamless interoperability of software analysis tools across platform, geographical and organizational boundaries. We realize software analysis tools as services that can be accessed and composed over the Internet. These distributed analysis services shall be widely accessible in our incrementally augmented Software Analysis Broker software analysis broker where organizations and tool providers can register and share their tools. To allow (semi-) automatic use and composition of these tools, they are classified and mapped into a software analysis taxonomy and adhere to specific meta-models and ontologiesontologies for their category of analysis.

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.

DPOI: Distributed software system development platform for ocean information service

NASA Astrophysics Data System (ADS)

Guo, Zhongwen; Hu, Keyong; Jiang, Yongguo; Sun, Zhaosui

2015-02-01

Ocean information management is of great importance as it has been employed in many areas of ocean science and technology. However, the developments of Ocean Information Systems (OISs) often suffer from low efficiency because of repetitive work and continuous modifications caused by dynamic requirements. In this paper, the basic requirements of OISs are analyzed first, and then a novel platform DPOI is proposed to improve development efficiency and enhance software quality of OISs by providing off-the-shelf resources. In the platform, the OIS is decomposed hierarchically into a set of modules, which can be reused in different system developments. These modules include the acquisition middleware and data loader that collect data from instruments and files respectively, the database that stores data consistently, the components that support fast application generation, the web services that make the data from distributed sources syntactical by use of predefined schemas and the configuration toolkit that enables software customization. With the assistance of the development platform, the software development needs no programming and the development procedure is thus accelerated greatly. We have applied the development platform in practical developments and evaluated its efficiency in several development practices and different development approaches. The results show that DPOI significantly improves development efficiency and software quality.

Crux: Rapid Open Source Protein Tandem Mass Spectrometry Analysis

PubMed Central

2015-01-01

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

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

PubMed

Wang, Anliang; Yan, Xiaolong; Wei, Zhijun

2018-04-27

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

OMPC: an Open-Source MATLAB®-to-Python Compiler

PubMed Central

Jurica, Peter; van Leeuwen, Cees

2008-01-01

Free access to scientific information facilitates scientific progress. Open-access scientific journals are a first step in this direction; a further step is to make auxiliary and supplementary materials that accompany scientific publications, such as methodological procedures and data-analysis tools, open and accessible to the scientific community. To this purpose it is instrumental to establish a software base, which will grow toward a comprehensive free and open-source language of technical and scientific computing. Endeavors in this direction are met with an important obstacle. MATLAB®, the predominant computation tool in many fields of research, is a closed-source commercial product. To facilitate the transition to an open computation platform, we propose Open-source MATLAB®-to-Python Compiler (OMPC), a platform that uses syntax adaptation and emulation to allow transparent import of existing MATLAB® functions into Python programs. The imported MATLAB® modules will run independently of MATLAB®, relying on Python's numerical and scientific libraries. Python offers a stable and mature open source platform that, in many respects, surpasses commonly used, expensive commercial closed source packages. The proposed software will therefore facilitate the transparent transition towards a free and general open-source lingua franca for scientific computation, while enabling access to the existing methods and algorithms of technical computing already available in MATLAB®. OMPC is available at http://ompc.juricap.com. PMID:19225577

PLUME and research sotware

NASA Astrophysics Data System (ADS)

Baudin, Veronique; Gomez-Diaz, Teresa

2013-04-01

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

REVEAL: Software Documentation and Platform Migration

NASA Technical Reports Server (NTRS)

Wilson, Michael A.; Veibell, Victoir T.

2011-01-01

The Research Environment for Vehicle Embedded Analysis on Linux (REVEAL) is reconfigurable data acquisition software designed for network-distributed test and measurement applications. In development since 2001, it has been successfully demonstrated in support of a number of actual missions within NASA's Suborbital Science Program. Improvements to software configuration control were needed to properly support both an ongoing transition to operational status and continued evolution of REVEAL capabilities. For this reason the project described in this report targets REVEAL software source documentation and deployment of the software on a small set of hardware platforms different from what is currently used in the baseline system implementation. This presentation specifically describes the actions taken over a ten week period by two undergraduate student interns and serves as an overview of the content of the final report for that internship.

Open-Source 3-D Platform for Low-Cost Scientific Instrument Ecosystem.

PubMed

Zhang, C; Wijnen, B; Pearce, J M

2016-08-01

The combination of open-source software and hardware provides technically feasible methods to create low-cost, highly customized scientific research equipment. Open-source 3-D printers have proven useful for fabricating scientific tools. Here the capabilities of an open-source 3-D printer are expanded to become a highly flexible scientific platform. An automated low-cost 3-D motion control platform is presented that has the capacity to perform scientific applications, including (1) 3-D printing of scientific hardware; (2) laboratory auto-stirring, measuring, and probing; (3) automated fluid handling; and (4) shaking and mixing. The open-source 3-D platform not only facilities routine research while radically reducing the cost, but also inspires the creation of a diverse array of custom instruments that can be shared and replicated digitally throughout the world to drive down the cost of research and education further. © 2016 Society for Laboratory Automation and Screening.

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.

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

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

PubMed

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

2017-08-15

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

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

PubMed Central

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

2017-01-01

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

QGene 4.0, an extensible Java QTL-analysis platform.

PubMed

Joehanes, Roby; Nelson, James C

2008-12-01

Of many statistical methods developed to date for quantitative trait locus (QTL) analysis, only a limited subset are available in public software allowing their exploration, comparison and practical application by researchers. We have developed QGene 4.0, a plug-in platform that allows execution and comparison of a variety of modern QTL-mapping methods and supports third-party addition of new ones. The software accommodates line-cross mating designs consisting of any arbitrary sequence of selfing, backcrossing, intercrossing and haploid-doubling steps that includes map, population, and trait simulators; and is scriptable. Software and documentation are available at http://coding.plantpath.ksu.edu/qgene. Source code is available on request.

Final Report. Center for Scalable Application Development Software

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

Mellor-Crummey, John

2014-10-26

The Center for Scalable Application Development Software (CScADS) was established as a part- nership between Rice University, Argonne National Laboratory, University of California Berkeley, University of Tennessee – Knoxville, and University of Wisconsin – Madison. CScADS pursued an integrated set of activities with the aim of increasing the productivity of DOE computational scientists by catalyzing the development of systems software, libraries, compilers, and tools for leadership computing platforms. Principal Center activities were workshops to engage the research community in the challenges of leadership computing, research and development of open-source software, and work with computational scientists to help them develop codesmore » for leadership computing platforms. This final report summarizes CScADS activities at Rice University in these areas.« less

An Incremental Life-cycle Assurance Strategy for Critical System Certification

DTIC Science & Technology

2014-11-04

for Safe Aircraft Operation Embedded software systems introduce a new class of problems not addressed by traditional system modeling & analysis...Platform Runtime Architecture Application Software Embedded SW System Engineer Data Stream Characteristics Latency jitter affects control behavior...do system level failures still occur despite fault tolerance techniques being deployed in systems ? Embedded software system as major source of

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

PubMed

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

2016-08-30

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

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

NASA Astrophysics Data System (ADS)

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

2016-02-01

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

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.

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

PubMed Central

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

2014-01-01

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

A Software Development Platform for Wearable Medical Applications.

PubMed

Zhang, Ruikai; Lin, Wei

2015-10-01

Wearable medical devices have become a leading trend in healthcare industry. Microcontrollers are computers on a chip with sufficient processing power and preferred embedded computing units in those devices. We have developed a software platform specifically for the design of the wearable medical applications with a small code footprint on the microcontrollers. It is supported by the open source real time operating system FreeRTOS and supplemented with a set of standard APIs for the architectural specific hardware interfaces on the microcontrollers for data acquisition and wireless communication. We modified the tick counter routine in FreeRTOS to include a real time soft clock. When combined with the multitasking features in the FreeRTOS, the platform offers the quick development of wearable applications and easy porting of the application code to different microprocessors. Test results have demonstrated that the application software developed using this platform are highly efficient in CPU usage while maintaining a small code foot print to accommodate the limited memory space in microcontrollers.

Co Modeling and Co Synthesis of Safety Critical Multi threaded Embedded Software for Multi Core Embedded Platforms

DTIC Science & Technology

2017-03-20

computation, Prime Implicates, Boolean Abstraction, real- time embedded software, software synthesis, correct by construction software design , model...types for time -dependent data-flow networks". J.-P. Talpin, P. Jouvelot, S. Shukla. ACM-IEEE Conference on Methods and Models for System Design ...information is estimated to average 1 hour per response, including the time for reviewing instructions, searching existing   data sources, gathering and

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

Apte, A; Veeraraghavan, H; Oh, J

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

Software Transition Project Retrospectives and the Application of SEL Effort Estimation Model and Boehm's COCOMO to Complex Software Transition Projects

NASA Technical Reports Server (NTRS)

McNeill, Justin

1995-01-01

The Multimission Image Processing Subsystem (MIPS) at the Jet Propulsion Laboratory (JPL) has managed transitions of application software sets from one operating system and hardware platform to multiple operating systems and hardware platforms. As a part of these transitions, cost estimates were generated from the personal experience of in-house developers and managers to calculate the total effort required for such projects. Productivity measures have been collected for two such transitions, one very large and the other relatively small in terms of source lines of code. These estimates used a cost estimation model similar to the Software Engineering Laboratory (SEL) Effort Estimation Model. Experience in transitioning software within JPL MIPS have uncovered a high incidence of interface complexity. Interfaces, both internal and external to individual software applications, have contributed to software transition project complexity, and thus to scheduling difficulties and larger than anticipated design work on software to be ported.

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.

Source Lines Counter (SLiC) Version 4.0

NASA Technical Reports Server (NTRS)

Monson, Erik W.; Smith, Kevin A.; Newport, Brian J.; Gostelow, Roli D.; Hihn, Jairus M.; Kandt, Ronald K.

2011-01-01

Source Lines Counter (SLiC) is a software utility designed to measure software source code size using logical source statements and other common measures for 22 of the programming languages commonly used at NASA and the aerospace industry. Such metrics can be used in a wide variety of applications, from parametric cost estimation to software defect analysis. SLiC has a variety of unique features such as automatic code search, automatic file detection, hierarchical directory totals, and spreadsheet-compatible output. SLiC was written for extensibility; new programming language support can be added with minimal effort in a short amount of time. SLiC runs on a variety of platforms including UNIX, Windows, and Mac OSX. Its straightforward command-line interface allows for customization and incorporation into the software build process for tracking development metrics. T

Friendly Extensible Transfer Tool Beta Version

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

Collins, William P.; Gutierrez, Kenneth M.; McRee, Susan R.

2016-04-15

Often data transfer software is designed to meet specific requirements or apply to specific environments. Frequently, this requires source code integration for added functionality. An extensible data transfer framework is needed to more easily incorporate new capabilities, in modular fashion. Using FrETT framework, functionality may be incorporated (in many cases without need of source code) to handle new platform capabilities: I/O methods (e.g., platform specific data access), network transport methods, data processing (e.g., data compression.).

OMPC: an Open-Source MATLAB-to-Python Compiler.

PubMed

Jurica, Peter; van Leeuwen, Cees

2009-01-01

Free access to scientific information facilitates scientific progress. Open-access scientific journals are a first step in this direction; a further step is to make auxiliary and supplementary materials that accompany scientific publications, such as methodological procedures and data-analysis tools, open and accessible to the scientific community. To this purpose it is instrumental to establish a software base, which will grow toward a comprehensive free and open-source language of technical and scientific computing. Endeavors in this direction are met with an important obstacle. MATLAB((R)), the predominant computation tool in many fields of research, is a closed-source commercial product. To facilitate the transition to an open computation platform, we propose Open-source MATLAB((R))-to-Python Compiler (OMPC), a platform that uses syntax adaptation and emulation to allow transparent import of existing MATLAB((R)) functions into Python programs. The imported MATLAB((R)) modules will run independently of MATLAB((R)), relying on Python's numerical and scientific libraries. Python offers a stable and mature open source platform that, in many respects, surpasses commonly used, expensive commercial closed source packages. The proposed software will therefore facilitate the transparent transition towards a free and general open-source lingua franca for scientific computation, while enabling access to the existing methods and algorithms of technical computing already available in MATLAB((R)). OMPC is available at http://ompc.juricap.com.

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…

Open Source in Education

ERIC Educational Resources Information Center

Lakhan, Shaheen E.; Jhunjhunwala, Kavita

2008-01-01

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

Developing Digital Competences Using an Educational Software. A Pedagogical Research

ERIC Educational Resources Information Center

Magdas, Ioana; Bontea, Timea

2011-01-01

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

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

PubMed

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

2012-10-01

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

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…

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).

Celeris: A GPU-accelerated open source software with a Boussinesq-type wave solver for real-time interactive simulation and visualization

NASA Astrophysics Data System (ADS)

Tavakkol, Sasan; Lynett, Patrick

2017-08-01

In this paper, we introduce an interactive coastal wave simulation and visualization software, called Celeris. Celeris is an open source software which needs minimum preparation to run on a Windows machine. The software solves the extended Boussinesq equations using a hybrid finite volume-finite difference method and supports moving shoreline boundaries. The simulation and visualization are performed on the GPU using Direct3D libraries, which enables the software to run faster than real-time. Celeris provides a first-of-its-kind interactive modeling platform for coastal wave applications and it supports simultaneous visualization with both photorealistic and colormapped rendering capabilities. We validate our software through comparison with three standard benchmarks for non-breaking and breaking waves.

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

ERIC Educational Resources Information Center

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

2008-01-01

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

Software Tech News. The DoD Source for Software Technology Information. Software Testing Series: Part 2, Volume 3, Number 3, 1999

DTIC Science & Technology

1999-01-01

published in December of 1998. In addition, Mr. Drake is the author of a theme article entitled: "Measuring Software Quality: A Case Study...and services may run on different platforms in differing combinations , • Partial application failure (e.g., a client running, service down) is...result in a combined utility function that is some aggregation of the underlying utility functions. The benefit a client receives from a service

Current trends for customized biomedical software tools.

PubMed

Khan, Haseeb Ahmad

2017-01-01

In the past, biomedical scientists were solely dependent on expensive commercial software packages for various applications. However, the advent of user-friendly programming languages and open source platforms has revolutionized the development of simple and efficient customized software tools for solving specific biomedical problems. Many of these tools are designed and developed by biomedical scientists independently or with the support of computer experts and often made freely available for the benefit of scientific community. The current trends for customized biomedical software tools are highlighted in this short review.

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

NASA Astrophysics Data System (ADS)

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

2016-04-01

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

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

PubMed Central

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

2008-01-01

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

Rich internet application system for patient-centric healthcare data management using handheld devices.

PubMed

Constantinescu, L; Pradana, R; Kim, J; Gong, P; Fulham, Michael; Feng, D

2009-01-01

Rich Internet Applications (RIAs) are an emerging software platform that blurs the line between web service and native application, and is a powerful tool for handheld device deployment. By democratizing health data management and widening its availability, this software platform has the potential to revolutionize telemedicine, clinical practice, medical education and information distribution, particularly in rural areas, and to make patient-centric medical computing a reality. In this paper, we propose a telemedicine application that leverages the ability of a mobile RIA platform to transcode, organise and present textual and multimedia data, which are sourced from medical database software. We adopted a web-based approach to communicate, in real-time, with an established hospital information system via a custom RIA. The proposed solution allows communication between handheld devices and a hospital information system for media streaming with support for real-time encryption, on any RIA enabled platform. We demonstrate our prototype's ability to securely and rapidly access, without installation requirements, medical data ranging from simple textual records to multi-slice PET-CT images and maximum intensity (MIP) projections.

An open-source java platform for automated reaction mapping.

PubMed

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

2010-09-27

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

RSEIS and RFOC: Seismic Analysis in R

NASA Astrophysics Data System (ADS)

Lees, J. M.

2015-12-01

Open software is essential for reproducible scientific exchange. R-packages provide a platform for development of seismological investigation software that can be properly documented and traced for data processing. A suite of R packages designed for a wide range of seismic analysis is currently available in the free software platform called R. R is a software platform based on the S-language developed at Bell Labs decades ago. Routines in R can be run as standalone function calls, or developed in object-oriented mode. R comes with a base set of routines, and thousands of user developed packages. The packages developed at UNC include subroutines and interactive codes for processing seismic data, analyzing geographic information (GIS) and inverting data involved in a variety of geophysical applications. On CRAN (Comprehensive R Archive Network, http://www.r-project.org/) currently available packages related to seismic analysis are RSEIS, Rquake, GEOmap, RFOC, zoeppritz, RTOMO, and geophys, Rwave, PEIP, hht, rFDSN. These include signal processing, data management, mapping, earthquake location, deconvolution, focal mechanisms, wavelet transforms, Hilbert-Huang Transforms, tomographic inversion, and Mogi deformation among other useful functionality. All software in R packages is required to have detailed documentation, making the exchange and modification of existing software easy. In this presentation, I will focus on packages RSEIS and RFOC, showing examples from a variety of seismic analyses. The R approach has similarities to the popular (and expensive) MATLAB platform, although R is open source and free to down load.

Virtual Observer Controller (VOC) for Small Unit Infantry Laser Simulation Training

DTIC Science & Technology

2007-04-01

per-seat license when deployed. As a result, ViaVoice was abandoned early in development. Next, the SPHINX engine from Carnegie Mellon University was...examined. Sphinx is Java-based software, providing cross-platform functionality, and it is also free, open-source software. Software developers at...IST had experience using SPHINX , so it was initially selected it to be the VOC speech engine. After implementing a small portion of the VOC grammar

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…

A Real-Time Linux for Multicore Platforms

DTIC Science & Technology

2013-12-20

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

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

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

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

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

PubMed

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

2016-10-01

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

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

PubMed

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

2016-10-01

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

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.

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

NASA Technical Reports Server (NTRS)

Samareh, Jamshid A.

2011-01-01

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

Raspberry Pi-powered imaging for plant phenotyping.

PubMed

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

2018-03-01

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

A Randomized Trial Comparing Classical Participatory Design to VandAID, an Interactive CrowdSourcing Platform to Facilitate User-centered Design.

PubMed

Dufendach, Kevin R; Koch, Sabine; Unertl, Kim M; Lehmann, Christoph U

2017-10-26

Early involvement of stakeholders in the design of medical software is particularly important due to the need to incorporate complex knowledge and actions associated with clinical work. Standard user-centered design methods include focus groups and participatory design sessions with individual stakeholders, which generally limit user involvement to a small number of individuals due to the significant time investments from designers and end users. The goal of this project was to reduce the effort for end users to participate in co-design of a software user interface by developing an interactive web-based crowdsourcing platform. In a randomized trial, we compared a new web-based crowdsourcing platform to standard participatory design sessions. We developed an interactive, modular platform that allows responsive remote customization and design feedback on a visual user interface based on user preferences. The responsive canvas is a dynamic HTML template that responds in real time to user preference selections. Upon completion, the design team can view the user's interface creations through an administrator portal and download the structured selections through a REDCap interface. We have created a software platform that allows users to customize a user interface and see the results of that customization in real time, receiving immediate feedback on the impact of their design choices. Neonatal clinicians used the new platform to successfully design and customize a neonatal handoff tool. They received no specific instruction and yet were able to use the software easily and reported high usability. VandAID, a new web-based crowdsourcing platform, can involve multiple users in user-centered design simultaneously and provides means of obtaining design feedback remotely. The software can provide design feedback at any stage in the design process, but it will be of greatest utility for specifying user requirements and evaluating iterative designs with multiple options.

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;

Increasing Flight Software Reuse with OpenSatKit

NASA Technical Reports Server (NTRS)

McComas, David C.

2018-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2015-12-01

The Southern California Earthquake Center (SCEC) Broadband Platform (BBP) is a carefully integrated collection of open-source scientific software programs that can simulate broadband (0-100Hz) ground motions for earthquakes at regional scales. The BBP scientific software modules implement kinematic rupture generation, low and high-frequency seismogram synthesis using wave propagation through 1D layered velocity structures, seismogram ground motion amplitude calculations, and goodness of fit measurements. These modules are integrated into a software system that provides user-defined, repeatable, calculation of ground motion seismograms, using multiple alternative ground motion simulation methods, and software utilities that can generate plots, charts, and maps. The BBP has been developed over the last five years in a collaborative scientific, engineering, and software development project involving geoscientists, earthquake engineers, graduate students, and SCEC scientific software developers. The BBP can run earthquake rupture and wave propagation modeling software to simulate ground motions for well-observed historical earthquakes and to quantify how well the simulated broadband seismograms match the observed seismograms. The BBP can also run simulations for hypothetical earthquakes. In this case, users input an earthquake location and magnitude description, a list of station locations, and a 1D velocity model for the region of interest, and the BBP software then calculates ground motions for the specified stations. The SCEC BBP software released in 2015 can be compiled and run on recent Linux systems with GNU compilers. It includes 5 simulation methods, 7 simulation regions covering California, Japan, and Eastern North America, the ability to compare simulation results against GMPEs, updated ground motion simulation methods, and a simplified command line user interface.

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

PubMed

Geissmann, Quentin

2013-01-01

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

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

PubMed

Wenig, Philip; Odermatt, Juergen

2010-07-30

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

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

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

Managing a Real-Time Embedded Linux Platform with Buildroot

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

Diamond, J.; Martin, K.

2015-01-01

Developers of real-time embedded software often need to build the operating system, kernel, tools and supporting applications from source to work with the differences in their hardware configuration. The first attempts to introduce Linux-based real-time embedded systems into the Fermilab accelerator controls system used this approach but it was found to be time-consuming, difficult to maintain and difficult to adapt to different hardware configurations. Buildroot is an open source build system with a menu-driven configuration tool (similar to the Linux kernel build system) that automates this process. A customized Buildroot [1] system has been developed for use in the Fermilabmore » accelerator controls system that includes several hardware configuration profiles (including Intel, ARM and PowerPC) and packages for Fermilab support software. A bootable image file is produced containing the Linux kernel, shell and supporting software suite that varies from 3 to 20 megabytes large – ideal for network booting. The result is a platform that is easier to maintain and deploy in diverse hardware configurations« less

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

PubMed

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

2016-01-01

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

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.

Genetic Constructor: An Online DNA Design Platform.

PubMed

Bates, Maxwell; Lachoff, Joe; Meech, Duncan; Zulkower, Valentin; Moisy, Anaïs; Luo, Yisha; Tekotte, Hille; Franziska Scheitz, Cornelia Johanna; Khilari, Rupal; Mazzoldi, Florencio; Chandran, Deepak; Groban, Eli

2017-12-15

Genetic Constructor is a cloud Computer Aided Design (CAD) application developed to support synthetic biologists from design intent through DNA fabrication and experiment iteration. The platform allows users to design, manage, and navigate complex DNA constructs and libraries, using a new visual language that focuses on functional parts abstracted from sequence. Features like combinatorial libraries and automated primer design allow the user to separate design from construction by focusing on functional intent, and design constraints aid iterative refinement of designs. A plugin architecture enables contributions from scientists and coders to leverage existing powerful software and connect to DNA foundries. The software is easily accessible and platform agnostic, free for academics, and available in an open-source community edition. Genetic Constructor seeks to democratize DNA design, manufacture, and access to tools and services from the synthetic biology community.

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

NASA Astrophysics Data System (ADS)

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

2015-04-01

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

GUIdock: Using Docker Containers with a Common Graphics User Interface to Address the Reproducibility of Research

PubMed Central

Yeung, Ka Yee

2016-01-01

Reproducibility is vital in science. For complex computational methods, it is often necessary, not just to recreate the code, but also the software and hardware environment to reproduce results. Virtual machines, and container software such as Docker, make it possible to reproduce the exact environment regardless of the underlying hardware and operating system. However, workflows that use Graphical User Interfaces (GUIs) remain difficult to replicate on different host systems as there is no high level graphical software layer common to all platforms. GUIdock allows for the facile distribution of a systems biology application along with its graphics environment. Complex graphics based workflows, ubiquitous in systems biology, can now be easily exported and reproduced on many different platforms. GUIdock uses Docker, an open source project that provides a container with only the absolutely necessary software dependencies and configures a common X Windows (X11) graphic interface on Linux, Macintosh and Windows platforms. As proof of concept, we present a Docker package that contains a Bioconductor application written in R and C++ called networkBMA for gene network inference. Our package also includes Cytoscape, a java-based platform with a graphical user interface for visualizing and analyzing gene networks, and the CyNetworkBMA app, a Cytoscape app that allows the use of networkBMA via the user-friendly Cytoscape interface. PMID:27045593

GUIdock: Using Docker Containers with a Common Graphics User Interface to Address the Reproducibility of Research.

PubMed

Hung, Ling-Hong; Kristiyanto, Daniel; Lee, Sung Bong; Yeung, Ka Yee

2016-01-01

Reproducibility is vital in science. For complex computational methods, it is often necessary, not just to recreate the code, but also the software and hardware environment to reproduce results. Virtual machines, and container software such as Docker, make it possible to reproduce the exact environment regardless of the underlying hardware and operating system. However, workflows that use Graphical User Interfaces (GUIs) remain difficult to replicate on different host systems as there is no high level graphical software layer common to all platforms. GUIdock allows for the facile distribution of a systems biology application along with its graphics environment. Complex graphics based workflows, ubiquitous in systems biology, can now be easily exported and reproduced on many different platforms. GUIdock uses Docker, an open source project that provides a container with only the absolutely necessary software dependencies and configures a common X Windows (X11) graphic interface on Linux, Macintosh and Windows platforms. As proof of concept, we present a Docker package that contains a Bioconductor application written in R and C++ called networkBMA for gene network inference. Our package also includes Cytoscape, a java-based platform with a graphical user interface for visualizing and analyzing gene networks, and the CyNetworkBMA app, a Cytoscape app that allows the use of networkBMA via the user-friendly Cytoscape interface.

Seqcrawler: biological data indexing and browsing platform.

PubMed

Sallou, Olivier; Bretaudeau, Anthony; Roult, Aurelien

2012-07-24

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

CILogon: An Integrated Identity and Access Management Platform for Science

NASA Astrophysics Data System (ADS)

Basney, J.

2016-12-01

When scientists work together, they use web sites and other software to share their ideas and data. To ensure the integrity of their work, these systems require the scientists to log in and verify that they are part of the team working on a particular science problem. Too often, the identity and access verification process is a stumbling block for the scientists. Scientific research projects are forced to invest time and effort into developing and supporting Identity and Access Management (IAM) services, distracting them from the core goals of their research collaboration. CILogon provides an IAM platform that enables scientists to work together to meet their IAM needs more effectively so they can allocate more time and effort to their core mission of scientific research. The CILogon platform enables federated identity management and collaborative organization management. Federated identity management enables researchers to use their home organization identities to access cyberinfrastructure, rather than requiring yet another username and password to log on. Collaborative organization management enables research projects to define user groups for authorization to collaboration platforms (e.g., wikis, mailing lists, and domain applications). CILogon's IAM platform serves the unique needs of research collaborations, namely the need to dynamically form collaboration groups across organizations and countries, sharing access to data, instruments, compute clusters, and other resources to enable scientific discovery. CILogon provides a software-as-a-service platform to ease integration with cyberinfrastructure, while making all software components publicly available under open source licenses to enable re-use. Figure 1 illustrates the components and interfaces of this platform. CILogon has been operational since 2010 and has been used by over 7,000 researchers from more than 170 identity providers to access cyberinfrastructure including Globus, LIGO, Open Science Grid, SeedMe, and XSEDE. The "CILogon 2.0" platform, launched in 2016, adds support for virtual organization (VO) membership management, identity linking, international collaborations, and standard integration protocols, through integration with the Internet2 COmanage collaboration software.

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

NASA Astrophysics Data System (ADS)

Delipetrev, Blagoj

2016-04-01

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

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

The Southern California Earthquake Center (SCEC) Broadband Platform (BBP) is a carefully integrated collection of open-source scientific software programs that can simulate broadband (0-100 Hz) ground motions for earthquakes at regional scales. The BBP can run earthquake rupture and wave propagation modeling software to simulate ground motions for well-observed historical earthquakes and to quantify how well the simulated broadband seismograms match the observed seismograms. The BBP can also run simulations for hypothetical earthquakes. In this case, users input an earthquake location and magnitude description, a list of station locations, and a 1D velocity model for the region of interest, and the BBP software then calculates ground motions for the specified stations. The BBP scientific software modules implement kinematic rupture generation, low- and high-frequency seismogram synthesis using wave propagation through 1D layered velocity structures, several ground motion intensity measure calculations, and various ground motion goodness-of-fit tools. These modules are integrated into a software system that provides user-defined, repeatable, calculation of ground-motion seismograms, using multiple alternative ground motion simulation methods, and software utilities to generate tables, plots, and maps. The BBP has been developed over the last five years in a collaborative project involving geoscientists, earthquake engineers, graduate students, and SCEC scientific software developers. The SCEC BBP software released in 2016 can be compiled and run on recent Linux and Mac OS X systems with GNU compilers. It includes five simulation methods, seven simulation regions covering California, Japan, and Eastern North America, and the ability to compare simulation results against empirical ground motion models (aka GMPEs). The latest version includes updated ground motion simulation methods, a suite of new validation metrics and a simplified command line user interface.

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

PubMed

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

2013-08-02

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

GABBs: Cyberinfrastructure for Self-Service Geospatial Data Exploration, Computation, and Sharing

NASA Astrophysics Data System (ADS)

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

2016-12-01

Geospatial data are present everywhere today with the proliferation of location-aware computing devices. This is especially true in the scientific community where large amounts of data are driving research and education activities in many domains. Collaboration over geospatial data, for example, in modeling, data analysis and visualization, must still overcome the barriers of specialized software and expertise among other challenges. In addressing these needs, the Geospatial data Analysis Building Blocks (GABBs) project aims at building geospatial modeling, data analysis and visualization capabilities in an open source web platform, HUBzero. Funded by NSF's Data Infrastructure Building Blocks initiative, GABBs is creating a geospatial data architecture that integrates spatial data management, mapping and visualization, and interfaces in the HUBzero platform for scientific collaborations. The geo-rendering enabled Rappture toolkit, a generic Python mapping library, geospatial data exploration and publication tools, and an integrated online geospatial data management solution are among the software building blocks from the project. The GABBS software will be available through Amazon's AWS Marketplace VM images and open source. Hosting services are also available to the user community. The outcome of the project will enable researchers and educators to self-manage their scientific data, rapidly create GIS-enable tools, share geospatial data and tools on the web, and build dynamic workflows connecting data and tools, all without requiring significant software development skills, GIS expertise or IT administrative privileges. This presentation will describe the GABBs architecture, toolkits and libraries, and showcase the scientific use cases that utilize GABBs capabilities, as well as the challenges and solutions for GABBs to interoperate with other cyberinfrastructure platforms.

RAPID and DDS

NASA Technical Reports Server (NTRS)

Utz, Hans Heinrich

2011-01-01

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

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

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

NASA Astrophysics Data System (ADS)

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

2016-03-01

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

The ImageJ ecosystem: an open platform for biomedical image analysis

PubMed Central

Schindelin, Johannes; Rueden, Curtis T.; Hiner, Mark C.; Eliceiri, Kevin W.

2015-01-01

Technology in microscopy advances rapidly, enabling increasingly affordable, faster, and more precise quantitative biomedical imaging, which necessitates correspondingly more-advanced image processing and analysis techniques. A wide range of software is available – from commercial to academic, special-purpose to Swiss army knife, small to large–but a key characteristic of software that is suitable for scientific inquiry is its accessibility. Open-source software is ideal for scientific endeavors because it can be freely inspected, modified, and redistributed; in particular, the open-software platform ImageJ has had a huge impact on life sciences, and continues to do so. From its inception, ImageJ has grown significantly due largely to being freely available and its vibrant and helpful user community. Scientists as diverse as interested hobbyists, technical assistants, students, scientific staff, and advanced biology researchers use ImageJ on a daily basis, and exchange knowledge via its dedicated mailing list. Uses of ImageJ range from data visualization and teaching to advanced image processing and statistical analysis. The software's extensibility continues to attract biologists at all career stages as well as computer scientists who wish to effectively implement specific image-processing algorithms. In this review, we use the ImageJ project as a case study of how open-source software fosters its suites of software tools, making multitudes of image-analysis technology easily accessible to the scientific community. We specifically explore what makes ImageJ so popular, how it impacts life science, how it inspires other projects, and how it is self-influenced by coevolving projects within the ImageJ ecosystem. PMID:26153368

The ImageJ ecosystem: An open platform for biomedical image analysis.

PubMed

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

2015-01-01

Technology in microscopy advances rapidly, enabling increasingly affordable, faster, and more precise quantitative biomedical imaging, which necessitates correspondingly more-advanced image processing and analysis techniques. A wide range of software is available-from commercial to academic, special-purpose to Swiss army knife, small to large-but a key characteristic of software that is suitable for scientific inquiry is its accessibility. Open-source software is ideal for scientific endeavors because it can be freely inspected, modified, and redistributed; in particular, the open-software platform ImageJ has had a huge impact on the life sciences, and continues to do so. From its inception, ImageJ has grown significantly due largely to being freely available and its vibrant and helpful user community. Scientists as diverse as interested hobbyists, technical assistants, students, scientific staff, and advanced biology researchers use ImageJ on a daily basis, and exchange knowledge via its dedicated mailing list. Uses of ImageJ range from data visualization and teaching to advanced image processing and statistical analysis. The software's extensibility continues to attract biologists at all career stages as well as computer scientists who wish to effectively implement specific image-processing algorithms. In this review, we use the ImageJ project as a case study of how open-source software fosters its suites of software tools, making multitudes of image-analysis technology easily accessible to the scientific community. We specifically explore what makes ImageJ so popular, how it impacts the life sciences, how it inspires other projects, and how it is self-influenced by coevolving projects within the ImageJ ecosystem. © 2015 Wiley Periodicals, Inc.

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

NASA Astrophysics Data System (ADS)

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

2013-12-01

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

Automated glycopeptide analysis—review of current state and future directions

PubMed Central

Dallas, David C.; Martin, William F.; Hua, Serenus

2013-01-01

Glycosylation of proteins is involved in immune defense, cell–cell adhesion, cellular recognition and pathogen binding and is one of the most common and complex post-translational modifications. Science is still struggling to assign detailed mechanisms and functions to this form of conjugation. Even the structural analysis of glycoproteins—glycoproteomics—remains in its infancy due to the scarcity of high-throughput analytical platforms capable of determining glycopeptide composition and structure, especially platforms for complex biological mixtures. Glycopeptide composition and structure can be determined with high mass-accuracy mass spectrometry, particularly when combined with chromatographic separation, but the sheer volume of generated data necessitates computational software for interpretation. This review discusses the current state of glycopeptide assignment software—advances made to date and issues that remain to be addressed. The various software and algorithms developed so far provide important insights into glycoproteomics. However, there is currently no freely available software that can analyze spectral data in batch and unambiguously determine glycopeptide compositions for N- and O-linked glycopeptides from relevant biological sources such as human milk and serum. Few programs are capable of aiding in structural determination of the glycan component. To significantly advance the field of glycoproteomics, analytical software and algorithms are required that: (i) solve for both N- and O-linked glycopeptide compositions, structures and glycosites in biological mixtures; (ii) are high-throughput and process data in batches; (iii) can interpret mass spectral data from a variety of sources and (iv) are open source and freely available. PMID:22843980

Building Interactive Visualizations for Geochronological Data

NASA Astrophysics Data System (ADS)

Zeringue, J.; Bowring, J. F.; McLean, N. M.; Pastor, F.

2014-12-01

Since the early 1990s, Ken Ludwig's Isoplot software has been the tool of choice for visualization and analysis of isotopic data used for geochronology. The software is an add-in to Microsoft Excel that allows users to generate visual representations of data. However, recent changes to Excel have made Isoplot more difficult to use and maintain, and the software is no longer supported. In the last several years, the Cyber Infrastructure Research and Development Lab for the Earth Sciences (CIRDLES), at the College of Charleston, has worked collaboratively with geochronologists to develop U-Pb_Redux, a software product that provides some of Isoplot's functionality for U-Pb geochronology. However, the community needs a full and complete Isoplot replacement that is open source, platform independent, and not dependent on proprietary software. This temporary lapse in tooling also presents a tremendous opportunity for scientific computing in the earth sciences. When Isoplot was written for Excel, it gained much of the platform's flexibility and power but also was burdened with its limitations. For example, Isoplot could not be used outside of Excel, could not be cross-platform (so long as Excel wasn't), could not be embedded in other applications, and only static images could be produced. Nonetheless this software was and still is a powerful tool that has served the community for more than two decades and the trade-offs were more than acceptable. In 2014, we seek to gain flexibility not available with Excel. We propose that the next generation of charting software be reusable, platform-agnostic, and interactive. This new software should allow scientists to easily explore—not just passively view—their data. Beginning in the fall of 2013, researchers at CIRDLES began planning for and prototyping a 21st-century replacement for Isoplot, which we call Topsoil, an anagram of Isoplot. This work is being conducted in the public domain at https://github.com/CIRDLES/topsoil. We welcome and encourage community participation and contributions.

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

NASA Astrophysics Data System (ADS)

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

2017-05-01

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

A Roadmap for using Agile Development in a Traditional System

NASA Technical Reports Server (NTRS)

Streiffert, Barbara; Starbird, Thomas

2006-01-01

I. Ensemble Development Group: a) Produces activity planning software for in spacecraft; b) Built on Eclipse Rich Client Platform (open source development and runtime software); c) Funded by multiple sources including the Mars Technology Program; d) Incorporated the use of Agile Development. II. Next Generation Uplink Planning System: a) Researches the Activity Planning and Sequencing Subsystem for Mars Science Laboratory (APSS); b) APSS includes Ensemble, Activity Modeling, Constraint Checking, Command Editing and Sequencing tools plus other uplink generation utilities; c) Funded by the Mars Technology Program; d) Integrates all of the tools for APSS.

The AppScale Cloud Platform

PubMed Central

Krintz, Chandra

2013-01-01

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

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.

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

PubMed Central

Geissmann, Quentin

2013-01-01

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

Lenstronomy: Multi-purpose gravitational lens modeling software package

NASA Astrophysics Data System (ADS)

Birrer, Simon; Amara, Adam

2018-04-01

Lenstronomy is a multi-purpose open-source gravitational lens modeling python package. Lenstronomy reconstructs the lens mass and surface brightness distributions of strong lensing systems using forward modelling and supports a wide range of analytic lens and light models in arbitrary combination. The software is also able to reconstruct complex extended sources as well as point sources. Lenstronomy is flexible and numerically accurate, with a clear user interface that could be deployed across different platforms. Lenstronomy has been used to derive constraints on dark matter properties in strong lenses, measure the expansion history of the universe with time-delay cosmography, measure cosmic shear with Einstein rings, and decompose quasar and host galaxy light.

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

PubMed Central

2013-01-01

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

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

PubMed

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

2014-02-07

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

General Aviation Data Framework

NASA Technical Reports Server (NTRS)

Blount, Elaine M.; Chung, Victoria I.

2006-01-01

The Flight Research Services Directorate at the NASA Langley Research Center (LaRC) provides development and operations services associated with three general aviation (GA) aircraft used for research experiments. The GA aircraft includes a Cessna 206X Stationair, a Lancair Colombia 300X, and a Cirrus SR22X. Since 2004, the GA Data Framework software was designed and implemented to gather data from a varying set of hardware and software sources as well as enable transfer of the data to other computers or devices. The key requirements for the GA Data Framework software include platform independence, the ability to reuse the framework for different projects without changing the framework code, graphics display capabilities, and the ability to vary the interfaces and their performance. Data received from the various devices is stored in shared memory. This paper concentrates on the object oriented software design patterns within the General Aviation Data Framework, and how they enable the construction of project specific software without changing the base classes. The issues of platform independence and multi-threading which enable interfaces to run at different frame rates are also discussed in this paper.

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

PubMed

Loening, Andreas Markus; Gambhir, Sanjiv Sam

2003-07-01

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

Distributed Processing of Sentinel-2 Products using the BIGEARTH Platform

NASA Astrophysics Data System (ADS)

Bacu, Victor; Stefanut, Teodor; Nandra, Constantin; Mihon, Danut; Gorgan, Dorian

2017-04-01

The constellation of observational satellites orbiting around Earth is constantly increasing, providing more data that need to be processed in order to extract meaningful information and knowledge from it. Sentinel-2 satellites, part of the Copernicus Earth Observation program, aim to be used in agriculture, forestry and many other land management applications. ESA's SNAP toolbox can be used to process data gathered by Sentinel-2 satellites but is limited to the resources provided by a stand-alone computer. In this paper we present a cloud based software platform that makes use of this toolbox together with other remote sensing software applications to process Sentinel-2 products. The BIGEARTH software platform [1] offers an integrated solution for processing Earth Observation data coming from different sources (such as satellites or on-site sensors). The flow of processing is defined as a chain of tasks based on the WorDeL description language [2]. Each task could rely on a different software technology (such as Grass GIS and ESA's SNAP) in order to process the input data. One important feature of the BIGEARTH platform comes from this possibility of interconnection and integration, throughout the same flow of processing, of the various well known software technologies. All this integration is transparent from the user perspective. The proposed platform extends the SNAP capabilities by enabling specialists to easily scale the processing over distributed architectures, according to their specific needs and resources. The software platform [3] can be used in multiple configurations. In the basic one the software platform runs as a standalone application inside a virtual machine. Obviously in this case the computational resources are limited but it will give an overview of the functionalities of the software platform, and also the possibility to define the flow of processing and later on to execute it on a more complex infrastructure. The most complex and robust configuration is based on cloud computing and allows the installation on a private or public cloud infrastructure. In this configuration, the processing resources can be dynamically allocated and the execution time can be considerably improved by the available virtual resources and the number of parallelizable sequences in the processing flow. The presentation highlights the benefits and issues of the proposed solution by analyzing some significant experimental use cases. Main references for further information: [1] BigEarth project, http://cgis.utcluj.ro/projects/bigearth [2] Constantin Nandra, Dorian Gorgan: "Defining Earth data batch processing tasks by means of a flexible workflow description language", ISPRS Ann. Photogramm. Remote Sens. Spatial Inf. Sci., III-4, 59-66, (2016). [3] Victor Bacu, Teodor Stefanut, Dorian Gorgan, "Adaptive Processing of Earth Observation Data on Cloud Infrastructures Based on Workflow Description", Proceedings of the Intelligent Computer Communication and Processing (ICCP), IEEE-Press, pp.444-454, (2015).

Increasing Flight Software Reuse with OpenSatKit

NASA Technical Reports Server (NTRS)

McComas, David

2018-01-01

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

A Roadmap to Continuous Integration for ATLAS Software Development

NASA Astrophysics Data System (ADS)

Elmsheuser, J.; Krasznahorkay, A.; Obreshkov, E.; Undrus, A.; ATLAS Collaboration

2017-10-01

The ATLAS software infrastructure facilitates efforts of more than 1000 developers working on the code base of 2200 packages with 4 million lines of C++ and 1.4 million lines of python code. The ATLAS offline code management system is the powerful, flexible framework for processing new package versions requests, probing code changes in the Nightly Build System, migration to new platforms and compilers, deployment of production releases for worldwide access and supporting physicists with tools and interfaces for efficient software use. It maintains multi-stream, parallel development environment with about 70 multi-platform branches of nightly releases and provides vast opportunities for testing new packages, for verifying patches to existing software and for migrating to new platforms and compilers. The system evolution is currently aimed on the adoption of modern continuous integration (CI) practices focused on building nightly releases early and often, with rigorous unit and integration testing. This paper describes the CI incorporation program for the ATLAS software infrastructure. It brings modern open source tools such as Jenkins and GitLab into the ATLAS Nightly System, rationalizes hardware resource allocation and administrative operations, provides improved feedback and means to fix broken builds promptly for developers. Once adopted, ATLAS CI practices will improve and accelerate innovation cycles and result in increased confidence in new software deployments. The paper reports the status of Jenkins integration with the ATLAS Nightly System as well as short and long term plans for the incorporation of CI practices.

Waggle: A Framework for Intelligent Attentive Sensing and Actuation

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

ViPAR: a software platform for the Virtual Pooling and Analysis of Research Data.

PubMed

Carter, Kim W; Francis, Richard W; Carter, K W; Francis, R W; Bresnahan, M; Gissler, M; Grønborg, T K; Gross, R; Gunnes, N; Hammond, G; Hornig, M; Hultman, C M; Huttunen, J; Langridge, A; Leonard, H; Newman, S; Parner, E T; Petersson, G; Reichenberg, A; Sandin, S; Schendel, D E; Schalkwyk, L; Sourander, A; Steadman, C; Stoltenberg, C; Suominen, A; Surén, P; Susser, E; Sylvester Vethanayagam, A; Yusof, Z

2016-04-01

Research studies exploring the determinants of disease require sufficient statistical power to detect meaningful effects. Sample size is often increased through centralized pooling of disparately located datasets, though ethical, privacy and data ownership issues can often hamper this process. Methods that facilitate the sharing of research data that are sympathetic with these issues and which allow flexible and detailed statistical analyses are therefore in critical need. We have created a software platform for the Virtual Pooling and Analysis of Research data (ViPAR), which employs free and open source methods to provide researchers with a web-based platform to analyse datasets housed in disparate locations. Database federation permits controlled access to remotely located datasets from a central location. The Secure Shell protocol allows data to be securely exchanged between devices over an insecure network. ViPAR combines these free technologies into a solution that facilitates 'virtual pooling' where data can be temporarily pooled into computer memory and made available for analysis without the need for permanent central storage. Within the ViPAR infrastructure, remote sites manage their own harmonized research dataset in a database hosted at their site, while a central server hosts the data federation component and a secure analysis portal. When an analysis is initiated, requested data are retrieved from each remote site and virtually pooled at the central site. The data are then analysed by statistical software and, on completion, results of the analysis are returned to the user and the virtually pooled data are removed from memory. ViPAR is a secure, flexible and powerful analysis platform built on open source technology that is currently in use by large international consortia, and is made publicly available at [http://bioinformatics.childhealthresearch.org.au/software/vipar/]. © The Author 2015. Published by Oxford University Press on behalf of the International Epidemiological Association.

NDEx - the Network Data Exchange, A Network Commons for Biologists | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

Network models of biology, whether curated or derived from large-scale data analysis, are critical tools in the understanding of cancer mechanisms and in the design and personalization of therapies. The NDEx Project (Network Data Exchange) will create, deploy, and maintain an open-source, web-based software platform and public website to enable scientists, organizations, and software applications to share, store, manipulate, and publish biological networks.

UltraPse: A Universal and Extensible Software Platform for Representing Biological Sequences.

PubMed

Du, Pu-Feng; Zhao, Wei; Miao, Yang-Yang; Wei, Le-Yi; Wang, Likun

2017-11-14

With the avalanche of biological sequences in public databases, one of the most challenging problems in computational biology is to predict their biological functions and cellular attributes. Most of the existing prediction algorithms can only handle fixed-length numerical vectors. Therefore, it is important to be able to represent biological sequences with various lengths using fixed-length numerical vectors. Although several algorithms, as well as software implementations, have been developed to address this problem, these existing programs can only provide a fixed number of representation modes. Every time a new sequence representation mode is developed, a new program will be needed. In this paper, we propose the UltraPse as a universal software platform for this problem. The function of the UltraPse is not only to generate various existing sequence representation modes, but also to simplify all future programming works in developing novel representation modes. The extensibility of UltraPse is particularly enhanced. It allows the users to define their own representation mode, their own physicochemical properties, or even their own types of biological sequences. Moreover, UltraPse is also the fastest software of its kind. The source code package, as well as the executables for both Linux and Windows platforms, can be downloaded from the GitHub repository.

CompactPCI/Linux Platform in FTU Slow Control System

NASA Astrophysics Data System (ADS)

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

2004-12-01

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

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

PubMed

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

2010-10-26

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

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

PubMed Central

2010-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

AlgoRun: a Docker-based packaging system for platform-agnostic implemented algorithms.

PubMed

Hosny, Abdelrahman; Vera-Licona, Paola; Laubenbacher, Reinhard; Favre, Thibauld

2016-08-01

There is a growing need in bioinformatics for easy-to-use software implementations of algorithms that are usable across platforms. At the same time, reproducibility of computational results is critical and often a challenge due to source code changes over time and dependencies. The approach introduced in this paper addresses both of these needs with AlgoRun, a dedicated packaging system for implemented algorithms, using Docker technology. Implemented algorithms, packaged with AlgoRun, can be executed through a user-friendly interface directly from a web browser or via a standardized RESTful web API to allow easy integration into more complex workflows. The packaged algorithm includes the entire software execution environment, thereby eliminating the common problem of software dependencies and the irreproducibility of computations over time. AlgoRun-packaged algorithms can be published on http://algorun.org, a centralized searchable directory to find existing AlgoRun-packaged algorithms. AlgoRun is available at http://algorun.org and the source code under GPL license is available at https://github.com/algorun laubenbacher@uchc.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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

PubMed

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

2005-08-01

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

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.

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.

KiT: a MATLAB package for kinetochore tracking.

PubMed

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

2016-06-15

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

LK Scripting Language

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

The LK scripting language is a simple and fast computer programming language designed for easy integration with existing software to enable automation of tasks. The LK language is used by NREL’s System Advisor Model (SAM), the SAM Software Development Kit (SDK), and SolTrace products. LK is easy extensible and adaptable to new software due to its small footprint and is designed to be statically linked into other software. It is written in standard C++, is cross-platform (Windows, Linux, and OSX), and includes optional portions that enable direct integration with graphical user interfaces written in the open source C++ wxWidgets Versionmore » 3.0+ toolkit.« less

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.

Image processing in biodosimetry: A proposal of a generic free software platform.

PubMed

Dumpelmann, Matthias; Cadena da Matta, Mariel; Pereira de Lemos Pinto, Marcela Maria; de Salazar E Fernandes, Thiago; Borges da Silva, Edvane; Amaral, Ademir

2015-08-01

The scoring of chromosome aberrations is the most reliable biological method for evaluating individual exposure to ionizing radiation. However, microscopic analyses of chromosome human metaphases, generally employed to identify aberrations mainly dicentrics (chromosome with two centromeres), is a laborious task. This method is time consuming and its application in biological dosimetry would be almost impossible in case of a large scale radiation incidents. In this project, a generic software was enhanced for automatic chromosome image processing from a framework originally developed for the Framework V project Simbio, of the European Union for applications in the area of source localization from electroencephalographic signals. The platforms capability is demonstrated by a study comparing automatic segmentation strategies of chromosomes from microscopic images.

GeolOkit 1.0: a new Open Source, Cross-Platform software for geological data visualization in Google Earth environment

NASA Astrophysics Data System (ADS)

Triantafyllou, Antoine; Bastin, Christophe; Watlet, Arnaud

2016-04-01

GIS software suites are today's essential tools to gather and visualise geological data, to apply spatial and temporal analysis and in fine, to create and share interactive maps for further geosciences' investigations. For these purposes, we developed GeolOkit: an open-source, freeware and lightweight software, written in Python, a high-level, cross-platform programming language. GeolOkit software is accessible through a graphical user interface, designed to run in parallel with Google Earth. It is a super user-friendly toolbox that allows 'geo-users' to import their raw data (e.g. GPS, sample locations, structural data, field pictures, maps), to use fast data analysis tools and to plot these one into Google Earth environment using KML code. This workflow requires no need of any third party software, except Google Earth itself. GeolOkit comes with large number of geosciences' labels, symbols, colours and placemarks and may process : (i) multi-points data, (ii) contours via several interpolations methods, (iii) discrete planar and linear structural data in 2D or 3D supporting large range of structures input format, (iv) clustered stereonets and rose diagram, (v) drawn cross-sections as vertical sections, (vi) georeferenced maps and vectors, (vii) field pictures using either geo-tracking metadata from a camera built-in GPS module, or the same-day track of an external GPS. We are looking for you to discover all the functionalities of GeolOkit software. As this project is under development, we are definitely looking to discussions regarding your proper needs, your ideas and contributions to GeolOkit project.

Open source Modeling and optimization tools for Planning

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

Peles, S.

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

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

PubMed

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

2017-11-01

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

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

DTIC Science & Technology

2016-01-01

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

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

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

PubMed

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

2007-11-01

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

A Versatile Phenotyping System and Analytics Platform Reveals Diverse Temporal Responses to Water Availability in Setaria.

PubMed

Fahlgren, Noah; Feldman, Maximilian; Gehan, Malia A; Wilson, Melinda S; Shyu, Christine; Bryant, Douglas W; Hill, Steven T; McEntee, Colton J; Warnasooriya, Sankalpi N; Kumar, Indrajit; Ficor, Tracy; Turnipseed, Stephanie; Gilbert, Kerrigan B; Brutnell, Thomas P; Carrington, James C; Mockler, Todd C; Baxter, Ivan

2015-10-05

Phenotyping has become the rate-limiting step in using large-scale genomic data to understand and improve agricultural crops. Here, the Bellwether Phenotyping Platform for controlled-environment plant growth and automated multimodal phenotyping is described. The system has capacity for 1140 plants, which pass daily through stations to record fluorescence, near-infrared, and visible images. Plant Computer Vision (PlantCV) was developed as open-source, hardware platform-independent software for quantitative image analysis. In a 4-week experiment, wild Setaria viridis and domesticated Setaria italica had fundamentally different temporal responses to water availability. While both lines produced similar levels of biomass under limited water conditions, Setaria viridis maintained the same water-use efficiency under water replete conditions, while Setaria italica shifted to less efficient growth. Overall, the Bellwether Phenotyping Platform and PlantCV software detected significant effects of genotype and environment on height, biomass, water-use efficiency, color, plant architecture, and tissue water status traits. All ∼ 79,000 images acquired during the course of the experiment are publicly available. Copyright © 2015 The Author. Published by Elsevier Inc. All rights reserved.

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

PubMed Central

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

2018-01-01

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

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

PubMed

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

2018-03-29

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

A New Effort for Atmospherical Forecast: Meteorological Image Processing Software (MIPS) for Astronomical Observations

NASA Astrophysics Data System (ADS)

Shameoni Niaei, M.; Kilic, Y.; Yildiran, B. E.; Yüzlükoglu, F.; Yesilyaprak, C.

2016-12-01

We have described a new software (MIPS) about the analysis and image processing of the meteorological satellite (Meteosat) data for an astronomical observatory. This software will be able to help to make some atmospherical forecast (cloud, humidity, rain) using meteosat data for robotic telescopes. MIPS uses a python library for Eumetsat data that aims to be completely open-source and licenced under GNU/General Public Licence (GPL). MIPS is a platform independent and uses h5py, numpy, and PIL with the general-purpose and high-level programming language Python and the QT framework.

Canary: An NLP Platform for Clinicians and Researchers.

PubMed

Malmasi, Shervin; Sandor, Nicolae L; Hosomura, Naoshi; Goldberg, Matt; Skentzos, Stephen; Turchin, Alexander

2017-05-03

Information Extraction methods can help discover critical knowledge buried in the vast repositories of unstructured clinical data. However, these methods are underutilized in clinical research, potentially due to the absence of free software geared towards clinicians with little technical expertise. The skills required for developing/using such software constitute a major barrier for medical researchers wishing to employ these methods. To address this, we have developed Canary, a free and open-source solution designed for users without natural language processing (NLP) or software engineering experience. It was designed to be fast and work out of the box via a user-friendly graphical interface.

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

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

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

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

Aziz, Azizan; Lasternas, Bertrand; Alschuler, Elena

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

ScaMo: Realisation of an OO-functional DSL for cross platform mobile applications development

NASA Astrophysics Data System (ADS)

Macos, Dragan; Solymosi, Andreas

2013-10-01

The software market is dynamically changing: the Internet is going mobile, the software applications are shifting from the desktop hardware onto the mobile devices. The largest markets are the mobile applications for iOS, Android and Windows Phone and for the purpose the typical programming languages include Objective-C, Java and C ♯. The realization of the native applications implies the integration of the developed software into the environments of mentioned mobile operating systems to enable the access to different hardware components of the devices: GPS module, display, GSM module, etc. This paper deals with the definition and possible implementation of an environment for the automatic application generation for multiple mobile platforms. It is based on a DSL for mobile application development, which includes the programming language Scala and a DSL defined in Scala. As part of a multi-stage cross-compiling algorithm, this language is translated into the language of the affected mobile platform. The advantage of our method lies in the expressiveness of the defined language and the transparent source code translation between different languages, which implies, for example, the advantages of debugging and development of the generated code.

The NCI High Performance Computing (HPC) and High Performance Data (HPD) Platform to Support the Analysis of Petascale Environmental Data Collections

NASA Astrophysics Data System (ADS)

Evans, B. J. K.; Pugh, T.; Wyborn, L. A.; Porter, D.; Allen, C.; Smillie, J.; Antony, J.; Trenham, C.; Evans, B. J.; Beckett, D.; Erwin, T.; King, E.; Hodge, J.; Woodcock, R.; Fraser, R.; Lescinsky, D. T.

2014-12-01

The National Computational Infrastructure (NCI) has co-located a priority set of national data assets within a HPC research platform. This powerful in-situ computational platform has been created to help serve and analyse the massive amounts of data across the spectrum of environmental collections - in particular the climate, observational data and geoscientific domains. This paper examines the infrastructure, innovation and opportunity for this significant research platform. NCI currently manages nationally significant data collections (10+ PB) categorised as 1) earth system sciences, climate and weather model data assets and products, 2) earth and marine observations and products, 3) geosciences, 4) terrestrial ecosystem, 5) water management and hydrology, and 6) astronomy, social science and biosciences. The data is largely sourced from the NCI partners (who include the custodians of many of the national scientific records), major research communities, and collaborating overseas organisations. By co-locating these large valuable data assets, new opportunities have arisen by harmonising the data collections, making a powerful transdisciplinary research platformThe data is accessible within an integrated HPC-HPD environment - a 1.2 PFlop supercomputer (Raijin), a HPC class 3000 core OpenStack cloud system and several highly connected large scale and high-bandwidth Lustre filesystems. New scientific software, cloud-scale techniques, server-side visualisation and data services have been harnessed and integrated into the platform, so that analysis is performed seamlessly across the traditional boundaries of the underlying data domains. Characterisation of the techniques along with performance profiling ensures scalability of each software component, all of which can either be enhanced or replaced through future improvements. A Development-to-Operations (DevOps) framework has also been implemented to manage the scale of the software complexity alone. This ensures that software is both upgradable and maintainable, and can be readily reused with complexly integrated systems and become part of the growing global trusted community tools for cross-disciplinary research.

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.

Fast software-based volume rendering using multimedia instructions on PC platforms and its application to virtual endoscopy

NASA Astrophysics Data System (ADS)

Mori, Kensaku; Suenaga, Yasuhito; Toriwaki, Jun-ichiro

2003-05-01

This paper describes a software-based fast volume rendering (VolR) method on a PC platform by using multimedia instructions, such as SIMD instructions, which are currently available in PCs' CPUs. This method achieves fast rendering speed through highly optimizing software rather than an improved rendering algorithm. In volume rendering using a ray casting method, the system requires fast execution of the following processes: (a) interpolation of voxel or color values at sample points, (b) computation of normal vectors (gray-level gradient vectors), (c) calculation of shaded values obtained by dot-products of normal vectors and light source direction vectors, (d) memory access to a huge area, and (e) efficient ray skipping at translucent regions. The proposed software implements these fundamental processes in volume rending by using special instruction sets for multimedia processing. The proposed software can generate virtual endoscopic images of a 3-D volume of 512x512x489 voxel size by volume rendering with perspective projection, specular reflection, and on-the-fly normal vector computation on a conventional PC without any special hardware at thirteen frames per second. Semi-translucent display is also possible.

CONRAD—A software framework for cone-beam imaging in radiology

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

Maier, Andreas; Choi, Jang-Hwan; Riess, Christian

2013-11-15

Purpose: In the community of x-ray imaging, there is a multitude of tools and applications that are used in scientific practice. Many of these tools are proprietary and can only be used within a certain lab. Often the same algorithm is implemented multiple times by different groups in order to enable comparison. In an effort to tackle this problem, the authors created CONRAD, a software framework that provides many of the tools that are required to simulate basic processes in x-ray imaging and perform image reconstruction with consideration of nonlinear physical effects.Methods: CONRAD is a Java-based state-of-the-art software platform withmore » extensive documentation. It is based on platform-independent technologies. Special libraries offer access to hardware acceleration such as OpenCL. There is an easy-to-use interface for parallel processing. The software package includes different simulation tools that are able to generate up to 4D projection and volume data and respective vector motion fields. Well known reconstruction algorithms such as FBP, DBP, and ART are included. All algorithms in the package are referenced to a scientific source.Results: A total of 13 different phantoms and 30 processing steps have already been integrated into the platform at the time of writing. The platform comprises 74.000 nonblank lines of code out of which 19% are used for documentation. The software package is available for download at http://conrad.stanford.edu. To demonstrate the use of the package, the authors reconstructed images from two different scanners, a table top system and a clinical C-arm system. Runtimes were evaluated using the RabbitCT platform and demonstrate state-of-the-art runtimes with 2.5 s for the 256 problem size and 12.4 s for the 512 problem size.Conclusions: As a common software framework, CONRAD enables the medical physics community to share algorithms and develop new ideas. In particular this offers new opportunities for scientific collaboration and quantitative performance comparison between the methods of different groups.« less

OpenSQUID: A Flexible Open-Source Software Framework for the Control of SQUID Electronics

DOE PAGES

Jaeckel, Felix T.; Lafler, Randy J.; Boyd, S. T. P.

2013-02-06

We report commercially available computer-controlled SQUID electronics are usually delivered with software providing a basic user interface for adjustment of SQUID tuning parameters, such as bias current, flux offset, and feedback loop settings. However, in a research context it would often be useful to be able to modify this code and/or to have full control over all these parameters from researcher-written software. In the case of the STAR Cryoelectronics PCI/PFL family of SQUID control electronics, the supplied software contains modules for automatic tuning and noise characterization, but does not provide an interface for user code. On the other hand, themore » Magnicon SQUIDViewer software package includes a public application programming interface (API), but lacks auto-tuning and noise characterization features. To overcome these and other limitations, we are developing an "open-source" framework for controlling SQUID electronics which should provide maximal interoperability with user software, a unified user interface for electronics from different manufacturers, and a flexible platform for the rapid development of customized SQUID auto-tuning and other advanced features. Finally, we have completed a first implementation for the STAR Cryoelectronics hardware and have made the source code for this ongoing project available to the research community on SourceForge (http://opensquid.sourceforge.net) under the GNU public license.« less

An Open Source Model for Open Access Journal Publication

PubMed Central

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

2005-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2014-04-01

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

FreeTure: A Free software to capTure meteors for FRIPON

NASA Astrophysics Data System (ADS)

Audureau, Yoan; Marmo, Chiara; Bouley, Sylvain; Kwon, Min-Kyung; Colas, François; Vaubaillon, Jérémie; Birlan, Mirel; Zanda, Brigitte; Vernazza, Pierre; Caminade, Stephane; Gattecceca, Jérôme

2014-02-01

The Fireball Recovery and Interplanetary Observation Network (FRIPON) is a French project started in 2014 which will monitor the sky, using 100 all-sky cameras to detect meteors and to retrieve related meteorites on the ground. There are several detection software all around. Some of them are proprietary. Also, some of them are hardware dependent. We present here the open source software for meteor detection to be installed on the FRIPON network's stations. The software will run on Linux with gigabit Ethernet cameras and we plan to make it cross platform. This paper is focused on the meteor detection method used for the pipeline development and the present capabilities.

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

ERIC Educational Resources Information Center

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

2014-01-01

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

A Virtual Laboratory for Digital Signal Processing

ERIC Educational Resources Information Center

Dow, Chyi-Ren; Li, Yi-Hsung; Bai, Jin-Yu

2006-01-01

This work designs and implements a virtual digital signal processing laboratory, VDSPL. VDSPL consists of four parts: mobile agent execution environments, mobile agents, DSP development software, and DSP experimental platforms. The network capability of VDSPL is created by using mobile agent and wrapper techniques without modifying the source code…

Get It Together: Integrating Data with XML.

ERIC Educational Resources Information Center

Miller, Ron

2003-01-01

Discusses the use of XML for data integration to move data across different platforms, including across the Internet, from a variety of sources. Topics include flexibility; standards; organizing databases; unstructured data and the use of meta tags to encode it with XML information; cost effectiveness; and eliminating client software licenses.…

Open source pipeline for ESPaDOnS reduction and analysis

NASA Astrophysics Data System (ADS)

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

2012-09-01

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

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

PubMed Central

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

2013-01-01

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

NeuroPG: open source software for optical pattern generation and data acquisition

PubMed Central

Avants, Benjamin W.; Murphy, Daniel B.; Dapello, Joel A.; Robinson, Jacob T.

2015-01-01

Patterned illumination using a digital micromirror device (DMD) is a powerful tool for optogenetics. Compared to a scanning laser, DMDs are inexpensive and can easily create complex illumination patterns. Combining these complex spatiotemporal illumination patterns with optogenetics allows DMD-equipped microscopes to probe neural circuits by selectively manipulating the activity of many individual cells or many subcellular regions at the same time. To use DMDs to study neural activity, scientists must develop specialized software to coordinate optical stimulation patterns with the acquisition of electrophysiological and fluorescence data. To meet this growing need we have developed an open source optical pattern generation software for neuroscience—NeuroPG—that combines, DMD control, sample visualization, and data acquisition in one application. Built on a MATLAB platform, NeuroPG can also process, analyze, and visualize data. The software is designed specifically for the Mightex Polygon400; however, as an open source package, NeuroPG can be modified to incorporate any data acquisition, imaging, or illumination equipment that is compatible with MATLAB’s Data Acquisition and Image Acquisition toolboxes. PMID:25784873

A High-Speed, Real-Time Visualization and State Estimation Platform for Monitoring and Control of Electric Distribution Systems: Implementation and Field Results

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

Lundstrom, Blake; Gotseff, Peter; Giraldez, Julieta

Continued deployment of renewable and distributed energy resources is fundamentally changing the way that electric distribution systems are controlled and operated; more sophisticated active system control and greater situational awareness are needed. Real-time measurements and distribution system state estimation (DSSE) techniques enable more sophisticated system control and, when combined with visualization applications, greater situational awareness. This paper presents a novel demonstration of a high-speed, real-time DSSE platform and related control and visualization functionalities, implemented using existing open-source software and distribution system monitoring hardware. Live scrolling strip charts of meter data and intuitive annotated map visualizations of the entire state (obtainedmore » via DSSE) of a real-world distribution circuit are shown. The DSSE implementation is validated to demonstrate provision of accurate voltage data. This platform allows for enhanced control and situational awareness using only a minimum quantity of distribution system measurement units and modest data and software infrastructure.« less

Software platform virtualization in chemistry research and university teaching

PubMed Central

2009-01-01

Background Modern chemistry laboratories operate with a wide range of software applications under different operating systems, such as Windows, LINUX or Mac OS X. Instead of installing software on different computers it is possible to install those applications on a single computer using Virtual Machine software. Software platform virtualization allows a single guest operating system to execute multiple other operating systems on the same computer. We apply and discuss the use of virtual machines in chemistry research and teaching laboratories. Results Virtual machines are commonly used for cheminformatics software development and testing. Benchmarking multiple chemistry software packages we have confirmed that the computational speed penalty for using virtual machines is low and around 5% to 10%. Software virtualization in a teaching environment allows faster deployment and easy use of commercial and open source software in hands-on computer teaching labs. Conclusion Software virtualization in chemistry, mass spectrometry and cheminformatics is needed for software testing and development of software for different operating systems. In order to obtain maximum performance the virtualization software should be multi-core enabled and allow the use of multiprocessor configurations in the virtual machine environment. Server consolidation, by running multiple tasks and operating systems on a single physical machine, can lead to lower maintenance and hardware costs especially in small research labs. The use of virtual machines can prevent software virus infections and security breaches when used as a sandbox system for internet access and software testing. Complex software setups can be created with virtual machines and are easily deployed later to multiple computers for hands-on teaching classes. We discuss the popularity of bioinformatics compared to cheminformatics as well as the missing cheminformatics education at universities worldwide. PMID:20150997

Software platform virtualization in chemistry research and university teaching.

PubMed

Kind, Tobias; Leamy, Tim; Leary, Julie A; Fiehn, Oliver

2009-11-16

Modern chemistry laboratories operate with a wide range of software applications under different operating systems, such as Windows, LINUX or Mac OS X. Instead of installing software on different computers it is possible to install those applications on a single computer using Virtual Machine software. Software platform virtualization allows a single guest operating system to execute multiple other operating systems on the same computer. We apply and discuss the use of virtual machines in chemistry research and teaching laboratories. Virtual machines are commonly used for cheminformatics software development and testing. Benchmarking multiple chemistry software packages we have confirmed that the computational speed penalty for using virtual machines is low and around 5% to 10%. Software virtualization in a teaching environment allows faster deployment and easy use of commercial and open source software in hands-on computer teaching labs. Software virtualization in chemistry, mass spectrometry and cheminformatics is needed for software testing and development of software for different operating systems. In order to obtain maximum performance the virtualization software should be multi-core enabled and allow the use of multiprocessor configurations in the virtual machine environment. Server consolidation, by running multiple tasks and operating systems on a single physical machine, can lead to lower maintenance and hardware costs especially in small research labs. The use of virtual machines can prevent software virus infections and security breaches when used as a sandbox system for internet access and software testing. Complex software setups can be created with virtual machines and are easily deployed later to multiple computers for hands-on teaching classes. We discuss the popularity of bioinformatics compared to cheminformatics as well as the missing cheminformatics education at universities worldwide.

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.

NiftyPET: a High-throughput Software Platform for High Quantitative Accuracy and Precision PET Imaging and Analysis.

PubMed

Markiewicz, Pawel J; Ehrhardt, Matthias J; Erlandsson, Kjell; Noonan, Philip J; Barnes, Anna; Schott, Jonathan M; Atkinson, David; Arridge, Simon R; Hutton, Brian F; Ourselin, Sebastien

2018-01-01

We present a standalone, scalable and high-throughput software platform for PET image reconstruction and analysis. We focus on high fidelity modelling of the acquisition processes to provide high accuracy and precision quantitative imaging, especially for large axial field of view scanners. All the core routines are implemented using parallel computing available from within the Python package NiftyPET, enabling easy access, manipulation and visualisation of data at any processing stage. The pipeline of the platform starts from MR and raw PET input data and is divided into the following processing stages: (1) list-mode data processing; (2) accurate attenuation coefficient map generation; (3) detector normalisation; (4) exact forward and back projection between sinogram and image space; (5) estimation of reduced-variance random events; (6) high accuracy fully 3D estimation of scatter events; (7) voxel-based partial volume correction; (8) region- and voxel-level image analysis. We demonstrate the advantages of this platform using an amyloid brain scan where all the processing is executed from a single and uniform computational environment in Python. The high accuracy acquisition modelling is achieved through span-1 (no axial compression) ray tracing for true, random and scatter events. Furthermore, the platform offers uncertainty estimation of any image derived statistic to facilitate robust tracking of subtle physiological changes in longitudinal studies. The platform also supports the development of new reconstruction and analysis algorithms through restricting the axial field of view to any set of rings covering a region of interest and thus performing fully 3D reconstruction and corrections using real data significantly faster. All the software is available as open source with the accompanying wiki-page and test data.

PyGaze: an open-source, cross-platform toolbox for minimal-effort programming of eyetracking experiments.

PubMed

Dalmaijer, Edwin S; Mathôt, Sebastiaan; Van der Stigchel, Stefan

2014-12-01

The PyGaze toolbox is an open-source software package for Python, a high-level programming language. It is designed for creating eyetracking experiments in Python syntax with the least possible effort, and it offers programming ease and script readability without constraining functionality and flexibility. PyGaze can be used for visual and auditory stimulus presentation; for response collection via keyboard, mouse, joystick, and other external hardware; and for the online detection of eye movements using a custom algorithm. A wide range of eyetrackers of different brands (EyeLink, SMI, and Tobii systems) are supported. The novelty of PyGaze lies in providing an easy-to-use layer on top of the many different software libraries that are required for implementing eyetracking experiments. Essentially, PyGaze is a software bridge for eyetracking research.

BEARS: a multi-mission anomaly response system

NASA Astrophysics Data System (ADS)

Roberts, Bryce A.

2009-05-01

The Mission Operations Group at UC Berkeley's Space Sciences Laboratory operates a highly automated ground station and presently a fleet of seven satellites, each with its own associated command and control console. However, the requirement for prompt anomaly detection and resolution is shared commonly between the ground segment and all spacecraft. The efficient, low-cost operation and "lights-out" staffing of the Mission Operations Group requires that controllers and engineers be notified of spacecraft and ground system problems around the clock. The Berkeley Emergency Anomaly and Response System (BEARS) is an in-house developed web- and paging-based software system that meets this need. BEARS was developed as a replacement for an existing emergency reporting software system that was too closedsource, platform-specific, expensive, and antiquated to expand or maintain. To avoid these limitations, the new system design leverages cross-platform, open-source software products such as MySQL, PHP, and Qt. Anomaly notifications and responses make use of the two-way paging capabilities of modern smart phones.

GFam: a platform for automatic annotation of gene families.

PubMed

Sasidharan, Rajkumar; Nepusz, Tamás; Swarbreck, David; Huala, Eva; Paccanaro, Alberto

2012-10-01

We have developed GFam, a platform for automatic annotation of gene/protein families. GFam provides a framework for genome initiatives and model organism resources to build domain-based families, derive meaningful functional labels and offers a seamless approach to propagate functional annotation across periodic genome updates. GFam is a hybrid approach that uses a greedy algorithm to chain component domains from InterPro annotation provided by its 12 member resources followed by a sequence-based connected component analysis of un-annotated sequence regions to derive consensus domain architecture for each sequence and subsequently generate families based on common architectures. Our integrated approach increases sequence coverage by 7.2 percentage points and residue coverage by 14.6 percentage points higher than the coverage relative to the best single-constituent database within InterPro for the proteome of Arabidopsis. The true power of GFam lies in maximizing annotation provided by the different InterPro data sources that offer resource-specific coverage for different regions of a sequence. GFam's capability to capture higher sequence and residue coverage can be useful for genome annotation, comparative genomics and functional studies. GFam is a general-purpose software and can be used for any collection of protein sequences. The software is open source and can be obtained from http://www.paccanarolab.org/software/gfam/.

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

PubMed

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

2008-11-01

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

Research on sudden environmental pollution public service platform construction based on WebGIS

NASA Astrophysics Data System (ADS)

Bi, T. P.; Gao, D. Y.; Zhong, X. Y.

2016-08-01

In order to actualize the social sharing and service of the emergency-response information for sudden pollution accidents, the public can share the risk source information service, dangerous goods control technology service and so on, The SQL Server and ArcSDE software are used to establish a spatial database to restore all kinds of information including risk sources, hazardous chemicals and handling methods in case of accidents. Combined with Chinese atmospheric environmental assessment standards, the SCREEN3 atmospheric dispersion model and one-dimensional liquid diffusion model are established to realize the query of related information and the display of the diffusion effect under B/S structure. Based on the WebGIS technology, C#.Net language is used to develop the sudden environmental pollution public service platform. As a result, the public service platform can make risk assessments and provide the best emergency processing services.

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

PubMed

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

2016-01-01

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

Web accessibility and open source software.

PubMed

Obrenović, Zeljko

2009-07-01

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

Open source software and low cost sensors for teaching UAV science

NASA Astrophysics Data System (ADS)

Kefauver, S. C.; Sanchez-Bragado, R.; El-Haddad, G.; Araus, J. L.

2016-12-01

Drones, also known as UASs (unmanned aerial systems), UAVs (Unmanned Aerial Vehicles) or RPAS (Remotely piloted aircraft systems), are both useful advanced scientific platforms and recreational toys that are appealing to younger generations. As such, they can make for excellent education tools as well as low-cost scientific research project alternatives. However, the process of taking pretty pictures to remote sensing science can be daunting if one is presented with only expensive software and sensor options. There are a number of open-source tools and low cost platform and sensor options available that can provide excellent scientific research results, and, by often requiring more user-involvement than commercial software and sensors, provide even greater educational benefits. Scale-invariant feature transform (SIFT) algorithm implementations, such as the Microsoft Image Composite Editor (ICE), which can create quality 2D image mosaics with some motion and terrain adjustments and VisualSFM (Structure from Motion), which can provide full image mosaicking with movement and orthorectification capacities. RGB image quantification using alternate color space transforms, such as the BreedPix indices, can be calculated via plugins in the open-source software Fiji (http://fiji.sc/Fiji; http://github.com/george-haddad/CIMMYT). Recent analyses of aerial images from UAVs over different vegetation types and environments have shown RGB metrics can outperform more costly commercial sensors. Specifically, Hue-based pixel counts, the Triangle Greenness Index (TGI), and the Normalized Green Red Difference Index (NGRDI) consistently outperformed NDVI in estimating abiotic and biotic stress impacts on crop health. Also, simple kits are available for NDVI camera conversions. Furthermore, suggestions for multivariate analyses of the different RGB indices in the "R program for statistical computing", such as classification and regression trees can allow for a more approachable interpretation of results in the classroom.

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

NASA Astrophysics Data System (ADS)

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

2010-12-01

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

Benchmarking of dynamic simulation predictions in two software platforms using an upper limb musculoskeletal model

PubMed Central

Saul, Katherine R.; Hu, Xiao; Goehler, Craig M.; Vidt, Meghan E.; Daly, Melissa; Velisar, Anca; Murray, Wendy M.

2014-01-01

Several opensource or commercially available software platforms are widely used to develop dynamic simulations of movement. While computational approaches are conceptually similar across platforms, technical differences in implementation may influence output. We present a new upper limb dynamic model as a tool to evaluate potential differences in predictive behavior between platforms. We evaluated to what extent differences in technical implementations in popular simulation software environments result in differences in kinematic predictions for single and multijoint movements using EMG- and optimization-based approaches for deriving control signals. We illustrate the benchmarking comparison using SIMM-Dynamics Pipeline-SD/Fast and OpenSim platforms. The most substantial divergence results from differences in muscle model and actuator paths. This model is a valuable resource and is available for download by other researchers. The model, data, and simulation results presented here can be used by future researchers to benchmark other software platforms and software upgrades for these two platforms. PMID:24995410

Benchmarking of dynamic simulation predictions in two software platforms using an upper limb musculoskeletal model.

PubMed

Saul, Katherine R; Hu, Xiao; Goehler, Craig M; Vidt, Meghan E; Daly, Melissa; Velisar, Anca; Murray, Wendy M

2015-01-01

Several opensource or commercially available software platforms are widely used to develop dynamic simulations of movement. While computational approaches are conceptually similar across platforms, technical differences in implementation may influence output. We present a new upper limb dynamic model as a tool to evaluate potential differences in predictive behavior between platforms. We evaluated to what extent differences in technical implementations in popular simulation software environments result in differences in kinematic predictions for single and multijoint movements using EMG- and optimization-based approaches for deriving control signals. We illustrate the benchmarking comparison using SIMM-Dynamics Pipeline-SD/Fast and OpenSim platforms. The most substantial divergence results from differences in muscle model and actuator paths. This model is a valuable resource and is available for download by other researchers. The model, data, and simulation results presented here can be used by future researchers to benchmark other software platforms and software upgrades for these two platforms.

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

PubMed

Mathôt, Sebastiaan; Schreij, Daniel; Theeuwes, Jan

2012-06-01

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

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.

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

NASA Astrophysics Data System (ADS)

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

2014-01-01

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

Development of Cross-Platform Software for Well Logging Data Visualization

NASA Astrophysics Data System (ADS)

Akhmadulin, R. K.; Miraev, A. I.

2017-07-01

Well logging data processing is one of the main sources of information in the oil-gas field analysis and is of great importance in the process of its development and operation. Therefore, it is important to have the software which would accurately and clearly provide the user with processed data in the form of well logs. In this work, there have been developed a software product which not only has the basic functionality for this task (loading data from .las files, well log curves display, etc.), but can be run in different operating systems and on different devices. In the article a subject field analysis and task formulation have been performed, and the software design stage has been considered. At the end of the work the resulting software product interface has been described.

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

PubMed

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

2015-03-01

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

Millstone: software for multiplex microbial genome analysis and engineering

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

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

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

Millstone: software for multiplex microbial genome analysis and engineering.

PubMed

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

2017-05-25

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

Millstone: software for multiplex microbial genome analysis and engineering

DOE PAGES

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

2017-05-25

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

Dynamic online surveys and experiments with the free open-source software dynQuest.

PubMed

Rademacher, Jens D M; Lippke, Sonia

2007-08-01

With computers and the World Wide Web widely available, collecting data through Web browsers is an attractive method utilized by the social sciences. In this article, conducting PC- and Web-based trials with the software package dynQuest is described. The software manages dynamic questionnaire-based trials over the Internet or on single computers, possibly as randomized control trials (RCT), if two or more groups are involved. The choice of follow-up questions can depend on previous responses, as needed for matched interventions. Data are collected in a simple text-based database that can be imported easily into other programs for postprocessing and statistical analysis. The software consists of platform-independent scripts written in the programming language PERL that use the common gateway interface between Web browser and server for submission of data through HTML forms. Advantages of dynQuest are parsimony, simplicity in use and installation, transparency, and reliability. The program is available as open-source freeware from the authors.

Publishing Platform for Scientific Software - Lessons Learned

NASA Astrophysics Data System (ADS)

Hammitzsch, Martin; Fritzsch, Bernadette; Reusser, Dominik; Brembs, Björn; Deinzer, Gernot; Loewe, Peter; Fenner, Martin; van Edig, Xenia; Bertelmann, Roland; Pampel, Heinz; Klump, Jens; Wächter, Joachim

2015-04-01

Scientific software has become an indispensable commodity for the production, processing and analysis of empirical data but also for modelling and simulation of complex processes. Software has a significant influence on the quality of research results. For strengthening the recognition of the academic performance of scientific software development, for increasing its visibility and for promoting the reproducibility of research results, concepts for the publication of scientific software have to be developed, tested, evaluated, and then transferred into operations. For this, the publication and citability of scientific software have to fulfil scientific criteria by means of defined processes and the use of persistent identifiers, similar to data publications. The SciForge project is addressing these challenges. Based on interviews a blueprint for a scientific software publishing platform and a systematic implementation plan has been designed. In addition, the potential of journals, software repositories and persistent identifiers have been evaluated to improve the publication and dissemination of reusable software solutions. It is important that procedures for publishing software as well as methods and tools for software engineering are reflected in the architecture of the platform, in order to improve the quality of the software and the results of research. In addition, it is necessary to work continuously on improving specific conditions that promote the adoption and sustainable utilization of scientific software publications. Among others, this would include policies for the development and publication of scientific software in the institutions but also policies for establishing the necessary competencies and skills of scientists and IT personnel. To implement the concepts developed in SciForge a combined bottom-up / top-down approach is considered that will be implemented in parallel in different scientific domains, e.g. in earth sciences, climate research and the life sciences. Based on the developed blueprints a scientific software publishing platform will be iteratively implemented, tested, and evaluated. Thus the platform should be developed continuously on the basis of gained experiences and results. The platform services will be extended one by one corresponding to the requirements of the communities. Thus the implemented platform for the publication of scientific software can be improved and stabilized incrementally as a tool with software, science, publishing, and user oriented features.

Software for Photometric and Astrometric Reduction of Video Meteors

NASA Astrophysics Data System (ADS)

Atreya, Prakash; Christou, Apostolos

2007-12-01

SPARVM is a Software for Photometric and Astrometric Reduction of Video Meteors being developed at Armagh Observatory. It is written in Interactive Data Language (IDL) and is designed to run primarily under Linux platform. The basic features of the software will be derivation of light curves, estimation of angular velocity and radiant position for single station data. For double station data, calculation of 3D coordinates of meteors, velocity, brightness, and estimation of meteoroid's orbit including uncertainties. Currently, the software supports extraction of time and date from video frames, estimation of position of cameras (Azimuth, Altitude), finding stellar sources in video frames and transformation of coordinates from video, frames to Horizontal coordinate system (Azimuth, Altitude), and Equatorial coordinate system (RA, Dec).

Java Mission Evaluation Workstation System

NASA Technical Reports Server (NTRS)

Pettinger, Ross; Watlington, Tim; Ryley, Richard; Harbour, Jeff

2006-01-01

The Java Mission Evaluation Workstation System (JMEWS) is a collection of applications designed to retrieve, display, and analyze both real-time and recorded telemetry data. This software is currently being used by both the Space Shuttle Program (SSP) and the International Space Station (ISS) program. JMEWS was written in the Java programming language to satisfy the requirement of platform independence. An object-oriented design was used to satisfy additional requirements and to make the software easily extendable. By virtue of its platform independence, JMEWS can be used on the UNIX workstations in the Mission Control Center (MCC) and on office computers. JMEWS includes an interactive editor that allows users to easily develop displays that meet their specific needs. The displays can be developed and modified while viewing data. By simply selecting a data source, the user can view real-time, recorded, or test data.

NeuroVR 1.5 - a free virtual reality platform for the assessment and treatment in clinical psychology and neuroscience.

PubMed

Riva, Giuseppe; Carelli, Laura; Gaggioli, Andrea; Gorini, Alessandra; Vigna, Cinzia; Corsi, Riccardo; Faletti, Gianluca; Vezzadini, Luca

2009-01-01

At MMVR 2007 we presented NeuroVR (http://www.neurovr.org) a free virtual reality platform based on open-source software. The software allows non-expert users to adapt the content of 14 pre-designed virtual environments to the specific needs of the clinical or experimental setting. Following the feedbacks of the 700 users who downloaded the first version, we developed a new version - NeuroVR 1.5 - that improves the possibility for the therapist to enhance the patient's feeling of familiarity and intimacy with the virtual scene, by using external sounds, photos or videos. Specifically, the new version now includes full sound support and the ability of triggering external sounds and videos using the keyboard. The outcomes of different trials made using NeuroVR will be presented and discussed.

Technological choices for mobile clinical applications.

PubMed

Ehrler, Frederic; Issom, David; Lovis, Christian

2011-01-01

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

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

PubMed

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

2013-03-01

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

Rapid prototyping of an adaptive light-source for mobile manipulators with EasyKit and EasyLab

NASA Astrophysics Data System (ADS)

Wojtczyk, Martin; Barner, Simon; Geisinger, Michael; Knoll, Alois

2008-08-01

While still not common in day-to-day business, mobile robot platforms form a growing market in robotics. Mobile platforms equipped with a manipulator for increased flexibility have been used successfully in biotech laboratories for sample management as shown on the well-known ESACT meetings. Navigation and object recognition is carried out by the utilization of a mounted machine vision camera. To cope with the different illumination conditions in a large laboratory, development of an adaptive light source was indispensable. We present our approach of rapid developing a computer controlled, adaptive LED light within one single business day, by utilizing the hardware toolbox EasyKit and our appropriate software counterpart EasyLab.

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.

CONNJUR Workflow Builder: A software integration environment for spectral reconstruction

PubMed Central

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

2015-01-01

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

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

PubMed

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

2015-07-01

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

BioRuby: bioinformatics software for the Ruby programming language.

PubMed

Goto, Naohisa; Prins, Pjotr; Nakao, Mitsuteru; Bonnal, Raoul; Aerts, Jan; Katayama, Toshiaki

2010-10-15

The BioRuby software toolkit contains a comprehensive set of free development tools and libraries for bioinformatics and molecular biology, written in the Ruby programming language. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO. BioRuby comes with a tutorial, documentation and an interactive environment, which can be used in the shell, and in the web browser. BioRuby is free and open source software, made available under the Ruby license. BioRuby runs on all platforms that support Ruby, including Linux, Mac OS X and Windows. And, with JRuby, BioRuby runs on the Java Virtual Machine. The source code is available from http://www.bioruby.org/. katayama@bioruby.org

[Porting Radiotherapy Software of Varian to Cloud Platform].

PubMed

Zou, Lian; Zhang, Weisha; Liu, Xiangxiang; Xie, Zhao; Xie, Yaoqin

2017-09-30

To develop a low-cost private cloud platform of radiotherapy software. First, a private cloud platform which was based on OpenStack and the virtual GPU hardware was builded. Then on the private cloud platform, all the Varian radiotherapy software modules were installed to the virtual machine, and the corresponding function configuration was completed. Finally the software on the cloud was able to be accessed by virtual desktop client. The function test results of the cloud workstation show that a cloud workstation is equivalent to an isolated physical workstation, and any clients on the LAN can use the cloud workstation smoothly. The cloud platform transplantation in this study is economical and practical. The project not only improves the utilization rates of radiotherapy software, but also makes it possible that the cloud computing technology can expand its applications to the field of radiation oncology.

Collaborative data model and data base development for paleoenvironmental and archaeological domain using Semantic MediaWiki

NASA Astrophysics Data System (ADS)

Willmes, C.

2017-12-01

In the frame of the Collaborative Research Centre 806 (CRC 806) an interdisciplinary research project, that needs to manage data, information and knowledge from heterogeneous domains, such as archeology, cultural sciences, and the geosciences, a collaborative internal knowledge base system was developed. The system is based on the open source MediaWiki software, that is well known as the software that enables Wikipedia, for its facilitation of a web based collaborative knowledge and information management platform. This software is additionally enhanced with the Semantic MediaWiki (SMW) extension, that allows to store and manage structural data within the Wiki platform, as well as it facilitates complex query and API interfaces to the structured data stored in the SMW data base. Using an additional open source software called mobo, it is possible to improve the data model development process, as well as automated data imports, from small spreadsheets to large relational databases. Mobo is a command line tool that helps building and deploying SMW structure in an agile, Schema-Driven Development way, and allows to manage and collaboratively develop the data model formalizations, that are formalized in JSON-Schema format, using version control systems like git. The combination of a well equipped collaborative web platform facilitated by Mediawiki, the possibility to store and query structured data in this collaborative database provided by SMW, as well as the possibility for automated data import and data model development enabled by mobo, result in a powerful but flexible system to build and develop a collaborative knowledge base system. Furthermore, SMW allows the application of Semantic Web technology, the structured data can be exported into RDF, thus it is possible to set a triple-store including a SPARQL endpoint on top of the database. The JSON-Schema based data models, can be enhanced into JSON-LD, to facilitate and profit from the possibilities of Linked Data technology.

Constructing graph models for software system development and analysis

NASA Astrophysics Data System (ADS)

Pogrebnoy, Andrey V.

2017-01-01

We propose a concept for creating the instrumentation for functional and structural decisions rationale during the software system (SS) development. We propose to develop SS simultaneously on two models - functional (FM) and structural (SM). FM is a source code of the SS. Adequate representation of the FM in the form of a graph model (GM) is made automatically and called SM. The problem of creating and visualizing GM is considered from the point of applying it as a uniform platform for the adequate representation of the SS source code. We propose three levels of GM detailing: GM1 - for visual analysis of the source code and for SS version control, GM2 - for resources optimization and analysis of connections between SS components, GM3 - for analysis of the SS functioning in dynamics. The paper includes examples of constructing all levels of GM.

Software designs of image processing tasks with incremental refinement of computation.

PubMed

Anastasia, Davide; Andreopoulos, Yiannis

2010-08-01

Software realizations of computationally-demanding image processing tasks (e.g., image transforms and convolution) do not currently provide graceful degradation when their clock-cycles budgets are reduced, e.g., when delay deadlines are imposed in a multitasking environment to meet throughput requirements. This is an important obstacle in the quest for full utilization of modern programmable platforms' capabilities since worst-case considerations must be in place for reasonable quality of results. In this paper, we propose (and make available online) platform-independent software designs performing bitplane-based computation combined with an incremental packing framework in order to realize block transforms, 2-D convolution and frame-by-frame block matching. The proposed framework realizes incremental computation: progressive processing of input-source increments improves the output quality monotonically. Comparisons with the equivalent nonincremental software realization of each algorithm reveal that, for the same precision of the result, the proposed approach can lead to comparable or faster execution, while it can be arbitrarily terminated and provide the result up to the computed precision. Application examples with region-of-interest based incremental computation, task scheduling per frame, and energy-distortion scalability verify that our proposal provides significant performance scalability with graceful degradation.

Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework

PubMed Central

Easterly, Caleb; Gruening, Bjoern; Johnson, James; Kolmeder, Carolin A.; Kumar, Praveen; May, Damon; Mehta, Subina; Mesuere, Bart; Brown, Zachary; Elias, Joshua E.; Hervey, W. Judson; McGowan, Thomas; Muth, Thilo; Rudney, Joel; Griffin, Timothy J.

2018-01-01

The impact of microbial communities, also known as the microbiome, on human health and the environment is receiving increased attention. Studying translated gene products (proteins) and comparing metaproteomic profiles may elucidate how microbiomes respond to specific environmental stimuli, and interact with host organisms. Characterizing proteins expressed by a complex microbiome and interpreting their functional signature requires sophisticated informatics tools and workflows tailored to metaproteomics. Additionally, there is a need to disseminate these informatics resources to researchers undertaking metaproteomic studies, who could use them to make new and important discoveries in microbiome research. The Galaxy for proteomics platform (Galaxy-P) offers an open source, web-based bioinformatics platform for disseminating metaproteomics software and workflows. Within this platform, we have developed easily-accessible and documented metaproteomic software tools and workflows aimed at training researchers in their operation and disseminating the tools for more widespread use. The modular workflows encompass the core requirements of metaproteomic informatics: (a) database generation; (b) peptide spectral matching; (c) taxonomic analysis and (d) functional analysis. Much of the software available via the Galaxy-P platform was selected, packaged and deployed through an online metaproteomics “Contribution Fest“ undertaken by a unique consortium of expert software developers and users from the metaproteomics research community, who have co-authored this manuscript. These resources are documented on GitHub and freely available through the Galaxy Toolshed, as well as a publicly accessible metaproteomics gateway Galaxy instance. These documented workflows are well suited for the training of novice metaproteomics researchers, through online resources such as the Galaxy Training Network, as well as hands-on training workshops. Here, we describe the metaproteomics tools available within these Galaxy-based resources, as well as the process by which they were selected and implemented in our community-based work. We hope this description will increase access to and utilization of metaproteomics tools, as well as offer a framework for continued community-based development and dissemination of cutting edge metaproteomics software. PMID:29385081

Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework.

PubMed

Blank, Clemens; Easterly, Caleb; Gruening, Bjoern; Johnson, James; Kolmeder, Carolin A; Kumar, Praveen; May, Damon; Mehta, Subina; Mesuere, Bart; Brown, Zachary; Elias, Joshua E; Hervey, W Judson; McGowan, Thomas; Muth, Thilo; Nunn, Brook; Rudney, Joel; Tanca, Alessandro; Griffin, Timothy J; Jagtap, Pratik D

2018-01-31

The impact of microbial communities, also known as the microbiome, on human health and the environment is receiving increased attention. Studying translated gene products (proteins) and comparing metaproteomic profiles may elucidate how microbiomes respond to specific environmental stimuli, and interact with host organisms. Characterizing proteins expressed by a complex microbiome and interpreting their functional signature requires sophisticated informatics tools and workflows tailored to metaproteomics. Additionally, there is a need to disseminate these informatics resources to researchers undertaking metaproteomic studies, who could use them to make new and important discoveries in microbiome research. The Galaxy for proteomics platform (Galaxy-P) offers an open source, web-based bioinformatics platform for disseminating metaproteomics software and workflows. Within this platform, we have developed easily-accessible and documented metaproteomic software tools and workflows aimed at training researchers in their operation and disseminating the tools for more widespread use. The modular workflows encompass the core requirements of metaproteomic informatics: (a) database generation; (b) peptide spectral matching; (c) taxonomic analysis and (d) functional analysis. Much of the software available via the Galaxy-P platform was selected, packaged and deployed through an online metaproteomics "Contribution Fest" undertaken by a unique consortium of expert software developers and users from the metaproteomics research community, who have co-authored this manuscript. These resources are documented on GitHub and freely available through the Galaxy Toolshed, as well as a publicly accessible metaproteomics gateway Galaxy instance. These documented workflows are well suited for the training of novice metaproteomics researchers, through online resources such as the Galaxy Training Network, as well as hands-on training workshops. Here, we describe the metaproteomics tools available within these Galaxy-based resources, as well as the process by which they were selected and implemented in our community-based work. We hope this description will increase access to and utilization of metaproteomics tools, as well as offer a framework for continued community-based development and dissemination of cutting edge metaproteomics software.

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

PubMed

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

2018-06-01

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

Open-source framework for documentation of scientific software written on MATLAB-compatible programming languages

NASA Astrophysics Data System (ADS)

Konnik, Mikhail V.; Welsh, James

2012-09-01

Numerical simulators for adaptive optics systems have become an essential tool for the research and development of the future advanced astronomical instruments. However, growing software code of the numerical simulator makes it difficult to continue to support the code itself. The problem of adequate documentation of the astronomical software for adaptive optics simulators may complicate the development since the documentation must contain up-to-date schemes and mathematical descriptions implemented in the software code. Although most modern programming environments like MATLAB or Octave have in-built documentation abilities, they are often insufficient for the description of a typical adaptive optics simulator code. This paper describes a general cross-platform framework for the documentation of scientific software using open-source tools such as LATEX, mercurial, Doxygen, and Perl. Using the Perl script that translates M-files MATLAB comments into C-like, one can use Doxygen to generate and update the documentation for the scientific source code. The documentation generated by this framework contains the current code description with mathematical formulas, images, and bibliographical references. A detailed description of the framework components is presented as well as the guidelines for the framework deployment. Examples of the code documentation for the scripts and functions of a MATLAB-based adaptive optics simulator are provided.

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

PubMed

Zdravkovski, Zoran

2014-01-01

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

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

PubMed Central

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

2011-01-01

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

Survey of Non-Rigid Registration Tools in Medicine.

PubMed

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

2017-02-01

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

Creating Math Videos: Comparing Platforms and Software

ERIC Educational Resources Information Center

Abbasian, Reza O.; Sieben, John T.

2016-01-01

In this paper we present a short tutorial on creating mini-videos using two platforms--PCs and tablets such as iPads--and software packages that work with these devices. Specifically, we describe the step-by-step process of creating and editing videos using a Wacom Intuos pen-tablet plus Camtasia software on a PC platform and using the software…

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

PubMed

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

2014-01-01

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

Multiattribute selection of acute stroke imaging software platform for Extending the Time for Thrombolysis in Emergency Neurological Deficits (EXTEND) clinical trial.

PubMed

Churilov, Leonid; Liu, Daniel; Ma, Henry; Christensen, Soren; Nagakane, Yoshinari; Campbell, Bruce; Parsons, Mark W; Levi, Christopher R; Davis, Stephen M; Donnan, Geoffrey A

2013-04-01

The appropriateness of a software platform for rapid MRI assessment of the amount of salvageable brain tissue after stroke is critical for both the validity of the Extending the Time for Thrombolysis in Emergency Neurological Deficits (EXTEND) Clinical Trial of stroke thrombolysis beyond 4.5 hours and for stroke patient care outcomes. The objective of this research is to develop and implement a methodology for selecting the acute stroke imaging software platform most appropriate for the setting of a multi-centre clinical trial. A multi-disciplinary decision making panel formulated the set of preferentially independent evaluation attributes. Alternative Multi-Attribute Value Measurement methods were used to identify the best imaging software platform followed by sensitivity analysis to ensure the validity and robustness of the proposed solution. Four alternative imaging software platforms were identified. RApid processing of PerfusIon and Diffusion (RAPID) software was selected as the most appropriate for the needs of the EXTEND trial. A theoretically grounded generic multi-attribute selection methodology for imaging software was developed and implemented. The developed methodology assured both a high quality decision outcome and a rational and transparent decision process. This development contributes to stroke literature in the area of comprehensive evaluation of MRI clinical software. At the time of evaluation, RAPID software presented the most appropriate imaging software platform for use in the EXTEND clinical trial. The proposed multi-attribute imaging software evaluation methodology is based on sound theoretical foundations of multiple criteria decision analysis and can be successfully used for choosing the most appropriate imaging software while ensuring both robust decision process and outcomes. © 2012 The Authors. International Journal of Stroke © 2012 World Stroke Organization.

Easy and effective--web-based information systems designed and maintained by physicians: experience with two gynecological projects.

PubMed

Kupka, M S; Dorn, C; Richter, O; van der Ven, H; Baur, M

2003-08-01

It is well established that medical information sources develop continuously from printed media to digital online sources. To demonstrate effectiveness and feasibility of decentralized performed web-based information sources for health professionals, two projects are described. The information platform of the German Working Group for Information Technologies in Gynecology and Obstetrics (AIG) and the information source concerning the German Registry for in vitro fertilization (DIR) were implemented using ordinary software and standard computer equipment. Only minimal resources and training were necessary to perform safe and reliable web-based information sources with a high correlation of effectiveness in costs and time exposure.

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

ERIC Educational Resources Information Center

Carrier, Nathalie

2017-01-01

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

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

Katipamula, Srinivas; Gowri, Krishnan; Hernandez, George

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

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

ERIC Educational Resources Information Center

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

2016-01-01

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

Unified Geophysical Cloud Platform (UGCP) for Seismic Monitoring and other Geophysical Applications.

NASA Astrophysics Data System (ADS)

Synytsky, R.; Starovoit, Y. O.; Henadiy, S.; Lobzakov, V.; Kolesnikov, L.

2016-12-01

We present Unified Geophysical Cloud Platform (UGCP) or UniGeoCloud as an innovative approach for geophysical data processing in the Cloud environment with the ability to run any type of data processing software in isolated environment within the single Cloud platform. We've developed a simple and quick method of several open-source widely known software seismic packages (SeisComp3, Earthworm, Geotool, MSNoise) installation which does not require knowledge of system administration, configuration, OS compatibility issues etc. and other often annoying details preventing time wasting for system configuration work. Installation process is simplified as "mouse click" on selected software package from the Cloud market place. The main objective of the developed capability was the software tools conception with which users are able to design and install quickly their own highly reliable and highly available virtual IT-infrastructure for the organization of seismic (and in future other geophysical) data processing for either research or monitoring purposes. These tools provide access to any seismic station data available in open IP configuration from the different networks affiliated with different Institutions and Organizations. It allows also setting up your own network as you desire by selecting either regionally deployed stations or the worldwide global network based on stations selection form the global map. The processing software and products and research results could be easily monitored from everywhere using variety of user's devices form desk top computers to IT gadgets. Currents efforts of the development team are directed to achieve Scalability, Reliability and Sustainability (SRS) of proposed solutions allowing any user to run their applications with the confidence of no data loss and no failure of the monitoring or research software components. The system is suitable for quick rollout of NDC-in-Box software package developed for State Signatories and aimed for promotion of data processing collected by the IMS Network.

Final Scientific/Technical Report for "Enabling Exascale Hardware and Software Design through Scalable System Virtualization"

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

Dinda, Peter August

2015-03-17

This report describes the activities, findings, and products of the Northwestern University component of the "Enabling Exascale Hardware and Software Design through Scalable System Virtualization" project. The purpose of this project has been to extend the state of the art of systems software for high-end computing (HEC) platforms, and to use systems software to better enable the evaluation of potential future HEC platforms, for example exascale platforms. Such platforms, and their systems software, have the goal of providing scientific computation at new scales, thus enabling new research in the physical sciences and engineering. Over time, the innovations in systems softwaremore » for such platforms also become applicable to more widely used computing clusters, data centers, and clouds. This was a five-institution project, centered on the Palacios virtual machine monitor (VMM) systems software, a project begun at Northwestern, and originally developed in a previous collaboration between Northwestern University and the University of New Mexico. In this project, Northwestern (including via our subcontract to the University of Pittsburgh) contributed to the continued development of Palacios, along with other team members. We took the leadership role in (1) continued extension of support for emerging Intel and AMD hardware, (2) integration and performance enhancement of overlay networking, (3) connectivity with architectural simulation, (4) binary translation, and (5) support for modern Non-Uniform Memory Access (NUMA) hosts and guests. We also took a supporting role in support for specialized hardware for I/O virtualization, profiling, configurability, and integration with configuration tools. The efforts we led (1-5) were largely successful and executed as expected, with code and papers resulting from them. The project demonstrated the feasibility of a virtualization layer for HEC computing, similar to such layers for cloud or datacenter computing. For effort (3), although a prototype connecting Palacios with the GEM5 architectural simulator was demonstrated, our conclusion was that such a platform was less useful for design space exploration than anticipated due to inherent complexity of the connection between the instruction set architecture level and the microarchitectural level. For effort (4), we found that a code injection approach proved to be more fruitful. The results of our efforts are publicly available in the open source Palacios codebase and published papers, all of which are available from the project web site, v3vee.org. Palacios is currently one of the two codebases (the other being Sandia’s Kitten lightweight kernel) that underlies the node operating system for the DOE Hobbes Project, one of two projects tasked with building a systems software prototype for the national exascale computing effort.« less

Explicet: graphical user interface software for metadata-driven management, analysis and visualization of microbiome data.

PubMed

Robertson, Charles E; Harris, J Kirk; Wagner, Brandie D; Granger, David; Browne, Kathy; Tatem, Beth; Feazel, Leah M; Park, Kristin; Pace, Norman R; Frank, Daniel N

2013-12-01

Studies of the human microbiome, and microbial community ecology in general, have blossomed of late and are now a burgeoning source of exciting research findings. Along with the advent of next-generation sequencing platforms, which have dramatically increased the scope of microbiome-related projects, several high-performance sequence analysis pipelines (e.g. QIIME, MOTHUR, VAMPS) are now available to investigators for microbiome analysis. The subject of our manuscript, the graphical user interface-based Explicet software package, fills a previously unmet need for a robust, yet intuitive means of integrating the outputs of the software pipelines with user-specified metadata and then visualizing the combined data.

Application of the GNU Radio platform in the multistatic radar

NASA Astrophysics Data System (ADS)

Szlachetko, Boguslaw; Lewandowski, Andrzej

2009-06-01

This document presents the application of the Software Defined Radio-based platform in the multistatic radar. This platform consists of four-sensor linear antenna, Universal Software Radio Peripheral (USRP) hardware (radio frequency frontend) and GNU-Radio PC software. The paper provides information about architecture of digital signal processing performed by USRP's FPGA (digital down converting blocks) and PC host (implementation of the multichannel digital beamforming). The preliminary results of the signal recording performed by our experimental platform are presented.

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

Peffer, Therese; Blumstein, Carl; Culler, David

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

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

PubMed

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

2017-02-01

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

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

PubMed Central

Kitson, Philip J; Glatzel, Stefan

2016-01-01

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

Scintillation-Hardened GPS Receiver

NASA Technical Reports Server (NTRS)

Stephens, Donald R.

2015-01-01

CommLargo, Inc., has developed a scintillation-hardened Global Positioning System (GPS) receiver that improves reliability for low-orbit missions and complies with NASA's Space Telecommunications Radio System (STRS) architecture standards. A software-defined radio (SDR) implementation allows a single hardware element to function as either a conventional radio or as a GPS receiver, providing backup and redundancy for platforms such as the International Space Station (ISS) and high-value remote sensing platforms. The innovation's flexible SDR implementation reduces cost, weight, and power requirements. Scintillation hardening improves mission reliability and variability. In Phase I, CommLargo refactored an open-source GPS software package with Kalman filter-based tracking loops to improve performance during scintillation and also demonstrated improved navigation during a geomagnetic storm. In Phase II, the company generated a new field-programmable gate array (FPGA)-based GPS waveform to demonstrate on NASA's Space Communication and Navigation (SCaN) test bed.

xQTL workbench: a scalable web environment for multi-level QTL analysis.

PubMed

Arends, Danny; van der Velde, K Joeri; Prins, Pjotr; Broman, Karl W; Möller, Steffen; Jansen, Ritsert C; Swertz, Morris A

2012-04-01

xQTL workbench is a scalable web platform for the mapping of quantitative trait loci (QTLs) at multiple levels: for example gene expression (eQTL), protein abundance (pQTL), metabolite abundance (mQTL) and phenotype (phQTL) data. Popular QTL mapping methods for model organism and human populations are accessible via the web user interface. Large calculations scale easily on to multi-core computers, clusters and Cloud. All data involved can be uploaded and queried online: markers, genotypes, microarrays, NGS, LC-MS, GC-MS, NMR, etc. When new data types come available, xQTL workbench is quickly customized using the Molgenis software generator. xQTL workbench runs on all common platforms, including Linux, Mac OS X and Windows. An online demo system, installation guide, tutorials, software and source code are available under the LGPL3 license from http://www.xqtl.org. m.a.swertz@rug.nl.

xQTL workbench: a scalable web environment for multi-level QTL analysis

PubMed Central

Arends, Danny; van der Velde, K. Joeri; Prins, Pjotr; Broman, Karl W.; Möller, Steffen; Jansen, Ritsert C.; Swertz, Morris A.

2012-01-01

Summary: xQTL workbench is a scalable web platform for the mapping of quantitative trait loci (QTLs) at multiple levels: for example gene expression (eQTL), protein abundance (pQTL), metabolite abundance (mQTL) and phenotype (phQTL) data. Popular QTL mapping methods for model organism and human populations are accessible via the web user interface. Large calculations scale easily on to multi-core computers, clusters and Cloud. All data involved can be uploaded and queried online: markers, genotypes, microarrays, NGS, LC-MS, GC-MS, NMR, etc. When new data types come available, xQTL workbench is quickly customized using the Molgenis software generator. Availability: xQTL workbench runs on all common platforms, including Linux, Mac OS X and Windows. An online demo system, installation guide, tutorials, software and source code are available under the LGPL3 license from http://www.xqtl.org. Contact: m.a.swertz@rug.nl PMID:22308096

A Generic Software Architecture For Prognostics

NASA Technical Reports Server (NTRS)

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

2017-01-01

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

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

PubMed

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

2018-05-08

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

FRACOR-software toolbox for deterministic mapping of fracture corridors in oil fields on AutoCAD platform

NASA Astrophysics Data System (ADS)

Ozkaya, Sait I.

2018-03-01

Fracture corridors are interconnected large fractures in a narrow sub vertical tabular array, which usually traverse entire reservoir vertically and extended for several hundreds of meters laterally. Fracture corridors with their huge conductivities constitute an important element of many fractured reservoirs. Unlike small diffuse fractures, actual fracture corridors must be mapped deterministically for simulation or field development purposes. Fracture corridors can be identified and quantified definitely with borehole image logs and well testing. However, there are rarely sufficient image logs or well tests, and it is necessary to utilize various fracture corridor indicators with varying degrees of reliability. Integration of data from many different sources, in turn, requires a platform with powerful editing and layering capability. Available commercial reservoir characterization software packages, with layering and editing capabilities, can be cost intensive. CAD packages are far more affordable and may easily acquire the versatility and power of commercial software packages with addition of a small software toolbox. The objective of this communication is to present FRACOR, a software toolbox which enables deterministic 2D fracture corridor mapping and modeling on AutoCAD platform. The FRACOR toolbox is written in AutoLISPand contains several independent routines to import and integrate available fracture corridor data from an oil field, and export results as text files. The resulting fracture corridor maps consists mainly of fracture corridors with different confidence levels from combination of static and dynamic data and exclusion zones where no fracture corridor can exist. The exported text file of fracture corridors from FRACOR can be imported into an upscaling programs to generate fracture grid for dual porosity simulation or used for field development and well planning.

Neurophysiological analytics for all! Free open-source software tools for documenting, analyzing, visualizing, and sharing using electronic notebooks.

PubMed

Rosenberg, David M; Horn, Charles C

2016-08-01

Neurophysiology requires an extensive workflow of information analysis routines, which often includes incompatible proprietary software, introducing limitations based on financial costs, transfer of data between platforms, and the ability to share. An ecosystem of free open-source software exists to fill these gaps, including thousands of analysis and plotting packages written in Python and R, which can be implemented in a sharable and reproducible format, such as the Jupyter electronic notebook. This tool chain can largely replace current routines by importing data, producing analyses, and generating publication-quality graphics. An electronic notebook like Jupyter allows these analyses, along with documentation of procedures, to display locally or remotely in an internet browser, which can be saved as an HTML, PDF, or other file format for sharing with team members and the scientific community. The present report illustrates these methods using data from electrophysiological recordings of the musk shrew vagus-a model system to investigate gut-brain communication, for example, in cancer chemotherapy-induced emesis. We show methods for spike sorting (including statistical validation), spike train analysis, and analysis of compound action potentials in notebooks. Raw data and code are available from notebooks in data supplements or from an executable online version, which replicates all analyses without installing software-an implementation of reproducible research. This demonstrates the promise of combining disparate analyses into one platform, along with the ease of sharing this work. In an age of diverse, high-throughput computational workflows, this methodology can increase efficiency, transparency, and the collaborative potential of neurophysiological research. Copyright © 2016 the American Physiological Society.

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.

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

NASA Astrophysics Data System (ADS)

Yu, Xiaoyuan; Yuan, Jian; Chen, Shi

2013-03-01

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

OrChem - An open source chemistry search engine for Oracle(R).

PubMed

Rijnbeek, Mark; Steinbeck, Christoph

2009-10-22

Registration, indexing and searching of chemical structures in relational databases is one of the core areas of cheminformatics. However, little detail has been published on the inner workings of search engines and their development has been mostly closed-source. We decided to develop an open source chemistry extension for Oracle, the de facto database platform in the commercial world. Here we present OrChem, an extension for the Oracle 11G database that adds registration and indexing of chemical structures to support fast substructure and similarity searching. The cheminformatics functionality is provided by the Chemistry Development Kit. OrChem provides similarity searching with response times in the order of seconds for databases with millions of compounds, depending on a given similarity cut-off. For substructure searching, it can make use of multiple processor cores on today's powerful database servers to provide fast response times in equally large data sets. OrChem is free software and can be redistributed and/or modified under the terms of the GNU Lesser General Public License as published by the Free Software Foundation. All software is available via http://orchem.sourceforge.net.

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.

WarpEngine, a Flexible Platform for Distributed Computing Implemented in the VEGA Program and Specially Targeted for Virtual Screening Studies.

PubMed

Pedretti, Alessandro; Mazzolari, Angelica; Vistoli, Giulio

2018-05-21

The manuscript describes WarpEngine, a novel platform implemented within the VEGA ZZ suite of software for performing distributed simulations both in local and wide area networks. Despite being tailored for structure-based virtual screening campaigns, WarpEngine possesses the required flexibility to carry out distributed calculations utilizing various pieces of software, which can be easily encapsulated within this platform without changing their source codes. WarpEngine takes advantages of all cheminformatics features implemented in the VEGA ZZ program as well as of its largely customizable scripting architecture thus allowing an efficient distribution of various time-demanding simulations. To offer an example of the WarpEngine potentials, the manuscript includes a set of virtual screening campaigns based on the ACE data set of the DUD-E collections using PLANTS as the docking application. Benchmarking analyses revealed a satisfactory linearity of the WarpEngine performances, the speed-up values being roughly equal to the number of utilized cores. Again, the computed scalability values emphasized that a vast majority (i.e., >90%) of the performed simulations benefit from the distributed platform presented here. WarpEngine can be freely downloaded along with the VEGA ZZ program at www.vegazz.net .

SU-D-BRD-02: A Web-Based Image Processing and Plan Evaluation Platform (WIPPEP) for Future Cloud-Based Radiotherapy

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

Chai, X; Liu, L; Xing, L

Purpose: Visualization and processing of medical images and radiation treatment plan evaluation have traditionally been constrained to local workstations with limited computation power and ability of data sharing and software update. We present a web-based image processing and planning evaluation platform (WIPPEP) for radiotherapy applications with high efficiency, ubiquitous web access, and real-time data sharing. Methods: This software platform consists of three parts: web server, image server and computation server. Each independent server communicates with each other through HTTP requests. The web server is the key component that provides visualizations and user interface through front-end web browsers and relay informationmore » to the backend to process user requests. The image server serves as a PACS system. The computation server performs the actual image processing and dose calculation. The web server backend is developed using Java Servlets and the frontend is developed using HTML5, Javascript, and jQuery. The image server is based on open source DCME4CHEE PACS system. The computation server can be written in any programming language as long as it can send/receive HTTP requests. Our computation server was implemented in Delphi, Python and PHP, which can process data directly or via a C++ program DLL. Results: This software platform is running on a 32-core CPU server virtually hosting the web server, image server, and computation servers separately. Users can visit our internal website with Chrome browser, select a specific patient, visualize image and RT structures belonging to this patient and perform image segmentation running Delphi computation server and Monte Carlo dose calculation on Python or PHP computation server. Conclusion: We have developed a webbased image processing and plan evaluation platform prototype for radiotherapy. This system has clearly demonstrated the feasibility of performing image processing and plan evaluation platform through a web browser and exhibited potential for future cloud based radiotherapy.« less

A Padawan Programmer's Guide to Developing Software Libraries.

PubMed

Yurkovich, James T; Yurkovich, Benjamin J; Dräger, Andreas; Palsson, Bernhard O; King, Zachary A

2017-11-22

With the rapid adoption of computational tools in the life sciences, scientists are taking on the challenge of developing their own software libraries and releasing them for public use. This trend is being accelerated by popular technologies and platforms, such as GitHub, Jupyter, R/Shiny, that make it easier to develop scientific software and by open-source licenses that make it easier to release software. But how do you build a software library that people will use? And what characteristics do the best libraries have that make them enduringly popular? Here, we provide a reference guide, based on our own experiences, for developing software libraries along with real-world examples to help provide context for scientists who are learning about these concepts for the first time. While we can only scratch the surface of these topics, we hope that this article will act as a guide for scientists who want to write great software that is built to last. Copyright © 2017 Elsevier Inc. All rights reserved.

HashDist: Reproducible, Relocatable, Customizable, Cross-Platform Software Stacks for Open Hydrological Science

NASA Astrophysics Data System (ADS)

Ahmadia, A. J.; Kees, C. E.

2014-12-01

Developing scientific software is a continuous balance between not reinventing the wheel and getting fragile codes to interoperate with one another. Binary software distributions such as Anaconda provide a robust starting point for many scientific software packages, but this solution alone is insufficient for many scientific software developers. HashDist provides a critical component of the development workflow, enabling highly customizable, source-driven, and reproducible builds for scientific software stacks, available from both the IPython Notebook and the command line. To address these issues, the Coastal and Hydraulics Laboratory at the US Army Engineer Research and Development Center has funded the development of HashDist in collaboration with Simula Research Laboratories and the University of Texas at Austin. HashDist is motivated by a functional approach to package build management, and features intelligent caching of sources and builds, parametrized build specifications, and the ability to interoperate with system compilers and packages. HashDist enables the easy specification of "software stacks", which allow both the novice user to install a default environment and the advanced user to configure every aspect of their build in a modular fashion. As an advanced feature, HashDist builds can be made relocatable, allowing the easy redistribution of binaries on all three major operating systems as well as cloud, and supercomputing platforms. As a final benefit, all HashDist builds are reproducible, with a build hash specifying exactly how each component of the software stack was installed. This talk discusses the role of HashDist in the hydrological sciences, including its use by the Coastal and Hydraulics Laboratory in the development and deployment of the Proteus Toolkit as well as the Rapid Operational Access and Maneuver Support project. We demonstrate HashDist in action, and show how it can effectively support development, deployment, teaching, and reproducibility for scientists working in the hydrological sciences. The HashDist documentation is available from: http://hashdist.readthedocs.org/en/latest/ HashDist is currently hosted at: https://github.com/hashdist/hashdist

The role of 3D printing in treating craniomaxillofacial congenital anomalies.

PubMed

Lopez, Christopher D; Witek, Lukasz; Torroni, Andrea; Flores, Roberto L; Demissie, David B; Young, Simon; Cronstein, Bruce N; Coelho, Paulo G

2018-05-20

Craniomaxillofacial congenital anomalies comprise approximately one third of all congenital birth defects and include deformities such as alveolar clefts, craniosynostosis, and microtia. Current surgical treatments commonly require the use of autogenous graft material which are difficult to shape, limited in supply, associated with donor site morbidity and cannot grow with a maturing skeleton. Our group has demonstrated that 3D printed bio-ceramic scaffolds can generate vascularized bone within large, critical-sized defects (defects too large to heal spontaneously) of the craniomaxillofacial skeleton. Furthermore, these scaffolds are also able to function as a delivery vehicle for a new osteogenic agent with a well-established safety profile. The same 3D printers and imaging software platforms have been leveraged by our team to create sterilizable patient-specific intraoperative models for craniofacial reconstruction. For microtia repair, the current standard of care surgical guide is a two-dimensional drawing taken from the contralateral ear. Our laboratory has used 3D printers and open source software platforms to design personalized microtia surgical models. In this review, we report on the advancements in tissue engineering principles, digital imaging software platforms and 3D printing that have culminated in the application of this technology to repair large bone defects in skeletally immature transitional models and provide in-house manufactured, sterilizable patient-specific models for craniofacial reconstruction. © 2018 Wiley Periodicals, Inc.

Software design for analysis of multichannel intracardial and body surface electrocardiograms.

PubMed

Potse, Mark; Linnenbank, André C; Grimbergen, Cornelis A

2002-11-01

Analysis of multichannel ECG recordings (body surface maps (BSMs) and intracardial maps) requires special software. We created a software package and a user interface on top of a commercial data analysis package (MATLAB) by a combination of high-level and low-level programming. Our software was created to satisfy the needs of a diverse group of researchers. It can handle a large variety of recording configurations. It allows for interactive usage through a fast and robust user interface, and batch processing for the analysis of large amounts of data. The package is user-extensible, includes routines for both common and experimental data processing tasks, and works on several computer platforms. The source code is made intelligible using software for structured documentation and is available to the users. The package is currently used by more than ten research groups analysing ECG data worldwide.

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

NASA Technical Reports Server (NTRS)

McComas, David; Strege, Susanne; Wilmot, Jonathan

2015-01-01

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

Updates in metabolomics tools and resources: 2014-2015.

PubMed

Misra, Biswapriya B; van der Hooft, Justin J J

2016-01-01

Data processing and interpretation represent the most challenging and time-consuming steps in high-throughput metabolomic experiments, regardless of the analytical platforms (MS or NMR spectroscopy based) used for data acquisition. Improved machinery in metabolomics generates increasingly complex datasets that create the need for more and better processing and analysis software and in silico approaches to understand the resulting data. However, a comprehensive source of information describing the utility of the most recently developed and released metabolomics resources--in the form of tools, software, and databases--is currently lacking. Thus, here we provide an overview of freely-available, and open-source, tools, algorithms, and frameworks to make both upcoming and established metabolomics researchers aware of the recent developments in an attempt to advance and facilitate data processing workflows in their metabolomics research. The major topics include tools and researches for data processing, data annotation, and data visualization in MS and NMR-based metabolomics. Most in this review described tools are dedicated to untargeted metabolomics workflows; however, some more specialist tools are described as well. All tools and resources described including their analytical and computational platform dependencies are summarized in an overview Table. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Framework for Risk Analysis in Multimedia Environmental Systems: Modeling Individual Steps of a Risk Assessment Process

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

Shah, Anuj; Castleton, Karl J.; Hoopes, Bonnie L.

2004-06-01

The study of the release and effects of chemicals in the environment and their associated risks to humans is central to public and private decision making. FRAMES 1.X, Framework for Risk Analysis in Multimedia Environmental Systems, is a systems modeling software platform, developed by PNNL, Pacific Northwest National Laboratory, that helps scientists study the release and effects of chemicals on a source to outcome basis, create environmental models for similar risk assessment and management problems. The unique aspect of FRAMES is to dynamically introduce software modules representing individual components of a risk assessment (e.g., source release of contaminants, fate andmore » transport in various environmental media, exposure, etc.) within a software framework, manipulate their attributes and run simulations to obtain results. This paper outlines the fundamental constituents of FRAMES 2.X, an enhanced version of FRAMES 1.X, that greatly improve the ability of the module developers to “plug” their self-developed software modules into the system. The basic design, the underlying principles and a discussion of the guidelines for module developers are presented.« less

Launching GUPPI: the Green Bank Ultimate Pulsar Processing Instrument

NASA Astrophysics Data System (ADS)

DuPlain, Ron; Ransom, Scott; Demorest, Paul; Brandt, Patrick; Ford, John; Shelton, Amy L.

2008-08-01

The National Radio Astronomy Observatory (NRAO) is launching the Green Bank Ultimate Pulsar Processing Instrument (GUPPI), a prototype flexible digital signal processor designed for pulsar observations with the Robert C. Byrd Green Bank Telescope (GBT). GUPPI uses field programmable gate array (FPGA) hardware and design tools developed by the Center for Astronomy Signal Processing and Electronics Research (CASPER) at the University of California, Berkeley. The NRAO has been concurrently developing GUPPI software and hardware using minimal software resources. The software handles instrument monitor and control, data acquisition, and hardware interfacing. GUPPI is currently an expert-only spectrometer, but supports future integration with the full GBT production system. The NRAO was able to take advantage of the unique flexibility of the CASPER FPGA hardware platform, develop hardware and software in parallel, and build a suite of software tools for monitoring, controlling, and acquiring data with a new instrument over a short timeline of just a few months. The NRAO interacts regularly with CASPER and its users, and GUPPI stands as an example of what reconfigurable computing and open-source development can do for radio astronomy. GUPPI is modular for portability, and the NRAO provides the results of development as an open-source resource.

Development of a Web-Enabled Learning Platform for Geospatial Laboratories: Improving the Undergraduate Learning Experience

ERIC Educational Resources Information Center

Mui, Amy B.; Nelson, Sarah; Huang, Bruce; He, Yuhong; Wilson, Kathi

2015-01-01

This paper describes a web-enabled learning platform providing remote access to geospatial software that extends the learning experience outside of the laboratory setting. The platform was piloted in two undergraduate courses, and includes a software server, a data server, and remote student users. The platform was designed to improve the quality…

ChiMS: Open-source instrument control software platform on LabVIEW for imaging/depth profiling mass spectrometers.

PubMed

Cui, Yang; Hanley, Luke

2015-06-01

ChiMS is an open-source data acquisition and control software program written within LabVIEW for high speed imaging and depth profiling mass spectrometers. ChiMS can also transfer large datasets from a digitizer to computer memory at high repetition rate, save data to hard disk at high throughput, and perform high speed data processing. The data acquisition mode generally simulates a digital oscilloscope, but with peripheral devices integrated for control as well as advanced data sorting and processing capabilities. Customized user-designed experiments can be easily written based on several included templates. ChiMS is additionally well suited to non-laser based mass spectrometers imaging and various other experiments in laser physics, physical chemistry, and surface science.

ChiMS: Open-source instrument control software platform on LabVIEW for imaging/depth profiling mass spectrometers

PubMed Central

Cui, Yang; Hanley, Luke

2015-01-01

ChiMS is an open-source data acquisition and control software program written within LabVIEW for high speed imaging and depth profiling mass spectrometers. ChiMS can also transfer large datasets from a digitizer to computer memory at high repetition rate, save data to hard disk at high throughput, and perform high speed data processing. The data acquisition mode generally simulates a digital oscilloscope, but with peripheral devices integrated for control as well as advanced data sorting and processing capabilities. Customized user-designed experiments can be easily written based on several included templates. ChiMS is additionally well suited to non-laser based mass spectrometers imaging and various other experiments in laser physics, physical chemistry, and surface science. PMID:26133872

Proteomics to go: Proteomatic enables the user-friendly creation of versatile MS/MS data evaluation workflows.

PubMed

Specht, Michael; Kuhlgert, Sebastian; Fufezan, Christian; Hippler, Michael

2011-04-15

We present Proteomatic, an operating system independent and user-friendly platform that enables the construction and execution of MS/MS data evaluation pipelines using free and commercial software. Required external programs such as for peptide identification are downloaded automatically in the case of free software. Due to a strict separation of functionality and presentation, and support for multiple scripting languages, new processing steps can be added easily. Proteomatic is implemented in C++/Qt, scripts are implemented in Ruby, Python and PHP. All source code is released under the LGPL. Source code and installers for Windows, Mac OS X, and Linux are freely available at http://www.proteomatic.org. michael.specht@uni-muenster.de Supplementary data are available at Bioinformatics online.

ChiMS: Open-source instrument control software platform on LabVIEW for imaging/depth profiling mass spectrometers

NASA Astrophysics Data System (ADS)

Cui, Yang; Hanley, Luke

2015-06-01

ChiMS is an open-source data acquisition and control software program written within LabVIEW for high speed imaging and depth profiling mass spectrometers. ChiMS can also transfer large datasets from a digitizer to computer memory at high repetition rate, save data to hard disk at high throughput, and perform high speed data processing. The data acquisition mode generally simulates a digital oscilloscope, but with peripheral devices integrated for control as well as advanced data sorting and processing capabilities. Customized user-designed experiments can be easily written based on several included templates. ChiMS is additionally well suited to non-laser based mass spectrometers imaging and various other experiments in laser physics, physical chemistry, and surface science.

Application research of Ganglia in Hadoop monitoring and management

NASA Astrophysics Data System (ADS)

Li, Gang; Ding, Jing; Zhou, Lixia; Yang, Yi; Liu, Lei; Wang, Xiaolei

2017-03-01

There are many applications of Hadoop System in the field of large data, cloud computing. The test bench of storage and application in seismic network at Earthquake Administration of Tianjin use with Hadoop system, which is used the open source software of Ganglia to operate and monitor. This paper reviews the function, installation and configuration process, application effect of operating and monitoring in Hadoop system of the Ganglia system. It briefly introduces the idea and effect of Nagios software monitoring Hadoop system. It is valuable for the industry in the monitoring system of cloud computing platform.

HTML5 PivotViewer: high-throughput visualization and querying of image data on the web.

PubMed

Taylor, Stephen; Noble, Roger

2014-09-15

Visualization and analysis of large numbers of biological images has generated a bottle neck in research. We present HTML5 PivotViewer, a novel, open source, platform-independent viewer making use of the latest web technologies that allows seamless access to images and associated metadata for each image. This provides a powerful method to allow end users to mine their data. Documentation, examples and links to the software are available from http://www.cbrg.ox.ac.uk/data/pivotviewer/. The software is licensed under GPLv2. © The Author 2014. Published by Oxford University Press.

Software LS-MIDA for efficient mass isotopomer distribution analysis in metabolic modelling.

PubMed

Ahmed, Zeeshan; Zeeshan, Saman; Huber, Claudia; Hensel, Michael; Schomburg, Dietmar; Münch, Richard; Eisenreich, Wolfgang; Dandekar, Thomas

2013-07-09

The knowledge of metabolic pathways and fluxes is important to understand the adaptation of organisms to their biotic and abiotic environment. The specific distribution of stable isotope labelled precursors into metabolic products can be taken as fingerprints of the metabolic events and dynamics through the metabolic networks. An open-source software is required that easily and rapidly calculates from mass spectra of labelled metabolites, derivatives and their fragments global isotope excess and isotopomer distribution. The open-source software "Least Square Mass Isotopomer Analyzer" (LS-MIDA) is presented that processes experimental mass spectrometry (MS) data on the basis of metabolite information such as the number of atoms in the compound, mass to charge ratio (m/e or m/z) values of the compounds and fragments under study, and the experimental relative MS intensities reflecting the enrichments of isotopomers in 13C- or 15 N-labelled compounds, in comparison to the natural abundances in the unlabelled molecules. The software uses Brauman's least square method of linear regression. As a result, global isotope enrichments of the metabolite or fragment under study and the molar abundances of each isotopomer are obtained and displayed. The new software provides an open-source platform that easily and rapidly converts experimental MS patterns of labelled metabolites into isotopomer enrichments that are the basis for subsequent observation-driven analysis of pathways and fluxes, as well as for model-driven metabolic flux calculations.

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.

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.

UNESCO's HOPE Initiative—Providing Free and Open-Source Hydrologic Software for Effective and Sustainable Management of Africa's Water Resources Temporary Title

NASA Astrophysics Data System (ADS)

Barlow, P. M.; Filali-Meknassi, Y.; Sanford, W. E.; Winston, R. B.; Kuniansky, E.; Dawson, C.

2015-12-01

UNESCO's HOPE Initiative—the Hydro Free and (or) Open-source Platform of Experts—was launched in June 2013 as part of UNESCO's International Hydrological Programme. The Initiative arose in response to a recognized need to make free and (or) open-source water-resources software more widely accessible to Africa's water sector. A kit of software is being developed to provide African water authorities, teachers, university lecturers, and researchers with a set of programs that can be enhanced and (or) applied to the development of efficient and sustainable management strategies for Africa's water resources. The Initiative brings together experts from the many fields of water resources to identify software that might be included in the kit, to oversee an objective process for selecting software for the kit, and to engage in training and other modes of capacity building to enhance dissemination of the software. To date, teams of experts from the fields of wastewater treatment, groundwater hydrology, surface-water hydrology, and data management have been formed to identify relevant software from their respective fields. An initial version of the HOPE Software Kit was released in late August 2014 and consists of the STOAT model for wastewater treatment developed by the Water Research Center (United Kingdom) and the MODFLOW-2005 model for groundwater-flow simulation developed by the U.S. Geological Survey. The Kit is available on the UNESCO HOPE website (http://www.hope-initiative.net/).Training in the theory and use of MODFLOW-2005 is planned in southern Africa in conjunction with UNESCO's study of the Kalahari-Karoo/Stampriet Transboundary Aquifer, which extends over an area that includes parts of Botswana, Namibia, and South Africa, and in support of the European Commission's Horizon 2020 FREEWAT project (FREE and open source software tools for WATer resource management; see the UNESCO HOPE website).

FluxPyt: a Python-based free and open-source software for 13C-metabolic flux analyses.

PubMed

Desai, Trunil S; Srivastava, Shireesh

2018-01-01

13 C-Metabolic flux analysis (MFA) is a powerful approach to estimate intracellular reaction rates which could be used in strain analysis and design. Processing and analysis of labeling data for calculation of fluxes and associated statistics is an essential part of MFA. However, various software currently available for data analysis employ proprietary platforms and thus limit accessibility. We developed FluxPyt, a Python-based truly open-source software package for conducting stationary 13 C-MFA data analysis. The software is based on the efficient elementary metabolite unit framework. The standard deviations in the calculated fluxes are estimated using the Monte-Carlo analysis. FluxPyt also automatically creates flux maps based on a template for visualization of the MFA results. The flux distributions calculated by FluxPyt for two separate models: a small tricarboxylic acid cycle model and a larger Corynebacterium glutamicum model, were found to be in good agreement with those calculated by a previously published software. FluxPyt was tested in Microsoft™ Windows 7 and 10, as well as in Linux Mint 18.2. The availability of a free and open 13 C-MFA software that works in various operating systems will enable more researchers to perform 13 C-MFA and to further modify and develop the package.

FluxPyt: a Python-based free and open-source software for 13C-metabolic flux analyses

PubMed Central

Desai, Trunil S.

2018-01-01

13C-Metabolic flux analysis (MFA) is a powerful approach to estimate intracellular reaction rates which could be used in strain analysis and design. Processing and analysis of labeling data for calculation of fluxes and associated statistics is an essential part of MFA. However, various software currently available for data analysis employ proprietary platforms and thus limit accessibility. We developed FluxPyt, a Python-based truly open-source software package for conducting stationary 13C-MFA data analysis. The software is based on the efficient elementary metabolite unit framework. The standard deviations in the calculated fluxes are estimated using the Monte-Carlo analysis. FluxPyt also automatically creates flux maps based on a template for visualization of the MFA results. The flux distributions calculated by FluxPyt for two separate models: a small tricarboxylic acid cycle model and a larger Corynebacterium glutamicum model, were found to be in good agreement with those calculated by a previously published software. FluxPyt was tested in Microsoft™ Windows 7 and 10, as well as in Linux Mint 18.2. The availability of a free and open 13C-MFA software that works in various operating systems will enable more researchers to perform 13C-MFA and to further modify and develop the package. PMID:29736347

OpenSatKit Enables Quick Startup for CubeSat Missions

NASA Technical Reports Server (NTRS)

McComas, David; Melton, Ryan

2017-01-01

The software required to develop, integrate, and operate a spacecraft is substantial regardless of whether its a large or small satellite. Even getting started can be a monumental task. To solve this problem, NASAs Core Flight System (cFS), NASA's 42 spacecraft dynamics simulator, and Ball Aerospaces COSMOS ground system have been integrated together into a kit called OpenSatKit that provides a complete and open source software solution for starting a new satellite mission. Users can have a working system with flight software, dynamics simulation, and a ground command and control system up and running within hours.Every satellite mission requires three primary categories of software to function. The first is Flight Software (FSW) which provides the onboard control of the satellites and its payload(s). NASA's cFS provides a great platform for developing this software. Second, while developing a satellite on earth, it is necessary to simulate the satellites orbit, attitude, and actuators, to ensure that the systems that control these aspects will work correctly in the real environment. NASAs 42 simulator provides these functionalities. Finally, the ground has to be able to communicate with the satellite, monitor its performance and health, and display its data. Additionally, test scripts have to be written to verify the system on the ground. Ball Aerospace's COSMOS command and control system provides this functionality. Once the OpenSatKit is up and running, the next step is to customize the platform and get it running on the end target. Starting from a fully working system makes porting the cFS from Linux to a users platform much easier. An example Raspberry Pi target is included in the kit so users can gain experience working with a low cost hardware target. All users can benefit from OpenSatKit but the greatest impact and benefits will be to SmallSat missions with constrained budgets and small software teams. This paper describes OpenSatKits system design, the steps necessary to run the system to target the Raspberry Pi, and future plans. OpenSatKit is a free fully functional spacecraft software system that we hope will greatly benefit the SmallSat community.

Open Marketplace for Simulation Software on the Basis of a Web Platform

NASA Astrophysics Data System (ADS)

Kryukov, A. P.; Demichev, A. P.

2016-02-01

The focus in development of a new generation of middleware shifts from the global grid systems to building convenient and efficient web platforms for remote access to individual computing resources. Further line of their development, suggested in this work, is related not only with the quantitative increase in their number and with the expansion of scientific, engineering, and manufacturing areas in which they are used, but also with improved technology for remote deployment of application software on the resources interacting with the web platforms. Currently, the services for providers of application software in the context of scientific-oriented web platforms is not developed enough. The proposed in this work new web platforms of application software market should have all the features of the existing web platforms for submissions of jobs to remote resources plus the provision of specific web services for interaction on market principles between the providers and consumers of application packages. The suggested approach will be approved on the example of simulation applications in the field of nonlinear optics.

Singularity: Scientific containers for mobility of compute.

PubMed

Kurtzer, Gregory M; Sochat, Vanessa; Bauer, Michael W

2017-01-01

Here we present Singularity, software developed to bring containers and reproducibility to scientific computing. Using Singularity containers, developers can work in reproducible environments of their choosing and design, and these complete environments can easily be copied and executed on other platforms. Singularity is an open source initiative that harnesses the expertise of system and software engineers and researchers alike, and integrates seamlessly into common workflows for both of these groups. As its primary use case, Singularity brings mobility of computing to both users and HPC centers, providing a secure means to capture and distribute software and compute environments. This ability to create and deploy reproducible environments across these centers, a previously unmet need, makes Singularity a game changing development for computational science.

Singularity: Scientific containers for mobility of compute

PubMed Central

Kurtzer, Gregory M.; Bauer, Michael W.

2017-01-01

Here we present Singularity, software developed to bring containers and reproducibility to scientific computing. Using Singularity containers, developers can work in reproducible environments of their choosing and design, and these complete environments can easily be copied and executed on other platforms. Singularity is an open source initiative that harnesses the expertise of system and software engineers and researchers alike, and integrates seamlessly into common workflows for both of these groups. As its primary use case, Singularity brings mobility of computing to both users and HPC centers, providing a secure means to capture and distribute software and compute environments. This ability to create and deploy reproducible environments across these centers, a previously unmet need, makes Singularity a game changing development for computational science. PMID:28494014

InDEx: Open Source iOS and Android Software for Self-Reporting and Monitoring of Alcohol Consumption.

PubMed

Leightley, Daniel; Puddephatt, Jo-Anne; Goodwin, Laura; Rona, Roberto; Fear, Nicola T

2018-03-23

InDEx is a software package for reporting and monitoring alcohol consumption via a smartphone application. Consumption of alcohol is self-reported by the user, and the app provides a visual representation of drinking behaviour and offers feedback on consumption levels compared to the general population. InDEx is intended as an exemplar app, operating as a standalone smartphone application and is highly customisable for a variety of research domains. InDEx is written in JavaScript, using IONIC framework which is cross-platform and is available under the liberal GNU General Public License (v3). The software is available from GitHub (https://github.com/DrDanL/index-app-public).

InDEx: Open Source iOS and Android Software for Self-Reporting and Monitoring of Alcohol Consumption

PubMed Central

Leightley, Daniel; Puddephatt, Jo-Anne; Goodwin, Laura; Rona, Roberto; Fear, Nicola T.

2018-01-01

InDEx is a software package for reporting and monitoring alcohol consumption via a smartphone application. Consumption of alcohol is self-reported by the user, and the app provides a visual representation of drinking behaviour and offers feedback on consumption levels compared to the general population. InDEx is intended as an exemplar app, operating as a standalone smartphone application and is highly customisable for a variety of research domains. InDEx is written in JavaScript, using IONIC framework which is cross-platform and is available under the liberal GNU General Public License (v3). The software is available from GitHub (https://github.com/DrDanL/index-app-public). PMID:29795769

CWA 15793 2011 Planning and Implementation Tool

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

Gross, Alan; Nail, George

This software, built on an open source platform called Electron (runs on Chromium and Node.js), is designed to assist organizations in the implementation of a biorisk management system consistent with the requirements of the international, publicly available guidance document CEN Workshop Agreement 15793:2011 (CWA 15793). The software includes tools for conducting organizational gap analysis against CWA 15793 requirements, planning tools to support the implementation of CWA 15793 requirements, and performance monitoring support. The gap analysis questions are based on the text of CWA 15793, and its associated guidance document, CEN Workshop Agreement 16393:2012. The authors have secured permission from themore » publisher of CWA 15793, the European Committee for Standardization (CEN), to use language from the document in the software, with the understanding that the software will be made available freely, without charge.« less

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

PubMed Central

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

2015-01-01

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

TRACC: An open source software for processing sap flux data from thermal dissipation probes

DOE PAGES

Ward, Eric J.; Domec, Jean-Christophe; King, John; ...

2017-05-02

Here, thermal dissipation probes (TDPs) have become a widely used method of monitoring plant water use in recent years. The use of TDPs requires calibration to a theoretical zero-flow value (ΔT0); usually based upon the assumption that at least some nighttime measurements represent zero-flow conditions. Fully automating the processing of data from TDPs is made exceedingly difficult due to errors arising from many sources. However, it is desirable to minimize variation arising from different researchers’ processing data, and thus, a common platform for processing data, including editing raw data and determination of ΔT0, is useful and increases the transparency andmore » replicability of TDP-based research. Here, we present the TDP data processing software TRACC (Thermal dissipation Review Assessment Cleaning and Conversion) to serve this purpose. TRACC is an open-source software written in the language R, using graphical presentation of data and on screen prompts with yes/no or simple numerical responses. It allows the user to select several important options, such as calibration coefficients and the exclusion of nights when vapor pressure deficit does not approach zero. Although it is designed for users with no coding experience, the outputs of TRACC could be easily incorporated into more complex models or software.« less

TRACC: An open source software for processing sap flux data from thermal dissipation probes

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

Ward, Eric J.; Domec, Jean-Christophe; King, John

Here, thermal dissipation probes (TDPs) have become a widely used method of monitoring plant water use in recent years. The use of TDPs requires calibration to a theoretical zero-flow value (ΔT0); usually based upon the assumption that at least some nighttime measurements represent zero-flow conditions. Fully automating the processing of data from TDPs is made exceedingly difficult due to errors arising from many sources. However, it is desirable to minimize variation arising from different researchers’ processing data, and thus, a common platform for processing data, including editing raw data and determination of ΔT0, is useful and increases the transparency andmore » replicability of TDP-based research. Here, we present the TDP data processing software TRACC (Thermal dissipation Review Assessment Cleaning and Conversion) to serve this purpose. TRACC is an open-source software written in the language R, using graphical presentation of data and on screen prompts with yes/no or simple numerical responses. It allows the user to select several important options, such as calibration coefficients and the exclusion of nights when vapor pressure deficit does not approach zero. Although it is designed for users with no coding experience, the outputs of TRACC could be easily incorporated into more complex models or software.« less

Embracing Open Software Development in Solar Physics

NASA Astrophysics Data System (ADS)

Hughitt, V. K.; Ireland, J.; Christe, S.; Mueller, D.

2012-12-01

We discuss two ongoing software projects in solar physics that have adopted best practices of the open source software community. The first, the Helioviewer Project, is a powerful data visualization tool which includes online and Java interfaces inspired by Google Maps (tm). This effort allows users to find solar features and events of interest, and download the corresponding data. Having found data of interest, the user now has to analyze it. The dominant solar data analysis platform is an open-source library called SolarSoft (SSW). Although SSW itself is open-source, the programming language used is IDL, a proprietary language with licensing costs that are prohibative for many institutions and individuals. SSW is composed of a collection of related scripts written by missions and individuals for solar data processing and analysis, without any consistent data structures or common interfaces. Further, at the time when SSW was initially developed, many of the best software development processes of today (mirrored and distributed version control, unit testing, continuous integration, etc.) were not standard, and have not since been adopted. The challenges inherent in developing SolarSoft led to a second software project known as SunPy. SunPy is an open-source Python-based library which seeks to create a unified solar data analysis environment including a number of core datatypes such as Maps, Lightcurves, and Spectra which have consistent interfaces and behaviors. By taking advantage of the large and sophisticated body of scientific software already available in Python (e.g. SciPy, NumPy, Matplotlib), and by adopting many of the best practices refined in open-source software development, SunPy has been able to develop at a very rapid pace while still ensuring a high level of reliability. The Helioviewer Project and SunPy represent two pioneering technologies in solar physics - simple yet flexible data visualization and a powerful, new data analysis environment. We discuss the development of both these efforts and how they are beginning to influence the solar physics community.

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.

Future Directions for Astronomical Image Display

NASA Technical Reports Server (NTRS)

Mandel, Eric

2000-01-01

In the "Future Directions for Astronomical Image Displav" project, the Smithsonian Astrophysical Observatory (SAO) and the National Optical Astronomy Observatories (NOAO) evolved our existing image display program into fully extensible. cross-platform image display software. We also devised messaging software to support integration of image display into astronomical analysis systems. Finally, we migrated our software from reliance on Unix and the X Window System to a platform-independent architecture that utilizes the cross-platform Tcl/Tk technology.

QuantWorm: a comprehensive software package for Caenorhabditis elegans phenotypic assays.

PubMed

Jung, Sang-Kyu; Aleman-Meza, Boanerges; Riepe, Celeste; Zhong, Weiwei

2014-01-01

Phenotypic assays are crucial in genetics; however, traditional methods that rely on human observation are unsuitable for quantitative, large-scale experiments. Furthermore, there is an increasing need for comprehensive analyses of multiple phenotypes to provide multidimensional information. Here we developed an automated, high-throughput computer imaging system for quantifying multiple Caenorhabditis elegans phenotypes. Our imaging system is composed of a microscope equipped with a digital camera and a motorized stage connected to a computer running the QuantWorm software package. Currently, the software package contains one data acquisition module and four image analysis programs: WormLifespan, WormLocomotion, WormLength, and WormEgg. The data acquisition module collects images and videos. The WormLifespan software counts the number of moving worms by using two time-lapse images; the WormLocomotion software computes the velocity of moving worms; the WormLength software measures worm body size; and the WormEgg software counts the number of eggs. To evaluate the performance of our software, we compared the results of our software with manual measurements. We then demonstrated the application of the QuantWorm software in a drug assay and a genetic assay. Overall, the QuantWorm software provided accurate measurements at a high speed. Software source code, executable programs, and sample images are available at www.quantworm.org. Our software package has several advantages over current imaging systems for C. elegans. It is an all-in-one package for quantifying multiple phenotypes. The QuantWorm software is written in Java and its source code is freely available, so it does not require use of commercial software or libraries. It can be run on multiple platforms and easily customized to cope with new methods and requirements.

AirShow 1.0 CFD Software Users' Guide

NASA Technical Reports Server (NTRS)

Mohler, Stanley R., Jr.

2005-01-01

AirShow is visualization post-processing software for Computational Fluid Dynamics (CFD). Upon reading binary PLOT3D grid and solution files into AirShow, the engineer can quickly see how hundreds of complex 3-D structured blocks are arranged and numbered. Additionally, chosen grid planes can be displayed and colored according to various aerodynamic flow quantities such as Mach number and pressure. The user may interactively rotate and translate the graphical objects using the mouse. The software source code was written in cross-platform Java, C++, and OpenGL, and runs on Unix, Linux, and Windows. The graphical user interface (GUI) was written using Java Swing. Java also provides multiple synchronized threads. The Java Native Interface (JNI) provides a bridge between the Java code and the C++ code where the PLOT3D files are read, the OpenGL graphics are rendered, and numerical calculations are performed. AirShow is easy to learn and simple to use. The source code is available for free from the NASA Technology Transfer and Partnership Office.

Open-source telemedicine platform for wireless medical video communication.

PubMed

Panayides, A; Eleftheriou, I; Pantziaris, M

2013-01-01

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

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

NASA Astrophysics Data System (ADS)

Knörchen, Achim; Ketzler, Gunnar; Schneider, Christoph

2015-01-01

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

Open-Source Telemedicine Platform for Wireless Medical Video Communication

PubMed Central

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

2013-01-01

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

Open-source platforms for navigated image-guided interventions.

PubMed

Ungi, Tamas; Lasso, Andras; Fichtinger, Gabor

2016-10-01

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

PharmTeX: a LaTeX-Based Open-Source Platform for Automated Reporting Workflow.

PubMed

Rasmussen, Christian Hove; Smith, Mike K; Ito, Kaori; Sundararajan, Vijayakumar; Magnusson, Mats O; Niclas Jonsson, E; Fostvedt, Luke; Burger, Paula; McFadyen, Lynn; Tensfeldt, Thomas G; Nicholas, Timothy

2018-03-16

Every year, the pharmaceutical industry generates a large number of scientific reports related to drug research, development, and regulatory submissions. Many of these reports are created using text processing tools such as Microsoft Word. Given the large number of figures, tables, references, and other elements, this is often a tedious task involving hours of copying and pasting and substantial efforts in quality control (QC). In the present article, we present the LaTeX-based open-source reporting platform, PharmTeX, a community-based effort to make reporting simple, reproducible, and user-friendly. The PharmTeX creators put a substantial effort into simplifying the sometimes complex elements of LaTeX into user-friendly functions that rely on advanced LaTeX and Perl code running in the background. Using this setup makes LaTeX much more accessible for users with no prior LaTeX experience. A software collection was compiled for users not wanting to manually install the required software components. The PharmTeX templates allow for inclusion of tables directly from mathematical software output as well and figures from several formats. Code listings can be included directly from source. No previous experience and only a few hours of training are required to start writing reports using PharmTeX. PharmTeX significantly reduces the time required for creating a scientific report fully compliant with regulatory and industry expectations. QC is made much simpler, since there is a direct link between analysis output and report input. PharmTeX makes available to report authors the strengths of LaTeX document processing without the need for extensive training. Graphical Abstract ᅟ.

VA's Integrated Imaging System on three platforms.

PubMed

Dayhoff, R E; Maloney, D L; Majurski, W J

1992-01-01

The DHCP Integrated Imaging System provides users with integrated patient data including text, image and graphics data. This system has been transferred from its original two screen DOS-based MUMPS platform to an X window workstation and a Microsoft Windows-based workstation. There are differences between these various platforms that impact on software design and on software development strategy. Data structures and conventions were used to isolate hardware, operating system, imaging software, and user-interface differences between platforms in the implementation of functionality for text and image display and interaction. The use of an object-oriented approach greatly increased system portability.

VA's Integrated Imaging System on three platforms.

PubMed Central

Dayhoff, R. E.; Maloney, D. L.; Majurski, W. J.

1992-01-01

The DHCP Integrated Imaging System provides users with integrated patient data including text, image and graphics data. This system has been transferred from its original two screen DOS-based MUMPS platform to an X window workstation and a Microsoft Windows-based workstation. There are differences between these various platforms that impact on software design and on software development strategy. Data structures and conventions were used to isolate hardware, operating system, imaging software, and user-interface differences between platforms in the implementation of functionality for text and image display and interaction. The use of an object-oriented approach greatly increased system portability. PMID:1482983

A Platform-Independent Plugin for Navigating Online Radiology Cases.

PubMed

Balkman, Jason D; Awan, Omer A

2016-06-01

Software methods that enable navigation of radiology cases on various digital platforms differ between handheld devices and desktop computers. This has resulted in poor compatibility of online radiology teaching files across mobile smartphones, tablets, and desktop computers. A standardized, platform-independent, or "agnostic" approach for presenting online radiology content was produced in this work by leveraging modern hypertext markup language (HTML) and JavaScript web software technology. We describe the design and evaluation of this software, demonstrate its use across multiple viewing platforms, and make it publicly available as a model for future development efforts.

Integrated Power, Avionics, and Software (iPAS) Space Telecommunications Radio System (STRS) Radio User's Guide -- Advanced Exploration Systems (AES)

NASA Technical Reports Server (NTRS)

Roche, Rigoberto; Shalkhauser, Mary Jo Windmille

2017-01-01

The Integrated Power, Avionics and Software (IPAS) software defined radio (SDR) was implemented on the Reconfigurable, Intelligently-Adaptive Communication System (RAICS) platform, for radio development at NASA Johnson Space Center. Software and hardware description language (HDL) code were delivered by NASA Glenn Research Center for use in the IPAS test bed and for development of their own Space Telecommunications Radio System (STRS) waveforms on the RAICS platform. The purpose of this document is to describe how to setup and operate the IPAS STRS Radio platform with its delivered test waveform.

Testing RISKGIS Platform with Students to Improve Learning and Teaching Skills

NASA Astrophysics Data System (ADS)

Olyazadeh, R.; Aye, Z. C.; Jaboyedoff, M.; Derron, M. H.

2016-12-01

Nowadays, open-source developments in the field of natural hazards and risk management increase rapidly. The governments, NGOs and other research institutes are producing data for risk and disaster analysis, but a few platforms are available to bring a real-life experience to the students. This work focuses on the preliminary results of testing a WebGIS platform called RISKGIS with the bachelor students at the University of Lausanne. The platform is designed based on a geospatial open-source technology called OpenGeo (Boundless). This platform can calculate the potential risk of the buildings and assist the students to understand the situations for risk reduction mitigation and decision-making. The center of Jomsom in Nepal was selected for the first exercise that may be affected by amplifications of earthquake. The shaking intensity map was designed by an expert based on the geological characteristics and DEM (Digital Elevation Model) of the area. All buildings data were extracted from OpenStreetMap using QGIS and adapted to the platform. The video tutorial was prepared to guide the students through the platform, and 80 students have tested the application online successfully and 40 of them participated in Moodle (a free Open Source software package for educators) for online feedback and quiz. Among those, 30 of them have completely answered to both. We had interesting results for effectiveness, efficiency and satisfaction based on System Usability Scale (SUS). The SUS score for this platform was 68.6 out of 100. The average result of the quiz was 9.39 out of 10 with a duration of 8 to 33 minutes to answer the quiz. There were several outliers for this duration with 2 minutes (two students) and 9 to 18 hours (three students). Further exercises will be carried out with students by adding more advanced functions to the platform and improving the willingness of participation in this online learning platform. This project is funded by Fonds d'innovation pédagogique de l'Université de Lausanne (FIP). We think this initial, ongoing platform can help both students and teachers to improve their skills in the field of risk and disaster management.Keywords: Risk and disaster Management, GIS, Open-Source, Boundless, Moodle, Teaching and learning

Wavelet-Based Peak Detection and a New Charge Inference Procedure for MS/MS Implemented in ProteoWizard’s msConvert

PubMed Central

2015-01-01

We report the implementation of high-quality signal processing algorithms into ProteoWizard, an efficient, open-source software package designed for analyzing proteomics tandem mass spectrometry data. Specifically, a new wavelet-based peak-picker (CantWaiT) and a precursor charge determination algorithm (Turbocharger) have been implemented. These additions into ProteoWizard provide universal tools that are independent of vendor platform for tandem mass spectrometry analyses and have particular utility for intralaboratory studies requiring the advantages of different platforms convergent on a particular workflow or for interlaboratory investigations spanning multiple platforms. We compared results from these tools to those obtained using vendor and commercial software, finding that in all cases our algorithms resulted in a comparable number of identified peptides for simple and complex samples measured on Waters, Agilent, and AB SCIEX quadrupole time-of-flight and Thermo Q-Exactive mass spectrometers. The mass accuracy of matched precursor ions also compared favorably with vendor and commercial tools. Additionally, typical analysis runtimes (∼1–100 ms per MS/MS spectrum) were short enough to enable the practical use of these high-quality signal processing tools for large clinical and research data sets. PMID:25411686

Wavelet-based peak detection and a new charge inference procedure for MS/MS implemented in ProteoWizard's msConvert.

PubMed

French, William R; Zimmerman, Lisa J; Schilling, Birgit; Gibson, Bradford W; Miller, Christine A; Townsend, R Reid; Sherrod, Stacy D; Goodwin, Cody R; McLean, John A; Tabb, David L

2015-02-06

We report the implementation of high-quality signal processing algorithms into ProteoWizard, an efficient, open-source software package designed for analyzing proteomics tandem mass spectrometry data. Specifically, a new wavelet-based peak-picker (CantWaiT) and a precursor charge determination algorithm (Turbocharger) have been implemented. These additions into ProteoWizard provide universal tools that are independent of vendor platform for tandem mass spectrometry analyses and have particular utility for intralaboratory studies requiring the advantages of different platforms convergent on a particular workflow or for interlaboratory investigations spanning multiple platforms. We compared results from these tools to those obtained using vendor and commercial software, finding that in all cases our algorithms resulted in a comparable number of identified peptides for simple and complex samples measured on Waters, Agilent, and AB SCIEX quadrupole time-of-flight and Thermo Q-Exactive mass spectrometers. The mass accuracy of matched precursor ions also compared favorably with vendor and commercial tools. Additionally, typical analysis runtimes (∼1-100 ms per MS/MS spectrum) were short enough to enable the practical use of these high-quality signal processing tools for large clinical and research data sets.

Integrative structure modeling with the Integrative Modeling Platform.

PubMed

Webb, Benjamin; Viswanath, Shruthi; Bonomi, Massimiliano; Pellarin, Riccardo; Greenberg, Charles H; Saltzberg, Daniel; Sali, Andrej

2018-01-01

Building models of a biological system that are consistent with the myriad data available is one of the key challenges in biology. Modeling the structure and dynamics of macromolecular assemblies, for example, can give insights into how biological systems work, evolved, might be controlled, and even designed. Integrative structure modeling casts the building of structural models as a computational optimization problem, for which information about the assembly is encoded into a scoring function that evaluates candidate models. Here, we describe our open source software suite for integrative structure modeling, Integrative Modeling Platform (https://integrativemodeling.org), and demonstrate its use. © 2017 The Protein Society.

Build and Execute Environment

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

Guan, Qiang

At exascale, the challenge becomes to develop applications that run at scale and use exascale platforms reliably, efficiently, and flexibly. Workflows become much more complex because they must seamlessly integrate simulation and data analytics. They must include down-sampling, post-processing, feature extraction, and visualization. Power and data transfer limitations require these analysis tasks to be run in-situ or in-transit. We expect successful workflows will comprise multiple linked simulations along with tens of analysis routines. Users will have limited development time at scale and, therefore, must have rich tools to develop, debug, test, and deploy applications. At this scale, successful workflows willmore » compose linked computations from an assortment of reliable, well-defined computation elements, ones that can come and go as required, based on the needs of the workflow over time. We propose a novel framework that utilizes both virtual machines (VMs) and software containers to create a workflow system that establishes a uniform build and execution environment (BEE) beyond the capabilities of current systems. In this environment, applications will run reliably and repeatably across heterogeneous hardware and software. Containers, both commercial (Docker and Rocket) and open-source (LXC and LXD), define a runtime that isolates all software dependencies from the machine operating system. Workflows may contain multiple containers that run different operating systems, different software, and even different versions of the same software. We will run containers in open-source virtual machines (KVM) and emulators (QEMU) so that workflows run on any machine entirely in user-space. On this platform of containers and virtual machines, we will deliver workflow software that provides services, including repeatable execution, provenance, checkpointing, and future proofing. We will capture provenance about how containers were launched and how they interact to annotate workflows for repeatable and partial re-execution. We will coordinate the physical snapshots of virtual machines with parallel programming constructs, such as barriers, to automate checkpoint and restart. We will also integrate with HPC-specific container runtimes to gain access to accelerators and other specialized hardware to preserve native performance. Containers will link development to continuous integration. When application developers check code in, it will automatically be tested on a suite of different software and hardware architectures.« less

Database Organisation in a Web-Enabled Free and Open-Source Software (foss) Environment for Spatio-Temporal Landslide Modelling

NASA Astrophysics Data System (ADS)

Das, I.; Oberai, K.; Sarathi Roy, P.

2012-07-01

Landslides exhibit themselves in different mass movement processes and are considered among the most complex natural hazards occurring on the earth surface. Making landslide database available online via WWW (World Wide Web) promotes the spreading and reaching out of the landslide information to all the stakeholders. The aim of this research is to present a comprehensive database for generating landslide hazard scenario with the help of available historic records of landslides and geo-environmental factors and make them available over the Web using geospatial Free & Open Source Software (FOSS). FOSS reduces the cost of the project drastically as proprietary software's are very costly. Landslide data generated for the period 1982 to 2009 were compiled along the national highway road corridor in Indian Himalayas. All the geo-environmental datasets along with the landslide susceptibility map were served through WEBGIS client interface. Open source University of Minnesota (UMN) mapserver was used as GIS server software for developing web enabled landslide geospatial database. PHP/Mapscript server-side application serve as a front-end application and PostgreSQL with PostGIS extension serve as a backend application for the web enabled landslide spatio-temporal databases. This dynamic virtual visualization process through a web platform brings an insight into the understanding of the landslides and the resulting damage closer to the affected people and user community. The landslide susceptibility dataset is also made available as an Open Geospatial Consortium (OGC) Web Feature Service (WFS) which can be accessed through any OGC compliant open source or proprietary GIS Software.

LabKey Server: an open source platform for scientific data integration, analysis and collaboration.

PubMed

Nelson, Elizabeth K; Piehler, Britt; Eckels, Josh; Rauch, Adam; Bellew, Matthew; Hussey, Peter; Ramsay, Sarah; Nathe, Cory; Lum, Karl; Krouse, Kevin; Stearns, David; Connolly, Brian; Skillman, Tom; Igra, Mark

2011-03-09

Broad-based collaborations are becoming increasingly common among disease researchers. For example, the Global HIV Enterprise has united cross-disciplinary consortia to speed progress towards HIV vaccines through coordinated research across the boundaries of institutions, continents and specialties. New, end-to-end software tools for data and specimen management are necessary to achieve the ambitious goals of such alliances. These tools must enable researchers to organize and integrate heterogeneous data early in the discovery process, standardize processes, gain new insights into pooled data and collaborate securely. To meet these needs, we enhanced the LabKey Server platform, formerly known as CPAS. This freely available, open source software is maintained by professional engineers who use commercially proven practices for software development and maintenance. Recent enhancements support: (i) Submitting specimens requests across collaborating organizations (ii) Graphically defining new experimental data types, metadata and wizards for data collection (iii) Transitioning experimental results from a multiplicity of spreadsheets to custom tables in a shared database (iv) Securely organizing, integrating, analyzing, visualizing and sharing diverse data types, from clinical records to specimens to complex assays (v) Interacting dynamically with external data sources (vi) Tracking study participants and cohorts over time (vii) Developing custom interfaces using client libraries (viii) Authoring custom visualizations in a built-in R scripting environment. Diverse research organizations have adopted and adapted LabKey Server, including consortia within the Global HIV Enterprise. Atlas is an installation of LabKey Server that has been tailored to serve these consortia. It is in production use and demonstrates the core capabilities of LabKey Server. Atlas now has over 2,800 active user accounts originating from approximately 36 countries and 350 organizations. It tracks roughly 27,000 assay runs, 860,000 specimen vials and 1,300,000 vial transfers. Sharing data, analysis tools and infrastructure can speed the efforts of large research consortia by enhancing efficiency and enabling new insights. The Atlas installation of LabKey Server demonstrates the utility of the LabKey platform for collaborative research. Stable, supported builds of LabKey Server are freely available for download at http://www.labkey.org. Documentation and source code are available under the Apache License 2.0.

LabKey Server: An open source platform for scientific data integration, analysis and collaboration

PubMed Central

2011-01-01

Background Broad-based collaborations are becoming increasingly common among disease researchers. For example, the Global HIV Enterprise has united cross-disciplinary consortia to speed progress towards HIV vaccines through coordinated research across the boundaries of institutions, continents and specialties. New, end-to-end software tools for data and specimen management are necessary to achieve the ambitious goals of such alliances. These tools must enable researchers to organize and integrate heterogeneous data early in the discovery process, standardize processes, gain new insights into pooled data and collaborate securely. Results To meet these needs, we enhanced the LabKey Server platform, formerly known as CPAS. This freely available, open source software is maintained by professional engineers who use commercially proven practices for software development and maintenance. Recent enhancements support: (i) Submitting specimens requests across collaborating organizations (ii) Graphically defining new experimental data types, metadata and wizards for data collection (iii) Transitioning experimental results from a multiplicity of spreadsheets to custom tables in a shared database (iv) Securely organizing, integrating, analyzing, visualizing and sharing diverse data types, from clinical records to specimens to complex assays (v) Interacting dynamically with external data sources (vi) Tracking study participants and cohorts over time (vii) Developing custom interfaces using client libraries (viii) Authoring custom visualizations in a built-in R scripting environment. Diverse research organizations have adopted and adapted LabKey Server, including consortia within the Global HIV Enterprise. Atlas is an installation of LabKey Server that has been tailored to serve these consortia. It is in production use and demonstrates the core capabilities of LabKey Server. Atlas now has over 2,800 active user accounts originating from approximately 36 countries and 350 organizations. It tracks roughly 27,000 assay runs, 860,000 specimen vials and 1,300,000 vial transfers. Conclusions Sharing data, analysis tools and infrastructure can speed the efforts of large research consortia by enhancing efficiency and enabling new insights. The Atlas installation of LabKey Server demonstrates the utility of the LabKey platform for collaborative research. Stable, supported builds of LabKey Server are freely available for download at http://www.labkey.org. Documentation and source code are available under the Apache License 2.0. PMID:21385461

Leveraging Existing Mission Tools in a Re-Usable, Component-Based Software Environment

NASA Technical Reports Server (NTRS)

Greene, Kevin; Grenander, Sven; Kurien, James; z,s (fshir. z[orttr); z,scer; O'Reilly, Taifun

2006-01-01

Emerging methods in component-based software development offer significant advantages but may seem incompatible with existing mission operations applications. In this paper we relate our positive experiences integrating existing mission applications into component-based tools we are delivering to three missions. In most operations environments, a number of software applications have been integrated together to form the mission operations software. In contrast, with component-based software development chunks of related functionality and data structures, referred to as components, can be individually delivered, integrated and re-used. With the advent of powerful tools for managing component-based development, complex software systems can potentially see significant benefits in ease of integration, testability and reusability from these techniques. These benefits motivate us to ask how component-based development techniques can be relevant in a mission operations environment, where there is significant investment in software tools that are not component-based and may not be written in languages for which component-based tools even exist. Trusted and complex software tools for sequencing, validation, navigation, and other vital functions cannot simply be re-written or abandoned in order to gain the advantages offered by emerging component-based software techniques. Thus some middle ground must be found. We have faced exactly this issue, and have found several solutions. Ensemble is an open platform for development, integration, and deployment of mission operations software that we are developing. Ensemble itself is an extension of an open source, component-based software development platform called Eclipse. Due to the advantages of component-based development, we have been able to vary rapidly develop mission operations tools for three surface missions by mixing and matching from a common set of mission operation components. We have also had to determine how to integrate existing mission applications for sequence development, sequence validation, and high level activity planning, and other functions into a component-based environment. For each of these, we used a somewhat different technique based upon the structure and usage of the existing application.

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.

Harnessing the power of emerging petascale platforms

NASA Astrophysics Data System (ADS)

Mellor-Crummey, John

2007-07-01

As part of the US Department of Energy's Scientific Discovery through Advanced Computing (SciDAC-2) program, science teams are tackling problems that require computational simulation and modeling at the petascale. A grand challenge for computer science is to develop software technology that makes it easier to harness the power of these systems to aid scientific discovery. As part of its activities, the SciDAC-2 Center for Scalable Application Development Software (CScADS) is building open source software tools to support efficient scientific computing on the emerging leadership-class platforms. In this paper, we describe two tools for performance analysis and tuning that are being developed as part of CScADS: a tool for analyzing scalability and performance, and a tool for optimizing loop nests for better node performance. We motivate these tools by showing how they apply to S3D, a turbulent combustion code under development at Sandia National Laboratory. For S3D, our node performance analysis tool helped uncover several performance bottlenecks. Using our loop nest optimization tool, we transformed S3D's most costly loop nest to reduce execution time by a factor of 2.94 for a processor working on a 503 domain.

The new meaning of quality in the information age.

PubMed

Prahalad, C K; Krishnan, M S

1999-01-01

Software applications are now a mission-critical source of competitive advantage for most companies. They are also a source of great risk, as the Y2K bug has made clear. Yet many line managers still haven't confronted software issues--partly because they aren't sure how best to define the quality of the applications in their IT infrastructures. Some companies such as Wal-Mart and the Gap have successfully integrated the software in their networks, but most have accumulated an unwidely number of incompatible applications--all designed to perform the same tasks. The authors provide a framework for measuring the performance of software in a company's IT portfolio. Quality traditionally has been measured according to a product's ability to meet certain specifications; other views of quality have emerged that measure a product's adaptability to customers' needs and a product's ability to encourage innovation. To judge software quality properly, argue the authors, managers must measure applications against all three approaches. Understanding the domain of a software application is an important part of that process. The domain is the body of knowledge about a user's needs and expectations for a product. Software domains change frequently based on how a consumer chooses to use, for example, Microsoft Word or a spreadsheet application. The domain can also be influenced by general changes in technology, such as the development of a new software platform. Thus, applications can't be judged only according to whether they conform to specifications. The authors discuss how to identify domain characteristics and software risks and suggest ways to reduce the variability of software domains.

Framework programmable platform for the advanced software development workstation. Integration mechanism design document

NASA Technical Reports Server (NTRS)

Mayer, Richard J.; Blinn, Thomas M.; Mayer, Paula S. D.; Reddy, Uday; Ackley, Keith; Futrell, Mike

1991-01-01

The Framework Programmable Software Development Platform (FPP) is a project aimed at combining effective tool and data integration mechanisms with a model of the software development process in an intelligent integrated software development environment. Guided by this model, this system development framework will take advantage of an integrated operating environment to automate effectively the management of the software development process so that costly mistakes during the development phase can be eliminated.

CellShape: A user-friendly image analysis tool for quantitative visualization of bacterial cell factories inside.

PubMed

Goñi-Moreno, Ángel; Kim, Juhyun; de Lorenzo, Víctor

2017-02-01

Visualization of the intracellular constituents of individual bacteria while performing as live biocatalysts is in principle doable through more or less sophisticated fluorescence microscopy. Unfortunately, rigorous quantitation of the wealth of data embodied in the resulting images requires bioinformatic tools that are not widely extended within the community-let alone that they are often subject to licensing that impedes software reuse. In this context we have developed CellShape, a user-friendly platform for image analysis with subpixel precision and double-threshold segmentation system for quantification of fluorescent signals stemming from single-cells. CellShape is entirely coded in Python, a free, open-source programming language with widespread community support. For a developer, CellShape enhances extensibility (ease of software improvements) by acting as an interface to access and use existing Python modules; for an end-user, CellShape presents standalone executable files ready to open without installation. We have adopted this platform to analyse with an unprecedented detail the tridimensional distribution of the constituents of the gene expression flow (DNA, RNA polymerase, mRNA and ribosomal proteins) in individual cells of the industrial platform strain Pseudomonas putida KT2440. While the CellShape first release version (v0.8) is readily operational, users and/or developers are enabled to expand the platform further. Copyright © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Towards an Open, Distributed Software Architecture for UxS Operations

NASA Technical Reports Server (NTRS)

Cross, Charles D.; Motter, Mark A.; Neilan, James H.; Qualls, Garry D.; Rothhaar, Paul M.; Tran, Loc; Trujillo, Anna C.; Allen, B. Danette

2015-01-01

To address the growing need to evaluate, test, and certify an ever expanding ecosystem of UxS platforms in preparation of cultural integration, NASA Langley Research Center's Autonomy Incubator (AI) has taken on the challenge of developing a software framework in which UxS platforms developed by third parties can be integrated into a single system which provides evaluation and testing, mission planning and operation, and out-of-the-box autonomy and data fusion capabilities. This software framework, named AEON (Autonomous Entity Operations Network), has two main goals. The first goal is the development of a cross-platform, extensible, onboard software system that provides autonomy at the mission execution and course-planning level, a highly configurable data fusion framework sensitive to the platform's available sensor hardware, and plug-and-play compatibility with a wide array of computer systems, sensors, software, and controls hardware. The second goal is the development of a ground control system that acts as a test-bed for integration of the proposed heterogeneous fleet, and allows for complex mission planning, tracking, and debugging capabilities. The ground control system should also be highly extensible and allow plug-and-play interoperability with third party software systems. In order to achieve these goals, this paper proposes an open, distributed software architecture which utilizes at its core the Data Distribution Service (DDS) standards, established by the Object Management Group (OMG), for inter-process communication and data flow. The design decisions proposed herein leverage the advantages of existing robotics software architectures and the DDS standards to develop software that is scalable, high-performance, fault tolerant, modular, and readily interoperable with external platforms and software.

OrChem - An open source chemistry search engine for Oracle®

PubMed Central

2009-01-01

Background Registration, indexing and searching of chemical structures in relational databases is one of the core areas of cheminformatics. However, little detail has been published on the inner workings of search engines and their development has been mostly closed-source. We decided to develop an open source chemistry extension for Oracle, the de facto database platform in the commercial world. Results Here we present OrChem, an extension for the Oracle 11G database that adds registration and indexing of chemical structures to support fast substructure and similarity searching. The cheminformatics functionality is provided by the Chemistry Development Kit. OrChem provides similarity searching with response times in the order of seconds for databases with millions of compounds, depending on a given similarity cut-off. For substructure searching, it can make use of multiple processor cores on today's powerful database servers to provide fast response times in equally large data sets. Availability OrChem is free software and can be redistributed and/or modified under the terms of the GNU Lesser General Public License as published by the Free Software Foundation. All software is available via http://orchem.sourceforge.net. PMID:20298521

Architecture and Implementation of OpenPET Firmware and Embedded Software

PubMed Central

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

2016-01-01

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

The NifTK software platform for image-guided interventions: platform overview and NiftyLink messaging.

PubMed

Clarkson, Matthew J; Zombori, Gergely; Thompson, Steve; Totz, Johannes; Song, Yi; Espak, Miklos; Johnsen, Stian; Hawkes, David; Ourselin, Sébastien

2015-03-01

To perform research in image-guided interventions, researchers need a wide variety of software components, and assembling these components into a flexible and reliable system can be a challenging task. In this paper, the NifTK software platform is presented. A key focus has been high-performance streaming of stereo laparoscopic video data, ultrasound data and tracking data simultaneously. A new messaging library called NiftyLink is introduced that uses the OpenIGTLink protocol and provides the user with easy-to-use asynchronous two-way messaging, high reliability and comprehensive error reporting. A small suite of applications called NiftyGuide has been developed, containing lightweight applications for grabbing data, currently from position trackers and ultrasound scanners. These applications use NiftyLink to stream data into NiftyIGI, which is a workstation-based application, built on top of MITK, for visualisation and user interaction. Design decisions, performance characteristics and initial applications are described in detail. NiftyLink was tested for latency when transmitting images, tracking data, and interleaved imaging and tracking data. NiftyLink can transmit tracking data at 1,024 frames per second (fps) with latency of 0.31 milliseconds, and 512 KB images with latency of 6.06 milliseconds at 32 fps. NiftyIGI was tested, receiving stereo high-definition laparoscopic video at 30 fps, tracking data from 4 rigid bodies at 20-30 fps and ultrasound data at 20 fps with rendering refresh rates between 2 and 20 Hz with no loss of user interaction. These packages form part of the NifTK platform and have proven to be successful in a variety of image-guided surgery projects. Code and documentation for the NifTK platform are available from http://www.niftk.org . NiftyLink is provided open-source under a BSD license and available from http://github.com/NifTK/NiftyLink . The code for this paper is tagged IJCARS-2014.

Applications of Sentinel-2 data for agriculture and forest monitoring using the absolute difference (ZABUD) index derived from the AgroEye software (ESA)

NASA Astrophysics Data System (ADS)

de Kok, R.; WeŻyk, P.; PapieŻ, M.; Migo, L.

2017-10-01

To convince new users of the advantages of the Sentinel_2 sensor, a simplification of classic remote sensing tools allows to create a platform of communication among domain specialists of agricultural analysis, visual image interpreters and remote sensing programmers. An index value, known in the remote sensing user domain as "Zabud" was selected to represent, in color, the essentials of a time series analysis. The color index used in a color atlas offers a working platform for an agricultural field control. This creates a database of test and training areas that enables rapid anomaly detection in the agricultural domain. The use cases and simplifications now function as an introduction to Sentinel_2 based remote sensing, in an area that before relies on VHR imagery and aerial data, to serve mainly the visual interpretation. The database extension with detected anomalies allows developers of open source software to design solutions for further agricultural control with remote sensing.

Efficient visualization of high-throughput targeted proteomics experiments: TAPIR.

PubMed

Röst, Hannes L; Rosenberger, George; Aebersold, Ruedi; Malmström, Lars

2015-07-15

Targeted mass spectrometry comprises a set of powerful methods to obtain accurate and consistent protein quantification in complex samples. To fully exploit these techniques, a cross-platform and open-source software stack based on standardized data exchange formats is required. We present TAPIR, a fast and efficient Python visualization software for chromatograms and peaks identified in targeted proteomics experiments. The input formats are open, community-driven standardized data formats (mzML for raw data storage and TraML encoding the hierarchical relationships between transitions, peptides and proteins). TAPIR is scalable to proteome-wide targeted proteomics studies (as enabled by SWATH-MS), allowing researchers to visualize high-throughput datasets. The framework integrates well with existing automated analysis pipelines and can be extended beyond targeted proteomics to other types of analyses. TAPIR is available for all computing platforms under the 3-clause BSD license at https://github.com/msproteomicstools/msproteomicstools. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

TomoMiner and TomoMinerCloud: A software platform for large-scale subtomogram structural analysis

PubMed Central

Frazier, Zachary; Xu, Min; Alber, Frank

2017-01-01

SUMMARY Cryo-electron tomography (cryoET) captures the 3D electron density distribution of macromolecular complexes in close to native state. With the rapid advance of cryoET acquisition technologies, it is possible to generate large numbers (>100,000) of subtomograms, each containing a macromolecular complex. Often, these subtomograms represent a heterogeneous sample due to variations in structure and composition of a complex in situ form or because particles are a mixture of different complexes. In this case subtomograms must be classified. However, classification of large numbers of subtomograms is a time-intensive task and often a limiting bottleneck. This paper introduces an open source software platform, TomoMiner, for large-scale subtomogram classification, template matching, subtomogram averaging, and alignment. Its scalable and robust parallel processing allows efficient classification of tens to hundreds of thousands of subtomograms. Additionally, TomoMiner provides a pre-configured TomoMinerCloud computing service permitting users without sufficient computing resources instant access to TomoMiners high-performance features. PMID:28552576

The tensor network theory library

NASA Astrophysics Data System (ADS)

Al-Assam, S.; Clark, S. R.; Jaksch, D.

2017-09-01

In this technical paper we introduce the tensor network theory (TNT) library—an open-source software project aimed at providing a platform for rapidly developing robust, easy to use and highly optimised code for TNT calculations. The objectives of this paper are (i) to give an overview of the structure of TNT library, and (ii) to help scientists decide whether to use the TNT library in their research. We show how to employ the TNT routines by giving examples of ground-state and dynamical calculations of one-dimensional bosonic lattice system. We also discuss different options for gaining access to the software available at www.tensornetworktheory.org.

MVAPACK: A Complete Data Handling Package for NMR Metabolomics

PubMed Central

2015-01-01

Data handling in the field of NMR metabolomics has historically been reliant on either in-house mathematical routines or long chains of expensive commercial software. Thus, while the relatively simple biochemical protocols of metabolomics maintain a low barrier to entry, new practitioners of metabolomics experiments are forced to either purchase expensive software packages or craft their own data handling solutions from scratch. This inevitably complicates the standardization and communication of data handling protocols in the field. We report a newly developed open-source platform for complete NMR metabolomics data handling, MVAPACK, and describe its application on an example metabolic fingerprinting data set. PMID:24576144

Ethoscopes: An open platform for high-throughput ethomics.

PubMed

Geissmann, Quentin; Garcia Rodriguez, Luis; Beckwith, Esteban J; French, Alice S; Jamasb, Arian R; Gilestro, Giorgio F

2017-10-01

Here, we present the use of ethoscopes, which are machines for high-throughput analysis of behavior in Drosophila and other animals. Ethoscopes provide a software and hardware solution that is reproducible and easily scalable. They perform, in real-time, tracking and profiling of behavior by using a supervised machine learning algorithm, are able to deliver behaviorally triggered stimuli to flies in a feedback-loop mode, and are highly customizable and open source. Ethoscopes can be built easily by using 3D printing technology and rely on Raspberry Pi microcomputers and Arduino boards to provide affordable and flexible hardware. All software and construction specifications are available at http://lab.gilest.ro/ethoscope.

BeadArray Expression Analysis Using Bioconductor

PubMed Central

Ritchie, Matthew E.; Dunning, Mark J.; Smith, Mike L.; Shi, Wei; Lynch, Andy G.

2011-01-01

Illumina whole-genome expression BeadArrays are a popular choice in gene profiling studies. Aside from the vendor-provided software tools for analyzing BeadArray expression data (GenomeStudio/BeadStudio), there exists a comprehensive set of open-source analysis tools in the Bioconductor project, many of which have been tailored to exploit the unique properties of this platform. In this article, we explore a number of these software packages and demonstrate how to perform a complete analysis of BeadArray data in various formats. The key steps of importing data, performing quality assessments, preprocessing, and annotation in the common setting of assessing differential expression in designed experiments will be covered. PMID:22144879

pyam: Python Implementation of YaM

NASA Technical Reports Server (NTRS)

Myint, Steven; Jain, Abhinandan

2012-01-01

pyam is a software development framework with tools for facilitating the rapid development of software in a concurrent software development environment. pyam provides solutions for development challenges associated with software reuse, managing multiple software configurations, developing software product lines, and multiple platform development and build management. pyam uses release-early, release-often development cycles to allow developers to integrate their changes incrementally into the system on a continual basis. It facilitates the creation and merging of branches to support the isolated development of immature software to avoid impacting the stability of the development effort. It uses modules and packages to organize and share software across multiple software products, and uses the concepts of link and work modules to reduce sandbox setup times even when the code-base is large. One sidebenefit is the enforcement of a strong module-level encapsulation of a module s functionality and interface. This increases design transparency, system stability, and software reuse. pyam is written in Python and is organized as a set of utilities on top of the open source SVN software version control package. All development software is organized into a collection of modules. pyam packages are defined as sub-collections of the available modules. Developers can set up private sandboxes for module/package development. All module/package development takes place on private SVN branches. High-level pyam commands support the setup, update, and release of modules and packages. Released and pre-built versions of modules are available to developers. Developers can tailor the source/link module mix for their sandboxes so that new sandboxes (even large ones) can be built up easily and quickly by pointing to pre-existing module releases. All inter-module interfaces are publicly exported via links. A minimal, but uniform, convention is used for building modules.

Framework Programmable Platform for the Advanced Software Development Workstation: Preliminary system design document

NASA Technical Reports Server (NTRS)

Mayer, Richard J.; Blinn, Thomas M.; Mayer, Paula S. D.; Ackley, Keith A.; Crump, John W., IV; Henderson, Richard; Futrell, Michael T.

1991-01-01

The Framework Programmable Software Development Platform (FPP) is a project aimed at combining effective tool and data integration mechanisms with a model of the software development process in an intelligent integrated software environment. Guided by the model, this system development framework will take advantage of an integrated operating environment to automate effectively the management of the software development process so that costly mistakes during the development phase can be eliminated. The focus here is on the design of components that make up the FPP. These components serve as supporting systems for the Integration Mechanism and the Framework Processor and provide the 'glue' that ties the FPP together. Also discussed are the components that allow the platform to operate in a distributed, heterogeneous environment and to manage the development and evolution of software system artifacts.

Hyperspectral Soil Mapper (HYSOMA) software interface: Review and future plans

NASA Astrophysics Data System (ADS)

Chabrillat, Sabine; Guillaso, Stephane; Eisele, Andreas; Rogass, Christian

2014-05-01

With the upcoming launch of the next generation of hyperspectral satellites that will routinely deliver high spectral resolution images for the entire globe (e.g. EnMAP, HISUI, HyspIRI, HypXIM, PRISMA), an increasing demand for the availability/accessibility of hyperspectral soil products is coming from the geoscience community. Indeed, many robust methods for the prediction of soil properties based on imaging spectroscopy already exist and have been successfully used for a wide range of soil mapping airborne applications. Nevertheless, these methods require expert know-how and fine-tuning, which makes them used sparingly. More developments are needed toward easy-to-access soil toolboxes as a major step toward the operational use of hyperspectral soil products for Earth's surface processes monitoring and modelling, to allow non-experienced users to obtain new information based on non-expensive software packages where repeatability of the results is an important prerequisite. In this frame, based on the EU-FP7 EUFAR (European Facility for Airborne Research) project and EnMAP satellite science program, higher performing soil algorithms were developed at the GFZ German Research Center for Geosciences as demonstrators for end-to-end processing chains with harmonized quality measures. The algorithms were built-in into the HYSOMA (Hyperspectral SOil MApper) software interface, providing an experimental platform for soil mapping applications of hyperspectral imagery that gives the choice of multiple algorithms for each soil parameter. The software interface focuses on fully automatic generation of semi-quantitative soil maps such as soil moisture, soil organic matter, iron oxide, clay content, and carbonate content. Additionally, a field calibration option calculates fully quantitative soil maps provided ground truth soil data are available. Implemented soil algorithms have been tested and validated using extensive in-situ ground truth data sets. The source of the HYSOMA code was developed as standalone IDL software to allow easy implementation in the hyperspectral and non-hyperspectral communities. Indeed, within the hyperspectral community, IDL language is very widely used, and for non-expert users that do not have an ENVI license, such software can be executed as a binary version using the free IDL virtual machine under various operating systems. Based on the growing interest of users in the software interface, the experimental software was adapted for public release version in 2012, and since then ~80 users of hyperspectral soil products downloaded the soil algorithms at www.gfz-potsdam.de/hysoma. The software interface was distributed for free as IDL plug-ins under the IDL-virtual machine. Up-to-now distribution of HYSOMA was based on a close source license model, for non-commercial and educational purposes. Currently, the HYSOMA is being under further development in the context of the EnMAP satellite mission, for extension and implementation in the EnMAP Box as EnSoMAP (EnMAP SOil MAPper). The EnMAP Box is a freely available, platform-independent software distributed under an open source license. In the presentation we will focus on an update of the HYSOMA software interface status and upcoming implementation in the EnMAP Box. Scientific software validation, associated publication record and users responses as well as software management and transition to open source will be discussed.

cPath: open source software for collecting, storing, and querying biological pathways.

PubMed

Cerami, Ethan G; Bader, Gary D; Gross, Benjamin E; Sander, Chris

2006-11-13

Biological pathways, including metabolic pathways, protein interaction networks, signal transduction pathways, and gene regulatory networks, are currently represented in over 220 diverse databases. These data are crucial for the study of specific biological processes, including human diseases. Standard exchange formats for pathway information, such as BioPAX, CellML, SBML and PSI-MI, enable convenient collection of this data for biological research, but mechanisms for common storage and communication are required. We have developed cPath, an open source database and web application for collecting, storing, and querying biological pathway data. cPath makes it easy to aggregate custom pathway data sets available in standard exchange formats from multiple databases, present pathway data to biologists via a customizable web interface, and export pathway data via a web service to third-party software, such as Cytoscape, for visualization and analysis. cPath is software only, and does not include new pathway information. Key features include: a built-in identifier mapping service for linking identical interactors and linking to external resources; built-in support for PSI-MI and BioPAX standard pathway exchange formats; a web service interface for searching and retrieving pathway data sets; and thorough documentation. The cPath software is freely available under the LGPL open source license for academic and commercial use. cPath is a robust, scalable, modular, professional-grade software platform for collecting, storing, and querying biological pathways. It can serve as the core data handling component in information systems for pathway visualization, analysis and modeling.

Rule-based interface generation on mobile devices for structured documentation.

PubMed

Kock, Ann-Kristin; Andersen, Björn; Handels, Heinz; Ingenerf, Josef

2014-01-01

In many software systems to date, interactive graphical user interfaces (GUIs) are represented implicitly in the source code, together with the application logic. Hence, the re-use, development, and modification of these interfaces is often very laborious. Flexible adjustments of GUIs for various platforms and devices as well as individual user preferences are furthermore difficult to realize. These problems motivate a software-based separation of content and GUI models on the one hand, and application logic on the other. In this project, a software solution for structured reporting on mobile devices is developed. Clinical content archetypes developed in a previous project serve as the content model while the Android SDK provides the GUI model. The necessary bindings between the models are specified using the Jess Rule Language.

BIAS: Bioinformatics Integrated Application Software.

PubMed

Finak, G; Godin, N; Hallett, M; Pepin, F; Rajabi, Z; Srivastava, V; Tang, Z

2005-04-15

We introduce a development platform especially tailored to Bioinformatics research and software development. BIAS (Bioinformatics Integrated Application Software) provides the tools necessary for carrying out integrative Bioinformatics research requiring multiple datasets and analysis tools. It follows an object-relational strategy for providing persistent objects, allows third-party tools to be easily incorporated within the system and supports standards and data-exchange protocols common to Bioinformatics. BIAS is an OpenSource project and is freely available to all interested users at http://www.mcb.mcgill.ca/~bias/. This website also contains a paper containing a more detailed description of BIAS and a sample implementation of a Bayesian network approach for the simultaneous prediction of gene regulation events and of mRNA expression from combinations of gene regulation events. hallett@mcb.mcgill.ca.

Parallelization of Rocket Engine System Software (Press)

NASA Technical Reports Server (NTRS)

Cezzar, Ruknet

1996-01-01

The main goal is to assess parallelization requirements for the Rocket Engine Numeric Simulator (RENS) project which, aside from gathering information on liquid-propelled rocket engines and setting forth requirements, involve a large FORTRAN based package at NASA Lewis Research Center and TDK software developed by SUBR/UWF. The ultimate aim is to develop, test, integrate, and suitably deploy a family of software packages on various aspects and facets of rocket engines using liquid-propellants. At present, all project efforts by the funding agency, NASA Lewis Research Center, and the HBCU participants are disseminated over the internet using world wide web home pages. Considering obviously expensive methods of actual field trails, the benefits of software simulators are potentially enormous. When realized, these benefits will be analogous to those provided by numerous CAD/CAM packages and flight-training simulators. According to the overall task assignments, Hampton University's role is to collect all available software, place them in a common format, assess and evaluate, define interfaces, and provide integration. Most importantly, the HU's mission is to see to it that the real-time performance is assured. This involves source code translations, porting, and distribution. The porting will be done in two phases: First, place all software on Cray XMP platform using FORTRAN. After testing and evaluation on the Cray X-MP, the code will be translated to C + + and ported to the parallel nCUBE platform. At present, we are evaluating another option of distributed processing over local area networks using Sun NFS, Ethernet, TCP/IP. Considering the heterogeneous nature of the present software (e.g., first started as an expert system using LISP machines) which now involve FORTRAN code, the effort is expected to be quite challenging.

A Problem-Solving Environment for Biological Network Informatics: Bio-Spice

DTIC Science & Technology

2007-06-01

user an environment to access software tools. The Dashboard is built upon the NetBeans Integrated Development Environment (IDE), an open source Java...based integration platform was demonstrated. During the subsequent six month development cycle, the first version of the NetBeans based Bio-SPICE...frameworks (OAA, NetBeans , and Systems Biology Workbench (SBW)[15]), it becomes possible for Bio-SPICE tools to truly interoperate. This interoperation

OASYS (OrAnge SYnchrotron Suite): an open-source graphical environment for x-ray virtual experiments

NASA Astrophysics Data System (ADS)

Rebuffi, Luca; Sanchez del Rio, Manuel

2017-08-01

The evolution of the hardware platforms, the modernization of the software tools, the access to the codes of a large number of young people and the popularization of the open source software for scientific applications drove us to design OASYS (ORange SYnchrotron Suite), a completely new graphical environment for modelling X-ray experiments. The implemented software architecture allows to obtain not only an intuitive and very-easy-to-use graphical interface, but also provides high flexibility and rapidity for interactive simulations, making configuration changes to quickly compare multiple beamline configurations. Its purpose is to integrate in a synergetic way the most powerful calculation engines available. OASYS integrates different simulation strategies via the implementation of adequate simulation tools for X-ray Optics (e.g. ray tracing and wave optics packages). It provides a language to make them to communicate by sending and receiving encapsulated data. Python has been chosen as main programming language, because of its universality and popularity in scientific computing. The software Orange, developed at the University of Ljubljana (SLO), is the high level workflow engine that provides the interaction with the user and communication mechanisms.

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

PubMed Central

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

2014-01-01

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

A software platform for phase contrast x-ray breast imaging research.

PubMed

Bliznakova, K; Russo, P; Mettivier, G; Requardt, H; Popov, P; Bravin, A; Buliev, I

2015-06-01

To present and validate a computer-based simulation platform dedicated for phase contrast x-ray breast imaging research. The software platform, developed at the Technical University of Varna on the basis of a previously validated x-ray imaging software simulator, comprises modules for object creation and for x-ray image formation. These modules were updated to take into account the refractive index for phase contrast imaging as well as implementation of the Fresnel-Kirchhoff diffraction theory of the propagating x-ray waves. Projection images are generated in an in-line acquisition geometry. To test and validate the platform, several phantoms differing in their complexity were constructed and imaged at 25 keV and 60 keV at the beamline ID17 of the European Synchrotron Radiation Facility. The software platform was used to design computational phantoms that mimic those used in the experimental study and to generate x-ray images in absorption and phase contrast modes. The visual and quantitative results of the validation process showed an overall good correlation between simulated and experimental images and show the potential of this platform for research in phase contrast x-ray imaging of the breast. The application of the platform is demonstrated in a feasibility study for phase contrast images of complex inhomogeneous and anthropomorphic breast phantoms, compared to x-ray images generated in absorption mode. The improved visibility of mammographic structures suggests further investigation and optimisation of phase contrast x-ray breast imaging, especially when abnormalities are present. The software platform can be exploited also for educational purposes. Copyright © 2015 Elsevier Ltd. All rights reserved.

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.

Encourage student learning of hydraulic matters by the use of Arduino platform

NASA Astrophysics Data System (ADS)

Rodriguez Sinobas, Leonor; Granja García, Javier; Sánchez Calvo, Raúl

2014-05-01

Arduino is an open-source electronics prototyping platform based on flexible, easy-to-use hardware and software. It's intended for several purposes to anyone interested in creating interactive objects or environments. The hydraulic matters teach at the Agricultural Engineering School at the Technical University of Madrid deal with practical issues regarding the measurement of variables such as pressure, discharge, temperature and soil water content. Most of the data loggers available in the market for these variables at expensive and not always affordable. On the other hand, current students are eager to manage new technological devices thus, their skills could be oriented not only to the application of an electronic platform as Arduino to build low cost data loggers for different purposes, but to encourage their learning in the hydraulic matters improving their self esteem

Craniux: A LabVIEW-Based Modular Software Framework for Brain-Machine Interface Research

PubMed Central

Degenhart, Alan D.; Kelly, John W.; Ashmore, Robin C.; Collinger, Jennifer L.; Tyler-Kabara, Elizabeth C.; Weber, Douglas J.; Wang, Wei

2011-01-01

This paper presents “Craniux,” an open-access, open-source software framework for brain-machine interface (BMI) research. Developed in LabVIEW, a high-level graphical programming environment, Craniux offers both out-of-the-box functionality and a modular BMI software framework that is easily extendable. Specifically, it allows researchers to take advantage of multiple features inherent to the LabVIEW environment for on-the-fly data visualization, parallel processing, multithreading, and data saving. This paper introduces the basic features and system architecture of Craniux and describes the validation of the system under real-time BMI operation using simulated and real electrocorticographic (ECoG) signals. Our results indicate that Craniux is able to operate consistently in real time, enabling a seamless work flow to achieve brain control of cursor movement. The Craniux software framework is made available to the scientific research community to provide a LabVIEW-based BMI software platform for future BMI research and development. PMID:21687575

Craniux: a LabVIEW-based modular software framework for brain-machine interface research.

PubMed

Degenhart, Alan D; Kelly, John W; Ashmore, Robin C; Collinger, Jennifer L; Tyler-Kabara, Elizabeth C; Weber, Douglas J; Wang, Wei

2011-01-01

This paper presents "Craniux," an open-access, open-source software framework for brain-machine interface (BMI) research. Developed in LabVIEW, a high-level graphical programming environment, Craniux offers both out-of-the-box functionality and a modular BMI software framework that is easily extendable. Specifically, it allows researchers to take advantage of multiple features inherent to the LabVIEW environment for on-the-fly data visualization, parallel processing, multithreading, and data saving. This paper introduces the basic features and system architecture of Craniux and describes the validation of the system under real-time BMI operation using simulated and real electrocorticographic (ECoG) signals. Our results indicate that Craniux is able to operate consistently in real time, enabling a seamless work flow to achieve brain control of cursor movement. The Craniux software framework is made available to the scientific research community to provide a LabVIEW-based BMI software platform for future BMI research and development.

Historical review of computer-assisted cognitive retraining.

PubMed

Lynch, Bill

2002-10-01

This article details the introduction and development of the use of microcomputers as adjuncts to traditional cognitive rehabilitation of persons with acquired brain injury. The initial application of video games as therapeutic recreation in the late 1970s was soon followed in the early 1980s by the use of the first personal computers and available educational software. By the mid-1980s, both the IBM PC and Macintosh platforms were established, along with simplified programming languages that allowed individuals without extensive technical expertise to develop their own software. Several rehabilitation clinicians began to produce and market specially written cognitive retraining software for one or the other platform. Their work was detailed and reviewed, as was recently released software from commercial sources. The latter discussion included the latest developments in the rehabilitation applications of personal digital assistants and related organizing, reminding, and dictation devices. A summary of research on the general and specific efficacy of computer-assisted cognitive retraining illustrated the lingering controversy and skepticism that have been associated with this field since its inception. Computer-assisted cognitive retraining (CACR) can be an effective adjunct to a comprehensive program of cognitive rehabilitation. Training needs to be focused, structured, monitored, and as ecologically relevant as possible for optimum effect. Transfer or training or generalizability of skills remains a key issue in the field and should be considered the key criterion in evaluating whether to initiate or continue CACR.

A Unified Algebraic and Logic-Based Framework Towards Safe Routing Implementations

DTIC Science & Technology

2015-08-13

Software - defined Networks ( SDN ). We developed a declarative platform for implementing SDN protocols using declarative...and debugging several SDN applications. Example-based SDN synthesis. Recent emergence of software - defined networks offers an opportunity to design...domain of Software - defined Networks ( SDN ). We developed a declarative platform for implementing SDN protocols using declarative networking

Open Source Hardware for DIY Environmental Sensing

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

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

PubMed

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

2013-05-01

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

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

NASA Astrophysics Data System (ADS)

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

2013-05-01

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

P-TRAP: a Panicle TRAit Phenotyping tool.

PubMed

A L-Tam, Faroq; Adam, Helene; Anjos, António dos; Lorieux, Mathias; Larmande, Pierre; Ghesquière, Alain; Jouannic, Stefan; Shahbazkia, Hamid Reza

2013-08-29

In crops, inflorescence complexity and the shape and size of the seed are among the most important characters that influence yield. For example, rice panicles vary considerably in the number and order of branches, elongation of the axis, and the shape and size of the seed. Manual low-throughput phenotyping methods are time consuming, and the results are unreliable. However, high-throughput image analysis of the qualitative and quantitative traits of rice panicles is essential for understanding the diversity of the panicle as well as for breeding programs. This paper presents P-TRAP software (Panicle TRAit Phenotyping), a free open source application for high-throughput measurements of panicle architecture and seed-related traits. The software is written in Java and can be used with different platforms (the user-friendly Graphical User Interface (GUI) uses Netbeans Platform 7.3). The application offers three main tools: a tool for the analysis of panicle structure, a spikelet/grain counting tool, and a tool for the analysis of seed shape. The three tools can be used independently or simultaneously for analysis of the same image. Results are then reported in the Extensible Markup Language (XML) and Comma Separated Values (CSV) file formats. Images of rice panicles were used to evaluate the efficiency and robustness of the software. Compared to data obtained by manual processing, P-TRAP produced reliable results in a much shorter time. In addition, manual processing is not repeatable because dry panicles are vulnerable to damage. The software is very useful, practical and collects much more data than human operators. P-TRAP is a new open source software that automatically recognizes the structure of a panicle and the seeds on the panicle in numeric images. The software processes and quantifies several traits related to panicle structure, detects and counts the grains, and measures their shape parameters. In short, P-TRAP offers both efficient results and a user-friendly environment for experiments. The experimental results showed very good accuracy compared to field operator, expert verification and well-known academic methods.

P-TRAP: a Panicle Trait Phenotyping tool

PubMed Central

2013-01-01

Background In crops, inflorescence complexity and the shape and size of the seed are among the most important characters that influence yield. For example, rice panicles vary considerably in the number and order of branches, elongation of the axis, and the shape and size of the seed. Manual low-throughput phenotyping methods are time consuming, and the results are unreliable. However, high-throughput image analysis of the qualitative and quantitative traits of rice panicles is essential for understanding the diversity of the panicle as well as for breeding programs. Results This paper presents P-TRAP software (Panicle TRAit Phenotyping), a free open source application for high-throughput measurements of panicle architecture and seed-related traits. The software is written in Java and can be used with different platforms (the user-friendly Graphical User Interface (GUI) uses Netbeans Platform 7.3). The application offers three main tools: a tool for the analysis of panicle structure, a spikelet/grain counting tool, and a tool for the analysis of seed shape. The three tools can be used independently or simultaneously for analysis of the same image. Results are then reported in the Extensible Markup Language (XML) and Comma Separated Values (CSV) file formats. Images of rice panicles were used to evaluate the efficiency and robustness of the software. Compared to data obtained by manual processing, P-TRAP produced reliable results in a much shorter time. In addition, manual processing is not repeatable because dry panicles are vulnerable to damage. The software is very useful, practical and collects much more data than human operators. Conclusions P-TRAP is a new open source software that automatically recognizes the structure of a panicle and the seeds on the panicle in numeric images. The software processes and quantifies several traits related to panicle structure, detects and counts the grains, and measures their shape parameters. In short, P-TRAP offers both efficient results and a user-friendly environment for experiments. The experimental results showed very good accuracy compared to field operator, expert verification and well-known academic methods. PMID:23987653

The Prodiguer Messaging Platform

NASA Astrophysics Data System (ADS)

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

2014-05-01

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

An architecture for genomics analysis in a clinical setting using Galaxy and Docker

PubMed Central

Digan, W; Countouris, H; Barritault, M; Baudoin, D; Laurent-Puig, P; Blons, H; Burgun, A

2017-01-01

Abstract Next-generation sequencing is used on a daily basis to perform molecular analysis to determine subtypes of disease (e.g., in cancer) and to assist in the selection of the optimal treatment. Clinical bioinformatics handles the manipulation of the data generated by the sequencer, from the generation to the analysis and interpretation. Reproducibility and traceability are crucial issues in a clinical setting. We have designed an approach based on Docker container technology and Galaxy, the popular bioinformatics analysis support open-source software. Our solution simplifies the deployment of a small-size analytical platform and simplifies the process for the clinician. From the technical point of view, the tools embedded in the platform are isolated and versioned through Docker images. Along the Galaxy platform, we also introduce the AnalysisManager, a solution that allows single-click analysis for biologists and leverages standardized bioinformatics application programming interfaces. We added a Shiny/R interactive environment to ease the visualization of the outputs. The platform relies on containers and ensures the data traceability by recording analytical actions and by associating inputs and outputs of the tools to EDAM ontology through ReGaTe. The source code is freely available on Github at https://github.com/CARPEM/GalaxyDocker. PMID:29048555

An architecture for genomics analysis in a clinical setting using Galaxy and Docker.

PubMed

Digan, W; Countouris, H; Barritault, M; Baudoin, D; Laurent-Puig, P; Blons, H; Burgun, A; Rance, B

2017-11-01

Next-generation sequencing is used on a daily basis to perform molecular analysis to determine subtypes of disease (e.g., in cancer) and to assist in the selection of the optimal treatment. Clinical bioinformatics handles the manipulation of the data generated by the sequencer, from the generation to the analysis and interpretation. Reproducibility and traceability are crucial issues in a clinical setting. We have designed an approach based on Docker container technology and Galaxy, the popular bioinformatics analysis support open-source software. Our solution simplifies the deployment of a small-size analytical platform and simplifies the process for the clinician. From the technical point of view, the tools embedded in the platform are isolated and versioned through Docker images. Along the Galaxy platform, we also introduce the AnalysisManager, a solution that allows single-click analysis for biologists and leverages standardized bioinformatics application programming interfaces. We added a Shiny/R interactive environment to ease the visualization of the outputs. The platform relies on containers and ensures the data traceability by recording analytical actions and by associating inputs and outputs of the tools to EDAM ontology through ReGaTe. The source code is freely available on Github at https://github.com/CARPEM/GalaxyDocker. © The Author 2017. Published by Oxford University Press.

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

NASA Astrophysics Data System (ADS)

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

2012-09-01

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

Neurophysiological analytics for all! Free open-source software tools for documenting, analyzing, visualizing, and sharing using electronic notebooks

PubMed Central

2016-01-01

Neurophysiology requires an extensive workflow of information analysis routines, which often includes incompatible proprietary software, introducing limitations based on financial costs, transfer of data between platforms, and the ability to share. An ecosystem of free open-source software exists to fill these gaps, including thousands of analysis and plotting packages written in Python and R, which can be implemented in a sharable and reproducible format, such as the Jupyter electronic notebook. This tool chain can largely replace current routines by importing data, producing analyses, and generating publication-quality graphics. An electronic notebook like Jupyter allows these analyses, along with documentation of procedures, to display locally or remotely in an internet browser, which can be saved as an HTML, PDF, or other file format for sharing with team members and the scientific community. The present report illustrates these methods using data from electrophysiological recordings of the musk shrew vagus—a model system to investigate gut-brain communication, for example, in cancer chemotherapy-induced emesis. We show methods for spike sorting (including statistical validation), spike train analysis, and analysis of compound action potentials in notebooks. Raw data and code are available from notebooks in data supplements or from an executable online version, which replicates all analyses without installing software—an implementation of reproducible research. This demonstrates the promise of combining disparate analyses into one platform, along with the ease of sharing this work. In an age of diverse, high-throughput computational workflows, this methodology can increase efficiency, transparency, and the collaborative potential of neurophysiological research. PMID:27098025

Future-saving audiovisual content for Data Science: Preservation of geoinformatics video heritage with the TIB|AV-Portal

NASA Astrophysics Data System (ADS)

Löwe, Peter; Plank, Margret; Ziedorn, Frauke

2015-04-01

In data driven research, the access to citation and preservation of the full triad consisting of journal article, research data and -software has started to become good scientific practice. To foster the adoption of this practice the significance of software tools has to be acknowledged, which enable scientists to harness auxiliary audiovisual content in their research work. The advent of ubiquitous computer-based audiovisual recording and corresponding Web 2.0 hosting platforms like Youtube, Slideshare and GitHub has created new ecosystems for contextual information related to scientific software and data, which continues to grow both in size and variety of content. The current Web 2.0 platforms lack capabilities for long term archiving and scientific citation, such as persistent identifiers allowing to reference specific intervals of the overall content. The audiovisual content currently shared by scientists ranges from commented howto-demonstrations on software handling, installation and data-processing, to aggregated visual analytics of the evolution of software projects over time. Such content are crucial additions to the scientific message, as they ensure that software-based data-processing workflows can be assessed, understood and reused in the future. In the context of data driven research, such content needs to be accessible by effective search capabilities, enabling the content to be retrieved and ensuring that the content producers receive credit for their efforts within the scientific community. Improved multimedia archiving and retrieval services for scientific audiovisual content which meet these requirements are currently implemented by the scientific library community. This paper exemplifies the existing challenges, requirements, benefits and the potential of the preservation, accessibility and citability of such audiovisual content for the Open Source communities based on the new audiovisual web service TIB|AV Portal of the German National Library of Science and Technology. The web-based portal allows for extended search capabilities based on enhanced metadata derived by automated video analysis. By combining state-of-the-art multimedia retrieval techniques such as speech-, text-, and image recognition with semantic analysis, content-based access to videos at the segment level is provided. Further, by using the open standard Media Fragment Identifier (MFID), a citable Digital Object Identifier is displayed for each video segment. In addition to the continuously growing footprint of contemporary content, the importance of vintage audiovisual information needs to be considered: This paper showcases the successful application of the TIB|AV-Portal in the preservation and provision of a newly discovered version of a GRASS GIS promotional video produced by US Army -Corps of Enginers Laboratory (US-CERL) in 1987. The video is provides insight into the constraints of the very early days of the GRASS GIS project, which is the oldest active Free and Open Source Software (FOSS) GIS project which has been active for over thirty years. GRASS itself has turned into a collaborative scientific platform and a repository of scientific peer-reviewed code and algorithm/knowledge hub for future generation of scientists [1]. This is a reference case for future preservation activities regarding semantic-enhanced Web 2.0 content from geospatial software projects within Academia and beyond. References: [1] Chemin, Y., Petras V., Petrasova, A., Landa, M., Gebbert, S., Zambelli, P., Neteler, M., Löwe, P.: GRASS GIS: a peer-reviewed scientific platform and future research Repository, Geophysical Research Abstracts, Vol. 17, EGU2015-8314-1, 2015 (submitted)

Framework Programmable Platform for the Advanced Software Development Workstation (FPP/ASDW). Demonstration framework document. Volume 1: Concepts and activity descriptions

NASA Technical Reports Server (NTRS)

Mayer, Richard J.; Blinn, Thomas M.; Dewitte, Paul S.; Crump, John W.; Ackley, Keith A.

1992-01-01

The Framework Programmable Software Development Platform (FPP) is a project aimed at effectively combining tool and data integration mechanisms with a model of the software development process to provide an intelligent integrated software development environment. Guided by the model, this system development framework will take advantage of an integrated operating environment to automate effectively the management of the software development process so that costly mistakes during the development phase can be eliminated. The Advanced Software Development Workstation (ASDW) program is conducting research into development of advanced technologies for Computer Aided Software Engineering (CASE).

A software platform for the analysis of dermatology images

NASA Astrophysics Data System (ADS)

Vlassi, Maria; Mavraganis, Vlasios; Asvestas, Panteleimon

2017-11-01

The purpose of this paper is to present a software platform developed in Python programming environment that can be used for the processing and analysis of dermatology images. The platform provides the capability for reading a file that contains a dermatology image. The platform supports image formats such as Windows bitmaps, JPEG, JPEG2000, portable network graphics, TIFF. Furthermore, it provides suitable tools for selecting, either manually or automatically, a region of interest (ROI) on the image. The automated selection of a ROI includes filtering for smoothing the image and thresholding. The proposed software platform has a friendly and clear graphical user interface and could be a useful second-opinion tool to a dermatologist. Furthermore, it could be used to classify images including from other anatomical parts such as breast or lung, after proper re-training of the classification algorithms.

ePMV embeds molecular modeling into professional animation software environments.

PubMed

Johnson, Graham T; Autin, Ludovic; Goodsell, David S; Sanner, Michel F; Olson, Arthur J

2011-03-09

Increasingly complex research has made it more difficult to prepare data for publication, education, and outreach. Many scientists must also wade through black-box code to interface computational algorithms from diverse sources to supplement their bench work. To reduce these barriers we have developed an open-source plug-in, embedded Python Molecular Viewer (ePMV), that runs molecular modeling software directly inside of professional 3D animation applications (hosts) to provide simultaneous access to the capabilities of these newly connected systems. Uniting host and scientific algorithms into a single interface allows users from varied backgrounds to assemble professional quality visuals and to perform computational experiments with relative ease. By enabling easy exchange of algorithms, ePMV can facilitate interdisciplinary research, smooth communication between broadly diverse specialties, and provide a common platform to frame and visualize the increasingly detailed intersection(s) of cellular and molecular biology. Copyright © 2011 Elsevier Ltd. All rights reserved.

ePMV Embeds Molecular Modeling into Professional Animation Software Environments

PubMed Central

Johnson, Graham T.; Autin, Ludovic; Goodsell, David S.; Sanner, Michel F.; Olson, Arthur J.

2011-01-01

SUMMARY Increasingly complex research has made it more difficult to prepare data for publication, education, and outreach. Many scientists must also wade through black-box code to interface computational algorithms from diverse sources to supplement their bench work. To reduce these barriers, we have developed an open-source plug-in, embedded Python Molecular Viewer (ePMV), that runs molecular modeling software directly inside of professional 3D animation applications (hosts) to provide simultaneous access to the capabilities of these newly connected systems. Uniting host and scientific algorithms into a single interface allows users from varied backgrounds to assemble professional quality visuals and to perform computational experiments with relative ease. By enabling easy exchange of algorithms, ePMV can facilitate interdisciplinary research, smooth communication between broadly diverse specialties and provide a common platform to frame and visualize the increasingly detailed intersection(s) of cellular and molecular biology. PMID:21397181

ATLAS Live: Collaborative Information Streams

NASA Astrophysics Data System (ADS)

Goldfarb, Steven; ATLAS Collaboration

2011-12-01

I report on a pilot project launched in 2010 focusing on facilitating communication and information exchange within the ATLAS Collaboration, through the combination of digital signage software and webcasting. The project, called ATLAS Live, implements video streams of information, ranging from detailed detector and data status to educational and outreach material. The content, including text, images, video and audio, is collected, visualised and scheduled using digital signage software. The system is robust and flexible, utilizing scripts to input data from remote sources, such as the CERN Document Server, Indico, or any available URL, and to integrate these sources into professional-quality streams, including text scrolling, transition effects, inter and intra-screen divisibility. Information is published via the encoding and webcasting of standard video streams, viewable on all common platforms, using a web browser or other common video tool. Authorisation is enforced at the level of the streaming and at the web portals, using the CERN SSO system.

Building Energy Management Open Source Software

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

Rahman, Saifur

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

Integrated Design and Implementation of Embedded Control Systems with Scilab

PubMed Central

Ma, Longhua; Xia, Feng; Peng, Zhe

2008-01-01

Embedded systems are playing an increasingly important role in control engineering. Despite their popularity, embedded systems are generally subject to resource constraints and it is therefore difficult to build complex control systems on embedded platforms. Traditionally, the design and implementation of control systems are often separated, which causes the development of embedded control systems to be highly time-consuming and costly. To address these problems, this paper presents a low-cost, reusable, reconfigurable platform that enables integrated design and implementation of embedded control systems. To minimize the cost, free and open source software packages such as Linux and Scilab are used. Scilab is ported to the embedded ARM-Linux system. The drivers for interfacing Scilab with several communication protocols including serial, Ethernet, and Modbus are developed. Experiments are conducted to test the developed embedded platform. The use of Scilab enables implementation of complex control algorithms on embedded platforms. With the developed platform, it is possible to perform all phases of the development cycle of embedded control systems in a unified environment, thus facilitating the reduction of development time and cost. PMID:27873827

Integrated Design and Implementation of Embedded Control Systems with Scilab.

PubMed

Ma, Longhua; Xia, Feng; Peng, Zhe

2008-09-05

Embedded systems are playing an increasingly important role in control engineering. Despite their popularity, embedded systems are generally subject to resource constraints and it is therefore difficult to build complex control systems on embedded platforms. Traditionally, the design and implementation of control systems are often separated, which causes the development of embedded control systems to be highly timeconsuming and costly. To address these problems, this paper presents a low-cost, reusable, reconfigurable platform that enables integrated design and implementation of embedded control systems. To minimize the cost, free and open source software packages such as Linux and Scilab are used. Scilab is ported to the embedded ARM-Linux system. The drivers for interfacing Scilab with several communication protocols including serial, Ethernet, and Modbus are developed. Experiments are conducted to test the developed embedded platform. The use of Scilab enables implementation of complex control algorithms on embedded platforms. With the developed platform, it is possible to perform all phases of the development cycle of embedded control systems in a unified environment, thus facilitating the reduction of development time and cost.

Framework Programmable Platform for the advanced software development workstation: Framework processor design document

NASA Technical Reports Server (NTRS)

Mayer, Richard J.; Blinn, Thomas M.; Mayer, Paula S. D.; Ackley, Keith A.; Crump, Wes; Sanders, Les

1991-01-01

The design of the Framework Processor (FP) component of the Framework Programmable Software Development Platform (FFP) is described. The FFP is a project aimed at combining effective tool and data integration mechanisms with a model of the software development process in an intelligent integrated software development environment. Guided by the model, this Framework Processor will take advantage of an integrated operating environment to provide automated support for the management and control of the software development process so that costly mistakes during the development phase can be eliminated.

Solar Asset Management Software

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

Iverson, Aaron; Zviagin, George

Ra Power Management (RPM) has developed a cloud based software platform that manages the financial and operational functions of third party financed solar projects throughout their lifecycle. RPM’s software streamlines and automates the sales, financing, and management of a portfolio of solar assets. The software helps solar developers automate the most difficult aspects of asset management, leading to increased transparency, efficiency, and reduction in human error. More importantly, our platform will help developers save money by improving their operating margins.

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

PubMed

Ratib, Osman; Rosset, Antoine; Heuberger, Joris

2011-05-01

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

Integrating Distributed Interactive Simulations With the Project Darkstar Open-Source Massively Multiplayer Online Game (MMOG) Middleware

DTIC Science & Technology

2009-09-01

be complete MMOG solutions such as Multiverse are not within the scope of this thesis, though it is recommended that readers compare this type of...software to the middleware described here ( Multiverse , 2009). 1. University of Munster: Real-Time Framework The Real-Time Framework (RTF) project is...10, 2009, from http://wiki.secondlife.com/wiki/MMOX Multiverse . (2009). Multiverse platform architecture. Retrieved September 9, 2009, from http

CGI: Java Software for Mapping and Visualizing Data from Array-based Comparative Genomic Hybridization and Expression Profiling

PubMed Central

Gu, Joyce Xiuweu-Xu; Wei, Michael Yang; Rao, Pulivarthi H.; Lau, Ching C.; Behl, Sanjiv; Man, Tsz-Kwong

2007-01-01

With the increasing application of various genomic technologies in biomedical research, there is a need to integrate these data to correlate candidate genes/regions that are identified by different genomic platforms. Although there are tools that can analyze data from individual platforms, essential software for integration of genomic data is still lacking. Here, we present a novel Java-based program called CGI (Cytogenetics-Genomics Integrator) that matches the BAC clones from array-based comparative genomic hybridization (aCGH) to genes from RNA expression profiling datasets. The matching is computed via a fast, backend MySQL database containing UCSC Genome Browser annotations. This program also provides an easy-to-use graphical user interface for visualizing and summarizing the correlation of DNA copy number changes and RNA expression patterns from a set of experiments. In addition, CGI uses a Java applet to display the copy number values of a specific BAC clone in aCGH experiments side by side with the expression levels of genes that are mapped back to that BAC clone from the microarray experiments. The CGI program is built on top of extensible, reusable graphic components specifically designed for biologists. It is cross-platform compatible and the source code is freely available under the General Public License. PMID:19936083

CGI: Java software for mapping and visualizing data from array-based comparative genomic hybridization and expression profiling.

PubMed

Gu, Joyce Xiuweu-Xu; Wei, Michael Yang; Rao, Pulivarthi H; Lau, Ching C; Behl, Sanjiv; Man, Tsz-Kwong

2007-10-06

With the increasing application of various genomic technologies in biomedical research, there is a need to integrate these data to correlate candidate genes/regions that are identified by different genomic platforms. Although there are tools that can analyze data from individual platforms, essential software for integration of genomic data is still lacking. Here, we present a novel Java-based program called CGI (Cytogenetics-Genomics Integrator) that matches the BAC clones from array-based comparative genomic hybridization (aCGH) to genes from RNA expression profiling datasets. The matching is computed via a fast, backend MySQL database containing UCSC Genome Browser annotations. This program also provides an easy-to-use graphical user interface for visualizing and summarizing the correlation of DNA copy number changes and RNA expression patterns from a set of experiments. In addition, CGI uses a Java applet to display the copy number values of a specific BAC clone in aCGH experiments side by side with the expression levels of genes that are mapped back to that BAC clone from the microarray experiments. The CGI program is built on top of extensible, reusable graphic components specifically designed for biologists. It is cross-platform compatible and the source code is freely available under the General Public License.

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.

FInd Gas Source

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

Travis, Bryan; Sauer, Jeremy; Dubey, Manvendra

2017-02-24

FIGS is a neural network software that ingests real time synchronized field data on environmental flow fields and turbulence and gas concentration variations at high frequency and uses an error minimization algorithm to locate the gas source and quantify its strength. The software can be interfaced with atmospheric, oceanic and subsurface instruments in a variety of platforms stationary or mobile (e.g. cars, UAVs, submersible vehicles or boreholes) and used to find gas sources by smart use of data and phenomenology. FIGS can be trained by phenomenological model of the flow fields in the environment of interest and/or be calibrated bymore » controlled release. After initial deployment the FIGS learning will grow with time as it accumulates data on source quantification. FIGS can be installed on any computer from small beagle-bones for field deployment/end-use to PC/MACs/main-frame for training/analysis. FIGS has been trained (using LANL's high resolution atmospheric simulations) and calibrated, tested and evaluated in the field and shown to perform well in finding and quantifying methane leaks at 10-100m scales at well pads by ingesting atmospheric measurements. The code is applicable to gas and particle source location at large scales.« less

Building a virtual simulation platform for quasistatic breast ultrasound elastography using open source software: A preliminary investigation.

PubMed

Wang, Yu; Helminen, Emily; Jiang, Jingfeng

2015-09-01

Quasistatic ultrasound elastography (QUE) is being used to augment in vivo characterization of breast lesions. Results from early clinical trials indicated that there was a lack of confidence in image interpretation. Such confidence can only be gained through rigorous imaging tests using complex, heterogeneous but known media. The objective of this study is to build a virtual breast QUE simulation platform in the public domain that can be used not only for innovative QUE research but also for rigorous imaging tests. The main thrust of this work is to streamline biomedical ultrasound simulations by leveraging existing open source software packages including Field II (ultrasound simulator), VTK (geometrical visualization and processing), FEBio [finite element (FE) analysis], and Tetgen (mesh generator). However, integration of these open source packages is nontrivial and requires interdisciplinary knowledge. In the first step, a virtual breast model containing complex anatomical geometries was created through a novel combination of image-based landmark structures and randomly distributed (small) structures. Image-based landmark structures were based on data from the NIH Visible Human Project. Subsequently, an unstructured FE-mesh was created by Tetgen. In the second step, randomly positioned point scatterers were placed within the meshed breast model through an octree-based algorithm to make a virtual breast ultrasound phantom. In the third step, an ultrasound simulator (Field II) was used to interrogate the virtual breast phantom to obtain simulated ultrasound echo data. Of note, tissue deformation generated using a FE-simulator (FEBio) was the basis of deforming the original virtual breast phantom in order to obtain the postdeformation breast phantom for subsequent ultrasound simulations. Using the procedures described above, a full cycle of QUE simulations involving complex and highly heterogeneous virtual breast phantoms can be accomplished for the first time. Representative examples were used to demonstrate capabilities of this virtual simulation platform. In the first set of three ultrasound simulation examples, three heterogeneous volumes of interest were selected from a virtual breast ultrasound phantom to perform sophisticated ultrasound simulations. These resultant B-mode images realistically represented the underlying complex but known media. In the second set of three QUE examples, advanced applications in QUE were simulated. The first QUE example was to show breast tumors with complex shapes and/or compositions. The resultant strain images showed complex patterns that were normally seen in freehand clinical ultrasound data. The second and third QUE examples demonstrated (deformation-dependent) nonlinear strain imaging and time-dependent strain imaging, respectively. The proposed virtual QUE platform was implemented and successfully tested in this study. Through show-case examples, the proposed work has demonstrated its capabilities of creating sophisticated QUE data in a way that cannot be done through the manufacture of physical tissue-mimicking phantoms and other software. This open software architecture will soon be made available in the public domain and can be readily adapted to meet specific needs of different research groups to drive innovations in QUE.

Software platform for simulation of a prototype proton CT scanner.

PubMed

Giacometti, Valentina; Bashkirov, Vladimir A; Piersimoni, Pierluigi; Guatelli, Susanna; Plautz, Tia E; Sadrozinski, Hartmut F-W; Johnson, Robert P; Zatserklyaniy, Andriy; Tessonnier, Thomas; Parodi, Katia; Rosenfeld, Anatoly B; Schulte, Reinhard W

2017-03-01

Proton computed tomography (pCT) is a promising imaging technique to substitute or at least complement x-ray CT for more accurate proton therapy treatment planning as it allows calculating directly proton relative stopping power from proton energy loss measurements. A proton CT scanner with a silicon-based particle tracking system and a five-stage scintillating energy detector has been completed. In parallel a modular software platform was developed to characterize the performance of the proposed pCT. The modular pCT software platform consists of (1) a Geant4-based simulation modeling the Loma Linda proton therapy beam line and the prototype proton CT scanner, (2) water equivalent path length (WEPL) calibration of the scintillating energy detector, and (3) image reconstruction algorithm for the reconstruction of the relative stopping power (RSP) of the scanned object. In this work, each component of the modular pCT software platform is described and validated with respect to experimental data and benchmarked against theoretical predictions. In particular, the RSP reconstruction was validated with both experimental scans, water column measurements, and theoretical calculations. The results show that the pCT software platform accurately reproduces the performance of the existing prototype pCT scanner with a RSP agreement between experimental and simulated values to better than 1.5%. The validated platform is a versatile tool for clinical proton CT performance and application studies in a virtual setting. The platform is flexible and can be modified to simulate not yet existing versions of pCT scanners and higher proton energies than those currently clinically available. © 2017 American Association of Physicists in Medicine.

Thermal Analysis for Monitoring Effects of Shock-Induced Physical, Mechanical, and Chemical Changes in Materials

DTIC Science & Technology

2015-01-19

MS WINDOWS platform, which enables multitasking with simultaneous evaluation and operation 1. REPORT DATE (DD-MM-YYYY) 4. TITLE AND SUBTITLE 13...measurement and analysis software for data acquisition, storage and evaluation with MS WINDOWS platform, which enables multitasking with simultaneous...Proteus measurement and analysis software for data acquisition, storage and evaluation with MS WINDOWS platform, which enables multitasking with

Design, Fabrication, and Testing of a Hopper Spacecraft Simulator

NASA Astrophysics Data System (ADS)

Mucasey, Evan Phillip Krell

A robust test bed is needed to facilitate future development of guidance, navigation, and control software for future vehicles capable of vertical takeoff and landings. Specifically, this work aims to develop both a hardware and software simulator that can be used for future flight software development for extra-planetary vehicles. To achieve the program requirements of a high thrust to weight ratio with large payload capability, the vehicle is designed to have a novel combination of electric motors and a micro jet engine is used to act as the propulsion elements. The spacecraft simulator underwent several iterations of hardware development using different materials and fabrication methods. The final design used a combination of carbon fiber and fiberglass that was cured under vacuum to serve as the frame of the vehicle which provided a strong, lightweight platform for all flight components and future payloads. The vehicle also uses an open source software development platform, Arduino, to serve as the initial flight computer and has onboard accelerometers, gyroscopes, and magnetometers to sense the vehicles attitude. To prevent instability due to noise, a polynomial kalman filter was designed and this fed the sensed angles and rates into a robust attitude controller which autonomously control the vehicle' s yaw, pitch, and roll angles. In addition to the hardware development of the vehicle itself, both a software simulation and a real time data acquisition interface was written in MATLAB/SIMULINK so that real flight data could be taken and then correlated to the simulation to prove the accuracy of the analytical model. In result, the full scale vehicle was designed and own outside of the lab environment and data showed that the software model accurately predicted the flight dynamics of the vehicle.

Architecture for the Next Generation System Management Tools

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

Gallard, Jerome; Lebre, I Adrien; Morin, Christine

2011-01-01

To get more results or greater accuracy, computational scientists execute their applications on distributed computing platforms such as Clusters, Grids and Clouds. These platforms are different in terms of hardware and software resources as well as locality: some span across multiple sites and multiple administrative domains whereas others are limited to a single site/domain. As a consequence, in order to scale their applica- tions up the scientists have to manage technical details for each target platform. From our point of view, this complexity should be hidden from the scientists who, in most cases, would prefer to focus on their researchmore » rather than spending time dealing with platform configuration concerns. In this article, we advocate for a system management framework that aims to automatically setup the whole run-time environment according to the applications needs. The main difference with regards to usual approaches is that they generally only focus on the software layer whereas we address both the hardware and the software expecta- tions through a unique system. For each application, scientists describe their requirements through the definition of a Virtual Platform (VP) and a Virtual System Environment (VSE). Relying on the VP/VSE definitions, the framework is in charge of: (i) the configuration of the physical infrastructure to satisfy the VP requirements, (ii) the setup of the VP, and (iii) the customization of the execution environment (VSE) upon the former VP. We propose a new formalism that the system can rely upon to successfully perform each of these three steps without burdening the user with the specifics of the configuration for the physical resources, and system management tools. This formalism leverages Goldberg s theory for recursive virtual machines by introducing new concepts based on system virtualization (identity, partitioning, aggregation) and emulation (simple, abstraction). This enables the definition of complex VP/VSE configurations without making assumptions about the hardware and the software re- sources. For each requirement, the system executes the corresponding operation with the appropriate management tool. As a proof of concept, we implemented a first prototype that currently interacts with several system management tools (e.g., OSCAR, the Grid 5000 toolkit, and XtreemOS) and that can be easily extended to integrate new resource brokers or cloud systems such as Nimbus, OpenNebula or Eucalyptus for instance.« less

HTML5 PivotViewer: high-throughput visualization and querying of image data on the web

PubMed Central

Taylor, Stephen; Noble, Roger

2014-01-01

Motivation: Visualization and analysis of large numbers of biological images has generated a bottle neck in research. We present HTML5 PivotViewer, a novel, open source, platform-independent viewer making use of the latest web technologies that allows seamless access to images and associated metadata for each image. This provides a powerful method to allow end users to mine their data. Availability and implementation: Documentation, examples and links to the software are available from http://www.cbrg.ox.ac.uk/data/pivotviewer/. The software is licensed under GPLv2. Contact:  stephen.taylor@imm.ox.ac.uk and roger@coritsu.com PMID:24849578

Ethoscopes: An open platform for high-throughput ethomics

PubMed Central

Geissmann, Quentin; Garcia Rodriguez, Luis; Beckwith, Esteban J.; French, Alice S.; Jamasb, Arian R.

2017-01-01

Here, we present the use of ethoscopes, which are machines for high-throughput analysis of behavior in Drosophila and other animals. Ethoscopes provide a software and hardware solution that is reproducible and easily scalable. They perform, in real-time, tracking and profiling of behavior by using a supervised machine learning algorithm, are able to deliver behaviorally triggered stimuli to flies in a feedback-loop mode, and are highly customizable and open source. Ethoscopes can be built easily by using 3D printing technology and rely on Raspberry Pi microcomputers and Arduino boards to provide affordable and flexible hardware. All software and construction specifications are available at http://lab.gilest.ro/ethoscope. PMID:29049280

HEPData: a repository for high energy physics data

NASA Astrophysics Data System (ADS)

Maguire, Eamonn; Heinrich, Lukas; Watt, Graeme

2017-10-01

The Durham High Energy Physics Database (HEPData) has been built up over the past four decades as a unique open-access repository for scattering data from experimental particle physics papers. It comprises data points underlying several thousand publications. Over the last two years, the HEPData software has been completely rewritten using modern computing technologies as an overlay on the Invenio v3 digital library framework. The software is open source with the new site available at https://hepdata.net now replacing the previous site at http://hepdata.cedar.ac.uk. In this write-up, we describe the development of the new site and explain some of the advantages it offers over the previous platform.

FAIMS Mobile: Flexible, open-source software for field research

NASA Astrophysics Data System (ADS)

Ballsun-Stanton, Brian; Ross, Shawn A.; Sobotkova, Adela; Crook, Penny

2018-01-01

FAIMS Mobile is a native Android application supported by an Ubuntu server facilitating human-mediated field research across disciplines. It consists of 'core' Java and Ruby software providing a platform for data capture, which can be deeply customised using 'definition packets' consisting of XML documents (data schema and UI) and Beanshell scripts (automation). Definition packets can also be generated using an XML-based domain-specific language, making customisation easier. FAIMS Mobile includes features allowing rich and efficient data capture tailored to the needs of fieldwork. It also promotes synthetic research and improves transparency and reproducibility through the production of comprehensive datasets that can be mapped to vocabularies or ontologies as they are created.

Quality control, analysis and secure sharing of Luminex® immunoassay data using the open source LabKey Server platform

PubMed Central

2013-01-01

Background Immunoassays that employ multiplexed bead arrays produce high information content per sample. Such assays are now frequently used to evaluate humoral responses in clinical trials. Integrated software is needed for the analysis, quality control, and secure sharing of the high volume of data produced by such multiplexed assays. Software that facilitates data exchange and provides flexibility to perform customized analyses (including multiple curve fits and visualizations of assay performance over time) could increase scientists’ capacity to use these immunoassays to evaluate human clinical trials. Results The HIV Vaccine Trials Network and the Statistical Center for HIV/AIDS Research and Prevention collaborated with LabKey Software to enhance the open source LabKey Server platform to facilitate workflows for multiplexed bead assays. This system now supports the management, analysis, quality control, and secure sharing of data from multiplexed immunoassays that leverage Luminex xMAP® technology. These assays may be custom or kit-based. Newly added features enable labs to: (i) import run data from spreadsheets output by Bio-Plex Manager™ software; (ii) customize data processing, curve fits, and algorithms through scripts written in common languages, such as R; (iii) select script-defined calculation options through a graphical user interface; (iv) collect custom metadata for each titration, analyte, run and batch of runs; (v) calculate dose–response curves for titrations; (vi) interpolate unknown concentrations from curves for titrated standards; (vii) flag run data for exclusion from analysis; (viii) track quality control metrics across runs using Levey-Jennings plots; and (ix) automatically flag outliers based on expected values. Existing system features allow researchers to analyze, integrate, visualize, export and securely share their data, as well as to construct custom user interfaces and workflows. Conclusions Unlike other tools tailored for Luminex immunoassays, LabKey Server allows labs to customize their Luminex analyses using scripting while still presenting users with a single, graphical interface for processing and analyzing data. The LabKey Server system also stands out among Luminex tools for enabling smooth, secure transfer of data, quality control information, and analyses between collaborators. LabKey Server and its Luminex features are freely available as open source software at http://www.labkey.com under the Apache 2.0 license. PMID:23631706

Quality control, analysis and secure sharing of Luminex® immunoassay data using the open source LabKey Server platform.

PubMed

Eckels, Josh; Nathe, Cory; Nelson, Elizabeth K; Shoemaker, Sara G; Nostrand, Elizabeth Van; Yates, Nicole L; Ashley, Vicki C; Harris, Linda J; Bollenbeck, Mark; Fong, Youyi; Tomaras, Georgia D; Piehler, Britt

2013-04-30

Immunoassays that employ multiplexed bead arrays produce high information content per sample. Such assays are now frequently used to evaluate humoral responses in clinical trials. Integrated software is needed for the analysis, quality control, and secure sharing of the high volume of data produced by such multiplexed assays. Software that facilitates data exchange and provides flexibility to perform customized analyses (including multiple curve fits and visualizations of assay performance over time) could increase scientists' capacity to use these immunoassays to evaluate human clinical trials. The HIV Vaccine Trials Network and the Statistical Center for HIV/AIDS Research and Prevention collaborated with LabKey Software to enhance the open source LabKey Server platform to facilitate workflows for multiplexed bead assays. This system now supports the management, analysis, quality control, and secure sharing of data from multiplexed immunoassays that leverage Luminex xMAP® technology. These assays may be custom or kit-based. Newly added features enable labs to: (i) import run data from spreadsheets output by Bio-Plex Manager™ software; (ii) customize data processing, curve fits, and algorithms through scripts written in common languages, such as R; (iii) select script-defined calculation options through a graphical user interface; (iv) collect custom metadata for each titration, analyte, run and batch of runs; (v) calculate dose-response curves for titrations; (vi) interpolate unknown concentrations from curves for titrated standards; (vii) flag run data for exclusion from analysis; (viii) track quality control metrics across runs using Levey-Jennings plots; and (ix) automatically flag outliers based on expected values. Existing system features allow researchers to analyze, integrate, visualize, export and securely share their data, as well as to construct custom user interfaces and workflows. Unlike other tools tailored for Luminex immunoassays, LabKey Server allows labs to customize their Luminex analyses using scripting while still presenting users with a single, graphical interface for processing and analyzing data. The LabKey Server system also stands out among Luminex tools for enabling smooth, secure transfer of data, quality control information, and analyses between collaborators. LabKey Server and its Luminex features are freely available as open source software at http://www.labkey.com under the Apache 2.0 license.

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

3D Slicer as an Image Computing Platform for the Quantitative Imaging Network

PubMed Central

Fedorov, Andriy; Beichel, Reinhard; Kalpathy-Cramer, Jayashree; Finet, Julien; Fillion-Robin, Jean-Christophe; Pujol, Sonia; Bauer, Christian; Jennings, Dominique; Fennessy, Fiona; Sonka, Milan; Buatti, John; Aylward, Stephen; Miller, James V.; Pieper, Steve; Kikinis, Ron

2012-01-01

Quantitative analysis has tremendous but mostly unrealized potential in healthcare to support objective and accurate interpretation of the clinical imaging. In 2008, the National Cancer Institute began building the Quantitative Imaging Network (QIN) initiative with the goal of advancing quantitative imaging in the context of personalized therapy and evaluation of treatment response. Computerized analysis is an important component contributing to reproducibility and efficiency of the quantitative imaging techniques. The success of quantitative imaging is contingent on robust analysis methods and software tools to bring these methods from bench to bedside. 3D Slicer is a free open source software application for medical image computing. As a clinical research tool, 3D Slicer is similar to a radiology workstation that supports versatile visualizations but also provides advanced functionality such as automated segmentation and registration for a variety of application domains. Unlike a typical radiology workstation, 3D Slicer is free and is not tied to specific hardware. As a programming platform, 3D Slicer facilitates translation and evaluation of the new quantitative methods by allowing the biomedical researcher to focus on the implementation of the algorithm, and providing abstractions for the common tasks of data communication, visualization and user interface development. Compared to other tools that provide aspects of this functionality, 3D Slicer is fully open source and can be readily extended and redistributed. In addition, 3D Slicer is designed to facilitate the development of new functionality in the form of 3D Slicer extensions. In this paper, we present an overview of 3D Slicer as a platform for prototyping, development and evaluation of image analysis tools for clinical research applications. To illustrate the utility of the platform in the scope of QIN, we discuss several use cases of 3D Slicer by the existing QIN teams, and we elaborate on the future directions that can further facilitate development and validation of imaging biomarkers using 3D Slicer. PMID:22770690

A mass spectrometry proteomics data management platform.

PubMed

Sharma, Vagisha; Eng, Jimmy K; Maccoss, Michael J; Riffle, Michael

2012-09-01

Mass spectrometry-based proteomics is increasingly being used in biomedical research. These experiments typically generate a large volume of highly complex data, and the volume and complexity are only increasing with time. There exist many software pipelines for analyzing these data (each typically with its own file formats), and as technology improves, these file formats change and new formats are developed. Files produced from these myriad software programs may accumulate on hard disks or tape drives over time, with older files being rendered progressively more obsolete and unusable with each successive technical advancement and data format change. Although initiatives exist to standardize the file formats used in proteomics, they do not address the core failings of a file-based data management system: (1) files are typically poorly annotated experimentally, (2) files are "organically" distributed across laboratory file systems in an ad hoc manner, (3) files formats become obsolete, and (4) searching the data and comparing and contrasting results across separate experiments is very inefficient (if possible at all). Here we present a relational database architecture and accompanying web application dubbed Mass Spectrometry Data Platform that is designed to address the failings of the file-based mass spectrometry data management approach. The database is designed such that the output of disparate software pipelines may be imported into a core set of unified tables, with these core tables being extended to support data generated by specific pipelines. Because the data are unified, they may be queried, viewed, and compared across multiple experiments using a common web interface. Mass Spectrometry Data Platform is open source and freely available at http://code.google.com/p/msdapl/.

Architecture and Implementation of OpenPET Firmware and Embedded Software

DOE PAGES

Abu-Nimeh, Faisal T.; Ito, Jennifer; Moses, William W.; ...

2016-01-11

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

An Open Software Platform for Sharing Water Resource Models, Code and Data

NASA Astrophysics Data System (ADS)

Knox, Stephen; Meier, Philipp; Mohamed, Khaled; Korteling, Brett; Matrosov, Evgenii; Huskova, Ivana; Harou, Julien; Rosenberg, David; Tilmant, Amaury; Medellin-Azuara, Josue; Wicks, Jon

2016-04-01

The modelling of managed water resource systems requires new approaches in the face of increasing future uncertainty. Water resources management models, even if applied to diverse problem areas, use common approaches such as representing the problem as a network of nodes and links. We propose a data management software platform, called Hydra, that uses this commonality to allow multiple models using a node-link structure to be managed and run using a single software system. Hydra's user interface allows users to manage network topology and associated data. Hydra feeds this data directly into a model, importing from and exporting to different file formats using Apps. An App connects Hydra to a custom model, a modelling system such as GAMS or MATLAB or to different file formats such as MS Excel, CSV and ESRI Shapefiles. Hydra allows users to manage their data in a single, consistent place. Apps can be used to run domain-specific models and allow users to work with their own required file formats. The Hydra App Store offers a collaborative space where model developers can publish, review and comment on Apps, models and data. Example Apps and open-source libraries are available in a variety of languages (Python, Java and .NET). The App Store can act as a hub for water resource modellers to view and share Apps, models and data easily. This encourages an ecosystem of development using a shared platform, resulting in more model integration and potentially greater unity within resource modelling communities. www.hydraplatform.org www.hydraappstore.com

GiNA, an Efficient and High-Throughput Software for Horticultural Phenotyping

PubMed Central

Diaz-Garcia, Luis; Covarrubias-Pazaran, Giovanny; Schlautman, Brandon; Zalapa, Juan

2016-01-01

Traditional methods for trait phenotyping have been a bottleneck for research in many crop species due to their intensive labor, high cost, complex implementation, lack of reproducibility and propensity to subjective bias. Recently, multiple high-throughput phenotyping platforms have been developed, but most of them are expensive, species-dependent, complex to use, and available only for major crops. To overcome such limitations, we present the open-source software GiNA, which is a simple and free tool for measuring horticultural traits such as shape- and color-related parameters of fruits, vegetables, and seeds. GiNA is multiplatform software available in both R and MATLAB® programming languages and uses conventional images from digital cameras with minimal requirements. It can process up to 11 different horticultural morphological traits such as length, width, two-dimensional area, volume, projected skin, surface area, RGB color, among other parameters. Different validation tests produced highly consistent results under different lighting conditions and camera setups making GiNA a very reliable platform for high-throughput phenotyping. In addition, five-fold cross validation between manually generated and GiNA measurements for length and width in cranberry fruits were 0.97 and 0.92. In addition, the same strategy yielded prediction accuracies above 0.83 for color estimates produced from images of cranberries analyzed with GiNA compared to total anthocyanin content (TAcy) of the same fruits measured with the standard methodology of the industry. Our platform provides a scalable, easy-to-use and affordable tool for massive acquisition of phenotypic data of fruits, seeds, and vegetables. PMID:27529547

GiNA, an Efficient and High-Throughput Software for Horticultural Phenotyping.

PubMed

Diaz-Garcia, Luis; Covarrubias-Pazaran, Giovanny; Schlautman, Brandon; Zalapa, Juan

2016-01-01

Traditional methods for trait phenotyping have been a bottleneck for research in many crop species due to their intensive labor, high cost, complex implementation, lack of reproducibility and propensity to subjective bias. Recently, multiple high-throughput phenotyping platforms have been developed, but most of them are expensive, species-dependent, complex to use, and available only for major crops. To overcome such limitations, we present the open-source software GiNA, which is a simple and free tool for measuring horticultural traits such as shape- and color-related parameters of fruits, vegetables, and seeds. GiNA is multiplatform software available in both R and MATLAB® programming languages and uses conventional images from digital cameras with minimal requirements. It can process up to 11 different horticultural morphological traits such as length, width, two-dimensional area, volume, projected skin, surface area, RGB color, among other parameters. Different validation tests produced highly consistent results under different lighting conditions and camera setups making GiNA a very reliable platform for high-throughput phenotyping. In addition, five-fold cross validation between manually generated and GiNA measurements for length and width in cranberry fruits were 0.97 and 0.92. In addition, the same strategy yielded prediction accuracies above 0.83 for color estimates produced from images of cranberries analyzed with GiNA compared to total anthocyanin content (TAcy) of the same fruits measured with the standard methodology of the industry. Our platform provides a scalable, easy-to-use and affordable tool for massive acquisition of phenotypic data of fruits, seeds, and vegetables.

cPath: open source software for collecting, storing, and querying biological pathways

PubMed Central

Cerami, Ethan G; Bader, Gary D; Gross, Benjamin E; Sander, Chris

2006-01-01

Background Biological pathways, including metabolic pathways, protein interaction networks, signal transduction pathways, and gene regulatory networks, are currently represented in over 220 diverse databases. These data are crucial for the study of specific biological processes, including human diseases. Standard exchange formats for pathway information, such as BioPAX, CellML, SBML and PSI-MI, enable convenient collection of this data for biological research, but mechanisms for common storage and communication are required. Results We have developed cPath, an open source database and web application for collecting, storing, and querying biological pathway data. cPath makes it easy to aggregate custom pathway data sets available in standard exchange formats from multiple databases, present pathway data to biologists via a customizable web interface, and export pathway data via a web service to third-party software, such as Cytoscape, for visualization and analysis. cPath is software only, and does not include new pathway information. Key features include: a built-in identifier mapping service for linking identical interactors and linking to external resources; built-in support for PSI-MI and BioPAX standard pathway exchange formats; a web service interface for searching and retrieving pathway data sets; and thorough documentation. The cPath software is freely available under the LGPL open source license for academic and commercial use. Conclusion cPath is a robust, scalable, modular, professional-grade software platform for collecting, storing, and querying biological pathways. It can serve as the core data handling component in information systems for pathway visualization, analysis and modeling. PMID:17101041

OsiriX: an open-source software for navigating in multidimensional DICOM images.

PubMed

Rosset, Antoine; Spadola, Luca; Ratib, Osman

2004-09-01

A multidimensional image navigation and display software was designed for display and interpretation of large sets of multidimensional and multimodality images such as combined PET-CT studies. The software is developed in Objective-C on a Macintosh platform under the MacOS X operating system using the GNUstep development environment. It also benefits from the extremely fast and optimized 3D graphic capabilities of the OpenGL graphic standard widely used for computer games optimized for taking advantage of any hardware graphic accelerator boards available. In the design of the software special attention was given to adapt the user interface to the specific and complex tasks of navigating through large sets of image data. An interactive jog-wheel device widely used in the video and movie industry was implemented to allow users to navigate in the different dimensions of an image set much faster than with a traditional mouse or on-screen cursors and sliders. The program can easily be adapted for very specific tasks that require a limited number of functions, by adding and removing tools from the program's toolbar and avoiding an overwhelming number of unnecessary tools and functions. The processing and image rendering tools of the software are based on the open-source libraries ITK and VTK. This ensures that all new developments in image processing that could emerge from other academic institutions using these libraries can be directly ported to the OsiriX program. OsiriX is provided free of charge under the GNU open-source licensing agreement at http://homepage.mac.com/rossetantoine/osirix.

A noninvasive technique for real-time detection of bruises in apple surface based on machine vision

NASA Astrophysics Data System (ADS)

Zhao, Juan; Peng, Yankun; Dhakal, Sagar; Zhang, Leilei; Sasao, Akira

2013-05-01

Apple is one of the highly consumed fruit item in daily life. However, due to its high damage potential and massive influence on taste and export, the quality of apple has to be detected before it reaches the consumer's hand. This study was aimed to develop a hardware and software unit for real-time detection of apple bruises based on machine vision technology. The hardware unit consisted of a light shield installed two monochrome cameras at different angles, LED light source to illuminate the sample, and sensors at the entrance of box to signal the positioning of sample. Graphical Users Interface (GUI) was developed in VS2010 platform to control the overall hardware and display the image processing result. The hardware-software system was developed to acquire the images of 3 samples from each camera and display the image processing result in real time basis. An image processing algorithm was developed in Opencv and C++ platform. The software is able to control the hardware system to classify the apple into two grades based on presence/absence of surface bruises with the size of 5mm. The experimental result is promising and the system with further modification can be applicable for industrial production in near future.

Different source image fusion based on FPGA

NASA Astrophysics Data System (ADS)

Luo, Xiao; Piao, Yan

2016-03-01

The fusion technology of video image is to make the video obtained by different image sensors complementary to each other by some technical means, so as to obtain the video information which is rich in information and suitable for the human eye system. Infrared cameras in harsh environments such as when smoke, fog and low light situations penetrating power, but the ability to obtain the details of the image is poor, does not meet the human visual system. Single visible light imaging can be rich in detail, high resolution images and for the visual system, but the visible image easily affected by the external environment. Infrared image and visible image fusion process involved in the video image fusion algorithm complexity and high calculation capacity, have occupied more memory resources, high clock rate requirements, such as software, c ++, c, etc. to achieve more, but based on Hardware platform less. In this paper, based on the imaging characteristics of infrared images and visible light images, the software and hardware are combined to obtain the registration parameters through software matlab, and the gray level weighted average method is used to implement the hardware platform. Information fusion, and finally the fusion image can achieve the goal of effectively improving the acquisition of information to increase the amount of information in the image.

Flexible Software Architecture for Visualization and Seismic Data Analysis

NASA Astrophysics Data System (ADS)

Petunin, S.; Pavlov, I.; Mogilenskikh, D.; Podzyuban, D.; Arkhipov, A.; Baturuin, N.; Lisin, A.; Smith, A.; Rivers, W.; Harben, P.

2007-12-01

Research in the field of seismology requires software and signal processing utilities for seismogram manipulation and analysis. Seismologists and data analysts often encounter a major problem in the use of any particular software application specific to seismic data analysis: the tuning of commands and windows to the specific waveforms and hot key combinations so as to fit their familiar informational environment. The ability to modify the user's interface independently from the developer requires an adaptive code structure. An adaptive code structure also allows for expansion of software capabilities such as new signal processing modules and implementation of more efficient algorithms. Our approach is to use a flexible "open" architecture for development of geophysical software. This report presents an integrated solution for organizing a logical software architecture based on the Unix version of the Geotool software implemented on the Microsoft NET 2.0 platform. Selection of this platform greatly expands the variety and number of computers that can implement the software, including laptops that can be utilized in field conditions. It also facilitates implementation of communication functions for seismic data requests from remote databases through the Internet. The main principle of the new architecture for Geotool is that scientists should be able to add new routines for digital waveform analysis via software plug-ins that utilize the basic Geotool display for GUI interaction. The use of plug-ins allows the efficient integration of diverse signal-processing software, including software still in preliminary development, into an organized platform without changing the fundamental structure of that platform itself. An analyst's use of Geotool is tracked via a metadata file so that future studies can reconstruct, and alter, the original signal processing operations. The work has been completed in the framework of a joint Russian- American project.

Campus Energy Model for Control and Performance Validation

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

2014-09-19

The core of the modeling platform is an extensible block library for the MATLAB/Simulink software suite. The platform enables true co-simulation (interaction at each simulation time step) with NREL's state-of-the-art modeling tools and other energy modeling software.

PRISM Software: Processing and Review Interface for Strong‐Motion Data

USGS Publications Warehouse

Jones, Jeanne M.; Kalkan, Erol; Stephens, Christopher D.; Ng, Peter

2017-01-01

A continually increasing number of high‐quality digital strong‐motion records from stations of the National Strong Motion Project (NSMP) of the U.S. Geological Survey, as well as data from regional seismic networks within the United States, calls for automated processing of strong‐motion records with human review limited to selected significant or flagged records. The NSMP has developed the Processing and Review Interface for Strong Motion data (PRISM) software to meet this need. In combination with the Advanced National Seismic System Quake Monitoring System (AQMS), PRISM automates the processing of strong‐motion records. When used without AQMS, PRISM provides batch‐processing capabilities. The PRISM software is platform independent (coded in Java), open source, and does not depend on any closed‐source or proprietary software. The software consists of two major components: a record processing engine composed of modules for each processing step, and a review tool, which is a graphical user interface for manual review, edit, and processing. To facilitate use by non‐NSMP earthquake engineers and scientists, PRISM (both its processing engine and review tool) is easy to install and run as a stand‐alone system on common operating systems such as Linux, OS X, and Windows. PRISM was designed to be flexible and extensible to accommodate implementation of new processing techniques. All the computing features have been thoroughly tested.

Tethys: A Platform for Water Resources Modeling and Decision Support Apps

NASA Astrophysics Data System (ADS)

Swain, N. R.; Christensen, S. D.; Jones, N.; Nelson, E. J.

2014-12-01

Cloud-based applications or apps are a promising medium through which water resources models and data can be conveyed in a user-friendly environment—making them more accessible to decision-makers and stakeholders. In the context of this work, a water resources web app is a web application that exposes limited modeling functionality for a scenario exploration activity in a structured workflow (e.g.: land use change runoff analysis, snowmelt runoff prediction, and flood potential analysis). The technical expertise required to develop water resources web apps can be a barrier to many potential developers of water resources apps. One challenge that developers face is in providing spatial storage, analysis, and visualization for the spatial data that is inherent to water resources models. The software projects that provide this functionality are non-standard to web development and there are a large number of free and open source software (FOSS) projects to choose from. In addition, it is often required to synthesize several software projects to provide all of the needed functionality. Another challenge for the developer will be orchestrating the use of several software components. Consequently, the initial software development investment required to deploy an effective water resources cloud-based application can be substantial. The Tethys Platform has been developed to lower the technical barrier and minimize the initial development investment that prohibits many scientists and engineers from making use of the web app medium. Tethys synthesizes several software projects including PostGIS for spatial storage, 52°North WPS for spatial analysis, GeoServer for spatial publishing, Google Earth™, Google Maps™ and OpenLayers for spatial visualization, and Highcharts for plotting tabular data. The software selection came after a literature review of software projects being used to create existing earth sciences web apps. All of the software is linked via a Python-powered software development kit (SDK). Tethys developers use the SDK to build their apps and incorporate the needed functionality from the software suite. The presentation will include several apps that have been developed using Tethys to demonstrate its capabilities. Based upon work supported by the National Science Foundation under Grant No. 1135483.

Software project management tools in global software development: a systematic mapping study.

PubMed

Chadli, Saad Yasser; Idri, Ali; Ros, Joaquín Nicolás; Fernández-Alemán, José Luis; de Gea, Juan M Carrillo; Toval, Ambrosio

2016-01-01

Global software development (GSD) which is a growing trend in the software industry is characterized by a highly distributed environment. Performing software project management (SPM) in such conditions implies the need to overcome new limitations resulting from cultural, temporal and geographic separation. The aim of this research is to discover and classify the various tools mentioned in literature that provide GSD project managers with support and to identify in what way they support group interaction. A systematic mapping study has been performed by means of automatic searches in five sources. We have then synthesized the data extracted and presented the results of this study. A total of 102 tools were identified as being used in SPM activities in GSD. We have classified these tools, according to the software life cycle process on which they focus and how they support the 3C collaboration model (communication, coordination and cooperation). The majority of the tools found are standalone tools (77%). A small number of platforms (8%) also offer a set of interacting tools that cover the software development lifecycle. Results also indicate that SPM areas in GSD are not adequately supported by corresponding tools and deserve more attention from tool builders.

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

PubMed

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

2017-10-30

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

Deploying a Route Optimization EFB Application for Commercial Airline Operational Trials

NASA Technical Reports Server (NTRS)

Roscoe, David A.; Vivona, Robert A.; Woods, Sharon E.; Karr, David A.; Wing, David J.

2016-01-01

The Traffic Aware Planner (TAP), developed for NASA Langley Research Center to support the Traffic Aware Strategic Aircrew Requests (TASAR) project, is a flight-efficiency software application developed for an Electronic Flight Bag (EFB). Tested in two flight trials and planned for operational testing by two commercial airlines, TAP is a real-time trajectory optimization application that leverages connectivity with onboard avionics and broadband Internet sources to compute and recommend route modifications to flight crews to improve fuel and time performance. The application utilizes a wide range of data, including Automatic Dependent Surveillance Broadcast (ADS-B) traffic, Flight Management System (FMS) guidance and intent, on-board sensors, published winds and weather, and Special Use Airspace (SUA) schedules. This paper discusses the challenges of developing and deploying TAP to various EFB platforms, our solutions to some of these challenges, and lessons learned, to assist commercial software developers and hardware manufacturers in their efforts to implement and extend TAP functionality in their environments. EFB applications (such as TAP) typically access avionics data via an ARINC 834 Simple Text Avionics Protocol (STAP) server hosted by an Aircraft Interface Device (AID) or other installed hardware. While the protocol is standardized, the data sources, content, and transmission rates can vary from aircraft to aircraft. Additionally, the method of communicating with the AID may vary depending on EFB hardware and/or the availability of onboard networking services, such as Ethernet, WIFI, Bluetooth, or other mechanisms. EFBs with portable and installed components can be implemented using a variety of operating systems, and cockpits are increasingly incorporating tablet-based technologies, further expanding the number of platforms the application may need to support. Supporting multiple EFB platforms, AIDs, avionics datasets, and user interfaces presents a challenge for software developers and the management of their code baselines. Maintaining multiple baselines to support all deployment targets can be extremely cumbersome and expensive. Certification also needs to be considered when developing the application. Regardless of whether the software is itself destined to be certified, data requirements in support of the application and user interface elements may introduce certification requirements for EFB manufacturers and the airlines. The example of TAP, the challenges faced, solutions implemented, and lessons learned will give EFB application and hardware developers insight into future potential requirements in deploying TAP or similar flight-deck EFB applications.

A LabVIEW®-based software for the control of the AUTORAD platform: a fully automated multisequential flow injection analysis Lab-on-Valve (MSFIA-LOV) system for radiochemical analysis.

PubMed

Barbesi, Donato; Vicente Vilas, Víctor; Millet, Sylvain; Sandow, Miguel; Colle, Jean-Yves; Aldave de Las Heras, Laura

2017-01-01

A LabVIEW ® -based software for the control of the fully automated multi-sequential flow injection analysis Lab-on-Valve (MSFIA-LOV) platform AutoRAD performing radiochemical analysis is described. The analytical platform interfaces an Arduino ® -based device triggering multiple detectors providing a flexible and fit for purpose choice of detection systems. The different analytical devices are interfaced to the PC running LabVIEW ® VI software using USB and RS232 interfaces, both for sending commands and receiving confirmation or error responses. The AUTORAD platform has been successfully applied for the chemical separation and determination of Sr, an important fission product pertinent to nuclear waste.

Numerical simulation and experimental verification of extended source interferometer

NASA Astrophysics Data System (ADS)

Hou, Yinlong; Li, Lin; Wang, Shanshan; Wang, Xiao; Zang, Haijun; Zhu, Qiudong

2013-12-01

Extended source interferometer, compared with the classical point source interferometer, can suppress coherent noise of environment and system, decrease dust scattering effects and reduce high-frequency error of reference surface. Numerical simulation and experimental verification of extended source interferometer are discussed in this paper. In order to provide guidance for the experiment, the modeling of the extended source interferometer is realized by using optical design software Zemax. Matlab codes are programmed to rectify the field parameters of the optical system automatically and get a series of interferometric data conveniently. The communication technique of DDE (Dynamic Data Exchange) was used to connect Zemax and Matlab. Then the visibility of interference fringes can be calculated through adding the collected interferometric data. Combined with the simulation, the experimental platform of the extended source interferometer was established, which consists of an extended source, interference cavity and image collection system. The decrease of high-frequency error of reference surface and coherent noise of the environment is verified. The relation between the spatial coherence and the size, shape, intensity distribution of the extended source is also verified through the analysis of the visibility of interference fringes. The simulation result is in line with the result given by real extended source interferometer. Simulation result shows that the model can simulate the actual optical interference of the extended source interferometer quite well. Therefore, the simulation platform can be used to guide the experiment of interferometer which is based on various extended sources.

Upgrades to the Probabilistic NAS Platform Air Traffic Simulation Software

NASA Technical Reports Server (NTRS)

Hunter, George; Boisvert, Benjamin

2013-01-01

This document is the final report for the project entitled "Upgrades to the Probabilistic NAS Platform Air Traffic Simulation Software." This report consists of 17 sections which document the results of the several subtasks of this effort. The Probabilistic NAS Platform (PNP) is an air operations simulation platform developed and maintained by the Saab Sensis Corporation. The improvements made to the PNP simulation include the following: an airborne distributed separation assurance capability, a required time of arrival assignment and conformance capability, and a tactical and strategic weather avoidance capability.

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

Systems biology driven software design for the research enterprise.

PubMed

Boyle, John; Cavnor, Christopher; Killcoyne, Sarah; Shmulevich, Ilya

2008-06-25

In systems biology, and many other areas of research, there is a need for the interoperability of tools and data sources that were not originally designed to be integrated. Due to the interdisciplinary nature of systems biology, and its association with high throughput experimental platforms, there is an additional need to continually integrate new technologies. As scientists work in isolated groups, integration with other groups is rarely a consideration when building the required software tools. We illustrate an approach, through the discussion of a purpose built software architecture, which allows disparate groups to reuse tools and access data sources in a common manner. The architecture allows for: the rapid development of distributed applications; interoperability, so it can be used by a wide variety of developers and computational biologists; development using standard tools, so that it is easy to maintain and does not require a large development effort; extensibility, so that new technologies and data types can be incorporated; and non intrusive development, insofar as researchers need not to adhere to a pre-existing object model. By using a relatively simple integration strategy, based upon a common identity system and dynamically discovered interoperable services, a light-weight software architecture can become the focal point through which scientists can both get access to and analyse the plethora of experimentally derived data.

Conversion of the Aerodynamic Preliminary Analysis System (APAS) to an IBM PC Compatible Format

NASA Technical Reports Server (NTRS)

Kruep, John M.

1995-01-01

The conversion of the Aerodynamic Preliminary Analysis System (APAS) software from a Silicon Graphics UNIX-based platform to a DOS-based IBM PC compatible is discussed. Relevant background information is given, followed by a discussion of the steps taken to accomplish the conversion and a discussion of the type of problems encountered during the conversion. A brief comparison of aerodynamic data obtained using APAS with data from another source is also made.

Programmable Logic Device (PLD) Design Description for the Integrated Power, Avionics, and Software (iPAS) Space Telecommunications Radio System (STRS) Radio

NASA Technical Reports Server (NTRS)

Shalkhauser, Mary Jo W.

2017-01-01

The Space Telecommunications Radio System (STRS) provides a common, consistent framework for software defined radios (SDRs) to abstract the application software from the radio platform hardware. The STRS standard aims to reduce the cost and risk of using complex, configurable and reprogrammable radio systems across NASA missions. To promote the use of the STRS architecture for future NASA advanced exploration missions, NASA Glenn Research Center (GRC) developed an STRS compliant SDR on a radio platform used by the Advance Exploration System program at the Johnson Space Center (JSC) in their Integrated Power, Avionics, and Software (iPAS) laboratory. At the conclusion of the development, the software and hardware description language (HDL) code was delivered to JSC for their use in their iPAS test bed to get hands-on experience with the STRS standard, and for development of their own STRS Waveforms on the now STRS compliant platform.The iPAS STRS Radio was implemented on the Reconfigurable, Intelligently-Adaptive Communication System (RIACS) platform, currently being used for radio development at JSC. The platform consists of a Xilinx ML605 Virtex-6 FPGA board, an Analog Devices FMCOMMS1-EBZ RF transceiver board, and an Embedded PC (Axiomtek eBox 620-110-FL) running the Ubuntu 12.4 operating system. Figure 1 shows the RIACS platform hardware. The result of this development is a very low cost STRS compliant platform that can be used for waveform developments for multiple applications.The purpose of this document is to describe the design of the HDL code for the FPGA portion of the iPAS STRS Radio particularly the design of the FPGA wrapper and the test waveform.

Reducing user error in dipstick urinalysis with a low-cost slipping manifold and mobile phone platform (Conference Presentation)

NASA Astrophysics Data System (ADS)

Smith, Gennifer T.; Dwork, Nicholas; Khan, Saara A.; Millet, Matthew; Magar, Kiran; Javanmard, Mehdi; Bowden, Audrey K.

2017-03-01

Urinalysis dipsticks were designed to revolutionize urine-based medical diagnosis. They are cheap, extremely portable, and have multiple assays patterned on a single platform. They were also meant to be incredibly easy to use. Unfortunately, there are many aspects in both the preparation and the analysis of the dipsticks that are plagued by user error. This high error is one reason that dipsticks have failed to flourish in both the at-home market and in low-resource settings. Sources of error include: inaccurate volume deposition, varying lighting conditions, inconsistent timing measurements, and misinterpreted color comparisons. We introduce a novel manifold and companion software for dipstick urinalysis that eliminates the aforementioned error sources. A micro-volume slipping manifold ensures precise sample delivery, an opaque acrylic box guarantees consistent lighting conditions, a simple sticker-based timing mechanism maintains accurate timing, and custom software that processes video data captured by a mobile phone ensures proper color comparisons. We show that the results obtained with the proposed device are as accurate and consistent as a properly executed dip-and-wipe method, the industry gold-standard, suggesting the potential for this strategy to enable confident urinalysis testing. Furthermore, the proposed all-acrylic slipping manifold is reusable and low in cost, making it a potential solution for at-home users and low-resource settings.

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

PubMed

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

2014-08-01

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

Evolution of a Reconfigurable Processing Platform for a Next Generation Space Software Defined Radio

NASA Technical Reports Server (NTRS)

Kacpura, Thomas J.; Downey, Joseph A.; Anderson, Keffery R.; Baldwin, Keith

2014-01-01

The National Aeronautics and Space Administration (NASA)Harris Ka-Band Software Defined Radio (SDR) is the first, fully reprogrammable space-qualified SDR operating in the Ka-Band frequency range. Providing exceptionally higher data communication rates than previously possible, this SDR offers in-orbit reconfiguration, multi-waveform operation, and fast deployment due to its highly modular hardware and software architecture. Currently in operation on the International Space Station (ISS), this new paradigm of reconfigurable technology is enabling experimenters to investigate navigation and networking in the space environment.The modular SDR and the NASA developed Space Telecommunications Radio System (STRS) architecture standard are the basis for Harris reusable, digital signal processing space platform trademarked as AppSTAR. As a result, two new space radio products are a synthetic aperture radar payload and an Automatic Detection Surveillance Broadcast (ADS-B) receiver. In addition, Harris is currently developing many new products similar to the Ka-Band software defined radio for other applications. For NASAs next generation flight Ka-Band radio development, leveraging these advancements could lead to a more robust and more capable software defined radio.The space environment has special considerations different from terrestrial applications that must be considered for any system operated in space. Each space mission has unique requirements that can make these systems unique. These unique requirements can make products that are expensive and limited in reuse. Space systems put a premium on size, weight and power. A key trade is the amount of reconfigurability in a space system. The more reconfigurable the hardware platform, the easier it is to adapt to the platform to the next mission, and this reduces the amount of non-recurring engineering costs. However, the more reconfigurable platforms often use more spacecraft resources. Software has similar considerations to hardware. Having an architecture standard promotes reuse of software and firmware. Space platforms have limited processor capability, which makes the trade on the amount of amount of flexibility paramount.

Technical Note: PLASTIMATCH MABS, an open source tool for automatic image segmentation

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

Zaffino, Paolo; Spadea, Maria Francesca

Purpose: Multiatlas based segmentation is largely used in many clinical and research applications. Due to its good performances, it has recently been included in some commercial platforms for radiotherapy planning and surgery guidance. Anyway, to date, a software with no restrictions about the anatomical district and image modality is still missing. In this paper we introduce PLASTIMATCH MABS, an open source software that can be used with any image modality for automatic segmentation. Methods: PLASTIMATCH MABS workflow consists of two main parts: (1) an offline phase, where optimal registration and voting parameters are tuned and (2) an online phase, wheremore » a new patient is labeled from scratch by using the same parameters as identified in the former phase. Several registration strategies, as well as different voting criteria can be selected. A flexible atlas selection scheme is also available. To prove the effectiveness of the proposed software across anatomical districts and image modalities, it was tested on two very different scenarios: head and neck (H&N) CT segmentation for radiotherapy application, and magnetic resonance image brain labeling for neuroscience investigation. Results: For the neurological study, minimum dice was equal to 0.76 (investigated structures: left and right caudate, putamen, thalamus, and hippocampus). For head and neck case, minimum dice was 0.42 for the most challenging structures (optic nerves and submandibular glands) and 0.62 for the other ones (mandible, brainstem, and parotid glands). Time required to obtain the labels was compatible with a real clinical workflow (35 and 120 min). Conclusions: The proposed software fills a gap in the multiatlas based segmentation field, since all currently available tools (both for commercial and for research purposes) are restricted to a well specified application. Furthermore, it can be adopted as a platform for exploring MABS parameters and as a reference implementation for comparing against other segmentation algorithms.« less

Reconstructing evolutionary trees in parallel for massive sequences.

PubMed

Zou, Quan; Wan, Shixiang; Zeng, Xiangxiang; Ma, Zhanshan Sam

2017-12-14

Building the evolutionary trees for massive unaligned DNA sequences is challenging and crucial. However, reconstructing evolutionary tree for ultra-large sequences is hard. Massive multiple sequence alignment is also challenging and time/space consuming. Hadoop and Spark are developed recently, which bring spring light for the classical computational biology problems. In this paper, we tried to solve the multiple sequence alignment and evolutionary reconstruction in parallel. HPTree, which is developed in this paper, can deal with big DNA sequence files quickly. It works well on the >1GB files, and gets better performance than other evolutionary reconstruction tools. Users could use HPTree for reonstructing evolutioanry trees on the computer clusters or cloud platform (eg. Amazon Cloud). HPTree could help on population evolution research and metagenomics analysis. In this paper, we employ the Hadoop and Spark platform and design an evolutionary tree reconstruction software tool for unaligned massive DNA sequences. Clustering and multiple sequence alignment are done in parallel. Neighbour-joining model was employed for the evolutionary tree building. We opened our software together with source codes via http://lab.malab.cn/soft/HPtree/ .

Probabilistic consensus scoring improves tandem mass spectrometry peptide identification.

PubMed

Nahnsen, Sven; Bertsch, Andreas; Rahnenführer, Jörg; Nordheim, Alfred; Kohlbacher, Oliver

2011-08-05

Database search is a standard technique for identifying peptides from their tandem mass spectra. To increase the number of correctly identified peptides, we suggest a probabilistic framework that allows the combination of scores from different search engines into a joint consensus score. Central to the approach is a novel method to estimate scores for peptides not found by an individual search engine. This approach allows the estimation of p-values for each candidate peptide and their combination across all search engines. The consensus approach works better than any single search engine across all different instrument types considered in this study. Improvements vary strongly from platform to platform and from search engine to search engine. Compared to the industry standard MASCOT, our approach can identify up to 60% more peptides. The software for consensus predictions is implemented in C++ as part of OpenMS, a software framework for mass spectrometry. The source code is available in the current development version of OpenMS and can easily be used as a command line application or via a graphical pipeline designer TOPPAS.

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.

How Conoco uses GIS technology to map geology, geography through time

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

Foley, D.C.; Ghazi, T.Y.

1995-05-08

Conoco Inc.`s Advanced Exploration Organization (AEO) is in the business of studying foreign sedimentary basins from a regional perspective to evaluate their potential for petroleum exploration. Recently the company decided to focus some of the AEO`s resources on developing a global ranking system for those areas of the world where hydrocarbons might occur. AEO obtained software from the University of Texas, Arlington that rotates continents or portions of continents through time. Using the software, company geoscientists have created a series of maps, known as a PaleoAtlas, that depicts the geography and selected geological features for different periods in Phanerozoic time.more » In addition, the AEO has developed a software package based on ARC/INFO (ESRI Inc., Redlands, Calif.), a commercial GIS platform, to manage, integrate, and analyze those time-slice maps. Entitled PaleoAtlas Geographic Evaluation system (Pages), this software also sequences portions of the maps in a montage effect that geoscientists can use to study the geological evolution of petroleum source rocks. The paper describes the AEO project and its software.« less

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

PubMed

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

2018-03-11

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

New virtual laboratories presenting advanced motion control concepts

NASA Astrophysics Data System (ADS)

Goubej, Martin; Krejčí, Alois; Reitinger, Jan

2015-11-01

The paper deals with development of software framework for rapid generation of remote virtual laboratories. Client-server architecture is chosen in order to employ real-time simulation core which is running on a dedicated server. Ordinary web browser is used as a final renderer to achieve hardware independent solution which can be run on different target platforms including laptops, tablets or mobile phones. The provided toolchain allows automatic generation of the virtual laboratory source code from the configuration file created in the open- source Inkscape graphic editor. Three virtual laboratories presenting advanced motion control algorithms have been developed showing the applicability of the proposed approach.

3-D interactive visualisation tools for Hi spectral line imaging

NASA Astrophysics Data System (ADS)

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

2017-06-01

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

ValWorkBench: an open source Java library for cluster validation, with applications to microarray data analysis.

PubMed

Giancarlo, R; Scaturro, D; Utro, F

2015-02-01

The prediction of the number of clusters in a dataset, in particular microarrays, is a fundamental task in biological data analysis, usually performed via validation measures. Unfortunately, it has received very little attention and in fact there is a growing need for software tools/libraries dedicated to it. Here we present ValWorkBench, a software library consisting of eleven well known validation measures, together with novel heuristic approximations for some of them. The main objective of this paper is to provide the interested researcher with the full software documentation of an open source cluster validation platform having the main features of being easily extendible in a homogeneous way and of offering software components that can be readily re-used. Consequently, the focus of the presentation is on the architecture of the library, since it provides an essential map that can be used to access the full software documentation, which is available at the supplementary material website [1]. The mentioned main features of ValWorkBench are also discussed and exemplified, with emphasis on software abstraction design and re-usability. A comparison with existing cluster validation software libraries, mainly in terms of the mentioned features, is also offered. It suggests that ValWorkBench is a much needed contribution to the microarray software development/algorithm engineering community. For completeness, it is important to mention that previous accurate algorithmic experimental analysis of the relative merits of each of the implemented measures [19,23,25], carried out specifically on microarray data, gives useful insights on the effectiveness of ValWorkBench for cluster validation to researchers in the microarray community interested in its use for the mentioned task. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Engineering and algorithm design for an image processing Api: a technical report on ITK--the Insight Toolkit.

PubMed

Yoo, Terry S; Ackerman, Michael J; Lorensen, William E; Schroeder, Will; Chalana, Vikram; Aylward, Stephen; Metaxas, Dimitris; Whitaker, Ross

2002-01-01

We present the detailed planning and execution of the Insight Toolkit (ITK), an application programmers interface (API) for the segmentation and registration of medical image data. This public resource has been developed through the NLM Visible Human Project, and is in beta test as an open-source software offering under cost-free licensing. The toolkit concentrates on 3D medical data segmentation and registration algorithms, multimodal and multiresolution capabilities, and portable platform independent support for Windows, Linux/Unix systems. This toolkit was built using current practices in software engineering. Specifically, we embraced the concept of generic programming during the development of these tools, working extensively with C++ templates and the freedom and flexibility they allow. Software development tools for distributed consortium-based code development have been created and are also publicly available. We discuss our assumptions, design decisions, and some lessons learned.

Project Management Software for Distributed Industrial Companies

NASA Astrophysics Data System (ADS)

Dobrojević, M.; Medjo, B.; Rakin, M.; Sedmak, A.

This paper gives an overview of the development of a new software solution for project management, intended mainly to use in industrial environment. The main concern of the proposed solution is application in everyday engineering practice in various, mainly distributed industrial companies. Having this in mind, special care has been devoted to development of appropriate tools for tracking, storing and analysis of the information about the project, and in-time delivering to the right team members or other responsible persons. The proposed solution is Internet-based and uses LAMP/WAMP (Linux or Windows - Apache - MySQL - PHP) platform, because of its stability, versatility, open source technology and simple maintenance. Modular structure of the software makes it easy for customization according to client specific needs, with a very short implementation period. Its main advantages are simple usage, quick implementation, easy system maintenance, short training and only basic computer skills needed for operators.

Thoth: Software for data visualization & statistics

NASA Astrophysics Data System (ADS)

Laher, R. R.

2016-10-01

Thoth is a standalone software application with a graphical user interface for making it easy to query, display, visualize, and analyze tabular data stored in relational databases and data files. From imported data tables, it can create pie charts, bar charts, scatter plots, and many other kinds of data graphs with simple menus and mouse clicks (no programming required), by leveraging the open-source JFreeChart library. It also computes useful table-column data statistics. A mature tool, having underwent development and testing over several years, it is written in the Java computer language, and hence can be run on any computing platform that has a Java Virtual Machine and graphical-display capability. It can be downloaded and used by anyone free of charge, and has general applicability in science, engineering, medical, business, and other fields. Special tools and features for common tasks in astronomy and astrophysical research are included in the software.

Hardware Interface Description for the Integrated Power, Avionics, and Software (iPAS) Space Telecommunications Radio Ssystem (STRS) Radio

NASA Technical Reports Server (NTRS)

Shalkhauser, Mary Jo W.; Roche, Rigoberto

2017-01-01

The Space Telecommunications Radio System (STRS) provides a common, consistent framework for software defined radios (SDRs) to abstract the application software from the radio platform hardware. The STRS standard aims to reduce the cost and risk of using complex, configurable and reprogrammable radio systems across NASA missions. To promote the use of the STRS architecture for future NASA advanced exploration missions, NASA Glenn Research Center (GRC) developed an STRS-compliant SDR on a radio platform used by the Advance Exploration System program at the Johnson Space Center (JSC) in their Integrated Power, Avionics, and Software (iPAS) laboratory. The iPAS STRS Radio was implemented on the Reconfigurable, Intelligently-Adaptive Communication System (RIACS) platform, currently being used for radio development at JSC. The platform consists of a Xilinx ML605 Virtex-6 FPGA board, an Analog Devices FMCOMMS1-EBZ RF transceiver board, and an Embedded PC (Axiomtek eBox 620-110-FL) running the Ubuntu 12.4 operating system. Figure 1 shows the RIACS platform hardware. The result of this development is a very low cost STRS compliant platform that can be used for waveform developments for multiple applications.The purpose of this document is to describe how to develop a new waveform using the RIACS platform and the Very High Speed Integrated Circuits (VHSIC) Hardware Description Language (VHDL) FPGA wrapper code and the STRS implementation on the Axiomtek processor.

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

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

PubMed

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

2014-01-01

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

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

PubMed

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

2015-01-01

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

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

PubMed Central

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

2015-01-01

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

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

Iverson, Aaron

Ra Power Management (RPM) has developed a cloud based software platform that manages the financial and operational functions of third party financed solar projects throughout their lifecycle. RPM’s software streamlines and automates the sales, financing, and management of a portfolio of solar assets. The software helps solar developers automate the most difficult aspects of asset management, leading to increased transparency, efficiency, and reduction in human error. More importantly, our platform will help developers save money by improving their operating margins

From Oss CAD to Bim for Cultural Heritage Digital Representation

NASA Astrophysics Data System (ADS)

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

2017-02-01

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

Creating an X Window Terminal-Based Information Technology Center.

ERIC Educational Resources Information Center

Klassen, Tim W.

1997-01-01

The creation of an information technology center at the University of Oregon Science Library is described. Goals included providing access to Internet-based resources and multimedia software, platforms for running science-oriented software, and resources so students can create multimedia materials. A mixed-lab platform was created with Unix-based…

Use of the NetBeans Platform for NASA Robotic Conjunction Assessment Risk Analysis

NASA Technical Reports Server (NTRS)

Sabey, Nickolas J.

2014-01-01

The latest Java and JavaFX technologies are very attractive software platforms for customers involved in space mission operations such as those of NASA and the US Air Force. For NASA Robotic Conjunction Assessment Risk Analysis (CARA), the NetBeans platform provided an environment in which scalable software solutions could be developed quickly and efficiently. Both Java 8 and the NetBeans platform are in the process of simplifying CARA development in secure environments by providing a significant amount of capability in a single accredited package, where accreditation alone can account for 6-8 months for each library or software application. Capabilities either in use or being investigated by CARA include: 2D and 3D displays with JavaFX, parallelization with the new Streams API, and scalability through the NetBeans plugin architecture.

Open-Source 3D-Printable Optics Equipment

PubMed Central

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

2013-01-01

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

Open-source 3D-printable optics equipment.

PubMed

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

2013-01-01

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

GUIDEseq: a bioconductor package to analyze GUIDE-Seq datasets for CRISPR-Cas nucleases.

PubMed

Zhu, Lihua Julie; Lawrence, Michael; Gupta, Ankit; Pagès, Hervé; Kucukural, Alper; Garber, Manuel; Wolfe, Scot A

2017-05-15

Genome editing technologies developed around the CRISPR-Cas9 nuclease system have facilitated the investigation of a broad range of biological questions. These nucleases also hold tremendous promise for treating a variety of genetic disorders. In the context of their therapeutic application, it is important to identify the spectrum of genomic sequences that are cleaved by a candidate nuclease when programmed with a particular guide RNA, as well as the cleavage efficiency of these sites. Powerful new experimental approaches, such as GUIDE-seq, facilitate the sensitive, unbiased genome-wide detection of nuclease cleavage sites within the genome. Flexible bioinformatics analysis tools for processing GUIDE-seq data are needed. Here, we describe an open source, open development software suite, GUIDEseq, for GUIDE-seq data analysis and annotation as a Bioconductor package in R. The GUIDEseq package provides a flexible platform with more than 60 adjustable parameters for the analysis of datasets associated with custom nuclease applications. These parameters allow data analysis to be tailored to different nuclease platforms with different length and complexity in their guide and PAM recognition sequences or their DNA cleavage position. They also enable users to customize sequence aggregation criteria, and vary peak calling thresholds that can influence the number of potential off-target sites recovered. GUIDEseq also annotates potential off-target sites that overlap with genes based on genome annotation information, as these may be the most important off-target sites for further characterization. In addition, GUIDEseq enables the comparison and visualization of off-target site overlap between different datasets for a rapid comparison of different nuclease configurations or experimental conditions. For each identified off-target, the GUIDEseq package outputs mapped GUIDE-Seq read count as well as cleavage score from a user specified off-target cleavage score prediction algorithm permitting the identification of genomic sequences with unexpected cleavage activity. The GUIDEseq package enables analysis of GUIDE-data from various nuclease platforms for any species with a defined genomic sequence. This software package has been used successfully to analyze several GUIDE-seq datasets. The software, source code and documentation are freely available at http://www.bioconductor.org/packages/release/bioc/html/GUIDEseq.html .

Falcon: a highly flexible open-source software for closed-loop neuroscience.

PubMed

Ciliberti, Davide; Kloosterman, Fabian

2017-08-01

Closed-loop experiments provide unique insights into brain dynamics and function. To facilitate a wide range of closed-loop experiments, we created an open-source software platform that enables high-performance real-time processing of streaming experimental data. We wrote Falcon, a C++ multi-threaded software in which the user can load and execute an arbitrary processing graph. Each node of a Falcon graph is mapped to a single thread and nodes communicate with each other through thread-safe buffers. The framework allows for easy implementation of new processing nodes and data types. Falcon was tested both on a 32-core and a 4-core workstation. Streaming data was read from either a commercial acquisition system (Neuralynx) or the open-source Open Ephys hardware, while closed-loop TTL pulses were generated with a USB module for digital output. We characterized the round-trip latency of our Falcon-based closed-loop system, as well as the specific latency contribution of the software architecture, by testing processing graphs with up to 32 parallel pipelines and eight serial stages. We finally deployed Falcon in a task of real-time detection of population bursts recorded live from the hippocampus of a freely moving rat. On Neuralynx hardware, round-trip latency was well below 1 ms and stable for at least 1 h, while on Open Ephys hardware latencies were below 15 ms. The latency contribution of the software was below 0.5 ms. Round-trip and software latencies were similar on both 32- and 4-core workstations. Falcon was used successfully to detect population bursts online with ~40 ms average latency. Falcon is a novel open-source software for closed-loop neuroscience. It has sub-millisecond intrinsic latency and gives the experimenter direct control of CPU resources. We envisage Falcon to be a useful tool to the neuroscientific community for implementing a wide variety of closed-loop experiments, including those requiring use of complex data structures and real-time execution of computationally intensive algorithms, such as population neural decoding/encoding from large cell assemblies.

Falcon: a highly flexible open-source software for closed-loop neuroscience

NASA Astrophysics Data System (ADS)

Ciliberti, Davide; Kloosterman, Fabian

2017-08-01

Objective. Closed-loop experiments provide unique insights into brain dynamics and function. To facilitate a wide range of closed-loop experiments, we created an open-source software platform that enables high-performance real-time processing of streaming experimental data. Approach. We wrote Falcon, a C++ multi-threaded software in which the user can load and execute an arbitrary processing graph. Each node of a Falcon graph is mapped to a single thread and nodes communicate with each other through thread-safe buffers. The framework allows for easy implementation of new processing nodes and data types. Falcon was tested both on a 32-core and a 4-core workstation. Streaming data was read from either a commercial acquisition system (Neuralynx) or the open-source Open Ephys hardware, while closed-loop TTL pulses were generated with a USB module for digital output. We characterized the round-trip latency of our Falcon-based closed-loop system, as well as the specific latency contribution of the software architecture, by testing processing graphs with up to 32 parallel pipelines and eight serial stages. We finally deployed Falcon in a task of real-time detection of population bursts recorded live from the hippocampus of a freely moving rat. Main results. On Neuralynx hardware, round-trip latency was well below 1 ms and stable for at least 1 h, while on Open Ephys hardware latencies were below 15 ms. The latency contribution of the software was below 0.5 ms. Round-trip and software latencies were similar on both 32- and 4-core workstations. Falcon was used successfully to detect population bursts online with ~40 ms average latency. Significance. Falcon is a novel open-source software for closed-loop neuroscience. It has sub-millisecond intrinsic latency and gives the experimenter direct control of CPU resources. We envisage Falcon to be a useful tool to the neuroscientific community for implementing a wide variety of closed-loop experiments, including those requiring use of complex data structures and real-time execution of computationally intensive algorithms, such as population neural decoding/encoding from large cell assemblies.

BioSmalltalk: a pure object system and library for bioinformatics.

PubMed

Morales, Hernán F; Giovambattista, Guillermo

2013-09-15

We have developed BioSmalltalk, a new environment system for pure object-oriented bioinformatics programming. Adaptive end-user programming systems tend to become more important for discovering biological knowledge, as is demonstrated by the emergence of open-source programming toolkits for bioinformatics in the past years. Our software is intended to bridge the gap between bioscientists and rapid software prototyping while preserving the possibility of scaling to whole-system biology applications. BioSmalltalk performs better in terms of execution time and memory usage than Biopython and BioPerl for some classical situations. BioSmalltalk is cross-platform and freely available (MIT license) through the Google Project Hosting at http://code.google.com/p/biosmalltalk hernan.morales@gmail.com Supplementary data are available at Bioinformatics online.

The Bio-Community Perl toolkit for microbial ecology.

PubMed

Angly, Florent E; Fields, Christopher J; Tyson, Gene W

2014-07-01

The development of bioinformatic solutions for microbial ecology in Perl is limited by the lack of modules to represent and manipulate microbial community profiles from amplicon and meta-omics studies. Here we introduce Bio-Community, an open-source, collaborative toolkit that extends BioPerl. Bio-Community interfaces with commonly used programs using various file formats, including BIOM, and provides operations such as rarefaction and taxonomic summaries. Bio-Community will help bioinformaticians to quickly piece together custom analysis pipelines and develop novel software. Availability an implementation: Bio-Community is cross-platform Perl code available from http://search.cpan.org/dist/Bio-Community under the Perl license. A readme file describes software installation and how to contribute. © The Author 2014. Published by Oxford University Press.

Architecture of a platform for hardware-in-the-loop simulation of flying vehicle control systems

NASA Astrophysics Data System (ADS)

Belokon', S. A.; Zolotukhin, Yu. N.; Filippov, M. N.

2017-07-01

A hardware-software platform is presented, which is designed for the development and hardware-in-the-loop simulation of flying vehicle control systems. This platform ensures the construction of the mathematical model of the plant, development of algorithms and software for onboard radioelectronic equipment and ground control station, and visualization of the three-dimensional model of the vehicle and external environment of the cockpit in the simulator training mode.

Supporting in- and off-Hospital Patient Management Using a Web-based Integrated Software Platform.

PubMed

Spyropoulos, Basile; Botsivali, Maria; Tzavaras, Aris; Pierros, Vasileios

2015-01-01

In this paper, a Web-based software platform appropriately designed to support the continuity of health care information and management for both in and out of hospital care is presented. The system has some additional features as it is the formation of continuity of care records and the transmission of referral letters with a semantically annotated web service. The platform's Web-orientation provides significant advantages, allowing for easily accomplished remote access.

Waveform Developer's Guide for the Integrated Power, Avionics, and Software (iPAS) Space Telecommunications Radio System (STRS) Radio

NASA Technical Reports Server (NTRS)

Shalkhauser, Mary Jo W.; Roche, Rigoberto

2017-01-01

The Space Telecommunications Radio System (STRS) provides a common, consistent framework for software defined radios (SDRs) to abstract the application software from the radio platform hardware. The STRS standard aims to reduce the cost and risk of using complex, configurable and reprogrammable radio systems across NASA missions. To promote the use of the STRS architecture for future NASA advanced exploration missions, NASA Glenn Research Center (GRC) developed an STRS-compliant SDR on a radio platform used by the Advance Exploration System program at the Johnson Space Center (JSC) in their Integrated Power, Avionics, and Software (iPAS) laboratory. The iPAS STRS Radio was implemented on the Reconfigurable, Intelligently-Adaptive Communication System (RIACS) platform, currently being used for radio development at JSC. The platform consists of a Xilinx(Trademark) ML605 Virtex(Trademark)-6 FPGA board, an Analog Devices FMCOMMS1-EBZ RF transceiver board, and an Embedded PC (Axiomtek(Trademark) eBox 620-110-FL) running the Ubuntu 12.4 operating system. The result of this development is a very low cost STRS compliant platform that can be used for waveform developments for multiple applications. The purpose of this document is to describe how to develop a new waveform using the RIACS platform and the Very High Speed Integrated Circuits (VHSIC) Hardware Description Language (VHDL) FPGA wrapper code and the STRS implementation on the Axiomtek processor.

SMART Platforms: Building the App Store for Biosurveillance

PubMed Central

Mandl, Kenneth D.

2013-01-01

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

Bringing Legacy Visualization Software to Modern Computing Devices via Application Streaming

NASA Astrophysics Data System (ADS)

Fisher, Ward

2014-05-01

Planning software compatibility across forthcoming generations of computing platforms is a problem commonly encountered in software engineering and development. While this problem can affect any class of software, data analysis and visualization programs are particularly vulnerable. This is due in part to their inherent dependency on specialized hardware and computing environments. A number of strategies and tools have been designed to aid software engineers with this task. While generally embraced by developers at 'traditional' software companies, these methodologies are often dismissed by the scientific software community as unwieldy, inefficient and unnecessary. As a result, many important and storied scientific software packages can struggle to adapt to a new computing environment; for example, one in which much work is carried out on sub-laptop devices (such as tablets and smartphones). Rewriting these packages for a new platform often requires significant investment in terms of development time and developer expertise. In many cases, porting older software to modern devices is neither practical nor possible. As a result, replacement software must be developed from scratch, wasting resources better spent on other projects. Enabled largely by the rapid rise and adoption of cloud computing platforms, 'Application Streaming' technologies allow legacy visualization and analysis software to be operated wholly from a client device (be it laptop, tablet or smartphone) while retaining full functionality and interactivity. It mitigates much of the developer effort required by other more traditional methods while simultaneously reducing the time it takes to bring the software to a new platform. This work will provide an overview of Application Streaming and how it compares against other technologies which allow scientific visualization software to be executed from a remote computer. We will discuss the functionality and limitations of existing application streaming frameworks and how a developer might prepare their software for application streaming. We will also examine the secondary benefits realized by moving legacy software to the cloud. Finally, we will examine the process by which a legacy Java application, the Integrated Data Viewer (IDV), is to be adapted for tablet computing via Application Streaming.

Methodology for automating software systems. Task 1 of the foundations for automating software systems

NASA Technical Reports Server (NTRS)

Moseley, Warren

1989-01-01

The early stages of a research program designed to establish an experimental research platform for software engineering are described. Major emphasis is placed on Computer Assisted Software Engineering (CASE). The Poor Man's CASE Tool is based on the Apple Macintosh system, employing available software including Focal Point II, Hypercard, XRefText, and Macproject. These programs are functional in themselves, but through advanced linking are available for operation from within the tool being developed. The research platform is intended to merge software engineering technology with artificial intelligence (AI). In the first prototype of the PMCT, however, the sections of AI are not included. CASE tools assist the software engineer in planning goals, routes to those goals, and ways to measure progress. The method described allows software to be synthesized instead of being written or built.

Low Cost Real Time Autonomous Remote Monitoring Platform

NASA Astrophysics Data System (ADS)

Rodríguez, J. R.; Maldonado, P. M.; Pierson, J. J.; Harris, L.

2016-02-01

Environmental scientists have a need for gathering multiple parameters during specific time periods to answer their research questions. Most available monitoring systems are very expensive and closed systems, which limits the potential to scale up research projects. We developed a low cost, autonomous, real-time monitoring platform that is both open hardware/software and easy to build, deploy, manage and maintain. The hardware is built with off-the-shelf components and a credit card sized computer called Raspberry Pi, running an open source operating (Raspbian). The system runs off a set of batteries and a solar panel, which makes it ideal for remote locations. The software is divided into three parts: 1) a framework for abstracting the sensors (initializing, pooling and communications) designed in python and using a fully object-oriented design, making it easy for new sensor to be added with minimal code changes, 2) a web front end for managing the entire system, 3) a data store (database) framework for local and remote data retrieval and reporting services. Connectivity to the system can be accomplished through a Wi-Fi or cellular Internet connection. Scientists are being forced to do more with less, in response our platform will provide them with a flexible system that can improve the process of data gathering with an accessible, modular, low-cost, and efficient monitoring system. Currently, we have the required permits from the Department of Natural Resources in Puerto Rico to deploy the platform at the Laguna Grande Bioluminescence Lagoon in Fajardo, PR. This station will include probes for pH, DO, Conductivity and water temperature.

SimulatorToFMU v0.1

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

Nouidui, Thierry; Wetter, Michael

SimulatorToFMU is a software package written in Python which allows users to export a memoryless Python-driven simulation program or script as a Functional Mock-up Unit (FMU) for model exchange or co-simulation.In CyDER (Cyber Physical Co-simulation Platform for Distributed Energy Resources in Smart Grids), SimulatorToFMU will allow exporting OPAL-RT as an FMU. This will enable OPAL-RT to be linked to CYMDIST and GridDyn FMUs through a standardized open source interface.

A novel informatics concept for high-throughput shotgun lipidomics based on the molecular fragmentation query language

PubMed Central

2011-01-01

Shotgun lipidome profiling relies on direct mass spectrometric analysis of total lipid extracts from cells, tissues or organisms and is a powerful tool to elucidate the molecular composition of lipidomes. We present a novel informatics concept of the molecular fragmentation query language implemented within the LipidXplorer open source software kit that supports accurate quantification of individual species of any ionizable lipid class in shotgun spectra acquired on any mass spectrometry platform. PMID:21247462

Governance in Open Source Software Development Projects: Towards a Model for Network-Centric Edge Organizations

DTIC Science & Technology

2008-06-01

project is not an isolated OSSD project. Instead, the NetBeans IDE which is the focus of development activities in the NetBeans.org project community...facilitate or constrain the intended usage of the NetBeans IDE. Figure 1 provides a rendering of some of the more visible OSSD projects that...as BioBeans and RefactorIT communities build tools on top of or extending the NetBeans platform or IDE. How do these organizations interact with

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

DOE PAGES

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

2017-10-30

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

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

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

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

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

ITK: enabling reproducible research and open science

PubMed Central

McCormick, Matthew; Liu, Xiaoxiao; Jomier, Julien; Marion, Charles; Ibanez, Luis

2014-01-01

Reproducibility verification is essential to the practice of the scientific method. Researchers report their findings, which are strengthened as other independent groups in the scientific community share similar outcomes. In the many scientific fields where software has become a fundamental tool for capturing and analyzing data, this requirement of reproducibility implies that reliable and comprehensive software platforms and tools should be made available to the scientific community. The tools will empower them and the public to verify, through practice, the reproducibility of observations that are reported in the scientific literature. Medical image analysis is one of the fields in which the use of computational resources, both software and hardware, are an essential platform for performing experimental work. In this arena, the introduction of the Insight Toolkit (ITK) in 1999 has transformed the field and facilitates its progress by accelerating the rate at which algorithmic implementations are developed, tested, disseminated and improved. By building on the efficiency and quality of open source methodologies, ITK has provided the medical image community with an effective platform on which to build a daily workflow that incorporates the true scientific practices of reproducibility verification. This article describes the multiple tools, methodologies, and practices that the ITK community has adopted, refined, and followed during the past decade, in order to become one of the research communities with the most modern reproducibility verification infrastructure. For example, 207 contributors have created over 2400 unit tests that provide over 84% code line test coverage. The Insight Journal, an open publication journal associated with the toolkit, has seen over 360,000 publication downloads. The median normalized closeness centrality, a measure of knowledge flow, resulting from the distributed peer code review system was high, 0.46. PMID:24600387

A Mass Spectrometry Proteomics Data Management Platform*

PubMed Central

Sharma, Vagisha; Eng, Jimmy K.; MacCoss, Michael J.; Riffle, Michael

2012-01-01

Mass spectrometry-based proteomics is increasingly being used in biomedical research. These experiments typically generate a large volume of highly complex data, and the volume and complexity are only increasing with time. There exist many software pipelines for analyzing these data (each typically with its own file formats), and as technology improves, these file formats change and new formats are developed. Files produced from these myriad software programs may accumulate on hard disks or tape drives over time, with older files being rendered progressively more obsolete and unusable with each successive technical advancement and data format change. Although initiatives exist to standardize the file formats used in proteomics, they do not address the core failings of a file-based data management system: (1) files are typically poorly annotated experimentally, (2) files are “organically” distributed across laboratory file systems in an ad hoc manner, (3) files formats become obsolete, and (4) searching the data and comparing and contrasting results across separate experiments is very inefficient (if possible at all). Here we present a relational database architecture and accompanying web application dubbed Mass Spectrometry Data Platform that is designed to address the failings of the file-based mass spectrometry data management approach. The database is designed such that the output of disparate software pipelines may be imported into a core set of unified tables, with these core tables being extended to support data generated by specific pipelines. Because the data are unified, they may be queried, viewed, and compared across multiple experiments using a common web interface. Mass Spectrometry Data Platform is open source and freely available at http://code.google.com/p/msdapl/. PMID:22611296

Knowledge Management tools integration within DLR's concurrent engineering facility

NASA Astrophysics Data System (ADS)

Lopez, R. P.; Soragavi, G.; Deshmukh, M.; Ludtke, D.

The complexity of space endeavors has increased the need for Knowledge Management (KM) tools. The concept of KM involves not only the electronic storage of knowledge, but also the process of making this knowledge available, reusable and traceable. Establishing a KM concept within the Concurrent Engineering Facility (CEF) has been a research topic of the German Aerospace Centre (DLR). This paper presents the current KM tools of the CEF: the Software Platform for Organizing and Capturing Knowledge (S.P.O.C.K.), the data model Virtual Satellite (VirSat), and the Simulation Model Library (SimMoLib), and how their usage improved the Concurrent Engineering (CE) process. This paper also exposes the lessons learned from the introduction of KM practices into the CEF and elaborates a roadmap for the further development of KM in CE activities at DLR. The results of the application of the Knowledge Management tools have shown the potential of merging the three software platforms with their functionalities, as the next step towards the fully integration of KM practices into the CE process. VirSat will stay as the main software platform used within a CE study, and S.P.O.C.K. and SimMoLib will be integrated into VirSat. These tools will support the data model as a reference and documentation source, and as an access to simulation and calculation models. The use of KM tools in the CEF aims to become a basic practice during the CE process. The settlement of this practice will result in a much more extended knowledge and experience exchange within the Concurrent Engineering environment and, consequently, the outcome of the studies will comprise higher quality in the design of space systems.

ITK: enabling reproducible research and open science.

PubMed

McCormick, Matthew; Liu, Xiaoxiao; Jomier, Julien; Marion, Charles; Ibanez, Luis

2014-01-01

Reproducibility verification is essential to the practice of the scientific method. Researchers report their findings, which are strengthened as other independent groups in the scientific community share similar outcomes. In the many scientific fields where software has become a fundamental tool for capturing and analyzing data, this requirement of reproducibility implies that reliable and comprehensive software platforms and tools should be made available to the scientific community. The tools will empower them and the public to verify, through practice, the reproducibility of observations that are reported in the scientific literature. Medical image analysis is one of the fields in which the use of computational resources, both software and hardware, are an essential platform for performing experimental work. In this arena, the introduction of the Insight Toolkit (ITK) in 1999 has transformed the field and facilitates its progress by accelerating the rate at which algorithmic implementations are developed, tested, disseminated and improved. By building on the efficiency and quality of open source methodologies, ITK has provided the medical image community with an effective platform on which to build a daily workflow that incorporates the true scientific practices of reproducibility verification. This article describes the multiple tools, methodologies, and practices that the ITK community has adopted, refined, and followed during the past decade, in order to become one of the research communities with the most modern reproducibility verification infrastructure. For example, 207 contributors have created over 2400 unit tests that provide over 84% code line test coverage. The Insight Journal, an open publication journal associated with the toolkit, has seen over 360,000 publication downloads. The median normalized closeness centrality, a measure of knowledge flow, resulting from the distributed peer code review system was high, 0.46.

A wellness software platform with smart wearable devices and the demonstration report for personal wellness management

NASA Astrophysics Data System (ADS)

Kang, Won-Seok; Son, Chang-Sik; Lee, Sangho; Choi, Rock-Hyun; Ha, Yeong-Mi

2017-07-01

In this paper, we introduce a wellness software platform, called WellnessHumanCare, is a semi-automatic wellness management software platform which has the functions of complex wellness data acquisition(mental, physical and environmental one) with smart wearable devices, complex wellness condition analysis, private-aware online/offline recommendation, real-time monitoring apps (Smartphone-based, Web-based) and so on and we has demonstrated a wellness management service with 79 participants (experimental group: 39, control group: 40) who has worked at experimental group (H Corp.) and control group (K Corp.), Korea and 3 months in order to show the efficiency of the WellnessHumanCare.

Raven-II: an open platform for surgical robotics research.

PubMed

Hannaford, Blake; Rosen, Jacob; Friedman, Diana W; King, Hawkeye; Roan, Phillip; Cheng, Lei; Glozman, Daniel; Ma, Ji; Kosari, Sina Nia; White, Lee

2013-04-01

The Raven-II is a platform for collaborative research on advances in surgical robotics. Seven universities have begun research using this platform. The Raven-II system has two 3-DOF spherical positioning mechanisms capable of attaching interchangeable four DOF instruments. The Raven-II software is based on open standards such as Linux and ROS to maximally facilitate software development. The mechanism is robust enough for repeated experiments and animal surgery experiments, but is not engineered to sufficient safety standards for human use. Mechanisms in place for interaction among the user community and dissemination of results include an electronic forum, an online software SVN repository, and meetings and workshops at major robotics conferences.

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

PubMed

Kieslich, Pascal J; Henninger, Felix

2017-10-01

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

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Building a virtual simulation platform for quasistatic breast ultrasound elastography using open source software: A preliminary investigation

PubMed Central

Wang, Yu; Helminen, Emily; Jiang, Jingfeng

2015-01-01

Purpose: Quasistatic ultrasound elastography (QUE) is being used to augment in vivo characterization of breast lesions. Results from early clinical trials indicated that there was a lack of confidence in image interpretation. Such confidence can only be gained through rigorous imaging tests using complex, heterogeneous but known media. The objective of this study is to build a virtual breast QUE simulation platform in the public domain that can be used not only for innovative QUE research but also for rigorous imaging tests. Methods: The main thrust of this work is to streamline biomedical ultrasound simulations by leveraging existing open source software packages including Field II (ultrasound simulator), VTK (geometrical visualization and processing), FEBio [finite element (FE) analysis], and Tetgen (mesh generator). However, integration of these open source packages is nontrivial and requires interdisciplinary knowledge. In the first step, a virtual breast model containing complex anatomical geometries was created through a novel combination of image-based landmark structures and randomly distributed (small) structures. Image-based landmark structures were based on data from the NIH Visible Human Project. Subsequently, an unstructured FE-mesh was created by Tetgen. In the second step, randomly positioned point scatterers were placed within the meshed breast model through an octree-based algorithm to make a virtual breast ultrasound phantom. In the third step, an ultrasound simulator (Field II) was used to interrogate the virtual breast phantom to obtain simulated ultrasound echo data. Of note, tissue deformation generated using a FE-simulator (FEBio) was the basis of deforming the original virtual breast phantom in order to obtain the postdeformation breast phantom for subsequent ultrasound simulations. Using the procedures described above, a full cycle of QUE simulations involving complex and highly heterogeneous virtual breast phantoms can be accomplished for the first time. Results: Representative examples were used to demonstrate capabilities of this virtual simulation platform. In the first set of three ultrasound simulation examples, three heterogeneous volumes of interest were selected from a virtual breast ultrasound phantom to perform sophisticated ultrasound simulations. These resultant B-mode images realistically represented the underlying complex but known media. In the second set of three QUE examples, advanced applications in QUE were simulated. The first QUE example was to show breast tumors with complex shapes and/or compositions. The resultant strain images showed complex patterns that were normally seen in freehand clinical ultrasound data. The second and third QUE examples demonstrated (deformation-dependent) nonlinear strain imaging and time-dependent strain imaging, respectively. Conclusions: The proposed virtual QUE platform was implemented and successfully tested in this study. Through show-case examples, the proposed work has demonstrated its capabilities of creating sophisticated QUE data in a way that cannot be done through the manufacture of physical tissue-mimicking phantoms and other software. This open software architecture will soon be made available in the public domain and can be readily adapted to meet specific needs of different research groups to drive innovations in QUE. PMID:26328994

Software engineering and automatic continuous verification of scientific software

NASA Astrophysics Data System (ADS)

Piggott, M. D.; Hill, J.; Farrell, P. E.; Kramer, S. C.; Wilson, C. R.; Ham, D.; Gorman, G. J.; Bond, T.

2011-12-01

Software engineering of scientific code is challenging for a number of reasons including pressure to publish and a lack of awareness of the pitfalls of software engineering by scientists. The Applied Modelling and Computation Group at Imperial College is a diverse group of researchers that employ best practice software engineering methods whilst developing open source scientific software. Our main code is Fluidity - a multi-purpose computational fluid dynamics (CFD) code that can be used for a wide range of scientific applications from earth-scale mantle convection, through basin-scale ocean dynamics, to laboratory-scale classic CFD problems, and is coupled to a number of other codes including nuclear radiation and solid modelling. Our software development infrastructure consists of a number of free tools that could be employed by any group that develops scientific code and has been developed over a number of years with many lessons learnt. A single code base is developed by over 30 people for which we use bazaar for revision control, making good use of the strong branching and merging capabilities. Using features of Canonical's Launchpad platform, such as code review, blueprints for designing features and bug reporting gives the group, partners and other Fluidity uers an easy-to-use platform to collaborate and allows the induction of new members of the group into an environment where software development forms a central part of their work. The code repositoriy are coupled to an automated test and verification system which performs over 20,000 tests, including unit tests, short regression tests, code verification and large parallel tests. Included in these tests are build tests on HPC systems, including local and UK National HPC services. The testing of code in this manner leads to a continuous verification process; not a discrete event performed once development has ceased. Much of the code verification is done via the "gold standard" of comparisons to analytical solutions via the method of manufactured solutions. By developing and verifying code in tandem we avoid a number of pitfalls in scientific software development and advocate similar procedures for other scientific code applications.

Utilizing Technology for FCS Education: Selecting Appropriate Interactive Webinar Software

ERIC Educational Resources Information Center

Zoumenou, Virginie; Sigman-Grant, Madeleine; Coleman, Gayle; Malekian, Fatemeh; Zee, Julia M. K.; Fountain, Brent J.; Marsh, Akela

2015-01-01

The purpose of this research was to identify commonly used interactive webinar software platforms and to conduct a testing session on best practices related to an interactive webinar. The study employed the Adobe Connect and the Maestro Conference platforms. The 15 participants experienced five best practices: pre-work, polling, breakout room,…

Development and Validation of an Interactive Internet Platform for Older People: The Healthy Ageing Through Internet Counselling in the Elderly Study.

PubMed

Jongstra, Susan; Beishuizen, Cathrien; Andrieu, Sandrine; Barbera, Mariagnese; van Dorp, Matthijs; van de Groep, Bram; Guillemont, Juliette; Mangialasche, Francesca; van Middelaar, Tessa; Moll van Charante, Eric; Soininen, Hilkka; Kivipelto, Miia; Richard, Edo

2017-02-01

A myriad of Web-based applications on self-management have been developed, but few focus on older people. In the face of global aging, older people form an important target population for cardiovascular prevention. This article describes the full development of an interactive Internet platform for older people, which was designed for the Healthy Ageing Through Internet Counselling in the Elderly (HATICE) study. We provide recommendations to design senior-friendly Web-based applications for a new approach to multicomponent cardiovascular prevention. The development of the platform followed five phases: (1) conceptual framework; (2) platform concept and functional design; (3) platform building (software and content); (4) testing and pilot study; and (5) final product. We performed a meta-analysis, reviewed guidelines for cardiovascular diseases, and consulted end users, experts, and software developers to create the platform concept and content. The software was built in iterative cycles. In the pilot study, 41 people aged ≥65 years used the platform for 8 weeks. Participants used the interactive features of the platform and appreciated the coach support. During all phases adjustments were made to incorporate all improvements from the previous phases. The final platform is a personal, secured, and interactive platform supported by a coach. When carefully designed, an interactive Internet platform is acceptable and feasible for use by older people with basic computer skills. To improve acceptability by older people, we recommend involving the end users in the process of development, to personalize the platform and to combine the application with human support. The interactive HATICE platform will be tested for efficacy in a multinational randomized controlled trial (ISRCTN48151589).

PYCHEM: a multivariate analysis package for python.

PubMed

Jarvis, Roger M; Broadhurst, David; Johnson, Helen; O'Boyle, Noel M; Goodacre, Royston

2006-10-15

We have implemented a multivariate statistical analysis toolbox, with an optional standalone graphical user interface (GUI), using the Python scripting language. This is a free and open source project that addresses the need for a multivariate analysis toolbox in Python. Although the functionality provided does not cover the full range of multivariate tools that are available, it has a broad complement of methods that are widely used in the biological sciences. In contrast to tools like MATLAB, PyChem 2.0.0 is easily accessible and free, allows for rapid extension using a range of Python modules and is part of the growing amount of complementary and interoperable scientific software in Python based upon SciPy. One of the attractions of PyChem is that it is an open source project and so there is an opportunity, through collaboration, to increase the scope of the software and to continually evolve a user-friendly platform that has applicability across a wide range of analytical and post-genomic disciplines. http://sourceforge.net/projects/pychem

Development of Analytical Plug-ins for ENSITE: Version 1.0

DTIC Science & Technology

2017-11-01

ENSITE’s core-software platform builds upon leading geospatial platforms already in use by the Army and is designed to offer an easy-to-use, customized ...use by the Army and is designed to offer an easy-to-use, customized set of workflows for CB planners. Within this platform are added software compo...public good . Find out more at www.erdc.usace.army.mil. To search for other technical reports published by ERDC, visit the ERDC online library at

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

PubMed

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

2013-03-01

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

MSiReader v1.0: Evolving Open-Source Mass Spectrometry Imaging Software for Targeted and Untargeted Analyses.

PubMed

Bokhart, Mark T; Nazari, Milad; Garrard, Kenneth P; Muddiman, David C

2018-01-01

A major update to the mass spectrometry imaging (MSI) software MSiReader is presented, offering a multitude of newly added features critical to MSI analyses. MSiReader is a free, open-source, and vendor-neutral software written in the MATLAB platform and is capable of analyzing most common MSI data formats. A standalone version of the software, which does not require a MATLAB license, is also distributed. The newly incorporated data analysis features expand the utility of MSiReader beyond simple visualization of molecular distributions. The MSiQuantification tool allows researchers to calculate absolute concentrations from quantification MSI experiments exclusively through MSiReader software, significantly reducing data analysis time. An image overlay feature allows the incorporation of complementary imaging modalities to be displayed with the MSI data. A polarity filter has also been incorporated into the data loading step, allowing the facile analysis of polarity switching experiments without the need for data parsing prior to loading the data file into MSiReader. A quality assurance feature to generate a mass measurement accuracy (MMA) heatmap for an analyte of interest has also been added to allow for the investigation of MMA across the imaging experiment. Most importantly, as new features have been added performance has not degraded, in fact it has been dramatically improved. These new tools and the improvements to the performance in MSiReader v1.0 enable the MSI community to evaluate their data in greater depth and in less time. Graphical Abstract ᅟ.

Operational use of open satellite data for marine water quality monitoring

NASA Astrophysics Data System (ADS)

Symeonidis, Panagiotis; Vakkas, Theodoros

2017-09-01

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

The CARIBU EBIS control and synchronization system

NASA Astrophysics Data System (ADS)

Dickerson, Clayton; Peters, Christopher

2015-01-01

The Californium Rare Isotope Breeder Upgrade (CARIBU) Electron Beam Ion Source (EBIS) charge breeder has been built and tested. The bases of the CARIBU EBIS electrical system are four voltage platforms on which both DC and pulsed high voltage outputs are controlled. The high voltage output pulses are created with either a combination of a function generator and a high voltage amplifier, or two high voltage DC power supplies and a high voltage solid state switch. Proper synchronization of the pulsed voltages, fundamental to optimizing the charge breeding performance, is achieved with triggering from a digital delay pulse generator. The control system is based on National Instruments realtime controllers and LabVIEW software implementing Functional Global Variables (FGV) to store and access instrument parameters. Fiber optic converters enable network communication and triggering across the platforms.

A Re-Engineered Software Interface and Workflow for the Open-Source SimVascular Cardiovascular Modeling Package.

PubMed

Lan, Hongzhi; Updegrove, Adam; Wilson, Nathan M; Maher, Gabriel D; Shadden, Shawn C; Marsden, Alison L

2018-02-01

Patient-specific simulation plays an important role in cardiovascular disease research, diagnosis, surgical planning and medical device design, as well as education in cardiovascular biomechanics. simvascular is an open-source software package encompassing an entire cardiovascular modeling and simulation pipeline from image segmentation, three-dimensional (3D) solid modeling, and mesh generation, to patient-specific simulation and analysis. SimVascular is widely used for cardiovascular basic science and clinical research as well as education, following increased adoption by users and development of a GATEWAY web portal to facilitate educational access. Initial efforts of the project focused on replacing commercial packages with open-source alternatives and adding increased functionality for multiscale modeling, fluid-structure interaction (FSI), and solid modeling operations. In this paper, we introduce a major SimVascular (SV) release that includes a new graphical user interface (GUI) designed to improve user experience. Additional improvements include enhanced data/project management, interactive tools to facilitate user interaction, new boundary condition (BC) functionality, plug-in mechanism to increase modularity, a new 3D segmentation tool, and new computer-aided design (CAD)-based solid modeling capabilities. Here, we focus on major changes to the software platform and outline features added in this new release. We also briefly describe our recent experiences using SimVascular in the classroom for bioengineering education.

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.

Evaluation of DICOM viewer software for workflow integration in clinical trials

NASA Astrophysics Data System (ADS)

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

2015-03-01

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

Toward an integrated software platform for systems pharmacology

PubMed Central

Ghosh, Samik; Matsuoka, Yukiko; Asai, Yoshiyuki; Hsin, Kun-Yi; Kitano, Hiroaki

2013-01-01

Understanding complex biological systems requires the extensive support of computational tools. This is particularly true for systems pharmacology, which aims to understand the action of drugs and their interactions in a systems context. Computational models play an important role as they can be viewed as an explicit representation of biological hypotheses to be tested. A series of software and data resources are used for model development, verification and exploration of the possible behaviors of biological systems using the model that may not be possible or not cost effective by experiments. Software platforms play a dominant role in creativity and productivity support and have transformed many industries, techniques that can be applied to biology as well. Establishing an integrated software platform will be the next important step in the field. © 2013 The Authors. Biopharmaceutics & Drug Disposition published by John Wiley & Sons, Ltd. PMID:24150748

Final Report Ra Power Management 1255 10-15-16 FINAL_Public

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

Iverson, Aaron

Ra Power Management (RPM) has developed a cloud based software platform that manages the financial and operational functions of third party financed solar projects throughout their lifecycle. RPM’s software streamlines and automates the sales, financing, and management of a portfolio of solar assets. The software helps solar developers automate the most difficult aspects of asset management, leading to increased transparency, efficiency, and reduction in human error. More importantly, our platform will help developers save money by improving their operating margins

mMass 3: a cross-platform software environment for precise analysis of mass spectrometric data.

PubMed

Strohalm, Martin; Kavan, Daniel; Novák, Petr; Volný, Michael; Havlícek, Vladimír

2010-06-01

While tools for the automated analysis of MS and LC-MS/MS data are continuously improving, it is still often the case that at the end of an experiment, the mass spectrometrist will spend time carefully examining individual spectra. Current software support is mostly provided only by the instrument vendors, and the available software tools are often instrument-dependent. Here we present a new generation of mMass, a cross-platform environment for the precise analysis of individual mass spectra. The software covers a wide range of processing tasks such as import from various data formats, smoothing, baseline correction, peak picking, deisotoping, charge determination, and recalibration. Functions presented in the earlier versions such as in silico digestion and fragmentation were redesigned and improved. In addition to Mascot, an interface for ProFound has been implemented. A specific tool is available for isotopic pattern modeling to enable precise data validation. The largest available lipid database (from the LIPID MAPS Consortium) has been incorporated and together with the new compound search tool lipids can be rapidly identified. In addition, the user can define custom libraries of compounds and use them analogously. The new version of mMass is based on a stand-alone Python library, which provides the basic functionality for data processing and interpretation. This library can serve as a good starting point for other developers in their projects. Binary distributions of mMass, its source code, a detailed user's guide, and video tutorials are freely available from www.mmass.org .

A resilient and secure software platform and architecture for distributed spacecraft

NASA Astrophysics Data System (ADS)

Otte, William R.; Dubey, Abhishek; Karsai, Gabor

2014-06-01

A distributed spacecraft is a cluster of independent satellite modules flying in formation that communicate via ad-hoc wireless networks. This system in space is a cloud platform that facilitates sharing sensors and other computing and communication resources across multiple applications, potentially developed and maintained by different organizations. Effectively, such architecture can realize the functions of monolithic satellites at a reduced cost and with improved adaptivity and robustness. Openness of these architectures pose special challenges because the distributed software platform has to support applications from different security domains and organizations, and where information flows have to be carefully managed and compartmentalized. If the platform is used as a robust shared resource its management, configuration, and resilience becomes a challenge in itself. We have designed and prototyped a distributed software platform for such architectures. The core element of the platform is a new operating system whose services were designed to restrict access to the network and the file system, and to enforce resource management constraints for all non-privileged processes Mixed-criticality applications operating at different security labels are deployed and controlled by a privileged management process that is also pre-configuring all information flows. This paper describes the design and objective of this layer.

Avoidable Software Procurements

DTIC Science & Technology

2012-09-01

software license, software usage, ELA, Software as a Service , SaaS , Software Asset...PaaS Platform as a Service SaaS Software as a Service SAM Software Asset Management SMS System Management Server SEWP Solutions for Enterprise Wide...delivery of full Cloud Services , we will see the transition of the Cloud Computing service model from Iaas to SaaS , or Software as a Service . Software

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

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

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

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

ProFound: Source Extraction and Application to Modern Survey Data

NASA Astrophysics Data System (ADS)

Robotham, A. S. G.; Davies, L. J. M.; Driver, S. P.; Koushan, S.; Taranu, D. S.; Casura, S.; Liske, J.

2018-05-01

We introduce PROFOUND, a source finding and image analysis package. PROFOUND provides methods to detect sources in noisy images, generate segmentation maps identifying the pixels belonging to each source, and measure statistics like flux, size, and ellipticity. These inputs are key requirements of PROFIT, our recently released galaxy profiling package, where the design aim is that these two software packages will be used in unison to semi-automatically profile large samples of galaxies. The key novel feature introduced in PROFOUND is that all photometry is executed on dilated segmentation maps that fully contain the identifiable flux, rather than using more traditional circular or ellipse-based photometry. Also, to be less sensitive to pathological segmentation issues, the de-blending is made across saddle points in flux. We apply PROFOUND in a number of simulated and real-world cases, and demonstrate that it behaves reasonably given its stated design goals. In particular, it offers good initial parameter estimation for PROFIT, and also segmentation maps that follow the sometimes complex geometry of resolved sources, whilst capturing nearly all of the flux. A number of bulge-disc decomposition projects are already making use of the PROFOUND and PROFIT pipeline, and adoption is being encouraged by publicly releasing the software for the open source R data analysis platform under an LGPL-3 license on GitHub (github.com/asgr/ProFound).

Xi-cam: Flexible High Throughput Data Processing for GISAXS

NASA Astrophysics Data System (ADS)

Pandolfi, Ronald; Kumar, Dinesh; Venkatakrishnan, Singanallur; Sarje, Abinav; Krishnan, Hari; Pellouchoud, Lenson; Ren, Fang; Fournier, Amanda; Jiang, Zhang; Tassone, Christopher; Mehta, Apurva; Sethian, James; Hexemer, Alexander

With increasing capabilities and data demand for GISAXS beamlines, supporting software is under development to handle larger data rates, volumes, and processing needs. We aim to provide a flexible and extensible approach to GISAXS data treatment as a solution to these rising needs. Xi-cam is the CAMERA platform for data management, analysis, and visualization. The core of Xi-cam is an extensible plugin-based GUI platform which provides users an interactive interface to processing algorithms. Plugins are available for SAXS/GISAXS data and data series visualization, as well as forward modeling and simulation through HipGISAXS. With Xi-cam's advanced mode, data processing steps are designed as a graph-based workflow, which can be executed locally or remotely. Remote execution utilizes HPC or de-localized resources, allowing for effective reduction of high-throughput data. Xi-cam is open-source and cross-platform. The processing algorithms in Xi-cam include parallel cpu and gpu processing optimizations, also taking advantage of external processing packages such as pyFAI. Xi-cam is available for download online.

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Open source software in a practical approach for post processing of radiologic images.

PubMed

Valeri, Gianluca; Mazza, Francesco Antonino; Maggi, Stefania; Aramini, Daniele; La Riccia, Luigi; Mazzoni, Giovanni; Giovagnoni, Andrea

2015-03-01

The purpose of this paper is to evaluate the use of open source software (OSS) to process DICOM images. We selected 23 programs for Windows and 20 programs for Mac from 150 possible OSS programs including DICOM viewers and various tools (converters, DICOM header editors, etc.). The programs selected all meet the basic requirements such as free availability, stand-alone application, presence of graphical user interface, ease of installation and advanced features beyond simple display monitor. Capabilities of data import, data export, metadata, 2D viewer, 3D viewer, support platform and usability of each selected program were evaluated on a scale ranging from 1 to 10 points. Twelve programs received a score higher than or equal to eight. Among them, five obtained a score of 9: 3D Slicer, MedINRIA, MITK 3M3, VolView, VR Render; while OsiriX received 10. OsiriX appears to be the only program able to perform all the operations taken into consideration, similar to a workstation equipped with proprietary software, allowing the analysis and interpretation of images in a simple and intuitive way. OsiriX is a DICOM PACS workstation for medical imaging and software for image processing for medical research, functional imaging, 3D imaging, confocal microscopy and molecular imaging. This application is also a good tool for teaching activities because it facilitates the attainment of learning objectives among students and other specialists.

Math Description Engine Software Development Kit

NASA Technical Reports Server (NTRS)

Shelton, Robert O.; Smith, Stephanie L.; Dexter, Dan E.; Hodgson, Terry R.

2010-01-01

The Math Description Engine Software Development Kit (MDE SDK) can be used by software developers to make computer-rendered graphs more accessible to blind and visually-impaired users. The MDE SDK generates alternative graph descriptions in two forms: textual descriptions and non-verbal sound renderings, or sonification. It also enables display of an animated trace of a graph sonification on a visual graph component, with color and line-thickness options for users having low vision or color-related impairments. A set of accessible graphical user interface widgets is provided for operation by end users and for control of accessible graph displays. Version 1.0 of the MDE SDK generates text descriptions for 2D graphs commonly seen in math and science curriculum (and practice). The mathematically rich text descriptions can also serve as a virtual math and science assistant for blind and sighted users, making graphs more accessible for everyone. The MDE SDK has a simple application programming interface (API) that makes it easy for programmers and Web-site developers to make graphs accessible with just a few lines of code. The source code is written in Java for cross-platform compatibility and to take advantage of Java s built-in support for building accessible software application interfaces. Compiled-library and NASA Open Source versions are available with API documentation and Programmer s Guide at http:/ / prim e.jsc.n asa. gov.

Systems biology driven software design for the research enterprise

PubMed Central

Boyle, John; Cavnor, Christopher; Killcoyne, Sarah; Shmulevich, Ilya

2008-01-01

Background In systems biology, and many other areas of research, there is a need for the interoperability of tools and data sources that were not originally designed to be integrated. Due to the interdisciplinary nature of systems biology, and its association with high throughput experimental platforms, there is an additional need to continually integrate new technologies. As scientists work in isolated groups, integration with other groups is rarely a consideration when building the required software tools. Results We illustrate an approach, through the discussion of a purpose built software architecture, which allows disparate groups to reuse tools and access data sources in a common manner. The architecture allows for: the rapid development of distributed applications; interoperability, so it can be used by a wide variety of developers and computational biologists; development using standard tools, so that it is easy to maintain and does not require a large development effort; extensibility, so that new technologies and data types can be incorporated; and non intrusive development, insofar as researchers need not to adhere to a pre-existing object model. Conclusion By using a relatively simple integration strategy, based upon a common identity system and dynamically discovered interoperable services, a light-weight software architecture can become the focal point through which scientists can both get access to and analyse the plethora of experimentally derived data. PMID:18578887

Software Reliability Analysis of NASA Space Flight Software: A Practical Experience

PubMed Central

Sukhwani, Harish; Alonso, Javier; Trivedi, Kishor S.; Mcginnis, Issac

2017-01-01

In this paper, we present the software reliability analysis of the flight software of a recently launched space mission. For our analysis, we use the defect reports collected during the flight software development. We find that this software was developed in multiple releases, each release spanning across all software life-cycle phases. We also find that the software releases were developed and tested for four different hardware platforms, spanning from off-the-shelf or emulation hardware to actual flight hardware. For releases that exhibit reliability growth or decay, we fit Software Reliability Growth Models (SRGM); otherwise we fit a distribution function. We find that most releases exhibit reliability growth, with Log-Logistic (NHPP) and S-Shaped (NHPP) as the best-fit SRGMs. For the releases that experience reliability decay, we investigate the causes for the same. We find that such releases were the first software releases to be tested on a new hardware platform, and hence they encountered major hardware integration issues. Also such releases seem to have been developed under time pressure in order to start testing on the new hardware platform sooner. Such releases exhibit poor reliability growth, and hence exhibit high predicted failure rate. Other problems include hardware specification changes and delivery delays from vendors. Thus, our analysis provides critical insights and inputs to the management to improve the software development process. As NASA has moved towards a product line engineering for its flight software development, software for future space missions will be developed in a similar manner and hence the analysis results for this mission can be considered as a baseline for future flight software missions. PMID:29278255

Software Reliability Analysis of NASA Space Flight Software: A Practical Experience.

PubMed

Sukhwani, Harish; Alonso, Javier; Trivedi, Kishor S; Mcginnis, Issac

2016-01-01

In this paper, we present the software reliability analysis of the flight software of a recently launched space mission. For our analysis, we use the defect reports collected during the flight software development. We find that this software was developed in multiple releases, each release spanning across all software life-cycle phases. We also find that the software releases were developed and tested for four different hardware platforms, spanning from off-the-shelf or emulation hardware to actual flight hardware. For releases that exhibit reliability growth or decay, we fit Software Reliability Growth Models (SRGM); otherwise we fit a distribution function. We find that most releases exhibit reliability growth, with Log-Logistic (NHPP) and S-Shaped (NHPP) as the best-fit SRGMs. For the releases that experience reliability decay, we investigate the causes for the same. We find that such releases were the first software releases to be tested on a new hardware platform, and hence they encountered major hardware integration issues. Also such releases seem to have been developed under time pressure in order to start testing on the new hardware platform sooner. Such releases exhibit poor reliability growth, and hence exhibit high predicted failure rate. Other problems include hardware specification changes and delivery delays from vendors. Thus, our analysis provides critical insights and inputs to the management to improve the software development process. As NASA has moved towards a product line engineering for its flight software development, software for future space missions will be developed in a similar manner and hence the analysis results for this mission can be considered as a baseline for future flight software missions.

MPHASYS: a mouse phenotype analysis system

PubMed Central

Calder, R Brent; Beems, Rudolf B; van Steeg, Harry; Mian, I Saira; Lohman, Paul HM; Vijg, Jan

2007-01-01

Background Systematic, high-throughput studies of mouse phenotypes have been hampered by the inability to analyze individual animal data from a multitude of sources in an integrated manner. Studies generally make comparisons at the level of genotype or treatment thereby excluding associations that may be subtle or involve compound phenotypes. Additionally, the lack of integrated, standardized ontologies and methodologies for data exchange has inhibited scientific collaboration and discovery. Results Here we introduce a Mouse Phenotype Analysis System (MPHASYS), a platform for integrating data generated by studies of mouse models of human biology and disease such as aging and cancer. This computational platform is designed to provide a standardized methodology for working with animal data; a framework for data entry, analysis and sharing; and ontologies and methodologies for ensuring accurate data capture. We describe the tools that currently comprise MPHASYS, primarily ones related to mouse pathology, and outline its use in a study of individual animal-specific patterns of multiple pathology in mice harboring a specific germline mutation in the DNA repair and transcription-specific gene Xpd. Conclusion MPHASYS is a system for analyzing multiple data types from individual animals. It provides a framework for developing data analysis applications, and tools for collecting and distributing high-quality data. The software is platform independent and freely available under an open-source license [1]. PMID:17553167

OptFlux: an open-source software platform for in silico metabolic engineering.

PubMed

Rocha, Isabel; Maia, Paulo; Evangelista, Pedro; Vilaça, Paulo; Soares, Simão; Pinto, José P; Nielsen, Jens; Patil, Kiran R; Ferreira, Eugénio C; Rocha, Miguel

2010-04-19

Over the last few years a number of methods have been proposed for the phenotype simulation of microorganisms under different environmental and genetic conditions. These have been used as the basis to support the discovery of successful genetic modifications of the microbial metabolism to address industrial goals. However, the use of these methods has been restricted to bioinformaticians or other expert researchers. The main aim of this work is, therefore, to provide a user-friendly computational tool for Metabolic Engineering applications. OptFlux is an open-source and modular software aimed at being the reference computational application in the field. It is the first tool to incorporate strain optimization tasks, i.e., the identification of Metabolic Engineering targets, using Evolutionary Algorithms/Simulated Annealing metaheuristics or the previously proposed OptKnock algorithm. It also allows the use of stoichiometric metabolic models for (i) phenotype simulation of both wild-type and mutant organisms, using the methods of Flux Balance Analysis, Minimization of Metabolic Adjustment or Regulatory on/off Minimization of Metabolic flux changes, (ii) Metabolic Flux Analysis, computing the admissible flux space given a set of measured fluxes, and (iii) pathway analysis through the calculation of Elementary Flux Modes. OptFlux also contemplates several methods for model simplification and other pre-processing operations aimed at reducing the search space for optimization algorithms. The software supports importing/exporting to several flat file formats and it is compatible with the SBML standard. OptFlux has a visualization module that allows the analysis of the model structure that is compatible with the layout information of Cell Designer, allowing the superimposition of simulation results with the model graph. The OptFlux software is freely available, together with documentation and other resources, thus bridging the gap from research in strain optimization algorithms and the final users. It is a valuable platform for researchers in the field that have available a number of useful tools. Its open-source nature invites contributions by all those interested in making their methods available for the community. Given its plug-in based architecture it can be extended with new functionalities. Currently, several plug-ins are being developed, including network topology analysis tools and the integration with Boolean network based regulatory models.

OptFlux: an open-source software platform for in silico metabolic engineering

PubMed Central

2010-01-01

Background Over the last few years a number of methods have been proposed for the phenotype simulation of microorganisms under different environmental and genetic conditions. These have been used as the basis to support the discovery of successful genetic modifications of the microbial metabolism to address industrial goals. However, the use of these methods has been restricted to bioinformaticians or other expert researchers. The main aim of this work is, therefore, to provide a user-friendly computational tool for Metabolic Engineering applications. Results OptFlux is an open-source and modular software aimed at being the reference computational application in the field. It is the first tool to incorporate strain optimization tasks, i.e., the identification of Metabolic Engineering targets, using Evolutionary Algorithms/Simulated Annealing metaheuristics or the previously proposed OptKnock algorithm. It also allows the use of stoichiometric metabolic models for (i) phenotype simulation of both wild-type and mutant organisms, using the methods of Flux Balance Analysis, Minimization of Metabolic Adjustment or Regulatory on/off Minimization of Metabolic flux changes, (ii) Metabolic Flux Analysis, computing the admissible flux space given a set of measured fluxes, and (iii) pathway analysis through the calculation of Elementary Flux Modes. OptFlux also contemplates several methods for model simplification and other pre-processing operations aimed at reducing the search space for optimization algorithms. The software supports importing/exporting to several flat file formats and it is compatible with the SBML standard. OptFlux has a visualization module that allows the analysis of the model structure that is compatible with the layout information of Cell Designer, allowing the superimposition of simulation results with the model graph. Conclusions The OptFlux software is freely available, together with documentation and other resources, thus bridging the gap from research in strain optimization algorithms and the final users. It is a valuable platform for researchers in the field that have available a number of useful tools. Its open-source nature invites contributions by all those interested in making their methods available for the community. Given its plug-in based architecture it can be extended with new functionalities. Currently, several plug-ins are being developed, including network topology analysis tools and the integration with Boolean network based regulatory models. PMID:20403172

MATtrack: A MATLAB-Based Quantitative Image Analysis Platform for Investigating Real-Time Photo-Converted Fluorescent Signals in Live Cells.

PubMed

Courtney, Jane; Woods, Elena; Scholz, Dimitri; Hall, William W; Gautier, Virginie W

2015-01-01

We introduce here MATtrack, an open source MATLAB-based computational platform developed to process multi-Tiff files produced by a photo-conversion time lapse protocol for live cell fluorescent microscopy. MATtrack automatically performs a series of steps required for image processing, including extraction and import of numerical values from Multi-Tiff files, red/green image classification using gating parameters, noise filtering, background extraction, contrast stretching and temporal smoothing. MATtrack also integrates a series of algorithms for quantitative image analysis enabling the construction of mean and standard deviation images, clustering and classification of subcellular regions and injection point approximation. In addition, MATtrack features a simple user interface, which enables monitoring of Fluorescent Signal Intensity in multiple Regions of Interest, over time. The latter encapsulates a region growing method to automatically delineate the contours of Regions of Interest selected by the user, and performs background and regional Average Fluorescence Tracking, and automatic plotting. Finally, MATtrack computes convenient visualization and exploration tools including a migration map, which provides an overview of the protein intracellular trajectories and accumulation areas. In conclusion, MATtrack is an open source MATLAB-based software package tailored to facilitate the analysis and visualization of large data files derived from real-time live cell fluorescent microscopy using photoconvertible proteins. It is flexible, user friendly, compatible with Windows, Mac, and Linux, and a wide range of data acquisition software. MATtrack is freely available for download at eleceng.dit.ie/courtney/MATtrack.zip.

Intraoperative visualization and assessment of electromagnetic tracking error

NASA Astrophysics Data System (ADS)

Harish, Vinyas; Ungi, Tamas; Lasso, Andras; MacDonald, Andrew; Nanji, Sulaiman; Fichtinger, Gabor

2015-03-01

Electromagnetic tracking allows for increased flexibility in designing image-guided interventions, however it is well understood that electromagnetic tracking is prone to error. Visualization and assessment of the tracking error should take place in the operating room with minimal interference with the clinical procedure. The goal was to achieve this ideal in an open-source software implementation in a plug and play manner, without requiring programming from the user. We use optical tracking as a ground truth. An electromagnetic sensor and optical markers are mounted onto a stylus device, pivot calibrated for both trackers. Electromagnetic tracking error is defined as difference of tool tip position between electromagnetic and optical readings. Multiple measurements are interpolated into the thin-plate B-spline transform visualized in real time using 3D Slicer. All tracked devices are used in a plug and play manner through the open-source SlicerIGT and PLUS extensions of the 3D Slicer platform. Tracking error was measured multiple times to assess reproducibility of the method, both with and without placing ferromagnetic objects in the workspace. Results from exhaustive grid sampling and freehand sampling were similar, indicating that a quick freehand sampling is sufficient to detect unexpected or excessive field distortion in the operating room. The software is available as a plug-in for the 3D Slicer platforms. Results demonstrate potential for visualizing electromagnetic tracking error in real time for intraoperative environments in feasibility clinical trials in image-guided interventions.

MATtrack: A MATLAB-Based Quantitative Image Analysis Platform for Investigating Real-Time Photo-Converted Fluorescent Signals in Live Cells

PubMed Central

Courtney, Jane; Woods, Elena; Scholz, Dimitri; Hall, William W.; Gautier, Virginie W.

2015-01-01

We introduce here MATtrack, an open source MATLAB-based computational platform developed to process multi-Tiff files produced by a photo-conversion time lapse protocol for live cell fluorescent microscopy. MATtrack automatically performs a series of steps required for image processing, including extraction and import of numerical values from Multi-Tiff files, red/green image classification using gating parameters, noise filtering, background extraction, contrast stretching and temporal smoothing. MATtrack also integrates a series of algorithms for quantitative image analysis enabling the construction of mean and standard deviation images, clustering and classification of subcellular regions and injection point approximation. In addition, MATtrack features a simple user interface, which enables monitoring of Fluorescent Signal Intensity in multiple Regions of Interest, over time. The latter encapsulates a region growing method to automatically delineate the contours of Regions of Interest selected by the user, and performs background and regional Average Fluorescence Tracking, and automatic plotting. Finally, MATtrack computes convenient visualization and exploration tools including a migration map, which provides an overview of the protein intracellular trajectories and accumulation areas. In conclusion, MATtrack is an open source MATLAB-based software package tailored to facilitate the analysis and visualization of large data files derived from real-time live cell fluorescent microscopy using photoconvertible proteins. It is flexible, user friendly, compatible with Windows, Mac, and Linux, and a wide range of data acquisition software. MATtrack is freely available for download at eleceng.dit.ie/courtney/MATtrack.zip. PMID:26485569

An integrated development framework for rapid development of platform-independent and reusable satellite on-board software

NASA Astrophysics Data System (ADS)

Ziemke, Claas; Kuwahara, Toshinori; Kossev, Ivan

2011-09-01

Even in the field of small satellites, the on-board data handling subsystem has become complex and powerful. With the introduction of powerful CPUs and the availability of considerable amounts of memory on-board a small satellite it has become possible to utilize the flexibility and power of contemporary platform-independent real-time operating systems. Especially the non-commercial sector such like university institutes and community projects such as AMSAT or SSETI are characterized by the inherent lack of financial as well as manpower resources. The opportunity to utilize such real-time operating systems will contribute significantly to achieve a successful mission. Nevertheless the on-board software of a satellite is much more than just an operating system. It has to fulfill a multitude of functional requirements such as: Telecommand interpretation and execution, execution of control loops, generation of telemetry data and frames, failure detection isolation and recovery, the communication with peripherals and so on. Most of the aforementioned tasks are of generic nature and have to be conducted on any satellite with only minor modifications. A general set of functional requirements as well as a protocol for communication is defined in the SA ECSS-E-70-41A standard "Telemetry and telecommand packet utilization". This standard not only defines the communication protocol of the satellite-ground link but also defines a set of so called services which have to be available on-board of every compliant satellite and which are of generic nature. In this paper, a platform-independent and reusable framework is described which is implementing not only the ECSS-E-70-41A standard but also functionalities for interprocess communication, scheduling and a multitude of tasks commonly performed on-board of a satellite. By making use of the capabilities of the high-level programming language C/C++, the powerful open source library BOOST, the real-time operating system RTEMS and finally by providing generic functionalities compliant to the ECSS-E-70-41A standard the proposed framework can provide a great boost in productivity. Together with open source tools such like the GNU tool-chain, Eclipse SDK, the simulation framework OpenSimKit, the emulator QEMU, the proposed on-board software framework forms an integrated development framework. It is possible to design, code and build the on-board software together with the operating system and then run it on a simulated satellite for performance analysis and debugging purposes. This makes it possible to rapidly develop and deploy a full-fledged satellite on-board software with minimal cost and in a limited time frame.

The development of data acquisition and processing application system for RF ion source

NASA Astrophysics Data System (ADS)

Zhang, Xiaodan; Wang, Xiaoying; Hu, Chundong; Jiang, Caichao; Xie, Yahong; Zhao, Yuanzhe

2017-07-01

As the key ion source component of nuclear fusion auxiliary heating devices, the radio frequency (RF) ion source is developed and applied gradually to offer a source plasma with the advantages of ease of control and high reliability. In addition, it easily achieves long-pulse steady-state operation. During the process of the development and testing of the RF ion source, a lot of original experimental data will be generated. Therefore, it is necessary to develop a stable and reliable computer data acquisition and processing application system for realizing the functions of data acquisition, storage, access, and real-time monitoring. In this paper, the development of a data acquisition and processing application system for the RF ion source is presented. The hardware platform is based on the PXI system and the software is programmed on the LabVIEW development environment. The key technologies that are used for the implementation of this software programming mainly include the long-pulse data acquisition technology, multi-threading processing technology, transmission control communication protocol, and the Lempel-Ziv-Oberhumer data compression algorithm. Now, this design has been tested and applied on the RF ion source. The test results show that it can work reliably and steadily. With the help of this design, the stable plasma discharge data of the RF ion source are collected, stored, accessed, and monitored in real-time. It is shown that it has a very practical application significance for the RF experiments.

Informatic search strategies to discover analogues and variants of natural product archetypes.

PubMed

Johnston, Chad W; Connaty, Alex D; Skinnider, Michael A; Li, Yong; Grunwald, Alyssa; Wyatt, Morgan A; Kerr, Russell G; Magarvey, Nathan A

2016-03-01

Natural products are a crucial source of antimicrobial agents, but reliance on low-resolution bioactivity-guided approaches has led to diminishing interest in discovery programmes. Here, we demonstrate that two in-house automated informatic platforms can be used to target classes of biologically active natural products, specifically, peptaibols. We demonstrate that mass spectrometry-based informatic approaches can be used to detect natural products with high sensitivity, identifying desired agents present in complex microbial extracts. Using our specialised software packages, we could elaborate specific branches of chemical space, uncovering new variants of trichopolyn and demonstrating a way forward in mining natural products as a valuable source of potential pharmaceutical agents.

VAGUE: a graphical user interface for the Velvet assembler.

PubMed

Powell, David R; Seemann, Torsten

2013-01-15

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

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

PubMed Central

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

2015-01-01

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

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

PubMed

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

2015-03-01

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

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.

Software-Defined Radio for Space-to-Space Communications

NASA Technical Reports Server (NTRS)

Fisher, Ken; Jih, Cindy; Moore, Michael S.; Price, Jeremy C.; Abbott, Ben A.; Fritz, Justin A.

2011-01-01

A paper describes the Space- to-Space Communications System (SSCS) Software- Defined Radio (SDR) research project to determine the most appropriate method for creating flexible and reconfigurable radios to implement wireless communications channels for space vehicles so that fewer radios are required, and commonality in hardware and software architecture can be leveraged for future missions. The ability to reconfigure the SDR through software enables one radio platform to be reconfigured to interoperate with many different waveforms. This means a reduction in the number of physical radio platforms necessary to support a space mission s communication requirements, thus decreasing the total size, weight, and power needed for a mission.

The Orthanc Ecosystem for Medical Imaging.

PubMed

Jodogne, Sébastien

2018-05-03

This paper reviews the components of Orthanc, a free and open-source, highly versatile ecosystem for medical imaging. At the core of the Orthanc ecosystem, the Orthanc server is a lightweight vendor neutral archive that provides PACS managers with a powerful environment to automate and optimize the imaging flows that are very specific to each hospital. The Orthanc server can be extended with plugins that provide solutions for teleradiology, digital pathology, or enterprise-ready databases. It is shown how software developers and research engineers can easily develop external software or Web portals dealing with medical images, with minimal knowledge of the DICOM standard, thanks to the advanced programming interface of the Orthanc server. The paper concludes by introducing the Stone of Orthanc, an innovative toolkit for the cross-platform rendering of medical images.

Space Station Furnace Facility Management Information System (SSFF-MIS) Development

NASA Technical Reports Server (NTRS)

Meade, Robert M.

1996-01-01

This report summarizes the chronology, results, and lessons learned from the development of the SSFF-MIS. This system has been nearly two years in development and has yielded some valuable insights into specialized MIS development. General: In December of 1994, the Camber Corporation and Science Applications International Corporation (SAIC) were contracted to design, develop, and implement a MIS for Marshall Space Flight Center's Space Station Furnace Facility Project. The system was to be accessible from both EBM-Compatible PC and Macintosh platforms. The system was required to contain data manually entered into the MIS as well as data imported from other MSFC sources. Electronic interfaces were established for each data source and retrieval was to be performed at prescribed time intervals. The SOW requirement that predominantly drove the development software selection was the dual-platform (IBM-PC and Macintosh) requirement. The requirement that the system would be maintained by Government personnel influenced the selection of Commercial Off-the-shelf software because of its inherent stability and readily available documentation and support. Microsoft FoxPro Professional 2.6 for Windows and Macintosh was selected as the development tool. This is a software development tool that has been in use for many years. It is stable and powerful. Microsoft has since released the replacement for this product, Microsoft Visual FoxPro, but at the time of this development, it was only available on the Windows platform. The initial contract included included the requirement for capabilities relating to the Work- and Organizational Breakdown Structures, cost (plan and actuals), workforce (plan and actuals), critical path scheduling, trend analysis, procurements and contracts, interface to manufacturing, Safety and Mission Assurance, risk analysis, and technical performance indicators. It also required full documentation of the system and training of users. During the course of the contract, the requirements for Safety and Mission Assurance interface, risk analysis, and technical performance indicators were deleted. Additional capabilities were added as reflected in the Contract Chronology below. Modification 4 added the requirement for Support Contractor manpower data, the ability to manually input data not imported from non-nal sources, a general 'health' indicator screen, and remote usage. Mod 6 included the ability to change the level of planning of Civil Service Manpower at any time and the ability to manually enter Op Codes in the manufacturing data where such codes were not provided by the EMPACS database. Modification 9 included a number of changes to report contents and formats. Modification 11 required the preparation of a detailed System Design Document.

ALFA: The new ALICE-FAIR software framework

NASA Astrophysics Data System (ADS)

Al-Turany, M.; Buncic, P.; Hristov, P.; Kollegger, T.; Kouzinopoulos, C.; Lebedev, A.; Lindenstruth, V.; Manafov, A.; Richter, M.; Rybalchenko, A.; Vande Vyvre, P.; Winckler, N.

2015-12-01

The commonalities between the ALICE and FAIR experiments and their computing requirements led to the development of large parts of a common software framework in an experiment independent way. The FairRoot project has already shown the feasibility of such an approach for the FAIR experiments and extending it beyond FAIR to experiments at other facilities[1, 2]. The ALFA framework is a joint development between ALICE Online- Offline (O2) and FairRoot teams. ALFA is designed as a flexible, elastic system, which balances reliability and ease of development with performance using multi-processing and multithreading. A message- based approach has been adopted; such an approach will support the use of the software on different hardware platforms, including heterogeneous systems. Each process in ALFA assumes limited communication and reliance on other processes. Such a design will add horizontal scaling (multiple processes) to vertical scaling provided by multiple threads to meet computing and throughput demands. ALFA does not dictate any application protocols. Potentially, any content-based processor or any source can change the application protocol. The framework supports different serialization standards for data exchange between different hardware and software languages.

A Web-Based Earth-Systems Knowledge Portal and Collaboration Platform

NASA Astrophysics Data System (ADS)

D'Agnese, F. A.; Turner, A. K.

2010-12-01

In support of complex water-resource sustainability projects in the Great Basin region of the United States, Earth Knowledge, Inc. has developed several web-based data management and analysis platforms that have been used by its scientists, clients, and public to facilitate information exchanges, collaborations, and decision making. These platforms support accurate water-resource decision-making by combining second-generation internet (Web 2.0) technologies with traditional 2D GIS and web-based 2D and 3D mapping systems such as Google Maps, and Google Earth. Most data management and analysis systems use traditional software systems to address the data needs and usage behavior of the scientific community. In contrast, these platforms employ more accessible open-source and “off-the-shelf” consumer-oriented, hosted web-services. They exploit familiar software tools using industry standard protocols, formats, and APIs to discover, process, fuse, and visualize earth, engineering, and social science datasets. Thus, they respond to the information needs and web-interface expectations of both subject-matter experts and the public. Because the platforms continue to gather and store all the contributions of their broad-spectrum of users, each new assessment leverages the data, information, and expertise derived from previous investigations. In the last year, Earth Knowledge completed a conceptual system design and feasibility study for a platform, which has a Knowledge Portal providing access to users wishing to retrieve information or knowledge developed by the science enterprise and a Collaboration Environment Module, a framework that links the user-access functions to a Technical Core supporting technical and scientific analyses including Data Management, Analysis and Modeling, and Decision Management, and to essential system administrative functions within an Administrative Module. The over-riding technical challenge is the design and development of a single technical platform that is accessed through a flexible series of knowledge portal and collaboration environment styles reflecting the information needs and user expectations of a diverse community of users. Recent investigations have defined the information needs and expectations of the major end-users and also have reviewed and assessed a wide variety of modern web-based technologies. Combining these efforts produced design specifications and recommendations for the selection and integration of web- and client-based tools. When fully developed, the resulting platform will: -Support new, advanced information systems and decision environments that take full advantage of multiple data sources and platforms; -Provide a distribution network tailored to the timely delivery of products to a broad range of users that are needed to support applications in disaster management, resource management, energy, and urban sustainability; -Establish new integrated multiple-user requirements and knowledge databases that support researchers and promote infusion of successful technologies into existing processes; and -Develop new decision support strategies and presentation methodologies for applied earth science applications to reduce risk, cost, and time.

JIP: Java image processing on the Internet

NASA Astrophysics Data System (ADS)

Wang, Dongyan; Lin, Bo; Zhang, Jun

1998-12-01

In this paper, we present JIP - Java Image Processing on the Internet, a new Internet based application for remote education and software presentation. JIP offers an integrate learning environment on the Internet where remote users not only can share static HTML documents and lectures notes, but also can run and reuse dynamic distributed software components, without having the source code or any extra work of software compilation, installation and configuration. By implementing a platform-independent distributed computational model, local computational resources are consumed instead of the resources on a central server. As an extended Java applet, JIP allows users to selected local image files on their computers or specify any image on the Internet using an URL as input. Multimedia lectures such as streaming video/audio and digital images are integrated into JIP and intelligently associated with specific image processing functions. Watching demonstrations an practicing the functions with user-selected input data dramatically encourages leaning interest, while promoting the understanding of image processing theory. The JIP framework can be easily applied to other subjects in education or software presentation, such as digital signal processing, business, mathematics, physics, or other areas such as employee training and charged software consumption.

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

PubMed

Kumar, Sudhir; Stecher, Glen; Li, Michael; Knyaz, Christina; Tamura, Koichiro

2018-06-01

The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.

Arsenic removal from contaminated groundwater by membrane-integrated hybrid plant: optimization and control using Visual Basic platform.

PubMed

Chakrabortty, S; Sen, M; Pal, P

2014-03-01

A simulation software (ARRPA) has been developed in Microsoft Visual Basic platform for optimization and control of a novel membrane-integrated arsenic separation plant in the backdrop of absence of such software. The user-friendly, menu-driven software is based on a dynamic linearized mathematical model, developed for the hybrid treatment scheme. The model captures the chemical kinetics in the pre-treating chemical reactor and the separation and transport phenomena involved in nanofiltration. The software has been validated through extensive experimental investigations. The agreement between the outputs from computer simulation program and the experimental findings are excellent and consistent under varying operating conditions reflecting high degree of accuracy and reliability of the software. High values of the overall correlation coefficient (R (2) = 0.989) and Willmott d-index (0.989) are indicators of the capability of the software in analyzing performance of the plant. The software permits pre-analysis, manipulation of input data, helps in optimization and exhibits performance of an integrated plant visually on a graphical platform. Performance analysis of the whole system as well as the individual units is possible using the tool. The software first of its kind in its domain and in the well-known Microsoft Excel environment is likely to be very useful in successful design, optimization and operation of an advanced hybrid treatment plant for removal of arsenic from contaminated groundwater.

OpenQuake, a platform for collaborative seismic hazard and risk assessment

NASA Astrophysics Data System (ADS)

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

2013-04-01

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

Potential of the Cogex Software Platform to Replace Logbooks in Capstone Design Projects

ERIC Educational Resources Information Center

Foley, David; Charron, François; Plante, Jean-Sébastien

2018-01-01

Recent technologies are offering the power to share and grow knowledge and ideas in unprecedented ways. The CogEx software platform was developed to take advantage of the digital world with innovative ideas to support designers work in both industrial and academic contexts. This paper presents a qualitative study on the usage of CogEx during…

A Software Platform for Post-Processing Waveform-Based NDE

NASA Technical Reports Server (NTRS)

Roth, Donald J.; Martin, Richard E.; Seebo, Jeff P.; Trinh, Long B.; Walker, James L.; Winfree, William P.

2007-01-01

Ultrasonic, microwave, and terahertz nondestructive evaluation imaging systems generally require the acquisition of waveforms at each scan point to form an image. For such systems, signal and image processing methods are commonly needed to extract information from the waves and improve resolution of, and highlight, defects in the image. Since some similarity exists for all waveform-based NDE methods, it would seem a common software platform containing multiple signal and image processing techniques to process the waveforms and images makes sense where multiple techniques, scientists, engineers, and organizations are involved. This presentation describes NASA Glenn Research Center's approach in developing a common software platform for processing waveform-based NDE signals and images. This platform is currently in use at NASA Glenn and at Lockheed Martin Michoud Assembly Facility for processing of pulsed terahertz and ultrasonic data. Highlights of the software operation will be given. A case study will be shown for use with terahertz data. The authors also request scientists and engineers who are interested in sharing customized signal and image processing algorithms to contribute to this effort by letting the authors code up and include these algorithms in future releases.

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.

Cross-platform validation and analysis environment for particle physics

NASA Astrophysics Data System (ADS)

Chekanov, S. V.; Pogrebnyak, I.; Wilbern, D.

2017-11-01

A multi-platform validation and analysis framework for public Monte Carlo simulation for high-energy particle collisions is discussed. The front-end of this framework uses the Python programming language, while the back-end is written in Java, which provides a multi-platform environment that can be run from a web browser and can easily be deployed at the grid sites. The analysis package includes all major software tools used in high-energy physics, such as Lorentz vectors, jet algorithms, histogram packages, graphic canvases, and tools for providing data access. This multi-platform software suite, designed to minimize OS-specific maintenance and deployment time, is used for online validation of Monte Carlo event samples through a web interface.

LIMAO: Cross-platform software for simulating laser-induced alignment and orientation dynamics of linear-, symmetric- and asymmetric tops

NASA Astrophysics Data System (ADS)

Szidarovszky, Tamás; Jono, Maho; Yamanouchi, Kaoru

2018-07-01

A user-friendly and cross-platform software called Laser-Induced Molecular Alignment and Orientation simulator (LIMAO) has been developed. The program can be used to simulate within the rigid rotor approximation the rotational dynamics of gas phase molecules induced by linearly polarized intense laser fields at a given temperature. The software is implemented in the Java and Mathematica programming languages. The primary aim of LIMAO is to aid experimental scientists in predicting and analyzing experimental data representing laser-induced spatial alignment and orientation of molecules.

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

PubMed Central

Alistar, Mirela; Gaudenz, Urs

2017-01-01

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

Radiation and scattering from printed antennas on cylindrically conformal platforms

NASA Technical Reports Server (NTRS)

Kempel, Leo C.; Volakis, John L.; Bindiganavale, Sunil

1994-01-01

The goal was to develop suitable methods and software for the analysis of antennas on cylindrical coated and uncoated platforms. Specifically, the finite element boundary integral and finite element ABC methods were employed successfully and associated software were developed for the analysis and design of wraparound and discrete cavity-backed arrays situated on cylindrical platforms. This work led to the successful implementation of analysis software for such antennas. Developments which played a role in this respect are the efficient implementation of the 3D Green's function for a metallic cylinder, the incorporation of the fast Fourier transform in computing the matrix-vector products executed in the solver of the finite element-boundary integral system, and the development of a new absorbing boundary condition for terminating the finite element mesh on cylindrical surfaces.

Hierarchical Petascale Simulation Framework For Stress Corrosion Cracking

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

Grama, Ananth

2013-12-18

A number of major accomplishments resulted from the project. These include: • Data Structures, Algorithms, and Numerical Methods for Reactive Molecular Dynamics. We have developed a range of novel data structures, algorithms, and solvers (amortized ILU, Spike) for use with ReaxFF and charge equilibration. • Parallel Formulations of ReactiveMD (Purdue ReactiveMolecular Dynamics Package, PuReMD, PuReMD-GPU, and PG-PuReMD) for Messaging, GPU, and GPU Cluster Platforms. We have developed efficient serial, parallel (MPI), GPU (Cuda), and GPU Cluster (MPI/Cuda) implementations. Our implementations have been demonstrated to be significantly better than the state of the art, both in terms of performance and scalability.more » • Comprehensive Validation in the Context of Diverse Applications. We have demonstrated the use of our software in diverse systems, including silica-water, silicon-germanium nanorods, and as part of other projects, extended it to applications ranging from explosives (RDX) to lipid bilayers (biomembranes under oxidative stress). • Open Source Software Packages for Reactive Molecular Dynamics. All versions of our soft- ware have been released over the public domain. There are over 100 major research groups worldwide using our software. • Implementation into the Department of Energy LAMMPS Software Package. We have also integrated our software into the Department of Energy LAMMPS software package.« less

OpenROCS: a software tool to control robotic observatories

NASA Astrophysics Data System (ADS)

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

2012-09-01

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