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

NASA Astrophysics Data System (ADS)

Yetman, G.; Downs, R. R.

2011-12-01

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

Building the Scientific Modeling Assistant: An interactive environment for specialized software design

NASA Technical Reports Server (NTRS)

Keller, Richard M.

1991-01-01

The construction of scientific software models is an integral part of doing science, both within NASA and within the scientific community at large. Typically, model-building is a time-intensive and painstaking process, involving the design of very large, complex computer programs. Despite the considerable expenditure of resources involved, completed scientific models cannot easily be distributed and shared with the larger scientific community due to the low-level, idiosyncratic nature of the implemented code. To address this problem, we have initiated a research project aimed at constructing a software tool called the Scientific Modeling Assistant. This tool provides automated assistance to the scientist in developing, using, and sharing software models. We describe the Scientific Modeling Assistant, and also touch on some human-machine interaction issues relevant to building a successful tool of this type.

GUIdock-VNC: using a graphical desktop sharing system to provide a browser-based interface for containerized software

PubMed Central

Mittal, Varun; Hung, Ling-Hong; Keswani, Jayant; Kristiyanto, Daniel; Lee, Sung Bong

2017-01-01

Abstract Background: Software container technology such as Docker can be used to package and distribute bioinformatics workflows consisting of multiple software implementations and dependencies. However, Docker is a command line–based tool, and many bioinformatics pipelines consist of components that require a graphical user interface. Results: We present a container tool called GUIdock-VNC that uses a graphical desktop sharing system to provide a browser-based interface for containerized software. GUIdock-VNC uses the Virtual Network Computing protocol to render the graphics within most commonly used browsers. We also present a minimal image builder that can add our proposed graphical desktop sharing system to any Docker packages, with the end result that any Docker packages can be run using a graphical desktop within a browser. In addition, GUIdock-VNC uses the Oauth2 authentication protocols when deployed on the cloud. Conclusions: As a proof-of-concept, we demonstrated the utility of GUIdock-noVNC in gene network inference. We benchmarked our container implementation on various operating systems and showed that our solution creates minimal overhead. PMID:28327936

GUIdock-VNC: using a graphical desktop sharing system to provide a browser-based interface for containerized software.

PubMed

Mittal, Varun; Hung, Ling-Hong; Keswani, Jayant; Kristiyanto, Daniel; Lee, Sung Bong; Yeung, Ka Yee

2017-04-01

Software container technology such as Docker can be used to package and distribute bioinformatics workflows consisting of multiple software implementations and dependencies. However, Docker is a command line-based tool, and many bioinformatics pipelines consist of components that require a graphical user interface. We present a container tool called GUIdock-VNC that uses a graphical desktop sharing system to provide a browser-based interface for containerized software. GUIdock-VNC uses the Virtual Network Computing protocol to render the graphics within most commonly used browsers. We also present a minimal image builder that can add our proposed graphical desktop sharing system to any Docker packages, with the end result that any Docker packages can be run using a graphical desktop within a browser. In addition, GUIdock-VNC uses the Oauth2 authentication protocols when deployed on the cloud. As a proof-of-concept, we demonstrated the utility of GUIdock-noVNC in gene network inference. We benchmarked our container implementation on various operating systems and showed that our solution creates minimal overhead. © The Authors 2017. Published by Oxford University Press.

A Dozen Years after Open Source's 1998 Birth, It's Time for "OpenTechComm"

ERIC Educational Resources Information Center

Still, Brian

2010-01-01

2008 marked the 10-year Anniversary of the Open Source movement, which has had a substantial impact on not only software production and adoption, but also on the sharing and distribution of information. Technical communication as a discipline has taken some advantage of the movement or its derivative software, but this article argues not as much…

Scalable Architecture for Federated Translational Inquiries Network (SAFTINet) Technology Infrastructure for a Distributed Data Network

PubMed Central

Schilling, Lisa M.; Kwan, Bethany M.; Drolshagen, Charles T.; Hosokawa, Patrick W.; Brandt, Elias; Pace, Wilson D.; Uhrich, Christopher; Kamerick, Michael; Bunting, Aidan; Payne, Philip R.O.; Stephens, William E.; George, Joseph M.; Vance, Mark; Giacomini, Kelli; Braddy, Jason; Green, Mika K.; Kahn, Michael G.

2013-01-01

Introduction: Distributed Data Networks (DDNs) offer infrastructure solutions for sharing electronic health data from across disparate data sources to support comparative effectiveness research. Data sharing mechanisms must address technical and governance concerns stemming from network security and data disclosure laws and best practices, such as HIPAA. Methods: The Scalable Architecture for Federated Translational Inquiries Network (SAFTINet) deploys TRIAD grid technology, a common data model, detailed technical documentation, and custom software for data harmonization to facilitate data sharing in collaboration with stakeholders in the care of safety net populations. Data sharing partners host TRIAD grid nodes containing harmonized clinical data within their internal or hosted network environments. Authorized users can use a central web-based query system to request analytic data sets. Discussion: SAFTINet DDN infrastructure achieved a number of data sharing objectives, including scalable and sustainable systems for ensuring harmonized data structures and terminologies and secure distributed queries. Initial implementation challenges were resolved through iterative discussions, development and implementation of technical documentation, governance, and technology solutions. PMID:25848567

Scalable Architecture for Federated Translational Inquiries Network (SAFTINet) Technology Infrastructure for a Distributed Data Network.

PubMed

Schilling, Lisa M; Kwan, Bethany M; Drolshagen, Charles T; Hosokawa, Patrick W; Brandt, Elias; Pace, Wilson D; Uhrich, Christopher; Kamerick, Michael; Bunting, Aidan; Payne, Philip R O; Stephens, William E; George, Joseph M; Vance, Mark; Giacomini, Kelli; Braddy, Jason; Green, Mika K; Kahn, Michael G

2013-01-01

Distributed Data Networks (DDNs) offer infrastructure solutions for sharing electronic health data from across disparate data sources to support comparative effectiveness research. Data sharing mechanisms must address technical and governance concerns stemming from network security and data disclosure laws and best practices, such as HIPAA. The Scalable Architecture for Federated Translational Inquiries Network (SAFTINet) deploys TRIAD grid technology, a common data model, detailed technical documentation, and custom software for data harmonization to facilitate data sharing in collaboration with stakeholders in the care of safety net populations. Data sharing partners host TRIAD grid nodes containing harmonized clinical data within their internal or hosted network environments. Authorized users can use a central web-based query system to request analytic data sets. SAFTINet DDN infrastructure achieved a number of data sharing objectives, including scalable and sustainable systems for ensuring harmonized data structures and terminologies and secure distributed queries. Initial implementation challenges were resolved through iterative discussions, development and implementation of technical documentation, governance, and technology solutions.

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

PubMed

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

2012-06-28

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

IHE cross-enterprise document sharing for imaging: interoperability testing software

PubMed Central

2010-01-01

Background With the deployments of Electronic Health Records (EHR), interoperability testing in healthcare is becoming crucial. EHR enables access to prior diagnostic information in order to assist in health decisions. It is a virtual system that results from the cooperation of several heterogeneous distributed systems. Interoperability between peers is therefore essential. Achieving interoperability requires various types of testing. Implementations need to be tested using software that simulates communication partners, and that provides test data and test plans. Results In this paper we describe a software that is used to test systems that are involved in sharing medical images within the EHR. Our software is used as part of the Integrating the Healthcare Enterprise (IHE) testing process to test the Cross Enterprise Document Sharing for imaging (XDS-I) integration profile. We describe its architecture and functionalities; we also expose the challenges encountered and discuss the elected design solutions. Conclusions EHR is being deployed in several countries. The EHR infrastructure will be continuously evolving to embrace advances in the information technology domain. Our software is built on a web framework to allow for an easy evolution with web technology. The testing software is publicly available; it can be used by system implementers to test their implementations. It can also be used by site integrators to verify and test the interoperability of systems, or by developers to understand specifications ambiguities, or to resolve implementations difficulties. PMID:20858241

IHE cross-enterprise document sharing for imaging: interoperability testing software.

PubMed

Noumeir, Rita; Renaud, Bérubé

2010-09-21

With the deployments of Electronic Health Records (EHR), interoperability testing in healthcare is becoming crucial. EHR enables access to prior diagnostic information in order to assist in health decisions. It is a virtual system that results from the cooperation of several heterogeneous distributed systems. Interoperability between peers is therefore essential. Achieving interoperability requires various types of testing. Implementations need to be tested using software that simulates communication partners, and that provides test data and test plans. In this paper we describe a software that is used to test systems that are involved in sharing medical images within the EHR. Our software is used as part of the Integrating the Healthcare Enterprise (IHE) testing process to test the Cross Enterprise Document Sharing for imaging (XDS-I) integration profile. We describe its architecture and functionalities; we also expose the challenges encountered and discuss the elected design solutions. EHR is being deployed in several countries. The EHR infrastructure will be continuously evolving to embrace advances in the information technology domain. Our software is built on a web framework to allow for an easy evolution with web technology. The testing software is publicly available; it can be used by system implementers to test their implementations. It can also be used by site integrators to verify and test the interoperability of systems, or by developers to understand specifications ambiguities, or to resolve implementations difficulties.

The Raid distributed database system

NASA Technical Reports Server (NTRS)

Bhargava, Bharat; Riedl, John

1989-01-01

Raid, a robust and adaptable distributed database system for transaction processing (TP), is described. Raid is a message-passing system, with server processes on each site to manage concurrent processing, consistent replicated copies during site failures, and atomic distributed commitment. A high-level layered communications package provides a clean location-independent interface between servers. The latest design of the package delivers messages via shared memory in a configuration with several servers linked into a single process. Raid provides the infrastructure to investigate various methods for supporting reliable distributed TP. Measurements on TP and server CPU time are presented, along with data from experiments on communications software, consistent replicated copy control during site failures, and concurrent distributed checkpointing. A software tool for evaluating the implementation of TP algorithms in an operating-system kernel is proposed.

Dataworks for GNSS: Software for Supporting Data Sharing and Federation of Geodetic Networks

NASA Astrophysics Data System (ADS)

Boler, F. M.; Meertens, C. M.; Miller, M. M.; Wier, S.; Rost, M.; Matykiewicz, J.

2015-12-01

Continuously-operating Global Navigation Satellite System (GNSS) networks are increasingly being installed globally for a wide variety of science and societal applications. GNSS enables Earth science research in areas including tectonic plate interactions, crustal deformation in response to loading by tectonics, magmatism, water and ice, and the dynamics of water - and thereby energy transfer - in the atmosphere at regional scale. The many individual scientists and organizations that set up GNSS stations globally are often open to sharing data, but lack the resources or expertise to deploy systems and software to manage and curate data and metadata and provide user tools that would support data sharing. UNAVCO previously gained experience in facilitating data sharing through the NASA-supported development of the Geodesy Seamless Archive Centers (GSAC) open source software. GSAC provides web interfaces and simple web services for data and metadata discovery and access, supports federation of multiple data centers, and simplifies transfer of data and metadata to long-term archives. The NSF supported the dissemination of GSAC to multiple European data centers forming the European Plate Observing System. To expand upon GSAC to provide end-to-end, instrument-to-distribution capability, UNAVCO developed Dataworks for GNSS with NSF funding to the COCONet project, and deployed this software on systems that are now operating as Regional GNSS Data Centers as part of the NSF-funded TLALOCNet and COCONet projects. Dataworks consists of software modules written in Python and Java for data acquisition, management and sharing. There are modules for GNSS receiver control and data download, a database schema for metadata, tools for metadata handling, ingest software to manage file metadata, data file management scripts, GSAC, scripts for mirroring station data and metadata from partner GSACs, and extensive software and operator documentation. UNAVCO plans to provide a cloud VM image of Dataworks that would allow standing up a Dataworks-enabled GNSS data center without requiring upfront investment in server hardware. By enabling data creators to organize their data and metadata for sharing, Dataworks helps scientists expand their data curation awareness and responsibility, and enhances data access for all.

Bringing your tools to CyVerse Discovery Environment using Docker

PubMed Central

Devisetty, Upendra Kumar; Kennedy, Kathleen; Sarando, Paul; Merchant, Nirav; Lyons, Eric

2016-01-01

Docker has become a very popular container-based virtualization platform for software distribution that has revolutionized the way in which scientific software and software dependencies (software stacks) can be packaged, distributed, and deployed. Docker makes the complex and time-consuming installation procedures needed for scientific software a one-time process. Because it enables platform-independent installation, versioning of software environments, and easy redeployment and reproducibility, Docker is an ideal candidate for the deployment of identical software stacks on different compute environments such as XSEDE and Amazon AWS. CyVerse’s Discovery Environment also uses Docker for integrating its powerful, community-recommended software tools into CyVerse’s production environment for public use. This paper will help users bring their tools into CyVerse Discovery Environment (DE) which will not only allows users to integrate their tools with relative ease compared to the earlier method of tool deployment in DE but will also help users to share their apps with collaborators and release them for public use. PMID:27803802

Bringing your tools to CyVerse Discovery Environment using Docker.

PubMed

Devisetty, Upendra Kumar; Kennedy, Kathleen; Sarando, Paul; Merchant, Nirav; Lyons, Eric

2016-01-01

Docker has become a very popular container-based virtualization platform for software distribution that has revolutionized the way in which scientific software and software dependencies (software stacks) can be packaged, distributed, and deployed. Docker makes the complex and time-consuming installation procedures needed for scientific software a one-time process. Because it enables platform-independent installation, versioning of software environments, and easy redeployment and reproducibility, Docker is an ideal candidate for the deployment of identical software stacks on different compute environments such as XSEDE and Amazon AWS. CyVerse's Discovery Environment also uses Docker for integrating its powerful, community-recommended software tools into CyVerse's production environment for public use. This paper will help users bring their tools into CyVerse Discovery Environment (DE) which will not only allows users to integrate their tools with relative ease compared to the earlier method of tool deployment in DE but will also help users to share their apps with collaborators and release them for public use.

Design distributed simulation platform for vehicle management system

NASA Astrophysics Data System (ADS)

Wen, Zhaodong; Wang, Zhanlin; Qiu, Lihua

2006-11-01

Next generation military aircraft requires the airborne management system high performance. General modules, data integration, high speed data bus and so on are needed to share and manage information of the subsystems efficiently. The subsystems include flight control system, propulsion system, hydraulic power system, environmental control system, fuel management system, electrical power system and so on. The unattached or mixed architecture is changed to integrated architecture. That means the whole airborne system is regarded into one system to manage. So the physical devices are distributed but the system information is integrated and shared. The process function of each subsystem are integrated (including general process modules, dynamic reconfiguration), furthermore, the sensors and the signal processing functions are shared. On the other hand, it is a foundation for power shared. Establish a distributed vehicle management system using 1553B bus and distributed processors which can provide a validation platform for the research of airborne system integrated management. This paper establishes the Vehicle Management System (VMS) simulation platform. Discuss the software and hardware configuration and analyze the communication and fault-tolerant method.

A multiarchitecture parallel-processing development environment

NASA Technical Reports Server (NTRS)

Townsend, Scott; Blech, Richard; Cole, Gary

1993-01-01

A description is given of the hardware and software of a multiprocessor test bed - the second generation Hypercluster system. The Hypercluster architecture consists of a standard hypercube distributed-memory topology, with multiprocessor shared-memory nodes. By using standard, off-the-shelf hardware, the system can be upgraded to use rapidly improving computer technology. The Hypercluster's multiarchitecture nature makes it suitable for researching parallel algorithms in computational field simulation applications (e.g., computational fluid dynamics). The dedicated test-bed environment of the Hypercluster and its custom-built software allows experiments with various parallel-processing concepts such as message passing algorithms, debugging tools, and computational 'steering'. Such research would be difficult, if not impossible, to achieve on shared, commercial systems.

Community-driven computational biology with Debian Linux.

PubMed

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

2010-12-21

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

A Content Markup Language for Data Services

NASA Astrophysics Data System (ADS)

Noviello, C.; Acampa, P.; Mango Furnari, M.

Network content delivery and documents sharing is possible using a variety of technologies, such as distributed databases, service-oriented applications, and so forth. The development of such systems is a complex job, because document life cycle involves a strong cooperation between domain experts and software developers. Furthermore, the emerging software methodologies, such as the service-oriented architecture and knowledge organization (e.g., semantic web) did not really solve the problems faced in a real distributed and cooperating settlement. In this chapter the authors' efforts to design and deploy a distribute and cooperating content management system are described. The main features of the system are a user configurable document type definition and a management middleware layer. It allows CMS developers to orchestrate the composition of specialized software components around the structure of a document. In this chapter are also reported some of the experiences gained on deploying the developed framework in a cultural heritage dissemination settlement.

Hardware/software codesign for embedded RISC core

NASA Astrophysics Data System (ADS)

Liu, Peng

2001-12-01

This paper describes hardware/software codesign method of the extendible embedded RISC core VIRGO, which based on MIPS-I instruction set architecture. VIRGO is described by Verilog hardware description language that has five-stage pipeline with shared 32-bit cache/memory interface, and it is controlled by distributed control scheme. Every pipeline stage has one small controller, which controls the pipeline stage status and cooperation among the pipeline phase. Since description use high level language and structure is distributed, VIRGO core has highly extension that can meet the requirements of application. We take look at the high-definition television MPEG2 MPHL decoder chip, constructed the hardware/software codesign virtual prototyping machine that can research on VIRGO core instruction set architecture, and system on chip memory size requirements, and system on chip software, etc. We also can evaluate the system on chip design and RISC instruction set based on the virtual prototyping machine platform.

The National Capital Region closed circuit television video interoperability project.

PubMed

Contestabile, John; Patrone, David; Babin, Steven

2016-01-01

The National Capital Region (NCR) includes many government jurisdictions and agencies using different closed circuit TV (CCTV) cameras and video management software. Because these agencies often must work together to respond to emergencies and events, a means of providing interoperability for CCTV video is critically needed. Video data from different CCTV systems that are not inherently interoperable is represented in the "data layer." An "integration layer" ingests the data layer source video and normalizes the different video formats. It then aggregates and distributes this video to a "presentation layer" where it can be viewed by almost any application used by other agencies and without any proprietary software. A native mobile video viewing application is also developed that uses the presentation layer to provide video to different kinds of smartphones. The NCR includes Washington, DC, and surrounding counties in Maryland and Virginia. The video sharing architecture allows one agency to see another agency's video in their native viewing application without the need to purchase new CCTV software or systems. A native smartphone application was also developed to enable them to share video via mobile devices even when they use different video management systems. A video sharing architecture has been developed for the NCR that creates an interoperable environment for sharing CCTV video in an efficient and cost effective manner. In addition, it provides the desired capability of sharing video via a native mobile application.

The NIH BD2K center for big data in translational genomics

PubMed Central

Paten, Benedict; Diekhans, Mark; Druker, Brian J; Friend, Stephen; Guinney, Justin; Gassner, Nadine; Guttman, Mitchell; James Kent, W; Mantey, Patrick; Margolin, Adam A; Massie, Matt; Novak, Adam M; Nothaft, Frank; Pachter, Lior; Patterson, David; Smuga-Otto, Maciej; Stuart, Joshua M; Van’t Veer, Laura; Haussler, David

2015-01-01

The world’s genomics data will never be stored in a single repository – rather, it will be distributed among many sites in many countries. No one site will have enough data to explain genotype to phenotype relationships in rare diseases; therefore, sites must share data. To accomplish this, the genetics community must forge common standards and protocols to make sharing and computing data among many sites a seamless activity. Through the Global Alliance for Genomics and Health, we are pioneering the development of shared application programming interfaces (APIs) to connect the world’s genome repositories. In parallel, we are developing an open source software stack (ADAM) that uses these APIs. This combination will create a cohesive genome informatics ecosystem. Using containers, we are facilitating the deployment of this software in a diverse array of environments. Through benchmarking efforts and big data driver projects, we are ensuring ADAM’s performance and utility. PMID:26174866

Evaluation of a low-end architecture for collaborative software development, remote observing, and data analysis from multiple sites

NASA Astrophysics Data System (ADS)

Messerotti, Mauro; Otruba, Wolfgang; Hanslmeier, Arnold

2000-06-01

The Kanzelhoehe Solar Observatory is an observing facility located in Carinthia (Austria) and operated by the Institute of Geophysics, Astrophysics and Meteorology of the Karl- Franzens University Graz. A set of instruments for solar surveillance at different wavelengths bands is continuously operated in automatic mode and is presently being upgraded to be used in supplying near-real-time solar activity indexes for space weather applications. In this frame, we tested a low-end software/hardware architecture running on the PC platform in a non-homogeneous, remotely distributed environment that allows efficient or moderately efficient application sharing at the Intranet and Extranet (i.e., Wide Area Network) levels respectively. Due to the geographical distributed of participating teams (Trieste, Italy; Kanzelhoehe and Graz, Austria), we have been using such features for collaborative remote software development and testing, data analysis and calibration, and observing run emulation from multiple sites as well. In this work, we describe the used architecture and its performances based on a series of application sharing tests we carried out to ascertain its effectiveness in real collaborative remote work, observations and data exchange. The system proved to be reliable at the Intranet level for most distributed tasks, limited to less demanding ones at the Extranet level, but quite effective in remote instrument control when real time response is not needed.

Distributed visualization of gridded geophysical data: the Carbon Data Explorer, version 0.2.3

NASA Astrophysics Data System (ADS)

Endsley, K. A.; Billmire, M. G.

2016-01-01

Due to the proliferation of geophysical models, particularly climate models, the increasing resolution of their spatiotemporal estimates of Earth system processes, and the desire to easily share results with collaborators, there is a genuine need for tools to manage, aggregate, visualize, and share data sets. We present a new, web-based software tool - the Carbon Data Explorer - that provides these capabilities for gridded geophysical data sets. While originally developed for visualizing carbon flux, this tool can accommodate any time-varying, spatially explicit scientific data set, particularly NASA Earth system science level III products. In addition, the tool's open-source licensing and web presence facilitate distributed scientific visualization, comparison with other data sets and uncertainty estimates, and data publishing and distribution.

Programming model for distributed intelligent systems

NASA Technical Reports Server (NTRS)

Sztipanovits, J.; Biegl, C.; Karsai, G.; Bogunovic, N.; Purves, B.; Williams, R.; Christiansen, T.

1988-01-01

A programming model and architecture which was developed for the design and implementation of complex, heterogeneous measurement and control systems is described. The Multigraph Architecture integrates artificial intelligence techniques with conventional software technologies, offers a unified framework for distributed and shared memory based parallel computational models and supports multiple programming paradigms. The system can be implemented on different hardware architectures and can be adapted to strongly different applications.

Experiences using OpenMP based on Computer Directed Software DSM on a PC Cluster

NASA Technical Reports Server (NTRS)

Hess, Matthias; Jost, Gabriele; Mueller, Matthias; Ruehle, Roland

2003-01-01

In this work we report on our experiences running OpenMP programs on a commodity cluster of PCs running a software distributed shared memory (DSM) system. We describe our test environment and report on the performance of a subset of the NAS Parallel Benchmarks that have been automaticaly parallelized for OpenMP. We compare the performance of the OpenMP implementations with that of their message passing counterparts and discuss performance differences.

Low cost and compact quantum key distribution

NASA Astrophysics Data System (ADS)

Duligall, J. L.; Godfrey, M. S.; Harrison, K. A.; Munro, W. J.; Rarity, J. G.

2006-10-01

We present the design of a novel free-space quantum cryptography system, complete with purpose-built software, that can operate in daylight conditions. The transmitter and receiver modules are built using inexpensive off-the-shelf components. Both modules are compact allowing the generation of renewed shared secrets on demand over a short range of a few metres. An analysis of the software is shown as well as results of error rates and therefore shared secret yields at varying background light levels. As the system is designed to eventually work in short-range consumer applications, we also present a use scenario where the consumer can regularly 'top up' a store of secrets for use in a variety of one-time-pad (OTP) and authentication protocols.

Reconfigurable Software for Controlling Formation Flying

NASA Technical Reports Server (NTRS)

Mueller, Joseph B.

2006-01-01

Software for a system to control the trajectories of multiple spacecraft flying in formation is being developed to reflect underlying concepts of (1) a decentralized approach to guidance and control and (2) reconfigurability of the control system, including reconfigurability of the software and of control laws. The software is organized as a modular network of software tasks. The computational load for both determining relative trajectories and planning maneuvers is shared equally among all spacecraft in a cluster. The flexibility and robustness of the software are apparent in the fact that tasks can be added, removed, or replaced during flight. In a computational simulation of a representative formation-flying scenario, it was demonstrated that the following are among the services performed by the software: Uploading of commands from a ground station and distribution of the commands among the spacecraft, Autonomous initiation and reconfiguration of formations, Autonomous formation of teams through negotiations among the spacecraft, Working out details of high-level commands (e.g., shapes and sizes of geometrically complex formations), Implementation of a distributed guidance law providing autonomous optimization and assignment of target states, and Implementation of a decentralized, fuel-optimal, impulsive control law for planning maneuvers.

Community-driven computational biology with Debian Linux

PubMed Central

2010-01-01

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

Experiences Using OpenMP Based on Compiler Directed Software DSM on a PC Cluster

NASA Technical Reports Server (NTRS)

Hess, Matthias; Jost, Gabriele; Mueller, Matthias; Ruehle, Roland; Biegel, Bryan (Technical Monitor)

2002-01-01

In this work we report on our experiences running OpenMP (message passing) programs on a commodity cluster of PCs (personal computers) running a software distributed shared memory (DSM) system. We describe our test environment and report on the performance of a subset of the NAS (NASA Advanced Supercomputing) Parallel Benchmarks that have been automatically parallelized for OpenMP. We compare the performance of the OpenMP implementations with that of their message passing counterparts and discuss performance differences.

Hypercluster Parallel Processor

NASA Technical Reports Server (NTRS)

Blech, Richard A.; Cole, Gary L.; Milner, Edward J.; Quealy, Angela

1992-01-01

Hypercluster computer system includes multiple digital processors, operation of which coordinated through specialized software. Configurable according to various parallel-computing architectures of shared-memory or distributed-memory class, including scalar computer, vector computer, reduced-instruction-set computer, and complex-instruction-set computer. Designed as flexible, relatively inexpensive system that provides single programming and operating environment within which one can investigate effects of various parallel-computing architectures and combinations on performance in solution of complicated problems like those of three-dimensional flows in turbomachines. Hypercluster software and architectural concepts are in public domain.

Software for Sharing and Management of Information

NASA Technical Reports Server (NTRS)

Chen, James R.; Wolfe, Shawn R.; Wragg, Stephen D.

2003-01-01

DIAMS is a set of computer programs that implements a system of collaborative agents that serve multiple, geographically distributed users communicating via the Internet. DIAMS provides a user interface as a Java applet that runs on each user s computer and that works within the context of the user s Internet-browser software. DIAMS helps all its users to manage, gain access to, share, and exchange information in databases that they maintain on their computers. One of the DIAMS agents is a personal agent that helps its owner find information most relevant to current needs. It provides software tools and utilities for users to manage their information repositories with dynamic organization and virtual views. Capabilities for generating flexible hierarchical displays are integrated with capabilities for indexed- query searching to support effective access to information. Automatic indexing methods are employed to support users queries and communication between agents. The catalog of a repository is kept in object-oriented storage to facilitate sharing of information. Collaboration between users is aided by matchmaker agents and by automated exchange of information. The matchmaker agents are designed to establish connections between users who have similar interests and expertise.

A Grid Infrastructure for Supporting Space-based Science Operations

NASA Technical Reports Server (NTRS)

Bradford, Robert N.; Redman, Sandra H.; McNair, Ann R. (Technical Monitor)

2002-01-01

Emerging technologies for computational grid infrastructures have the potential for revolutionizing the way computers are used in all aspects of our lives. Computational grids are currently being implemented to provide a large-scale, dynamic, and secure research and engineering environments based on standards and next-generation reusable software, enabling greater science and engineering productivity through shared resources and distributed computing for less cost than traditional architectures. Combined with the emerging technologies of high-performance networks, grids provide researchers, scientists and engineers the first real opportunity for an effective distributed collaborative environment with access to resources such as computational and storage systems, instruments, and software tools and services for the most computationally challenging applications.

Moving code - Sharing geoprocessing logic on the Web

NASA Astrophysics Data System (ADS)

Müller, Matthias; Bernard, Lars; Kadner, Daniel

2013-09-01

Efficient data processing is a long-standing challenge in remote sensing. Effective and efficient algorithms are required for product generation in ground processing systems, event-based or on-demand analysis, environmental monitoring, and data mining. Furthermore, the increasing number of survey missions and the exponentially growing data volume in recent years have created demand for better software reuse as well as an efficient use of scalable processing infrastructures. Solutions that address both demands simultaneously have begun to slowly appear, but they seldom consider the possibility to coordinate development and maintenance efforts across different institutions, community projects, and software vendors. This paper presents a new approach to share, reuse, and possibly standardise geoprocessing logic in the field of remote sensing. Drawing from the principles of service-oriented design and distributed processing, this paper introduces moving-code packages as self-describing software components that contain algorithmic code and machine-readable descriptions of the provided functionality, platform, and infrastructure, as well as basic information about exploitation rights. Furthermore, the paper presents a lean publishing mechanism by which to distribute these packages on the Web and to integrate them in different processing environments ranging from monolithic workstations to elastic computational environments or "clouds". The paper concludes with an outlook toward community repositories for reusable geoprocessing logic and their possible impact on data-driven science in general.

Software modifications to the Demonstration Advanced Avionics Systems (DAAS)

NASA Technical Reports Server (NTRS)

Nedell, B. F.; Hardy, G. H.

1984-01-01

Critical information required for the design of integrated avionics suitable for generation aviation is applied towards software modifications for the Demonstration Advanced Avionics System (DAAS). The program emphasizes the use of data busing, distributed microprocessors, shared electronic displays and data entry devices, and improved functional capability. A demonstration advanced avionics system (DAAS) is designed, built, and flight tested in a Cessna 402, twin engine, general aviation aircraft. Software modifications are made to DAAS at Ames concurrent with the flight test program. The changes are the result of the experience obtained with the system at Ames, and the comments of the pilots who evaluated the system.

ImTK: an open source multi-center information management toolkit

NASA Astrophysics Data System (ADS)

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

2008-03-01

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

Climate tools in mainstream Linux distributions

NASA Astrophysics Data System (ADS)

McKinstry, Alastair

2015-04-01

Debian/meterology is a project to integrate climate tools and analysis software into the mainstream Debian/Ubuntu Linux distributions. This work describes lessons learnt, and recommends practices for scientific software to be adopted and maintained in OS distributions. In addition to standard analysis tools (cdo,, grads, ferret, metview, ncl, etc.), software used by the Earth System Grid Federation was chosen for integraion, to enable ESGF portals to be built on this base; however exposing scientific codes via web APIs enables security weaknesses, normally ignorable, to be exposed. How tools are hardened, and what changes are required to handle security upgrades, are described. Secondly, to enable libraries and components (e.g. Python modules) to be integrated requires planning by writers: it is not sufficient to assume users can upgrade their code when you make incompatible changes. Here, practices are recommended to enable upgrades and co-installability of C, C++, Fortran and Python codes. Finally, software packages such as NetCDF and HDF5 can be built in multiple configurations. Tools may then expect incompatible versions of these libraries (e.g. serial and parallel) to be simultaneously available; how this was solved in Debian using "pkg-config" and shared library interfaces is described, and best practices for software writers to enable this are summarised.

Making it Easy to Construct Accurate Hydrological Models that Exploit High Performance Computers (Invited)

NASA Astrophysics Data System (ADS)

Kees, C. E.; Farthing, M. W.; Terrel, A.; Certik, O.; Seljebotn, D.

2013-12-01

This presentation will focus on two barriers to progress in the hydrological modeling community, and research and development conducted to lessen or eliminate them. The first is a barrier to sharing hydrological models among specialized scientists that is caused by intertwining the implementation of numerical methods with the implementation of abstract numerical modeling information. In the Proteus toolkit for computational methods and simulation, we have decoupled these two important parts of computational model through separate "physics" and "numerics" interfaces. More recently we have begun developing the Strong Form Language for easy and direct representation of the mathematical model formulation in a domain specific language embedded in Python. The second major barrier is sharing ANY scientific software tools that have complex library or module dependencies, as most parallel, multi-physics hydrological models must have. In this setting, users and developer are dependent on an entire distribution, possibly depending on multiple compilers and special instructions depending on the environment of the target machine. To solve these problem we have developed, hashdist, a stateless package management tool and a resulting portable, open source scientific software distribution.

Parallel computing for probabilistic fatigue analysis

NASA Technical Reports Server (NTRS)

Sues, Robert H.; Lua, Yuan J.; Smith, Mark D.

1993-01-01

This paper presents the results of Phase I research to investigate the most effective parallel processing software strategies and hardware configurations for probabilistic structural analysis. We investigate the efficiency of both shared and distributed-memory architectures via a probabilistic fatigue life analysis problem. We also present a parallel programming approach, the virtual shared-memory paradigm, that is applicable across both types of hardware. Using this approach, problems can be solved on a variety of parallel configurations, including networks of single or multiprocessor workstations. We conclude that it is possible to effectively parallelize probabilistic fatigue analysis codes; however, special strategies will be needed to achieve large-scale parallelism to keep large number of processors busy and to treat problems with the large memory requirements encountered in practice. We also conclude that distributed-memory architecture is preferable to shared-memory for achieving large scale parallelism; however, in the future, the currently emerging hybrid-memory architectures will likely be optimal.

Parallel Computing for Probabilistic Response Analysis of High Temperature Composites

NASA Technical Reports Server (NTRS)

Sues, R. H.; Lua, Y. J.; Smith, M. D.

1994-01-01

The objective of this Phase I research was to establish the required software and hardware strategies to achieve large scale parallelism in solving PCM problems. To meet this objective, several investigations were conducted. First, we identified the multiple levels of parallelism in PCM and the computational strategies to exploit these parallelisms. Next, several software and hardware efficiency investigations were conducted. These involved the use of three different parallel programming paradigms and solution of two example problems on both a shared-memory multiprocessor and a distributed-memory network of workstations.

Application of SLURM, BOINC, and GlusterFS as Software System for Sustainable Modeling and Data Analytics

NASA Astrophysics Data System (ADS)

Kashansky, Vladislav V.; Kaftannikov, Igor L.

2018-02-01

Modern numerical modeling experiments and data analytics problems in various fields of science and technology reveal a wide variety of serious requirements for distributed computing systems. Many scientific computing projects sometimes exceed the available resource pool limits, requiring extra scalability and sustainability. In this paper we share the experience and findings of our own on combining the power of SLURM, BOINC and GlusterFS as software system for scientific computing. Especially, we suggest a complete architecture and highlight important aspects of systems integration.

A synchronized computational architecture for generalized bilateral control of robot arms

NASA Technical Reports Server (NTRS)

Bejczy, Antal K.; Szakaly, Zoltan

1987-01-01

This paper describes a computational architecture for an interconnected high speed distributed computing system for generalized bilateral control of robot arms. The key method of the architecture is the use of fully synchronized, interrupt driven software. Since an objective of the development is to utilize the processing resources efficiently, the synchronization is done in the hardware level to reduce system software overhead. The architecture also achieves a balaced load on the communication channel. The paper also describes some architectural relations to trading or sharing manual and automatic control.

SDMtoolbox 2.0: the next generation Python-based GIS toolkit for landscape genetic, biogeographic and species distribution model analyses.

PubMed

Brown, Jason L; Bennett, Joseph R; French, Connor M

2017-01-01

SDMtoolbox 2.0 is a software package for spatial studies of ecology, evolution, and genetics. The release of SDMtoolbox 2.0 allows researchers to use the most current ArcGIS software and MaxEnt software, and reduces the amount of time that would be spent developing common solutions. The central aim of this software is to automate complicated and repetitive spatial analyses in an intuitive graphical user interface. One core tenant facilitates careful parameterization of species distribution models (SDMs) to maximize each model's discriminatory ability and minimize overfitting. This includes carefully processing of occurrence data, environmental data, and model parameterization. This program directly interfaces with MaxEnt, one of the most powerful and widely used species distribution modeling software programs, although SDMtoolbox 2.0 is not limited to species distribution modeling or restricted to modeling in MaxEnt. Many of the SDM pre- and post-processing tools have 'universal' analogs for use with any modeling software. The current version contains a total of 79 scripts that harness the power of ArcGIS for macroecology, landscape genetics, and evolutionary studies. For example, these tools allow for biodiversity quantification (such as species richness or corrected weighted endemism), generation of least-cost paths and corridors among shared haplotypes, assessment of the significance of spatial randomizations, and enforcement of dispersal limitations of SDMs projected into future climates-to only name a few functions contained in SDMtoolbox 2.0. Lastly, dozens of generalized tools exists for batch processing and conversion of GIS data types or formats, which are broadly useful to any ArcMap user.

Tools for Supporting Distributed Agile Project Planning

NASA Astrophysics Data System (ADS)

Wang, Xin; Maurer, Frank; Morgan, Robert; Oliveira, Josyleuda

Agile project planning plays an important part in agile software development. In distributed settings, project planning is severely impacted by the lack of face-to-face communication and the inability to share paper index cards amongst all meeting participants. To address these issues, several distributed agile planning tools were developed. The tools vary in features, functions and running platforms. In this chapter, we first summarize the requirements for distributed agile planning. Then we give an overview on existing agile planning tools. We also evaluate existing tools based on tool requirements. Finally, we present some practical advices for both designers and users of distributed agile planning tools.

Supporting geoscience with graphical-user-interface Internet tools for the Macintosh

NASA Astrophysics Data System (ADS)

Robin, Bernard

1995-07-01

This paper describes a suite of Macintosh graphical-user-interface (GUI) software programs that can be used in conjunction with the Internet to support geoscience education. These software programs allow science educators to access and retrieve a large body of resources from an increasing number of network sites, taking advantage of the intuitive, simple-to-use Macintosh operating system. With these tools, educators easily can locate, download, and exchange not only text files but also sound resources, video movie clips, and software application files from their desktop computers. Another major advantage of these software tools is that they are available at no cost and may be distributed freely. The following GUI software tools are described including examples of how they can be used in an educational setting: ∗ Eudora—an e-mail program ∗ NewsWatcher—a newsreader ∗ TurboGopher—a Gopher program ∗ Fetch—a software application for easy File Transfer Protocol (FTP) ∗ NCSA Mosaic—a worldwide hypertext browsing program. An explosive growth of online archives currently is underway as new electronic sites are being added continuously to the Internet. Many of these resources may be of interest to science educators who learn they can share not only ASCII text files, but also graphic image files, sound resources, QuickTime movie clips, and hypermedia projects with colleagues from locations around the world. These powerful, yet simple to learn GUI software tools are providing a revolution in how knowledge can be accessed, retrieved, and shared.

e!DAL - a framework to store, share and publish research data

PubMed Central

2014-01-01

Background The life-science community faces a major challenge in handling “big data”, highlighting the need for high quality infrastructures capable of sharing and publishing research data. Data preservation, analysis, and publication are the three pillars in the “big data life cycle”. The infrastructures currently available for managing and publishing data are often designed to meet domain-specific or project-specific requirements, resulting in the repeated development of proprietary solutions and lower quality data publication and preservation overall. Results e!DAL is a lightweight software framework for publishing and sharing research data. Its main features are version tracking, metadata management, information retrieval, registration of persistent identifiers (DOI), an embedded HTTP(S) server for public data access, access as a network file system, and a scalable storage backend. e!DAL is available as an API for local non-shared storage and as a remote API featuring distributed applications. It can be deployed “out-of-the-box” as an on-site repository. Conclusions e!DAL was developed based on experiences coming from decades of research data management at the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK). Initially developed as a data publication and documentation infrastructure for the IPK’s role as a data center in the DataCite consortium, e!DAL has grown towards being a general data archiving and publication infrastructure. The e!DAL software has been deployed into the Maven Central Repository. Documentation and Software are also available at: http://edal.ipk-gatersleben.de. PMID:24958009

e!DAL--a framework to store, share and publish research data.

PubMed

Arend, Daniel; Lange, Matthias; Chen, Jinbo; Colmsee, Christian; Flemming, Steffen; Hecht, Denny; Scholz, Uwe

2014-06-24

The life-science community faces a major challenge in handling "big data", highlighting the need for high quality infrastructures capable of sharing and publishing research data. Data preservation, analysis, and publication are the three pillars in the "big data life cycle". The infrastructures currently available for managing and publishing data are often designed to meet domain-specific or project-specific requirements, resulting in the repeated development of proprietary solutions and lower quality data publication and preservation overall. e!DAL is a lightweight software framework for publishing and sharing research data. Its main features are version tracking, metadata management, information retrieval, registration of persistent identifiers (DOI), an embedded HTTP(S) server for public data access, access as a network file system, and a scalable storage backend. e!DAL is available as an API for local non-shared storage and as a remote API featuring distributed applications. It can be deployed "out-of-the-box" as an on-site repository. e!DAL was developed based on experiences coming from decades of research data management at the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK). Initially developed as a data publication and documentation infrastructure for the IPK's role as a data center in the DataCite consortium, e!DAL has grown towards being a general data archiving and publication infrastructure. The e!DAL software has been deployed into the Maven Central Repository. Documentation and Software are also available at: http://edal.ipk-gatersleben.de.

Aho-Corasick String Matching on Shared and Distributed Memory Parallel Architectures

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

Tumeo, Antonino; Villa, Oreste; Chavarría-Miranda, Daniel

String matching is at the core of many critical applications, including network intrusion detection systems, search engines, virus scanners, spam filters, DNA and protein sequencing, and data mining. For all of these applications string matching requires a combination of (sometimes all) the following characteristics: high and/or predictable performance, support for large data sets and flexibility of integration and customization. Many software based implementations targeting conventional cache-based microprocessors fail to achieve high and predictable performance requirements, while Field-Programmable Gate Array (FPGA) implementations and dedicated hardware solutions fail to support large data sets (dictionary sizes) and are difficult to integrate and customize.more » The advent of multicore, multithreaded, and GPU-based systems is opening the possibility for software based solutions to reach very high performance at a sustained rate. This paper compares several software-based implementations of the Aho-Corasick string searching algorithm for high performance systems. We discuss the implementation of the algorithm on several types of shared-memory high-performance architectures (Niagara 2, large x86 SMPs and Cray XMT), distributed memory with homogeneous processing elements (InfiniBand cluster of x86 multicores) and heterogeneous processing elements (InfiniBand cluster of x86 multicores with NVIDIA Tesla C10 GPUs). We describe in detail how each solution achieves the objectives of supporting large dictionaries, sustaining high performance, and enabling customization and flexibility using various data sets.« less

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.

A knowledge based software engineering environment testbed

NASA Technical Reports Server (NTRS)

Gill, C.; Reedy, A.; Baker, L.

1985-01-01

The Carnegie Group Incorporated and Boeing Computer Services Company are developing a testbed which will provide a framework for integrating conventional software engineering tools with Artifical Intelligence (AI) tools to promote automation and productivity. The emphasis is on the transfer of AI technology to the software development process. Experiments relate to AI issues such as scaling up, inference, and knowledge representation. In its first year, the project has created a model of software development by representing software activities; developed a module representation formalism to specify the behavior and structure of software objects; integrated the model with the formalism to identify shared representation and inheritance mechanisms; demonstrated object programming by writing procedures and applying them to software objects; used data-directed and goal-directed reasoning to, respectively, infer the cause of bugs and evaluate the appropriateness of a configuration; and demonstrated knowledge-based graphics. Future plans include introduction of knowledge-based systems for rapid prototyping or rescheduling; natural language interfaces; blackboard architecture; and distributed processing

Multiprocessor shared-memory information exchange

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

Santoline, L.L.; Bowers, M.D.; Crew, A.W.

1989-02-01

In distributed microprocessor-based instrumentation and control systems, the inter-and intra-subsystem communication requirements ultimately form the basis for the overall system architecture. This paper describes a software protocol which addresses the intra-subsystem communications problem. Specifically the protocol allows for multiple processors to exchange information via a shared-memory interface. The authors primary goal is to provide a reliable means for information to be exchanged between central application processor boards (masters) and dedicated function processor boards (slaves) in a single computer chassis. The resultant Multiprocessor Shared-Memory Information Exchange (MSMIE) protocol, a standard master-slave shared-memory interface suitable for use in nuclear safety systems, ismore » designed to pass unidirectional buffers of information between the processors while providing a minimum, deterministic cycle time for this data exchange.« less

SimBOX: a scalable architecture for aggregate distributed command and control of spaceport and service constellation

NASA Astrophysics Data System (ADS)

Prasad, Guru; Jayaram, Sanjay; Ward, Jami; Gupta, Pankaj

2004-08-01

In this paper, Aximetric proposes a decentralized Command and Control (C2) architecture for a distributed control of a cluster of on-board health monitoring and software enabled control systems called SimBOX that will use some of the real-time infrastructure (RTI) functionality from the current military real-time simulation architecture. The uniqueness of the approach is to provide a "plug and play environment" for various system components that run at various data rates (Hz) and the ability to replicate or transfer C2 operations to various subsystems in a scalable manner. This is possible by providing a communication bus called "Distributed Shared Data Bus" and a distributed computing environment used to scale the control needs by providing a self-contained computing, data logging and control function module that can be rapidly reconfigured to perform different functions. This kind of software-enabled control is very much needed to meet the needs of future aerospace command and control functions.

SimBox: a simulation-based scalable architecture for distributed command and control of spaceport and service constellations

NASA Astrophysics Data System (ADS)

Prasad, Guru; Jayaram, Sanjay; Ward, Jami; Gupta, Pankaj

2004-09-01

In this paper, Aximetric proposes a decentralized Command and Control (C2) architecture for a distributed control of a cluster of on-board health monitoring and software enabled control systems called SimBOX that will use some of the real-time infrastructure (RTI) functionality from the current military real-time simulation architecture. The uniqueness of the approach is to provide a "plug and play environment" for various system components that run at various data rates (Hz) and the ability to replicate or transfer C2 operations to various subsystems in a scalable manner. This is possible by providing a communication bus called "Distributed Shared Data Bus" and a distributed computing environment used to scale the control needs by providing a self-contained computing, data logging and control function module that can be rapidly reconfigured to perform different functions. This kind of software-enabled control is very much needed to meet the needs of future aerospace command and control functions.

The NIH BD2K center for big data in translational genomics.

PubMed

Paten, Benedict; Diekhans, Mark; Druker, Brian J; Friend, Stephen; Guinney, Justin; Gassner, Nadine; Guttman, Mitchell; Kent, W James; Mantey, Patrick; Margolin, Adam A; Massie, Matt; Novak, Adam M; Nothaft, Frank; Pachter, Lior; Patterson, David; Smuga-Otto, Maciej; Stuart, Joshua M; Van't Veer, Laura; Wold, Barbara; Haussler, David

2015-11-01

The world's genomics data will never be stored in a single repository - rather, it will be distributed among many sites in many countries. No one site will have enough data to explain genotype to phenotype relationships in rare diseases; therefore, sites must share data. To accomplish this, the genetics community must forge common standards and protocols to make sharing and computing data among many sites a seamless activity. Through the Global Alliance for Genomics and Health, we are pioneering the development of shared application programming interfaces (APIs) to connect the world's genome repositories. In parallel, we are developing an open source software stack (ADAM) that uses these APIs. This combination will create a cohesive genome informatics ecosystem. Using containers, we are facilitating the deployment of this software in a diverse array of environments. Through benchmarking efforts and big data driver projects, we are ensuring ADAM's performance and utility. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

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

Jones, J.P.; Bangs, A.L.; Butler, P.L.

Hetero Helix is a programming environment which simulates shared memory on a heterogeneous network of distributed-memory computers. The machines in the network may vary with respect to their native operating systems and internal representation of numbers. Hetero Helix presents a simple programming model to developers, and also considers the needs of designers, system integrators, and maintainers. The key software technology underlying Hetero Helix is the use of a compiler'' which analyzes the data structures in shared memory and automatically generates code which translates data representations from the format native to each machine into a common format, and vice versa. Themore » design of Hetero Helix was motivated in particular by the requirements of robotics applications. Hetero Helix has been used successfully in an integration effort involving 27 CPUs in a heterogeneous network and a body of software totaling roughly 100,00 lines of code. 25 refs., 6 figs.« less

Experimental Internet Environment Software Development

NASA Technical Reports Server (NTRS)

Maddux, Gary A.

1998-01-01

Geographically distributed project teams need an Internet based collaborative work environment or "Intranet." The Virtual Research Center (VRC) is an experimental Intranet server that combines several services such as desktop conferencing, file archives, on-line publishing, and security. Using the World Wide Web (WWW) as a shared space paradigm, the Graphical User Interface (GUI) presents users with images of a lunar colony. Each project has a wing of the colony and each wing has a conference room, library, laboratory, and mail station. In FY95, the VRC development team proved the feasibility of this shared space concept by building a prototype using a Netscape commerce server and several public domain programs. Successful demonstrations of the prototype resulted in approval for a second phase. Phase 2, documented by this report, will produce a seamlessly integrated environment by introducing new technologies such as Java and Adobe Web Links to replace less efficient interface software.

Static analysis of the hull plate using the finite element method

NASA Astrophysics Data System (ADS)

Ion, A.

2015-11-01

This paper aims at presenting the static analysis for two levels of a container ship's construction as follows: the first level is at the girder / hull plate and the second level is conducted at the entire strength hull of the vessel. This article will describe the work for the static analysis of a hull plate. We shall use the software package ANSYS Mechanical 14.5. The program is run on a computer with four Intel Xeon X5260 CPU processors at 3.33 GHz, 32 GB memory installed. In terms of software, the shared memory parallel version of ANSYS refers to running ANSYS across multiple cores on a SMP system. The distributed memory parallel version of ANSYS (Distributed ANSYS) refers to running ANSYS across multiple processors on SMP systems or DMP systems.

SDMtoolbox 2.0: the next generation Python-based GIS toolkit for landscape genetic, biogeographic and species distribution model analyses

PubMed Central

Bennett, Joseph R.; French, Connor M.

2017-01-01

SDMtoolbox 2.0 is a software package for spatial studies of ecology, evolution, and genetics. The release of SDMtoolbox 2.0 allows researchers to use the most current ArcGIS software and MaxEnt software, and reduces the amount of time that would be spent developing common solutions. The central aim of this software is to automate complicated and repetitive spatial analyses in an intuitive graphical user interface. One core tenant facilitates careful parameterization of species distribution models (SDMs) to maximize each model’s discriminatory ability and minimize overfitting. This includes carefully processing of occurrence data, environmental data, and model parameterization. This program directly interfaces with MaxEnt, one of the most powerful and widely used species distribution modeling software programs, although SDMtoolbox 2.0 is not limited to species distribution modeling or restricted to modeling in MaxEnt. Many of the SDM pre- and post-processing tools have ‘universal’ analogs for use with any modeling software. The current version contains a total of 79 scripts that harness the power of ArcGIS for macroecology, landscape genetics, and evolutionary studies. For example, these tools allow for biodiversity quantification (such as species richness or corrected weighted endemism), generation of least-cost paths and corridors among shared haplotypes, assessment of the significance of spatial randomizations, and enforcement of dispersal limitations of SDMs projected into future climates—to only name a few functions contained in SDMtoolbox 2.0. Lastly, dozens of generalized tools exists for batch processing and conversion of GIS data types or formats, which are broadly useful to any ArcMap user. PMID:29230356

A comparison of time-shared vs. batch development of space software

NASA Technical Reports Server (NTRS)

Forthofer, M.

1977-01-01

In connection with a study regarding the ground support software development for the Space Shuttle, an investigation was conducted concerning the most suitable software development techniques to be employed. A time-sharing 'trial period' was used to determine whether or not time-sharing would be a cost-effective software development technique for the Ground Based Shuttle system. It was found that time-sharing substantially improved job turnaround and programmer access to the computer for the representative group of ground support programmers. Moreover, this improvement resulted in an estimated saving of over fifty programmer days during the trial period.

Developing a Cyberinfrastructure for integrated assessments of environmental contaminants.

PubMed

Kaur, Taranjit; Singh, Jatinder; Goodale, Wing M; Kramar, David; Nelson, Peter

2005-03-01

The objective of this study was to design and implement prototype software for capturing field data and automating the process for reporting and analyzing the distribution of mercury. The four phase process used to design, develop, deploy and evaluate the prototype software is described. Two different development strategies were used: (1) design of a mobile data collection application intended to capture field data in a meaningful format and automate transfer into user databases, followed by (2) a re-engineering of the original software to develop an integrated database environment with improved methods for aggregating and sharing data. Results demonstrated that innovative use of commercially available hardware and software components can lead to the development of an end-to-end digital cyberinfrastructure that captures, records, stores, transmits, compiles and integrates multi-source data as it relates to mercury.

Panorama: A Targeted Proteomics Knowledge Base

PubMed Central

2015-01-01

Panorama is a web application for storing, sharing, analyzing, and reusing targeted assays created and refined with Skyline,1 an increasingly popular Windows client software tool for targeted proteomics experiments. Panorama allows laboratories to store and organize curated results contained in Skyline documents with fine-grained permissions, which facilitates distributed collaboration and secure sharing of published and unpublished data via a web-browser interface. It is fully integrated with the Skyline workflow and supports publishing a document directly to a Panorama server from the Skyline user interface. Panorama captures the complete Skyline document information content in a relational database schema. Curated results published to Panorama can be aggregated and exported as chromatogram libraries. These libraries can be used in Skyline to pick optimal targets in new experiments and to validate peak identification of target peptides. Panorama is open-source and freely available. It is distributed as part of LabKey Server,2 an open source biomedical research data management system. Laboratories and organizations can set up Panorama locally by downloading and installing the software on their own servers. They can also request freely hosted projects on https://panoramaweb.org, a Panorama server maintained by the Department of Genome Sciences at the University of Washington. PMID:25102069

TeCo3D: a 3D telecooperation application based on VRML and Java

NASA Astrophysics Data System (ADS)

Mauve, Martin

1998-12-01

In this paper we present a method for sharing collaboration- unaware VRML content, e.g. 3D models which were not specifically developed for use in a distributed environment. This functionality is an essential requirement for the inclusion of arbitrary VRML content, as generated by standard CAD or animation software, into teleconferencing sessions. We have developed a 3D TeleCooperation (TeCo3D) prototype to demonstrate the feasibility of our approach. The basic services provided by the prototype are the distribution of cooperation unaware VRML content, the sharing of user interactions, and the joint viewing of the content. In order to achieve maximum portability, the prototype was developed completely in Java. This paper presents general aspects of sharing VRML content as well as the concepts, the architecture and the services of the TeCo3D prototype. Our approach relies on existing VRML browsers as the VRML presentation and execution engines while reliable multicast is used as the means of communication to provide for scalability.

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

NASA Astrophysics Data System (ADS)

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

2015-04-01

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

Shared virtual environments for aerospace training

NASA Technical Reports Server (NTRS)

Loftin, R. Bowen; Voss, Mark

1994-01-01

Virtual environments have the potential to significantly enhance the training of NASA astronauts and ground-based personnel for a variety of activities. A critical requirement is the need to share virtual environments, in real or near real time, between remote sites. It has been hypothesized that the training of international astronaut crews could be done more cheaply and effectively by utilizing such shared virtual environments in the early stages of mission preparation. The Software Technology Branch at NASA's Johnson Space Center has developed the capability for multiple users to simultaneously share the same virtual environment. Each user generates the graphics needed to create the virtual environment. All changes of object position and state are communicated to all users so that each virtual environment maintains its 'currency.' Examples of these shared environments will be discussed and plans for the utilization of the Department of Defense's Distributed Interactive Simulation (DIS) protocols for shared virtual environments will be presented. Finally, the impact of this technology on training and education in general will be explored.

Distributing Data to Hand-Held Devices in a Wireless Network

NASA Technical Reports Server (NTRS)

Hodges, Mark; Simmons, Layne

2008-01-01

ADROIT is a developmental computer program for real-time distribution of complex data streams for display on Web-enabled, portable terminals held by members of an operational team of a spacecraft-command-and-control center who may be located away from the center. Examples of such terminals include personal data assistants, laptop computers, and cellular telephones. ADROIT would make it unnecessary to equip each terminal with platform- specific software for access to the data streams or with software that implements the information-sharing protocol used to deliver telemetry data to clients in the center. ADROIT is a combination of middleware plus software specific to the center. (Middleware enables one application program to communicate with another by performing such functions as conversion, translation, consolidation, and/or integration.) ADROIT translates a data stream (voice, video, or alphanumerical data) from the center into Extensible Markup Language, effectuates a subscription process to determine who gets what data when, and presents the data to each user in real time. Thus, ADROIT is expected to enable distribution of operations and to reduce the cost of operations by reducing the number of persons required to be in the center.

System For Research On Multiple-Arm Robots

NASA Technical Reports Server (NTRS)

Backes, Paul G.; Hayati, Samad; Tso, Kam S.; Hayward, Vincent

1991-01-01

Kali system of computer programs and equipment provides environment for research on distributed programming and distributed control of coordinated-multiple-arm robots. Suitable for telerobotics research involving sensing and execution of low level tasks. Software and configuration of hardware designed flexible so system modified easily to test various concepts in control and programming of robots, including multiple-arm control, redundant-arm control, shared control, traded control, force control, force/position hybrid control, design and integration of sensors, teleoperation, task-space description and control, methods of adaptive control, control of flexible arms, and human factors.

Engineering the CernVM-Filesystem as a High Bandwidth Distributed Filesystem for Auxiliary Physics Data

NASA Astrophysics Data System (ADS)

Dykstra, D.; Bockelman, B.; Blomer, J.; Herner, K.; Levshina, T.; Slyz, M.

2015-12-01

A common use pattern in the computing models of particle physics experiments is running many distributed applications that read from a shared set of data files. We refer to this data is auxiliary data, to distinguish it from (a) event data from the detector (which tends to be different for every job), and (b) conditions data about the detector (which tends to be the same for each job in a batch of jobs). Relatively speaking, conditions data also tends to be relatively small per job where both event data and auxiliary data are larger per job. Unlike event data, auxiliary data comes from a limited working set of shared files. Since there is spatial locality of the auxiliary data access, the use case appears to be identical to that of the CernVM- Filesystem (CVMFS). However, we show that distributing auxiliary data through CVMFS causes the existing CVMFS infrastructure to perform poorly. We utilize a CVMFS client feature called "alien cache" to cache data on existing local high-bandwidth data servers that were engineered for storing event data. This cache is shared between the worker nodes at a site and replaces caching CVMFS files on both the worker node local disks and on the site's local squids. We have tested this alien cache with the dCache NFSv4.1 interface, Lustre, and the Hadoop Distributed File System (HDFS) FUSE interface, and measured performance. In addition, we use high-bandwidth data servers at central sites to perform the CVMFS Stratum 1 function instead of the low-bandwidth web servers deployed for the CVMFS software distribution function. We have tested this using the dCache HTTP interface. As a result, we have a design for an end-to-end high-bandwidth distributed caching read-only filesystem, using existing client software already widely deployed to grid worker nodes and existing file servers already widely installed at grid sites. Files are published in a central place and are soon available on demand throughout the grid and cached locally on the site with a convenient POSIX interface. This paper discusses the details of the architecture and reports performance measurements.

Engineering the CernVM-Filesystem as a High Bandwidth Distributed Filesystem for Auxiliary Physics Data

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

Dykstra, D.; Bockelman, B.; Blomer, J.

A common use pattern in the computing models of particle physics experiments is running many distributed applications that read from a shared set of data files. We refer to this data is auxiliary data, to distinguish it from (a) event data from the detector (which tends to be different for every job), and (b) conditions data about the detector (which tends to be the same for each job in a batch of jobs). Relatively speaking, conditions data also tends to be relatively small per job where both event data and auxiliary data are larger per job. Unlike event data, auxiliarymore » data comes from a limited working set of shared files. Since there is spatial locality of the auxiliary data access, the use case appears to be identical to that of the CernVM- Filesystem (CVMFS). However, we show that distributing auxiliary data through CVMFS causes the existing CVMFS infrastructure to perform poorly. We utilize a CVMFS client feature called 'alien cache' to cache data on existing local high-bandwidth data servers that were engineered for storing event data. This cache is shared between the worker nodes at a site and replaces caching CVMFS files on both the worker node local disks and on the site's local squids. We have tested this alien cache with the dCache NFSv4.1 interface, Lustre, and the Hadoop Distributed File System (HDFS) FUSE interface, and measured performance. In addition, we use high-bandwidth data servers at central sites to perform the CVMFS Stratum 1 function instead of the low-bandwidth web servers deployed for the CVMFS software distribution function. We have tested this using the dCache HTTP interface. As a result, we have a design for an end-to-end high-bandwidth distributed caching read-only filesystem, using existing client software already widely deployed to grid worker nodes and existing file servers already widely installed at grid sites. Files are published in a central place and are soon available on demand throughout the grid and cached locally on the site with a convenient POSIX interface. This paper discusses the details of the architecture and reports performance measurements.« less

Globus | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

Globus software services provide secure cancer research data transfer, synchronization, and sharing in distributed environments at large scale. These services can be integrated into applications and research data gateways, leveraging Globus identity management, single sign-on, search, and authorization capabilities. Globus Genomics integrates Globus with the Galaxy genomics workflow engine and Amazon Web Services to enable cancer genomics analysis that can elastically scale compute resources with demand.

The open science grid

NASA Astrophysics Data System (ADS)

Pordes, Ruth; OSG Consortium; Petravick, Don; Kramer, Bill; Olson, Doug; Livny, Miron; Roy, Alain; Avery, Paul; Blackburn, Kent; Wenaus, Torre; Würthwein, Frank; Foster, Ian; Gardner, Rob; Wilde, Mike; Blatecky, Alan; McGee, John; Quick, Rob

2007-07-01

The Open Science Grid (OSG) provides a distributed facility where the Consortium members provide guaranteed and opportunistic access to shared computing and storage resources. OSG provides support for and evolution of the infrastructure through activities that cover operations, security, software, troubleshooting, addition of new capabilities, and support for existing and engagement with new communities. The OSG SciDAC-2 project provides specific activities to manage and evolve the distributed infrastructure and support it's use. The innovative aspects of the project are the maintenance and performance of a collaborative (shared & common) petascale national facility over tens of autonomous computing sites, for many hundreds of users, transferring terabytes of data a day, executing tens of thousands of jobs a day, and providing robust and usable resources for scientific groups of all types and sizes. More information can be found at the OSG web site: www.opensciencegrid.org.

SCSODC: Integrating Ocean Data for Visualization Sharing and Application

NASA Astrophysics Data System (ADS)

Xu, C.; Li, S.; Wang, D.; Xie, Q.

2014-02-01

The South China Sea Ocean Data Center (SCSODC) was founded in 2010 in order to improve collecting and managing of ocean data of the South China Sea Institute of Oceanology (SCSIO). The mission of SCSODC is to ensure the long term scientific stewardship of ocean data, information and products - collected through research groups, monitoring stations and observation cruises - and to facilitate the efficient use and distribution to possible users. However, data sharing and applications were limited due to the characteristics of distribution and heterogeneity that made it difficult to integrate the data. To surmount those difficulties, the Data Sharing System has been developed by the SCSODC using the most appropriate information management and information technology. The Data Sharing System uses open standards and tools to promote the capability to integrate ocean data and to interact with other data portals or users and includes a full range of processes such as data discovery, evaluation and access combining C/S and B/S mode. It provides a visualized management interface for the data managers and a transparent and seamless data access and application environment for users. Users are allowed to access data using the client software and to access interactive visualization application interface via a web browser. The architecture, key technologies and functionality of the system are discussed briefly in this paper. It is shown that the system of SCSODC is able to implement web visualization sharing and seamless access to ocean data in a distributed and heterogeneous environment.

SOLE: Applying Semantics and Social Web to Support Technology Enhanced Learning in Software Engineering

NASA Astrophysics Data System (ADS)

Colomo-Palacios, Ricardo; Jiménez-López, Diego; García-Crespo, Ángel; Blanco-Iglesias, Borja

eLearning educative processes are a challenge for educative institutions and education professionals. In an environment in which learning resources are being produced, catalogued and stored using innovative ways, SOLE provides a platform in which exam questions can be produced supported by Web 2.0 tools, catalogued and labeled via semantic web and stored and distributed using eLearning standards. This paper presents, SOLE, a social network of exam questions sharing particularized for Software Engineering domain, based on semantics and built using semantic web and eLearning standards, such as IMS Question and Test Interoperability specification 2.1.

Using Docker Compose for the Simple Deployment of an Integrated Drug Target Screening Platform.

PubMed

List, Markus

2017-06-10

Docker virtualization allows for software tools to be executed in an isolated and controlled environment referred to as a container. In Docker containers, dependencies are provided exactly as intended by the developer and, consequently, they simplify the distribution of scientific software and foster reproducible research. The Docker paradigm is that each container encapsulates one particular software tool. However, to analyze complex biomedical data sets, it is often necessary to combine several software tools into elaborate workflows. To address this challenge, several Docker containers need to be instantiated and properly integrated, which complicates the software deployment process unnecessarily. Here, we demonstrate how an extension to Docker, Docker compose, can be used to mitigate these problems by providing a unified setup routine that deploys several tools in an integrated fashion. We demonstrate the power of this approach by example of a Docker compose setup for a drug target screening platform consisting of five integrated web applications and shared infrastructure, deployable in just two lines of codes.

Software Defined Cyberinfrastructure

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

Foster, Ian; Blaiszik, Ben; Chard, Kyle

Within and across thousands of science labs, researchers and students struggle to manage data produced in experiments, simulations, and analyses. Largely manual research data lifecycle management processes mean that much time is wasted, research results are often irreproducible, and data sharing and reuse remain rare. In response, we propose a new approach to data lifecycle management in which researchers are empowered to define the actions to be performed at individual storage systems when data are created or modified: actions such as analysis, transformation, copying, and publication. We term this approach software-defined cyberinfrastructure because users can implement powerful data management policiesmore » by deploying rules to local storage systems, much as software-defined networking allows users to configure networks by deploying rules to switches.We argue that this approach can enable a new class of responsive distributed storage infrastructure that will accelerate research innovation by allowing any researcher to associate data workflows with data sources, whether local or remote, for such purposes as data ingest, characterization, indexing, and sharing. We report on early experiments with this approach in the context of experimental science, in which a simple if-trigger-then-action (IFTA) notation is used to define rules.« less

Migration of the Gaudi and LHCb software repositories from CVS to Subversion

NASA Astrophysics Data System (ADS)

Clemencic, M.; Degaudenzi, H.; LHCb Collaboration

2011-12-01

A common code repository is of primary importance in a distributed development environment such as large HEP experiments. CVS (Concurrent Versions System) has been used in the past years at CERN for the hosting of shared software repositories, among which were the repositories for the Gaudi Framework and the LHCb software projects. Many developers around the world produced alternative systems to share code and revisions among several developers, mainly to overcome the limitations in CVS, and CERN has recently started a new service for code hosting based on the version control system Subversion. The differences between CVS and Subversion and the way the code was organized in Gaudi and LHCb CVS repositories required careful study and planning of the migration. Special care was used to define the organization of the new Subversion repository. To avoid as much as possible disruption in the development cycle, the migration has been gradual with the help of tools developed explicitly to hide the differences between the two systems. The principles guiding the migration steps, the organization of the Subversion repository and the tools developed will be presented, as well as the problems encountered both from the librarian and the user points of view.

The AI Bus architecture for distributed knowledge-based systems

NASA Technical Reports Server (NTRS)

Schultz, Roger D.; Stobie, Iain

1991-01-01

The AI Bus architecture is layered, distributed object oriented framework developed to support the requirements of advanced technology programs for an order of magnitude improvement in software costs. The consequent need for highly autonomous computer systems, adaptable to new technology advances over a long lifespan, led to the design of an open architecture and toolbox for building large scale, robust, production quality systems. The AI Bus accommodates a mix of knowledge based and conventional components, running on heterogeneous, distributed real world and testbed environment. The concepts and design is described of the AI Bus architecture and its current implementation status as a Unix C++ library or reusable objects. Each high level semiautonomous agent process consists of a number of knowledge sources together with interagent communication mechanisms based on shared blackboards and message passing acquaintances. Standard interfaces and protocols are followed for combining and validating subsystems. Dynamic probes or demons provide an event driven means for providing active objects with shared access to resources, and each other, while not violating their security.

Parallel Computation of the Regional Ocean Modeling System (ROMS)

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

Wang, P; Song, Y T; Chao, Y

2005-04-05

The Regional Ocean Modeling System (ROMS) is a regional ocean general circulation modeling system solving the free surface, hydrostatic, primitive equations over varying topography. It is free software distributed world-wide for studying both complex coastal ocean problems and the basin-to-global scale ocean circulation. The original ROMS code could only be run on shared-memory systems. With the increasing need to simulate larger model domains with finer resolutions and on a variety of computer platforms, there is a need in the ocean-modeling community to have a ROMS code that can be run on any parallel computer ranging from 10 to hundreds ofmore » processors. Recently, we have explored parallelization for ROMS using the MPI programming model. In this paper, an efficient parallelization strategy for such a large-scale scientific software package, based on an existing shared-memory computing model, is presented. In addition, scientific applications and data-performance issues on a couple of SGI systems, including Columbia, the world's third-fastest supercomputer, are discussed.« less

ARX - A Comprehensive Tool for Anonymizing Biomedical Data

PubMed Central

Prasser, Fabian; Kohlmayer, Florian; Lautenschläger, Ronald; Kuhn, Klaus A.

2014-01-01

Collaboration and data sharing have become core elements of biomedical research. Especially when sensitive data from distributed sources are linked, privacy threats have to be considered. Statistical disclosure control allows the protection of sensitive data by introducing fuzziness. Reduction of data quality, however, needs to be balanced against gains in protection. Therefore, tools are needed which provide a good overview of the anonymization process to those responsible for data sharing. These tools require graphical interfaces and the use of intuitive and replicable methods. In addition, extensive testing, documentation and openness to reviews by the community are important. Existing publicly available software is limited in functionality, and often active support is lacking. We present ARX, an anonymization tool that i) implements a wide variety of privacy methods in a highly efficient manner, ii) provides an intuitive cross-platform graphical interface, iii) offers a programming interface for integration into other software systems, and iv) is well documented and actively supported. PMID:25954407

Information Sharing for Computing Trust Metrics on COTS Electronic Components

DTIC Science & Technology

2008-09-01

8 a. Standard SDLCs ...........................8 b. The Waterfall Model ......................9 c. V -shaped Model ...development of a system. There are many well-known SDLC models , the most popular of which are: • Waterfall • V -shaped • Spiral • Agile a. Standard...the SDLC or applied to software and hardware distribution chain. A. JØSANG’S MODEL DEFINED Jøsang expresses "opinions" mathematically as: 1

Lessons Learned In Developing Multiple Distributed Planning Systems for the International Space Station

NASA Technical Reports Server (NTRS)

Maxwell, Theresa G.; McNair, Ann R. (Technical Monitor)

2002-01-01

The planning processes for the International Space Station (ISS) Program are quite complex. Detailed mission planning for ISS on-orbit operations is a distributed function. Pieces of the on-orbit plan are developed by multiple planning organizations, located around the world, based on their respective expertise and responsibilities. The "pieces" are then integrated to yield the final detailed plan that will be executed onboard the ISS. Previous space programs have not distributed the planning and scheduling functions to this extent. Major ISS planning organizations are currently located in the United States (at both the NASA Johnson Space Center (JSC) and NASA Marshall Space Flight Center (MSFC)), in Russia, in Europe, and in Japan. Software systems have been developed by each of these planning organizations to support their assigned planning and scheduling functions. Although there is some cooperative development and sharing of key software components, each planning system has been tailored to meet the unique requirements and operational environment of the facility in which it operates. However, all the systems must operate in a coordinated fashion in order to effectively and efficiently produce a single integrated plan of ISS operations, in accordance with the established planning processes. This paper addresses lessons learned during the development of these multiple distributed planning systems, from the perspective of the developer of one of the software systems. The lessons focus on the coordination required to allow the multiple systems to operate together, rather than on the problems associated with the development of any particular system. Included in the paper is a discussion of typical problems faced during the development and coordination process, such as incompatible development schedules, difficulties in defining system interfaces, technical coordination and funding for shared tools, continually evolving planning concepts/requirements, programmatic and budget issues, and external influences. Techniques that mitigated some of these problems will also be addressed, along with recommendations for any future programs involving the development of multiple planning and scheduling systems. Many of these lessons learned are not unique to the area of planning and scheduling systems, so may be applied to other distributed ground systems that must operate in concert to successfully support space mission operations.

Lessons Learned in Developing Multiple Distributed Planning Systems for the International Space Station

NASA Technical Reports Server (NTRS)

Maxwell, Theresa G.

2002-01-01

The planning processes for the International Space Station (ISS) Program are quite complex. Detailed mission planning for ISS on-orbit operations is a distributed function. Pieces of the on-orbit plan are developed by multiple planning organizations, located around the world, based on their respective expertise and responsibilities. The pieces are then integrated to yield the final detailed plan that will be executed onboard the ISS. Previous space programs have not distributed the planning and scheduling functions to this extent. Major ISS planning organizations are currently located in the United States (at both the NASA Johnson Space Center (JSC) and NASA Marshall Space Flight Center (MSFC)), in Russia, in Europe, and in Japan. Software systems have been developed by each of these planning organizations to support their assigned planning and scheduling functions. Although there is some cooperative development and sharing of key software components, each planning system has been tailored to meet the unique requirements and operational environment of the facility in which it operates. However, all the systems must operate in a coordinated fashion in order to effectively and efficiently produce a single integrated plan of ISS operations, in accordance with the established planning processes. This paper addresses lessons learned during the development of these multiple distributed planning systems, from the perspective of the developer of one of the software systems. The lessons focus on the coordination required to allow the multiple systems to operate together, rather than on the problems associated with the development of any particular system. Included in the paper is a discussion of typical problems faced during the development and coordination process, such as incompatible development schedules, difficulties in defining system interfaces, technical coordination and funding for shared tools, continually evolving planning concepts/requirements, programmatic and budget issues, and external influences. Techniques that mitigated some of these problems will also be addressed, along with recommendations for any future programs involving the development of multiple planning and scheduling systems. Many of these lessons learned are not unique to the area of planning and scheduling systems, so may be applied to other distributed ground systems that must operate in concert to successfully support space mission operations.

MNE software for processing MEG and EEG data

PubMed Central

Gramfort, A.; Luessi, M.; Larson, E.; Engemann, D.; Strohmeier, D.; Brodbeck, C.; Parkkonen, L.; Hämäläinen, M.

2013-01-01

Magnetoencephalography and electroencephalography (M/EEG) measure the weak electromagnetic signals originating from neural currents in the brain. Using these signals to characterize and locate brain activity is a challenging task, as evidenced by several decades of methodological contributions. MNE, whose name stems from its capability to compute cortically-constrained minimum-norm current estimates from M/EEG data, is a software package that provides comprehensive analysis tools and workflows including preprocessing, source estimation, time–frequency analysis, statistical analysis, and several methods to estimate functional connectivity between distributed brain regions. The present paper gives detailed information about the MNE package and describes typical use cases while also warning about potential caveats in analysis. The MNE package is a collaborative effort of multiple institutes striving to implement and share best methods and to facilitate distribution of analysis pipelines to advance reproducibility of research. Full documentation is available at http://martinos.org/mne. PMID:24161808

Empirical analysis on the human dynamics of blogging behavior on GitHub

NASA Astrophysics Data System (ADS)

Yan, Deng-Cheng; Wei, Zong-Wen; Han, Xiao-Pu; Wang, Bing-Hong

2017-01-01

GitHub is a social collaborative coding platform on which software developers not only collaborate on codes but also share knowledge through blogs using GitHub Pages. In this article, we analyze the blogging behavior of software developers on GitHub Pages. The results show that both the commit number and the inter-event time of two consecutive blogging actions follow heavy-tailed distribution. We further observe a significant variety of activity among individual developers, and a strongly positive correlation between the activity and the power-law exponent of the inter-event time distribution. We also find a difference between the user behaviors of GitHub Pages and other online systems which is driven by the diversity of users and length of contents. In addition, our result shows an obvious difference between the majority of developers and elite developers in their burstiness property.

Hierarchical resilience with lightweight threads.

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

Wheeler, Kyle Bruce

2011-10-01

This paper proposes methodology for providing robustness and resilience for a highly threaded distributed- and shared-memory environment based on well-defined inputs and outputs to lightweight tasks. These inputs and outputs form a failure 'barrier', allowing tasks to be restarted or duplicated as necessary. These barriers must be expanded based on task behavior, such as communication between tasks, but do not prohibit any given behavior. One of the trends in high-performance computing codes seems to be a trend toward self-contained functions that mimic functional programming. Software designers are trending toward a model of software design where their core functions are specifiedmore » in side-effect free or low-side-effect ways, wherein the inputs and outputs of the functions are well-defined. This provides the ability to copy the inputs to wherever they need to be - whether that's the other side of the PCI bus or the other side of the network - do work on that input using local memory, and then copy the outputs back (as needed). This design pattern is popular among new distributed threading environment designs. Such designs include the Barcelona STARS system, distributed OpenMP systems, the Habanero-C and Habanero-Java systems from Vivek Sarkar at Rice University, the HPX/ParalleX model from LSU, as well as our own Scalable Parallel Runtime effort (SPR) and the Trilinos stateless kernels. This design pattern is also shared by CUDA and several OpenMP extensions for GPU-type accelerators (e.g. the PGI OpenMP extensions).« less

Fast implementation of length-adaptive privacy amplification in quantum key distribution

NASA Astrophysics Data System (ADS)

Zhang, Chun-Mei; Li, Mo; Huang, Jing-Zheng; Patcharapong, Treeviriyanupab; Li, Hong-Wei; Li, Fang-Yi; Wang, Chuan; Yin, Zhen-Qiang; Chen, Wei; Keattisak, Sripimanwat; Han, Zhen-Fu

2014-09-01

Post-processing is indispensable in quantum key distribution (QKD), which is aimed at sharing secret keys between two distant parties. It mainly consists of key reconciliation and privacy amplification, which is used for sharing the same keys and for distilling unconditional secret keys. In this paper, we focus on speeding up the privacy amplification process by choosing a simple multiplicative universal class of hash functions. By constructing an optimal multiplication algorithm based on four basic multiplication algorithms, we give a fast software implementation of length-adaptive privacy amplification. “Length-adaptive” indicates that the implementation of privacy amplification automatically adapts to different lengths of input blocks. When the lengths of the input blocks are 1 Mbit and 10 Mbit, the speed of privacy amplification can be as fast as 14.86 Mbps and 10.88 Mbps, respectively. Thus, it is practical for GHz or even higher repetition frequency QKD systems.

PANDA: A distributed multiprocessor operating system

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

Chubb, P.

1989-01-01

PANDA is a design for a distributed multiprocessor and an operating system. PANDA is designed to allow easy expansion of both hardware and software. As such, the PANDA kernel provides only message passing and memory and process management. The other features needed for the system (device drivers, secondary storage management, etc.) are provided as replaceable user tasks. The thesis presents PANDA's design and implementation, both hardware and software. PANDA uses multiple 68010 processors sharing memory on a VME bus, each such node potentially connected to others via a high speed network. The machine is completely homogeneous: there are no differencesmore » between processors that are detectable by programs running on the machine. A single two-processor node has been constructed. Each processor contains memory management circuits designed to allow processors to share page tables safely. PANDA presents a programmers' model similar to the hardware model: a job is divided into multiple tasks, each having its own address space. Within each task, multiple processes share code and data. Tasks can send messages to each other, and set up virtual circuits between themselves. Peripheral devices such as disc drives are represented within PANDA by tasks. PANDA divides secondary storage into volumes, each volume being accessed by a volume access task, or VAT. All knowledge about the way that data is stored on a disc is kept in its volume's VAT. The design is such that PANDA should provide a useful testbed for file systems and device drivers, as these can be installed without recompiling PANDA itself, and without rebooting the machine.« less

NA-42 TI Shared Software Component Library FY2011 Final Report

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

Knudson, Christa K.; Rutz, Frederick C.; Dorow, Kevin E.

The NA-42 TI program initiated an effort in FY2010 to standardize its software development efforts with the long term goal of migrating toward a software management approach that will allow for the sharing and reuse of code developed within the TI program, improve integration, ensure a level of software documentation, and reduce development costs. The Pacific Northwest National Laboratory (PNNL) has been tasked with two activities that support this mission. PNNL has been tasked with the identification, selection, and implementation of a Shared Software Component Library. The intent of the library is to provide a common repository that is accessiblemore » by all authorized NA-42 software development teams. The repository facilitates software reuse through a searchable and easy to use web based interface. As software is submitted to the repository, the component registration process captures meta-data and provides version control for compiled libraries, documentation, and source code. This meta-data is then available for retrieval and review as part of library search results. In FY2010, PNNL and staff from the Remote Sensing Laboratory (RSL) teamed up to develop a software application with the goal of replacing the aging Aerial Measuring System (AMS). The application under development includes an Advanced Visualization and Integration of Data (AVID) framework and associated AMS modules. Throughout development, PNNL and RSL have utilized a common AMS code repository for collaborative code development. The AMS repository is hosted by PNNL, is restricted to the project development team, is accessed via two different geographic locations and continues to be used. The knowledge gained from the collaboration and hosting of this repository in conjunction with PNNL software development and systems engineering capabilities were used in the selection of a package to be used in the implementation of the software component library on behalf of NA-42 TI. The second task managed by PNNL is the development and continued maintenance of the NA-42 TI Software Development Questionnaire. This questionnaire is intended to help software development teams working under NA-42 TI in documenting their development activities. When sufficiently completed, the questionnaire illustrates that the software development activities recorded incorporate significant aspects of the software engineering lifecycle. The questionnaire template is updated as comments are received from NA-42 and/or its development teams and revised versions distributed to those using the questionnaire. PNNL also maintains a list of questionnaire recipients. The blank questionnaire template, the AVID and AMS software being developed, and the completed AVID AMS specific questionnaire are being used as the initial content to be established in the TI Component Library. This report summarizes the approach taken to identify requirements, search for and evaluate technologies, and the approach taken for installation of the software needed to host the component library. Additionally, it defines the process by which users request access for the contribution and retrieval of library content.« less

32 CFR 37.550 - May I accept intellectual property as cost sharing?

Code of Federal Regulations, 2013 CFR

2013-07-01

... software) as cost sharing, because: (1) It is difficult to assign values to these intangible contributions... offer the use of commercially available software for which there is an established license fee for use of the product. The costs of the development of the software would not be a reasonable basis for...

32 CFR 37.550 - May I accept intellectual property as cost sharing?

Code of Federal Regulations, 2011 CFR

2011-07-01

... offer the use of commercially available software for which there is an established license fee for use of the product. The costs of the development of the software would not be a reasonable basis for... software) as cost sharing, because: (1) It is difficult to assign values to these intangible contributions...

AAS Publishing News: Astronomical Software Citation Workshop

NASA Astrophysics Data System (ADS)

Kohler, Susanna

2015-07-01

Do you write code for your research? Use astronomical software? Do you wish there were a better way of citing, sharing, archiving, or discovering software for astronomy research? You're not alone! In April 2015, AAS's publishing team joined other leaders in the astronomical software community in a meeting funded by the Sloan Foundation, with the purpose of discussing these issues and potential solutions. In attendance were representatives from academic astronomy, publishing, libraries, for-profit software sharing platforms, telescope facilities, and grantmaking institutions. The goal of the group was to establish “protocols, policies, and platforms for astronomical software citation, sharing, and archiving,” in the hopes of encouraging a set of normalized standards across the field. The AAS is now collaborating with leaders at GitHub to write grant proposals for a project to develop strategies for software discoverability and citation, in astronomy and beyond. If this topic interests you, you can find more details in this document released by the group after the meeting: http://astronomy-software-index.github.io/2015-workshop/ The group hopes to move this project forward with input and support from the broader community. Please share the above document, discuss it on social media using the hashtag #astroware (so that your conversations can be found!), or send private comments to julie.steffen@aas.org.

Distributed medical services within the ATM-based Berlin regional test bed

NASA Astrophysics Data System (ADS)

Thiel, Andreas; Bernarding, Johannes; Krauss, Manfred; Schulz, Sandra; Tolxdorff, Thomas

1996-05-01

The ATM-based Metropolitan Area Network (MAN) of Berlin connects two university hospitals (Benjamin Franklin University Hospital and Charite) with the computer resources of the Technical University of Berlin (TUB). Distributed new medical services have been implemented and will be evaluated within the highspeed MAN of Berlin. The network with its data transmission rates of up to 155 Mbit/s renders these medical services externally available to practicing physicians. Resource and application sharing is demonstrated by the use of two software systems. The first software system is an interactive 3D reconstruction tool (3D- Medbild), based on a client-server mechanism. This structure allows the use of high- performance computers at the TUB from the low-level workstations in the hospitals. A second software system, RAMSES, utilizes a tissue database of Magnetic Resonance Images. For the remote control of the software, the developed applications use standards such as DICOM 3.0 and features of the World Wide Web. Data security concepts are being tested and integrated for the needs of the sensitive medical data. The highspeed network is the necessary prerequisite for the clinical evaluation of data in a joint teleconference. The transmission of digitized real-time sequences such as video and ultrasound and the interactive manipulation of data are made possible by Multi Media tools.

Second International Workshop on Software Engineering and Code Design in Parallel Meteorological and Oceanographic Applications

NASA Technical Reports Server (NTRS)

OKeefe, Matthew (Editor); Kerr, Christopher L. (Editor)

1998-01-01

This report contains the abstracts and technical papers from the Second International Workshop on Software Engineering and Code Design in Parallel Meteorological and Oceanographic Applications, held June 15-18, 1998, in Scottsdale, Arizona. The purpose of the workshop is to bring together software developers in meteorology and oceanography to discuss software engineering and code design issues for parallel architectures, including Massively Parallel Processors (MPP's), Parallel Vector Processors (PVP's), Symmetric Multi-Processors (SMP's), Distributed Shared Memory (DSM) multi-processors, and clusters. Issues to be discussed include: (1) code architectures for current parallel models, including basic data structures, storage allocation, variable naming conventions, coding rules and styles, i/o and pre/post-processing of data; (2) designing modular code; (3) load balancing and domain decomposition; (4) techniques that exploit parallelism efficiently yet hide the machine-related details from the programmer; (5) tools for making the programmer more productive; and (6) the proliferation of programming models (F--, OpenMP, MPI, and HPF).

Eleven quick tips for architecting biomedical informatics workflows with cloud computing.

PubMed

Cole, Brian S; Moore, Jason H

2018-03-01

Cloud computing has revolutionized the development and operations of hardware and software across diverse technological arenas, yet academic biomedical research has lagged behind despite the numerous and weighty advantages that cloud computing offers. Biomedical researchers who embrace cloud computing can reap rewards in cost reduction, decreased development and maintenance workload, increased reproducibility, ease of sharing data and software, enhanced security, horizontal and vertical scalability, high availability, a thriving technology partner ecosystem, and much more. Despite these advantages that cloud-based workflows offer, the majority of scientific software developed in academia does not utilize cloud computing and must be migrated to the cloud by the user. In this article, we present 11 quick tips for architecting biomedical informatics workflows on compute clouds, distilling knowledge gained from experience developing, operating, maintaining, and distributing software and virtualized appliances on the world's largest cloud. Researchers who follow these tips stand to benefit immediately by migrating their workflows to cloud computing and embracing the paradigm of abstraction.

Eleven quick tips for architecting biomedical informatics workflows with cloud computing

PubMed Central

Moore, Jason H.

2018-01-01

Cloud computing has revolutionized the development and operations of hardware and software across diverse technological arenas, yet academic biomedical research has lagged behind despite the numerous and weighty advantages that cloud computing offers. Biomedical researchers who embrace cloud computing can reap rewards in cost reduction, decreased development and maintenance workload, increased reproducibility, ease of sharing data and software, enhanced security, horizontal and vertical scalability, high availability, a thriving technology partner ecosystem, and much more. Despite these advantages that cloud-based workflows offer, the majority of scientific software developed in academia does not utilize cloud computing and must be migrated to the cloud by the user. In this article, we present 11 quick tips for architecting biomedical informatics workflows on compute clouds, distilling knowledge gained from experience developing, operating, maintaining, and distributing software and virtualized appliances on the world’s largest cloud. Researchers who follow these tips stand to benefit immediately by migrating their workflows to cloud computing and embracing the paradigm of abstraction. PMID:29596416

Interface Specifications for the A-7E Shared Services Module.

DTIC Science & Technology

1982-09-08

To illustrate the principles, the onboard software for the Navy’s A-7E aircraft will be redesigned and rewritten. The Shared Services module provides...purpose of the Shared Services module is to allow the remainder of the software to remain unchanged when the requirements-based rules for these values and...services change. This report describes the modular structure of the Shared Services module, and contains the abstract interface specifications for all

A comparison of queueing, cluster and distributed computing systems

NASA Technical Reports Server (NTRS)

Kaplan, Joseph A.; Nelson, Michael L.

1993-01-01

Using workstation clusters for distributed computing has become popular with the proliferation of inexpensive, powerful workstations. Workstation clusters offer both a cost effective alternative to batch processing and an easy entry into parallel computing. However, a number of workstations on a network does not constitute a cluster. Cluster management software is necessary to harness the collective computing power. A variety of cluster management and queuing systems are compared: Distributed Queueing Systems (DQS), Condor, Load Leveler, Load Balancer, Load Sharing Facility (LSF - formerly Utopia), Distributed Job Manager (DJM), Computing in Distributed Networked Environments (CODINE), and NQS/Exec. The systems differ in their design philosophy and implementation. Based on published reports on the different systems and conversations with the system's developers and vendors, a comparison of the systems are made on the integral issues of clustered computing.

An Analysis of Security and Privacy Issues in Smart Grid Software Architectures on Clouds

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

Simmhan, Yogesh; Kumbhare, Alok; Cao, Baohua

2011-07-09

Power utilities globally are increasingly upgrading to Smart Grids that use bi-directional communication with the consumer to enable an information-driven approach to distributed energy management. Clouds offer features well suited for Smart Grid software platforms and applications, such as elastic resources and shared services. However, the security and privacy concerns inherent in an information rich Smart Grid environment are further exacerbated by their deployment on Clouds. Here, we present an analysis of security and privacy issues in a Smart Grids software architecture operating on different Cloud environments, in the form of a taxonomy. We use the Los Angeles Smart Gridmore » Project that is underway in the largest U.S. municipal utility to drive this analysis that will benefit both Cloud practitioners targeting Smart Grid applications, and Cloud researchers investigating security and privacy.« less

Browndye: A software package for Brownian dynamics

NASA Astrophysics Data System (ADS)

Huber, Gary A.; McCammon, J. Andrew

2010-11-01

A new software package, Browndye, is presented for simulating the diffusional encounter of two large biological molecules. It can be used to estimate second-order rate constants and encounter probabilities, and to explore reaction trajectories. Browndye builds upon previous knowledge and algorithms from software packages such as UHBD, SDA, and Macrodox, while implementing algorithms that scale to larger systems. Program summaryProgram title: Browndye Catalogue identifier: AEGT_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGT_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: MIT license, included in distribution No. of lines in distributed program, including test data, etc.: 143 618 No. of bytes in distributed program, including test data, etc.: 1 067 861 Distribution format: tar.gz Programming language: C++, OCaml ( http://caml.inria.fr/) Computer: PC, Workstation, Cluster Operating system: Linux Has the code been vectorised or parallelized?: Yes. Runs on multiple processors with shared memory using pthreads RAM: Depends linearly on size of physical system Classification: 3 External routines: uses the output of APBS [1] ( http://www.poissonboltzmann.org/apbs/) as input. APBS must be obtained and installed separately. Expat 2.0.1, CLAPACK, ocaml-expat, Mersenne Twister. These are included in the Browndye distribution. Nature of problem: Exploration and determination of rate constants of bimolecular interactions involving large biological molecules. Solution method: Brownian dynamics with electrostatic, excluded volume, van der Waals, and desolvation forces. Running time: Depends linearly on size of physical system and quadratically on precision of results. The included example executes in a few minutes.

GLobal Integrated Design Environment (GLIDE): A Concurrent Engineering Application

NASA Technical Reports Server (NTRS)

McGuire, Melissa L.; Kunkel, Matthew R.; Smith, David A.

2010-01-01

The GLobal Integrated Design Environment (GLIDE) is a client-server software application purpose-built to mitigate issues associated with real time data sharing in concurrent engineering environments and to facilitate discipline-to-discipline interaction between multiple engineers and researchers. GLIDE is implemented in multiple programming languages utilizing standardized web protocols to enable secure parameter data sharing between engineers and researchers across the Internet in closed and/or widely distributed working environments. A well defined, HyperText Transfer Protocol (HTTP) based Application Programming Interface (API) to the GLIDE client/server environment enables users to interact with GLIDE, and each other, within common and familiar tools. One such common tool, Microsoft Excel (Microsoft Corporation), paired with its add-in API for GLIDE, is discussed in this paper. The top-level examples given demonstrate how this interface improves the efficiency of the design process of a concurrent engineering study while reducing potential errors associated with manually sharing information between study participants.

Towards an Ontology-Based Approach to Support Monitoring the Data of the International Monitoring System (IMS)

NASA Astrophysics Data System (ADS)

Laban, Shaban; El-Desouky, Ali

2010-05-01

The heterogeneity of the distributed processing systems, monitored data and resources is an obvious challenge in monitoring the data of International Monitoring System (IMS) of the Comprehensive Nuclear Test-Ban Treaty organization (CTBTO). Processing engineers, analysts, operators and other interested parties seek for intelligent tools and software that hide the underlying complexity of the systems, allowing them to manage the operation and monitoring the systems at a higher level, focusing on what the expected behavior and results should be instead of how to specifically achieve it. Also, it is needed to share common understanding of the structure of organization information, data, and products among staff, software agents, and policy making organs. Additionally, introducing new monitoring object or system should not complicate the overall system and should be feasible. An ontologybased approach is presented in this paper aiming to support monitoring real-time data processing and supervising the various system resources, focusing on integrating and sharing same knowledge and status information of the system among different environments. The results of a prototype framework is presented and analyzed.

Caltrans WeatherShare Phase II System: An Application of Systems and Software Engineering Process to Project Development

DOT National Transportation Integrated Search

2009-08-25

In cooperation with the California Department of Transportation, Montana State University's Western Transportation Institute has developed the WeatherShare Phase II system by applying Systems Engineering and Software Engineering processes. The system...

Sharing lattice QCD data over a widely distributed file system

NASA Astrophysics Data System (ADS)

Amagasa, T.; Aoki, S.; Aoki, Y.; Aoyama, T.; Doi, T.; Fukumura, K.; Ishii, N.; Ishikawa, K.-I.; Jitsumoto, H.; Kamano, H.; Konno, Y.; Matsufuru, H.; Mikami, Y.; Miura, K.; Sato, M.; Takeda, S.; Tatebe, O.; Togawa, H.; Ukawa, A.; Ukita, N.; Watanabe, Y.; Yamazaki, T.; Yoshie, T.

2015-12-01

JLDG is a data-grid for the lattice QCD (LQCD) community in Japan. Several large research groups in Japan have been working on lattice QCD simulations using supercomputers distributed over distant sites. The JLDG provides such collaborations with an efficient method of data management and sharing. File servers installed on 9 sites are connected to the NII SINET VPN and are bound into a single file system with the GFarm. The file system looks the same from any sites, so that users can do analyses on a supercomputer on a site, using data generated and stored in the JLDG at a different site. We present a brief description of hardware and software of the JLDG, including a recently developed subsystem for cooperating with the HPCI shared storage, and report performance and statistics of the JLDG. As of April 2015, 15 research groups (61 users) store their daily research data of 4.7PB including replica and 68 million files in total. Number of publications for works which used the JLDG is 98. The large number of publications and recent rapid increase of disk usage convince us that the JLDG has grown up into a useful infrastructure for LQCD community in Japan.

Artificial intelligence support for scientific model-building

NASA Technical Reports Server (NTRS)

Keller, Richard M.

1992-01-01

Scientific model-building can be a time-intensive and painstaking process, often involving the development of large and complex computer programs. Despite the effort involved, scientific models cannot easily be distributed and shared with other scientists. In general, implemented scientific models are complex, idiosyncratic, and difficult for anyone but the original scientific development team to understand. We believe that artificial intelligence techniques can facilitate both the model-building and model-sharing process. In this paper, we overview our effort to build a scientific modeling software tool that aids the scientist in developing and using models. This tool includes an interactive intelligent graphical interface, a high-level domain specific modeling language, a library of physics equations and experimental datasets, and a suite of data display facilities.

[Research on tumor information grid framework].

PubMed

Zhang, Haowei; Qin, Zhu; Liu, Ying; Tan, Jianghao; Cao, Haitao; Chen, Youping; Zhang, Ke; Ding, Yuqing

2013-10-01

In order to realize tumor disease information sharing and unified management, we utilized grid technology to make the data and software resources which distributed in various medical institutions for effective integration so that we could make the heterogeneous resources consistent and interoperable in both semantics and syntax aspects. This article describes the tumor grid framework, the type of the service being packaged in Web Service Description Language (WSDL) and extensible markup language schemas definition (XSD), the client use the serialized document to operate the distributed resources. The service objects could be built by Unified Modeling Language (UML) as middle ware to create application programming interface. All of the grid resources are registered in the index and released in the form of Web Services based on Web Services Resource Framework (WSRF). Using the system we can build a multi-center, large sample and networking tumor disease resource sharing framework to improve the level of development in medical scientific research institutions and the patient's quality of life.

Plug into a Network.

ERIC Educational Resources Information Center

Vander Linden, Doug; Clark, Larry

1994-01-01

Stand-alone, single-user software programs for classroom use can be prohibitively expensive, compared to information-sharing network systems. Based on a Kansas district's experience, this article explains three types of networks (device-sharing, operating-system-based, and client-server-based) and discusses network protocols, software choices,…

Raising Virtual Laboratories in Australia onto global platforms

NASA Astrophysics Data System (ADS)

Wyborn, L. A.; Barker, M.; Fraser, R.; Evans, B. J. K.; Moloney, G.; Proctor, R.; Moise, A. F.; Hamish, H.

2016-12-01

Across the globe, Virtual Laboratories (VLs), Science Gateways (SGs), and Virtual Research Environments (VREs) are being developed that enable users who are not co-located to actively work together at various scales to share data, models, tools, software, workflows, best practices, etc. Outcomes range from enabling `long tail' researchers to more easily access specific data collections, to facilitating complex workflows on powerful supercomputers. In Australia, government funding has facilitated the development of a range of VLs through the National eResearch Collaborative Tools and Resources (NeCTAR) program. The VLs provide highly collaborative, research-domain oriented, integrated software infrastructures that meet user community needs. Twelve VLs have been funded since 2012, including the Virtual Geophysics Laboratory (VGL); Virtual Hazards, Impact and Risk Laboratory (VHIRL); Climate and Weather Science Laboratory (CWSLab); Marine Virtual Laboratory (MarVL); and Biodiversity and Climate Change Virtual Laboratory (BCCVL). These VLs share similar technical challenges, with common issues emerging on integration of tools, applications and access data collections via both cloud-based environments and other distributed resources. While each VL began with a focus on a specific research domain, communities of practice have now formed across the VLs around common issues, and facilitate identification of best practice case studies, and new standards. As a result, tools are now being shared where the VLs access data via data services using international standards such as ISO, OGC, W3C. The sharing of these approaches is starting to facilitate re-usability of infrastructure and is a step towards supporting interdisciplinary research. Whilst the focus of the VLs are Australia-centric, by using standards, these environments are able to be extended to analysis on other international datasets. Many VL datasets are subsets of global datasets and so extension to global is a small (and often requested) step. Similarly, most of the tools, software, and other technologies could be shared across infrastructures globally. Therefore, it is now time to better connect the Australian VLs with similar initiatives elsewhere to create international platforms that can contribute to global research challenges.

3D Visualization Development of SIUE Campus

NASA Astrophysics Data System (ADS)

Nellutla, Shravya

Geographic Information Systems (GIS) has progressed from the traditional map-making to the modern technology where the information can be created, edited, managed and analyzed. Like any other models, maps are simplified representations of real world. Hence visualization plays an essential role in the applications of GIS. The use of sophisticated visualization tools and methods, especially three dimensional (3D) modeling, has been rising considerably due to the advancement of technology. There are currently many off-the-shelf technologies available in the market to build 3D GIS models. One of the objectives of this research was to examine the available ArcGIS and its extensions for 3D modeling and visualization and use them to depict a real world scenario. Furthermore, with the advent of the web, a platform for accessing and sharing spatial information on the Internet, it is possible to generate interactive online maps. Integrating Internet capacity with GIS functionality redefines the process of sharing and processing the spatial information. Enabling a 3D map online requires off-the-shelf GIS software, 3D model builders, web server, web applications and client server technologies. Such environments are either complicated or expensive because of the amount of hardware and software involved. Therefore, the second objective of this research was to investigate and develop simpler yet cost-effective 3D modeling approach that uses available ArcGIS suite products and the free 3D computer graphics software for designing 3D world scenes. Both ArcGIS Explorer and ArcGIS Online will be used to demonstrate the way of sharing and distributing 3D geographic information on the Internet. A case study of the development of 3D campus for the Southern Illinois University Edwardsville is demonstrated.

Lowering the Barrier for Standards-Compliant and Discoverable Hydrological Data Publication

NASA Astrophysics Data System (ADS)

Kadlec, J.

2013-12-01

The growing need for sharing and integration of hydrological and climate data across multiple organizations has resulted in the development of distributed, services-based, standards-compliant hydrological data management and data hosting systems. The problem with these systems is complicated set-up and deployment. Many existing systems assume that the data publisher has remote-desktop access to a locally managed server and experience with computer network setup. For corporate websites, shared web hosting services with limited root access provide an inexpensive, dynamic web presence solution using the Linux, Apache, MySQL and PHP (LAMP) software stack. In this paper, we hypothesize that a webhosting service provides an optimal, low-cost solution for hydrological data hosting. We propose a software architecture of a standards-compliant, lightweight and easy-to-deploy hydrological data management system that can be deployed on the majority of existing shared internet webhosting services. The architecture and design is validated by developing Hydroserver Lite: a PHP and MySQL-based hydrological data hosting package that is fully standards-compliant and compatible with the Consortium of Universities for Advancement of Hydrologic Sciences (CUAHSI) hydrologic information system. It is already being used for management of field data collection by students of the McCall Outdoor Science School in Idaho. For testing, the Hydroserver Lite software has been installed on multiple different free and low-cost webhosting sites including Godaddy, Bluehost and 000webhost. The number of steps required to set-up the server is compared with the number of steps required to set-up other standards-compliant hydrologic data hosting systems including THREDDS, IstSOS and MapServer SOS.

High-Surety Telemedicine in a Distributed, 'Plug-andPlan' Environment

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

Craft, Richard L.; Funkhouser, Donald R.; Gallagher, Linda K.

1999-05-17

Commercial telemedicine systems are increasingly functional, incorporating video-conferencing capabilities, diagnostic peripherals, medication reminders, and patient education services. However, these systems (1) rarely utilize information architectures which allow them to be easily integrated with existing health information networks and (2) do not always protect patient confidentiality with adequate security mechanisms. Using object-oriented methods and software wrappers, we illustrate the transformation of an existing stand-alone telemedicine system into `plug-and-play' components that function in a distributed medical information environment. We show, through the use of open standards and published component interfaces, that commercial telemedicine offerings which were once incompatible with electronic patient recordmore » systems can now share relevant data with clinical information repositories while at the same time hiding the proprietary implementations of the respective systems. Additionally, we illustrate how leading-edge technology can secure this distributed telemedicine environment, maintaining patient confidentiality and the integrity of the associated electronic medical data. Information surety technology also encourages the development of telemedicine systems that have both read and write access to electronic medical records containing patient-identifiable information. The win-win approach to telemedicine information system development preserves investments in legacy software and hardware while promoting security and interoperability in a distributed environment.« less

A STUDY OF SOME SOFTWARE PARAMETERS IN TIME-SHARING SYSTEMS.

DTIC Science & Technology

A review is made of some existing time-sharing computer systems and an exploration of various software characteristics is conducted. This...of the various parameters upon the average response cycle time, the average number in the queue awaiting service , the average length of time a user is

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

PubMed

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

2004-09-24

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

MAGIC: Model and Graphic Information Converter

NASA Technical Reports Server (NTRS)

Herbert, W. C.

2009-01-01

MAGIC is a software tool capable of converting highly detailed 3D models from an open, standard format, VRML 2.0/97, into the proprietary DTS file format used by the Torque Game Engine from GarageGames. MAGIC is used to convert 3D simulations from authoritative sources into the data needed to run the simulations in NASA's Distributed Observer Network. The Distributed Observer Network (DON) is a simulation presentation tool built by NASA to facilitate the simulation sharing requirements of the Data Presentation and Visualization effort within the Constellation Program. DON is built on top of the Torque Game Engine (TGE) and has chosen TGE's Dynamix Three Space (DTS) file format to represent 3D objects within simulations.

Distributed shared memory for roaming large volumes.

PubMed

Castanié, Laurent; Mion, Christophe; Cavin, Xavier; Lévy, Bruno

2006-01-01

We present a cluster-based volume rendering system for roaming very large volumes. This system allows to move a gigabyte-sized probe inside a total volume of several tens or hundreds of gigabytes in real-time. While the size of the probe is limited by the total amount of texture memory on the cluster, the size of the total data set has no theoretical limit. The cluster is used as a distributed graphics processing unit that both aggregates graphics power and graphics memory. A hardware-accelerated volume renderer runs in parallel on the cluster nodes and the final image compositing is implemented using a pipelined sort-last rendering algorithm. Meanwhile, volume bricking and volume paging allow efficient data caching. On each rendering node, a distributed hierarchical cache system implements a global software-based distributed shared memory on the cluster. In case of a cache miss, this system first checks page residency on the other cluster nodes instead of directly accessing local disks. Using two Gigabit Ethernet network interfaces per node, we accelerate data fetching by a factor of 4 compared to directly accessing local disks. The system also implements asynchronous disk access and texture loading, which makes it possible to overlap data loading, volume slicing and rendering for optimal volume roaming.

Information Management for Unmanned Systems: Combining DL-Reasoning with Publish/Subscribe

NASA Astrophysics Data System (ADS)

Moser, Herwig; Reichelt, Toni; Oswald, Norbert; Förster, Stefan

Sharing capabilities and information between collaborating entities by using modem information- and communication-technology is a core principle in complex distributed civil or military mission scenarios. Previous work proved the suitability of Service-oriented Architectures for modelling and sharing the participating entities' capabilities. Albeit providing a satisfactory model for capabilities sharing, pure service-orientation curtails expressiveness for information exchange as opposed to dedicated data-centric communication principles. In this paper we introduce an Information Management System which combines OWL-Ontologies and automated reasoning with Publish/Subscribe-Systems, providing for a shared but decoupled data model. While confirming existing related research results, we emphasise the novel application and lack of practical experience of using Semantic Web technologies in areas other than originally intended. That is, aiding decision support and software design in the context of a mission scenario for an unmanned system. Experiments within a complex simulation environment show the immediate benefits of a semantic information-management and -dissemination platform: Clear separation of concerns in code and data model, increased service re-usability and extensibility as well as regulation of data flow and respective system behaviour through declarative rules.

A-7E Software Module Guide.

DTIC Science & Technology

1981-12-08

o 14 A& B:2.1 Function Driver Module.. ..... .... 14’ ’: B:2.2 Shared Services Module . . . o o . 0 -15 M’ 5:3 Software Decision Module...2.1.13 Weapon Release Functions... ........24 C:2.l.14 Ground Test Functions .. ........... 24 C:2.2 Shared Services Module Decomposition. ........24 C...Driver (FD) Module supported by a Shared Services (SS) Module. B:2.1 FUNCTION DRIVER MODULE The Function Driver Module consists of a set of individual

NSF Policies on Software and Data Sharing and their Implementation

NASA Astrophysics Data System (ADS)

Katz, Daniel

2014-01-01

Since January 2011, the National Science Foundation has required a Data Management plan to be submitted with all proposals. This plan should include a description of how the proposers will share the products of the research (http://www.nsf.gov/bfa/dias/policy/dmp.jsp). What constitutes such data will be determined by the community of interest through the process of peer review and program management. This may include, but is not limited to: data, publications, samples, physical collections, software and models. In particular, “investigators and grantees are encouraged to share software and inventions created under an award or otherwise make them or their products widely available and usable.”

OxMaR: open source free software for online minimization and randomization for clinical trials.

PubMed

O'Callaghan, Christopher A

2014-01-01

Minimization is a valuable method for allocating participants between the control and experimental arms of clinical studies. The use of minimization reduces differences that might arise by chance between the study arms in the distribution of patient characteristics such as gender, ethnicity and age. However, unlike randomization, minimization requires real time assessment of each new participant with respect to the preceding distribution of relevant participant characteristics within the different arms of the study. For multi-site studies, this necessitates centralized computational analysis that is shared between all study locations. Unfortunately, there is no suitable freely available open source or free software that can be used for this purpose. OxMaR was developed to enable researchers in any location to use minimization for patient allocation and to access the minimization algorithm using any device that can connect to the internet such as a desktop computer, tablet or mobile phone. The software is complete in itself and requires no special packages or libraries to be installed. It is simple to set up and run over the internet using online facilities which are very low cost or even free to the user. Importantly, it provides real time information on allocation to the study lead or administrator and generates real time distributed backups with each allocation. OxMaR can readily be modified and customised and can also be used for standard randomization. It has been extensively tested and has been used successfully in a low budget multi-centre study. Hitherto, the logistical difficulties involved in minimization have precluded its use in many small studies and this software should allow more widespread use of minimization which should lead to studies with better matched control and experimental arms. OxMaR should be particularly valuable in low resource settings.

Scalable, High-performance 3D Imaging Software Platform: System Architecture and Application to Virtual Colonoscopy

PubMed Central

Yoshida, Hiroyuki; Wu, Yin; Cai, Wenli; Brett, Bevin

2013-01-01

One of the key challenges in three-dimensional (3D) medical imaging is to enable the fast turn-around time, which is often required for interactive or real-time response. This inevitably requires not only high computational power but also high memory bandwidth due to the massive amount of data that need to be processed. In this work, we have developed a software platform that is designed to support high-performance 3D medical image processing for a wide range of applications using increasingly available and affordable commodity computing systems: multi-core, clusters, and cloud computing systems. To achieve scalable, high-performance computing, our platform (1) employs size-adaptive, distributable block volumes as a core data structure for efficient parallelization of a wide range of 3D image processing algorithms; (2) supports task scheduling for efficient load distribution and balancing; and (3) consists of a layered parallel software libraries that allow a wide range of medical applications to share the same functionalities. We evaluated the performance of our platform by applying it to an electronic cleansing system in virtual colonoscopy, with initial experimental results showing a 10 times performance improvement on an 8-core workstation over the original sequential implementation of the system. PMID:23366803

Information Metacatalog for a Grid

NASA Technical Reports Server (NTRS)

Kolano, Paul

2007-01-01

SWIM is a Software Information Metacatalog that gathers detailed information about the software components and packages installed on a grid resource. Information is currently gathered for Executable and Linking Format (ELF) executables and shared libraries, Java classes, shell scripts, and Perl and Python modules. SWIM is built on top of the POUR framework, which is described in the preceding article. SWIM consists of a set of Perl modules for extracting software information from a system, an XML schema defining the format of data that can be added by users, and a POUR XML configuration file that describes how these elements are used to generate periodic, on-demand, and user-specified information. Periodic software information is derived mainly from the package managers used on each system. SWIM collects information from native package managers in FreeBSD, Solaris, and IRX as well as the RPM, Perl, and Python package managers on multiple platforms. Because not all software is available, or installed in package form, SWIM also crawls the set of relevant paths from the File System Hierarchy Standard that defines the standard file system structure used by all major UNIX distributions. Using these two techniques, the vast majority of software installed on a system can be located. SWIM computes the same information gathered by the periodic routines for specific files on specific hosts, and locates software on a system given only its name and type.

It's Time to Consider Open Source Software

ERIC Educational Resources Information Center

Pfaffman, Jay

2007-01-01

In 1985 Richard Stallman, a computer programmer, released "The GNU Manifesto" in which he proclaimed a golden rule: One must share computer programs. Software vendors required him to agree to license agreements that forbade sharing programs with others, but he refused to "break solidarity" with other computer users whom he assumed also wanted to…

Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration.

PubMed

Sauro, Herbert M; Hucka, Michael; Finney, Andrew; Wellock, Cameron; Bolouri, Hamid; Doyle, John; Kitano, Hiroaki

2003-01-01

Researchers in quantitative systems biology make use of a large number of different software packages for modelling, analysis, visualization, and general data manipulation. In this paper, we describe the Systems Biology Workbench (SBW), a software framework that allows heterogeneous application components--written in diverse programming languages and running on different platforms--to communicate and use each others' capabilities via a fast binary encoded-message system. Our goal was to create a simple, high performance, opensource software infrastructure which is easy to implement and understand. SBW enables applications (potentially running on separate, distributed computers) to communicate via a simple network protocol. The interfaces to the system are encapsulated in client-side libraries that we provide for different programming languages. We describe in this paper the SBW architecture, a selection of current modules, including Jarnac, JDesigner, and SBWMeta-tool, and the close integration of SBW into BioSPICE, which enables both frameworks to share tools and compliment and strengthen each others capabilities.

Software system safety

NASA Technical Reports Server (NTRS)

Uber, James G.

1988-01-01

Software itself is not hazardous, but since software and hardware share common interfaces there is an opportunity for software to create hazards. Further, these software systems are complex, and proven methods for the design, analysis, and measurement of software safety are not yet available. Some past software failures, future NASA software trends, software engineering methods, and tools and techniques for various software safety analyses are reviewed. Recommendations to NASA are made based on this review.

Configurable software for satellite graphics

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

Hartzman, P D

An important goal in interactive computer graphics is to provide users with both quick system responses for basic graphics functions and enough computing power for complex calculations. One solution is to have a distributed graphics system in which a minicomputer and a powerful large computer share the work. The most versatile type of distributed system is an intelligent satellite system in which the minicomputer is programmable by the application user and can do most of the work while the large remote machine is used for difficult computations. At New York University, the hardware was configured from available equipment. The levelmore » of system intelligence resulted almost completely from software development. Unlike previous work with intelligent satellites, the resulting system had system control centered in the satellite. It also had the ability to reconfigure software during realtime operation. The design of the system was done at a very high level using set theoretic language. The specification clearly illustrated processor boundaries and interfaces. The high-level specification also produced a compact, machine-independent virtual graphics data structure for picture representation. The software was written in a systems implementation language; thus, only one set of programs was needed for both machines. A user can program both machines in a single language. Tests of the system with an application program indicate that is has very high potential. A major result of this work is the demonstration that a gigantic investment in new hardware is not necessary for computing facilities interested in graphics.« less

Data format standard for sharing light source measurements

NASA Astrophysics Data System (ADS)

Gregory, G. Groot; Ashdown, Ian; Brandenburg, Willi; Chabaud, Dominique; Dross, Oliver; Gangadhara, Sanjay; Garcia, Kevin; Gauvin, Michael; Hansen, Dirk; Haraguchi, Kei; Hasna, Günther; Jiao, Jianzhong; Kelley, Ryan; Koshel, John; Muschaweck, Julius

2013-09-01

Optical design requires accurate characterization of light sources for computer aided design (CAD) software. Various methods have been used to model sources, from accurate physical models to measurement of light output. It has become common practice for designers to include measured source data for design simulations. Typically, a measured source will contain rays which sample the output distribution of the source. The ray data must then be exported to various formats suitable for import into optical analysis or design software. Source manufacturers are also making measurements of their products and supplying CAD models along with ray data sets for designers. The increasing availability of data has been beneficial to the design community but has caused a large expansion in storage needs for the source manufacturers since each software program uses a unique format to describe the source distribution. In 2012, the Illuminating Engineering Society (IES) formed a working group to understand the data requirements for ray data and recommend a standard file format. The working group included representatives from software companies supplying the analysis and design tools, source measurement companies providing metrology, source manufacturers creating the data and users from the design community. Within one year the working group proposed a file format which was recently approved by the IES for publication as TM-25. This paper will discuss the process used to define the proposed format, highlight some of the significant decisions leading to the format and list the data to be included in the first version of the standard.

Sharing programming resources between Bio* projects through remote procedure call and native call stack strategies.

PubMed

Prins, Pjotr; Goto, Naohisa; Yates, Andrew; Gautier, Laurent; Willis, Scooter; Fields, Christopher; Katayama, Toshiaki

2012-01-01

Open-source software (OSS) encourages computer programmers to reuse software components written by others. In evolutionary bioinformatics, OSS comes in a broad range of programming languages, including C/C++, Perl, Python, Ruby, Java, and R. To avoid writing the same functionality multiple times for different languages, it is possible to share components by bridging computer languages and Bio* projects, such as BioPerl, Biopython, BioRuby, BioJava, and R/Bioconductor. In this chapter, we compare the two principal approaches for sharing software between different programming languages: either by remote procedure call (RPC) or by sharing a local call stack. RPC provides a language-independent protocol over a network interface; examples are RSOAP and Rserve. The local call stack provides a between-language mapping not over the network interface, but directly in computer memory; examples are R bindings, RPy, and languages sharing the Java Virtual Machine stack. This functionality provides strategies for sharing of software between Bio* projects, which can be exploited more often. Here, we present cross-language examples for sequence translation, and measure throughput of the different options. We compare calling into R through native R, RSOAP, Rserve, and RPy interfaces, with the performance of native BioPerl, Biopython, BioJava, and BioRuby implementations, and with call stack bindings to BioJava and the European Molecular Biology Open Software Suite. In general, call stack approaches outperform native Bio* implementations and these, in turn, outperform RPC-based approaches. To test and compare strategies, we provide a downloadable BioNode image with all examples, tools, and libraries included. The BioNode image can be run on VirtualBox-supported operating systems, including Windows, OSX, and Linux.

AirLab: a cloud-based platform to manage and share antibody-based single-cell research.

PubMed

Catena, Raúl; Özcan, Alaz; Jacobs, Andrea; Chevrier, Stephane; Bodenmiller, Bernd

2016-06-29

Single-cell analysis technologies are essential tools in research and clinical diagnostics. These methods include flow cytometry, mass cytometry, and other microfluidics-based technologies. Most laboratories that employ these methods maintain large repositories of antibodies. These ever-growing collections of antibodies, their multiple conjugates, and the large amounts of data generated in assays using specific antibodies and conditions makes a dedicated software solution necessary. We have developed AirLab, a cloud-based tool with web and mobile interfaces, for the organization of these data. AirLab streamlines the processes of antibody purchase, organization, and storage, antibody panel creation, results logging, and antibody validation data sharing and distribution. Furthermore, AirLab enables inventory of other laboratory stocks, such as primers or clinical samples, through user-controlled customization. Thus, AirLab is a mobile-powered and flexible tool that harnesses the capabilities of mobile tools and cloud-based technology to facilitate inventory and sharing of antibody and sample collections and associated validation data.

The Emergence of Open-Source Software in China

ERIC Educational Resources Information Center

Pan, Guohua; Bonk, Curtis J.

2007-01-01

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

STEMsalabim: A high-performance computing cluster friendly code for scanning transmission electron microscopy image simulations of thin specimens.

PubMed

Oelerich, Jan Oliver; Duschek, Lennart; Belz, Jürgen; Beyer, Andreas; Baranovskii, Sergei D; Volz, Kerstin

2017-06-01

We present a new multislice code for the computer simulation of scanning transmission electron microscope (STEM) images based on the frozen lattice approximation. Unlike existing software packages, the code is optimized to perform well on highly parallelized computing clusters, combining distributed and shared memory architectures. This enables efficient calculation of large lateral scanning areas of the specimen within the frozen lattice approximation and fine-grained sweeps of parameter space. Copyright © 2017 Elsevier B.V. All rights reserved.

Container-Based Clinical Solutions for Portable and Reproducible Image Analysis.

PubMed

Matelsky, Jordan; Kiar, Gregory; Johnson, Erik; Rivera, Corban; Toma, Michael; Gray-Roncal, William

2018-05-08

Medical imaging analysis depends on the reproducibility of complex computation. Linux containers enable the abstraction, installation, and configuration of environments so that software can be both distributed in self-contained images and used repeatably by tool consumers. While several initiatives in neuroimaging have adopted approaches for creating and sharing more reliable scientific methods and findings, Linux containers are not yet mainstream in clinical settings. We explore related technologies and their efficacy in this setting, highlight important shortcomings, demonstrate a simple use-case, and endorse the use of Linux containers for medical image analysis.

A numerical differentiation library exploiting parallel architectures

NASA Astrophysics Data System (ADS)

Voglis, C.; Hadjidoukas, P. E.; Lagaris, I. E.; Papageorgiou, D. G.

2009-08-01

We present a software library for numerically estimating first and second order partial derivatives of a function by finite differencing. Various truncation schemes are offered resulting in corresponding formulas that are accurate to order O(h), O(h), and O(h), h being the differencing step. The derivatives are calculated via forward, backward and central differences. Care has been taken that only feasible points are used in the case where bound constraints are imposed on the variables. The Hessian may be approximated either from function or from gradient values. There are three versions of the software: a sequential version, an OpenMP version for shared memory architectures and an MPI version for distributed systems (clusters). The parallel versions exploit the multiprocessing capability offered by computer clusters, as well as modern multi-core systems and due to the independent character of the derivative computation, the speedup scales almost linearly with the number of available processors/cores. Program summaryProgram title: NDL (Numerical Differentiation Library) Catalogue identifier: AEDG_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEDG_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 73 030 No. of bytes in distributed program, including test data, etc.: 630 876 Distribution format: tar.gz Programming language: ANSI FORTRAN-77, ANSI C, MPI, OPENMP Computer: Distributed systems (clusters), shared memory systems Operating system: Linux, Solaris Has the code been vectorised or parallelized?: Yes RAM: The library uses O(N) internal storage, N being the dimension of the problem Classification: 4.9, 4.14, 6.5 Nature of problem: The numerical estimation of derivatives at several accuracy levels is a common requirement in many computational tasks, such as optimization, solution of nonlinear systems, etc. The parallel implementation that exploits systems with multiple CPUs is very important for large scale and computationally expensive problems. Solution method: Finite differencing is used with carefully chosen step that minimizes the sum of the truncation and round-off errors. The parallel versions employ both OpenMP and MPI libraries. Restrictions: The library uses only double precision arithmetic. Unusual features: The software takes into account bound constraints, in the sense that only feasible points are used to evaluate the derivatives, and given the level of the desired accuracy, the proper formula is automatically employed. Running time: Running time depends on the function's complexity. The test run took 15 ms for the serial distribution, 0.6 s for the OpenMP and 4.2 s for the MPI parallel distribution on 2 processors.

Software Simplifies the Sharing of Numerical Models

NASA Technical Reports Server (NTRS)

2014-01-01

To ease the sharing of climate models with university students, Goddard Space Flight Center awarded SBIR funding to Reston, Virginia-based Parabon Computation Inc., a company that specializes in cloud computing. The firm developed a software program capable of running climate models over the Internet, and also created an online environment for people to collaborate on developing such models.

Storing, Browsing, Querying, and Sharing Data: the THREDDS Data Repository (TDR)

NASA Astrophysics Data System (ADS)

Wilson, A.; Lindholm, D.; Baltzer, T.

2005-12-01

The Unidata Internet Data Distribution (IDD) network delivers gigabytes of data per day in near real time to sites across the U.S. and beyond. The THREDDS Data Server (TDS) supports public browsing of metadata and data access via OPeNDAP enabled URLs for datasets such as these. With such large quantities of data, sites generally employ a simple data management policy, keeping the data for a relatively short term on the order of hours to perhaps a week or two. In order to save interesting data in longer term storage and make it available for sharing, a user must move the data herself. In this case the user is responsible for determining where space is available, executing the data movement, generating any desired metadata, and setting access control to enable sharing. This task sequence is generally based on execution of a sequence of low level operating system specific commands with significant user involvement. The LEAD (Linked Environments for Atmospheric Discovery) project is building a cyberinfrastructure to support research and education in mesoscale meteorology. LEAD orchestrations require large, robust, and reliable storage with speedy access to stage data and store both intermediate and final results. These requirements suggest storage solutions that involve distributed storage, replication, and interfacing to archival storage systems such as mass storage systems and tape or removable disks. LEAD requirements also include metadata generation and access in order to support querying. In support of both THREDDS and LEAD requirements, Unidata is designing and prototyping the THREDDS Data Repository (TDR), a framework for a modular data repository to support distributed data storage and retrieval using a variety of back end storage media and interchangeable software components. The TDR interface will provide high level abstractions for long term storage, controlled, fast and reliable access, and data movement capabilities via a variety of technologies such as OPeNDAP and gridftp. The modular structure will allow substitution of software components so that both simple and complex storage media can be integrated into the repository. It will also allow integration of different varieties of supporting software. For example, if replication is desired, replica management could be handled via a simple hash table or a complex solution such as Replica Locater Service (RLS). In order to ensure that metadata is available for all the data in the repository, the TDR will also generate THREDDS metadata when necessary. Users will be able to establish levels of access control to their metadata and data. Coupled with a THREDDS Data Server, both browsing via THREDDS catalogs and querying capabilities will be supported. This presentation will describe the motivating factors, current status, and future plans of the TDR. References: IDD: http://www.unidata.ucar.edu/content/software/idd/index.html THREDDS: http://www.unidata.ucar.edu/content/projects/THREDDS/tech/server/ServerStatus.html LEAD: http://lead.ou.edu/ RLS: http://www.isi.edu/~annc/papers/chervenakRLSjournal05.pdf

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

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

Ananthakrishnan, Rachana; Bell, Gavin; Cinquini, Luca

2013-01-01

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

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

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

Cinquini, Luca; Crichton, Daniel; Miller, Neill

2012-01-01

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

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

NASA Technical Reports Server (NTRS)

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

Sharing Research Models: Using Software Engineering Practices for Facilitation

PubMed Central

Bryant, Stephanie P.; Solano, Eric; Cantor, Susanna; Cooley, Philip C.; Wagener, Diane K.

2011-01-01

Increasingly, researchers are turning to computational models to understand the interplay of important variables on systems’ behaviors. Although researchers may develop models that meet the needs of their investigation, application limitations—such as nonintuitive user interface features and data input specifications—may limit the sharing of these tools with other research groups. By removing these barriers, other research groups that perform related work can leverage these work products to expedite their own investigations. The use of software engineering practices can enable managed application production and shared research artifacts among multiple research groups by promoting consistent models, reducing redundant effort, encouraging rigorous peer review, and facilitating research collaborations that are supported by a common toolset. This report discusses three established software engineering practices— the iterative software development process, object-oriented methodology, and Unified Modeling Language—and the applicability of these practices to computational model development. Our efforts to modify the MIDAS TranStat application to make it more user-friendly are presented as an example of how computational models that are based on research and developed using software engineering practices can benefit a broader audience of researchers. PMID:21687780

Characteristic Analysis of DC Electric Railway Systems with Superconducting Power Cables Connecting Power Substations

NASA Astrophysics Data System (ADS)

Ohsaki, H.; Matsushita, N.; Koseki, T.; Tomita, M.

2014-05-01

The application of superconducting power cables to DC electric railway systems has been studied. It could leads to an effective use of regenerative brake, improved energy efficiency, effective load sharing among the substations, etc. In this study, an electric circuit model of a DC feeding system is built and numerical simulation is carried out using MATLAB-Simulink software. A modified electric circuit model with an AC power grid connection taken into account is also created to simulate the influence of the grid connection. The analyses have proved that a certain amount of energy can be conserved by introducing superconducting cables, and that electric load distribution and concentration among the substations depend on the substation output voltage distribution.

Are the expected benefits of requirements reuse hampered by distance? An experiment.

PubMed

Carrillo de Gea, Juan M; Nicolás, Joaquín; Fernández-Alemán, José L; Toval, Ambrosio; Idri, Ali

2016-01-01

Software development processes are often performed by distributed teams which may be separated by great distances. Global software development (GSD) has undergone a significant growth in recent years. The challenges concerning GSD are especially relevant to requirements engineering (RE). Stakeholders need to share a common ground, but there are many difficulties as regards the potentially variable interpretation of the requirements in different contexts. We posit that the application of requirements reuse techniques could alleviate this problem through the diminution of the number of requirements open to misinterpretation. This paper presents a reuse-based approach with which to address RE in GSD, with special emphasis on specification techniques, namely parameterised requirements and traceability relationships. An experiment was carried out with the participation of 29 university students enrolled on a Computer Science and Engineering course. Two main scenarios that represented co-localisation and distribution in software development were portrayed by participants from Spain and Morocco. The global teams achieved a slightly better performance than the co-located teams as regards effectiveness , which could be a result of the worse productivity of the global teams in comparison to the co-located teams. Subjective perceptions were generally more positive in the case of the distributed teams ( difficulty , speed and understanding ), with the exception of quality . A theoretical model has been proposed as an evaluation framework with which to analyse, from the point of view of the factor of distance, the effect of requirements specification techniques on a set of performance and perception-based variables. The experiment utilised a new internationalisation requirements catalogue. None of the differences found between co-located and distributed teams were significant according to the outcome of our statistical tests. The well-known benefits of requirements reuse in traditional co-located projects could, therefore, also be expected in GSD projects.

A data management and publication workflow for a large-scale, heterogeneous sensor network.

PubMed

Jones, Amber Spackman; Horsburgh, Jeffery S; Reeder, Stephanie L; Ramírez, Maurier; Caraballo, Juan

2015-06-01

It is common for hydrology researchers to collect data using in situ sensors at high frequencies, for extended durations, and with spatial distributions that produce data volumes requiring infrastructure for data storage, management, and sharing. The availability and utility of these data in addressing scientific questions related to water availability, water quality, and natural disasters relies on effective cyberinfrastructure that facilitates transformation of raw sensor data into usable data products. It also depends on the ability of researchers to share and access the data in useable formats. In this paper, we describe a data management and publication workflow and software tools for research groups and sites conducting long-term monitoring using in situ sensors. Functionality includes the ability to track monitoring equipment inventory and events related to field maintenance. Linking this information to the observational data is imperative in ensuring the quality of sensor-based data products. We present these tools in the context of a case study for the innovative Urban Transitions and Aridregion Hydrosustainability (iUTAH) sensor network. The iUTAH monitoring network includes sensors at aquatic and terrestrial sites for continuous monitoring of common meteorological variables, snow accumulation and melt, soil moisture, surface water flow, and surface water quality. We present the overall workflow we have developed for effectively transferring data from field monitoring sites to ultimate end-users and describe the software tools we have deployed for storing, managing, and sharing the sensor data. These tools are all open source and available for others to use.

Collaborative medical informatics research using the Internet and the World Wide Web.

PubMed Central

Shortliffe, E. H.; Barnett, G. O.; Cimino, J. J.; Greenes, R. A.; Huff, S. M.; Patel, V. L.

1996-01-01

The InterMed Collaboratory is an interdisciplinary project involving six participating medical institutions. There are two broad mandates for the effort. The first is to further the development, sharing, and demonstration of numerous software and system components, data sets, procedures and tools that will facilitate the collaborations and support the application goals of these projects. The second is to provide a distributed suite of clinical applications, guidelines, and knowledge-bases for clinical, educational, and administrative purposes. To define the interactions among the components, datasets, procedures, and tools that we are producing and sharing, we have identified a model composed of seven tiers, each of which supports the levels above it. In this paper we briefly describe those tiers and the nature of the collaborative process with which we have experimented. PMID:8947641

Shared-resource computing for small research labs.

PubMed

Ackerman, M J

1982-04-01

A real time laboratory computer network is described. This network is composed of four real-time laboratory minicomputers located in each of four division laboratories and a larger minicomputer in a centrally located computer room. Off the shelf hardware and software were used with no customization. The network is configured for resource sharing using DECnet communications software and the RSX-11-M multi-user real-time operating system. The cost effectiveness of the shared resource network and multiple real-time processing using priority scheduling is discussed. Examples of utilization within a medical research department are given.

The OpenPlanetary initiative

NASA Astrophysics Data System (ADS)

Manaud, Nicolas; Rossi, Angelo Pio; Hare, Trent; Aye, Michael; Galluzzi, Valentina; van Gasselt, Stephan; Martinez, Santa; McAuliffe, Jonathan; Million, Chase; Nass, Andrea; Zinzi, Angelo

2016-10-01

"Open" has become attached to several concepts: science, data, and software are some of the most obvious. It is already common practice within the planetary science community to share spacecraft missions data freely and openly [1]. However, this is not historically the case for software tools, source code, and derived data sets, which are often reproduced independently by multiple individuals and groups. Sharing data, tools and overall knowledge would increase scientific return and benefits [e.g. 2], and recent projects and initiatives are helping toward this goal [e.g. 3,4,5,6].OpenPlanetary is a bottom-up initiative to address the need of the planetary science community for sharing ideas and collaborating on common planetary research and data analysis problems, new challenges, and opportunities. It started from an initial participants effort to stay connected and share information related to and beyond the ESA's first Planetary GIS Workshop [7]. It then continued during the 2nd (US) Planetary Data Workshop [8], and aggregated more people.Our objective is to build an online distributed framework enabling open collaborations within the planetary science community. We aim to co-create, curate and publish resource materials and data sets; to organise online events, to support community-based projects development; and to offer a real-time communication channel at and between conferences and workshops.We will present our current framework and resources, developing projects and ideas, and solicit for feedback and participation. OpenPlanetary is intended for research and education professionals: scientists, engineers, designers, teachers and students, as well as the general public that includes enthusiasts and citizen scientists. All are welcome to join and contribute at openplanetary.co[1] International Planetary Data Alliance, planetarydata.org. [2] Nosek et al (2015), dx.doi.org/10.1126/science.aab2374. [3] Erard S. et al. (2016), EGU2016-17527. [4] Proposal for a PDS Software Node, bit.ly/PDS_SN. [5] Zinzi et al. (2016), dx.doi.org/10.1016/j.ascom.2016.02.006. [6] Open Universe initiave, bit.ly/OpenUniverse, [7] Manaud N. et al. (2016), LPSC47-1387. [8] bit.ly/PlanetaryDataWorkshops

Automatic Tools for Enhancing the Collaborative Experience in Large Projects

NASA Astrophysics Data System (ADS)

Bourilkov, D.; Rodriquez, J. L.

2014-06-01

With the explosion of big data in many fields, the efficient management of knowledge about all aspects of the data analysis gains in importance. A key feature of collaboration in large scale projects is keeping a log of what is being done and how - for private use, reuse, and for sharing selected parts with collaborators and peers, often distributed geographically on an increasingly global scale. Even better if the log is automatically created on the fly while the scientist or software developer is working in a habitual way, without the need for extra efforts. This saves time and enables a team to do more with the same resources. The CODESH - COllaborative DEvelopment SHell - and CAVES - Collaborative Analysis Versioning Environment System projects address this problem in a novel way. They build on the concepts of virtual states and transitions to enhance the collaborative experience by providing automatic persistent virtual logbooks. CAVES is designed for sessions of distributed data analysis using the popular ROOT framework, while CODESH generalizes the approach for any type of work on the command line in typical UNIX shells like bash or tcsh. Repositories of sessions can be configured dynamically to record and make available the knowledge accumulated in the course of a scientific or software endeavor. Access can be controlled to define logbooks of private sessions or sessions shared within or between collaborating groups. A typical use case is building working scalable systems for analysis of Petascale volumes of data as encountered in the LHC experiments. Our approach is general enough to find applications in many fields.

Web based 3-D medical image visualization on the PC.

PubMed

Kim, N; Lee, D H; Kim, J H; Kim, Y; Cho, H J

1998-01-01

With the recent advance of Web and its associated technologies, information sharing on distribute computing environments has gained a great amount of attention from many researchers in many application areas, such as medicine, engineering, and business. One basic requirement of distributed medical consultation systems is that geographically dispersed, disparate participants are allowed to exchange information readily with each other. Such software also needs to be supported on a broad range of computer platforms to increase the softwares accessibility. In this paper, the development of world-wide-web based medical consultation system for radiology imaging is addressed to provide platform independence and greater accessibility. The system supports sharing of 3-dimensional objects. We use VRML (Virtual Reality Modeling Language), which is the defacto standard in 3-D modeling on the Web. 3-D objects are reconstructed from CT or MRI volume data using a VRML format, which can be viewed and manipulated easily in Web-browsers with a VRML plug-in. A Marching cubes method is used in the transformation of scanned volume data sets to polygonal surfaces of VRML. A decimation algorithm is adopted to reduce the number of meshes in the resulting VRML file. 3-D volume data are often very large in size, hence loading the data on PC level computers requires a significant reduction of the size of the data, while minimizing the loss of the original shape information. This is also important to decrease network delays. A prototype system has been implemented (http://cybernet5.snu.ac.kr/-cyber/mrivrml .html), and several sessions of experiments are carried out.

A Role-Playing Game for a Software Engineering Lab: Developing a Product Line

ERIC Educational Resources Information Center

Zuppiroli, Sara; Ciancarini, Paolo; Gabbrielli, Maurizio

2012-01-01

Software product line development refers to software engineering practices and techniques for creating families of similar software systems from a basic set of reusable components, called shared assets. Teaching how to deal with software product lines in a university lab course is a challenging task, because there are several practical issues that…

Bioboxes: standardised containers for interchangeable bioinformatics software.

PubMed

Belmann, Peter; Dröge, Johannes; Bremges, Andreas; McHardy, Alice C; Sczyrba, Alexander; Barton, Michael D

2015-01-01

Software is now both central and essential to modern biology, yet lack of availability, difficult installations, and complex user interfaces make software hard to obtain and use. Containerisation, as exemplified by the Docker platform, has the potential to solve the problems associated with sharing software. We propose bioboxes: containers with standardised interfaces to make bioinformatics software interchangeable.

Using DTSA-II to simulate and interpret energy dispersive spectra from particles.

PubMed

Ritchie, Nicholas W M

2010-06-01

A high quality X-ray spectrum image of a 3.3 mum diameter sphere of K411 glass resting on a copper substrate was collected at 25 keV. The same sample configuration was modeled using the NISTMonte Monte Carlo simulation of electron and X-ray transport as is integrated into the quantitative X-ray microanalysis software package DTSA-II. The distribution of measured and simulated X-ray intensity compare favorably for all the major lines present in the spectra. The simulation is further examined to investigate the influence of angle-of-incidence, sample thickness, and sample diameter on the generated and measured X-ray intensity. The distribution of generated X-rays is seen to deviate significantly from a naive model which assumes that the distribution of generated X-rays is similar to bulk within the volume they share in common. It is demonstrated that the angle at which the electron beam strikes the sample has nonnegligible consequences. It is also demonstrated that within the volume that the bulk and particle share in common that electrons, which have exited and later reentered the particle volume, generate a significant fraction of the X-rays. Any general model of X-ray generation in particles must take into account the lateral spread of the scattered electron beam.

From Data-Sharing to Model-Sharing: SCEC and the Development of Earthquake System Science (Invited)

NASA Astrophysics Data System (ADS)

Jordan, T. H.

2009-12-01

Earthquake system science seeks to construct system-level models of earthquake phenomena and use them to predict emergent seismic behavior—an ambitious enterprise that requires high degree of interdisciplinary, multi-institutional collaboration. This presentation will explore model-sharing structures that have been successful in promoting earthquake system science within the Southern California Earthquake Center (SCEC). These include disciplinary working groups to aggregate data into community models; numerical-simulation working groups to investigate system-specific phenomena (process modeling) and further improve the data models (inverse modeling); and interdisciplinary working groups to synthesize predictive system-level models. SCEC has developed a cyberinfrastructure, called the Community Modeling Environment, that can distribute the community models; manage large suites of numerical simulations; vertically integrate the hardware, software, and wetware needed for system-level modeling; and promote the interactions among working groups needed for model validation and refinement. Various socio-scientific structures contribute to successful model-sharing. Two of the most important are “communities of trust” and collaborations between government and academic scientists on mission-oriented objectives. The latter include improvements of earthquake forecasts and seismic hazard models and the use of earthquake scenarios in promoting public awareness and disaster management.

Telescience Resource Kit Software Capabilities and Future Enhancements

NASA Technical Reports Server (NTRS)

Schneider, Michelle

2004-01-01

The Telescience Resource Kit (TReK) is a suite of PC-based software applications that can be used to monitor and control a payload on board the International Space Station (ISS). This software provides a way for payload users to operate their payloads from their home sites. It can be used by an individual or a team of people. TReK provides both local ground support system services and an interface to utilize remote services provided by the Payload Operations Integration Center (POIC). by the POIC and to perform local data functions such as processing the data, storing it in local files, and forwarding it to other computer systems. TReK can also be used to build, send, and track payload commands. In addition to these features, work is in progress to add a new command management capability. This capability will provide a way to manage a multi- platform command environment that can include geographically distributed computers. This is intended to help those teams that need to manage a shared on-board resource such as a facility class payload. The environment can be configured such that one individual can manage all the command activities associated with that payload. This paper will provide a summary of existing TReK capabilities and a description of the new command management capability. For example, 7'ReK can be used to receive payload data distributed

A Web-based open-source database for the distribution of hyperspectral signatures

NASA Astrophysics Data System (ADS)

Ferwerda, J. G.; Jones, S. D.; Du, Pei-Jun

2006-10-01

With the coming of age of field spectroscopy as a non-destructive means to collect information on the physiology of vegetation, there is a need for storage of signatures, and, more importantly, their metadata. Without the proper organisation of metadata, the signatures itself become limited. In order to facilitate re-distribution of data, a database for the storage & distribution of hyperspectral signatures and their metadata was designed. The database was built using open-source software, and can be used by the hyperspectral community to share their data. Data is uploaded through a simple web-based interface. The database recognizes major file-formats by ASD, GER and International Spectronics. The database source code is available for download through the hyperspectral.info web domain, and we happily invite suggestion for additions & modification for the database to be submitted through the online forums on the same website.

Implementing the concurrent operation of sub-arrays in the ALMA correlator

NASA Astrophysics Data System (ADS)

Amestica, Rodrigo; Perez, Jesus; Lacasse, Richard; Saez, Alejandro

2016-07-01

The ALMA correlator processes the digitized signals from 64 individual antennas to produce a grand total of 2016 correlated base-lines, with runtime selectable lags resolution and integration time. The on-line software system can process a maximum of 125M visibilities per second, producing an archiving data rate close to one sixteenth of the former (7.8M visibilities per second with a network transfer limit of 60 MB/sec). Mechanisms in the correlator hardware design make it possible to split the total number of antennas in the array into smaller subsets, or sub-arrays, such that they can share correlator resources while executing independent observations. The software part of the sub-system is responsible for configuring and scheduling correlator resources in such a way that observations among independent subarrays occur simultaneously while internally sharing correlator resources under a cooperative arrangement. Configuration of correlator modes through its CAN-bus interface and periodic geometric delay updates are the most relevant activities to schedule concurrently while observations happen at the same time among a number of sub-arrays. For that to work correctly, the software interface to sub-arrays schedules shared correlator resources sequentially before observations actually start on each sub-array. Start times for specific observations are optimized and reported back to the higher level observing software. After that initial sequential phase has taken place then simultaneous executions and recording of correlated data across different sub-arrays move forward concurrently, sharing the local network to broadcast results to other software sub-systems. The present paper presents an overview of the different hardware and software actors within the correlator sub-system that implement some degree of concurrency and synchronization needed for seamless and simultaneous operation of multiple sub-arrays, limitations stemming from the resource-sharing nature of the correlator, limitations intrinsic to the digital technology available in the correlator hardware, and milestones so far reached by this new ALMA feature.

Publishing and Editing of Semantically-Enabled Scientific Metadata Across Multiple Web Platforms: Challenges and Experiences

NASA Astrophysics Data System (ADS)

Patton, E. W.; West, P.; Greer, R.; Jin, B.

2011-12-01

Following on work presented at the 2010 AGU Fall Meeting, we present a number of real-world collections of semantically-enabled scientific metadata ingested into the Tetherless World RDF2HTML system as structured data and presented and edited using that system. Two separate datasets from two different domains (oceanography and solar sciences) are made available using existing web standards and services, e.g. encoded using ontologies represented with the Web Ontology Language (OWL) and stored in a SPARQL endpoint for querying. These datasets are deployed for use in three different web environments, i.e. Drupal, MediaWiki, and a custom web portal written in Java, to highlight the cross-platform nature of the data presentation. Stylesheets used to transform concepts in each domain as well as shared terms into HTML will be presented to show the power of using common ontologies to publish data and support reuse of existing terminologies. In addition, a single domain dataset is shared between two separate portal instances to demonstrate the ability for this system to offer distributed access and modification of content across the Internet. Lastly, we will highlight challenges that arose in the software engineering process, outline the design choices we made in solving those issues, and discuss how future improvements to this and other systems will enable the evolution of distributed, decentralized collaborations for scientific data sharing across multiple research groups.

Software Sharing Enables Smarter Content Management

NASA Technical Reports Server (NTRS)

2007-01-01

In 2004, NASA established a technology partnership with Xerox Corporation to develop high-tech knowledge management systems while providing new tools and applications that support the Vision for Space Exploration. In return, NASA provides research and development assistance to Xerox to progress its product line. The first result of the technology partnership was a new system called the NX Knowledge Network (based on Xerox DocuShare CPX). Created specifically for NASA's purposes, this system combines Netmark-practical database content management software created by the Intelligent Systems Division of NASA's Ames Research Center-with complementary software from Xerox's global research centers and DocuShare. NX Knowledge Network was tested at the NASA Astrobiology Institute, and is widely used for document management at Ames, Langley Research Center, within the Mission Operations Directorate at Johnson Space Center, and at the Jet Propulsion Laboratory, for mission-related tasks.

Design of transnational mobile e-payment application based on SIM card

NASA Astrophysics Data System (ADS)

Qian, Tang; Zhen, Li

2018-05-01

Facing the stronger demands of transnational mobile communications and internet-based mobile wireless value-added services, the interconnection and interworking of multiple communication operators and their win-win cooperations become a crucial target in the new round of mobile economic development. Previous researches showed that mobile communications and value-add services are not only technical problems, but also more economic problems.we design a general oncard operating system based on SIM card that could be responsible for coordinating and distributing card hardware and software resources. These applications such as transnational mobile payment, consumption management and many other supplemented functions share the API interfaces, hardware and software resources provided by the operation system, although they are independent of each other. The layer structure of SIM card design not only greatly reduces the complexity of COS development, but also saves the most tense card resources and extends SIM cards applications.

The software architecture of climate models: a graphical comparison of CMIP5 and EMICAR5 configurations

NASA Astrophysics Data System (ADS)

Alexander, K.; Easterbrook, S. M.

2015-01-01

We analyse the source code of eight coupled climate models, selected from those that participated in the CMIP5 (Taylor et al., 2012) or EMICAR5 (Eby et al., 2013; Zickfeld et al., 2013) intercomparison projects. For each model, we sort the preprocessed code into components and subcomponents based on dependency structure. We then create software architecture diagrams which show the relative sizes of these components/subcomponents and the flow of data between them. The diagrams also illustrate several major classes of climate model design; the distribution of complexity between components, which depends on historical development paths as well as the conscious goals of each institution; and the sharing of components between different modelling groups. These diagrams offer insights into the similarities and differences between models, and have the potential to be useful tools for communication between scientists, scientific institutions, and the public.

The software architecture of climate models: a graphical comparison of CMIP5 and EMICAR5 configurations

NASA Astrophysics Data System (ADS)

Alexander, K.; Easterbrook, S. M.

2015-04-01

We analyze the source code of eight coupled climate models, selected from those that participated in the CMIP5 (Taylor et al., 2012) or EMICAR5 (Eby et al., 2013; Zickfeld et al., 2013) intercomparison projects. For each model, we sort the preprocessed code into components and subcomponents based on dependency structure. We then create software architecture diagrams that show the relative sizes of these components/subcomponents and the flow of data between them. The diagrams also illustrate several major classes of climate model design; the distribution of complexity between components, which depends on historical development paths as well as the conscious goals of each institution; and the sharing of components between different modeling groups. These diagrams offer insights into the similarities and differences in structure between climate models, and have the potential to be useful tools for communication between scientists, scientific institutions, and the public.

Method and apparatus for managing transactions with connected computers

DOEpatents

Goldsmith, Steven Y.; Phillips, Laurence R.; Spires, Shannon V.

2003-01-01

The present invention provides a method and apparatus that make use of existing computer and communication resources and that reduce the errors and delays common to complex transactions such as international shipping. The present invention comprises an agent-based collaborative work environment that assists geographically distributed commercial and government users in the management of complex transactions such as the transshipment of goods across the U.S.-Mexico border. Software agents can mediate the creation, validation and secure sharing of shipment information and regulatory documentation over the Internet, using the World-Wide Web to interface with human users.

Telearch - Integrated visual simulation environment for collaborative virtual archaeology.

NASA Astrophysics Data System (ADS)

Kurillo, Gregorij; Forte, Maurizio

Archaeologists collect vast amounts of digital data around the world; however, they lack tools for integration and collaborative interaction to support reconstruction and interpretation process. TeleArch software is aimed to integrate different data sources and provide real-time interaction tools for remote collaboration of geographically distributed scholars inside a shared virtual environment. The framework also includes audio, 2D and 3D video streaming technology to facilitate remote presence of users. In this paper, we present several experimental case studies to demonstrate the integration and interaction with 3D models and geographical information system (GIS) data in this collaborative environment.

New Interfaces to Web Documents and Services

NASA Technical Reports Server (NTRS)

Carlisle, W. H.

1996-01-01

This paper reports on investigations into how to extend capabilities of the Virtual Research Center (VRC) for NASA's Advanced Concepts Office. The work was performed as part of NASA's 1996 Summer Faculty Fellowship program, and involved research into and prototype development of software components that provide documents and services for the World Wide Web (WWW). The WWW has become a de-facto standard for sharing resources over the internet, primarily because web browsers are freely available for the most common hardware platforms and their operating systems. As a consequence of the popularity of the internet, tools, and techniques associated with web browsers are changing rapidly. New capabilities are offered by companies that support web browsers in order to achieve or remain a dominant participant in internet services. Because a goal of the VRC is to build an environment for NASA centers, universities, and industrial partners to share information associated with Advanced Concepts Office activities, the VRC tracks new techniques and services associated with the web in order to determine the their usefulness for distributed and collaborative engineering research activities. Most recently, Java has emerged as a new tool for providing internet services. Because the major web browser providers have decided to include Java in their software, investigations into Java were conducted this summer.

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

NASA Astrophysics Data System (ADS)

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

2017-09-01

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

Reducing Time to Science: Unidata and JupyterHub Technology Using the Jetstream Cloud

NASA Astrophysics Data System (ADS)

Chastang, J.; Signell, R. P.; Fischer, J. L.

2017-12-01

Cloud computing can accelerate scientific workflows, discovery, and collaborations by reducing research and data friction. We describe the deployment of Unidata and JupyterHub technologies on the NSF-funded XSEDE Jetstream cloud. With the aid of virtual machines and Docker technology, we deploy a Unidata JupyterHub server co-located with a Local Data Manager (LDM), THREDDS data server (TDS), and RAMADDA geoscience content management system. We provide Jupyter Notebooks and the pre-built Python environments needed to run them. The notebooks can be used for instruction and as templates for scientific experimentation and discovery. We also supply a large quantity of NCEP forecast model results to allow data-proximate analysis and visualization. In addition, users can transfer data using Globus command line tools, and perform their own data-proximate analysis and visualization with Notebook technology. These data can be shared with others via a dedicated TDS server for scientific distribution and collaboration. There are many benefits of this approach. Not only is the cloud computing environment fast, reliable and scalable, but scientists can analyze, visualize, and share data using only their web browser. No local specialized desktop software or a fast internet connection is required. This environment will enable scientists to spend less time managing their software and more time doing science.

bioboxes v510

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

Barton, Michael; Droge, Johannes; Belmann, Peter

2017-06-22

Software is now both central and essential to modern biology, yet lack of availability, difficult installations, and complex user interfaces make software hard to obtain and use. Containerisation, as exemplified by the Docker platform, has the potential to solve the problems associated with sharing software. The developers propose bioboxes: containers with standardised interfaces to make bioinformatics software interchangeable.

Social Networks as a Critical Pathway for Public Education in IYA2009

NASA Astrophysics Data System (ADS)

Plait, P.; Gay, P. L.

2008-11-01

Social networks are websites (or software that distributes media over the Internet) where users can share content to either a list of friends on that site or to anyone who surfs onto their page, and where those friends can interact and discuss the content. By linking to friends online, the users' personal content (pictures, songs, favorite movies, diaries, websites, and so on) is dynamically distributed, and can ``become viral,'' that is, get spread rapidly as more people see it and spread it themselves. Social networks are immensely popular around the planet, especially with teens, and by tapping into these networks IYA can excite and inspire a younger audience. IYA already has a small but growing presence on several of the larger social networks, and more are planned.

Optimizing CMS build infrastructure via Apache Mesos

NASA Astrophysics Data System (ADS)

Abdurachmanov, David; Degano, Alessandro; Elmer, Peter; Eulisse, Giulio; Mendez, David; Muzaffar, Shahzad

2015-12-01

The Offline Software of the CMS Experiment at the Large Hadron Collider (LHC) at CERN consists of 6M lines of in-house code, developed over a decade by nearly 1000 physicists, as well as a comparable amount of general use open-source code. A critical ingredient to the success of the construction and early operation of the WLCG was the convergence, around the year 2000, on the use of a homogeneous environment of commodity x86-64 processors and Linux. Apache Mesos is a cluster manager that provides efficient resource isolation and sharing across distributed applications, or frameworks. It can run Hadoop, Jenkins, Spark, Aurora, and other applications on a dynamically shared pool of nodes. We present how we migrated our continuous integration system to schedule jobs on a relatively small Apache Mesos enabled cluster and how this resulted in better resource usage, higher peak performance and lower latency thanks to the dynamic scheduling capabilities of Mesos.

Modeling the microstructure of surface by applying BRDF function

NASA Astrophysics Data System (ADS)

Plachta, Kamil

2017-06-01

The paper presents the modeling of surface microstructure using a bidirectional reflectance distribution function. This function contains full information about the reflectance properties of the flat surfaces - it is possible to determine the share of the specular, directional and diffuse components in the reflected luminous stream. The software is based on the authorial algorithm that uses selected elements of this function models, which allows to determine the share of each component. Basing on obtained data, the surface microstructure of each material can be modeled, which allows to determine the properties of this materials. The concentrator directs the reflected solar radiation onto the photovoltaic surface, increasing, at the same time, the value of the incident luminous stream. The paper presents an analysis of selected materials that can be used to construct the solar concentrator system. The use of concentrator increases the power output of the photovoltaic system by up to 17% as compared to the standard solution.

What Librarians Still Don't Know about Free Software

ERIC Educational Resources Information Center

Chudnov, Daniel

2009-01-01

Free software isn't about cost, and it isn't about hype, it isn't about taking business away from vendors. It's about four kinds of freedom--the freedom to use the software for any purpose, the freedom to study how the software works, the freedom to modify the software to adapt it to one's needs, and the freedom to copy and share copies of the…

Secure Peer-to-Peer Networks for Scientific Information Sharing

NASA Technical Reports Server (NTRS)

Karimabadi, Homa

2012-01-01

The most common means of remote scientific collaboration today includes the trio of e-mail for electronic communication, FTP for file sharing, and personalized Web sites for dissemination of papers and research results. With the growth of broadband Internet, there has been a desire to share large files (movies, files, scientific data files) over the Internet. Email has limits on the size of files that can be attached and transmitted. FTP is often used to share large files, but this requires the user to set up an FTP site for which it is hard to set group privileges, it is not straightforward for everyone, and the content is not searchable. Peer-to-peer technology (P2P), which has been overwhelmingly successful in popular content distribution, is the basis for development of a scientific collaboratory called Scientific Peer Network (SciPerNet). This technology combines social networking with P2P file sharing. SciPerNet will be a standalone application, written in Java and Swing, thus insuring portability to a number of different platforms. Some of the features include user authentication, search capability, seamless integration with a data center, the ability to create groups and social networks, and on-line chat. In contrast to P2P networks such as Gnutella, Bit Torrent, and others, SciPerNet incorporates three design elements that are critical to application of P2P for scientific purposes: User authentication, Data integrity validation, Reliable searching SciPerNet also provides a complementary solution to virtual observatories by enabling distributed collaboration and sharing of downloaded and/or processed data among scientists. This will, in turn, increase scientific returns from NASA missions. As such, SciPerNet can serve a two-fold purpose for NASA: a cost-savings software as well as a productivity tool for scientists working with data from NASA missions.

Dynamic Collaboration Infrastructure for Hydrologic Science

NASA Astrophysics Data System (ADS)

Tarboton, D. G.; Idaszak, R.; Castillo, C.; Yi, H.; Jiang, F.; Jones, N.; Goodall, J. L.

2016-12-01

Data and modeling infrastructure is becoming increasingly accessible to water scientists. HydroShare is a collaborative environment that currently offers water scientists the ability to access modeling and data infrastructure in support of data intensive modeling and analysis. It supports the sharing of and collaboration around "resources" which are social objects defined to include both data and models in a structured standardized format. Users collaborate around these objects via comments, ratings, and groups. HydroShare also supports web services and cloud based computation for the execution of hydrologic models and analysis and visualization of hydrologic data. However, the quantity and variety of data and modeling infrastructure available that can be accessed from environments like HydroShare is increasing. Storage infrastructure can range from one's local PC to campus or organizational storage to storage in the cloud. Modeling or computing infrastructure can range from one's desktop to departmental clusters to national HPC resources to grid and cloud computing resources. How does one orchestrate this vast number of data and computing infrastructure without needing to correspondingly learn each new system? A common limitation across these systems is the lack of efficient integration between data transport mechanisms and the corresponding high-level services to support large distributed data and compute operations. A scientist running a hydrology model from their desktop may require processing a large collection of files across the aforementioned storage and compute resources and various national databases. To address these community challenges a proof-of-concept prototype was created integrating HydroShare with RADII (Resource Aware Data-centric collaboration Infrastructure) to provide software infrastructure to enable the comprehensive and rapid dynamic deployment of what we refer to as "collaborative infrastructure." In this presentation we discuss the results of this proof-of-concept prototype which enabled HydroShare users to readily instantiate virtual infrastructure marshaling arbitrary combinations, varieties, and quantities of distributed data and computing infrastructure in addressing big problems in hydrology.

The Value of Open Source Software Tools in Qualitative Research

ERIC Educational Resources Information Center

Greenberg, Gary

2011-01-01

In an era of global networks, researchers using qualitative methods must consider the impact of any software they use on the sharing of data and findings. In this essay, I identify researchers' main areas of concern regarding the use of qualitative software packages for research. I then examine how open source software tools, wherein the publisher…

Toward an automated parallel computing environment for geosciences

NASA Astrophysics Data System (ADS)

Zhang, Huai; Liu, Mian; Shi, Yaolin; Yuen, David A.; Yan, Zhenzhen; Liang, Guoping

2007-08-01

Software for geodynamic modeling has not kept up with the fast growing computing hardware and network resources. In the past decade supercomputing power has become available to most researchers in the form of affordable Beowulf clusters and other parallel computer platforms. However, to take full advantage of such computing power requires developing parallel algorithms and associated software, a task that is often too daunting for geoscience modelers whose main expertise is in geosciences. We introduce here an automated parallel computing environment built on open-source algorithms and libraries. Users interact with this computing environment by specifying the partial differential equations, solvers, and model-specific properties using an English-like modeling language in the input files. The system then automatically generates the finite element codes that can be run on distributed or shared memory parallel machines. This system is dynamic and flexible, allowing users to address different problems in geosciences. It is capable of providing web-based services, enabling users to generate source codes online. This unique feature will facilitate high-performance computing to be integrated with distributed data grids in the emerging cyber-infrastructures for geosciences. In this paper we discuss the principles of this automated modeling environment and provide examples to demonstrate its versatility.

10 CFR 603.550 - Acceptability of intellectual property.

Code of Federal Regulations, 2011 CFR

2011-01-01

... property (e.g., copyrighted material, including software) as cost sharing because: (1) It is difficult to... the contribution. For example, a for-profit firm may offer the use of commercially available software... the software would not be a reasonable basis for valuing its use. ...

10 CFR 603.550 - Acceptability of intellectual property.

Code of Federal Regulations, 2012 CFR

2012-01-01

... property (e.g., copyrighted material, including software) as cost sharing because: (1) It is difficult to... the contribution. For example, a for-profit firm may offer the use of commercially available software... the software would not be a reasonable basis for valuing its use. ...

Collaborative Data Publication Utilizing the Open Data Repository's (ODR) Data Publisher

NASA Technical Reports Server (NTRS)

Stone, N.; Lafuente, B.; Bristow, T.; Keller, R. M.; Downs, R. T.; Blake, D.; Fonda, M.; Dateo, C.; Pires, A.

2017-01-01

Introduction: For small communities in diverse fields such as astrobiology, publishing and sharing data can be a difficult challenge. While large, homogenous fields often have repositories and existing data standards, small groups of independent researchers have few options for publishing standards and data that can be utilized within their community. In conjunction with teams at NASA Ames and the University of Arizona, the Open Data Repository's (ODR) Data Publisher has been conducting ongoing pilots to assess the needs of diverse research groups and to develop software to allow them to publish and share their data collaboratively. Objectives: The ODR's Data Publisher aims to provide an easy-to-use and implement software tool that will allow researchers to create and publish database templates and related data. The end product will facilitate both human-readable interfaces (web-based with embedded images, files, and charts) and machine-readable interfaces utilizing semantic standards. Characteristics: The Data Publisher software runs on the standard LAMP (Linux, Apache, MySQL, PHP) stack to provide the widest server base available. The software is based on Symfony (www.symfony.com) which provides a robust framework for creating extensible, object-oriented software in PHP. The software interface consists of a template designer where individual or master database templates can be created. A master database template can be shared by many researchers to provide a common metadata standard that will set a compatibility standard for all derivative databases. Individual researchers can then extend their instance of the template with custom fields, file storage, or visualizations that may be unique to their studies. This allows groups to create compatible databases for data discovery and sharing purposes while still providing the flexibility needed to meet the needs of scientists in rapidly evolving areas of research. Research: As part of this effort, a number of ongoing pilot and test projects are currently in progress. The Astrobiology Habitable Environments Database Working Group is developing a shared database standard using the ODR's Data Publisher and has a number of example databases where astrobiology data are shared. Soon these databases will be integrated via the template-based standard. Work with this group helps determine what data researchers in these diverse fields need to share and archive. Additionally, this pilot helps determine what standards are viable for sharing these types of data from internally developed standards to existing open standards such as the Dublin Core (http://dublincore.org) and Darwin Core (http://rs.twdg.org) metadata standards. Further studies are ongoing with the University of Arizona Department of Geosciences where a number of mineralogy databases are being constructed within the ODR Data Publisher system. Conclusions: Through the ongoing pilots and discussions with individual researchers and small research teams, a definition of the tools desired by these groups is coming into focus. As the software development moves forward, the goal is to meet the publication and collaboration needs of these scientists in an unobtrusive and functional way.

Sharing of Data Products From CPTEC/INPE and New Developments for Data Distribution

NASA Astrophysics Data System (ADS)

Almeida, W. G.; Lima, A. A.; Pessoa, A. S.; Ferreira, A. T.; Mendes, M. V.; Ferreira, N. J.; Silva Dias, M. F.; Yoksas, T.

2006-05-01

The CPTEC is the Center for Weather Forecast and Climatic Analysis, a division of the INPE, the Brazilian National Institute for Space Research. The CPTEC is an operational and research center, that runs the fastest supercomputer and is a pioneer in global and regional numerical weather forecasting in South America. The INPE is a traditional provider of data, softwares and services for researchers, forecasters and decision makers in Brazil and South America. The institution is a reference for space science, satellite imagery, and environmental studies. Several of the INPE's departments and centers, like the CPTEC, have a variety of valuable datasets, many of them freely available. Currently the politics of "free data and software" is being strengthened, as the INPE's administration has stated it as a priority for the following years. The CPTEC/INPE distributes outputs from several numerical models, like the COLA/CPTEC global model, and regional models for South America, among others. The web and FTP servers also are used to disseminate satellite imagery, satellite derived products, and data from INPE's automated reporting network. Products from the GTS data also are available. To improve these services new servers for FTP and internet are being installed. The data-sharing component of the Unidata Internet Data Distribution (IDD) also is being used to disseminate these data to university participants in both the South American IDD-Brazil and North American IDD. The IDD- Brasil is the expansion of the IDD system in Brazil, and now is delivering data to a rapidly increasing community of university users. Some months ago the CPTEC finished the installation of two new LDM/IDD servers for data relaying and dissemination. With this infrastructure the author believe that the LDM/IDD demand in South America must be attended for the next three years. Some projects and developments are under execution to provide external access to broader set of meteorological and hydro-meteorological data from CPTEC's databases. Under the auspices of the PROTIM (Program for Information Technology Applied to Meteorology), a project supported by one Brazilian governmental foundation (FINEP), the CPTEC embarked on several developments to open the internal databases for free external access. We view the data dissemination infrastructure installed in the INPE as the beginnings of a continent-wide network that can act for multi-way sharing of locally held data sets with peers worldwide.

A service-oriented distributed semantic mediator: integrating multiscale biomedical information.

PubMed

Mora, Oscar; Engelbrecht, Gerhard; Bisbal, Jesus

2012-11-01

Biomedical research continuously generates large amounts of heterogeneous and multimodal data spread over multiple data sources. These data, if appropriately shared and exploited, could dramatically improve the research practice itself, and ultimately the quality of health care delivered. This paper presents DISMED (DIstributed Semantic MEDiator), an open source semantic mediator that provides a unified view of a federated environment of multiscale biomedical data sources. DISMED is a Web-based software application to query and retrieve information distributed over a set of registered data sources, using semantic technologies. It also offers a userfriendly interface specifically designed to simplify the usage of these technologies by non-expert users. Although the architecture of the software mediator is generic and domain independent, in the context of this paper, DISMED has been evaluated for managing biomedical environments and facilitating research with respect to the handling of scientific data distributed in multiple heterogeneous data sources. As part of this contribution, a quantitative evaluation framework has been developed. It consist of a benchmarking scenario and the definition of five realistic use-cases. This framework, created entirely with public datasets, has been used to compare the performance of DISMED against other available mediators. It is also available to the scientific community in order to evaluate progress in the domain of semantic mediation, in a systematic and comparable manner. The results show an average improvement in the execution time by DISMED of 55% compared to the second best alternative in four out of the five use-cases of the experimental evaluation.

Development of a Dynamic Time Sharing Scheduled Environment Final Report CRADA No. TC-824-94E

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

Jette, M.; Caliga, D.

Massively parallel computers, such as the Cray T3D, have historically supported resource sharing solely with space sharing. In that method, multiple problems are solved by executing them on distinct processors. This project developed a dynamic time- and space-sharing scheduler to achieve greater interactivity and throughput than could be achieved with space-sharing alone. CRI and LLNL worked together on the design, testing, and review aspects of this project. There were separate software deliverables. CFU implemented a general purpose scheduling system as per the design specifications. LLNL ported the local gang scheduler software to the LLNL Cray T3D. In this approach, processorsmore » are allocated simultaneously to aU components of a parallel program (in a “gang”). Program execution is preempted as needed to provide for interactivity. Programs are also reIocated to different processors as needed to efficiently pack the computer’s torus of processors. In phase one, CRI developed an interface specification after discussions with LLNL for systemlevel software supporting a time- and space-sharing environment on the LLNL T3D. The two parties also discussed interface specifications for external control tools (such as scheduling policy tools, system administration tools) and applications programs. CRI assumed responsibility for the writing and implementation of all the necessary system software in this phase. In phase two, CRI implemented job-rolling on the Cray T3D, a mechanism for preempting a program, saving its state to disk, and later restoring its state to memory for continued execution. LLNL ported its gang scheduler to the LLNL T3D utilizing the CRI interface implemented in phases one and two. During phase three, the functionality and effectiveness of the LLNL gang scheduler was assessed to provide input to CRI time- and space-sharing, efforts. CRI will utilize this information in the development of general schedulers suitable for other sites and future architectures.« less

Surgical model-view-controller simulation software framework for local and collaborative applications

PubMed Central

Sankaranarayanan, Ganesh; Halic, Tansel; Arikatla, Venkata Sreekanth; Lu, Zhonghua; De, Suvranu

2010-01-01

Purpose Surgical simulations require haptic interactions and collaboration in a shared virtual environment. A software framework for decoupled surgical simulation based on a multi-controller and multi-viewer model-view-controller (MVC) pattern was developed and tested. Methods A software framework for multimodal virtual environments was designed, supporting both visual interactions and haptic feedback while providing developers with an integration tool for heterogeneous architectures maintaining high performance, simplicity of implementation, and straightforward extension. The framework uses decoupled simulation with updates of over 1,000 Hz for haptics and accommodates networked simulation with delays of over 1,000 ms without performance penalty. Results The simulation software framework was implemented and was used to support the design of virtual reality-based surgery simulation systems. The framework supports the high level of complexity of such applications and the fast response required for interaction with haptics. The efficacy of the framework was tested by implementation of a minimally invasive surgery simulator. Conclusion A decoupled simulation approach can be implemented as a framework to handle simultaneous processes of the system at the various frame rates each process requires. The framework was successfully used to develop collaborative virtual environments (VEs) involving geographically distributed users connected through a network, with the results comparable to VEs for local users. PMID:20714933

Experimenting with an Evolving Ground/Space-based Software Architecture to Enable Sensor Webs

NASA Technical Reports Server (NTRS)

mandl, Daniel; Frye, Stuart

2005-01-01

A series of ongoing experiments are being conducted at the NASA Goddard Space Flight Center to explore integrated ground and space-based software architectures enabling sensor webs. A sensor web, as defined by Steve Talabac at NASA Goddard Space Flight Center(GSFC), is a coherent set of distributed nodes interconnected by a communications fabric, that collectively behave as a single, dynamically adaptive, observing system. The nodes can be comprised of satellites, ground instruments, computing nodes etc. Sensor web capability requires autonomous management of constellation resources. This becomes progressively more important as more and more satellites share resource, such as communication channels and ground station,s while automatically coordinating their activities. There have been five ongoing activities which include an effort to standardize a set of middleware. This paper will describe one set of activities using the Earth Observing 1 satellite, which used a variety of ground and flight software along with other satellites and ground sensors to prototype a sensor web. This activity allowed us to explore where the difficulties that occur in the assembly of sensor webs given today s technology. We will present an overview of the software system architecture, some key experiments and lessons learned to facilitate better sensor webs in the future.

Surgical model-view-controller simulation software framework for local and collaborative applications.

PubMed

Maciel, Anderson; Sankaranarayanan, Ganesh; Halic, Tansel; Arikatla, Venkata Sreekanth; Lu, Zhonghua; De, Suvranu

2011-07-01

Surgical simulations require haptic interactions and collaboration in a shared virtual environment. A software framework for decoupled surgical simulation based on a multi-controller and multi-viewer model-view-controller (MVC) pattern was developed and tested. A software framework for multimodal virtual environments was designed, supporting both visual interactions and haptic feedback while providing developers with an integration tool for heterogeneous architectures maintaining high performance, simplicity of implementation, and straightforward extension. The framework uses decoupled simulation with updates of over 1,000 Hz for haptics and accommodates networked simulation with delays of over 1,000 ms without performance penalty. The simulation software framework was implemented and was used to support the design of virtual reality-based surgery simulation systems. The framework supports the high level of complexity of such applications and the fast response required for interaction with haptics. The efficacy of the framework was tested by implementation of a minimally invasive surgery simulator. A decoupled simulation approach can be implemented as a framework to handle simultaneous processes of the system at the various frame rates each process requires. The framework was successfully used to develop collaborative virtual environments (VEs) involving geographically distributed users connected through a network, with the results comparable to VEs for local users.

Small Business Innovations

NASA Technical Reports Server (NTRS)

1993-01-01

Under an Army Small Business Innovation Research (SBIR) grant, Symbiotics, Inc. developed a software system that permits users to upgrade products from standalone applications so they can communicate in a distributed computing environment. Under a subsequent NASA SBIR grant, Symbiotics added additional tools to the SOCIAL product to enable NASA to coordinate conventional systems for planning Shuttle launch support operations. Using SOCIAL, data may be shared among applications in a computer network even when the applications are written in different programming languages. The product was introduced to the commercial market in 1993 and is used to monitor and control equipment for operation support and to integrate financial networks. The SBIR program was established to increase small business participation in federal R&D activities and to transfer government research to industry. InQuisiX is a reuse library providing high performance classification, cataloging, searching, browsing, retrieval and synthesis capabilities. These form the foundation for software reuse, producing higher quality software at lower cost and in less time. Software Productivity Solutions, Inc. developed the technology under Small Business Innovation Research (SBIR) projects funded by NASA and the Army and is marketing InQuisiX in conjunction with Science Applications International Corporation (SAIC). The SBIR program was established to increase small business participation in federal R&D activities and to transfer government research to industry.

A Semantic Web Management Model for Integrative Biomedical Informatics

PubMed Central

Deus, Helena F.; Stanislaus, Romesh; Veiga, Diogo F.; Behrens, Carmen; Wistuba, Ignacio I.; Minna, John D.; Garner, Harold R.; Swisher, Stephen G.; Roth, Jack A.; Correa, Arlene M.; Broom, Bradley; Coombes, Kevin; Chang, Allen; Vogel, Lynn H.; Almeida, Jonas S.

2008-01-01

Background Data, data everywhere. The diversity and magnitude of the data generated in the Life Sciences defies automated articulation among complementary efforts. The additional need in this field for managing property and access permissions compounds the difficulty very significantly. This is particularly the case when the integration involves multiple domains and disciplines, even more so when it includes clinical and high throughput molecular data. Methodology/Principal Findings The emergence of Semantic Web technologies brings the promise of meaningful interoperation between data and analysis resources. In this report we identify a core model for biomedical Knowledge Engineering applications and demonstrate how this new technology can be used to weave a management model where multiple intertwined data structures can be hosted and managed by multiple authorities in a distributed management infrastructure. Specifically, the demonstration is performed by linking data sources associated with the Lung Cancer SPORE awarded to The University of Texas MDAnderson Cancer Center at Houston and the Southwestern Medical Center at Dallas. A software prototype, available with open source at www.s3db.org, was developed and its proposed design has been made publicly available as an open source instrument for shared, distributed data management. Conclusions/Significance The Semantic Web technologies have the potential to addresses the need for distributed and evolvable representations that are critical for systems Biology and translational biomedical research. As this technology is incorporated into application development we can expect that both general purpose productivity software and domain specific software installed on our personal computers will become increasingly integrated with the relevant remote resources. In this scenario, the acquisition of a new dataset should automatically trigger the delegation of its analysis. PMID:18698353

Using Java for distributed computing in the Gaia satellite data processing

NASA Astrophysics Data System (ADS)

O'Mullane, William; Luri, Xavier; Parsons, Paul; Lammers, Uwe; Hoar, John; Hernandez, Jose

2011-10-01

In recent years Java has matured to a stable easy-to-use language with the flexibility of an interpreter (for reflection etc.) but the performance and type checking of a compiled language. When we started using Java for astronomical applications around 1999 they were the first of their kind in astronomy. Now a great deal of astronomy software is written in Java as are many business applications. We discuss the current environment and trends concerning the language and present an actual example of scientific use of Java for high-performance distributed computing: ESA's mission Gaia. The Gaia scanning satellite will perform a galactic census of about 1,000 million objects in our galaxy. The Gaia community has chosen to write its processing software in Java. We explore the manifold reasons for choosing Java for this large science collaboration. Gaia processing is numerically complex but highly distributable, some parts being embarrassingly parallel. We describe the Gaia processing architecture and its realisation in Java. We delve into the astrometric solution which is the most advanced and most complex part of the processing. The Gaia simulator is also written in Java and is the most mature code in the system. This has been successfully running since about 2005 on the supercomputer "Marenostrum" in Barcelona. We relate experiences of using Java on a large shared machine. Finally we discuss Java, including some of its problems, for scientific computing.

PCI bus content-addressable-memory (CAM) implementation on FPGA for pattern recognition/image retrieval in a distributed environment

NASA Astrophysics Data System (ADS)

Megherbi, Dalila B.; Yan, Yin; Tanmay, Parikh; Khoury, Jed; Woods, C. L.

2004-11-01

Recently surveillance and Automatic Target Recognition (ATR) applications are increasing as the cost of computing power needed to process the massive amount of information continues to fall. This computing power has been made possible partly by the latest advances in FPGAs and SOPCs. In particular, to design and implement state-of-the-Art electro-optical imaging systems to provide advanced surveillance capabilities, there is a need to integrate several technologies (e.g. telescope, precise optics, cameras, image/compute vision algorithms, which can be geographically distributed or sharing distributed resources) into a programmable system and DSP systems. Additionally, pattern recognition techniques and fast information retrieval, are often important components of intelligent systems. The aim of this work is using embedded FPGA as a fast, configurable and synthesizable search engine in fast image pattern recognition/retrieval in a distributed hardware/software co-design environment. In particular, we propose and show a low cost Content Addressable Memory (CAM)-based distributed embedded FPGA hardware architecture solution with real time recognition capabilities and computing for pattern look-up, pattern recognition, and image retrieval. We show how the distributed CAM-based architecture offers a performance advantage of an order-of-magnitude over RAM-based architecture (Random Access Memory) search for implementing high speed pattern recognition for image retrieval. The methods of designing, implementing, and analyzing the proposed CAM based embedded architecture are described here. Other SOPC solutions/design issues are covered. Finally, experimental results, hardware verification, and performance evaluations using both the Xilinx Virtex-II and the Altera Apex20k are provided to show the potential and power of the proposed method for low cost reconfigurable fast image pattern recognition/retrieval at the hardware/software co-design level.

Knowledge Sharing through Pair Programming in Learning Environments: An Empirical Study

ERIC Educational Resources Information Center

Kavitha, R. K.; Ahmed, M. S.

2015-01-01

Agile software development is an iterative and incremental methodology, where solutions evolve from self-organizing, cross-functional teams. Pair programming is a type of agile software development technique where two programmers work together with one computer for developing software. This paper reports the results of the pair programming…

Open Source Bayesian Models. 1. Application to ADME/Tox and Drug Discovery Datasets.

PubMed

Clark, Alex M; Dole, Krishna; Coulon-Spektor, Anna; McNutt, Andrew; Grass, George; Freundlich, Joel S; Reynolds, Robert C; Ekins, Sean

2015-06-22

On the order of hundreds of absorption, distribution, metabolism, excretion, and toxicity (ADME/Tox) models have been described in the literature in the past decade which are more often than not inaccessible to anyone but their authors. Public accessibility is also an issue with computational models for bioactivity, and the ability to share such models still remains a major challenge limiting drug discovery. We describe the creation of a reference implementation of a Bayesian model-building software module, which we have released as an open source component that is now included in the Chemistry Development Kit (CDK) project, as well as implemented in the CDD Vault and in several mobile apps. We use this implementation to build an array of Bayesian models for ADME/Tox, in vitro and in vivo bioactivity, and other physicochemical properties. We show that these models possess cross-validation receiver operator curve values comparable to those generated previously in prior publications using alternative tools. We have now described how the implementation of Bayesian models with FCFP6 descriptors generated in the CDD Vault enables the rapid production of robust machine learning models from public data or the user's own datasets. The current study sets the stage for generating models in proprietary software (such as CDD) and exporting these models in a format that could be run in open source software using CDK components. This work also demonstrates that we can enable biocomputation across distributed private or public datasets to enhance drug discovery.

Open Source Bayesian Models. 1. Application to ADME/Tox and Drug Discovery Datasets

PubMed Central

2015-01-01

On the order of hundreds of absorption, distribution, metabolism, excretion, and toxicity (ADME/Tox) models have been described in the literature in the past decade which are more often than not inaccessible to anyone but their authors. Public accessibility is also an issue with computational models for bioactivity, and the ability to share such models still remains a major challenge limiting drug discovery. We describe the creation of a reference implementation of a Bayesian model-building software module, which we have released as an open source component that is now included in the Chemistry Development Kit (CDK) project, as well as implemented in the CDD Vault and in several mobile apps. We use this implementation to build an array of Bayesian models for ADME/Tox, in vitro and in vivo bioactivity, and other physicochemical properties. We show that these models possess cross-validation receiver operator curve values comparable to those generated previously in prior publications using alternative tools. We have now described how the implementation of Bayesian models with FCFP6 descriptors generated in the CDD Vault enables the rapid production of robust machine learning models from public data or the user’s own datasets. The current study sets the stage for generating models in proprietary software (such as CDD) and exporting these models in a format that could be run in open source software using CDK components. This work also demonstrates that we can enable biocomputation across distributed private or public datasets to enhance drug discovery. PMID:25994950

TRENCADIS - secure architecture to share and manage DICOM objects in a ontological framework based on OGSA.

PubMed

Blanquer, Ignacio; Hernandez, Vicente; Segrelles, Damià; Torres, Erik

2007-01-01

Today most European healthcare centers use the digital format for their databases of images. TRENCADIS is a software architecture comprising a set of services as a solution for interconnecting, managing and sharing selected parts of medical DICOM data for the development of training and decision support tools. The organization of the distributed information in virtual repositories is based on semantic criteria. Different groups of researchers could organize themselves to propose a Virtual Organization (VO). These VOs will be interested in specific target areas, and will share information concerning each area. Although the private part of the information to be shared will be removed, special considerations will be taken into account to avoid the access by non-authorized users. This paper describes the security model implemented as part of TRENCADIS. The paper is organized as follows. First introduces the problem and presents our motivations. Section 1 defines the objectives. Section 2 presents an overview of the existing proposals per objective. Section 3 outlines the overall architecture. Section 4 describes how TRENCADIS is architected to realize the security goals discussed in the previous sections. The different security services and components of the infrastructure are briefly explained, as well as the exposed interfaces. Finally, Section 5 concludes and gives some remarks on our future work.

Moving Virtual Research Environments from high maintenance Stovepipes to Multi-purpose Sustainable Service-oriented Science Platforms

NASA Astrophysics Data System (ADS)

Klump, Jens; Fraser, Ryan; Wyborn, Lesley; Friedrich, Carsten; Squire, Geoffrey; Barker, Michelle; Moloney, Glenn

2017-04-01

The researcher of today is likely to be part of a team distributed over multiple sites that will access data from an external repository and then process the data on a public or private cloud or even on a large centralised supercomputer. They are increasingly likely to use a mixture of their own code, third party software and libraries, or even access global community codes. These components will be connected into a Virtual Research Environments (VREs) that will enable members of the research team who are not co-located to actively work together at various scales to share data, models, tools, software, workflows, best practices, infrastructures, etc. Many VRE's are built in isolation: designed to meet a specific research program with components tightly coupled and not capable of being repurposed for other use cases - they are becoming 'stovepipes'. The limited number of users of some VREs also means that the cost of maintenance per researcher can be unacceptably high. The alternative is to develop service-oriented Science Platforms that enable multiple communities to develop specialised solutions for specific research programs. The platforms can offer access to data, software tools and processing infrastructures (cloud, supercomputers) through globally distributed, interconnected modules. In Australia, the Virtual Geophysics Laboratory (VGL) was initially built to enable a specific set of researchers in government agencies access to specific data sets and a limited number of tools, that is now rapidly evolving into a multi-purpose Earth science platform with access to an increased variety of data, a broader range of tools, users from more sectors and a diversity of computational infrastructures. The expansion has been relatively easy, because of the architecture whereby data, tools and compute resources are loosely coupled via interfaces that are built on international standards and accessed as services wherever possible. In recent years, investments in discoverability and accessibility of data via online services in Australia mean that data resources can be easily added to the virtual environments as and when required. Another key to increasing to reusability and uptake of the VRE is the capability to capturing workflows so that they can be reused and repurposed both within and beyond the community that that defined the original use case. Unfortunately, Software-as-a-Service in the research sector is not yet mature. In response, we developed a Scientific Software solutions Center (SSSC) that enables researchers to discover, deploy and then share computational codes, code snippets or processes both in a human and machine-readable manner. Growth has come not only from within the Earth science community but from the Australian Virtual Laboratory community which is building VREs for a diversity of communities such as astronomy, genomics, environment, humanities, climate etc. Components such as access control, provenance, visualisation, accounting etc. are common to all scientific domains and sharing of these across multiple domains reduces costs, but more importantly increases the ability to undertake interdisciplinary science. These efforts are transitioning VREs to more sustainable Service-oriented Science Platforms that can be delivered in an agile, adaptable manner for broader community interests.

Expanding Software Productivity and Power while Reducing Costs.

ERIC Educational Resources Information Center

Winer, Ellen N.

1988-01-01

Microcomputer efficiency and software economy can be achieved through file transfer and data sharing. Costs can be reduced by purchasing computer systems that allow for expansion and portability of data. (MLF)

Earth Exploration Toolbook Workshops: Helping Teachers and Students Analyze Web-based Scientific Data

NASA Astrophysics Data System (ADS)

McAuliffe, C.; Ledley, T.; Dahlman, L.; Haddad, N.

2007-12-01

One of the challenges faced by Earth science teachers, particularly in K-12 settings, is that of connecting scientific research to classroom experiences. Helping teachers and students analyze Web-based scientific data is one way to bring scientific research to the classroom. The Earth Exploration Toolbook (EET) was developed as an online resource to accomplish precisely that. The EET consists of chapters containing step-by-step instructions for accessing Web-based scientific data and for using a software analysis tool to explore issues or concepts in science, technology, and mathematics. For example, in one EET chapter, users download Earthquake data from the USGS and bring it into a geographic information system (GIS), analyzing factors affecting the distribution of earthquakes. The goal of the EET Workshops project is to provide professional development that enables teachers to incorporate Web-based scientific data and analysis tools in ways that meet their curricular needs. In the EET Workshops project, Earth science teachers participate in a pair of workshops that are conducted in a combined teleconference and Web-conference format. In the first workshop, the EET Data Analysis Workshop, participants are introduced to the National Science Digital Library (NSDL) and the Digital Library for Earth System Education (DLESE). They also walk through an Earth Exploration Toolbook (EET) chapter and discuss ways to use Earth science datasets and tools with their students. In a follow-up second workshop, the EET Implementation Workshop, teachers share how they used these materials in the classroom by describing the projects and activities that they carried out with students. The EET Workshops project offers unique and effective professional development. Participants work at their own Internet-connected computers, and dial into a toll-free group teleconference for step-by-step facilitation and interaction. They also receive support via Elluminate, a Web-conferencing software program. The software allows participants to see the facilitator's computer as the analysis techniques of an EET chapter are demonstrated. If needed, the facilitator can also view individual participant's computers, assisting with technical difficulties. In addition, it enables a large number of end users, often widely distributed, to engage in interactive, real-time instruction. In this presentation, we will describe the elements of an EET Workshop pair, highlighting the capabilities and use of Elluminate. We will share lessons learned through several years of conducting this type of professional development. We will also share findings from survey data gathered from teachers who have participated in our workshops.

cOSPREY: A Cloud-Based Distributed Algorithm for Large-Scale Computational Protein Design

PubMed Central

Pan, Yuchao; Dong, Yuxi; Zhou, Jingtian; Hallen, Mark; Donald, Bruce R.; Xu, Wei

2016-01-01

Abstract Finding the global minimum energy conformation (GMEC) of a huge combinatorial search space is the key challenge in computational protein design (CPD) problems. Traditional algorithms lack a scalable and efficient distributed design scheme, preventing researchers from taking full advantage of current cloud infrastructures. We design cloud OSPREY (cOSPREY), an extension to a widely used protein design software OSPREY, to allow the original design framework to scale to the commercial cloud infrastructures. We propose several novel designs to integrate both algorithm and system optimizations, such as GMEC-specific pruning, state search partitioning, asynchronous algorithm state sharing, and fault tolerance. We evaluate cOSPREY on three different cloud platforms using different technologies and show that it can solve a number of large-scale protein design problems that have not been possible with previous approaches. PMID:27154509

Multimedia Shared Stories: Teaching Literacy Skills to Diverse Learners

ERIC Educational Resources Information Center

Rivera, Christopher J.

2013-01-01

Through research, shared stories have demonstrated their effectiveness in teaching literacy skills to students with disabilities, including students who are culturally and linguistically diverse. In an effort to keep pace with ever-changing technology, shared stories can be transformed into a multimedia experience using software that is commonly…

Sharing of Needles and Syringes among Men Who Inject Drugs: HIV Risk in Northwest Bangladesh.

PubMed

Pasa, M Kamal; Alom, Kazi Robiul; Bashri, Zubaida; Vermund, Sten H

2016-01-01

Injection drug use is prevalent in northwestern Bangladesh. We sought to explore the context of needle/syringe sharing among persons who inject drugs (PWID), examining risk exposures to blood-borne infections like the human immunodeficiency virus (HIV) and hepatitis in a region where these dual epidemics are likely to expand. We used a qualitative research approach to learn about injection practices, conducting 60 in-depth interviews among PWID. We then conducted 12 focus group discussions (FGDs) that generated a checklist of salient issues, and followed up with personal observations of typical days at the drug-use venues. Content and interpretative frameworks were used to analyze qualitative information and socio-demographic information, using SPSS software. We found that needle/syringe-sharing behaviours were integrated into the overall social and cultural lives of drug users. Sharing behaviours were an central component of PWID social organization. Sharing was perceived as an inherent element within reciprocal relationships, and sharing was tied to beliefs about drug effects, economic adversity, and harassment due to their drug user status. Carrying used needles/syringes to drug-use venues was deemed essential since user-unfriendly needle-syringe distribution schedules of harm reduction programmes made it difficult to access clean needles/syringes in off-hours. PWID had low self-esteem. Unequal power relationships were reported between the field workers of harm reduction programmes and PWID. Field workers expressed anti-PWID bias and judgmental attitudes, and also had had misconceptions about HIV and hepatitis transmission. PWID were especially disturbed that no assistance was forthcoming from risk reduction programme staff when drug users manifested withdrawal symptoms. Interventions must take social context into account when scaling up programmes in diverse settings. The social organization of PWID include values that foster needle-syringe sharing. Utilization and impact of risk reduction programmes might be improved with expanded clean needle/syringe distribution at times and venues convenient for PWID, better trained and non-judgmental staff, and medical assistance for health problems, including drug withdrawal symptoms.

The effects of a shared, Intranet science learning environment on the academic behaviors of problem-solving and metacognitive reflection

NASA Astrophysics Data System (ADS)

Parker, Mary Jo

This study investigated the effects of a shared, Intranet science environment on the academic behaviors of problem-solving and metacognitive reflection. Seventy-eight subjects included 9th and 10th grade male and female biology students. A quasi-experimental design with pre- and post-test data collection and randomization occurring through assignment of biology classes to traditional or shared, Intranet learning groups was employed. Pilot, web-based distance education software (CourseInfo) created the Intranet learning environment. A modified ecology curriculum provided contextualization and content for traditional and shared learning environments. The effect of this environment on problem-solving, was measured using the standardized Watson-Glaser Critical Thinking Appraisal test. Metacognitive reflection, was measured in three ways: (a) number of concepts used, (b) number of concept links noted, and (c) number of concept nodes noted. Visual learning software, Inspiration, generated concept maps. Secondary research questions evaluated the pilot CourseInfo software for (a) tracked user movement, (b) discussion forum findings, and (c) difficulties experienced using CourseInfo software. Analysis of problem-solving group means reached no levels of significance resulting from the shared, Intranet environment. Paired t-Test of individual differences in problem-solving reached levels of significance. Analysis of metacognitive reflection by number of concepts reached levels of significance. Metacognitive reflection by number of concept links noted also reach significance. No significance was found for metacognitive reflection by number of concept nodes. No gender differences in problem-solving ability and metacognitive reflection emerged. Lack of gender differences in the shared, Intranet environment strongly suggests an equalizing effect due to the cooperative, collaborative nature of Intranet environments. Such environments appeal to, and rank high with, the female gender. Tracking learner movements in web-based, science environments has metacognitive and problem-solving learner implications. CourseInfo software offers one method of informing instruction within web-based learning environments focusing on academic behaviors. A shared, technology-supported learning environment may pose one model which science classrooms can use to create equitable scientific study across gender. The lack of significant differences resulting from this environment presents one model for improvement of individual problem-solving ability and metacognitive reflection across gender.

The key image and case log application: new radiology software for teaching file creation and case logging that incorporates elements of a social network.

PubMed

Rowe, Steven P; Siddiqui, Adeel; Bonekamp, David

2014-07-01

To create novel radiology key image software that is easy to use for novice users, incorporates elements adapted from social networking Web sites, facilitates resident and fellow education, and can serve as the engine for departmental sharing of interesting cases and follow-up studies. Using open-source programming languages and software, radiology key image software (the key image and case log application, KICLA) was developed. This system uses a lightweight interface with the institutional picture archiving and communications systems and enables the storage of key images, image series, and cine clips. It was designed to operate with minimal disruption to the radiologists' daily workflow. Many features of the user interface have been inspired by social networking Web sites, including image organization into private or public folders, flexible sharing with other users, and integration of departmental teaching files into the system. We also review the performance, usage, and acceptance of this novel system. KICLA was implemented at our institution and achieved widespread popularity among radiologists. A large number of key images have been transmitted to the system since it became available. After this early experience period, the most commonly encountered radiologic modalities are represented. A survey distributed to users revealed that most of the respondents found the system easy to use (89%) and fast at allowing them to record interesting cases (100%). Hundred percent of respondents also stated that they would recommend a system such as KICLA to their colleagues. The system described herein represents a significant upgrade to the Digital Imaging and Communications in Medicine teaching file paradigm with efforts made to maximize its ease of use and inclusion of characteristics inspired by social networking Web sites that allow the system additional functionality such as individual case logging. Copyright © 2014 AUR. Published by Elsevier Inc. All rights reserved.

Metadata based management and sharing of distributed biomedical data

PubMed Central

Vergara-Niedermayr, Cristobal; Liu, Peiya

2014-01-01

Biomedical research data sharing is becoming increasingly important for researchers to reuse experiments, pool expertise and validate approaches. However, there are many hurdles for data sharing, including the unwillingness to share, lack of flexible data model for providing context information, difficulty to share syntactically and semantically consistent data across distributed institutions, and high cost to provide tools to share the data. SciPort is a web-based collaborative biomedical data sharing platform to support data sharing across distributed organisations. SciPort provides a generic metadata model to flexibly customise and organise the data. To enable convenient data sharing, SciPort provides a central server based data sharing architecture with a one-click data sharing from a local server. To enable consistency, SciPort provides collaborative distributed schema management across distributed sites. To enable semantic consistency, SciPort provides semantic tagging through controlled vocabularies. SciPort is lightweight and can be easily deployed for building data sharing communities. PMID:24834105

Infusing Reliability Techniques into Software Safety Analysis

NASA Technical Reports Server (NTRS)

Shi, Ying

2015-01-01

Software safety analysis for a large software intensive system is always a challenge. Software safety practitioners need to ensure that software related hazards are completely identified, controlled, and tracked. This paper discusses in detail how to incorporate the traditional reliability techniques into the entire software safety analysis process. In addition, this paper addresses how information can be effectively shared between the various practitioners involved in the software safety analyses. The author has successfully applied the approach to several aerospace applications. Examples are provided to illustrate the key steps of the proposed approach.

The UNIX Operating System: A Model for Software Design.

ERIC Educational Resources Information Center

Kernighan, Brian W.; Morgan, Samuel P.

1982-01-01

Describes UNIX time-sharing operating system, including the program environment, software development tools, flexibility and ease of change, portability and other advantages, and five applications and three nonapplications of the system. (JN)

The CECAM Electronic Structure Library: community-driven development of software libraries for electronic structure simulations

NASA Astrophysics Data System (ADS)

Oliveira, Micael

The CECAM Electronic Structure Library (ESL) is a community-driven effort to segregate shared pieces of software as libraries that could be contributed and used by the community. Besides allowing to share the burden of developing and maintaining complex pieces of software, these can also become a target for re-coding by software engineers as hardware evolves, ensuring that electronic structure codes remain at the forefront of HPC trends. In a series of workshops hosted at the CECAM HQ in Lausanne, the tools and infrastructure for the project were prepared, and the first contributions were included and made available online (http://esl.cecam.org). In this talk I will present the different aspects and aims of the ESL and how these can be useful for the electronic structure community.

Coast to Coast Support of the E-2C Hawkeye using Distributed TSP

DTIC Science & Technology

2008-05-02

Share history of each subgroup and establish a vision f th f t f thi l f d to e u ure or s new y orme eam 3. Establish team operating principles...visits were made by team t th ld k t b d b ild th b id b t th Th ff t NAVAIR Systems/Software Support Center (NSSC) Slide 18 managemen so ey cou now...Success • High quality products from multiple teams delivered on ti d t d tme an cos o no happen in a vacuum • There is a need for common processes

A Novel College Network Resource Management Method using Cloud Computing

NASA Astrophysics Data System (ADS)

Lin, Chen

At present information construction of college mainly has construction of college networks and management information system; there are many problems during the process of information. Cloud computing is development of distributed processing, parallel processing and grid computing, which make data stored on the cloud, make software and services placed in the cloud and build on top of various standards and protocols, you can get it through all kinds of equipments. This article introduces cloud computing and function of cloud computing, then analyzes the exiting problems of college network resource management, the cloud computing technology and methods are applied in the construction of college information sharing platform.

Built But Not Used, Needed But Not Built: Ground System Guidance Based On Cassini-Huygens Experience

NASA Technical Reports Server (NTRS)

Larsen, Barbara S.

2006-01-01

These reflections share insight gleaned from Cassini-Huygens experience in supporting uplink operations tasks with software. Of particular interest are developed applications that were not widely adopted and tasks for which the appropriate application was not planned. After several years of operations, tasks are better understood providing a clearer picture of the mapping of requirements to applications. The impact on system design of the changing user profile due to distributed operations and greater participation of scientists in operations is also explored. Suggestions are made for improving the architecture, requirements, and design of future systems for uplink operations.

Implementing Extreme Programming in Distributed Software Project Teams: Strategies and Challenges

NASA Astrophysics Data System (ADS)

Maruping, Likoebe M.

Agile software development methods and distributed forms of organizing teamwork are two team process innovations that are gaining prominence in today's demanding software development environment. Individually, each of these innovations has yielded gains in the practice of software development. Agile methods have enabled software project teams to meet the challenges of an ever turbulent business environment through enhanced flexibility and responsiveness to emergent customer needs. Distributed software project teams have enabled organizations to access highly specialized expertise across geographic locations. Although much progress has been made in understanding how to more effectively manage agile development teams and how to manage distributed software development teams, managers have little guidance on how to leverage these two potent innovations in combination. In this chapter, I outline some of the strategies and challenges associated with implementing agile methods in distributed software project teams. These are discussed in the context of a study of a large-scale software project in the United States that lasted four months.

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

Grant, Robert

Under this grant, three significant software packages were developed or improved, all with the goal of improving the ease-of-use of HPC libraries. The first component is a Python package, named DistArray (originally named Odin), that provides a high-level interface to distributed array computing. This interface is based on the popular and widely used NumPy package and is integrated with the IPython project for enhanced interactive parallel distributed computing. The second Python package is the Distributed Array Protocol (DAP) that enables separate distributed array libraries to share arrays efficiently without copying or sending messages. If a distributed array library supports themore » DAP, it is then automatically able to communicate with any other library that also supports the protocol. This protocol allows DistArray to communicate with the Trilinos library via PyTrilinos, which was also enhanced during this project. A third package, PyTrilinos, was extended to support distributed structured arrays (in addition to the unstructured arrays of its original design), allow more flexible distributed arrays (i.e., the restriction to double precision data was lifted), and implement the DAP. DAP support includes both exporting the protocol so that external packages can use distributed Trilinos data structures, and importing the protocol so that PyTrilinos can work with distributed data from external packages.« less

Resource Sharing of Micro-Software, or, What Ever Happened to All That CP/M Compatibility?

ERIC Educational Resources Information Center

DeYoung, Barbara

1984-01-01

Explores incompatible operating systems as the basic reason why software packages will not work on different microcomputers; defines operating system; explores compatibility issues surrounding the IBM MS-DOS; and presents two future trends in hardware and software developments which indicate a return to true compatibility. (Author/MBR)

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.

CmapTools: A Software Environment for Knowledge Modeling and Sharing

NASA Technical Reports Server (NTRS)

Canas, Alberto J.

2004-01-01

In an ongoing collaborative effort between a group of NASA Ames scientists and researchers at the Institute for Human and Machine Cognition (IHMC) of the University of West Florida, a new version of CmapTools has been developed that enable scientists to construct knowledge models of their domain of expertise, share them with other scientists, make them available to anybody on the Internet with access to a Web browser, and peer-review other scientists models. These software tools have been successfully used at NASA to build a large-scale multimedia on Mars and in knowledge model on Habitability Assessment. The new version of the software places emphasis on greater usability for experts constructing their own knowledge models, and support for the creation of large knowledge models with large number of supporting resources in the forms of images, videos, web pages, and other media. Additionally, the software currently allows scientists to cooperate with each other in the construction, sharing and criticizing of knowledge models. Scientists collaborating from remote distances, for example researchers at the Astrobiology Institute, can concurrently manipulate the knowledge models they are viewing without having to do this at a special videoconferencing facility.

Using Ada to implement the operations management system in a community of experts

NASA Technical Reports Server (NTRS)

Frank, M. S.

1986-01-01

An architecture is described for the Space Station Operations Management System (OMS), consisting of a distributed expert system framework implemented in Ada. The motivation for such a scheme is based on the desire to integrate the very diverse elements of the OMS while taking maximum advantage of knowledge based systems technology. Part of the foundation of an Ada based distributed expert system was accomplished in the form of a proof of concept prototype for the KNOMES project (Knowledge-based Maintenance Expert System). This prototype successfully used concurrently active experts to accomplish monitoring and diagnosis for the Remote Manipulator System. The basic concept of this software architecture is named ACTORS for Ada Cognitive Task ORganization Scheme. It is when one considers the overall problem of integrating all of the OMS elements into a cooperative system that the AI solution stands out. By utilizing a distributed knowledge based system as the framework for OMS, it is possible to integrate those components which need to share information in an intelligent manner.

The Perfect Neuroimaging-Genetics-Computation Storm: Collision of Petabytes of Data, Millions of Hardware Devices and Thousands of Software Tools

PubMed Central

Dinov, Ivo D.; Petrosyan, Petros; Liu, Zhizhong; Eggert, Paul; Zamanyan, Alen; Torri, Federica; Macciardi, Fabio; Hobel, Sam; Moon, Seok Woo; Sung, Young Hee; Jiang, Zhiguo; Labus, Jennifer; Kurth, Florian; Ashe-McNalley, Cody; Mayer, Emeran; Vespa, Paul M.; Van Horn, John D.; Toga, Arthur W.

2013-01-01

The volume, diversity and velocity of biomedical data are exponentially increasing providing petabytes of new neuroimaging and genetics data every year. At the same time, tens-of-thousands of computational algorithms are developed and reported in the literature along with thousands of software tools and services. Users demand intuitive, quick and platform-agnostic access to data, software tools, and infrastructure from millions of hardware devices. This explosion of information, scientific techniques, computational models, and technological advances leads to enormous challenges in data analysis, evidence-based biomedical inference and reproducibility of findings. The Pipeline workflow environment provides a crowd-based distributed solution for consistent management of these heterogeneous resources. The Pipeline allows multiple (local) clients and (remote) servers to connect, exchange protocols, control the execution, monitor the states of different tools or hardware, and share complete protocols as portable XML workflows. In this paper, we demonstrate several advanced computational neuroimaging and genetics case-studies, and end-to-end pipeline solutions. These are implemented as graphical workflow protocols in the context of analyzing imaging (sMRI, fMRI, DTI), phenotypic (demographic, clinical), and genetic (SNP) data. PMID:23975276

Understanding Social OER Environments--A Quantitative Study on Factors Influencing the Motivation to Share and Collaborate

ERIC Educational Resources Information Center

Pirkkalainen, Henri; Jokinen, Jussi P. P.; Pawlowski, Jan M.

2014-01-01

Social software environments are increasingly used for open education: teachers and learners share and collaborate in these environments. While there are various possibilities for the inclusion of such social functionalities for OER, many organizational, individual and technological challenges can hinder the motivation of teachers to share and…

Library Information System Time-Sharing (LISTS) Project. Final Report.

ERIC Educational Resources Information Center

Black, Donald V.

The Library Information System Time-Sharing (LISTS) experiment was based on three innovations in data processing technology: (1) the advent of computer time-sharing on third-generation machines, (2) the development of general-purpose file-management software and (3) the introduction of large, library-oriented data bases. The main body of the…

Summary of the ACAT Round Table Discussion: Open-source, knowledge sharing and scientific collaboration

NASA Astrophysics Data System (ADS)

Carminati, Federico; Perret-Gallix, Denis; Riemann, Tord

2014-06-01

Round table discussions are in the tradition of ACAT. This year's plenary round table discussion was devoted to questions related to the use of scientific software in High Energy Physics and beyond. The 90 minutes of discussion were lively, and quite a lot of diverse opinions were spelled out. Although the discussion was, in part, controversial, the participants agreed unanimously on several basic issues in software sharing: • The importance of having various licensing models in academic research; • The basic value of proper recognition and attribution of intellectual property, including scientific software; • The user respect for the conditions of use, including licence statements, as formulated by the author. The need of a similar discussion on the issues of data sharing was emphasized and it was recommended to cover this subject at the conference round table discussion of next ACAT. In this contribution, we summarise selected topics that were covered in the introductory talks and in the following discussion.

Designing Distributed Learning Environments with Intelligent Software Agents

ERIC Educational Resources Information Center

Lin, Fuhua, Ed.

2005-01-01

"Designing Distributed Learning Environments with Intelligent Software Agents" reports on the most recent advances in agent technologies for distributed learning. Chapters are devoted to the various aspects of intelligent software agents in distributed learning, including the methodological and technical issues on where and how intelligent agents…

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

PubMed Central

Pronk, Sander; Páll, Szilárd; Schulz, Roland; Larsson, Per; Bjelkmar, Pär; Apostolov, Rossen; Shirts, Michael R.; Smith, Jeremy C.; Kasson, Peter M.; van der Spoel, David; Hess, Berk; Lindahl, Erik

2013-01-01

Motivation: Molecular simulation has historically been a low-throughput technique, but faster computers and increasing amounts of genomic and structural data are changing this by enabling large-scale automated simulation of, for instance, many conformers or mutants of biomolecules with or without a range of ligands. At the same time, advances in performance and scaling now make it possible to model complex biomolecular interaction and function in a manner directly testable by experiment. These applications share a need for fast and efficient software that can be deployed on massive scale in clusters, web servers, distributed computing or cloud resources. Results: Here, we present a range of new simulation algorithms and features developed during the past 4 years, leading up to the GROMACS 4.5 software package. The software now automatically handles wide classes of biomolecules, such as proteins, nucleic acids and lipids, and comes with all commonly used force fields for these molecules built-in. GROMACS supports several implicit solvent models, as well as new free-energy algorithms, and the software now uses multithreading for efficient parallelization even on low-end systems, including windows-based workstations. Together with hand-tuned assembly kernels and state-of-the-art parallelization, this provides extremely high performance and cost efficiency for high-throughput as well as massively parallel simulations. Availability: GROMACS is an open source and free software available from http://www.gromacs.org. Contact: erik.lindahl@scilifelab.se Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23407358

In silico tools for sharing data and knowledge on toxicity and metabolism: derek for windows, meteor, and vitic.

PubMed

Marchant, Carol A; Briggs, Katharine A; Long, Anthony

2008-01-01

ABSTRACT Lhasa Limited is a not-for-profit organization that exists to promote the sharing of data and knowledge in chemistry and the life sciences. It has developed the software tools Derek for Windows, Meteor, and Vitic to facilitate such sharing. Derek for Windows and Meteor are knowledge-based expert systems that predict the toxicity and metabolism of a chemical, respectively. Vitic is a chemically intelligent toxicity database. An overview of each software system is provided along with examples of the sharing of data and knowledge in the context of their development. These examples include illustrations of (1) the use of data entry and editing tools for the sharing of data and knowledge within organizations; (2) the use of proprietary data to develop nonconfidential knowledge that can be shared between organizations; (3) the use of shared expert knowledge to refine predictions; (4) the sharing of proprietary data between organizations through the formation of data-sharing groups; and (5) the use of proprietary data to validate predictions. Sharing of chemical toxicity and metabolism data and knowledge in this way offers a number of benefits including the possibilities of faster scientific progress and reductions in the use of animals in testing. Maximizing the accessibility of data also becomes increasingly crucial as in silico systems move toward the prediction of more complex phenomena for which limited data are available.

Distributed Virtual System (DIVIRS) Project

NASA Technical Reports Server (NTRS)

Schorr, Herbert; Neuman, B. Clifford

1993-01-01

As outlined in our continuation proposal 92-ISI-50R (revised) on contract NCC 2-539, we are (1) developing software, including a system manager and a job manager, that will manage available resources and that will enable programmers to program parallel applications in terms of a virtual configuration of processors, hiding the mapping to physical nodes; (2) developing communications routines that support the abstractions implemented in item one; (3) continuing the development of file and information systems based on the virtual system model; and (4) incorporating appropriate security measures to allow the mechanisms developed in items 1 through 3 to be used on an open network. The goal throughout our work is to provide a uniform model that can be applied to both parallel and distributed systems. We believe that multiprocessor systems should exist in the context of distributed systems, allowing them to be more easily shared by those that need them. Our work provides the mechanisms through which nodes on multiprocessors are allocated to jobs running within the distributed system and the mechanisms through which files needed by those jobs can be located and accessed.

DIstributed VIRtual System (DIVIRS) project

NASA Technical Reports Server (NTRS)

Schorr, Herbert; Neuman, B. Clifford

1994-01-01

As outlined in our continuation proposal 92-ISI-. OR (revised) on NASA cooperative agreement NCC2-539, we are (1) developing software, including a system manager and a job manager, that will manage available resources and that will enable programmers to develop and execute parallel applications in terms of a virtual configuration of processors, hiding the mapping to physical nodes; (2) developing communications routines that support the abstractions implemented in item one; (3) continuing the development of file and information systems based on the Virtual System Model; and (4) incorporating appropriate security measures to allow the mechanisms developed in items 1 through 3 to be used on an open network. The goal throughout our work is to provide a uniform model that can be applied to both parallel and distributed systems. We believe that multiprocessor systems should exist in the context of distributed systems, allowing them to be more easily shared by those that need them. Our work provides the mechanisms through which nodes on multiprocessors are allocated to jobs running within the distributed system and the mechanisms through which files needed by those jobs can be located and accessed.

DIstributed VIRtual System (DIVIRS) project

NASA Technical Reports Server (NTRS)

Schorr, Herbert; Neuman, Clifford B.

1995-01-01

As outlined in our continuation proposal 92-ISI-50R (revised) on NASA cooperative agreement NCC2-539, we are (1) developing software, including a system manager and a job manager, that will manage available resources and that will enable programmers to develop and execute parallel applications in terms of a virtual configuration of processors, hiding the mapping to physical nodes; (2) developing communications routines that support the abstractions implemented in item one; (3) continuing the development of file and information systems based on the Virtual System Model; and (4) incorporating appropriate security measures to allow the mechanisms developed in items 1 through 3 to be used on an open network. The goal throughout our work is to provide a uniform model that can be applied to both parallel and distributed systems. We believe that multiprocessor systems should exist in the context of distributed systems, allowing them to be more easily shared by those that need them. Our work provides the mechanisms through which nodes on multiprocessors are allocated to jobs running within the distributed system and the mechanisms through which files needed by those jobs can be located and accessed.

Distributed Virtual System (DIVIRS) project

NASA Technical Reports Server (NTRS)

Schorr, Herbert; Neuman, B. Clifford

1993-01-01

As outlined in the continuation proposal 92-ISI-50R (revised) on NASA cooperative agreement NCC 2-539, the investigators are developing software, including a system manager and a job manager, that will manage available resources and that will enable programmers to develop and execute parallel applications in terms of a virtual configuration of processors, hiding the mapping to physical nodes; developing communications routines that support the abstractions implemented; continuing the development of file and information systems based on the Virtual System Model; and incorporating appropriate security measures to allow the mechanisms developed to be used on an open network. The goal throughout the work is to provide a uniform model that can be applied to both parallel and distributed systems. The authors believe that multiprocessor systems should exist in the context of distributed systems, allowing them to be more easily shared by those that need them. The work provides the mechanisms through which nodes on multiprocessors are allocated to jobs running within the distributed system and the mechanisms through which files needed by those jobs can be located and accessed.

An approach for access differentiation design in medical distributed applications built on databases.

PubMed

Shoukourian, S K; Vasilyan, A M; Avagyan, A A; Shukurian, A K

1999-01-01

A formalized "top to bottom" design approach was described in [1] for distributed applications built on databases, which were considered as a medium between virtual and real user environments for a specific medical application. Merging different components within a unified distributed application posits new essential problems for software. Particularly protection tools, which are sufficient separately, become deficient during the integration due to specific additional links and relationships not considered formerly. E.g., it is impossible to protect a shared object in the virtual operating room using only DBMS protection tools, if the object is stored as a record in DB tables. The solution of the problem should be found only within the more general application framework. Appropriate tools are absent or unavailable. The present paper suggests a detailed outline of a design and testing toolset for access differentiation systems (ADS) in distributed medical applications which use databases. The appropriate formal model as well as tools for its mapping to a DMBS are suggested. Remote users connected via global networks are considered too.

University Approaches to Software Copyright and Licensure Policies.

ERIC Educational Resources Information Center

Hawkins, Brian L.

Issues of copyright policy and software licensure at Drexel University that were developed during the introduction of a new microcomputing program are discussed. Channels for software distribution include: individual purchase of externally-produced software, distribution of internally-developed software, institutional licensure, and "read…

Open source system OpenVPN in a function of Virtual Private Network

NASA Astrophysics Data System (ADS)

Skendzic, A.; Kovacic, B.

2017-05-01

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

Advanced data management system architectures testbed

NASA Technical Reports Server (NTRS)

Grant, Terry

1990-01-01

The objective of the Architecture and Tools Testbed is to provide a working, experimental focus to the evolving automation applications for the Space Station Freedom data management system. Emphasis is on defining and refining real-world applications including the following: the validation of user needs; understanding system requirements and capabilities; and extending capabilities. The approach is to provide an open, distributed system of high performance workstations representing both the standard data processors and networks and advanced RISC-based processors and multiprocessor systems. The system provides a base from which to develop and evaluate new performance and risk management concepts and for sharing the results. Participants are given a common view of requirements and capability via: remote login to the testbed; standard, natural user interfaces to simulations and emulations; special attention to user manuals for all software tools; and E-mail communication. The testbed elements which instantiate the approach are briefly described including the workstations, the software simulation and monitoring tools, and performance and fault tolerance experiments.

Statistics on continuous IBD data: Exact distribution evaluation for a pair of full(half)-sibs and a pair of a (great-) grandchild with a (great-) grandparent

PubMed Central

Stefanov, Valeri T

2002-01-01

Background Pairs of related individuals are widely used in linkage analysis. Most of the tests for linkage analysis are based on statistics associated with identity by descent (IBD) data. The current biotechnology provides data on very densely packed loci, and therefore, it may provide almost continuous IBD data for pairs of closely related individuals. Therefore, the distribution theory for statistics on continuous IBD data is of interest. In particular, distributional results which allow the evaluation of p-values for relevant tests are of importance. Results A technology is provided for numerical evaluation, with any given accuracy, of the cumulative probabilities of some statistics on continuous genome data for pairs of closely related individuals. In the case of a pair of full-sibs, the following statistics are considered: (i) the proportion of genome with 2 (at least 1) haplotypes shared identical-by-descent (IBD) on a chromosomal segment, (ii) the number of distinct pieces (subsegments) of a chromosomal segment, on each of which exactly 2 (at least 1) haplotypes are shared IBD. The natural counterparts of these statistics for the other relationships are also considered. Relevant Maple codes are provided for a rapid evaluation of the cumulative probabilities of such statistics. The genomic continuum model, with Haldane's model for the crossover process, is assumed. Conclusions A technology, together with relevant software codes for its automated implementation, are provided for exact evaluation of the distributions of relevant statistics associated with continuous genome data on closely related individuals. PMID:11996673

Catchment virtual observatory for sharing flow and transport models outputs: using residence time distribution to compare contrasting catchments

NASA Astrophysics Data System (ADS)

Thomas, Zahra; Rousseau-Gueutin, Pauline; Kolbe, Tamara; Abbott, Ben; Marcais, Jean; Peiffer, Stefan; Frei, Sven; Bishop, Kevin; Le Henaff, Geneviève; Squividant, Hervé; Pichelin, Pascal; Pinay, Gilles; de Dreuzy, Jean-Raynald

2017-04-01

The distribution of groundwater residence time in a catchment provides synoptic information about catchment functioning (e.g. nutrient retention and removal, hydrograph flashiness). In contrast with interpreted model results, which are often not directly comparable between studies, residence time distribution is a general output that could be used to compare catchment behaviors and test hypotheses about landscape controls on catchment functioning. In this goal, we created a virtual observatory platform called Catchment Virtual Observatory for Sharing Flow and Transport Model Outputs (COnSOrT). The main goal of COnSOrT is to collect outputs from calibrated groundwater models from a wide range of environments. By comparing a wide variety of catchments from different climatic, topographic and hydrogeological contexts, we expect to enhance understanding of catchment connectivity, resilience to anthropogenic disturbance, and overall functioning. The web-based observatory will also provide software tools to analyze model outputs. The observatory will enable modelers to test their models in a wide range of catchment environments to evaluate the generality of their findings and robustness of their post-processing methods. Researchers with calibrated numerical models can benefit from observatory by using the post-processing methods to implement a new approach to analyzing their data. Field scientists interested in contributing data could invite modelers associated with the observatory to test their models against observed catchment behavior. COnSOrT will allow meta-analyses with community contributions to generate new understanding and identify promising pathways forward to moving beyond single catchment ecohydrology. Keywords: Residence time distribution, Models outputs, Catchment hydrology, Inter-catchment comparison

Team Collaboration Software

NASA Technical Reports Server (NTRS)

Wang, Yeou-Fang; Schrock, Mitchell; Baldwin, John R.; Borden, Charles S.

2010-01-01

The Ground Resource Allocation and Planning Environment (GRAPE 1.0) is a Web-based, collaborative team environment based on the Microsoft SharePoint platform, which provides Deep Space Network (DSN) resource planners tools and services for sharing information and performing analysis.

SHARE: system design and case studies for statistical health information release

PubMed Central

Gardner, James; Xiong, Li; Xiao, Yonghui; Gao, Jingjing; Post, Andrew R; Jiang, Xiaoqian; Ohno-Machado, Lucila

2013-01-01

Objectives We present SHARE, a new system for statistical health information release with differential privacy. We present two case studies that evaluate the software on real medical datasets and demonstrate the feasibility and utility of applying the differential privacy framework on biomedical data. Materials and Methods SHARE releases statistical information in electronic health records with differential privacy, a strong privacy framework for statistical data release. It includes a number of state-of-the-art methods for releasing multidimensional histograms and longitudinal patterns. We performed a variety of experiments on two real datasets, the surveillance, epidemiology and end results (SEER) breast cancer dataset and the Emory electronic medical record (EeMR) dataset, to demonstrate the feasibility and utility of SHARE. Results Experimental results indicate that SHARE can deal with heterogeneous data present in medical data, and that the released statistics are useful. The Kullback–Leibler divergence between the released multidimensional histograms and the original data distribution is below 0.5 and 0.01 for seven-dimensional and three-dimensional data cubes generated from the SEER dataset, respectively. The relative error for longitudinal pattern queries on the EeMR dataset varies between 0 and 0.3. While the results are promising, they also suggest that challenges remain in applying statistical data release using the differential privacy framework for higher dimensional data. Conclusions SHARE is one of the first systems to provide a mechanism for custodians to release differentially private aggregate statistics for a variety of use cases in the medical domain. This proof-of-concept system is intended to be applied to large-scale medical data warehouses. PMID:23059729

WWWinda Orchestrator: a mechanism for coordinating distributed flocks of Java Applets

NASA Astrophysics Data System (ADS)

Gutfreund, Yechezkal-Shimon; Nicol, John R.

1997-01-01

The WWWinda Orchestrator is a simple but powerful tool for coordinating distributed Java applets. Loosely derived from the Linda programming language developed by David Gelernter and Nicholas Carriero of Yale, WWWinda implements a distributed shared object space called TupleSpace where applets can post, read, or permanently store arbitrary Java objects. In this manner, applets can easily share information without being aware of the underlying communication mechanisms. WWWinda is a very useful for orchestrating flocks of distributed Java applets. Coordination event scan be posted to WWWinda TupleSpace and used to orchestrate the actions of remote applets. Applets can easily share information via the TupleSpace. The technology combines several functions in one simple metaphor: distributed web objects, remote messaging between applets, distributed synchronization mechanisms, object- oriented database, and a distributed event signaling mechanisms. WWWinda can be used a s platform for implementing shared VRML environments, shared groupware environments, controlling remote devices such as cameras, distributed Karaoke, distributed gaming, and shared audio and video experiences.

Collaborative environments for capability-based planning

NASA Astrophysics Data System (ADS)

McQuay, William K.

2005-05-01

Distributed collaboration is an emerging technology for the 21st century that will significantly change how business is conducted in the defense and commercial sectors. Collaboration involves two or more geographically dispersed entities working together to create a "product" by sharing and exchanging data, information, and knowledge. A product is defined broadly to include, for example, writing a report, creating software, designing hardware, or implementing robust systems engineering and capability planning processes in an organization. Collaborative environments provide the framework and integrate models, simulations, domain specific tools, and virtual test beds to facilitate collaboration between the multiple disciplines needed in the enterprise. The Air Force Research Laboratory (AFRL) is conducting a leading edge program in developing distributed collaborative technologies targeted to the Air Force's implementation of systems engineering for a simulation-aided acquisition and capability-based planning. The research is focusing on the open systems agent-based framework, product and process modeling, structural architecture, and the integration technologies - the glue to integrate the software components. In past four years, two live assessment events have been conducted to demonstrate the technology in support of research for the Air Force Agile Acquisition initiatives. The AFRL Collaborative Environment concept will foster a major cultural change in how the acquisition, training, and operational communities conduct business.

BIO-Plex Information System Concept

NASA Technical Reports Server (NTRS)

Jones, Harry; Boulanger, Richard; Arnold, James O. (Technical Monitor)

1999-01-01

This paper describes a suggested design for an integrated information system for the proposed BIO-Plex (Bioregenerative Planetary Life Support Systems Test Complex) at Johnson Space Center (JSC), including distributed control systems, central control, networks, database servers, personal computers and workstations, applications software, and external communications. The system will have an open commercial computing and networking, architecture. The network will provide automatic real-time transfer of information to database server computers which perform data collection and validation. This information system will support integrated, data sharing applications for everything, from system alarms to management summaries. Most existing complex process control systems have information gaps between the different real time subsystems, between these subsystems and central controller, between the central controller and system level planning and analysis application software, and between the system level applications and management overview reporting. An integrated information system is vitally necessary as the basis for the integration of planning, scheduling, modeling, monitoring, and control, which will allow improved monitoring and control based on timely, accurate and complete data. Data describing the system configuration and the real time processes can be collected, checked and reconciled, analyzed and stored in database servers that can be accessed by all applications. The required technology is available. The only opportunity to design a distributed, nonredundant, integrated system is before it is built. Retrofit is extremely difficult and costly.

A Study about the 3S-based Great Ruins Monitoring and Early-warning System

NASA Astrophysics Data System (ADS)

Xuefeng, W.; Zhongyuan, H.; Gongli, L.; Li, Z.

2015-08-01

Large-scale urbanization construction and new countryside construction, frequent natural disasters, and natural corrosion pose severe threat to the great ruins. It is not uncommon that the cultural relics are damaged and great ruins are occupied. Now the ruins monitoring mainly adopt general monitoring data processing system which can not effectively exert management, display, excavation analysis and data sharing of the relics monitoring data. Meanwhile those general software systems require layout of large number of devices or apparatuses, but they are applied to small-scope relics monitoring only. Therefore, this paper proposes a method to make use of the stereoscopic cartographic satellite technology to improve and supplement the great ruins monitoring index system and combine GIS and GPS to establish a highly automatic, real-time and intelligent great ruins monitoring and early-warning system in order to realize collection, processing, updating, spatial visualization, analysis, distribution and sharing of the monitoring data, and provide scientific and effective data for the relics protection, scientific planning, reasonable development and sustainable utilization.

Optimizing CMS build infrastructure via Apache Mesos

DOE PAGES

Abdurachmanov, David; Degano, Alessandro; Elmer, Peter; ...

2015-12-23

The Offline Software of the CMS Experiment at the Large Hadron Collider (LHC) at CERN consists of 6M lines of in-house code, developed over a decade by nearly 1000 physicists, as well as a comparable amount of general use open-source code. A critical ingredient to the success of the construction and early operation of the WLCG was the convergence, around the year 2000, on the use of a homogeneous environment of commodity x86-64 processors and Linux.Apache Mesos is a cluster manager that provides efficient resource isolation and sharing across distributed applications, or frameworks. It can run Hadoop, Jenkins, Spark, Aurora,more » and other applications on a dynamically shared pool of nodes. Lastly, we present how we migrated our continuous integration system to schedule jobs on a relatively small Apache Mesos enabled cluster and how this resulted in better resource usage, higher peak performance and lower latency thanks to the dynamic scheduling capabilities of Mesos.« less

Distribution of genome shared identical by descent by two individuals in grandparent-type relationship.

PubMed Central

Stefanov, V T

2000-01-01

A methodology is introduced for numerical evaluation, with any given accuracy, of the cumulative probabilities of the proportion of genome shared identical by descent (IBD) on chromosome segments by two individuals in a grandparent-type relationship. Programs are provided in the popular software package Maple for rapidly implementing such evaluations in the cases of grandchild-grandparent and great-grandchild-great-grandparent relationships. Our results can be used to identify chromosomal segments that may contain disease genes. Also, exact P values in significance testing for resemblance of either a grandparent with a grandchild or a great-grandparent with a great-grandchild can be calculated. The genomic continuum model, with Haldane's model for the crossover process, is assumed. This is the model that has been used recently in the genetics literature devoted to IBD calculations. Our methodology is based on viewing the model as a special exponential family and elaborating on recent research results for such families. PMID:11063711

Optimizing CMS build infrastructure via Apache Mesos

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

Abdurachmanov, David; Degano, Alessandro; Elmer, Peter

The Offline Software of the CMS Experiment at the Large Hadron Collider (LHC) at CERN consists of 6M lines of in-house code, developed over a decade by nearly 1000 physicists, as well as a comparable amount of general use open-source code. A critical ingredient to the success of the construction and early operation of the WLCG was the convergence, around the year 2000, on the use of a homogeneous environment of commodity x86-64 processors and Linux.Apache Mesos is a cluster manager that provides efficient resource isolation and sharing across distributed applications, or frameworks. It can run Hadoop, Jenkins, Spark, Aurora,more » and other applications on a dynamically shared pool of nodes. Lastly, we present how we migrated our continuous integration system to schedule jobs on a relatively small Apache Mesos enabled cluster and how this resulted in better resource usage, higher peak performance and lower latency thanks to the dynamic scheduling capabilities of Mesos.« less

Remote software upload techniques in future vehicles and their performance analysis

NASA Astrophysics Data System (ADS)

Hossain, Irina

Updating software in vehicle Electronic Control Units (ECUs) will become a mandatory requirement for a variety of reasons, for examples, to update/fix functionality of an existing system, add new functionality, remove software bugs and to cope up with ITS infrastructure. Software modules of advanced vehicles can be updated using Remote Software Upload (RSU) technique. The RSU employs infrastructure-based wireless communication technique where the software supplier sends the software to the targeted vehicle via a roadside Base Station (BS). However, security is critically important in RSU to avoid any disasters due to malfunctions of the vehicle or to protect the proprietary algorithms from hackers, competitors or people with malicious intent. In this thesis, a mechanism of secure software upload in advanced vehicles is presented which employs mutual authentication of the software provider and the vehicle using a pre-shared authentication key before sending the software. The software packets are sent encrypted with a secret key along with the Message Digest (MD). In order to increase the security level, it is proposed the vehicle to receive more than one copy of the software along with the MD in each copy. The vehicle will install the new software only when it receives more than one identical copies of the software. In order to validate the proposition, analytical expressions of average number of packet transmissions for successful software update is determined. Different cases are investigated depending on the vehicle's buffer size and verification methods. The analytical and simulation results show that it is sufficient to send two copies of the software to the vehicle to thwart any security attack while uploading the software. The above mentioned unicast method for RSU is suitable when software needs to be uploaded to a single vehicle. Since multicasting is the most efficient method of group communication, updating software in an ECU of a large number of vehicles could benefit from it. However, like the unicast RSU, the security requirements of multicast communication, i.e., authenticity, confidentiality and integrity of the software transmitted and access control of the group members is challenging. In this thesis, an infrastructure-based mobile multicasting for RSU in vehicle ECUs is proposed where an ECU receives the software from a remote software distribution center using the road side BSs as gateways. The Vehicular Software Distribution Network (VSDN) is divided into small regions administered by a Regional Group Manager (RGM). Two multicast Group Key Management (GKM) techniques are proposed based on the degree of trust on the BSs named Fully-trusted (FT) and Semi-trusted (ST) systems. Analytical models are developed to find the multicast session establishment latency and handover latency for these two protocols. The average latency to perform mutual authentication of the software vendor and a vehicle, and to send the multicast session key by the software provider during multicast session initialization, and the handoff latency during multicast session is calculated. Analytical and simulation results show that the link establishment latency per vehicle of our proposed schemes is in the range of few seconds and the ST system requires few ms higher time than the FT system. The handoff latency is also in the range of few seconds and in some cases ST system requires less handoff time than the FT system. Thus, it is possible to build an efficient GKM protocol without putting too much trust on the BSs.

Lin4Neuro: a customized Linux distribution ready for neuroimaging analysis

PubMed Central

2011-01-01

Background A variety of neuroimaging software packages have been released from various laboratories worldwide, and many researchers use these packages in combination. Though most of these software packages are freely available, some people find them difficult to install and configure because they are mostly based on UNIX-like operating systems. We developed a live USB-bootable Linux package named "Lin4Neuro." This system includes popular neuroimaging analysis tools. The user interface is customized so that even Windows users can use it intuitively. Results The boot time of this system was only around 40 seconds. We performed a benchmark test of inhomogeneity correction on 10 subjects of three-dimensional T1-weighted MRI scans. The processing speed of USB-booted Lin4Neuro was as fast as that of the package installed on the hard disk drive. We also installed Lin4Neuro on a virtualization software package that emulates the Linux environment on a Windows-based operation system. Although the processing speed was slower than that under other conditions, it remained comparable. Conclusions With Lin4Neuro in one's hand, one can access neuroimaging software packages easily, and immediately focus on analyzing data. Lin4Neuro can be a good primer for beginners of neuroimaging analysis or students who are interested in neuroimaging analysis. It also provides a practical means of sharing analysis environments across sites. PMID:21266047

Lin4Neuro: a customized Linux distribution ready for neuroimaging analysis.

PubMed

Nemoto, Kiyotaka; Dan, Ippeita; Rorden, Christopher; Ohnishi, Takashi; Tsuzuki, Daisuke; Okamoto, Masako; Yamashita, Fumio; Asada, Takashi

2011-01-25

A variety of neuroimaging software packages have been released from various laboratories worldwide, and many researchers use these packages in combination. Though most of these software packages are freely available, some people find them difficult to install and configure because they are mostly based on UNIX-like operating systems. We developed a live USB-bootable Linux package named "Lin4Neuro." This system includes popular neuroimaging analysis tools. The user interface is customized so that even Windows users can use it intuitively. The boot time of this system was only around 40 seconds. We performed a benchmark test of inhomogeneity correction on 10 subjects of three-dimensional T1-weighted MRI scans. The processing speed of USB-booted Lin4Neuro was as fast as that of the package installed on the hard disk drive. We also installed Lin4Neuro on a virtualization software package that emulates the Linux environment on a Windows-based operation system. Although the processing speed was slower than that under other conditions, it remained comparable. With Lin4Neuro in one's hand, one can access neuroimaging software packages easily, and immediately focus on analyzing data. Lin4Neuro can be a good primer for beginners of neuroimaging analysis or students who are interested in neuroimaging analysis. It also provides a practical means of sharing analysis environments across sites.

Small PACS implementation using publicly available software

NASA Astrophysics Data System (ADS)

Passadore, Diego J.; Isoardi, Roberto A.; Gonzalez Nicolini, Federico J.; Ariza, P. P.; Novas, C. V.; Omati, S. A.

1998-07-01

Building cost effective PACS solutions is a main concern in developing countries. Hardware and software components are generally much more expensive than in developed countries and also more tightened financial constraints are the main reasons contributing to a slow rate of implementation of PACS. The extensive use of Internet for sharing resources and information has brought a broad number of freely available software packages to an ever-increasing number of users. In the field of medical imaging is possible to find image format conversion packages, DICOM compliant servers for all kinds of service classes, databases, web servers, image visualization, manipulation and analysis tools, etc. This paper describes a PACS implementation for review and storage built on freely available software. It currently integrates four diagnostic modalities (PET, CT, MR and NM), a Radiotherapy Treatment Planning workstation and several computers in a local area network, for image storage, database management and image review, processing and analysis. It also includes a web-based application that allows remote users to query the archive for studies from any workstation and to view the corresponding images and reports. We conclude that the advantage of using this approach is twofold. It allows a full understanding of all the issues involved in the implementation of a PACS and also contributes to keep costs down while enabling the development of a functional system for storage, distribution and review that can prove to be helpful for radiologists and referring physicians.

The distributed annotation system.

PubMed

Dowell, R D; Jokerst, R M; Day, A; Eddy, S R; Stein, L

2001-01-01

Currently, most genome annotation is curated by centralized groups with limited resources. Efforts to share annotations transparently among multiple groups have not yet been satisfactory. Here we introduce a concept called the Distributed Annotation System (DAS). DAS allows sequence annotations to be decentralized among multiple third-party annotators and integrated on an as-needed basis by client-side software. The communication between client and servers in DAS is defined by the DAS XML specification. Annotations are displayed in layers, one per server. Any client or server adhering to the DAS XML specification can participate in the system; we describe a simple prototype client and server example. The DAS specification is being used experimentally by Ensembl, WormBase, and the Berkeley Drosophila Genome Project. Continued success will depend on the readiness of the research community to adopt DAS and provide annotations. All components are freely available from the project website http://www.biodas.org/.

A distributed, graphical user interface based, computer control system for atomic physics experiments

NASA Astrophysics Data System (ADS)

Keshet, Aviv; Ketterle, Wolfgang

2013-01-01

Atomic physics experiments often require a complex sequence of precisely timed computer controlled events. This paper describes a distributed graphical user interface-based control system designed with such experiments in mind, which makes use of off-the-shelf output hardware from National Instruments. The software makes use of a client-server separation between a user interface for sequence design and a set of output hardware servers. Output hardware servers are designed to use standard National Instruments output cards, but the client-server nature should allow this to be extended to other output hardware. Output sequences running on multiple servers and output cards can be synchronized using a shared clock. By using a field programmable gate array-generated variable frequency clock, redundant buffers can be dramatically shortened, and a time resolution of 100 ns achieved over effectively arbitrary sequence lengths.

A distributed, graphical user interface based, computer control system for atomic physics experiments.

PubMed

Keshet, Aviv; Ketterle, Wolfgang

2013-01-01

Atomic physics experiments often require a complex sequence of precisely timed computer controlled events. This paper describes a distributed graphical user interface-based control system designed with such experiments in mind, which makes use of off-the-shelf output hardware from National Instruments. The software makes use of a client-server separation between a user interface for sequence design and a set of output hardware servers. Output hardware servers are designed to use standard National Instruments output cards, but the client-server nature should allow this to be extended to other output hardware. Output sequences running on multiple servers and output cards can be synchronized using a shared clock. By using a field programmable gate array-generated variable frequency clock, redundant buffers can be dramatically shortened, and a time resolution of 100 ns achieved over effectively arbitrary sequence lengths.

Networking and AI systems: Requirements and benefits

NASA Technical Reports Server (NTRS)

1988-01-01

The price performance benefits of network systems is well documented. The ability to share expensive resources sold timesharing for mainframes, department clusters of minicomputers, and now local area networks of workstations and servers. In the process, other fundamental system requirements emerged. These have now been generalized with open system requirements for hardware, software, applications and tools. The ability to interconnect a variety of vendor products has led to a specification of interfaces that allow new techniques to extend existing systems for new and exciting applications. As an example of the message passing system, local area networks provide a testbed for many of the issues addressed by future concurrent architectures: synchronization, load balancing, fault tolerance and scalability. Gold Hill has been working with a number of vendors on distributed architectures that range from a network of workstations to a hypercube of microprocessors with distributed memory. Results from early applications are promising both for performance and scalability.

Closing the loop on improvement: Packaging experience in the Software Engineering Laboratory

NASA Technical Reports Server (NTRS)

Waligora, Sharon R.; Landis, Linda C.; Doland, Jerry T.

1994-01-01

As part of its award-winning software process improvement program, the Software Engineering Laboratory (SEL) has developed an effective method for packaging organizational best practices based on real project experience into useful handbooks and training courses. This paper shares the SEL's experience over the past 12 years creating and updating software process handbooks and training courses. It provides cost models and guidelines for successful experience packaging derived from SEL experience.

Finite Control Set Model Predictive Control for Multiple Distributed Generators Microgrids

NASA Astrophysics Data System (ADS)

Babqi, Abdulrahman Jamal

This dissertation proposes two control strategies for AC microgrids that consist of multiple distributed generators (DGs). The control strategies are valid for both grid-connected and islanded modes of operation. In general, microgrid can operate as a stand-alone system (i.e., islanded mode) or while it is connected to the utility grid (i.e., grid connected mode). To enhance the performance of a micrgorid, a sophisticated control scheme should be employed. The control strategies of microgrids can be divided into primary and secondary controls. The primary control regulates the output active and reactive powers of each DG in grid-connected mode as well as the output voltage and frequency of each DG in islanded mode. The secondary control is responsible for regulating the microgrid voltage and frequency in the islanded mode. Moreover, it provides power sharing schemes among the DGs. In other words, the secondary control specifies the set points (i.e. reference values) for the primary controllers. In this dissertation, Finite Control Set Model Predictive Control (FCS-MPC) was proposed for controlling microgrids. FCS-MPC was used as the primary controller to regulate the output power of each DG (in the grid-connected mode) or the voltage of the point of DG coupling (in the islanded mode of operation). In the grid-connected mode, Direct Power Model Predictive Control (DPMPC) was implemented to manage the power flow between each DG and the utility grid. In the islanded mode, Voltage Model Predictive Control (VMPC), as the primary control, and droop control, as the secondary control, were employed to control the output voltage of each DG and system frequency. The controller was equipped with a supplementary current limiting technique in order to limit the output current of each DG in abnormal incidents. The control approach also enabled smooth transition between the two modes. The performance of the control strategy was investigated and verified using PSCAD/EMTDC software platform. This dissertation also proposes a control and power sharing strategy for small-scale microgrids in both grid-connected and islanded modes based on centralized FCS-MPC. In grid-connected mode, the controller was capable of managing the output power of each DG and enabling flexible power regulation between the microgrid and the utility grid. In islanded mode, the controller regulated the microgrid voltage and frequency, and provided a precise power sharing scheme among the DGs. In addition, the power sharing can be adjusted flexibly by changing the sharing ratio. The proposed control also enabled plug-and-play operation. Moreover, a smooth transition between the two modes of operation was achieved without any disturbance in the system. Case studies were carried out in order to validate the proposed control strategy with the PSCAD/EMTDA software package.

QMachine: commodity supercomputing in web browsers.

PubMed

Wilkinson, Sean R; Almeida, Jonas S

2014-06-09

Ongoing advancements in cloud computing provide novel opportunities in scientific computing, especially for distributed workflows. Modern web browsers can now be used as high-performance workstations for querying, processing, and visualizing genomics' "Big Data" from sources like The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) without local software installation or configuration. The design of QMachine (QM) was driven by the opportunity to use this pervasive computing model in the context of the Web of Linked Data in Biomedicine. QM is an open-sourced, publicly available web service that acts as a messaging system for posting tasks and retrieving results over HTTP. The illustrative application described here distributes the analyses of 20 Streptococcus pneumoniae genomes for shared suffixes. Because all analytical and data retrieval tasks are executed by volunteer machines, few server resources are required. Any modern web browser can submit those tasks and/or volunteer to execute them without installing any extra plugins or programs. A client library provides high-level distribution templates including MapReduce. This stark departure from the current reliance on expensive server hardware running "download and install" software has already gathered substantial community interest, as QM received more than 2.2 million API calls from 87 countries in 12 months. QM was found adequate to deliver the sort of scalable bioinformatics solutions that computation- and data-intensive workflows require. Paradoxically, the sandboxed execution of code by web browsers was also found to enable them, as compute nodes, to address critical privacy concerns that characterize biomedical environments.

OSiRIS: a distributed Ceph deployment using software defined networking for multi-institutional research

NASA Astrophysics Data System (ADS)

McKee, Shawn; Kissel, Ezra; Meekhof, Benjeman; Swany, Martin; Miller, Charles; Gregorowicz, Michael

2017-10-01

We report on the first year of the OSiRIS project (NSF Award #1541335, UM, IU, MSU and WSU) which is targeting the creation of a distributed Ceph storage infrastructure coupled together with software-defined networking to provide high-performance access for well-connected locations on any participating campus. The projects goal is to provide a single scalable, distributed storage infrastructure that allows researchers at each campus to read, write, manage and share data directly from their own computing locations. The NSF CC*DNI DIBBS program which funded OSiRIS is seeking solutions to the challenges of multi-institutional collaborations involving large amounts of data and we are exploring the creative use of Ceph and networking to address those challenges. While OSiRIS will eventually be serving a broad range of science domains, its first adopter will be the LHC ATLAS detector project via the ATLAS Great Lakes Tier-2 (AGLT2) jointly located at the University of Michigan and Michigan State University. Part of our presentation will cover how ATLAS is using the OSiRIS infrastructure and our experiences integrating our first user community. The presentation will also review the motivations for and goals of the project, the technical details of the OSiRIS infrastructure, the challenges in providing such an infrastructure, and the technical choices made to address those challenges. We will conclude with our plans for the remaining 4 years of the project and our vision for what we hope to deliver by the projects end.

Center for Adaptive Optics | Software

Science.gov Websites

Center for Adaptive Optics A University of California Science and Technology Center home Adaptive Optics Software The Center for Adaptive Optics acts as a clearing house for distributing Software to Institutes it gives specialists in Adaptive Optics a place to distribute their software. All software is

Support for User Interfaces for Distributed Systems

NASA Technical Reports Server (NTRS)

Eychaner, Glenn; Niessner, Albert

2005-01-01

An extensible Java(TradeMark) software framework supports the construction and operation of graphical user interfaces (GUIs) for distributed computing systems typified by ground control systems that send commands to, and receive telemetric data from, spacecraft. Heretofore, such GUIs have been custom built for each new system at considerable expense. In contrast, the present framework affords generic capabilities that can be shared by different distributed systems. Dynamic class loading, reflection, and other run-time capabilities of the Java language and JavaBeans component architecture enable the creation of a GUI for each new distributed computing system with a minimum of custom effort. By use of this framework, GUI components in control panels and menus can send commands to a particular distributed system with a minimum of system-specific code. The framework receives, decodes, processes, and displays telemetry data; custom telemetry data handling can be added for a particular system. The framework supports saving and later restoration of users configurations of control panels and telemetry displays with a minimum of effort in writing system-specific code. GUIs constructed within this framework can be deployed in any operating system with a Java run-time environment, without recompilation or code changes.

OFF, Open source Finite volume Fluid dynamics code: A free, high-order solver based on parallel, modular, object-oriented Fortran API

NASA Astrophysics Data System (ADS)

Zaghi, S.

2014-07-01

OFF, an open source (free software) code for performing fluid dynamics simulations, is presented. The aim of OFF is to solve, numerically, the unsteady (and steady) compressible Navier-Stokes equations of fluid dynamics by means of finite volume techniques: the research background is mainly focused on high-order (WENO) schemes for multi-fluids, multi-phase flows over complex geometries. To this purpose a highly modular, object-oriented application program interface (API) has been developed. In particular, the concepts of data encapsulation and inheritance available within Fortran language (from standard 2003) have been stressed in order to represent each fluid dynamics "entity" (e.g. the conservative variables of a finite volume, its geometry, etc…) by a single object so that a large variety of computational libraries can be easily (and efficiently) developed upon these objects. The main features of OFF can be summarized as follows: Programming LanguageOFF is written in standard (compliant) Fortran 2003; its design is highly modular in order to enhance simplicity of use and maintenance without compromising the efficiency; Parallel Frameworks Supported the development of OFF has been also targeted to maximize the computational efficiency: the code is designed to run on shared-memory multi-cores workstations and distributed-memory clusters of shared-memory nodes (supercomputers); the code's parallelization is based on Open Multiprocessing (OpenMP) and Message Passing Interface (MPI) paradigms; Usability, Maintenance and Enhancement in order to improve the usability, maintenance and enhancement of the code also the documentation has been carefully taken into account; the documentation is built upon comprehensive comments placed directly into the source files (no external documentation files needed): these comments are parsed by means of doxygen free software producing high quality html and latex documentation pages; the distributed versioning system referred as git has been adopted in order to facilitate the collaborative maintenance and improvement of the code; CopyrightsOFF is a free software that anyone can use, copy, distribute, study, change and improve under the GNU Public License version 3. The present paper is a manifesto of OFF code and presents the currently implemented features and ongoing developments. This work is focused on the computational techniques adopted and a detailed description of the main API characteristics is reported. OFF capabilities are demonstrated by means of one and two dimensional examples and a three dimensional real application.

The role of the host in a cooperating mainframe and workstation environment, volumes 1 and 2

NASA Technical Reports Server (NTRS)

Kusmanoff, Antone; Martin, Nancy L.

1989-01-01

In recent years, advancements made in computer systems have prompted a move from centralized computing based on timesharing a large mainframe computer to distributed computing based on a connected set of engineering workstations. A major factor in this advancement is the increased performance and lower cost of engineering workstations. The shift to distributed computing from centralized computing has led to challenges associated with the residency of application programs within the system. In a combined system of multiple engineering workstations attached to a mainframe host, the question arises as to how does a system designer assign applications between the larger mainframe host and the smaller, yet powerful, workstation. The concepts related to real time data processing are analyzed and systems are displayed which use a host mainframe and a number of engineering workstations interconnected by a local area network. In most cases, distributed systems can be classified as having a single function or multiple functions and as executing programs in real time or nonreal time. In a system of multiple computers, the degree of autonomy of the computers is important; a system with one master control computer generally differs in reliability, performance, and complexity from a system in which all computers share the control. This research is concerned with generating general criteria principles for software residency decisions (host or workstation) for a diverse yet coupled group of users (the clustered workstations) which may need the use of a shared resource (the mainframe) to perform their functions.

Common Data Models and Efficient Reproducible Workflows for Distributed Ocean Model Skill Assessment

NASA Astrophysics Data System (ADS)

Signell, R. P.; Snowden, D. P.; Howlett, E.; Fernandes, F. A.

2014-12-01

Model skill assessment requires discovery, access, analysis, and visualization of information from both sensors and models, and traditionally has been possible only by a few experts. The US Integrated Ocean Observing System (US-IOOS) consists of 17 Federal Agencies and 11 Regional Associations that produce data from various sensors and numerical models; exactly the information required for model skill assessment. US-IOOS is seeking to develop documented skill assessment workflows that are standardized, efficient, and reproducible so that a much wider community can participate in the use and assessment of model results. Standardization requires common data models for observational and model data. US-IOOS relies on the CF Conventions for observations and structured grid data, and on the UGRID Conventions for unstructured (e.g. triangular) grid data. This allows applications to obtain only the data they require in a uniform and parsimonious way using web services: OPeNDAP for model output and OGC Sensor Observation Service (SOS) for observed data. Reproducibility is enabled with IPython Notebooks shared on GitHub (http://github.com/ioos). These capture the entire skill assessment workflow, including user input, search, access, analysis, and visualization, ensuring that workflows are self-documenting and reproducible by anyone, using free software. Python packages for common data models are Pyugrid and the British Met Office Iris package. Python packages required to run the workflows (pyugrid, pyoos, and the British Met Office Iris package) are also available on GitHub and on Binstar.org so that users can run scenarios using the free Anaconda Python distribution. Hosted services such as Wakari enable anyone to reproduce these workflows for free, without installing any software locally, using just their web browser. We are also experimenting with Wakari Enterprise, which allows multi-user access from a web browser to an IPython Server running where large quantities of model output reside, increasing the efficiency. The open development and distribution of these workflows, and the software on which they depend, is an educational resource for those new to the field and a center of focus where practitioners can contribute new software and ideas.

Impact of Machine Virtualization on Timing Precision for Performance-critical Tasks

NASA Astrophysics Data System (ADS)

Karpov, Kirill; Fedotova, Irina; Siemens, Eduard

2017-07-01

In this paper we present a measurement study to characterize the impact of hardware virtualization on basic software timing, as well as on precise sleep operations of an operating system. We investigated how timer hardware is shared among heavily CPU-, I/O- and Network-bound tasks on a virtual machine as well as on the host machine. VMware ESXi and QEMU/KVM have been chosen as commonly used examples of hypervisor- and host-based models. Based on statistical parameters of retrieved distributions, our results provide a very good estimation of timing behavior. It is essential for real-time and performance-critical applications such as image processing or real-time control.

OntoMaton: a bioportal powered ontology widget for Google Spreadsheets.

PubMed

Maguire, Eamonn; González-Beltrán, Alejandra; Whetzel, Patricia L; Sansone, Susanna-Assunta; Rocca-Serra, Philippe

2013-02-15

Data collection in spreadsheets is ubiquitous, but current solutions lack support for collaborative semantic annotation that would promote shared and interdisciplinary annotation practices, supporting geographically distributed players. OntoMaton is an open source solution that brings ontology lookup and tagging capabilities into a cloud-based collaborative editing environment, harnessing Google Spreadsheets and the NCBO Web services. It is a general purpose, format-agnostic tool that may serve as a component of the ISA software suite. OntoMaton can also be used to assist the ontology development process. OntoMaton is freely available from Google widgets under the CPAL open source license; documentation and examples at: https://github.com/ISA-tools/OntoMaton.

Arranging computer architectures to create higher-performance controllers

NASA Technical Reports Server (NTRS)

Jacklin, Stephen A.

1988-01-01

Techniques for integrating microprocessors, array processors, and other intelligent devices in control systems are reviewed, with an emphasis on the (re)arrangement of components to form distributed or parallel processing systems. Consideration is given to the selection of the host microprocessor, increasing the power and/or memory capacity of the host, multitasking software for the host, array processors to reduce computation time, the allocation of real-time and non-real-time events to different computer subsystems, intelligent devices to share the computational burden for real-time events, and intelligent interfaces to increase communication speeds. The case of a helicopter vibration-suppression and stabilization controller is analyzed as an example, and significant improvements in computation and throughput rates are demonstrated.

Simulation of trading strategies in the electricity market

NASA Astrophysics Data System (ADS)

Charkiewicz, Kamil; Nowak, Robert

2011-10-01

The main objective of the energy market existence is reduction of the total cost of production, transport and distribution of energy, and so the prices paid by terminal consumers. Energy market contains few markets that are varying on operational rules, the important segments: the Futures Contract Market and Next Day Market are analyzed in presented approach. The computer system was developed to simulate the Polish Energy Market. This system use the multi-agent approach, where each agent is the separate shared library with defined interface. The software was used to compare strategies for players in energy market, where the strategies uses auto-regression, k-nearest neighbours, neural network and mixed algorithm, to predict the next price.

Network-based collaborative research environment LDRD final report

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

Davies, B.R.; McDonald, M.J.

1997-09-01

The Virtual Collaborative Environment (VCE) and Distributed Collaborative Workbench (DCW) are new technologies that make it possible for diverse users to synthesize and share mechatronic, sensor, and information resources. Using these technologies, university researchers, manufacturers, design firms, and others can directly access and reconfigure systems located throughout the world. The architecture for implementing VCE and DCW has been developed based on the proposed National Information Infrastructure or Information Highway and a tool kit of Sandia-developed software. Further enhancements to the VCE and DCW technologies will facilitate access to other mechatronic resources. This report describes characteristics of VCE and DCW andmore » also includes background information about the evolution of these technologies.« less

Towards structured sharing of raw and derived neuroimaging data across existing resources

PubMed Central

Keator, D.B.; Helmer, K.; Steffener, J.; Turner, J.A.; Van Erp, T.G.M.; Gadde, S.; Ashish, N.; Burns, G.A.; Nichols, B.N.

2013-01-01

Data sharing efforts increasingly contribute to the acceleration of scientific discovery. Neuroimaging data is accumulating in distributed domain-specific databases and there is currently no integrated access mechanism nor an accepted format for the critically important meta-data that is necessary for making use of the combined, available neuroimaging data. In this manuscript, we present work from the Derived Data Working Group, an open-access group sponsored by the Biomedical Informatics Research Network (BIRN) and the International Neuroimaging Coordinating Facility (INCF) focused on practical tools for distributed access to neuroimaging data. The working group develops models and tools facilitating the structured interchange of neuroimaging meta-data and is making progress towards a unified set of tools for such data and meta-data exchange. We report on the key components required for integrated access to raw and derived neuroimaging data as well as associated meta-data and provenance across neuroimaging resources. The components include (1) a structured terminology that provides semantic context to data, (2) a formal data model for neuroimaging with robust tracking of data provenance, (3) a web service-based application programming interface (API) that provides a consistent mechanism to access and query the data model, and (4) a provenance library that can be used for the extraction of provenance data by image analysts and imaging software developers. We believe that the framework and set of tools outlined in this manuscript have great potential for solving many of the issues the neuroimaging community faces when sharing raw and derived neuroimaging data across the various existing database systems for the purpose of accelerating scientific discovery. PMID:23727024

Compiling software for a hierarchical distributed processing system

DOEpatents

Archer, Charles J; Blocksome, Michael A; Ratterman, Joseph D; Smith, Brian E

2013-12-31

Compiling software for a hierarchical distributed processing system including providing to one or more compiling nodes software to be compiled, wherein at least a portion of the software to be compiled is to be executed by one or more nodes; compiling, by the compiling node, the software; maintaining, by the compiling node, any compiled software to be executed on the compiling node; selecting, by the compiling node, one or more nodes in a next tier of the hierarchy of the distributed processing system in dependence upon whether any compiled software is for the selected node or the selected node's descendents; sending to the selected node only the compiled software to be executed by the selected node or selected node's descendent.

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.

Merlin - Massively parallel heterogeneous computing

NASA Technical Reports Server (NTRS)

Wittie, Larry; Maples, Creve

1989-01-01

Hardware and software for Merlin, a new kind of massively parallel computing system, are described. Eight computers are linked as a 300-MIPS prototype to develop system software for a larger Merlin network with 16 to 64 nodes, totaling 600 to 3000 MIPS. These working prototypes help refine a mapped reflective memory technique that offers a new, very general way of linking many types of computer to form supercomputers. Processors share data selectively and rapidly on a word-by-word basis. Fast firmware virtual circuits are reconfigured to match topological needs of individual application programs. Merlin's low-latency memory-sharing interfaces solve many problems in the design of high-performance computing systems. The Merlin prototypes are intended to run parallel programs for scientific applications and to determine hardware and software needs for a future Teraflops Merlin network.

Sharing the Code.

ERIC Educational Resources Information Center

Olsen, Florence

2003-01-01

Colleges and universities are beginning to consider collaborating on open-source-code projects as a way to meet critical software and computing needs. Points out the attractive features of noncommercial open-source software and describes some examples in use now, especially for the creation of Web infrastructure. (SLD)

Neuroinformatics Software Applications Supporting Electronic Data Capture, Management, and Sharing for the Neuroimaging Community

PubMed Central

Nichols, B. Nolan; Pohl, Kilian M.

2017-01-01

Accelerating insight into the relation between brain and behavior entails conducting small and large-scale research endeavors that lead to reproducible results. Consensus is emerging between funding agencies, publishers, and the research community that data sharing is a fundamental requirement to ensure all such endeavors foster data reuse and fuel reproducible discoveries. Funding agency and publisher mandates to share data are bolstered by a growing number of data sharing efforts that demonstrate how information technologies can enable meaningful data reuse. Neuroinformatics evaluates scientific needs and develops solutions to facilitate the use of data across the cognitive and neurosciences. For example, electronic data capture and management tools designed to facilitate human neurocognitive research can decrease the setup time of studies, improve quality control, and streamline the process of harmonizing, curating, and sharing data across data repositories. In this article we outline the advantages and disadvantages of adopting software applications that support these features by reviewing the tools available and then presenting two contrasting neuroimaging study scenarios in the context of conducting a cross-sectional and a multisite longitudinal study. PMID:26267019

Probability distribution of extreme share returns in Malaysia

NASA Astrophysics Data System (ADS)

Zin, Wan Zawiah Wan; Safari, Muhammad Aslam Mohd; Jaaman, Saiful Hafizah; Yie, Wendy Ling Shin

2014-09-01

The objective of this study is to investigate the suitable probability distribution to model the extreme share returns in Malaysia. To achieve this, weekly and monthly maximum daily share returns are derived from share prices data obtained from Bursa Malaysia over the period of 2000 to 2012. The study starts with summary statistics of the data which will provide a clue on the likely candidates for the best fitting distribution. Next, the suitability of six extreme value distributions, namely the Gumbel, Generalized Extreme Value (GEV), Generalized Logistic (GLO) and Generalized Pareto (GPA), the Lognormal (GNO) and the Pearson (PE3) distributions are evaluated. The method of L-moments is used in parameter estimation. Based on several goodness of fit tests and L-moment diagram test, the Generalized Pareto distribution and the Pearson distribution are found to be the best fitted distribution to represent the weekly and monthly maximum share returns in Malaysia stock market during the studied period, respectively.

ESPC Common Model Architecture Earth System Modeling Framework (ESMF) Software and Application Development

DTIC Science & Technology

2015-09-30

originate from NASA , NOAA , and community modeling efforts, and support for creation of the suite was shared by sponsors from other agencies. ESPS...Framework (ESMF) Software and Application Development Cecelia Deluca NESII/CIRES/ NOAA Earth System Research Laboratory 325 Broadway Boulder, CO...Capability (NUOPC) was established between NOAA and Navy to develop a common software architecture for easy and efficient interoperability. The

First year of ALMA site software deployment: where everything comes together

NASA Astrophysics Data System (ADS)

González, Víctor; Mora, Matias; Araya, Rodrigo; Arredondo, Diego; Bartsch, Marcelo; Burgos, Pablo; Ibsen, Jorge; Reveco, Johnny; Sáez, Norman; Schemrl, Anton; Sepulveda, Jorge; Shen, Tzu-Chiang; Soto, Rubén; Troncoso, Nicolás; Zambrano, Mauricio; Barriga, Nicolás; Glendenning, Brian; Raffi, Gianni; Kern, Jeff

2010-07-01

Starting 2009, the ALMA project initiated one of its most exciting phases within construction: the first antenna from one of the vendors was delivered to the Assembly, Integration and Verification team. With this milestone and the closure of the ALMA Test Facility in New Mexico, the JAO Computing Group in Chile found itself in the front line of the project's software deployment and integration effort. Among the group's main responsibilities are the deployment, configuration and support of the observation systems, in addition to infrastructure administration, all of which needs to be done in close coordination with the development groups in Europe, North America and Japan. Software support has been the primary interaction key with the current users (mainly scientists, operators and hardware engineers), as the software is normally the most visible part of the system. During this first year of work with the production hardware, three consecutive software releases have been deployed and commissioned. Also, the first three antennas have been moved to the Array Operations Site, at 5.000 meters elevation, and the complete end-to-end system has been successfully tested. This paper shares the experience of this 15-people group as part of the construction team at the ALMA site, and working together with Computing IPT, on the achievements and problems overcomed during this period. It explores the excellent results of teamwork, and also some of the troubles that such a complex and geographically distributed project can run into. Finally, it approaches the challenges still to come, with the transition to the ALMA operations plan.

Challenges in Managing Trustworthy Large-scale Digital Science

NASA Astrophysics Data System (ADS)

Evans, B. J. K.

2017-12-01

The increased use of large-scale international digital science has opened a number of challenges for managing, handling, using and preserving scientific information. The large volumes of information are driven by three main categories - model outputs including coupled models and ensembles, data products that have been processing to a level of usability, and increasingly heuristically driven data analysis. These data products are increasingly the ones that are usable by the broad communities, and far in excess of the raw instruments data outputs. The data, software and workflows are then shared and replicated to allow broad use at an international scale, which places further demands of infrastructure to support how the information is managed reliably across distributed resources. Users necessarily rely on these underlying "black boxes" so that they are productive to produce new scientific outcomes. The software for these systems depend on computational infrastructure, software interconnected systems, and information capture systems. This ranges from the fundamentals of the reliability of the compute hardware, system software stacks and libraries, and the model software. Due to these complexities and capacity of the infrastructure, there is an increased emphasis of transparency of the approach and robustness of the methods over the full reproducibility. Furthermore, with large volume data management, it is increasingly difficult to store the historical versions of all model and derived data. Instead, the emphasis is on the ability to access the updated products and the reliability by which both previous outcomes are still relevant and can be updated for the new information. We will discuss these challenges and some of the approaches underway that are being used to address these issues.

A Web-based Distributed Voluntary Computing Platform for Large Scale Hydrological Computations

NASA Astrophysics Data System (ADS)

Demir, I.; Agliamzanov, R.

2014-12-01

Distributed volunteer computing can enable researchers and scientist to form large parallel computing environments to utilize the computing power of the millions of computers on the Internet, and use them towards running large scale environmental simulations and models to serve the common good of local communities and the world. Recent developments in web technologies and standards allow client-side scripting languages to run at speeds close to native application, and utilize the power of Graphics Processing Units (GPU). Using a client-side scripting language like JavaScript, we have developed an open distributed computing framework that makes it easy for researchers to write their own hydrologic models, and run them on volunteer computers. Users will easily enable their websites for visitors to volunteer sharing their computer resources to contribute running advanced hydrological models and simulations. Using a web-based system allows users to start volunteering their computational resources within seconds without installing any software. The framework distributes the model simulation to thousands of nodes in small spatial and computational sizes. A relational database system is utilized for managing data connections and queue management for the distributed computing nodes. In this paper, we present a web-based distributed volunteer computing platform to enable large scale hydrological simulations and model runs in an open and integrated environment.

Contingency theoretic methodology for agent-based web-oriented manufacturing systems

NASA Astrophysics Data System (ADS)

Durrett, John R.; Burnell, Lisa J.; Priest, John W.

2000-12-01

The development of distributed, agent-based, web-oriented, N-tier Information Systems (IS) must be supported by a design methodology capable of responding to the convergence of shifts in business process design, organizational structure, computing, and telecommunications infrastructures. We introduce a contingency theoretic model for the use of open, ubiquitous software infrastructure in the design of flexible organizational IS. Our basic premise is that developers should change in the way they view the software design process from a view toward the solution of a problem to one of the dynamic creation of teams of software components. We postulate that developing effective, efficient, flexible, component-based distributed software requires reconceptualizing the current development model. The basic concepts of distributed software design are merged with the environment-causes-structure relationship from contingency theory; the task-uncertainty of organizational- information-processing relationships from information processing theory; and the concept of inter-process dependencies from coordination theory. Software processes are considered as employees, groups of processes as software teams, and distributed systems as software organizations. Design techniques already used in the design of flexible business processes and well researched in the domain of the organizational sciences are presented. Guidelines that can be utilized in the creation of component-based distributed software will be discussed.

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

NASA Astrophysics Data System (ADS)

Dubenskaya, Julia; Kryukov, Alexander; Demichev, Andrey

2018-02-01

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

Reliable file sharing in distributed operating system using web RTC

NASA Astrophysics Data System (ADS)

Dukiya, Rajesh

2017-12-01

Since, the evolution of distributed operating system, distributed file system is come out to be important part in operating system. P2P is a reliable way in Distributed Operating System for file sharing. It was introduced in 1999, later it became a high research interest topic. Peer to Peer network is a type of network, where peers share network workload and other load related tasks. A P2P network can be a period of time connection, where a bunch of computers connected by a USB (Universal Serial Bus) port to transfer or enable disk sharing i.e. file sharing. Currently P2P requires special network that should be designed in P2P way. Nowadays, there is a big influence of browsers in our life. In this project we are going to study of file sharing mechanism in distributed operating system in web browsers, where we will try to find performance bottlenecks which our research will going to be an improvement in file sharing by performance and scalability in distributed file systems. Additionally, we will discuss the scope of Web Torrent file sharing and free-riding in peer to peer networks.

Sustaining an Online, Shared Community Resource for Models, Robust Open source Software Tools and Data for Volcanology - the Vhub Experience

NASA Astrophysics Data System (ADS)

Patra, A. K.; Valentine, G. A.; Bursik, M. I.; Connor, C.; Connor, L.; Jones, M.; Simakov, N.; Aghakhani, H.; Jones-Ivey, R.; Kosar, T.; Zhang, B.

2015-12-01

Over the last 5 years we have created a community collaboratory Vhub.org [Palma et al, J. App. Volc. 3:2 doi:10.1186/2191-5040-3-2] as a place to find volcanology-related resources, and a venue for users to disseminate tools, teaching resources, data, and an online platform to support collaborative efforts. As the community (current active users > 6000 from an estimated community of comparable size) embeds the tools in the collaboratory into educational and research workflows it became imperative to: a) redesign tools into robust, open source reusable software for online and offline usage/enhancement; b) share large datasets with remote collaborators and other users seamlessly with security; c) support complex workflows for uncertainty analysis, validation and verification and data assimilation with large data. The focus on tool development/redevelopment has been twofold - firstly to use best practices in software engineering and new hardware like multi-core and graphic processing units. Secondly we wish to enhance capabilities to support inverse modeling, uncertainty quantification using large ensembles and design of experiments, calibration, validation. Among software engineering practices we practice are open source facilitating community contributions, modularity and reusability. Our initial targets are four popular tools on Vhub - TITAN2D, TEPHRA2, PUFF and LAVA. Use of tools like these requires many observation driven data sets e.g. digital elevation models of topography, satellite imagery, field observations on deposits etc. These data are often maintained in private repositories that are privately shared by "sneaker-net". As a partial solution to this we tested mechanisms using irods software for online sharing of private data with public metadata and access limits. Finally, we adapted use of workflow engines (e.g. Pegasus) to support the complex data and computing workflows needed for usage like uncertainty quantification for hazard analysis using physical models.

Practice-Relevant Pedagogy for Mining Software Engineering Curricula Assets

DTIC Science & Technology

2007-06-20

permits the application of the Lean methods by virtually grouping shared services into eWorkcenters to which only non-routine requests are routed...engineering can be applied to IT shared services improvement and provide precise system improvement methods to complement the ITIL best practice. This...Vertical� or internal service- chain of primary business functions and enabling shared services Framework results - Mined patterns that relate

NHPP-Based Software Reliability Models Using Equilibrium Distribution

NASA Astrophysics Data System (ADS)

Xiao, Xiao; Okamura, Hiroyuki; Dohi, Tadashi

Non-homogeneous Poisson processes (NHPPs) have gained much popularity in actual software testing phases to estimate the software reliability, the number of remaining faults in software and the software release timing. In this paper, we propose a new modeling approach for the NHPP-based software reliability models (SRMs) to describe the stochastic behavior of software fault-detection processes. The fundamental idea is to apply the equilibrium distribution to the fault-detection time distribution in NHPP-based modeling. We also develop efficient parameter estimation procedures for the proposed NHPP-based SRMs. Through numerical experiments, it can be concluded that the proposed NHPP-based SRMs outperform the existing ones in many data sets from the perspective of goodness-of-fit and prediction performance.

Quantifying Scheduling Challenges for Exascale System Software

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

Mondragon, Oscar; Bridges, Patrick G.; Jones, Terry R

2015-01-01

The move towards high-performance computing (HPC) ap- plications comprised of coupled codes and the need to dra- matically reduce data movement is leading to a reexami- nation of time-sharing vs. space-sharing in HPC systems. In this paper, we discuss and begin to quantify the perfor- mance impact of a move away from strict space-sharing of nodes for HPC applications. Specifically, we examine the po- tential performance cost of time-sharing nodes between ap- plication components, we determine whether a simple coor- dinated scheduling mechanism can address these problems, and we research how suitable simple constraint-based opti- mization techniques are for solvingmore » scheduling challenges in this regime. Our results demonstrate that current general- purpose HPC system software scheduling and resource al- location systems are subject to significant performance de- ciencies which we quantify for six representative applica- tions. Based on these results, we discuss areas in which ad- ditional research is needed to meet the scheduling challenges of next-generation HPC systems.« less

Concurrent Image Processing Executive (CIPE). Volume 1: Design overview

NASA Technical Reports Server (NTRS)

Lee, Meemong; Groom, Steven L.; Mazer, Alan S.; Williams, Winifred I.

1990-01-01

The design and implementation of a Concurrent Image Processing Executive (CIPE), which is intended to become the support system software for a prototype high performance science analysis workstation are described. The target machine for this software is a JPL/Caltech Mark 3fp Hypercube hosted by either a MASSCOMP 5600 or a Sun-3, Sun-4 workstation; however, the design will accommodate other concurrent machines of similar architecture, i.e., local memory, multiple-instruction-multiple-data (MIMD) machines. The CIPE system provides both a multimode user interface and an applications programmer interface, and has been designed around four loosely coupled modules: user interface, host-resident executive, hypercube-resident executive, and application functions. The loose coupling between modules allows modification of a particular module without significantly affecting the other modules in the system. In order to enhance hypercube memory utilization and to allow expansion of image processing capabilities, a specialized program management method, incremental loading, was devised. To minimize data transfer between host and hypercube, a data management method which distributes, redistributes, and tracks data set information was implemented. The data management also allows data sharing among application programs. The CIPE software architecture provides a flexible environment for scientific analysis of complex remote sensing image data, such as planetary data and imaging spectrometry, utilizing state-of-the-art concurrent computation capabilities.

Thyroid Cancer and Tumor Collaborative Registry (TCCR).

PubMed

Shats, Oleg; Goldner, Whitney; Feng, Jianmin; Sherman, Alexander; Smith, Russell B; Sherman, Simon

2016-01-01

A multicenter, web-based Thyroid Cancer and Tumor Collaborative Registry (TCCR, http://tccr.unmc.edu) allows for the collection and management of various data on thyroid cancer (TC) and thyroid nodule (TN) patients. The TCCR is coupled with OpenSpecimen, an open-source biobank management system, to annotate biospecimens obtained from the TCCR subjects. The demographic, lifestyle, physical activity, dietary habits, family history, medical history, and quality of life data are provided and may be entered into the registry by subjects. Information on diagnosis, treatment, and outcome is entered by the clinical personnel. The TCCR uses advanced technical and organizational practices, such as (i) metadata-driven software architecture (design); (ii) modern standards and best practices for data sharing and interoperability (standardization); (iii) Agile methodology (project management); (iv) Software as a Service (SaaS) as a software distribution model (operation); and (v) the confederation principle as a business model (governance). This allowed us to create a secure, reliable, user-friendly, and self-sustainable system for TC and TN data collection and management that is compatible with various end-user devices and easily adaptable to a rapidly changing environment. Currently, the TCCR contains data on 2,261 subjects and data on more than 28,000 biospecimens. Data and biological samples collected by the TCCR are used in developing diagnostic, prevention, treatment, and survivorship strategies against TC.

Software metrics: Software quality metrics for distributed systems. [reliability engineering

NASA Technical Reports Server (NTRS)

Post, J. V.

1981-01-01

Software quality metrics was extended to cover distributed computer systems. Emphasis is placed on studying embedded computer systems and on viewing them within a system life cycle. The hierarchy of quality factors, criteria, and metrics was maintained. New software quality factors were added, including survivability, expandability, and evolvability.

76 FR 66012 - Partner's Distributive Share

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-25

[email protected] . SUPPLEMENTARY INFORMATION: Background Subchapter K is intended to permit taxpayers to... Revenue Code provides that a partner's distributive share of income, gain, loss, deduction, or credit... that a partner's distributive share of income, gain, loss, deduction, or credit (or item thereof) shall...

Using a Foundational Ontology for Reengineering a Software Enterprise Ontology

NASA Astrophysics Data System (ADS)

Perini Barcellos, Monalessa; de Almeida Falbo, Ricardo

The knowledge about software organizations is considerably relevant to software engineers. The use of a common vocabulary for representing the useful knowledge about software organizations involved in software projects is important for several reasons, such as to support knowledge reuse and to allow communication and interoperability between tools. Domain ontologies can be used to define a common vocabulary for sharing and reuse of knowledge about some domain. Foundational ontologies can be used for evaluating and re-designing domain ontologies, giving to these real-world semantics. This paper presents an evaluating of a Software Enterprise Ontology that was reengineered using the Unified Foundation Ontology (UFO) as basis.

SIF 3.0

ERIC Educational Resources Information Center

Waters, John K.

2009-01-01

This article introduces Schools Interoperability Framework (SIF), a specification for data sharing among educational software applications that has grown to 10 disparate software applications. This new version (code name Columbus) is likely to give districts more vendors to choose from--maybe a lot more--because it will be arriving with a profound…

Does Your Graphing Software Real-ly Work?

ERIC Educational Resources Information Center

Marchand, R. J.; McDevitt, T. J.; Bosse, Michael J.; Nandakumar, N. R.

2007-01-01

Many popular mathematical software products including Maple, Mathematica, Derive, Mathcad, Matlab, and some of the TI calculators produce incorrect graphs because they use complex arithmetic instead of "real" arithmetic. This article expounds on this issue, provides possible remedies for instructors to share with their students, and demonstrates…

Global Situational Awareness with Free Tools

DTIC Science & Technology

2015-01-15

Client Technical Solutions • Software Engineering Measurement and Analysis • Architecture Practices • Product Line Practice • Team Software Process...multiple data sources • Snort (Snorby on Security Onion ) • Nagios • SharePoint RSS • Flow • Others • Leverage standard data formats • Keyhole Markup Language

47 CFR 59.3 - Information concerning deployment of new services and equipment.

Code of Federal Regulations, 2010 CFR

2010-10-01

... services and equipment, including any software or upgrades of software integral to the use or operation of... services and equipment. 59.3 Section 59.3 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) COMMON CARRIER SERVICES (CONTINUED) INFRASTRUCTURE SHARING § 59.3 Information concerning deployment of...

Toward the Geoscience Paper of the Future: Best practices for documenting and sharing research from data to software to provenance

NASA Astrophysics Data System (ADS)

Gil, Yolanda; David, Cédric H.; Demir, Ibrahim; Essawy, Bakinam T.; Fulweiler, Robinson W.; Goodall, Jonathan L.; Karlstrom, Leif; Lee, Huikyo; Mills, Heath J.; Oh, Ji-Hyun; Pierce, Suzanne A.; Pope, Allen; Tzeng, Mimi W.; Villamizar, Sandra R.; Yu, Xuan

2016-10-01

Geoscientists now live in a world rich with digital data and methods, and their computational research cannot be fully captured in traditional publications. The Geoscience Paper of the Future (GPF) presents an approach to fully document, share, and cite all their research products including data, software, and computational provenance. This article proposes best practices for GPF authors to make data, software, and methods openly accessible, citable, and well documented. The publication of digital objects empowers scientists to manage their research products as valuable scientific assets in an open and transparent way that enables broader access by other scientists, students, decision makers, and the public. Improving documentation and dissemination of research will accelerate the pace of scientific discovery by improving the ability of others to build upon published work.

Large-scale P2P network based distributed virtual geographic environment (DVGE)

NASA Astrophysics Data System (ADS)

Tan, Xicheng; Yu, Liang; Bian, Fuling

2007-06-01

Virtual Geographic Environment has raised full concern as a kind of software information system that helps us understand and analyze the real geographic environment, and it has also expanded to application service system in distributed environment--distributed virtual geographic environment system (DVGE), and gets some achievements. However, limited by the factor of the mass data of VGE, the band width of network, as well as numerous requests and economic, etc. DVGE still faces some challenges and problems which directly cause the current DVGE could not provide the public with high-quality service under current network mode. The Rapid development of peer-to-peer network technology has offered new ideas of solutions to the current challenges and problems of DVGE. Peer-to-peer network technology is able to effectively release and search network resources so as to realize efficient share of information. Accordingly, this paper brings forth a research subject on Large-scale peer-to-peer network extension of DVGE as well as a deep study on network framework, routing mechanism, and DVGE data management on P2P network.

Perspectives on Sharing Models and Related Resources in Computational Biomechanics Research.

PubMed

Erdemir, Ahmet; Hunter, Peter J; Holzapfel, Gerhard A; Loew, Leslie M; Middleton, John; Jacobs, Christopher R; Nithiarasu, Perumal; Löhner, Rainlad; Wei, Guowei; Winkelstein, Beth A; Barocas, Victor H; Guilak, Farshid; Ku, Joy P; Hicks, Jennifer L; Delp, Scott L; Sacks, Michael; Weiss, Jeffrey A; Ateshian, Gerard A; Maas, Steve A; McCulloch, Andrew D; Peng, Grace C Y

2018-02-01

The role of computational modeling for biomechanics research and related clinical care will be increasingly prominent. The biomechanics community has been developing computational models routinely for exploration of the mechanics and mechanobiology of diverse biological structures. As a result, a large array of models, data, and discipline-specific simulation software has emerged to support endeavors in computational biomechanics. Sharing computational models and related data and simulation software has first become a utilitarian interest, and now, it is a necessity. Exchange of models, in support of knowledge exchange provided by scholarly publishing, has important implications. Specifically, model sharing can facilitate assessment of reproducibility in computational biomechanics and can provide an opportunity for repurposing and reuse, and a venue for medical training. The community's desire to investigate biological and biomechanical phenomena crossing multiple systems, scales, and physical domains, also motivates sharing of modeling resources as blending of models developed by domain experts will be a required step for comprehensive simulation studies as well as the enhancement of their rigor and reproducibility. The goal of this paper is to understand current perspectives in the biomechanics community for the sharing of computational models and related resources. Opinions on opportunities, challenges, and pathways to model sharing, particularly as part of the scholarly publishing workflow, were sought. A group of journal editors and a handful of investigators active in computational biomechanics were approached to collect short opinion pieces as a part of a larger effort of the IEEE EMBS Computational Biology and the Physiome Technical Committee to address model reproducibility through publications. A synthesis of these opinion pieces indicates that the community recognizes the necessity and usefulness of model sharing. There is a strong will to facilitate model sharing, and there are corresponding initiatives by the scientific journals. Outside the publishing enterprise, infrastructure to facilitate model sharing in biomechanics exists, and simulation software developers are interested in accommodating the community's needs for sharing of modeling resources. Encouragement for the use of standardized markups, concerns related to quality assurance, acknowledgement of increased burden, and importance of stewardship of resources are noted. In the short-term, it is advisable that the community builds upon recent strategies and experiments with new pathways for continued demonstration of model sharing, its promotion, and its utility. Nonetheless, the need for a long-term strategy to unify approaches in sharing computational models and related resources is acknowledged. Development of a sustainable platform supported by a culture of open model sharing will likely evolve through continued and inclusive discussions bringing all stakeholders at the table, e.g., by possibly establishing a consortium.

The role of open-source software in innovation and standardization in radiology.

PubMed

Erickson, Bradley J; Langer, Steve; Nagy, Paul

2005-11-01

The use of open-source software (OSS), in which developers release the source code to applications they have developed, is popular in the software industry. This is done to allow others to modify and improve software (which may or may not be shared back to the community) and to allow others to learn from the software. Radiology was an early participant in this model, supporting OSS that implemented the ACR-National Electrical Manufacturers Association (now Digital Imaging and Communications in Medicine) standard for medical image communications. In radiology and in other fields, OSS has promoted innovation and the adoption of standards. Popular OSS is of high quality because access to source code allows many people to identify and resolve errors. Open-source software is analogous to the peer-review scientific process: one must be able to see and reproduce results to understand and promote what is shared. The authors emphasize that support for OSS need not threaten vendors; most vendors embrace and benefit from standards. Open-source development does not replace vendors but more clearly defines their roles, typically focusing on areas in which proprietary differentiators benefit customers and on professional services such as implementation planning and service. Continued support for OSS is essential for the success of our field.

A modular approach to addressing model design, scale, and parameter estimation issues in distributed hydrological modelling

USGS Publications Warehouse

Leavesley, G.H.; Markstrom, S.L.; Restrepo, Pedro J.; Viger, R.J.

2002-01-01

A modular approach to model design and construction provides a flexible framework in which to focus the multidisciplinary research and operational efforts needed to facilitate the development, selection, and application of the most robust distributed modelling methods. A variety of modular approaches have been developed, but with little consideration for compatibility among systems and concepts. Several systems are proprietary, limiting any user interaction. The US Geological Survey modular modelling system (MMS) is a modular modelling framework that uses an open source software approach to enable all members of the scientific community to address collaboratively the many complex issues associated with the design, development, and application of distributed hydrological and environmental models. Implementation of a common modular concept is not a trivial task. However, it brings the resources of a larger community to bear on the problems of distributed modelling, provides a framework in which to compare alternative modelling approaches objectively, and provides a means of sharing the latest modelling advances. The concepts and components of the MMS are described and an example application of the MMS, in a decision-support system context, is presented to demonstrate current system capabilities. Copyright ?? 2002 John Wiley and Sons, Ltd.

A hybrid integrated services digital network-internet protocol solution for resident education.

PubMed

Erickson, Delnora; Greer, Lester; Belard, Arnaud; Tinnel, Brent; O'Connell, John

2010-05-01

The purpose of this study was to explore the effectiveness of incorporating Web-based application sharing of virtual medical simulation software within a multipoint video teleconference (VTC) as a training tool in graduate medical education. National Capital Consortium Radiation Oncology Residency Program resident and attending physicians participated in dosimetry teaching sessions held via VTC using Acrobat Connect application sharing. Residents at remote locations could take turns designing radiation treatments using standard three-dimensional planning software, whereas instructors gave immediate feedback and demonstrated proper techniques. Immediately after each dosimetry lesson, residents were asked to complete a survey that evaluated the effectiveness of the session. At the end of a 3-month trial of using Adobe Connect, residents completed a final survey that compared this teaching technology to the prior VTC-alone method. The mean difference from equality across all quality measures from the weekly survey was 0.8, where 0 indicated neither enhanced nor detracted from the learning experience and 1 indicated a minor enhancement in the learning experience. The mean difference from equality across all measures from the final survey comparing use of application sharing with VTC to VTC alone was 1.5, where 1 indicated slightly better and 2 indicated a somewhat better experience. The teaching efficacy of multipoint VTC is perceived by medical residents to be more effective when complemented by application-sharing software such as Adobe Acrobat Connect.

Integrated software environment based on COMKAT for analyzing tracer pharmacokinetics with molecular imaging.

PubMed

Fang, Yu-Hua Dean; Asthana, Pravesh; Salinas, Cristian; Huang, Hsuan-Ming; Muzic, Raymond F

2010-01-01

An integrated software package, Compartment Model Kinetic Analysis Tool (COMKAT), is presented in this report. COMKAT is an open-source software package with many functions for incorporating pharmacokinetic analysis in molecular imaging research and has both command-line and graphical user interfaces. With COMKAT, users may load and display images, draw regions of interest, load input functions, select kinetic models from a predefined list, or create a novel model and perform parameter estimation, all without having to write any computer code. For image analysis, COMKAT image tool supports multiple image file formats, including the Digital Imaging and Communications in Medicine (DICOM) standard. Image contrast, zoom, reslicing, display color table, and frame summation can be adjusted in COMKAT image tool. It also displays and automatically registers images from 2 modalities. Parametric imaging capability is provided and can be combined with the distributed computing support to enhance computation speeds. For users without MATLAB licenses, a compiled, executable version of COMKAT is available, although it currently has only a subset of the full COMKAT capability. Both the compiled and the noncompiled versions of COMKAT are free for academic research use. Extensive documentation, examples, and COMKAT itself are available on its wiki-based Web site, http://comkat.case.edu. Users are encouraged to contribute, sharing their experience, examples, and extensions of COMKAT. With integrated functionality specifically designed for imaging and kinetic modeling analysis, COMKAT can be used as a software environment for molecular imaging and pharmacokinetic analysis.

Code Sharing and Collaboration: Experiences from the Scientist's Expert Assistant Project and their Relevance to the Virtual Observatory

NASA Technical Reports Server (NTRS)

Jones, Jeremy; Grosvenor, Sandy; Wolf, Karl; Li, Connie; Koratkar, Anuradha; Powers, Edward I. (Technical Monitor)

2001-01-01

In the Virtual Observatory (VO), software tools will perform the functions that have traditionally been performed by physical observatories and their instruments. These tools will not be adjuncts to VO functionality but will make up the very core of the VO. Consequently, the tradition of observatory and system independent tools serving a small user base is not valid for the VO. For the VO to succeed, we must improve software collaboration and code sharing between projects and groups. A significant goal of the Scientist's Expert Assistant (SEA) project has been promoting effective collaboration and code sharing between groups. During the past three years, the SEA project has been developing prototypes for new observation planning software tools and strategies. Initially funded by the Next Generation Space Telescope, parts of the SEA code have since been adopted by the Space Telescope Science Institute. SEA has also supplied code for SOFIA, the SIRTF planning tools, and the JSky Open Source Java library. The potential benefits of sharing code are clear. The recipient gains functionality for considerably less cost. The provider gains additional developers working with their code. If enough users groups adopt a set of common code and tools, defacto standards can emerge (as demonstrated by the success of the FITS standard). Code sharing also raises a number of challenges related to the management of the code. In this talk, we will review our experiences with SEA - both successes and failures - and offer some lessons learned that may promote further successes in collaboration and re-use.

Code Sharing and Collaboration: Experiences From the Scientist's Expert Assistant Project and Their Relevance to the Virtual Observatory

NASA Technical Reports Server (NTRS)

Korathkar, Anuradha; Grosvenor, Sandy; Jones, Jeremy; Li, Connie; Mackey, Jennifer; Neher, Ken; Obenschain, Arthur F. (Technical Monitor)

2001-01-01

In the Virtual Observatory (VO), software tools will perform the functions that have traditionally been performed by physical observatories and their instruments. These tools will not be adjuncts to VO functionality but will make up the very core of the VO. Consequently, the tradition of observatory and system independent tools serving a small user base is not valid for the VO. For the VO to succeed, we must improve software collaboration and code sharing between projects and groups. A significant goal of the Scientist's Expert Assistant (SEA) project has been promoting effective collaboration and code sharing among groups. During the past three years, the SEA project has been developing prototypes for new observation planning software tools and strategies. Initially funded by the Next Generation Space Telescope, parts of the SEA code have since been adopted by the Space Telescope Science Institute. SEA has also supplied code for the SIRTF (Space Infrared Telescope Facility) planning tools, and the JSky Open Source Java library. The potential benefits of sharing code are clear. The recipient gains functionality for considerably less cost. The provider gains additional developers working with their code. If enough users groups adopt a set of common code and tools, de facto standards can emerge (as demonstrated by the success of the FITS standard). Code sharing also raises a number of challenges related to the management of the code. In this talk, we will review our experiences with SEA--both successes and failures, and offer some lessons learned that might promote further successes in collaboration and re-use.

Prospectus 2000

NASA Astrophysics Data System (ADS)

Holmes, Jon L.; Gettys, Nancy S.

2000-01-01

We begin 2000 with a message about our plans for JCE Software and what you will be seeing in this column as the year progresses. Floppy Disk --> CD-ROM Most software today is distributed on CD-ROM or by downloading from the Internet. Several new computers no longer include a floppy disk drive as "standard equipment". Today's software no longer fits on one or two floppies (the installation software alone can require two disks) and the cost of reproducing and distributing several disks is prohibitive. In short, distribution of software on floppy disks is no longer practical. Therefore, JCE Software will distribute all new software publications on CD-ROM rather than on disks. Regular Issues --> Collections Distribution of all our software on CD-ROM allows us to extend our concept of software collections that we started with the General Chemistry Collection. Such collections will contain all the previously published software that is still "in print" (i.e., is compatible with current operating systems and hardware) and any new programs that fall under the topic of the collection. Proposed topics in addition to General Chemistry currently include Advanced Chemistry, Instrument and Laboratory Simulations, and Spectroscopy. Eventually, all regular issues will be replaced by these collections, which will be updated annually or semiannually with new programs and updates to existing programs. Abstracts for all new programs will continue to appear in this column when a collection or its update is ready for publication. We will continue to offer special issues of single larger programs (e.g. Periodic Table Live!, Chemistry Comes Alive! volumes) on CD-ROM and video on videotape. Connect with Your Students outside Class JCE Software has always offered network licenses to allow instructors to make our software available to students in computer labs, but that model no longer fits the way many instructors and students work with computers. Many students (or their families) own a personal computer allowing them much more flexibility than a campus computer lab. Many instructors utilize the World Wide Web, creating HTML pages for students to use. JCE Software has options available to take advantage of both of these developments. Software Adoption To provide students who own computers access to JCE Software programs, consider adopting one or more of our CD-ROMs as you would a textbook. The General Chemistry Collection has been adopted by several general chemistry courses. We can arrange to bundle CDs with laboratory manuals or to be sold separately to students through the campus bookstore. The cost per CD can be quite low (as little as $5) when large numbers are ordered, making this a cost-effective method of allowing students access to the software they need whenever and wherever they desire. Web-Ready Publications Several JCE Software programs use HTML to present the material. Viewed with the ubiquitous Internet Browser, HTML is compatible with both Mac OS and Windows (as well most other current operating systems) and provides a flexible hypermedia interface that is familiar to an increasing number of instructors and students. HTML-based publications are also ready for use on local intranets, with appropriate licensing, and can be readily incorporated into other HTML-based materials. Already published in this format are: Chemistry Comes Alive!, Volumes 1 and 2 (Special Issues 18 and 21), Flying over Atoms (Special Issue 19), and Periodic Table Live! Second Edition (Special Issue 17). Solid State Resources Second Edition (Special Issue 12) and Chemistry Comes Alive!, Volume 3 (Special Issue 23) will be available soon. Other submissions being developed in HTML format include ChemPages Laboratory and Multimedia General Chemistry Problems. Contact the JCE Software office to learn about licensing alternatives that take advantage of the World Wide Web. Periodic Table Live! 2nd ed. is one of JCE Software's "Web-ready" publications. Publication Plans for 2000 We have several exciting new issues planned for publication in the coming year. Chemistry Comes Alive! The Chemistry Comes Alive! (CCA!) series continues with additional CD-ROMs for Mac OS and Windows. Each volume in this series contains video and animations of chemical reactions that can be easily incorporated into your own computer-based presentations. Our digital video now uses state-of-the-art compression that yields higher quality video with smaller file sizes and data rates more suited for WWW delivery. Video for Periodic Table Live! 2nd edition, Chemistry Comes Alive! Volumes 3, ChemPages Laboratory, and Multimedia General Chemistry Problems use this new format. We will be releasing updates of CCA! Volumes 1 and 2 to take advantage of this new technology. We are very pleased with the results and think you will be also. The reaction of aluminum with chlorine is included in Chemistry Comes Alive! Volume 3. ChemPages Laboratory ChemPages Laboratory, developed by the New Traditions Curriculum Project at the University of Wisconsin-Madison, is an HTML-based CD-ROM for Mac OS and Windows that contains lessons and tutorials to prepare introductory chemistry students to work in the laboratory. It includes text, photographs, computer graphics, animations, digital video, and voice narration to introduce students to the laboratory equipment and procedures. ChemPages Laboratory teaches introductory chemistry students about laboratory instruments, equipment, and procedures. Versatile Video Video demonstrating the "drinking bird" is included in the Chemistry Comes Alive! video collection. Video from this collection can be incorporated into many other projects. As an example, David Whisnant has used the drinking bird in his Multimedia General Chemistry Problems, where students view the video and are asked to explain why the bird bobs up and down. JCE Software anticipates publication of Multimedia General Chemistry Problems on CD-ROM for Mac OS and Windows in 2000. It will be "Web-ready". General Chemistry Collection, 4th Edition The General Chemistry Collection will be revised early in the summer and CDs will be shipped in time for fall adoptions. The 4th edition will include JCE Software publications for general chemistry published in 1999, as well as any programs for general chemistry accepted in 2000. Regular Issues We have had many recent submissions and submissions of work in progress. In 2000 we will work with the authors and our peer-reviewers to complete and publish these submissions individually or as part of a software collection on CD-ROM. An Invitation In collaboration with JCE Online we plan to make available in 2000 more support files for JCE Software. These will include not only troubleshooting tips and technical support notes, but also supporting information submitted by users such as lessons, specific assignments, and activities using JCE Software publications. All JCE Software users are invited to contribute to this area. Get in touch with JCE Software and let us know how you are using our materials so that we can share your ideas with others! Although the word software is in our name, many of our publications are not traditional software. We also publish video on videotape, videodisc, and CD-ROM and electronic documents (Mathcad and Mathematica, spreadsheet files and macros, HTML documents, and PowerPoint presentations). Most chemistry instructors who use a computer in their teaching have created or considered creating one or more of these for their classes. If you have an original computer presentation, electronic document, animation, video, or any other item that is not printed text it is probably an appropriate submission for JCE Software. By publishing your work in any branch of the Journal of Chemical Education, you will share your efforts with chemistry instructors and students all over the world and get professional recognition for your achievements. All JCE Software publications are Y2K compliant.

Software for Statistical Analysis of Weibull Distributions with Application to Gear Fatigue Data: User Manual with Verification

NASA Technical Reports Server (NTRS)

Krantz, Timothy L.

2002-01-01

The Weibull distribution has been widely adopted for the statistical description and inference of fatigue data. This document provides user instructions, examples, and verification for software to analyze gear fatigue test data. The software was developed presuming the data are adequately modeled using a two-parameter Weibull distribution. The calculations are based on likelihood methods, and the approach taken is valid for data that include type 1 censoring. The software was verified by reproducing results published by others.

Software for Statistical Analysis of Weibull Distributions with Application to Gear Fatigue Data: User Manual with Verification

NASA Technical Reports Server (NTRS)

Kranz, Timothy L.

2002-01-01

The Weibull distribution has been widely adopted for the statistical description and inference of fatigue data. This document provides user instructions, examples, and verification for software to analyze gear fatigue test data. The software was developed presuming the data are adequately modeled using a two-parameter Weibull distribution. The calculations are based on likelihood methods, and the approach taken is valid for data that include type I censoring. The software was verified by reproducing results published by others.

Information Technology Wants to Be Free

ERIC Educational Resources Information Center

Poritz, Jonathan A.

2012-01-01

It makes sense for college and university faculty to ally with the free and open-source software community. They share common values. A marvelous additional benefit is that free software on campuses would significantly advance pedagogy and scholarship, increase efficiency, and save money. Only unquestioning obedience to market fundamentalism--or…

Security Code Red or Ready? Leaders Sharing--For Tech Leaders

ERIC Educational Resources Information Center

Hall, Don; Kelly, Pat

2005-01-01

Increasingly, teachers rely on computer software and networks to both enhance curriculum management and provide engaging learning opportunities in instruction. New software is enabling more frequent formative assessments to better focus day-to-day lessons on the unique needs of individual learners. Administrators use increasingly complex data…

Data and Models as Social Objects in the HydroShare System for Collaboration in the Hydrology Community and Beyond

NASA Astrophysics Data System (ADS)

Tarboton, D. G.; Idaszak, R.; Horsburgh, J. S.; Ames, D. P.; Goodall, J. L.; Band, L. E.; Merwade, V.; Couch, A.; Hooper, R. P.; Maidment, D. R.; Dash, P. K.; Stealey, M.; Yi, H.; Gan, T.; Castronova, A. M.; Miles, B.; Li, Z.; Morsy, M. M.; Crawley, S.; Ramirez, M.; Sadler, J.; Xue, Z.; Bandaragoda, C.

2016-12-01

How do you share and publish hydrologic data and models for a large collaborative project? HydroShare is a new, web-based system for sharing hydrologic data and models with specific functionality aimed at making collaboration easier. HydroShare has been developed with U.S. National Science Foundation support under the auspices of the Consortium of Universities for the Advancement of Hydrologic Science, Inc. (CUAHSI) to support the collaboration and community cyberinfrastructure needs of the hydrology research community. Within HydroShare, we have developed new functionality for creating datasets, describing them with metadata, and sharing them with collaborators. We cast hydrologic datasets and models as "social objects" that can be shared, collaborated around, annotated, published and discovered. In addition to data and model sharing, HydroShare supports web application programs (apps) that can act on data stored in HydroShare, just as software programs on your PC act on your data locally. This can free you from some of the limitations of local computing capacity and challenges in installing and maintaining software on your own PC. HydroShare's web-based cyberinfrastructure can take work off your desk or laptop computer and onto infrastructure or "cloud" based data and processing servers. This presentation will describe HydroShare's collaboration functionality that enables both public and private sharing with individual users and collaborative user groups, and makes it easier for collaborators to iterate on shared datasets and models, creating multiple versions along the way, and publishing them with a permanent landing page, metadata description, and citable Digital Object Identifier (DOI) when the work is complete. This presentation will also describe the web app architecture that supports interoperability with third party servers functioning as application engines for analysis and processing of big hydrologic datasets. While developed to support the cyberinfrastructure needs of the hydrology community, the informatics infrastructure for programmatic interoperability of web resources has a generality beyond the solution of hydrology problems that will be discussed.

QMachine: commodity supercomputing in web browsers

PubMed Central

2014-01-01

Background Ongoing advancements in cloud computing provide novel opportunities in scientific computing, especially for distributed workflows. Modern web browsers can now be used as high-performance workstations for querying, processing, and visualizing genomics’ “Big Data” from sources like The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) without local software installation or configuration. The design of QMachine (QM) was driven by the opportunity to use this pervasive computing model in the context of the Web of Linked Data in Biomedicine. Results QM is an open-sourced, publicly available web service that acts as a messaging system for posting tasks and retrieving results over HTTP. The illustrative application described here distributes the analyses of 20 Streptococcus pneumoniae genomes for shared suffixes. Because all analytical and data retrieval tasks are executed by volunteer machines, few server resources are required. Any modern web browser can submit those tasks and/or volunteer to execute them without installing any extra plugins or programs. A client library provides high-level distribution templates including MapReduce. This stark departure from the current reliance on expensive server hardware running “download and install” software has already gathered substantial community interest, as QM received more than 2.2 million API calls from 87 countries in 12 months. Conclusions QM was found adequate to deliver the sort of scalable bioinformatics solutions that computation- and data-intensive workflows require. Paradoxically, the sandboxed execution of code by web browsers was also found to enable them, as compute nodes, to address critical privacy concerns that characterize biomedical environments. PMID:24913605

Specifying Software Behavior for Requirements and Design

DTIC Science & Technology

2013-01-01

e.g., Behavior Hiding is comprised of the Function Driver and Shared Services modules. Blacked-out modules, which are concerned with mechanisms for...and Shared Services modules. “The Func- tion Driver Module consists of a set of modules called Func- tion Drivers; each Function Driver is the sole...system environment. Functions that capture the rules determining these output values specify that behavior. The Shared Services module concerns aspects of

[Series: Medical Applications of the PHITS Code (2): Acceleration by Parallel Computing].

PubMed

Furuta, Takuya; Sato, Tatsuhiko

2015-01-01

Time-consuming Monte Carlo dose calculation becomes feasible owing to the development of computer technology. However, the recent development is due to emergence of the multi-core high performance computers. Therefore, parallel computing becomes a key to achieve good performance of software programs. A Monte Carlo simulation code PHITS contains two parallel computing functions, the distributed-memory parallelization using protocols of message passing interface (MPI) and the shared-memory parallelization using open multi-processing (OpenMP) directives. Users can choose the two functions according to their needs. This paper gives the explanation of the two functions with their advantages and disadvantages. Some test applications are also provided to show their performance using a typical multi-core high performance workstation.

DIMP: an interoperable solution for software integration and product data exchange

NASA Astrophysics Data System (ADS)

Wang, Xi Vincent; Xu, Xun William

2012-08-01

Today, globalisation has become one of the main trends of manufacturing business that has led to a world-wide decentralisation of resources amongst not only individual departments within one company but also business partners. However, despite the development and improvement in the last few decades, difficulties in information exchange and sharing still exist in heterogeneous applications environments. This article is divided into two parts. In the first part, related research work and integrating solutions are reviewed and discussed. The second part introduces a collaborative environment called distributed interoperable manufacturing platform, which is based on a module-based, service-oriented architecture (SOA). In the platform, the STEP-NC data model is used to facilitate data-exchange among heterogeneous CAD/CAM/CNC systems.

From Content to Practice: Sharing Educational Practice in Edu-Sharing

ERIC Educational Resources Information Center

Klebl, Michael; Kramer, Bernd J.; Zobel, Annett

2010-01-01

For technology-enhanced learning, the idea of "learning objects" transfers the technologies of content management, methods of software engineering and principles of open access to educational resources. This paper reports on CampusContent, a research project and competence centre for e-learning at FernUniversitat in Hagen that designed…

Design and implementation of an open source indexing solution for a large set of radiological reports and images.

PubMed

Voet, T; Devolder, P; Pynoo, B; Vercruysse, J; Duyck, P

2007-11-01

This paper hopes to share the insights we experienced during designing, building, and running an indexing solution for a large set of radiological reports and images in a production environment for more than 3 years. Several technical challenges were encountered and solved in the course of this project. One hundred four million words in 1.8 million radiological reports from 1989 to the present were indexed and became instantaneously searchable in a user-friendly fashion; the median query duration is only 31 ms. Currently, our highly tuned index holds 332,088 unique words in four languages. The indexing system is feature-rich and language-independent and allows for making complex queries. For research and training purposes it certainly is a valuable and convenient addition to our radiology informatics toolbox. Extended use of open-source technology dramatically reduced both implementation time and cost. All software we developed related to the indexing project has been made available to the open-source community covered by an unrestricted Berkeley Software Distribution-style license.

Emerging Technologies for Software-Reliant Systems

DTIC Science & Technology

2011-02-24

needs • Loose coupling • Global distribution of hardware, software and people • Horizontal integration and convergence • Virtualization...Webinar– February 2011 © 2011 Carnegie Mellon University Global Distribution of Hardware, Software and People Globalization is an essential part of...University Required Software Engineering Emphasis Due to Emerging Technologies (2) Defensive Programming • Security • Auto-adaptation • Globalization

Information Technology. DOD Needs to Strengthen Management of Its Statutorily Mandated Software and System Process Improvement Efforts

DTIC Science & Technology

2009-09-01

NII)/CIO Assistant Secretary of Defense for Networks and Information Integration/Chief Information Officer CMMI Capability Maturity Model...a Web-based portal to share knowledge about software process-related methodologies, such as the SEI’s Capability Maturity Model Integration ( CMMI ...19 SEI’s IDEALSM model, and Lean Six Sigma.20 For example, the portal features content areas such as software acquisition management, the SEI CMMI

EDGE3: A web-based solution for management and analysis of Agilent two color microarray experiments

PubMed Central

Vollrath, Aaron L; Smith, Adam A; Craven, Mark; Bradfield, Christopher A

2009-01-01

Background The ability to generate transcriptional data on the scale of entire genomes has been a boon both in the improvement of biological understanding and in the amount of data generated. The latter, the amount of data generated, has implications when it comes to effective storage, analysis and sharing of these data. A number of software tools have been developed to store, analyze, and share microarray data. However, a majority of these tools do not offer all of these features nor do they specifically target the commonly used two color Agilent DNA microarray platform. Thus, the motivating factor for the development of EDGE3 was to incorporate the storage, analysis and sharing of microarray data in a manner that would provide a means for research groups to collaborate on Agilent-based microarray experiments without a large investment in software-related expenditures or extensive training of end-users. Results EDGE3 has been developed with two major functions in mind. The first function is to provide a workflow process for the generation of microarray data by a research laboratory or a microarray facility. The second is to store, analyze, and share microarray data in a manner that doesn't require complicated software. To satisfy the first function, EDGE3 has been developed as a means to establish a well defined experimental workflow and information system for microarray generation. To satisfy the second function, the software application utilized as the user interface of EDGE3 is a web browser. Within the web browser, a user is able to access the entire functionality, including, but not limited to, the ability to perform a number of bioinformatics based analyses, collaborate between research groups through a user-based security model, and access to the raw data files and quality control files generated by the software used to extract the signals from an array image. Conclusion Here, we present EDGE3, an open-source, web-based application that allows for the storage, analysis, and controlled sharing of transcription-based microarray data generated on the Agilent DNA platform. In addition, EDGE3 provides a means for managing RNA samples and arrays during the hybridization process. EDGE3 is freely available for download at . PMID:19732451

EDGE(3): a web-based solution for management and analysis of Agilent two color microarray experiments.

PubMed

Vollrath, Aaron L; Smith, Adam A; Craven, Mark; Bradfield, Christopher A

2009-09-04

The ability to generate transcriptional data on the scale of entire genomes has been a boon both in the improvement of biological understanding and in the amount of data generated. The latter, the amount of data generated, has implications when it comes to effective storage, analysis and sharing of these data. A number of software tools have been developed to store, analyze, and share microarray data. However, a majority of these tools do not offer all of these features nor do they specifically target the commonly used two color Agilent DNA microarray platform. Thus, the motivating factor for the development of EDGE(3) was to incorporate the storage, analysis and sharing of microarray data in a manner that would provide a means for research groups to collaborate on Agilent-based microarray experiments without a large investment in software-related expenditures or extensive training of end-users. EDGE(3) has been developed with two major functions in mind. The first function is to provide a workflow process for the generation of microarray data by a research laboratory or a microarray facility. The second is to store, analyze, and share microarray data in a manner that doesn't require complicated software. To satisfy the first function, EDGE3 has been developed as a means to establish a well defined experimental workflow and information system for microarray generation. To satisfy the second function, the software application utilized as the user interface of EDGE(3) is a web browser. Within the web browser, a user is able to access the entire functionality, including, but not limited to, the ability to perform a number of bioinformatics based analyses, collaborate between research groups through a user-based security model, and access to the raw data files and quality control files generated by the software used to extract the signals from an array image. Here, we present EDGE(3), an open-source, web-based application that allows for the storage, analysis, and controlled sharing of transcription-based microarray data generated on the Agilent DNA platform. In addition, EDGE(3) provides a means for managing RNA samples and arrays during the hybridization process. EDGE(3) is freely available for download at http://edge.oncology.wisc.edu/.

A Simple Strategy for Implementing Standard Reference Terminologies in a Distributed Healthcare Delivery System with Minimal Impact to Existing Applications

PubMed Central

Bouhaddou, Omar; Lincoln, Michael J.; Maulden, Sarah; Murphy, Holli; Warnekar, Pradnya; Nguyen, Viet; Lam, Siew; Brown, Steven H; Frankson, Ferdinand J.; Crandall, Glen; Hughes, Carla; Sigley, Roger; Insley, Marcia; Graham, Gail

2006-01-01

The Veterans Administration (VA) has adopted an ambitious program to standardize its clinical terminology to comply with industry-wide standards. The VA is using commercially available tools and in-house software to create a high-quality reference terminology system. The terminology will be used by current and future applications with no planned disruption to operational systems. The first large customer of the group is the national VA Health Data Repository (HDR). Unique enterprise identifiers are assigned to each standard term, and a rich network of semantic relationships makes the resulting data not only recognizable, but highly computable and reusable in a variety of applications, including decision support and data sharing with partners such as the Department of Defense (DoD). This paper describes the specific methods and approaches that the VA has employed to develop and implement this innovative program in existing information system. The goal is to share with others our experience with key issues that face our industry as we move toward an electronic health record for every individual. PMID:17238306

Support of Herschel Key Programme Teams at the NASA Herschel Science Center

NASA Astrophysics Data System (ADS)

Shupe, David L.; Appleton, P. N.; Ardila, D.; Bhattacharya, B.; Mei, Y.; Morris, P.; Rector, J.; NHSC Team

2010-01-01

The first science data from the Herschel Space Observatory were distributed to Key Programme teams in September 2009. This poster describes a number of resources that have been developed by the NASA Herschel Science Center (NHSC) to support the first users of the observatory. The NHSC webpages and Helpdesk serve as the starting point for information and queries from the US community. Details about the use of the Herschel Common Science Software can be looked up in the Helpdesk Knowledgebase. The capability of real-time remote support through desktop sharing has been implemented. The NHSC continues to host workshops on data analysis and observation planning. Key Programme teams have been provided Wiki sites upon request for their team's private use and for sharing information with other teams. A secure data storage area is in place for troubleshooting purposes and for use by visitors. The NHSC draws upon close working relationships with Instrument Control Centers and the Herschel Science Center in Madrid in order to have the necessary expertise on hand to assist Herschel observers, including both Key Programme teams and respondents to upcoming open time proposal calls.

Assessment of risk factors for death in electrical injury.

PubMed

Dokov, William

2009-02-01

Fatal high-voltage injuries present a problem which has not yet been studied sufficiently in the context of interaction between the human body and electricity, as a technical, anthropogenic and natural phenomenon. The forensic medicine records of 291 cases of death caused by high-voltage current for a 41-year-long period (1965-2006) were examined in retrospect. The descriptive statistical analyses were made using the SPSS 11.0 software. Death was found to result most commonly from contact between the deceased and elements of the power transmission and distribution grid: (41.24%), and from the action of lightning: (32.3%), the difference in their relative share being insignificant. Much more rarely, death was due to contact with construction and repair electrical devices: (7.56%), or with elements of the power transport railway infrastructure: (6.87%). Death resulting from contact with agricultural electrical devices was only occasional: (0.68%). The victims' average age was 36.19 years. Our analysis indicates that the relative share (43.98%) of the victims is the highest in the age period between 25 and 44. The ratio between women and men is 1:21.38.

BioShaDock: a community driven bioinformatics shared Docker-based tools registry

PubMed Central

Moreews, François; Sallou, Olivier; Ménager, Hervé; Le bras, Yvan; Monjeaud, Cyril; Blanchet, Christophe; Collin, Olivier

2015-01-01

Linux container technologies, as represented by Docker, provide an alternative to complex and time-consuming installation processes needed for scientific software. The ease of deployment and the process isolation they enable, as well as the reproducibility they permit across environments and versions, are among the qualities that make them interesting candidates for the construction of bioinformatic infrastructures, at any scale from single workstations to high throughput computing architectures. The Docker Hub is a public registry which can be used to distribute bioinformatic software as Docker images. However, its lack of curation and its genericity make it difficult for a bioinformatics user to find the most appropriate images needed. BioShaDock is a bioinformatics-focused Docker registry, which provides a local and fully controlled environment to build and publish bioinformatic software as portable Docker images. It provides a number of improvements over the base Docker registry on authentication and permissions management, that enable its integration in existing bioinformatic infrastructures such as computing platforms. The metadata associated with the registered images are domain-centric, including for instance concepts defined in the EDAM ontology, a shared and structured vocabulary of commonly used terms in bioinformatics. The registry also includes user defined tags to facilitate its discovery, as well as a link to the tool description in the ELIXIR registry if it already exists. If it does not, the BioShaDock registry will synchronize with the registry to create a new description in the Elixir registry, based on the BioShaDock entry metadata. This link will help users get more information on the tool such as its EDAM operations, input and output types. This allows integration with the ELIXIR Tools and Data Services Registry, thus providing the appropriate visibility of such images to the bioinformatics community. PMID:26913191

BioShaDock: a community driven bioinformatics shared Docker-based tools registry.

PubMed

Moreews, François; Sallou, Olivier; Ménager, Hervé; Le Bras, Yvan; Monjeaud, Cyril; Blanchet, Christophe; Collin, Olivier

2015-01-01

Linux container technologies, as represented by Docker, provide an alternative to complex and time-consuming installation processes needed for scientific software. The ease of deployment and the process isolation they enable, as well as the reproducibility they permit across environments and versions, are among the qualities that make them interesting candidates for the construction of bioinformatic infrastructures, at any scale from single workstations to high throughput computing architectures. The Docker Hub is a public registry which can be used to distribute bioinformatic software as Docker images. However, its lack of curation and its genericity make it difficult for a bioinformatics user to find the most appropriate images needed. BioShaDock is a bioinformatics-focused Docker registry, which provides a local and fully controlled environment to build and publish bioinformatic software as portable Docker images. It provides a number of improvements over the base Docker registry on authentication and permissions management, that enable its integration in existing bioinformatic infrastructures such as computing platforms. The metadata associated with the registered images are domain-centric, including for instance concepts defined in the EDAM ontology, a shared and structured vocabulary of commonly used terms in bioinformatics. The registry also includes user defined tags to facilitate its discovery, as well as a link to the tool description in the ELIXIR registry if it already exists. If it does not, the BioShaDock registry will synchronize with the registry to create a new description in the Elixir registry, based on the BioShaDock entry metadata. This link will help users get more information on the tool such as its EDAM operations, input and output types. This allows integration with the ELIXIR Tools and Data Services Registry, thus providing the appropriate visibility of such images to the bioinformatics community.

Development practices and lessons learned in developing SimPEG

NASA Astrophysics Data System (ADS)

Cockett, R.; Heagy, L. J.; Kang, S.; Rosenkjaer, G. K.

2015-12-01

Inverse modelling provides a mathematical framework for constructing a model of physical property distributions in the subsurface that are consistent with the data collected in geophysical surveys. The geosciences are increasingly moving towards the integration of geological, geophysical, and hydrological information to better characterize the subsurface. This integration must span disciplines and is not only challenging scientifically, but additionally the inconsistencies between conventions often makes implementations complicated, non­ reproducible, or inefficient. SimPEG is an open-source, multi-university effort aimed at providing a generalized framework for solving forward and inverse problems. SimPEG includes finite volume discretizations on structured and unstructured meshes, interfaces to standard numerical solver packages, convex optimization algorithms, model parameterizations, and visualization routines. The SimPEG package (http://simpeg.xyz) supports an ecosystem of forward and inverse modelling applications, including electromagnetics, vadose zone flow, seismic, and potential­ fields, that are all written with a common interface and toolbox. The goal of SimPEG is to support a community of researchers with well-tested, extensible tools, and encourage transparency and reproducibility both of the SimPEG software and the geoscientific research it is applied to. In this presentation, we will share some of the lessons we have learned in designing the modular infrastructure, testing and development practices of SimPEG. We will discuss our use of version control, extensive unit-testing, continuous integration, documentation, issue tracking, and resources that facilitate communication between existing team members and allows new researchers to get involved. These practices have enabled the use of SimPEG in research, industry, and education as well as the ability to support a growing number of dependent repositories and applications. We hope that sharing our practices and experiences will help other researchers who are creating communities around their own scientific software. As this session suggests, "software is critical to the success of science," but, it is the *communities* of researchers that must be supported as we strive to create top quality research tools.

Lifelong personal health data and application software via virtual machines in the cloud.

PubMed

Van Gorp, Pieter; Comuzzi, Marco

2014-01-01

Personal Health Records (PHRs) should remain the lifelong property of patients, who should be able to show them conveniently and securely to selected caregivers and institutions. In this paper, we present MyPHRMachines, a cloud-based PHR system taking a radically new architectural solution to health record portability. In MyPHRMachines, health-related data and the application software to view and/or analyze it are separately deployed in the PHR system. After uploading their medical data to MyPHRMachines, patients can access them again from remote virtual machines that contain the right software to visualize and analyze them without any need for conversion. Patients can share their remote virtual machine session with selected caregivers, who will need only a Web browser to access the pre-loaded fragments of their lifelong PHR. We discuss a prototype of MyPHRMachines applied to two use cases, i.e., radiology image sharing and personalized medicine.

26 CFR 1.704-1 - Partner's distributive share.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 26 Internal Revenue 8 2014-04-01 2014-04-01 false Partner's distributive share. 1.704-1 Section 1.704-1 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED) INCOME TAX (CONTINUED) INCOME TAXES (CONTINUED) Partners and Partnerships § 1.704-1 Partner's distributive share. (a) Effect of partnership agreement. A partner'...

26 CFR 1.704-1 - Partner's distributive share.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 26 Internal Revenue 8 2013-04-01 2013-04-01 false Partner's distributive share. 1.704-1 Section 1.704-1 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED) INCOME TAX (CONTINUED) INCOME TAXES (CONTINUED) Partners and Partnerships § 1.704-1 Partner's distributive share. (a) Effect of partnership agreement. A partner'...

26 CFR 1.704-1 - Partner's distributive share.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 26 Internal Revenue 8 2010-04-01 2010-04-01 false Partner's distributive share. 1.704-1 Section 1.704-1 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED) INCOME TAX (CONTINUED) INCOME TAXES Partners and Partnerships § 1.704-1 Partner's distributive share. (a) Effect of partnership agreement. A partner's...

26 CFR 1.704-1 - Partner's distributive share.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 26 Internal Revenue 8 2012-04-01 2012-04-01 false Partner's distributive share. 1.704-1 Section 1.704-1 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED) INCOME TAX (CONTINUED) INCOME TAXES (CONTINUED) Partners and Partnerships § 1.704-1 Partner's distributive share. (a) Effect of partnership agreement. A partner'...

26 CFR 1.704-1 - Partner's distributive share.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 26 Internal Revenue 8 2011-04-01 2011-04-01 false Partner's distributive share. 1.704-1 Section 1.704-1 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED) INCOME TAX (CONTINUED) INCOME TAXES (CONTINUED) Partners and Partnerships § 1.704-1 Partner's distributive share. (a) Effect of partnership agreement. A partner'...

Social Networks and Performance in Distributed Learning Communities

ERIC Educational Resources Information Center

Cadima, Rita; Ojeda, Jordi; Monguet, Josep M.

2012-01-01

Social networks play an essential role in learning environments as a key channel for knowledge sharing and students' support. In distributed learning communities, knowledge sharing does not occur as spontaneously as when a working group shares the same physical space; knowledge sharing depends even more on student informal connections. In this…

Open-source, community-driven microfluidics with Metafluidics.

PubMed

Kong, David S; Thorsen, Todd A; Babb, Jonathan; Wick, Scott T; Gam, Jeremy J; Weiss, Ron; Carr, Peter A

2017-06-07

Microfluidic devices have the potential to automate and miniaturize biological experiments, but open-source sharing of device designs has lagged behind sharing of other resources such as software. Synthetic biologists have used microfluidics for DNA assembly, cell-free expression, and cell culture, but a combination of expense, device complexity, and reliance on custom set-ups hampers their widespread adoption. We present Metafluidics, an open-source, community-driven repository that hosts digital design files, assembly specifications, and open-source software to enable users to build, configure, and operate a microfluidic device. We use Metafluidics to share designs and fabrication instructions for both a microfluidic ring-mixer device and a 32-channel tabletop microfluidic controller. This device and controller are applied to build genetic circuits using standard DNA assembly methods including ligation, Gateway, Gibson, and Golden Gate. Metafluidics is intended to enable a broad community of engineers, DIY enthusiasts, and other nontraditional participants with limited fabrication skills to contribute to microfluidic research.

Ideas for Advancing Code Sharing: A Different Kind of Hack Day

NASA Astrophysics Data System (ADS)

Teuben, P.; Allen, A.; Berriman, B.; DuPrie, K.; Hanisch, R. J.; Mink, J.; Nemiroff, R. J.; Shamir, L.; Shortridge, K.; Taylor, M. B.; Wallin, J. F.

2014-05-01

How do we as a community encourage the reuse of software for telescope operations, data processing, and ? How can we support making codes used in research available for others to examine? Continuing the discussion from last year Bring out your codes! BoF session, participants separated into groups to brainstorm ideas to mitigate factors which inhibit code sharing and nurture those which encourage code sharing. The BoF concluded with the sharing of ideas that arose from the brainstorming sessions and a brief summary by the moderator.

Fault Tolerant Software Technology for Distributed Computer Systems

DTIC Science & Technology

1989-03-01

RAY.) &-TR-88-296 I Fin;.’ Technical Report ,r 19,39 i A28 3329 F’ULT TOLERANT SOFTWARE TECHNOLOGY FOR DISTRIBUTED COMPUTER SYSTEMS Georgia Institute...GrfisABN 34-70IiWftlI NO0. IN?3. NO IACCESSION NO. 158 21 7 11. TITLE (Incld security Cassification) FAULT TOLERANT SOFTWARE FOR DISTRIBUTED COMPUTER ...Technology for Distributed Computing Systems," a two year effort performed at Georgia Institute of Technology as part of the Clouds Project. The Clouds

MCdevelop - a universal framework for Stochastic Simulations

NASA Astrophysics Data System (ADS)

Slawinska, M.; Jadach, S.

2011-03-01

We present MCdevelop, a universal computer framework for developing and exploiting the wide class of Stochastic Simulations (SS) software. This powerful universal SS software development tool has been derived from a series of scientific projects for precision calculations in high energy physics (HEP), which feature a wide range of functionality in the SS software needed for advanced precision Quantum Field Theory calculations for the past LEP experiments and for the ongoing LHC experiments at CERN, Geneva. MCdevelop is a "spin-off" product of HEP to be exploited in other areas, while it will still serve to develop new SS software for HEP experiments. Typically SS involve independent generation of large sets of random "events", often requiring considerable CPU power. Since SS jobs usually do not share memory it makes them easy to parallelize. The efficient development, testing and running in parallel SS software requires a convenient framework to develop software source code, deploy and monitor batch jobs, merge and analyse results from multiple parallel jobs, even before the production runs are terminated. Throughout the years of development of stochastic simulations for HEP, a sophisticated framework featuring all the above mentioned functionality has been implemented. MCdevelop represents its latest version, written mostly in C++ (GNU compiler gcc). It uses Autotools to build binaries (optionally managed within the KDevelop 3.5.3 Integrated Development Environment (IDE)). It uses the open-source ROOT package for histogramming, graphics and the mechanism of persistency for the C++ objects. MCdevelop helps to run multiple parallel jobs on any computer cluster with NQS-type batch system. Program summaryProgram title:MCdevelop Catalogue identifier: AEHW_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHW_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 48 136 No. of bytes in distributed program, including test data, etc.: 355 698 Distribution format: tar.gz Programming language: ANSI C++ Computer: Any computer system or cluster with C++ compiler and UNIX-like operating system. Operating system: Most UNIX systems, Linux. The application programs were thoroughly tested under Ubuntu 7.04, 8.04 and CERN Scientific Linux 5. Has the code been vectorised or parallelised?: Tools (scripts) for optional parallelisation on a PC farm are included. RAM: 500 bytes Classification: 11.3 External routines: ROOT package version 5.0 or higher ( http://root.cern.ch/drupal/). Nature of problem: Developing any type of stochastic simulation program for high energy physics and other areas. Solution method: Object Oriented programming in C++ with added persistency mechanism, batch scripts for running on PC farms and Autotools.

Development of a Dynamically Configurable,Object-Oriented Framework for Distributed, Multi-modal Computational Aerospace Systems Simulation

NASA Technical Reports Server (NTRS)

Afjeh, Abdollah A.; Reed, John A.

2003-01-01

This research is aimed at developing a neiv and advanced simulation framework that will significantly improve the overall efficiency of aerospace systems design and development. This objective will be accomplished through an innovative integration of object-oriented and Web-based technologies ivith both new and proven simulation methodologies. The basic approach involves Ihree major areas of research: Aerospace system and component representation using a hierarchical object-oriented component model which enables the use of multimodels and enforces component interoperability. Collaborative software environment that streamlines the process of developing, sharing and integrating aerospace design and analysis models. . Development of a distributed infrastructure which enables Web-based exchange of models to simplify the collaborative design process, and to support computationally intensive aerospace design and analysis processes. Research for the first year dealt with the design of the basic architecture and supporting infrastructure, an initial implementation of that design, and a demonstration of its application to an example aircraft engine system simulation.

Automatic Parallelization of Numerical Python Applications using the Global Arrays Toolkit

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

Daily, Jeffrey A.; Lewis, Robert R.

2011-11-30

Global Arrays is a software system from Pacific Northwest National Laboratory that enables an efficient, portable, and parallel shared-memory programming interface to manipulate distributed dense arrays. The NumPy module is the de facto standard for numerical calculation in the Python programming language, a language whose use is growing rapidly in the scientific and engineering communities. NumPy provides a powerful N-dimensional array class as well as other scientific computing capabilities. However, like the majority of the core Python modules, NumPy is inherently serial. Using a combination of Global Arrays and NumPy, we have reimplemented NumPy as a distributed drop-in replacement calledmore » Global Arrays in NumPy (GAiN). Serial NumPy applications can become parallel, scalable GAiN applications with only minor source code changes. Scalability studies of several different GAiN applications will be presented showing the utility of developing serial NumPy codes which can later run on more capable clusters or supercomputers.« less

Educational Software Employing Group Competition Using an Interactive Electronic Whiteboard

ERIC Educational Resources Information Center

Otsuki, Yoko; Bandoh, Hirokazu; Kato, Naoki; Indurkhya, Bipin; Nakagawa, Masaki

2004-01-01

This article presents a design of educational software employing group competition using a large interactive electronic whiteboard, and a report on its experimental use. Group competition and collaboration are useful methods to cultivate originality and communication skills. To share the same space, the same large screen, and face-to-face…

Assessing the Utility of an Event-Step ASMD Model by Analysis of Surface Combatant Shared Self-Defense

DTIC Science & Technology

2001-09-01

Oriented Discrete Event Simulation,” Master’s Thesis in Operations Research, Naval Postgraduate School Monterey, CA, 1996. 12. Arntzen , A., “Software...Dependent Hit Probabilities”, Naval Research Logistics, Vol. 31, pp. 363-371, 1984. 3 Arntzen , A., “Software Components for Air Defense Planning

Voice-Recognition Augmented Performance Tools in Performance Poetry Pedagogy

ERIC Educational Resources Information Center

Devanny, David; McGowan, Jack

2016-01-01

This provocation shares findings from the use of bespoke voice-recognition performance software in a number of seminars (which took place in the 2014-2016 academic years at Glasgow School of Art, University of Warwick, and Falmouth University). The software, made available through this publication, is a web-app which uses Google Chrome's native…

"LearningPad" Conundrum: The Perils of Using Third-Party Software and Student Privacy

ERIC Educational Resources Information Center

O'Brien, Jason; Roller, Sarah; Lampley, Sandra

2017-01-01

This case focuses on the potential problems associated with sharing personally identifiable information (PII) when students are required to use third-party software. Specifically, third-grade students were required to complete "LearningPad" activities as a component of their homework grade in math, spelling, and language arts. As…

DataSync - sharing data via filesystem

NASA Astrophysics Data System (ADS)

Ulbricht, Damian; Klump, Jens

2014-05-01

Usually research work is a cycle of to hypothesize, to collect data, to corroborate the hypothesis, and finally to publish the results. In this sequence there are possibilities to base the own work on the work of others. Maybe there are candidates of physical samples listed in the IGSN-Registry and there is no need to go on excursion to acquire physical samples. Hopefully the DataCite catalogue lists already metadata of datasets that meet the constraints of the hypothesis and that are now open for reappraisal. After all, working with the measured data to corroborate the hypothesis involves new methods, and proven methods as well as different software tools. A cohort of intermediate data is created that can be shared with colleagues to discuss the research progress and receive a first evaluation. In consequence, the intermediate data should be versioned to easily get back to valid intermediate data, when you notice you get on the wrong track. Things are different for project managers. They want to know what is currently done, what has been done, and what is the last valid data, if somebody has to continue the work. To make life of members of small science projects easier we developed Datasync [1] as a software for sharing and versioning data. Datasync is designed to synchronize directory trees between different computers of a research team over the internet. The software is developed as JAVA application and watches a local directory tree for changes that are replicated as eSciDoc-objects into an eSciDoc-infrastructure [2] using the eSciDoc REST API. Modifications to the local filesystem automatically create a new version of an eSciDoc-object inside the eSciDoc-infrastructure. This way individual folders can be shared between team members while project managers can get a general idea of current status by synchronizing whole project inventories. Additionally XML metadata from separate files can be managed together with data files inside the eSciDoc-objects. While Datasync's major task is to distribute directory trees, we complement its functionality with the PHP-based application panMetaDocs [3]. panMetaDocs is the successor to panMetaWorks [4] and inherits most of its functionality. Through an internet browser PanMetaDocs provides a web-based overview of the datasets inside the eSciDoc-infrastructure. The software allows to upload further data, to add and edit metadata using the metadata editor, and it disseminates metadata through various channels. In addition, previous versions of a file can be downloaded and access rights can be defined on files and folders to control visibility of files for users of both panMetaDocs and Datasync. panMetaDocs serves as a publication agent for datasets and it serves as a registration agent for dataset DOIs. The application stack presented here allows sharing, versioning, and central storage of data from the very beginning of project activities by using the file synchronization service Datasync. The web-application panMetaDocs complements the functionality of DataSync by providing a dataset publication agent and other tools to handle administrative tasks on the data. [1] http://github.com/ulbricht/datasync [2] http://github.com/escidoc [3] http://panmetadocs.sf.net [4] http://metaworks.pangaea.de

Using an architectural approach to integrate heterogeneous, distributed software components

NASA Technical Reports Server (NTRS)

Callahan, John R.; Purtilo, James M.

1995-01-01

Many computer programs cannot be easily integrated because their components are distributed and heterogeneous, i.e., they are implemented in diverse programming languages, use different data representation formats, or their runtime environments are incompatible. In many cases, programs are integrated by modifying their components or interposing mechanisms that handle communication and conversion tasks. For example, remote procedure call (RPC) helps integrate heterogeneous, distributed programs. When configuring such programs, however, mechanisms like RPC must be used explicitly by software developers in order to integrate collections of diverse components. Each collection may require a unique integration solution. This paper describes improvements to the concepts of software packaging and some of our experiences in constructing complex software systems from a wide variety of components in different execution environments. Software packaging is a process that automatically determines how to integrate a diverse collection of computer programs based on the types of components involved and the capabilities of available translators and adapters in an environment. Software packaging provides a context that relates such mechanisms to software integration processes and reduces the cost of configuring applications whose components are distributed or implemented in different programming languages. Our software packaging tool subsumes traditional integration tools like UNIX make by providing a rule-based approach to software integration that is independent of execution environments.

Towards a New Paradigm of Software Development: an Ambassador Driven Process in Distributed Software Companies

NASA Astrophysics Data System (ADS)

Kumlander, Deniss

The globalization of companies operations and competitor between software vendors demand improving quality of delivered software and decreasing the overall cost. The same in fact introduce a lot of problem into software development process as produce distributed organization breaking the co-location rule of modern software development methodologies. Here we propose a reformulation of the ambassador position increasing its productivity in order to bridge communication and workflow gap by managing the entire communication process rather than concentrating purely on the communication result.

Online Concept Maps: Enhancing Collaborative Learning by Using Technology with Concept Maps.

ERIC Educational Resources Information Center

Canas, Alberto J.; Ford, Kenneth M.; Novak, Joseph D.; Hayes, Patrick; Reichherzer, Thomas R.; Suri, Niranjan

2001-01-01

Describes a collaborative software system that allows students from distant schools to share claims derived from their concept maps. Sharing takes place by accessing The Knowledge Soup, a repository of propositions submitted by students and stored on a computer server. Students can use propositions from other students to enhance their concept…

Investigating Why Teachers Reported Continued Use and Sharing of an Educational Innovation after the Research Has Ended

ERIC Educational Resources Information Center

Hegedus, Stephen J.; Dalton, Sara; Roschelle, Jeremy; Penuel, William; Dickey-Kurdziolek, Margaret; Tatar, Deborah

2014-01-01

We investigated prospects for reported sustainable adoption and sharing of an educational innovation through survey research including online questionnaires and telephone interviews. This investigation is part of the Scaling-Up SimCalc experimental program, which combines dynamic representational algebra software (SimCalc MathWorlds) with…

Software-Controlled Caches in the VMP Multiprocessor

DTIC Science & Technology

1986-03-01

programming system level that Processors is tuned for the VMP design. In this vein, we are interested in exploring how far the software support can go to ...handled in software, analogously to the handling agement of the shared program state is familiar and of virtual memory page faults. Hardware support for...ensure good behavior, as opposed to how Each cache miss results in bus traffic. Table 2 pro- vides the bus cost for the "average" cache miss. Fig

"WWW.MDTF.ORG": a World Wide Web forum for developing open-architecture, freely distributed, digital teaching file software by participant consensus.

PubMed

Katzman, G L; Morris, D; Lauman, J; Cochella, C; Goede, P; Harnsberger, H R

2001-06-01

To foster a community supported evaluation processes for open-source digital teaching file (DTF) development and maintenance. The mechanisms used to support this process will include standard web browsers, web servers, forum software, and custom additions to the forum software to potentially enable a mediated voting protocol. The web server will also serve as a focal point for beta and release software distribution, which is the desired end-goal of this process. We foresee that www.mdtf.org will provide for widespread distribution of open source DTF software that will include function and interface design decisions from community participation on the website forums.

Node Resource Manager: A Distributed Computing Software Framework Used for Solving Geophysical Problems

NASA Astrophysics Data System (ADS)

Lawry, B. J.; Encarnacao, A.; Hipp, J. R.; Chang, M.; Young, C. J.

2011-12-01

With the rapid growth of multi-core computing hardware, it is now possible for scientific researchers to run complex, computationally intensive software on affordable, in-house commodity hardware. Multi-core CPUs (Central Processing Unit) and GPUs (Graphics Processing Unit) are now commonplace in desktops and servers. Developers today have access to extremely powerful hardware that enables the execution of software that could previously only be run on expensive, massively-parallel systems. It is no longer cost-prohibitive for an institution to build a parallel computing cluster consisting of commodity multi-core servers. In recent years, our research team has developed a distributed, multi-core computing system and used it to construct global 3D earth models using seismic tomography. Traditionally, computational limitations forced certain assumptions and shortcuts in the calculation of tomographic models; however, with the recent rapid growth in computational hardware including faster CPU's, increased RAM, and the development of multi-core computers, we are now able to perform seismic tomography, 3D ray tracing and seismic event location using distributed parallel algorithms running on commodity hardware, thereby eliminating the need for many of these shortcuts. We describe Node Resource Manager (NRM), a system we developed that leverages the capabilities of a parallel computing cluster. NRM is a software-based parallel computing management framework that works in tandem with the Java Parallel Processing Framework (JPPF, http://www.jppf.org/), a third party library that provides a flexible and innovative way to take advantage of modern multi-core hardware. NRM enables multiple applications to use and share a common set of networked computers, regardless of their hardware platform or operating system. Using NRM, algorithms can be parallelized to run on multiple processing cores of a distributed computing cluster of servers and desktops, which results in a dramatic speedup in execution time. NRM is sufficiently generic to support applications in any domain, as long as the application is parallelizable (i.e., can be subdivided into multiple individual processing tasks). At present, NRM has been effective in decreasing the overall runtime of several algorithms: 1) the generation of a global 3D model of the compressional velocity distribution in the Earth using tomographic inversion, 2) the calculation of the model resolution matrix, model covariance matrix, and travel time uncertainty for the aforementioned velocity model, and 3) the correlation of waveforms with archival data on a massive scale for seismic event detection. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Technology Solutions | Distributed Generation Interconnection Collaborative

Science.gov Websites

technologies, both hardware and software, can support the wider adoption of distributed generation on the grid . As the penetration of distributed-generation photovoltaics (DGPV) has risen rapidly in recent years posed by high penetrations of distributed PV. Other promising technologies include new utility software

Resurrecting Legacy Code Using Ontosoft Knowledge-Sharing and Digital Object Management to Revitalize and Reproduce Software for Groundwater Management Research

NASA Astrophysics Data System (ADS)

Kwon, N.; Gentle, J.; Pierce, S. A.

2015-12-01

Software code developed for research is often used for a relatively short period of time before it is abandoned, lost, or becomes outdated. This unintentional abandonment of code is a valid problem in the 21st century scientific process, hindering widespread reusability and increasing the effort needed to develop research software. Potentially important assets, these legacy codes may be resurrected and documented digitally for long-term reuse, often with modest effort. Furthermore, the revived code may be openly accessible in a public repository for researchers to reuse or improve. For this study, the research team has begun to revive the codebase for Groundwater Decision Support System (GWDSS), originally developed for participatory decision making to aid urban planning and groundwater management, though it may serve multiple use cases beyond those originally envisioned. GWDSS was designed as a java-based wrapper with loosely federated commercial and open source components. If successfully revitalized, GWDSS will be useful for both practical applications as a teaching tool and case study for groundwater management, as well as informing theoretical research. Using the knowledge-sharing approaches documented by the NSF-funded Ontosoft project, digital documentation of GWDSS is underway, from conception to development, deployment, characterization, integration, composition, and dissemination through open source communities and geosciences modeling frameworks. Information assets, documentation, and examples are shared using open platforms for data sharing and assigned digital object identifiers. Two instances of GWDSS version 3.0 are being created: 1) a virtual machine instance for the original case study to serve as a live demonstration of the decision support tool, assuring the original version is usable, and 2) an open version of the codebase, executable installation files, and developer guide available via an open repository, assuring the source for the application is accessible with version control and potential for new branch developments. Finally, metadata about the software has been completed within the OntoSoft portal to provide descriptive curation, make GWDSS searchable, and complete documentation of the scientific software lifecycle.

77 FR 37941 - Order Granting a Limited Exemption From Exchange Act Rule 10b-17 to Certain Actively Managed...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-25

.... John McGuire, Esq., Morgan Lewis & Bockius LLP regarding AdvisorShares Trust (December 16, 2011... or rights or other subscription offering, of the amount in cash to be paid or distributed per share... or distribution and the rate of the dividend or distribution. \\2\\ If the exact per share cash...

Thyroid Cancer and Tumor Collaborative Registry (TCCR)

PubMed Central

Shats, Oleg; Goldner, Whitney; Feng, Jianmin; Sherman, Alexander; Smith, Russell B.; Sherman, Simon

2016-01-01

A multicenter, web-based Thyroid Cancer and Tumor Collaborative Registry (TCCR, http://tccr.unmc.edu) allows for the collection and management of various data on thyroid cancer (TC) and thyroid nodule (TN) patients. The TCCR is coupled with OpenSpecimen, an open-source biobank management system, to annotate biospecimens obtained from the TCCR subjects. The demographic, lifestyle, physical activity, dietary habits, family history, medical history, and quality of life data are provided and may be entered into the registry by subjects. Information on diagnosis, treatment, and outcome is entered by the clinical personnel. The TCCR uses advanced technical and organizational practices, such as (i) metadata-driven software architecture (design); (ii) modern standards and best practices for data sharing and interoperability (standardization); (iii) Agile methodology (project management); (iv) Software as a Service (SaaS) as a software distribution model (operation); and (v) the confederation principle as a business model (governance). This allowed us to create a secure, reliable, user-friendly, and self-sustainable system for TC and TN data collection and management that is compatible with various end-user devices and easily adaptable to a rapidly changing environment. Currently, the TCCR contains data on 2,261 subjects and data on more than 28,000 biospecimens. Data and biological samples collected by the TCCR are used in developing diagnostic, prevention, treatment, and survivorship strategies against TC. PMID:27168721

A Facility and Architecture for Autonomy Research

NASA Technical Reports Server (NTRS)

Pisanich, Greg; Clancy, Daniel (Technical Monitor)

2002-01-01

Autonomy is a key enabling factor in the advancement of the remote robotic exploration. There is currently a large gap between autonomy software at the research level and software that is ready for insertion into near-term space missions. The Mission Simulation Facility (MST) will bridge this gap by providing a simulation framework and suite of simulation tools to support research in autonomy for remote exploration. This system will allow developers of autonomy software to test their models in a high-fidelity simulation and evaluate their system's performance against a set of integrated, standardized simulations. The Mission Simulation ToolKit (MST) uses a distributed architecture with a communication layer that is built on top of the standardized High Level Architecture (HLA). This architecture enables the use of existing high fidelity models, allows mixing simulation components from various computing platforms and enforces the use of a standardized high-level interface among components. The components needed to achieve a realistic simulation can be grouped into four categories: environment generation (terrain, environmental features), robotic platform behavior (robot dynamics), instrument models (camera/spectrometer/etc.), and data analysis. The MST will provide basic components in these areas but allows users to plug-in easily any refined model by means of a communication protocol. Finally, a description file defines the robot and environment parameters for easy configuration and ensures that all the simulation models share the same information.

Customer Communication Challenges and Solutions in Globally Distributed Agile Software Development

NASA Astrophysics Data System (ADS)

Pikkarainen, Minna; Korkala, Mikko

Working in the globally distributed market is one of the key trends among the software organizations all over the world. [1-5]. Several factors have contributed to the growth of distributed software development; time-zone independent ”follow the sun” development, access to well-educated labour, maturation of the technical infrastructure and reduced costs are some of the most commonly cited benefits of distributed development [3, 6-8]. Furthermore, customers are often located in different countries because of the companies’ internationalization purposes or good market opportunities.

Similarities and Differences in the Academic Education of Software Engineering and Architectural Design Professionals

ERIC Educational Resources Information Center

Hazzan, Orit; Karni, Eyal

2006-01-01

This article focuses on the similarities and differences in the academic education of software engineers and architects. The rationale for this work stems from our observation, each from the perspective of her or his own discipline, that these two professional design and development processes share some similarities. A pilot study was performed,…

Using VirtualGL/TurboVNC Software on the Peregrine System |

Science.gov Websites

High-Performance Computing | NREL VirtualGL/TurboVNC Software on the Peregrine System Using , allowing users to access and share large-memory visualization nodes with high-end graphics processing units may be better than just using X11 forwarding when connecting from a remote site with low bandwidth and

Captivating Open University Students with Online Literature Search Tutorials Created Using Screen Capture Software

ERIC Educational Resources Information Center

Wales, Tim; Robertson, Penny

2008-01-01

Purpose: The aim of this paper is to share the experiences and challenges faced by the Open University Library (OUL) in using screen capture software to develop online literature search tutorials. Design/methodology/approach: A summary of information literacy support at the OUL is provided as background information to explain the decision to…

Quick and Easy: Use Screen Capture Software to Train and Communicate

ERIC Educational Resources Information Center

Schuster, Ellen

2011-01-01

Screen capture (screen cast) software can be used to develop short videos for training purposes. Developing videos is quick and easy. This article describes how these videos are used as tools to reinforce face-to-face and interactive TV curriculum training in a nutrition education program. Advantages of developing these videos are shared.…

Generalized Nuclear Data

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

Conlin, Jeremy

2017-03-15

This software is code related to reading/writing/manipulating nuclear data in the Generalized Nuclear Data (GND) format, a new format for sharing nuclear data among institutions. In addition to the software and its documentation, notes and documentation from the WPEC Subgroup 43 will be included. WPEC Subgroup 43 is an international committee charged with creating the API for the GND format.

Conducting a Trial of Web Conferencing Software: Why, How, and Perceptions from the Coalface

ERIC Educational Resources Information Center

Reushle, Shirley; Loch, Birgit

2008-01-01

This paper reports on the trial of web conferencing software conducted at a regional Australian university with a significant distance population. The paper shares preliminary findings, the views of participants and recommendations for future activity. To design and conduct the trial, an action research method was chosen because it is…

New Catalog of Resources Enables Paleogeosciences Research

NASA Astrophysics Data System (ADS)

Lingo, R. C.; Horlick, K. A.; Anderson, D. M.

2014-12-01

The 21st century promises a new era for scientists of all disciplines, the age where cyber infrastructure enables research and education and fuels discovery. EarthCube is a working community of over 2,500 scientists and students of many Earth Science disciplines who are looking to build bridges between disciplines. The EarthCube initiative will create a digital infrastructure that connects databases, software, and repositories. A catalog of resources (databases, software, repositories) has been produced by the Research Coordination Network for Paleogeosciences to improve the discoverability of resources. The Catalog is currently made available within the larger-scope CINERGI geosciences portal (http://hydro10.sdsc.edu/geoportal/catalog/main/home.page). Other distribution points and web services are planned, using linked data, content services for the web, and XML descriptions that can be harvested using metadata protocols. The databases provide searchable interfaces to find data sets that would otherwise remain dark data, hidden in drawers and on personal computers. The software will be described in catalog entries so just one click will lead users to methods and analytical tools that many geoscientists were unaware of. The repositories listed in the Paleogeosciences Catalog contain physical samples found all across the globe, from natural history museums to the basements of university buildings. EarthCube has over 250 databases, 300 software systems, and 200 repositories which will grow in the coming year. When completed, geoscientists across the world will be connected into a productive workflow for managing, sharing, and exploring geoscience data and information that expedites collaboration and innovation within the paleogeosciences, potentially bringing about new interdisciplinary discoveries.

Quantitative X-ray fluorescence computed tomography for low-Z samples using an iterative absorption correction algorithm

NASA Astrophysics Data System (ADS)

Huang, Rong; Limburg, Karin; Rohtla, Mehis

2017-05-01

X-ray fluorescence computed tomography is often used to measure trace element distributions within low-Z samples, using algorithms capable of X-ray absorption correction when sample self-absorption is not negligible. Its reconstruction is more complicated compared to transmission tomography, and therefore not widely used. We describe in this paper a very practical iterative method that uses widely available transmission tomography reconstruction software for fluorescence tomography. With this method, sample self-absorption can be corrected not only for the absorption within the measured layer but also for the absorption by material beyond that layer. By combining tomography with analysis for scanning X-ray fluorescence microscopy, absolute concentrations of trace elements can be obtained. By using widely shared software, we not only minimized the coding, took advantage of computing efficiency of fast Fourier transform in transmission tomography software, but also thereby accessed well-developed data processing tools coming with well-known and reliable software packages. The convergence of the iterations was also carefully studied for fluorescence of different attenuation lengths. As an example, fish eye lenses could provide valuable information about fish life-history and endured environmental conditions. Given the lens's spherical shape and sometimes the short distance from sample to detector for detecting low concentration trace elements, its tomography data are affected by absorption related to material beyond the measured layer but can be reconstructed well with our method. Fish eye lens tomography results are compared with sliced lens 2D fluorescence mapping with good agreement, and with tomography providing better spatial resolution.

MaROS: Information Management Service

NASA Technical Reports Server (NTRS)

Allard, Daniel A.; Gladden, Roy E.; Wright, Jesse J.; Hy, Franklin H.; Rabideau, Gregg R.; Wallick, Michael N.

2011-01-01

This software is provided by the Mars Relay Operations Service (MaROS) task to a variety of Mars projects for the purpose of coordinating communications sessions between landed spacecraft assets and orbiting spacecraft assets at Mars. The Information Management Service centralizes a set of functions previously distributed across multiple spacecraft operations teams, and as such, greatly improves visibility into the end-to-end strategic coordination process. Most of the process revolves around the scheduling of communications sessions between the spacecraft during periods of time when a landed asset on Mars is geometrically visible by an orbiting spacecraft. These relay sessions are used to transfer data both to and from the landed asset via the orbiting asset on behalf of Earth-based spacecraft operators. This software component is an application process running as a Java virtual machine. The component provides all service interfaces via a Representational State Transfer (REST) protocol over https to external clients. There are two general interaction modes with the service: upload and download of data. For data upload, the service must execute logic specific to the upload data type and trigger any applicable calculations including pass delivery latencies and overflight conflicts. For data download, the software must retrieve and correlate requested information and deliver to the requesting client. The provision of this service enables several key advancements over legacy processes and systems. For one, this service represents the first time that end-to-end relay information is correlated into a single shared repository. The software also provides the first multimission latency calculator; previous latency calculations had been performed on a mission-by-mission basis.

A distributed data acquisition software scheme for the Laboratory Telerobotic Manipulator

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

Butler, P.L.; Glassell, R.L.; Rowe, J.C.

1990-01-01

A custom software architecture was developed for use in the Laboratory Telerobotic Manipulator (LTM) to provide support for the distributed data acquisition electronics. This architecture was designed to provide a comprehensive development environment that proved to be useful for both hardware and software debugging. This paper describes the development environment and the operational characteristics of the real-time data acquisition software. 8 refs., 5 figs.

Distributed generation of shared RSA keys in mobile ad hoc networks

NASA Astrophysics Data System (ADS)

Liu, Yi-Liang; Huang, Qin; Shen, Ying

2005-12-01

Mobile Ad Hoc Networks is a totally new concept in which mobile nodes are able to communicate together over wireless links in an independent manner, independent of fixed physical infrastructure and centralized administrative infrastructure. However, the nature of Ad Hoc Networks makes them very vulnerable to security threats. Generation and distribution of shared keys for CA (Certification Authority) is challenging for security solution based on distributed PKI(Public-Key Infrastructure)/CA. The solutions that have been proposed in the literature and some related issues are discussed in this paper. The solution of a distributed generation of shared threshold RSA keys for CA is proposed in the present paper. During the process of creating an RSA private key share, every CA node only has its own private security. Distributed arithmetic is used to create the CA's private share locally, and that the requirement of centralized management institution is eliminated. Based on fully considering the Mobile Ad Hoc network's characteristic of self-organization, it avoids the security hidden trouble that comes by holding an all private security share of CA, with which the security and robustness of system is enhanced.

MicROS-drt: supporting real-time and scalable data distribution in distributed robotic systems.

PubMed

Ding, Bo; Wang, Huaimin; Fan, Zedong; Zhang, Pengfei; Liu, Hui

A primary requirement in distributed robotic software systems is the dissemination of data to all interested collaborative entities in a timely and scalable manner. However, providing such a service in a highly dynamic and resource-limited robotic environment is a challenging task, and existing robot software infrastructure has limitations in this aspect. This paper presents a novel robot software infrastructure, micROS-drt, which supports real-time and scalable data distribution. The solution is based on a loosely coupled data publish-subscribe model with the ability to support various time-related constraints. And to realize this model, a mature data distribution standard, the data distribution service for real-time systems (DDS), is adopted as the foundation of the transport layer of this software infrastructure. By elaborately adapting and encapsulating the capability of the underlying DDS middleware, micROS-drt can meet the requirement of real-time and scalable data distribution in distributed robotic systems. Evaluation results in terms of scalability, latency jitter and transport priority as well as the experiment on real robots validate the effectiveness of this work.

Facilitating Collaboration in Lecture-Based Learning through Shared Notes Using Wireless Technologies

ERIC Educational Resources Information Center

Valtonen, T.; Havu-Nuutinen, S.; Dillon, P.; Vesisenaho, M.

2011-01-01

This paper reports a case study for developing lecture teaching in higher education by connecting simultaneously the benefits of face-to-face teaching and social software for capturing and sharing students' lecture notes. The study was conducted with 12 university students taking a degree course on pre-primary education. Data were collected on (1)…

Discerning the Shared Beliefs of Teachers in a Secondary School Mathematics Department

ERIC Educational Resources Information Center

Beswick, Kim

2016-01-01

This study examined the shared beliefs among mathematics teachers in one secondary school in the United Kingdom across the first term of a school year and almost 4 years subsequently. Leximancer software was used to analyse the language used as teachers responded to questions concerning their beliefs about mathematics, mathematics teaching,…

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

NASA Astrophysics Data System (ADS)

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

2015-09-01

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

Distributed observing facility for remote access to multiple telescopes

NASA Astrophysics Data System (ADS)

Callegari, Massimo; Panciatici, Antonio; Pasian, Fabio; Pucillo, Mauro; Santin, Paolo; Aro, Simo; Linde, Peter; Duran, Maria A.; Rodriguez, Jose A.; Genova, Francoise; Ochsenbein, Francois; Ponz, J. D.; Talavera, Antonio

2000-06-01

The REMOT (Remote Experiment Monitoring and conTrol) project was financed by 1996 by the European Community in order to investigate the possibility of generalizing the remote access to scientific instruments. After the feasibility of this idea was demonstrated, the DYNACORE (DYNAmically, COnfigurable Remote Experiment monitoring and control) project was initiated as a REMOT follow-up. Its purpose is to develop software technology to support scientists in two different domains, astronomy and plasma physics. The resulting system allows (1) simultaneous multiple user access to different experimental facilities, (2) dynamic adaptability to different kinds of real instruments, (3) exploitation of the communication infrastructures features, (4) ease of use through intuitive graphical interfaces, and (5) additional inter-user communication using off-the-shelf projects such as video-conference tools, chat programs and shared blackboards.

Megatux

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

2012-09-25

The Megatux platform enables the emulation of large scale (multi-million node) distributed systems. In particular, it allows for the emulation of large-scale networks interconnecting a very large number of emulated computer systems. It does this by leveraging virtualization and associated technologies to allow hundreds of virtual computers to be hosted on a single moderately sized server or workstation. Virtualization technology provided by modern processors allows for multiple guest OSs to run at the same time, sharing the hardware resources. The Megatux platform can be deployed on a single PC, a small cluster of a few boxes or a large clustermore » of computers. With a modest cluster, the Megatux platform can emulate complex organizational networks. By using virtualization, we emulate the hardware, but run actual software enabling large scale without sacrificing fidelity.« less

BioImg.org: A Catalog of Virtual Machine Images for the Life Sciences

PubMed Central

Dahlö, Martin; Haziza, Frédéric; Kallio, Aleksi; Korpelainen, Eija; Bongcam-Rudloff, Erik; Spjuth, Ola

2015-01-01

Virtualization is becoming increasingly important in bioscience, enabling assembly and provisioning of complete computer setups, including operating system, data, software, and services packaged as virtual machine images (VMIs). We present an open catalog of VMIs for the life sciences, where scientists can share information about images and optionally upload them to a server equipped with a large file system and fast Internet connection. Other scientists can then search for and download images that can be run on the local computer or in a cloud computing environment, providing easy access to bioinformatics environments. We also describe applications where VMIs aid life science research, including distributing tools and data, supporting reproducible analysis, and facilitating education. BioImg.org is freely available at: https://bioimg.org. PMID:26401099

BioImg.org: A Catalog of Virtual Machine Images for the Life Sciences.

PubMed

Dahlö, Martin; Haziza, Frédéric; Kallio, Aleksi; Korpelainen, Eija; Bongcam-Rudloff, Erik; Spjuth, Ola

2015-01-01

Virtualization is becoming increasingly important in bioscience, enabling assembly and provisioning of complete computer setups, including operating system, data, software, and services packaged as virtual machine images (VMIs). We present an open catalog of VMIs for the life sciences, where scientists can share information about images and optionally upload them to a server equipped with a large file system and fast Internet connection. Other scientists can then search for and download images that can be run on the local computer or in a cloud computing environment, providing easy access to bioinformatics environments. We also describe applications where VMIs aid life science research, including distributing tools and data, supporting reproducible analysis, and facilitating education. BioImg.org is freely available at: https://bioimg.org.

Sharing electronic structure and crystallographic data with ETSF_IO

NASA Astrophysics Data System (ADS)

Caliste, D.; Pouillon, Y.; Verstraete, M. J.; Olevano, V.; Gonze, X.

2008-11-01

We present a library of routines whose main goal is to read and write exchangeable files (NetCDF file format) storing electronic structure and crystallographic information. It is based on the specification agreed inside the European Theoretical Spectroscopy Facility (ETSF). Accordingly, this library is nicknamed ETSF_IO. The purpose of this article is to give both an overview of the ETSF_IO library and a closer look at its usage. ETSF_IO is designed to be robust and easy to use, close to Fortran read and write routines. To facilitate its adoption, a complete documentation of the input and output arguments of the routines is available in the package, as well as six tutorials explaining in detail various possible uses of the library routines. Catalogue identifier: AEBG_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEBG_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Gnu Lesser General Public License No. of lines in distributed program, including test data, etc.: 63 156 No. of bytes in distributed program, including test data, etc.: 363 390 Distribution format: tar.gz Programming language: Fortran 95 Computer: All systems with a Fortran95 compiler Operating system: All systems with a Fortran95 compiler Classification: 7.3, 8 External routines: NetCDF, http://www.unidata.ucar.edu/software/netcdf Nature of problem: Store and exchange electronic structure data and crystallographic data independently of the computational platform, language and generating software Solution method: Implement a library based both on NetCDF file format and an open specification (http://etsf.eu/index.php?page=standardization)

The eGenVar data management system—cataloguing and sharing sensitive data and metadata for the life sciences

PubMed Central

Razick, Sabry; Močnik, Rok; Thomas, Laurent F.; Ryeng, Einar; Drabløs, Finn; Sætrom, Pål

2014-01-01

Systematic data management and controlled data sharing aim at increasing reproducibility, reducing redundancy in work, and providing a way to efficiently locate complementing or contradicting information. One method of achieving this is collecting data in a central repository or in a location that is part of a federated system and providing interfaces to the data. However, certain data, such as data from biobanks or clinical studies, may, for legal and privacy reasons, often not be stored in public repositories. Instead, we describe a metadata cataloguing system and a software suite for reporting the presence of data from the life sciences domain. The system stores three types of metadata: file information, file provenance and data lineage, and content descriptions. Our software suite includes both graphical and command line interfaces that allow users to report and tag files with these different metadata types. Importantly, the files remain in their original locations with their existing access-control mechanisms in place, while our system provides descriptions of their contents and relationships. Our system and software suite thereby provide a common framework for cataloguing and sharing both public and private data. Database URL: http://bigr.medisin.ntnu.no/data/eGenVar/ PMID:24682735

Stochastic modelling of human exposure to food chemicals and nutrients within the "Montecarlo" project: an exploration of the influence of brand loyalty and market share on intake estimates of intense sweeteners from sugar-free soft drinks.

PubMed

Leclercq, Catherine; Arcella, Davide; Le Donne, Cinzia; Piccinelli, Raffaela; Sette, Stefania; Soggiu, Maria Eleonora

2003-04-11

To get a more realistic view of exposure to food chemicals, risk managers are getting more interested in stochastic modelling as an alternative to deterministic approaches based on conservative assumptions. It allows to take into account all the available information in the concentration of the chemical present in foods and in food consumption patterns. Within the EC-funded "Montecarlo" project, a comprehensive set of mathematical algorithms was developed to take into account all the necessary components for stochastic modelling of a variety of food chemicals, nutrients and ingredients. An appropriate computer software is being developed. Since the concentration of food chemicals may vary among different brands of the same product, consumer behaviour with respect to brands may have an impact on exposure assessments. Numeric experiments were carried out on different ways of incorporating indicators of market share and brand loyalty in the mathematical algorithms developed within the stochastic model of exposure to intense sweeteners from sugar-free beverages. The 95th percentiles of intake were shown to vary according to the inclusion/exclusion of these indicators. The market share should be included in the model especially if the market is not equitably distributed between brands. If brand loyalty data are not available, the model may be run under theoretical scenarios.

A communication-avoiding, hybrid-parallel, rank-revealing orthogonalization method.

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

Hoemmen, Mark

2010-11-01

Orthogonalization consumes much of the run time of many iterative methods for solving sparse linear systems and eigenvalue problems. Commonly used algorithms, such as variants of Gram-Schmidt or Householder QR, have performance dominated by communication. Here, 'communication' includes both data movement between the CPU and memory, and messages between processors in parallel. Our Tall Skinny QR (TSQR) family of algorithms requires asymptotically fewer messages between processors and data movement between CPU and memory than typical orthogonalization methods, yet achieves the same accuracy as Householder QR factorization. Furthermore, in block orthogonalizations, TSQR is faster and more accurate than existing approaches formore » orthogonalizing the vectors within each block ('normalization'). TSQR's rank-revealing capability also makes it useful for detecting deflation in block iterative methods, for which existing approaches sacrifice performance, accuracy, or both. We have implemented a version of TSQR that exploits both distributed-memory and shared-memory parallelism, and supports real and complex arithmetic. Our implementation is optimized for the case of orthogonalizing a small number (5-20) of very long vectors. The shared-memory parallel component uses Intel's Threading Building Blocks, though its modular design supports other shared-memory programming models as well, including computation on the GPU. Our implementation achieves speedups of 2 times or more over competing orthogonalizations. It is available now in the development branch of the Trilinos software package, and will be included in the 10.8 release.« less

Microcomputer software development facilities

NASA Technical Reports Server (NTRS)

Gorman, J. S.; Mathiasen, C.

1980-01-01

A more efficient and cost effective method for developing microcomputer software is to utilize a host computer with high-speed peripheral support. Application programs such as cross assemblers, loaders, and simulators are implemented in the host computer for each of the microcomputers for which software development is a requirement. The host computer is configured to operate in a time share mode for multiusers. The remote terminals, printers, and down loading capabilities provided are based on user requirements. With this configuration a user, either local or remote, can use the host computer for microcomputer software development. Once the software is developed (through the code and modular debug stage) it can be downloaded to the development system or emulator in a test area where hardware/software integration functions can proceed. The microcomputer software program sources reside in the host computer and can be edited, assembled, loaded, and then downloaded as required until the software development project has been completed.

The Particle-in-Cell and Kinetic Simulation Software Center

NASA Astrophysics Data System (ADS)

Mori, W. B.; Decyk, V. K.; Tableman, A.; Fonseca, R. A.; Tsung, F. S.; Hu, Q.; Winjum, B. J.; An, W.; Dalichaouch, T. N.; Davidson, A.; Hildebrand, L.; Joglekar, A.; May, J.; Miller, K.; Touati, M.; Xu, X. L.

2017-10-01

The UCLA Particle-in-Cell and Kinetic Simulation Software Center (PICKSC) aims to support an international community of PIC and plasma kinetic software developers, users, and educators; to increase the use of this software for accelerating the rate of scientific discovery; and to be a repository of knowledge and history for PIC. We discuss progress towards making available and documenting illustrative open-source software programs and distinct production programs; developing and comparing different PIC algorithms; coordinating the development of resources for the educational use of kinetic software; and the outcomes of our first sponsored OSIRIS users workshop. We also welcome input and discussion from anyone interested in using or developing kinetic software, in obtaining access to our codes, in collaborating, in sharing their own software, or in commenting on how PICKSC can better serve the DPP community. Supported by NSF under Grant ACI-1339893 and by the UCLA Institute for Digital Research and Education.

Analysis of scalability of high-performance 3D image processing platform for virtual colonoscopy

NASA Astrophysics Data System (ADS)

Yoshida, Hiroyuki; Wu, Yin; Cai, Wenli

2014-03-01

One of the key challenges in three-dimensional (3D) medical imaging is to enable the fast turn-around time, which is often required for interactive or real-time response. This inevitably requires not only high computational power but also high memory bandwidth due to the massive amount of data that need to be processed. For this purpose, we previously developed a software platform for high-performance 3D medical image processing, called HPC 3D-MIP platform, which employs increasingly available and affordable commodity computing systems such as the multicore, cluster, and cloud computing systems. To achieve scalable high-performance computing, the platform employed size-adaptive, distributable block volumes as a core data structure for efficient parallelization of a wide range of 3D-MIP algorithms, supported task scheduling for efficient load distribution and balancing, and consisted of a layered parallel software libraries that allow image processing applications to share the common functionalities. We evaluated the performance of the HPC 3D-MIP platform by applying it to computationally intensive processes in virtual colonoscopy. Experimental results showed a 12-fold performance improvement on a workstation with 12-core CPUs over the original sequential implementation of the processes, indicating the efficiency of the platform. Analysis of performance scalability based on the Amdahl's law for symmetric multicore chips showed the potential of a high performance scalability of the HPC 3DMIP platform when a larger number of cores is available.

48 CFR 227.7203-9 - Copyright.

Code of Federal Regulations, 2010 CFR

2010-10-01

... Software and Computer Software Documentation 227.7203-9 Copyright. (a) Copyright license. (1) The clause at 252.227-7014, Rights in Noncommercial Computer Software and Noncommercial Computer Software... Government to reproduce the software or documentation, distribute copies, perform or display the software or...

48 CFR 227.7203-9 - Copyright.

Code of Federal Regulations, 2013 CFR

2013-10-01

... Software and Computer Software Documentation 227.7203-9 Copyright. (a) Copyright license. (1) The clause at 252.227-7014, Rights in Noncommercial Computer Software and Noncommercial Computer Software... Government to reproduce the software or documentation, distribute copies, perform or display the software or...

48 CFR 227.7203-9 - Copyright.

Code of Federal Regulations, 2011 CFR

2011-10-01

... Software and Computer Software Documentation 227.7203-9 Copyright. (a) Copyright license. (1) The clause at 252.227-7014, Rights in Noncommercial Computer Software and Noncommercial Computer Software... Government to reproduce the software or documentation, distribute copies, perform or display the software or...

48 CFR 227.7203-9 - Copyright.

Code of Federal Regulations, 2014 CFR

2014-10-01

... Software and Computer Software Documentation 227.7203-9 Copyright. (a) Copyright license. (1) The clause at 252.227-7014, Rights in Noncommercial Computer Software and Noncommercial Computer Software... Government to reproduce the software or documentation, distribute copies, perform or display the software or...

48 CFR 227.7203-9 - Copyright.

Code of Federal Regulations, 2012 CFR

2012-10-01

... Software and Computer Software Documentation 227.7203-9 Copyright. (a) Copyright license. (1) The clause at 252.227-7014, Rights in Noncommercial Computer Software and Noncommercial Computer Software... Government to reproduce the software or documentation, distribute copies, perform or display the software or...

Effects of Medical Device Regulations on the Development of Stand-Alone Medical Software: A Pilot Study.

PubMed

Blagec, Kathrin; Jungwirth, David; Haluza, Daniela; Samwald, Matthias

2018-01-01

Medical device regulations which aim to ensure safety standards do not only apply to hardware devices but also to standalone medical software, e.g. mobile apps. To explore the effects of these regulations on the development and distribution of medical standalone software. We invited a convenience sample of 130 domain experts to participate in an online survey about the impact of current regulations on the development and distribution of medical standalone software. 21 respondents completed the questionnaire. Participants reported slight positive effects on usability, reliability, and data security of their products, whereas the ability to modify already deployed software and customization by end users were negatively impacted. The additional time and costs needed to go through the regulatory process were perceived as the greatest obstacles in developing and distributing medical software. Further research is needed to compare positive effects on software quality with negative impacts on market access and innovation. Strategies for avoiding over-regulation while still ensuring safety standards need to be devised.

Overview of the LINCS architecture

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

Fletcher, J.G.; Watson, R.W.

1982-01-13

Computing at the Lawrence Livermore National Laboratory (LLNL) has evolved over the past 15 years with a computer network based resource sharing environment. The increasing use of low cost and high performance micro, mini and midi computers and commercially available local networking systems will accelerate this trend. Further, even the large scale computer systems, on which much of the LLNL scientific computing depends, are evolving into multiprocessor systems. It is our belief that the most cost effective use of this environment will depend on the development of application systems structured into cooperating concurrent program modules (processes) distributed appropriately over differentmore » nodes of the environment. A node is defined as one or more processors with a local (shared) high speed memory. Given the latter view, the environment can be characterized as consisting of: multiple nodes communicating over noisy channels with arbitrary delays and throughput, heterogenous base resources and information encodings, no single administration controlling all resources, distributed system state, and no uniform time base. The system design problem is - how to turn the heterogeneous base hardware/firmware/software resources of this environment into a coherent set of resources that facilitate development of cost effective, reliable, and human engineered applications. We believe the answer lies in developing a layered, communication oriented distributed system architecture; layered and modular to support ease of understanding, reconfiguration, extensibility, and hiding of implementation or nonessential local details; communication oriented because that is a central feature of the environment. The Livermore Interactive Network Communication System (LINCS) is a hierarchical architecture designed to meet the above needs. While having characteristics in common with other architectures, it differs in several respects.« less

Unleashing the Power of Distributed CPU/GPU Architectures: Massive Astronomical Data Analysis and Visualization Case Study

NASA Astrophysics Data System (ADS)

Hassan, A. H.; Fluke, C. J.; Barnes, D. G.

2012-09-01

Upcoming and future astronomy research facilities will systematically generate terabyte-sized data sets moving astronomy into the Petascale data era. While such facilities will provide astronomers with unprecedented levels of accuracy and coverage, the increases in dataset size and dimensionality will pose serious computational challenges for many current astronomy data analysis and visualization tools. With such data sizes, even simple data analysis tasks (e.g. calculating a histogram or computing data minimum/maximum) may not be achievable without access to a supercomputing facility. To effectively handle such dataset sizes, which exceed today's single machine memory and processing limits, we present a framework that exploits the distributed power of GPUs and many-core CPUs, with a goal of providing data analysis and visualizing tasks as a service for astronomers. By mixing shared and distributed memory architectures, our framework effectively utilizes the underlying hardware infrastructure handling both batched and real-time data analysis and visualization tasks. Offering such functionality as a service in a “software as a service” manner will reduce the total cost of ownership, provide an easy to use tool to the wider astronomical community, and enable a more optimized utilization of the underlying hardware infrastructure.

Dynamic Load-Balancing for Distributed Heterogeneous Computing of Parallel CFD Problems

NASA Technical Reports Server (NTRS)

Ecer, A.; Chien, Y. P.; Boenisch, T.; Akay, H. U.

2000-01-01

The developed methodology is aimed at improving the efficiency of executing block-structured algorithms on parallel, distributed, heterogeneous computers. The basic approach of these algorithms is to divide the flow domain into many sub- domains called blocks, and solve the governing equations over these blocks. Dynamic load balancing problem is defined as the efficient distribution of the blocks among the available processors over a period of several hours of computations. In environments with computers of different architecture, operating systems, CPU speed, memory size, load, and network speed, balancing the loads and managing the communication between processors becomes crucial. Load balancing software tools for mutually dependent parallel processes have been created to efficiently utilize an advanced computation environment and algorithms. These tools are dynamic in nature because of the chances in the computer environment during execution time. More recently, these tools were extended to a second operating system: NT. In this paper, the problems associated with this application will be discussed. Also, the developed algorithms were combined with the load sharing capability of LSF to efficiently utilize workstation clusters for parallel computing. Finally, results will be presented on running a NASA based code ADPAC to demonstrate the developed tools for dynamic load balancing.

A controlled experiment on the impact of software structure on maintainability

NASA Technical Reports Server (NTRS)

Rombach, Dieter H.

1987-01-01

The impact of software structure on maintainability aspects including comprehensibility, locality, modifiability, and reusability in a distributed system environment is studied in a controlled maintenance experiment involving six medium-size distributed software systems implemented in LADY (language for distributed systems) and six in an extended version of sequential PASCAL. For all maintenance aspects except reusability, the results were quantitatively given in terms of complexity metrics which could be automated. The results showed LADY to be better suited to the development of maintainable software than the extension of sequential PASCAL. The strong typing combined with high parametrization of units is suggested to improve the reusability of units in LADY.

Influence of Smartphones and Software on Acoustic Voice Measures

PubMed Central

GRILLO, ELIZABETH U.; BROSIOUS, JENNA N.; SORRELL, STACI L.; ANAND, SUPRAJA

2016-01-01

This study assessed the within-subject variability of voice measures captured using different recording devices (i.e., smartphones and head mounted microphone) and software programs (i.e., Analysis of Dysphonia in Speech and Voice (ADSV), Multi-dimensional Voice Program (MDVP), and Praat). Correlations between the software programs that calculated the voice measures were also analyzed. Results demonstrated no significant within-subject variability across devices and software and that some of the measures were highly correlated across software programs. The study suggests that certain smartphones may be appropriate to record daily voice measures representing the effects of vocal loading within individuals. In addition, even though different algorithms are used to compute voice measures across software programs, some of the programs and measures share a similar relationship. PMID:28775797

The Architecture Based Design Method

DTIC Science & Technology

2000-01-01

implementation of components of different types. The software templates include a description of how components interact with shared services and also include citizenship responsibilities for components.

Expert system technologies for Space Shuttle decision support: Two case studies

NASA Technical Reports Server (NTRS)

Ortiz, Christopher J.; Hasan, David A.

1994-01-01

This paper addresses the issue of integrating the C Language Integrated Production System (CLIPS) into distributed data acquisition environments. In particular, it presents preliminary results of some ongoing software development projects aimed at exploiting CLIPS technology in the new mission control center (MCC) being built at NASA Johnson Space Center. One interesting aspect of the control center is its distributed architecture; it consists of networked workstations which acquire and share data through the NASA/JSC-developed information sharing protocol (ISP). This paper outlines some approaches taken to integrate CLIPS and ISP in order to permit the development of intelligent data analysis applications which can be used in the MCC. Three approaches to CLIPS/IPS integration are discussed. The initial approach involves clearly separating CLIPS from ISP using user-defined functions for gathering and sending data to and from a local storage buffer. Memory and performance drawbacks of this design are summarized. The second approach involves taking full advantage of CLIPS and the CLIPS Object-Oriented Language (COOL) by using objects to directly transmit data and state changes from ISP to COOL. Any changes within the object slots eliminate the need for both a data structure and external function call thus taking advantage of the object matching capabilities within CLIPS 6.0. The final approach is to treat CLIPS and ISP as peer toolkits. Neither is embedded in the other; rather the application interweaves calls to each directly in the application source code.

Orthographic Learning and the Role of Text-to-Speech Software in Dutch Disabled Readers

ERIC Educational Resources Information Center

Staels, Eva; Van den Broeck, Wim

2015-01-01

In this study, we examined whether orthographic learning can be demonstrated in disabled readers learning to read in a transparent orthography (Dutch). In addition, we tested the effect of the use of text-to-speech software, a new form of direct instruction, on orthographic learning. Both research goals were investigated by replicating Share's…

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…

[Ecology suitability study of Chinese materia medica Gentianae Macrophyllae Radix].

PubMed

Lu, You-Yuan; Yang, Yan-Mei; Ma, Xiao-Hui; Zhang, Xiao-Bo; Zhu, Shou-Dong; Jin, Ling

2016-09-01

This paper is aimed to predict ecology suitability distribution of Gentianae Macrophyllae Radix and search the main ecological factors affecting the suitability distribution. The 313 distribution information about G. macrophylla, 186 distribution information about G. straminea, 343 distribution information about G. dauricaand 131 distribution information about G. crasicaulis were collected though investigation and network sharing platform data . The ecology suitable distribution factors for production Gentianae Macrophyllae Radix was analyzed respectively by the software of ArcGIS and MaxEnt with 55 environmental factors. The result of MaxEnt prediction was very well (AUC was above 0.9). The results of predominant factors analysis showed that precipitation and altitude were all the major factors impacting the ecology suitable of Getiana Macrophylla Radix production. G. macrophylla ecology suitable region was mainly concentrated in south of Gansu, Shanxi, central of Shaanxi and east of Qinghai provinces. G. straminea ecology suitable region was mainly concentrated in southwest of Gansu, east of Qinghai, north and northwest of Sichuan, east of Xizang province. G. daurica ecology suitable region was mainly concentrated in south and southwest of Gansu, east of Qinghai, Shanxi and north of Shaanxi province. G. crasicaulis ecology suitable region was mainly concentrated in Sichuan and north of Yunnan, east of Xizang, south of Gansu and east of Qinghai province. The ecological suitability distribution result of Gentianae Macrophyllae Radix was consistent with each species actual distribution. The study could provide reference for the collection and protection of wild resources, meanwhile, provide the basis for the selection of cultivation area of Gentiana Macrophylla Radix. Copyright© by the Chinese Pharmaceutical Association.

Communication and Organization in Software Development: An Empirical Study

NASA Technical Reports Server (NTRS)

Seaman, Carolyn B.; Basili, Victor R.

1996-01-01

The empirical study described in this paper addresses the issue of communication among members of a software development organization. The independent variables are various attributes of organizational structure. The dependent variable is the effort spent on sharing information which is required by the software development process in use. The research questions upon which the study is based ask whether or not these attributes of organizational structure have an effect on the amount of communication effort expended. In addition, there are a number of blocking variables which have been identified. These are used to account for factors other than organizational structure which may have an effect on communication effort. The study uses both quantitative and qualitative methods for data collection and analysis. These methods include participant observation, structured interviews, and graphical data presentation. The results of this study indicate that several attributes of organizational structure do affect communication effort, but not in a simple, straightforward way. In particular, the distances between communicators in the reporting structure of the organization, as well as in the physical layout of offices, affects how quickly they can share needed information, especially during meetings. These results provide a better understanding of how organizational structure helps or hinders communication in software development.

Sptrace

NASA Technical Reports Server (NTRS)

Burleigh, Scott C.

2011-01-01

Sptrace is a general-purpose space utilization tracing system that is conceptually similar to the commercial Purify product used to detect leaks and other memory usage errors. It is designed to monitor space utilization in any sort of heap, i.e., a region of data storage on some device (nominally memory; possibly shared and possibly persistent) with a flat address space. This software can trace usage of shared and/or non-volatile storage in addition to private RAM (random access memory). Sptrace is implemented as a set of C function calls that are invoked from within the software that is being examined. The function calls fall into two broad classes: (1) functions that are embedded within the heap management software [e.g., JPL's SDR (Simple Data Recorder) and PSM (Personal Space Management) systems] to enable heap usage analysis by populating a virtual time-sequenced log of usage activity, and (2) reporting functions that are embedded within the application program whose behavior is suspect. For ease of use, these functions may be wrapped privately inside public functions offered by the heap management software. Sptrace can be used for VxWorks or RTEMS realtime systems as easily as for Linux or OS/X systems.

ETICS: the international software engineering service for the grid

NASA Astrophysics Data System (ADS)

Meglio, A. D.; Bégin, M.-E.; Couvares, P.; Ronchieri, E.; Takacs, E.

2008-07-01

The ETICS system is a distributed software configuration, build and test system designed to fulfil the needs of improving the quality, reliability and interoperability of distributed software in general and grid software in particular. The ETICS project is a consortium of five partners (CERN, INFN, Engineering Ingegneria Informatica, 4D Soft and the University of Wisconsin-Madison). The ETICS service consists of a build and test job execution system based on the Metronome software and an integrated set of web services and software engineering tools to design, maintain and control build and test scenarios. The ETICS system allows taking into account complex dependencies among applications and middleware components and provides a rich environment to perform static and dynamic analysis of the software and execute deployment, system and interoperability tests. This paper gives an overview of the system architecture and functionality set and then describes how the EC-funded EGEE, DILIGENT and OMII-Europe projects are using the software engineering services to build, validate and distribute their software. Finally a number of significant use and test cases will be described to show how ETICS can be used in particular to perform interoperability tests of grid middleware using the grid itself.

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

An exchange format for use-cases of hospital information systems.

PubMed

Masuda, G; Sakamoto, N; Sakai, R; Yamamoto, R

2001-01-01

Object-oriented software development is a powerful methodology for development of large hospital information systems. We think use-case driven approach is particularly useful for the development. In the use-cases driven approach, use-cases are documented at the first stage in the software development process and they are used through the whole steps in a variety of ways. Therefore, it is important to exchange and share the use-cases and make effective use of them through the overall lifecycle of a development process. In this paper, we propose a method of sharing and exchanging use-case models between applications, developers, and projects. We design an XML based exchange format for use-cases. We then discuss an application of the exchange format to support several software development activities. We preliminarily implemented a support system for object-oriented analysis based on the exchange format. The result shows that using the structural and semantic information in the exchange format enables the support system to assist the object-oriented analysis successfully.

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

36 CFR 1206.45 - What rules govern subgrant distribution, cost sharing, grant administration, and reporting?

Code of Federal Regulations, 2010 CFR

2010-07-01

... distribution, cost sharing, grant administration, and reporting? 1206.45 Section 1206.45 Parks, Forests, and Public Property NATIONAL ARCHIVES AND RECORDS ADMINISTRATION GENERAL RULES NATIONAL HISTORICAL..., cost sharing, grant administration, and reporting? (a) The Commission will annually establish guidance...

Creating a YouTube-Like Collaborative Environment in Mathematics: Integrating Animated Geogebra Constructions and Student-Generated Screencast Videos

ERIC Educational Resources Information Center

Lazarus, Jill; Roulet, Geoffrey

2013-01-01

This article discusses the integration of student-generated GeoGebra applets and Jing screencast videos to create a YouTube-like medium for sharing in mathematics. The value of combining dynamic mathematics software and screencast videos for facilitating communication and representations in a digital era is demonstrated herein. We share our…

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

Computer Sciences and Data Systems, volume 1

NASA Technical Reports Server (NTRS)

1987-01-01

Topics addressed include: software engineering; university grants; institutes; concurrent processing; sparse distributed memory; distributed operating systems; intelligent data management processes; expert system for image analysis; fault tolerant software; and architecture research.

Managing a tier-2 computer centre with a private cloud infrastructure

NASA Astrophysics Data System (ADS)

Bagnasco, Stefano; Berzano, Dario; Brunetti, Riccardo; Lusso, Stefano; Vallero, Sara

2014-06-01

In a typical scientific computing centre, several applications coexist and share a single physical infrastructure. An underlying Private Cloud infrastructure eases the management and maintenance of such heterogeneous applications (such as multipurpose or application-specific batch farms, Grid sites, interactive data analysis facilities and others), allowing dynamic allocation resources to any application. Furthermore, the maintenance of large deployments of complex and rapidly evolving middleware and application software is eased by the use of virtual images and contextualization techniques. Such infrastructures are being deployed in some large centres (see e.g. the CERN Agile Infrastructure project), but with several open-source tools reaching maturity this is becoming viable also for smaller sites. In this contribution we describe the Private Cloud infrastructure at the INFN-Torino Computer Centre, that hosts a full-fledged WLCG Tier-2 centre, an Interactive Analysis Facility for the ALICE experiment at the CERN LHC and several smaller scientific computing applications. The private cloud building blocks include the OpenNebula software stack, the GlusterFS filesystem and the OpenWRT Linux distribution (used for network virtualization); a future integration into a federated higher-level infrastructure is made possible by exposing commonly used APIs like EC2 and OCCI.

Visualization in aerospace research with a large wall display system

NASA Astrophysics Data System (ADS)

Matsuo, Yuichi

2002-05-01

National Aerospace Laboratory of Japan has built a large- scale visualization system with a large wall-type display. The system has been operational since April 2001 and comprises a 4.6x1.5-meter (15x5-foot) rear projection screen with 3 BARCO 812 high-resolution CRT projectors. The reason we adopted the 3-gun CRT projectors is support for stereoscopic viewing, ease with color/luminosity matching and accuracy of edge-blending. The system is driven by a new SGI Onyx 3400 server of distributed shared-memory architecture with 32 CPUs, 64Gbytes memory, 1.5TBytes FC RAID disk and 6 IR3 graphics pipelines. Software is another important issue for us to make full use of the system. We have introduced some applications available in a multi- projector environment such as AVS/MPE, EnSight Gold and COVISE, and been developing some software tools that create volumetric images with using SGI graphics libraries. The system is mainly used for visualization fo computational fluid dynamics (CFD) simulation sin aerospace research. Visualized CFD results are of our help for designing an improved configuration of aerospace vehicles and analyzing their aerodynamic performances. These days we also use it for various collaborations among researchers.

EMMA: a new paradigm in configurable software

DOE PAGES

Nogiec, J. M.; Trombly-Freytag, K.

2017-11-23

EMMA is a framework designed to create a family of configurable software systems, with emphasis on extensibility and flexibility. It is based on a loosely coupled, event driven architecture. The EMMA framework has been built upon the premise of composing software systems from independent components. It opens up opportunities for reuse of components and their functionality and composing them together in many different ways. As a result, it provides the developer of test and measurement applications with a lightweight alternative to microservices, while sharing their various advantages, including composability, loose coupling, encapsulation, and reuse.

EMMA: A New Paradigm in Configurable Software

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

Nogiec, J. M.; Trombly-Freytag, K.

EMMA is a framework designed to create a family of configurable software systems, with emphasis on extensibility and flexibility. It is based on a loosely coupled, event driven architecture. The EMMA framework has been built upon the premise of composing software systems from independent components. It opens up opportunities for reuse of components and their functionality and composing them together in many different ways. It provides the developer of test and measurement applications with a lightweight alternative to microservices, while sharing their various advantages, including composability, loose coupling, encapsulation, and reuse.

EMMA: a new paradigm in configurable software

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

Nogiec, J. M.; Trombly-Freytag, K.

EMMA is a framework designed to create a family of configurable software systems, with emphasis on extensibility and flexibility. It is based on a loosely coupled, event driven architecture. The EMMA framework has been built upon the premise of composing software systems from independent components. It opens up opportunities for reuse of components and their functionality and composing them together in many different ways. As a result, it provides the developer of test and measurement applications with a lightweight alternative to microservices, while sharing their various advantages, including composability, loose coupling, encapsulation, and reuse.

EMMA: a new paradigm in configurable software

NASA Astrophysics Data System (ADS)

Nogiec, J. M.; Trombly-Freytag, K.

2017-10-01

EMMA is a framework designed to create a family of configurable software systems, with emphasis on extensibility and flexibility. It is based on a loosely coupled, event driven architecture. The EMMA framework has been built upon the premise of composing software systems from independent components. It opens up opportunities for reuse of components and their functionality and composing them together in many different ways. It provides the developer of test and measurement applications with a lightweight alternative to microservices, while sharing their various advantages, including composability, loose coupling, encapsulation, and reuse.

pFlogger: The Parallel Fortran Logging Utility

NASA Technical Reports Server (NTRS)

Clune, Tom; Cruz, Carlos A.

2017-01-01

In the context of high performance computing (HPC), software investments in support of text-based diagnostics, which monitor a running application, are typically limited compared to those for other types of IO. Examples of such diagnostics include reiteration of configuration parameters, progress indicators, simple metrics (e.g., mass conservation, convergence of solvers, etc.), and timers. To some degree, this difference in priority is justifiable as other forms of output are the primary products of a scientific model and, due to their large data volume, much more likely to be a significant performance concern. In contrast, text-based diagnostic content is generally not shared beyond the individual or group running an application and is most often used to troubleshoot when something goes wrong. We suggest that a more systematic approach enabled by a logging facility (or 'logger)' similar to those routinely used by many communities would provide significant value to complex scientific applications. In the context of high-performance computing, an appropriate logger would provide specialized support for distributed and shared-memory parallelism and have low performance overhead. In this paper, we present our prototype implementation of pFlogger - a parallel Fortran-based logging framework, and assess its suitability for use in a complex scientific application.

Modeling a distributed environment for a petroleum reservoir engineering application with software product line

NASA Astrophysics Data System (ADS)

de Faria Scheidt, Rafael; Vilain, Patrícia; Dantas, M. A. R.

2014-10-01

Petroleum reservoir engineering is a complex and interesting field that requires large amount of computational facilities to achieve successful results. Usually, software environments for this field are developed without taking care out of possible interactions and extensibilities required by reservoir engineers. In this paper, we present a research work which it is characterized by the design and implementation based on a software product line model for a real distributed reservoir engineering environment. Experimental results indicate successfully the utilization of this approach for the design of distributed software architecture. In addition, all components from the proposal provided greater visibility of the organization and processes for the reservoir engineers.

Cooperative Learning for Distributed In-Network Traffic Classification

NASA Astrophysics Data System (ADS)

Joseph, S. B.; Loo, H. R.; Ismail, I.; Andromeda, T.; Marsono, M. N.

2017-04-01

Inspired by the concept of autonomic distributed/decentralized network management schemes, we consider the issue of information exchange among distributed network nodes to network performance and promote scalability for in-network monitoring. In this paper, we propose a cooperative learning algorithm for propagation and synchronization of network information among autonomic distributed network nodes for online traffic classification. The results show that network nodes with sharing capability perform better with a higher average accuracy of 89.21% (sharing data) and 88.37% (sharing clusters) compared to 88.06% for nodes without cooperative learning capability. The overall performance indicates that cooperative learning is promising for distributed in-network traffic classification.

An Open Data Platform in the framework of the EGI-LifeWatch Competence Center

NASA Astrophysics Data System (ADS)

Aguilar Gómez, Fernando; de Lucas, Jesús Marco; Yaiza Rodríguez Marrero, Ana

2016-04-01

The working pilot of an Open Data Platform supporting the full data cycle in research is presented. It aims to preserve knowledge explicitly, starting with the description of the Case Studies, and integrating data and software management and preservation on equal basis. The uninterrupted support in the chain starts at the data acquisition level and covers up to the support for reuse and publication in an open framework, providing integrity and provenance controls. The Lifewatch Open Science Framework is a pilot web portal developed in collaboration with different commercial companies that tries to enrich and integrate different data lifecycle-related tools in order to address the management of the different steps: data planning, gathering, storing, curation, preservation, sharing, discovering, etc. To achieve this goal, the platform includes the following features: -Data Management Planning. Tool to set up an structure of the data, including what data will be generated, how it will be exploited, re-used, curated, preserved, etc. It has a semantic approach: includes reference to ontologies in order to express what data will be gathered. -Close to instrumentation. The portal includes a distributed storage system that can be used both for storing data from instruments and output data from analysis. All that data can be shared -Analysis. Resources from EGI Federated Cloud are accessible within the portal, so that users can exploit computing resources to perform analysis and other processes, including workflows. -Preservation. Data can be preserved in different systems and DOIs can be minted not only for datasets but also for software, DMPs, etc. The presentation will show the different components of the framework as well as how it can be extrapolated to other communities.

Using open source computational tools for predicting human metabolic stability and additional absorption, distribution, metabolism, excretion, and toxicity properties.

PubMed

Gupta, Rishi R; Gifford, Eric M; Liston, Ted; Waller, Chris L; Hohman, Moses; Bunin, Barry A; Ekins, Sean

2010-11-01

Ligand-based computational models could be more readily shared between researchers and organizations if they were generated with open source molecular descriptors [e.g., chemistry development kit (CDK)] and modeling algorithms, because this would negate the requirement for proprietary commercial software. We initially evaluated open source descriptors and model building algorithms using a training set of approximately 50,000 molecules and a test set of approximately 25,000 molecules with human liver microsomal metabolic stability data. A C5.0 decision tree model demonstrated that CDK descriptors together with a set of Smiles Arbitrary Target Specification (SMARTS) keys had good statistics [κ = 0.43, sensitivity = 0.57, specificity = 0.91, and positive predicted value (PPV) = 0.64], equivalent to those of models built with commercial Molecular Operating Environment 2D (MOE2D) and the same set of SMARTS keys (κ = 0.43, sensitivity = 0.58, specificity = 0.91, and PPV = 0.63). Extending the dataset to ∼193,000 molecules and generating a continuous model using Cubist with a combination of CDK and SMARTS keys or MOE2D and SMARTS keys confirmed this observation. When the continuous predictions and actual values were binned to get a categorical score we observed a similar κ statistic (0.42). The same combination of descriptor set and modeling method was applied to passive permeability and P-glycoprotein efflux data with similar model testing statistics. In summary, open source tools demonstrated predictive results comparable to those of commercial software with attendant cost savings. We discuss the advantages and disadvantages of open source descriptors and the opportunity for their use as a tool for organizations to share data precompetitively, avoiding repetition and assisting drug discovery.

Software Framework for Peer Data-Management Services

NASA Technical Reports Server (NTRS)

Hughes, John; Hardman, Sean; Crichton, Daniel; Hyon, Jason; Kelly, Sean; Tran, Thuy

2007-01-01

Object Oriented Data Technology (OODT) is a software framework for creating a Web-based system for exchange of scientific data that are stored in diverse formats on computers at different sites under the management of scientific peers. OODT software consists of a set of cooperating, distributed peer components that provide distributed peer-to-peer (P2P) services that enable one peer to search and retrieve data managed by another peer. In effect, computers running OODT software at different locations become parts of an integrated data-management system.

Measurement and analysis of operating system fault tolerance

NASA Technical Reports Server (NTRS)

Lee, I.; Tang, D.; Iyer, R. K.

1992-01-01

This paper demonstrates a methodology to model and evaluate the fault tolerance characteristics of operational software. The methodology is illustrated through case studies on three different operating systems: the Tandem GUARDIAN fault-tolerant system, the VAX/VMS distributed system, and the IBM/MVS system. Measurements are made on these systems for substantial periods to collect software error and recovery data. In addition to investigating basic dependability characteristics such as major software problems and error distributions, we develop two levels of models to describe error and recovery processes inside an operating system and on multiple instances of an operating system running in a distributed environment. Based on the models, reward analysis is conducted to evaluate the loss of service due to software errors and the effect of the fault-tolerance techniques implemented in the systems. Software error correlation in multicomputer systems is also investigated.

Federating Metadata Catalogs

NASA Astrophysics Data System (ADS)

Baru, C.; Lin, K.

2009-04-01

The Geosciences Network project (www.geongrid.org) has been developing cyberinfrastructure for data sharing in the Earth Science community based on a service-oriented architecture. The project defines a standard "software stack", which includes a standardized set of software modules and corresponding service interfaces. The system employs Grid certificates for distributed user authentication. The GEON Portal provides online access to these services via a set of portlets. This service-oriented approach has enabled the GEON network to easily expand to new sites and deploy the same infrastructure in new projects. To facilitate interoperation with other distributed geoinformatics environments, service standards are being defined and implemented for catalog services and federated search across distributed catalogs. The need arises because there may be multiple metadata catalogs in a distributed system, for example, for each institution, agency, geographic region, and/or country. Ideally, a geoinformatics user should be able to search across all such catalogs by making a single search request. In this paper, we describe our implementation for such a search capability across federated metadata catalogs in the GEON service-oriented architecture. The GEON catalog can be searched using spatial, temporal, and other metadata-based search criteria. The search can be invoked as a Web service and, thus, can be imbedded in any software application. The need for federated catalogs in GEON arises because, (i) GEON collaborators at the University of Hyderabad, India have deployed their own catalog, as part of the iGEON-India effort, to register information about local resources for broader access across the network, (ii) GEON collaborators in the GEO Grid (Global Earth Observations Grid) project at AIST, Japan have implemented a catalog for their ASTER data products, and (iii) we have recently deployed a search service to access all data products from the EarthScope project in the US (http://es-portal.geongrid.org), which are distributed across data archives at IRIS in Seattle, Washington, UNAVCO in Boulder, Colorado, and at the ICDP archives in GFZ, Potsdam, Germany. This service implements a "virtual" catalog--the actual/"physical" catalogs and data are stored at each of the remote locations. A federated search across all these catalogs would enable GEON users to discover data across all of these environments with a single search request. Our objective is to implement this search service via the OGC Catalog Services for the Web (CS-W) standard by providing appropriate CSW "wrappers" for each metadata catalog, as necessary. This paper will discuss technical issues in designing and deploying such a multi-catalog search service in GEON and describe an initial prototype of the federated search capability.

NASA JPL Distributed Systems Technology (DST) Object-Oriented Component Approach for Software Inter-Operability and Reuse

NASA Technical Reports Server (NTRS)

Hall, Laverne; Hung, Chaw-Kwei; Lin, Imin

2000-01-01

The purpose of this paper is to provide a description of NASA JPL Distributed Systems Technology (DST) Section's object-oriented component approach to open inter-operable systems software development and software reuse. It will address what is meant by the terminology object component software, give an overview of the component-based development approach and how it relates to infrastructure support of software architectures and promotes reuse, enumerate on the benefits of this approach, and give examples of application prototypes demonstrating its usage and advantages. Utilization of the object-oriented component technology approach for system development and software reuse will apply to several areas within JPL, and possibly across other NASA Centers.

Development of Ada language control software for the NASA power management and distribution test bed

NASA Technical Reports Server (NTRS)

Wright, Ted; Mackin, Michael; Gantose, Dave

1989-01-01

The Ada language software developed to control the NASA Lewis Research Center's Power Management and Distribution testbed is described. The testbed is a reduced-scale prototype of the electric power system to be used on space station Freedom. It is designed to develop and test hardware and software for a 20-kHz power distribution system. The distributed, multiprocessor, testbed control system has an easy-to-use operator interface with an understandable English-text format. A simple interface for algorithm writers that uses the same commands as the operator interface is provided, encouraging interactive exploration of the system.

Proceedings of Tenth Annual Software Engineering Workshop

NASA Technical Reports Server (NTRS)

1985-01-01

Papers are presented on the following topics: measurement of software technology, recent studies of the Software Engineering Lab, software management tools, expert systems, error seeding as a program validation technique, software quality assurance, software engineering environments (including knowledge-based environments), the Distributed Computing Design System, and various Ada experiments.

Using Scrum Practices in GSD Projects

NASA Astrophysics Data System (ADS)

Paasivaara, Maria; Lassenius, Casper

In this chapter we present advice for applying Scrum practices to globally distributed software development projects. The chapter is based on a multiple-case study of four distributed Scrum projects. We discuss the use of distributed daily Scrums, Scrum-of-Scrums, Sprints, Sprint planning meetings, Sprint Demos, Retrospective meetings, and Backlogs. Moreover, we present lessons that distributed Scrum projects can benefit from non-agile globally distributed software development projects: frequent visits and multiple communication modes.

The Role of Standards in Cloud-Computing Interoperability

DTIC Science & Technology

2012-10-01

services are not shared outside the organization. CloudStack, Eucalyptus, HP, Microsoft, OpenStack , Ubuntu, and VMWare provide tools for building...center requirements • Developing usage models for cloud ven- dors • Independent IT consortium OpenStack http://www.openstack.org • Open-source...software for running private clouds • Currently consists of three core software projects: OpenStack Compute (Nova), OpenStack Object Storage (Swift

A Case Study in Software Adaptation

DTIC Science & Technology

2002-01-01

1 A Case Study in Software Adaptation Giuseppe Valetto Telecom Italia Lab Via Reiss Romoli 274 10148, Turin, Italy +39 011 2288788...configuration of the service; monitoring of database connectivity from within the service; monitoring of crashes and shutdowns of IM servers; monitoring of...of the IM server all share a relational database and a common runtime state repository, which make up the backend tier, and allow replicas to

Learning from hackers: open-source clinical trials.

PubMed

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

2012-05-02

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

OpenEIS. Users Guide

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

Kim, Woohyun; Lutes, Robert G.; Katipamula, Srinivas

This document is a users guide for OpenEIS, a software code designed to provide standard methods for authoring, sharing, testing, using and improving algorithms for operational building energy efficiency.

ROS-IGTL-Bridge: an open network interface for image-guided therapy using the ROS environment.

PubMed

Frank, Tobias; Krieger, Axel; Leonard, Simon; Patel, Niravkumar A; Tokuda, Junichi

2017-08-01

With the growing interest in advanced image-guidance for surgical robot systems, rapid integration and testing of robotic devices and medical image computing software are becoming essential in the research and development. Maximizing the use of existing engineering resources built on widely accepted platforms in different fields, such as robot operating system (ROS) in robotics and 3D Slicer in medical image computing could simplify these tasks. We propose a new open network bridge interface integrated in ROS to ensure seamless cross-platform data sharing. A ROS node named ROS-IGTL-Bridge was implemented. It establishes a TCP/IP network connection between the ROS environment and external medical image computing software using the OpenIGTLink protocol. The node exports ROS messages to the external software over the network and vice versa simultaneously, allowing seamless and transparent data sharing between the ROS-based devices and the medical image computing platforms. Performance tests demonstrated that the bridge could stream transforms, strings, points, and images at 30 fps in both directions successfully. The data transfer latency was <1.2 ms for transforms, strings and points, and 25.2 ms for color VGA images. A separate test also demonstrated that the bridge could achieve 900 fps for transforms. Additionally, the bridge was demonstrated in two representative systems: a mock image-guided surgical robot setup consisting of 3D slicer, and Lego Mindstorms with ROS as a prototyping and educational platform for IGT research; and the smart tissue autonomous robot surgical setup with 3D Slicer. The study demonstrated that the bridge enabled cross-platform data sharing between ROS and medical image computing software. This will allow rapid and seamless integration of advanced image-based planning/navigation offered by the medical image computing software such as 3D Slicer into ROS-based surgical robot systems.

Unbreakable distributed storage with quantum key distribution network and password-authenticated secret sharing

PubMed Central

Fujiwara, M.; Waseda, A.; Nojima, R.; Moriai, S.; Ogata, W.; Sasaki, M.

2016-01-01

Distributed storage plays an essential role in realizing robust and secure data storage in a network over long periods of time. A distributed storage system consists of a data owner machine, multiple storage servers and channels to link them. In such a system, secret sharing scheme is widely adopted, in which secret data are split into multiple pieces and stored in each server. To reconstruct them, the data owner should gather plural pieces. Shamir’s (k, n)-threshold scheme, in which the data are split into n pieces (shares) for storage and at least k pieces of them must be gathered for reconstruction, furnishes information theoretic security, that is, even if attackers could collect shares of less than the threshold k, they cannot get any information about the data, even with unlimited computing power. Behind this scenario, however, assumed is that data transmission and authentication must be perfectly secure, which is not trivial in practice. Here we propose a totally information theoretically secure distributed storage system based on a user-friendly single-password-authenticated secret sharing scheme and secure transmission using quantum key distribution, and demonstrate it in the Tokyo metropolitan area (≤90 km). PMID:27363566

Unbreakable distributed storage with quantum key distribution network and password-authenticated secret sharing.

PubMed

Fujiwara, M; Waseda, A; Nojima, R; Moriai, S; Ogata, W; Sasaki, M

2016-07-01

Distributed storage plays an essential role in realizing robust and secure data storage in a network over long periods of time. A distributed storage system consists of a data owner machine, multiple storage servers and channels to link them. In such a system, secret sharing scheme is widely adopted, in which secret data are split into multiple pieces and stored in each server. To reconstruct them, the data owner should gather plural pieces. Shamir's (k, n)-threshold scheme, in which the data are split into n pieces (shares) for storage and at least k pieces of them must be gathered for reconstruction, furnishes information theoretic security, that is, even if attackers could collect shares of less than the threshold k, they cannot get any information about the data, even with unlimited computing power. Behind this scenario, however, assumed is that data transmission and authentication must be perfectly secure, which is not trivial in practice. Here we propose a totally information theoretically secure distributed storage system based on a user-friendly single-password-authenticated secret sharing scheme and secure transmission using quantum key distribution, and demonstrate it in the Tokyo metropolitan area (≤90 km).

Category representations in the brain are both discretely localized and widely distributed.

PubMed

Shehzad, Zarrar; McCarthy, Gregory

2018-06-01

Whether category information is discretely localized or represented widely in the brain remains a contentious issue. Initial functional MRI studies supported the localizationist perspective that category information is represented in discrete brain regions. More recent fMRI studies using machine learning pattern classification techniques provide evidence for widespread distributed representations. However, these latter studies have not typically accounted for shared information. Here, we find strong support for distributed representations when brain regions are considered separately. However, localized representations are revealed by using analytical methods that separate unique from shared information among brain regions. The distributed nature of shared information and the localized nature of unique information suggest that brain connectivity may encourage spreading of information but category-specific computations are carried out in distinct domain-specific regions. NEW & NOTEWORTHY Whether visual category information is localized in unique domain-specific brain regions or distributed in many domain-general brain regions is hotly contested. We resolve this debate by using multivariate analyses to parse functional MRI signals from different brain regions into unique and shared variance. Our findings support elements of both models and show information is initially localized and then shared among other regions leading to distributed representations being observed.

Space Physics Data Facility Web Services

NASA Technical Reports Server (NTRS)

Candey, Robert M.; Harris, Bernard T.; Chimiak, Reine A.

2005-01-01

The Space Physics Data Facility (SPDF) Web services provides a distributed programming interface to a portion of the SPDF software. (A general description of Web services is available at http://www.w3.org/ and in many current software-engineering texts and articles focused on distributed programming.) The SPDF Web services distributed programming interface enables additional collaboration and integration of the SPDF software system with other software systems, in furtherance of the SPDF mission to lead collaborative efforts in the collection and utilization of space physics data and mathematical models. This programming interface conforms to all applicable Web services specifications of the World Wide Web Consortium. The interface is specified by a Web Services Description Language (WSDL) file. The SPDF Web services software consists of the following components: 1) A server program for implementation of the Web services; and 2) A software developer s kit that consists of a WSDL file, a less formal description of the interface, a Java class library (which further eases development of Java-based client software), and Java source code for an example client program that illustrates the use of the interface.

48 CFR 227.7205 - Contracts for special works.

Code of Federal Regulations, 2014 CFR

2014-10-01

... Computer Software and Computer Software Documentation 227.7205 Contracts for special works. (a) Use the... a specific need to control the distribution of computer software or computer software documentation..., modification, reproduction, release, performance, display, or disclosure of such software or documentation. Use...

48 CFR 227.7205 - Contracts for special works.

Code of Federal Regulations, 2010 CFR

2010-10-01

... Computer Software and Computer Software Documentation 227.7205 Contracts for special works. (a) Use the... a specific need to control the distribution of computer software or computer software documentation..., modification, reproduction, release, performance, display, or disclosure of such software or documentation. Use...

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.

Complexity and Safety (FAA)

DTIC Science & Technology

2016-10-27

Software Engineering Institute Carnegie Mellon University Pittsburgh, PA 15213 © 2016 Carnegie Mellon University [DISTRIBUTION STATEMENT A: This... Carnegie Mellon University [DISTRIBUTION STATEMENT A: This material has been approved for public release and unlimited distribution] Copyright 2016 Carnegie ... Carnegie Mellon University for the operation of the Software Engineering Institute, a federally funded research and development center sponsored by

Computer-Based Patient Records: Better Planning and Oversight by VA, DOD, and IHS Would Enhance Health Data Sharing

DTIC Science & Technology

2001-04-01

IHS), could share information technology (IT) and patient medical information to provide greater continuity of care, accelerate VA eligibility... patient medical information to provide greater continuity of care, accelerate VA eligibility determinations, and save software development costs.1 In...system, which primarily includes information on patient hospital admission and discharge, patient medications , laboratory results, and radiology

Vehicle-to-Grid Automatic Load Sharing with Driver Preference in Micro-Grids

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

Wang, Yubo; Nazaripouya, Hamidreza; Chu, Chi-Cheng

Integration of Electrical Vehicles (EVs) with power grid not only brings new challenges for load management, but also opportunities for distributed storage and generation. This paper comprehensively models and analyzes distributed Vehicle-to-Grid (V2G) for automatic load sharing with driver preference. In a micro-grid with limited communications, V2G EVs need to decide load sharing based on their own power and voltage profile. A droop based controller taking into account driver preference is proposed in this paper to address the distributed control of EVs. Simulations are designed for three fundamental V2G automatic load sharing scenarios that include all system dynamics of suchmore » applications. Simulation results demonstrate that active power sharing is achieved proportionally among V2G EVs with consideration of driver preference. In additional, the results also verify the system stability and reactive power sharing analysis in system modelling, which sheds light on large scale V2G automatic load sharing in more complicated cases.« less

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.

SPICE Module for the Satellite Orbit Analysis Program (SOAP)

NASA Technical Reports Server (NTRS)

Coggi, John; Carnright, Robert; Hildebrand, Claude

2008-01-01

A SPICE module for the Satellite Orbit Analysis Program (SOAP) precisely represents complex motion and maneuvers in an interactive, 3D animated environment with support for user-defined quantitative outputs. (SPICE stands for Spacecraft, Planet, Instrument, Camera-matrix, and Events). This module enables the SOAP software to exploit NASA mission ephemeris represented in the JPL Ancillary Information Facility (NAIF) SPICE formats. Ephemeris types supported include position, velocity, and orientation for spacecraft and planetary bodies including the Sun, planets, natural satellites, comets, and asteroids. Entire missions can now be imported into SOAP for 3D visualization, playback, and analysis. The SOAP analysis and display features can now leverage detailed mission files to offer the analyst both a numerically correct and aesthetically pleasing combination of results that can be varied to study many hypothetical scenarios. The software provides a modeling and simulation environment that can encompass a broad variety of problems using orbital prediction. For example, ground coverage analysis, communications analysis, power and thermal analysis, and 3D visualization that provide the user with insight into complex geometric relations are included. The SOAP SPICE module allows distributed science and engineering teams to share common mission models of known pedigree, which greatly reduces duplication of effort and the potential for error. The use of the software spans all phases of the space system lifecycle, from the study of future concepts to operations and anomaly analysis. It allows SOAP software to correctly position and orient all of the principal bodies of the Solar System within a single simulation session along with multiple spacecraft trajectories and the orientation of mission payloads. In addition to the 3D visualization, the user can define numeric variables and x-y plots to quantitatively assess metrics of interest.

Program Management Tool

NASA Technical Reports Server (NTRS)

Gawadiak, Yuri; Wong, Alan; Maluf, David; Bell, David; Gurram, Mohana; Tran, Khai Peter; Hsu, Jennifer; Yagi, Kenji; Patel, Hemil

2007-01-01

The Program Management Tool (PMT) is a comprehensive, Web-enabled business intelligence software tool for assisting program and project managers within NASA enterprises in gathering, comprehending, and disseminating information on the progress of their programs and projects. The PMT provides planning and management support for implementing NASA programmatic and project management processes and requirements. It provides an online environment for program and line management to develop, communicate, and manage their programs, projects, and tasks in a comprehensive tool suite. The information managed by use of the PMT can include monthly reports as well as data on goals, deliverables, milestones, business processes, personnel, task plans, monthly reports, and budgetary allocations. The PMT provides an intuitive and enhanced Web interface to automate the tedious process of gathering and sharing monthly progress reports, task plans, financial data, and other information on project resources based on technical, schedule, budget, and management criteria and merits. The PMT is consistent with the latest Web standards and software practices, including the use of Extensible Markup Language (XML) for exchanging data and the WebDAV (Web Distributed Authoring and Versioning) protocol for collaborative management of documents. The PMT provides graphical displays of resource allocations in the form of bar and pie charts using Microsoft Excel Visual Basic for Application (VBA) libraries. The PMT has an extensible architecture that enables integration of PMT with other strategic-information software systems, including, for example, the Erasmus reporting system, now part of the NASA Integrated Enterprise Management Program (IEMP) tool suite, at NASA Marshall Space Flight Center (MSFC). The PMT data architecture provides automated and extensive software interfaces and reports to various strategic information systems to eliminate duplicative human entries and minimize data integrity issues among various NASA systems that impact schedules and planning.

Software design and code generation for the engineering graphical user interface of the ASTRI SST-2M prototype for the Cherenkov Telescope Array

NASA Astrophysics Data System (ADS)

Tanci, Claudio; Tosti, Gino; Antolini, Elisa; Gambini, Giorgio F.; Bruno, Pietro; Canestrari, Rodolfo; Conforti, Vito; Lombardi, Saverio; Russo, Federico; Sangiorgi, Pierluca; Scuderi, Salvatore

2016-08-01

ASTRI is an on-going project developed in the framework of the Cherenkov Telescope Array (CTA). An end- to-end prototype of a dual-mirror small-size telescope (SST-2M) has been installed at the INAF observing station on Mt. Etna, Italy. The next step is the development of the ASTRI mini-array composed of nine ASTRI SST-2M telescopes proposed to be installed at the CTA southern site. The ASTRI mini-array is a collaborative and international effort carried on by Italy, Brazil and South-Africa and led by the Italian National Institute of Astrophysics, INAF. To control the ASTRI telescopes, a specific ASTRI Mini-Array Software System (MASS) was designed using a scalable and distributed architecture to monitor all the hardware devices for the telescopes. Using code generation we built automatically from the ASTRI Interface Control Documents a set of communication libraries and extensive Graphical User Interfaces that provide full access to the capabilities offered by the telescope hardware subsystems for testing and maintenance. Leveraging these generated libraries and components we then implemented a human designed, integrated, Engineering GUI for MASS to perform the verification of the whole prototype and test shared services such as the alarms, configurations, control systems, and scientific on-line outcomes. In our experience the use of code generation dramatically reduced the amount of effort in development, integration and testing of the more basic software components and resulted in a fast software release life cycle. This approach could be valuable for the whole CTA project, characterized by a large diversity of hardware components.

A Probabilistic Software System Attribute Acceptance Paradigm for COTS Software Evaluation

NASA Technical Reports Server (NTRS)

Morris, A. Terry

2005-01-01

Standard software requirement formats are written from top-down perspectives only, that is, from an ideal notion of a client s needs. Despite the exactness of the standard format, software and system errors in designed systems have abounded. Bad and inadequate requirements have resulted in cost overruns, schedule slips and lost profitability. Commercial off-the-shelf (COTS) software components are even more troublesome than designed systems because they are often provided as is and subsequently delivered with unsubstantiated validation of described capabilities. For COTS software, there needs to be a way to express the client s software needs in a consistent and formal manner using software system attributes derived from software quality standards. Additionally, the format needs to be amenable to software evaluation processes that integrate observable evidence garnered from historical data. This paper presents a paradigm that effectively bridges the gap between what a client desires (top-down) and what has been demonstrated (bottom-up) for COTS software evaluation. The paradigm addresses the specification of needs before the software evaluation is performed and can be used to increase the shared understanding between clients and software evaluators about what is required and what is technically possible.

multiplierz v2.0: A Python-based ecosystem for shared access and analysis of native mass spectrometry data.

PubMed

Alexander, William M; Ficarro, Scott B; Adelmant, Guillaume; Marto, Jarrod A

2017-08-01

The continued evolution of modern mass spectrometry instrumentation and associated methods represents a critical component in efforts to decipher the molecular mechanisms which underlie normal physiology and understand how dysregulation of biological pathways contributes to human disease. The increasing scale of these experiments combined with the technological diversity of mass spectrometers presents several challenges for community-wide data access, analysis, and distribution. Here we detail a redesigned version of multiplierz, our Python software library which leverages our common application programming interface (mzAPI) for analysis and distribution of proteomic data. New features include support for a wider range of native mass spectrometry file types, interfaces to additional database search engines, compatibility with new reporting formats, and high-level tools to perform post-search proteomic analyses. A GUI desktop environment, mzDesktop, provides access to multiplierz functionality through a user friendly interface. multiplierz is available for download from: https://github.com/BlaisProteomics/multiplierz; and mzDesktop is available for download from: https://sourceforge.net/projects/multiplierz/. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Evaluating non-relational storage technology for HEP metadata and meta-data catalog

NASA Astrophysics Data System (ADS)

Grigorieva, M. A.; Golosova, M. V.; Gubin, M. Y.; Klimentov, A. A.; Osipova, V. V.; Ryabinkin, E. A.

2016-10-01

Large-scale scientific experiments produce vast volumes of data. These data are stored, processed and analyzed in a distributed computing environment. The life cycle of experiment is managed by specialized software like Distributed Data Management and Workload Management Systems. In order to be interpreted and mined, experimental data must be accompanied by auxiliary metadata, which are recorded at each data processing step. Metadata describes scientific data and represent scientific objects or results of scientific experiments, allowing them to be shared by various applications, to be recorded in databases or published via Web. Processing and analysis of constantly growing volume of auxiliary metadata is a challenging task, not simpler than the management and processing of experimental data itself. Furthermore, metadata sources are often loosely coupled and potentially may lead to an end-user inconsistency in combined information queries. To aggregate and synthesize a range of primary metadata sources, and enhance them with flexible schema-less addition of aggregated data, we are developing the Data Knowledge Base architecture serving as the intelligence behind GUIs and APIs.

A distributed cloud-based cyberinfrastructure framework for integrated bridge monitoring

NASA Astrophysics Data System (ADS)

Jeong, Seongwoon; Hou, Rui; Lynch, Jerome P.; Sohn, Hoon; Law, Kincho H.

2017-04-01

This paper describes a cloud-based cyberinfrastructure framework for the management of the diverse data involved in bridge monitoring. Bridge monitoring involves various hardware systems, software tools and laborious activities that include, for examples, a structural health monitoring (SHM), sensor network, engineering analysis programs and visual inspection. Very often, these monitoring systems, tools and activities are not coordinated, and the collected information are not shared. A well-designed integrated data management framework can support the effective use of the data and, thereby, enhance bridge management and maintenance operations. The cloud-based cyberinfrastructure framework presented herein is designed to manage not only sensor measurement data acquired from the SHM system, but also other relevant information, such as bridge engineering model and traffic videos, in an integrated manner. For the scalability and flexibility, cloud computing services and distributed database systems are employed. The information stored can be accessed through standard web interfaces. For demonstration, the cyberinfrastructure system is implemented for the monitoring of the bridges located along the I-275 Corridor in the state of Michigan.

A Parallel Rendering Algorithm for MIMD Architectures

NASA Technical Reports Server (NTRS)

Crockett, Thomas W.; Orloff, Tobias

1991-01-01

Applications such as animation and scientific visualization demand high performance rendering of complex three dimensional scenes. To deliver the necessary rendering rates, highly parallel hardware architectures are required. The challenge is then to design algorithms and software which effectively use the hardware parallelism. A rendering algorithm targeted to distributed memory MIMD architectures is described. For maximum performance, the algorithm exploits both object-level and pixel-level parallelism. The behavior of the algorithm is examined both analytically and experimentally. Its performance for large numbers of processors is found to be limited primarily by communication overheads. An experimental implementation for the Intel iPSC/860 shows increasing performance from 1 to 128 processors across a wide range of scene complexities. It is shown that minimal modifications to the algorithm will adapt it for use on shared memory architectures as well.

RPYFMM: Parallel adaptive fast multipole method for Rotne-Prager-Yamakawa tensor in biomolecular hydrodynamics simulations

NASA Astrophysics Data System (ADS)

Guan, W.; Cheng, X.; Huang, J.; Huber, G.; Li, W.; McCammon, J. A.; Zhang, B.

2018-06-01

RPYFMM is a software package for the efficient evaluation of the potential field governed by the Rotne-Prager-Yamakawa (RPY) tensor interactions in biomolecular hydrodynamics simulations. In our algorithm, the RPY tensor is decomposed as a linear combination of four Laplace interactions, each of which is evaluated using the adaptive fast multipole method (FMM) (Greengard and Rokhlin, 1997) where the exponential expansions are applied to diagonalize the multipole-to-local translation operators. RPYFMM offers a unified execution on both shared and distributed memory computers by leveraging the DASHMM library (DeBuhr et al., 2016, 2018). Preliminary numerical results show that the interactions for a molecular system of 15 million particles (beads) can be computed within one second on a Cray XC30 cluster using 12,288 cores, while achieving approximately 54% strong-scaling efficiency.

COSMIC: Software catalog 1991 edition diskette format

NASA Technical Reports Server (NTRS)

1991-01-01

The PC edition of the annual COSMIC Software contains descriptions of the over 1,200 computer programs available for use within the United States as of January 1, 1991. By using the PC version of the catalog, it is possible to conduct extensive searches of the software inventory for programs that meet specific criteria. Elements such as program keywords, hardware specifications, source code languages, and title acronyms can be used for the basis of such searches. After isolating those programs that might be of best interest to the user, it is then possible to either view at the monitor, or generate a hardcopy listing of all information on those packages. In addition to the program elements that the user can search on, information such as total program size, distribution media, and program price, as well as extensive abstracts on the program, are also available to the user at this time. Another useful feature of the catalog allows for the retention of programs that meet certain search criteria between individual sessions of using the catalog. This allows users to save the information on those programs that are of interest to them in different areas of application. They can then recall a specific collection of programs for information retrieval or further search reduction if desired. In addition, this version of the catalog is adaptable to a network/shared resource environment, allowing multiple users access to a single copy of the catalog database simultaneously.

Collecting, Visualising, Communicating and Modelling Geographic Data for the Sciences

NASA Astrophysics Data System (ADS)

Crooks, A.; Hudson-Smith, A.; Milton, R.; Smith, D.; Batty, M.; Neuhaus, F.

2009-12-01

New web technologies and task specific software packages and services are fundamentally changing the way we share, collect, visualise, communicate and distribute geographic information. Coupled with these new technologies is the emergence of rich fine scale and extensive geographical datasets of the built environment. Such technologies and data are providing opportunities for both the social and physical sciences that were unimaginable ten years ago. Within this paper we discus such change from our own experiences at the Centre of Advanced Spatial Analysis. Specifically, how it is now possible to harness the crowd to collect peoples’ opinions about topical events such as the current financial crisis, in real time and map the results, through the use of our GMapCreator software and the MapTube website. Furthermore, such tools allow for widespread dissemination and visualisation of geographic data to whoever has an internet connection. We will explore how one can use new datasets to visualise the city using our Virtual London model as an example. Within the model individual buildings are tagged with multiple attributes providing a lens to explore the urban structure offering a plethora of research applications. We then turn to how one can visualise and communicate such data through low cost software and virtual worlds such as Crysis and Second Life with a look into their potential for modelling and finally how we disseminated much of this information through weblogs (blogs) such as Digital Urban, GIS and Agent-based modelling and Urban Tick.

STARS 2.0: 2nd-generation open-source archiving and query software

NASA Astrophysics Data System (ADS)

Winegar, Tom

2008-07-01

The Subaru Telescope is in process of developing an open-source alternative to the 1st-generation software and databases (STARS 1) used for archiving and query. For STARS 2, we have chosen PHP and Python for scripting and MySQL as the database software. We have collected feedback from staff and observers, and used this feedback to significantly improve the design and functionality of our future archiving and query software. Archiving - We identified two weaknesses in 1st-generation STARS archiving software: a complex and inflexible table structure and uncoordinated system administration for our business model: taking pictures from the summit and archiving them in both Hawaii and Japan. We adopted a simplified and normalized table structure with passive keyword collection, and we are designing an archive-to-archive file transfer system that automatically reports real-time status and error conditions and permits error recovery. Query - We identified several weaknesses in 1st-generation STARS query software: inflexible query tools, poor sharing of calibration data, and no automatic file transfer mechanisms to observers. We are developing improved query tools and sharing of calibration data, and multi-protocol unassisted file transfer mechanisms for observers. In the process, we have redefined a 'query': from an invisible search result that can only transfer once in-house right now, with little status and error reporting and no error recovery - to a stored search result that can be monitored, transferred to different locations with multiple protocols, reporting status and error conditions and permitting recovery from errors.

Sharing data for public health research by members of an international online diabetes social network.

PubMed

Weitzman, Elissa R; Adida, Ben; Kelemen, Skyler; Mandl, Kenneth D

2011-04-27

Surveillance and response to diabetes may be accelerated through engaging online diabetes social networks (SNs) in consented research. We tested the willingness of an online diabetes community to share data for public health research by providing members with a privacy-preserving social networking software application for rapid temporal-geographic surveillance of glycemic control. SN-mediated collection of cross-sectional, member-reported data from an international online diabetes SN entered into a software application we made available in a "Facebook-like" environment to enable reporting, charting and optional sharing of recent hemoglobin A1c values through a geographic display. Self-enrollment by 17% (n = 1,136) of n = 6,500 active members representing 32 countries and 50 US states. Data were current with 83.1% of most recent A1c values reported obtained within the past 90 days. Sharing was high with 81.4% of users permitting data donation to the community display. 34.1% of users also displayed their A1cs on their SN profile page. Users selecting the most permissive sharing options had a lower average A1c (6.8%) than users not sharing with the community (7.1%, p = .038). 95% of users permitted re-contact. Unadjusted aggregate A1c reported by US users closely resembled aggregate 2007-2008 NHANES estimates (respectively, 6.9% and 6.9%, p = 0.85). Success within an early adopter community demonstrates that online SNs may comprise efficient platforms for bidirectional communication with and data acquisition from disease populations. Advancing this model for cohort and translational science and for use as a complementary surveillance approach will require understanding of inherent selection and publication (sharing) biases in the data and a technology model that supports autonomy, anonymity and privacy.

GIFT-Cloud: A data sharing and collaboration platform for medical imaging research.

PubMed

Doel, Tom; Shakir, Dzhoshkun I; Pratt, Rosalind; Aertsen, Michael; Moggridge, James; Bellon, Erwin; David, Anna L; Deprest, Jan; Vercauteren, Tom; Ourselin, Sébastien

2017-02-01

Clinical imaging data are essential for developing research software for computer-aided diagnosis, treatment planning and image-guided surgery, yet existing systems are poorly suited for data sharing between healthcare and academia: research systems rarely provide an integrated approach for data exchange with clinicians; hospital systems are focused towards clinical patient care with limited access for external researchers; and safe haven environments are not well suited to algorithm development. We have established GIFT-Cloud, a data and medical image sharing platform, to meet the needs of GIFT-Surg, an international research collaboration that is developing novel imaging methods for fetal surgery. GIFT-Cloud also has general applicability to other areas of imaging research. GIFT-Cloud builds upon well-established cross-platform technologies. The Server provides secure anonymised data storage, direct web-based data access and a REST API for integrating external software. The Uploader provides automated on-site anonymisation, encryption and data upload. Gateways provide a seamless process for uploading medical data from clinical systems to the research server. GIFT-Cloud has been implemented in a multi-centre study for fetal medicine research. We present a case study of placental segmentation for pre-operative surgical planning, showing how GIFT-Cloud underpins the research and integrates with the clinical workflow. GIFT-Cloud simplifies the transfer of imaging data from clinical to research institutions, facilitating the development and validation of medical research software and the sharing of results back to the clinical partners. GIFT-Cloud supports collaboration between multiple healthcare and research institutions while satisfying the demands of patient confidentiality, data security and data ownership. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

A Report of the Joint Development of a Prototype Communications Link to Share Nuclear Accident Dispersion and Dose Assessment Modeling Products Between JAERI/WSPEEDI and LLNL/NARAC

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

Sullivan, T J; Belles, R D; Ellis, J S

2001-05-01

In June of 1997, under an umbrella Memorandum of Understanding between the Japan Atomic Energy Research Institute (JAERI) and the U.S. Department of Energy (US/DOE) concerning matters of nuclear research and development, a Specific Memorandum of Agreement (SMA) entitled ''A Collaborative Programme of Development of a Prototype Communication Link to Share Atmospheric Dispersion and Dose Assessment Modelling Products'' was signed. This SMA formalized an informal collaborative exchange between the DOE's Lawrence Livermore National Laboratory (LLNL) Atmospheric Release Advisory Capability (ARAC) center and the Japan Atomic Energy Research Institute (JAERI) Worldwide System for Prediction of Environmental Emergency Dose Information (WSPEEDI). Themore » intended objective of this agreement was to explore various modes of information exchange, beyond facsimile transmission, which could provide for the quick exchange of information between two major nuclear emergency dose assessment and prediction national centers to provide consistency checks and data exchange before public release of their calculations. The extreme sensitivity of the general public to any nuclear accident information has been a strong motivation to seek peer preview prior to public release. Other intended objectives of this work are the development of an affordable/accessible system for distribution of prediction results to other countries having no prediction capabilities and utilization of the link for collaboration studies. To fulfill the objectives of this project JAERI and LLNL scientists determined to assess the evolving Internet and rapidly emerging communications application software. Our timing was a little early in 1997-1998 but nonetheless a few candidate software packages were found, evaluated and a selection was made for initial test and evaluation. Subsequently several new candidate software packages have arrived, albeit with limitations. This report outlines the ARAC and JAERI emergency response assessment systems, describes the prototype communications protocol system established and the tools evaluated in that process. Three real-time applications of the information exchange protocol and lessons learned are discussed and then some conclusions and future plans are presented.« less

Gencrypt: one-way cryptographic hashes to detect overlapping individuals across samples

PubMed Central

Turchin, Michael C.; Hirschhorn, Joel N.

2012-01-01

Summary: Meta-analysis across genome-wide association studies is a common approach for discovering genetic associations. However, in some meta-analysis efforts, individual-level data cannot be broadly shared by study investigators due to privacy and Institutional Review Board concerns. In such cases, researchers cannot confirm that each study represents a unique group of people, leading to potentially inflated test statistics and false positives. To resolve this problem, we created a software tool, Gencrypt, which utilizes a security protocol known as one-way cryptographic hashes to allow overlapping participants to be identified without sharing individual-level data. Availability: Gencrypt is freely available under the GNU general public license v3 at http://www.broadinstitute.org/software/gencrypt/ Contact: joelh@broadinstitute.org Supplementary information: Supplementary data are available at Bioinformatics online. PMID:22302573

Software Management for the NOνAExperiment

NASA Astrophysics Data System (ADS)

Davies, G. S.; Davies, J. P.; C Group; Rebel, B.; Sachdev, K.; Zirnstein, J.

2015-12-01

The NOvAsoftware (NOνASoft) is written in C++, and built on the Fermilab Computing Division's art framework that uses ROOT analysis software. NOνASoftmakes use of more than 50 external software packages, is developed by more than 50 developers and is used by more than 100 physicists from over 30 universities and laboratories in 3 continents. The software builds are handled by Fermilab's custom version of Software Release Tools (SRT), a UNIX based software management system for large, collaborative projects that is used by several experiments at Fermilab. The system provides software version control with SVN configured in a client-server mode and is based on the code originally developed by the BaBar collaboration. In this paper, we present efforts towards distributing the NOvA software via the CernVM File System distributed file system. We will also describe our recent work to use a CMake build system and Jenkins, the open source continuous integration system, for NOνASoft.

24 CFR 213.278 - Distribution of distributive share.

Code of Federal Regulations, 2010 CFR

2010-04-01

... AUTHORITIES COOPERATIVE HOUSING MORTGAGE INSURANCE Contract Rights and Obligations-Projects Cooperative... obligation of the Cooperative Management Housing Insurance Fund a share of the Participating Reserve Account... actuarial and accounting practice. ...

A Fault Oblivious Extreme-Scale Execution Environment

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

McKie, Jim

The FOX project, funded under the ASCR X-stack I program, developed systems software and runtime libraries for a new approach to the data and work distribution for massively parallel, fault oblivious application execution. Our work was motivated by the premise that exascale computing systems will provide a thousand-fold increase in parallelism and a proportional increase in failure rate relative to today’s machines. To deliver the capability of exascale hardware, the systems software must provide the infrastructure to support existing applications while simultaneously enabling efficient execution of new programming models that naturally express dynamic, adaptive, irregular computation; coupled simulations; and massivemore » data analysis in a highly unreliable hardware environment with billions of threads of execution. Our OS research has prototyped new methods to provide efficient resource sharing, synchronization, and protection in a many-core compute node. We have experimented with alternative task/dataflow programming models and shown scalability in some cases to hundreds of thousands of cores. Much of our software is in active development through open source projects. Concepts from FOX are being pursued in next generation exascale operating systems. Our OS work focused on adaptive, application tailored OS services optimized for multi → many core processors. We developed a new operating system NIX that supports role-based allocation of cores to processes which was released to open source. We contributed to the IBM FusedOS project, which promoted the concept of latency-optimized and throughput-optimized cores. We built a task queue library based on distributed, fault tolerant key-value store and identified scaling issues. A second fault tolerant task parallel library was developed, based on the Linda tuple space model, that used low level interconnect primitives for optimized communication. We designed fault tolerance mechanisms for task parallel computations employing work stealing for load balancing that scaled to the largest existing supercomputers. Finally, we implemented the Elastic Building Blocks runtime, a library to manage object-oriented distributed software components. To support the research, we won two INCITE awards for time on Intrepid (BG/P) and Mira (BG/Q). Much of our work has had impact in the OS and runtime community through the ASCR Exascale OS/R workshop and report, leading to the research agenda of the Exascale OS/R program. Our project was, however, also affected by attrition of multiple PIs. While the PIs continued to participate and offer guidance as time permitted, losing these key individuals was unfortunate both for the project and for the DOE HPC community.« less

Hardware-assisted software clock synchronization for homogeneous distributed systems

NASA Technical Reports Server (NTRS)

Ramanathan, P.; Kandlur, Dilip D.; Shin, Kang G.

1990-01-01

A clock synchronization scheme that strikes a balance between hardware and software solutions is proposed. The proposed is a software algorithm that uses minimal additional hardware to achieve reasonably tight synchronization. Unlike other software solutions, the guaranteed worst-case skews can be made insensitive to the maximum variation of message transit delay in the system. The scheme is particularly suitable for large partially connected distributed systems with topologies that support simple point-to-point broadcast algorithms. Examples of such topologies include the hypercube and the mesh interconnection structures.

26 CFR 13.10 - Distribution of money in lieu of fractional shares.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 26 Internal Revenue 14 2012-04-01 2012-04-01 false Distribution of money in lieu of fractional... Distribution of money in lieu of fractional shares. (a) In general. (1) Under the general rule of section 305... distribution is one) has the result of (i) the receipt of money or other property by some shareholders, and (ii...

26 CFR 13.10 - Distribution of money in lieu of fractional shares.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 26 Internal Revenue 14 2010-04-01 2010-04-01 false Distribution of money in lieu of fractional... Distribution of money in lieu of fractional shares. (a) In general. (1) Under the general rule of section 305... distribution is one) has the result of (i) the receipt of money or other property by some shareholders, and (ii...

Cyberinfrastructure to Support Collaborative and Reproducible Computational Hydrologic Modeling

NASA Astrophysics Data System (ADS)

Goodall, J. L.; Castronova, A. M.; Bandaragoda, C.; Morsy, M. M.; Sadler, J. M.; Essawy, B.; Tarboton, D. G.; Malik, T.; Nijssen, B.; Clark, M. P.; Liu, Y.; Wang, S. W.

2017-12-01

Creating cyberinfrastructure to support reproducibility of computational hydrologic models is an important research challenge. Addressing this challenge requires open and reusable code and data with machine and human readable metadata, organized in ways that allow others to replicate results and verify published findings. Specific digital objects that must be tracked for reproducible computational hydrologic modeling include (1) raw initial datasets, (2) data processing scripts used to clean and organize the data, (3) processed model inputs, (4) model results, and (5) the model code with an itemization of all software dependencies and computational requirements. HydroShare is a cyberinfrastructure under active development designed to help users store, share, and publish digital research products in order to improve reproducibility in computational hydrology, with an architecture supporting hydrologic-specific resource metadata. Researchers can upload data required for modeling, add hydrology-specific metadata to these resources, and use the data directly within HydroShare.org for collaborative modeling using tools like CyberGIS, Sciunit-CLI, and JupyterHub that have been integrated with HydroShare to run models using notebooks, Docker containers, and cloud resources. Current research aims to implement the Structure For Unifying Multiple Modeling Alternatives (SUMMA) hydrologic model within HydroShare to support hypothesis-driven hydrologic modeling while also taking advantage of the HydroShare cyberinfrastructure. The goal of this integration is to create the cyberinfrastructure that supports hypothesis-driven model experimentation, education, and training efforts by lowering barriers to entry, reducing the time spent on informatics technology and software development, and supporting collaborative research within and across research groups.

Software Hardware Asset Reuse Enterprise (SHARE) Repository Framework: Related Work and Development Plan

DTIC Science & Technology

2009-08-19

designed to collect the data and assist the analyst in drawing relationships between the data. Palantir Technologies has created one such software...application to support the DoD intelligence community by providing robust capabilities for managing data from various sources10. The Palantir tool...www.palantirtech.com/ - 38 - Figure 17. Palantir Graphical Interface (Gordon-Schlosberg, 2008) Similar examples of the use of ontologies to support data

An International Survey of Industrial Applications of Formal Methods. Volume 1: Purpose, Approach, Analysis, and Conclusions

DTIC Science & Technology

1993-09-30

97 Accesion For NTIS CRA&I DTIC TAB Unannounced 0 Justification ----- ---.......................... Ry Di. t ,:; t,.: 1...months of effort. The product was important for demonstrating to IBM management the potential of the Cleanroom methodology. 3.2.4 Software Architecture ...for Oscilloscopes Using Z (Tektronix) Tektronix in Beaverton, Oregon, used Z to develop a reusable software architecture to be shared among a number

CrossTalk: The Journal of Defense Software Engineering. Volume 22, Number 6, September/October 2009

DTIC Science & Technology

2009-10-01

software to improve the reliability, sustainability, and responsiveness of our warfighting capability. Subscriptions: Send correspondence concerning...endorsed by, the U.S. government, the DoD, the co-sponsors, or the STSC.All product names referenced in this issue are trademarks of their companies...Authors will use this section to share evidence of a demonstrative return on investment, process improvement , quality improvement , reductions to schedule

Evaluation of a deidentification (De-Id) software engine to share pathology reports and clinical documents for research.

PubMed

Gupta, Dilip; Saul, Melissa; Gilbertson, John

2004-02-01

We evaluated a comprehensive deidentification engine at the University of Pittsburgh Medical Center (UPMC), Pittsburgh, PA, that uses a complex set of rules, dictionaries, pattern-matching algorithms, and the Unified Medical Language System to identify and replace identifying text in clinical reports while preserving medical information for sharing in research. In our initial data set of 967 surgical pathology reports, the software did not suppress outside (103), UPMC (47), and non-UPMC (56) accession numbers; dates (7); names (9) or initials (25) of case pathologists; or hospital or laboratory names (46). In 150 reports, some clinical information was suppressed inadvertently (overmarking). The engine retained eponymic patient names, eg, Barrett and Gleason. In the second evaluation (1,000 reports), the software did not suppress outside (90) or UPMC (6) accession numbers or names (4) or initials (2) of case pathologists. In the third evaluation, the software removed names of patients, hospitals (297/300), pathologists (297/300), transcriptionists, residents and physicians, dates of procedures, and accession numbers (298/300). By the end of the evaluation, the system was reliably and specifically removing safe-harbor identifiers and producing highly readable deidentified text without removing important clinical information. Collaboration between pathology domain experts and system developers and continuous quality assurance are needed to optimize ongoing deidentification processes.

A Distributed Simulation Software System for Multi-Spacecraft Missions

NASA Technical Reports Server (NTRS)

Burns, Richard; Davis, George; Cary, Everett

2003-01-01

The paper will provide an overview of the web-based distributed simulation software system developed for end-to-end, multi-spacecraft mission design, analysis, and test at the NASA Goddard Space Flight Center (GSFC). This software system was developed for an internal research and development (IR&D) activity at GSFC called the Distributed Space Systems (DSS) Distributed Synthesis Environment (DSE). The long-term goal of the DSS-DSE is to integrate existing GSFC stand-alone test beds, models, and simulation systems to create a "hands on", end-to-end simulation environment for mission design, trade studies and simulations. The short-term goal of the DSE was therefore to develop the system architecture, and then to prototype the core software simulation capability based on a distributed computing approach, with demonstrations of some key capabilities by the end of Fiscal Year 2002 (FY02). To achieve the DSS-DSE IR&D objective, the team adopted a reference model and mission upon which FY02 capabilities were developed. The software was prototyped according to the reference model, and demonstrations were conducted for the reference mission to validate interfaces, concepts, etc. The reference model, illustrated in Fig. 1, included both space and ground elements, with functional capabilities such as spacecraft dynamics and control, science data collection, space-to-space and space-to-ground communications, mission operations, science operations, and data processing, archival and distribution addressed.

Remote control of an MR imaging study via tele-collaboration tools

NASA Astrophysics Data System (ADS)

Sullivan, John M., Jr.; Mullen, Julia S.; Benz, Udo A.; Schmidt, Karl F.; Murugavel, Murali; Chen, Wei; Ghadyani, Hamid

2005-04-01

In contrast to traditional 'video conferencing' the Access Grid (AG), developed by Argonne National Laboratory, is a collaboration of audio, video and shared application tools which provide the 'persistent presence' of each participant. Among the shared application tools are the ability to share viewing and control of presentations, browsers, images and movies. When used in conjunction with Virtual Network Computing (VNC) software, an investigator can interact with colleagues at a remote site, and control remote systems via local keyboard and mouse commands. This combination allows for effective viewing and discussion of information, i.e. data, images, and results. It is clear that such an approach when applied to the medical sciences will provide a means by which a team of experts can not only access, but interact and control medical devices for the purpose of experimentation, diagnosis, surgery and therapy. We present the development of an application node at our 4.7 Tesla MR magnet facility, and a demonstration of remote investigator control of the magnet. A local magnet operator performs manual tasks such as loading the test subject into the magnet and administering the stimulus associated with the functional MRI study. The remote investigator has complete control of the magnet console. S/he can adjust the gradient coil settings, the pulse sequence, image capture frequency, etc. A geographically distributed audience views and interacts with the remote investigator and local MR operator. This AG demonstration of MR magnet control illuminates the potential of untethered medical experiments, procedures and training.

General software design for multisensor data fusion

NASA Astrophysics Data System (ADS)

Zhang, Junliang; Zhao, Yuming

1999-03-01

In this paper a general method of software design for multisensor data fusion is discussed in detail, which adopts object-oriented technology under UNIX operation system. The software for multisensor data fusion is divided into six functional modules: data collection, database management, GIS, target display and alarming data simulation etc. Furthermore, the primary function, the components and some realization methods of each modular is given. The interfaces among these functional modular relations are discussed. The data exchange among each functional modular is performed by interprocess communication IPC, including message queue, semaphore and shared memory. Thus, each functional modular is executed independently, which reduces the dependence among functional modules and helps software programing and testing. This software for multisensor data fusion is designed as hierarchical structure by the inheritance character of classes. Each functional modular is abstracted and encapsulated through class structure, which avoids software redundancy and enhances readability.

PhysioNet: physiologic signals, time series and related open source software for basic, clinical, and applied research.

PubMed

Moody, George B; Mark, Roger G; Goldberger, Ary L

2011-01-01

PhysioNet provides free web access to over 50 collections of recorded physiologic signals and time series, and related open-source software, in support of basic, clinical, and applied research in medicine, physiology, public health, biomedical engineering and computing, and medical instrument design and evaluation. Its three components (PhysioBank, the archive of signals; PhysioToolkit, the software library; and PhysioNetWorks, the virtual laboratory for collaborative development of future PhysioBank data collections and PhysioToolkit software components) connect researchers and students who need physiologic signals and relevant software with researchers who have data and software to share. PhysioNet's annual open engineering challenges stimulate rapid progress on unsolved or poorly solved questions of basic or clinical interest, by focusing attention on achievable solutions that can be evaluated and compared objectively using freely available reference data.

Research and Design of the Three-tier Distributed Network Management System Based on COM / COM + and DNA

NASA Astrophysics Data System (ADS)

Liang, Likai; Bi, Yushen

Considered on the distributed network management system's demand of high distributives, extensibility and reusability, a framework model of Three-tier distributed network management system based on COM/COM+ and DNA is proposed, which adopts software component technology and N-tier application software framework design idea. We also give the concrete design plan of each layer of this model. Finally, we discuss the internal running process of each layer in the distributed network management system's framework model.

Design and implementation of a robot control system with traded and shared control capability

NASA Technical Reports Server (NTRS)

Hayati, S.; Venkataraman, S. T.

1989-01-01

Preliminary results are reported from efforts to design and develop a robotic system that will accept and execute commands from either a six-axis teleoperator device or an autonomous planner, or combine the two. Such a system should have both traded as well as shared control capability. A sharing strategy is presented whereby the overall system, while retaining positive features of teleoperated and autonomous operation, loses its individual negative features. A two-tiered shared control architecture is considered here, consisting of a task level and a servo level. Also presented is a computer architecture for the implementation of this system, including a description of the hardware and software.

A Legal Guide for the Software Developer.

ERIC Educational Resources Information Center

Minnesota Small Business Assistance Office, St. Paul.

This booklet has been prepared to familiarize the inventor, creator, or developer of a new computer software product or software invention with the basic legal issues involved in developing, protecting, and distributing the software in the United States. Basic types of software protection and related legal matters are discussed in detail,…

21 CFR 801.50 - Labeling requirements for stand-alone software.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Labeling requirements for stand-alone software....50 Labeling requirements for stand-alone software. (a) Stand-alone software that is not distributed... in packaged form, stand-alone software regulated as a medical device must provide its unique device...

Toward Baseline Software Anomalies in NASA Missions

NASA Technical Reports Server (NTRS)

Layman, Lucas; Zelkowitz, Marvin; Basili, Victor; Nikora, Allen P.

2012-01-01

In this fast abstract, we provide preliminary findings an analysis of 14,500 spacecraft anomalies from unmanned NASA missions. We provide some baselines for the distributions of software vs. non-software anomalies in spaceflight systems, the risk ratings of software anomalies, and the corrective actions associated with software anomalies.

Development of climate data storage and processing model

NASA Astrophysics Data System (ADS)

Okladnikov, I. G.; Gordov, E. P.; Titov, A. G.

2016-11-01

We present a storage and processing model for climate datasets elaborated in the framework of a virtual research environment (VRE) for climate and environmental monitoring and analysis of the impact of climate change on the socio-economic processes on local and regional scales. The model is based on a «shared nothings» distributed computing architecture and assumes using a computing network where each computing node is independent and selfsufficient. Each node holds a dedicated software for the processing and visualization of geospatial data providing programming interfaces to communicate with the other nodes. The nodes are interconnected by a local network or the Internet and exchange data and control instructions via SSH connections and web services. Geospatial data is represented by collections of netCDF files stored in a hierarchy of directories in the framework of a file system. To speed up data reading and processing, three approaches are proposed: a precalculation of intermediate products, a distribution of data across multiple storage systems (with or without redundancy), and caching and reuse of the previously obtained products. For a fast search and retrieval of the required data, according to the data storage and processing model, a metadata database is developed. It contains descriptions of the space-time features of the datasets available for processing, their locations, as well as descriptions and run options of the software components for data analysis and visualization. The model and the metadata database together will provide a reliable technological basis for development of a high- performance virtual research environment for climatic and environmental monitoring.

Scheduling for Locality in Shared-Memory Multiprocessors

DTIC Science & Technology

1993-05-01

Submitted in Partial Fulfillment of the Requirements for the Degree ’)iIC Q(JALfryT INSPECTED 5 DOCTOR OF PHILOSOPHY I Accesion For Supervised by NTIS CRAM... architecture on parallel program performance, explain the implications of this trend on popular parallel programming models, and propose system software to 0...decomoosition and scheduling algorithms. I. SUIUECT TERMS IS. NUMBER OF PAGES shared-memory multiprocessors; architecture trends; loop 110 scheduling

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

DTIC Science & Technology

2008-03-01

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

The A-7E Software Requirements Document: Three Years of Change Data.

DTIC Science & Technology

1982-11-08

Washington DC: Naval Research Laboratory. 1982. Interface Specifications for the A-7E Shared Services Module NRL Memorandum Report. Forthcoming...function driver module (Clements 1981), specifications for the extended computer module (Britton et al. 1982), and specifications for the shared ... services module (Clements 1982). The projected completion date for the SCR project is September 1985. As of the end of 1981, approximately 10 man-years of

Next generation tools for genomic data generation, distribution, and visualization

PubMed Central

2010-01-01

Background With the rapidly falling cost and availability of high throughput sequencing and microarray technologies, the bottleneck for effectively using genomic analysis in the laboratory and clinic is shifting to one of effectively managing, analyzing, and sharing genomic data. Results Here we present three open-source, platform independent, software tools for generating, analyzing, distributing, and visualizing genomic data. These include a next generation sequencing/microarray LIMS and analysis project center (GNomEx); an application for annotating and programmatically distributing genomic data using the community vetted DAS/2 data exchange protocol (GenoPub); and a standalone Java Swing application (GWrap) that makes cutting edge command line analysis tools available to those who prefer graphical user interfaces. Both GNomEx and GenoPub use the rich client Flex/Flash web browser interface to interact with Java classes and a relational database on a remote server. Both employ a public-private user-group security model enabling controlled distribution of patient and unpublished data alongside public resources. As such, they function as genomic data repositories that can be accessed manually or programmatically through DAS/2-enabled client applications such as the Integrated Genome Browser. Conclusions These tools have gained wide use in our core facilities, research laboratories and clinics and are freely available for non-profit use. See http://sourceforge.net/projects/gnomex/, http://sourceforge.net/projects/genoviz/, and http://sourceforge.net/projects/useq. PMID:20828407

Multi-party semi-quantum key distribution-convertible multi-party semi-quantum secret sharing

NASA Astrophysics Data System (ADS)

Yu, Kun-Fei; Gu, Jun; Hwang, Tzonelih; Gope, Prosanta

2017-08-01

This paper proposes a multi-party semi-quantum secret sharing (MSQSS) protocol which allows a quantum party (manager) to share a secret among several classical parties (agents) based on GHZ-like states. By utilizing the special properties of GHZ-like states, the proposed scheme can easily detect outside eavesdropping attacks and has the highest qubit efficiency among the existing MSQSS protocols. Then, we illustrate an efficient way to convert the proposed MSQSS protocol into a multi-party semi-quantum key distribution (MSQKD) protocol. The proposed approach is even useful to convert all the existing measure-resend type of semi-quantum secret sharing protocols into semi-quantum key distribution protocols.

Managing Written Directives: A Software Solution to Streamline Workflow.

PubMed

Wagner, Robert H; Savir-Baruch, Bital; Gabriel, Medhat S; Halama, James R; Bova, Davide

2017-06-01

A written directive is required by the U.S. Nuclear Regulatory Commission for any use of 131 I above 1.11 MBq (30 μCi) and for patients receiving radiopharmaceutical therapy. This requirement has also been adopted and must be enforced by the agreement states. As the introduction of new radiopharmaceuticals increases therapeutic options in nuclear medicine, time spent on regulatory paperwork also increases. The pressure of managing these time-consuming regulatory requirements may heighten the potential for inaccurate or incomplete directive data and subsequent regulatory violations. To improve on the paper-trail method of directive management, we created a software tool using a Health Insurance Portability and Accountability Act (HIPAA)-compliant database. This software allows for secure data-sharing among physicians, technologists, and managers while saving time, reducing errors, and eliminating the possibility of loss and duplication. Methods: The software tool was developed using Visual Basic, which is part of the Visual Studio development environment for the Windows platform. Patient data are deposited in an Access database on a local HIPAA-compliant secure server or hard disk. Once a working version had been developed, it was installed at our institution and used to manage directives. Updates and modifications of the software were released regularly until no more significant problems were found with its operation. Results: The software has been used at our institution for over 2 y and has reliably kept track of all directives. All physicians and technologists use the software daily and find it superior to paper directives. They can retrieve active directives at any stage of completion, as well as completed directives. Conclusion: We have developed a software solution for the management of written directives that streamlines and structures the departmental workflow. This solution saves time, centralizes the information for all staff to share, and decreases confusion about the creation, completion, filing, and retrieval of directives. © 2017 by the Society of Nuclear Medicine and Molecular Imaging.

Open Technology Approaches to Geospatial Interface Design

NASA Astrophysics Data System (ADS)

Crevensten, B.; Simmons, D.; Alaska Satellite Facility

2011-12-01

What problems do you not want your software developers to be solving? Choosing open technologies across the entire stack of software development-from low-level shared libraries to high-level user interaction implementations-is a way to help ensure that customized software yields innovative and valuable tools for Earth Scientists. This demonstration will review developments in web application technologies and the recurring patterns of interaction design regarding exploration and discovery of geospatial data through the Vertex: ASF's Dataportal interface, a project utilizing current open web application standards and technologies including HTML5, jQueryUI, Backbone.js and the Jasmine unit testing framework.

Behavior driven testing in ALMA telescope calibration software

NASA Astrophysics Data System (ADS)

Gil, Juan P.; Garces, Mario; Broguiere, Dominique; Shen, Tzu-Chiang

2016-07-01

ALMA software development cycle includes well defined testing stages that involves developers, testers and scientists. We adapted Behavior Driven Development (BDD) to testing activities applied to Telescope Calibration (TELCAL) software. BDD is an agile technique that encourages communication between roles by defining test cases using natural language to specify features and scenarios, what allows participants to share a common language and provides a high level set of automated tests. This work describes how we implemented and maintain BDD testing for TELCAL, the infrastructure needed to support it and proposals to expand this technique to other subsystems.

Concierge: Personal Database Software for Managing Digital Research Resources

PubMed Central

Sakai, Hiroyuki; Aoyama, Toshihiro; Yamaji, Kazutsuna; Usui, Shiro

2007-01-01

This article introduces a desktop application, named Concierge, for managing personal digital research resources. Using simple operations, it enables storage of various types of files and indexes them based on content descriptions. A key feature of the software is a high level of extensibility. By installing optional plug-ins, users can customize and extend the usability of the software based on their needs. In this paper, we also introduce a few optional plug-ins: literature management, electronic laboratory notebook, and XooNlps client plug-ins. XooNIps is a content management system developed to share digital research resources among neuroscience communities. It has been adopted as the standard database system in Japanese neuroinformatics projects. Concierge, therefore, offers comprehensive support from management of personal digital research resources to their sharing in open-access neuroinformatics databases such as XooNIps. This interaction between personal and open-access neuroinformatics databases is expected to enhance the dissemination of digital research resources. Concierge is developed as an open source project; Mac OS X and Windows XP versions have been released at the official site (http://concierge.sourceforge.jp). PMID:18974800

Technology collaboration by means of an open source government

NASA Astrophysics Data System (ADS)

Berardi, Steven M.

2009-05-01

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

Software Reliability 2002

NASA Technical Reports Server (NTRS)

Wallace, Dolores R.

2003-01-01

In FY01 we learned that hardware reliability models need substantial changes to account for differences in software, thus making software reliability measurements more effective, accurate, and easier to apply. These reliability models are generally based on familiar distributions or parametric methods. An obvious question is 'What new statistical and probability models can be developed using non-parametric and distribution-free methods instead of the traditional parametric method?" Two approaches to software reliability engineering appear somewhat promising. The first study, begin in FY01, is based in hardware reliability, a very well established science that has many aspects that can be applied to software. This research effort has investigated mathematical aspects of hardware reliability and has identified those applicable to software. Currently the research effort is applying and testing these approaches to software reliability measurement, These parametric models require much project data that may be difficult to apply and interpret. Projects at GSFC are often complex in both technology and schedules. Assessing and estimating reliability of the final system is extremely difficult when various subsystems are tested and completed long before others. Parametric and distribution free techniques may offer a new and accurate way of modeling failure time and other project data to provide earlier and more accurate estimates of system reliability.

Center-to-center : local self-evaluation report

DOT National Transportation Integrated Search

2003-04-01

Texas Department of Transportation implemented a software system to facilitate sharing of traffic management related information and control of Intelligent Transportation System field devices between Traffic Management Centers with heterogeneous Adva...