Developing an Open Source Option for NASA Software

NASA Technical Reports Server (NTRS)

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

2003-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2015-04-01

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

Exploring the Role of Value Networks for Software Innovation

NASA Astrophysics Data System (ADS)

Morgan, Lorraine; Conboy, Kieran

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

The 2016 Bioinformatics Open Source Conference (BOSC)

PubMed Central

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

2016-01-01

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

The GenABEL Project for statistical genomics.

PubMed

Karssen, Lennart C; van Duijn, Cornelia M; Aulchenko, Yurii S

2016-01-01

Development of free/libre open source software is usually done by a community of people with an interest in the tool. For scientific software, however, this is less often the case. Most scientific software is written by only a few authors, often a student working on a thesis. Once the paper describing the tool has been published, the tool is no longer developed further and is left to its own device. Here we describe the broad, multidisciplinary community we formed around a set of tools for statistical genomics. The GenABEL project for statistical omics actively promotes open interdisciplinary development of statistical methodology and its implementation in efficient and user-friendly software under an open source licence. The software tools developed withing the project collectively make up the GenABEL suite, which currently consists of eleven tools. The open framework of the project actively encourages involvement of the community in all stages, from formulation of methodological ideas to application of software to specific data sets. A web forum is used to channel user questions and discussions, further promoting the use of the GenABEL suite. Developer discussions take place on a dedicated mailing list, and development is further supported by robust development practices including use of public version control, code review and continuous integration. Use of this open science model attracts contributions from users and developers outside the "core team", facilitating agile statistical omics methodology development and fast dissemination.

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

None

An OpenStudio Measure is a script that can manipulate an OpenStudio model and associated data to apply energy conservation measures (ECMs), run supplemental simulations, or visualize simulation results. The OpenStudio software development kit (SDK) and accessibility of the Ruby scripting language makes measure authorship accessible to both software developers and energy modelers. This paper discusses the life cycle of an OpenStudio Measure from development, testing, and distribution, to application.

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

PubMed

Busby, Ben; Lesko, Matthew; Federer, Lisa

2016-01-01

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

Open Drug Discovery Toolkit (ODDT): a new open-source player in the drug discovery field.

PubMed

Wójcikowski, Maciej; Zielenkiewicz, Piotr; Siedlecki, Pawel

2015-01-01

There has been huge progress in the open cheminformatics field in both methods and software development. Unfortunately, there has been little effort to unite those methods and software into one package. We here describe the Open Drug Discovery Toolkit (ODDT), which aims to fulfill the need for comprehensive and open source drug discovery software. The Open Drug Discovery Toolkit was developed as a free and open source tool for both computer aided drug discovery (CADD) developers and researchers. ODDT reimplements many state-of-the-art methods, such as machine learning scoring functions (RF-Score and NNScore) and wraps other external software to ease the process of developing CADD pipelines. ODDT is an out-of-the-box solution designed to be easily customizable and extensible. Therefore, users are strongly encouraged to extend it and develop new methods. We here present three use cases for ODDT in common tasks in computer-aided drug discovery. Open Drug Discovery Toolkit is released on a permissive 3-clause BSD license for both academic and industrial use. ODDT's source code, additional examples and documentation are available on GitHub (https://github.com/oddt/oddt).

Open Source Molecular Modeling

PubMed Central

Pirhadi, Somayeh; Sunseri, Jocelyn; Koes, David Ryan

2016-01-01

The success of molecular modeling and computational chemistry efforts are, by definition, dependent on quality software applications. Open source software development provides many advantages to users of modeling applications, not the least of which is that the software is free and completely extendable. In this review we categorize, enumerate, and describe available open source software packages for molecular modeling and computational chemistry. PMID:27631126

Evaluation of software maintain ability with open EHR - a comparison of architectures.

PubMed

Atalag, Koray; Yang, Hong Yul; Tempero, Ewan; Warren, James R

2014-11-01

To assess whether it is easier to maintain a clinical information system developed using open EHR model driven development versus mainstream methods. A new open source application (GastrOS) has been developed following open EHR's multi-level modelling approach using .Net/C# based on the same requirements of an existing clinically used application developed using Microsoft Visual Basic and Access database. Almost all the domain knowledge was embedded into the software code and data model in the latter. The same domain knowledge has been expressed as a set of open EHR Archetypes in GastrOS. We then introduced eight real-world change requests that had accumulated during live clinical usage, and implemented these in both systems while measuring time for various development tasks and change in software size for each change request. Overall it took half the time to implement changes in GastrOS. However it was the more difficult application to modify for one change request, suggesting the nature of change is also important. It was not possible to implement changes by modelling only. Comparison of relative measures of time and software size change within each application highlights how architectural differences affected maintain ability across change requests. The use of open EHR model driven development can result in better software maintain ability. The degree to which open EHR affects software maintain ability depends on the extent and nature of domain knowledge involved in changes. Although we used relative measures for time and software size, confounding factors could not be totally excluded as a controlled study design was not feasible. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Open source software integrated into data services of Japanese planetary explorations

NASA Astrophysics Data System (ADS)

Yamamoto, Y.; Ishihara, Y.; Otake, H.; Imai, K.; Masuda, K.

2015-12-01

Scientific data obtained by Japanese scientific satellites and lunar and planetary explorations are archived in DARTS (Data ARchives and Transmission System). DARTS provides the data with a simple method such as HTTP directory listing for long-term preservation while DARTS tries to provide rich web applications for ease of access with modern web technologies based on open source software. This presentation showcases availability of open source software through our services. KADIAS is a web-based application to search, analyze, and obtain scientific data measured by SELENE(Kaguya), a Japanese lunar orbiter. KADIAS uses OpenLayers to display maps distributed from Web Map Service (WMS). As a WMS server, open source software MapServer is adopted. KAGUYA 3D GIS (KAGUYA 3D Moon NAVI) provides a virtual globe for the SELENE's data. The main purpose of this application is public outreach. NASA World Wind Java SDK is used to develop. C3 (Cross-Cutting Comparisons) is a tool to compare data from various observations and simulations. It uses Highcharts to draw graphs on web browsers. Flow is a tool to simulate a Field-Of-View of an instrument onboard a spacecraft. This tool itself is open source software developed by JAXA/ISAS, and the license is BSD 3-Caluse License. SPICE Toolkit is essential to compile FLOW. SPICE Toolkit is also open source software developed by NASA/JPL, and the website distributes many spacecrafts' data. Nowadays, open source software is an indispensable tool to integrate DARTS services.

Open-source software: not quite endsville.

PubMed

Stahl, Matthew T

2005-02-01

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

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

ERIC Educational Resources Information Center

Hirst, Tony

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

Introducing the CUAHSI Hydrologic Information System Desktop Application (HydroDesktop) and Open Development Community

NASA Astrophysics Data System (ADS)

Ames, D.; Kadlec, J.; Horsburgh, J. S.; Maidment, D. R.

2009-12-01

The Consortium of Universities for the Advancement of Hydrologic Sciences (CUAHSI) Hydrologic Information System (HIS) project includes extensive development of data storage and delivery tools and standards including WaterML (a language for sharing hydrologic data sets via web services); and HIS Server (a software tool set for delivering WaterML from a server); These and other CUASHI HIS tools have been under development and deployment for several years and together, present a relatively complete software “stack” to support the consistent storage and delivery of hydrologic and other environmental observation data. This presentation describes the development of a new HIS software tool called “HydroDesktop” and the development of an online open source software development community to update and maintain the software. HydroDesktop is a local (i.e. not server-based) client side software tool that ultimately will run on multiple operating systems and will provide a highly usable level of access to HIS services. The software provides many key capabilities including data query, map-based visualization, data download, local data maintenance, editing, graphing, data export to selected model-specific data formats, linkage with integrated modeling systems such as OpenMI, and ultimately upload to HIS servers from the local desktop software. As the software is presently in the early stages of development, this presentation will focus on design approach and paradigm and is viewed as an opportunity to encourage participation in the open development community. Indeed, recognizing the value of community based code development as a means of ensuring end-user adoption, this project has adopted an “iterative” or “spiral” software development approach which will be described in this presentation.

Expanding Human Capabilities through the Adoption and Utilization of Free, Libre, and Open Source Software

ERIC Educational Resources Information Center

Simpson, James Daniel

2014-01-01

Free, libre, and open source software (FLOSS) is software that is collaboratively developed. FLOSS provides end-users with the source code and the freedom to adapt or modify a piece of software to fit their needs (Deek & McHugh, 2008; Stallman, 2010). FLOSS has a 30 year history that dates to the open hacker community at the Massachusetts…

Maintaining Quality and Confidence in Open-Source, Evolving Software: Lessons Learned with PFLOTRAN

NASA Astrophysics Data System (ADS)

Frederick, J. M.; Hammond, G. E.

2017-12-01

Software evolution in an open-source framework poses a major challenge to a geoscientific simulator, but when properly managed, the pay-off can be enormous for both the developers and the community at large. Developers must juggle implementing new scientific process models, adopting increasingly efficient numerical methods and programming paradigms, changing funding sources (or total lack of funding), while also ensuring that legacy code remains functional and reported bugs are fixed in a timely manner. With robust software engineering and a plan for long-term maintenance, a simulator can evolve over time incorporating and leveraging many advances in the computational and domain sciences. In this positive light, what practices in software engineering and code maintenance can be employed within open-source development to maximize the positive aspects of software evolution and community contributions while minimizing its negative side effects? This presentation will discusses steps taken in the development of PFLOTRAN (www.pflotran.org), an open source, massively parallel subsurface simulator for multiphase, multicomponent, and multiscale reactive flow and transport processes in porous media. As PFLOTRAN's user base and development team continues to grow, it has become increasingly important to implement strategies which ensure sustainable software development while maintaining software quality and community confidence. In this presentation, we will share our experiences and "lessons learned" within the context of our open-source development framework and community engagement efforts. Topics discussed will include how we've leveraged both standard software engineering principles, such as coding standards, version control, and automated testing, as well unique advantages of object-oriented design in process model coupling, to ensure software quality and confidence. We will also be prepared to discuss the major challenges faced by most open-source software teams, such as on-boarding new developers or one-time contributions, dealing with competitors or lookie-loos, and other downsides of complete transparency, as well as our approach to community engagement, including a user group email list, hosting short courses and workshops for new users, and maintaining a website. SAND2017-8174A

Open source posturography.

PubMed

Rey-Martinez, Jorge; Pérez-Fernández, Nicolás

2016-12-01

The proposed validation goal of 0.9 in intra-class correlation coefficient was reached with the results of this study. With the obtained results we consider that the developed software (RombergLab) is a validated balance assessment software. The reliability of this software is dependent of the used force platform technical specifications. Develop and validate a posturography software and share its source code in open source terms. Prospective non-randomized validation study: 20 consecutive adults underwent two balance assessment tests, six condition posturography was performed using a clinical approved software and force platform and the same conditions were measured using the new developed open source software using a low cost force platform. Intra-class correlation index of the sway area obtained from the center of pressure variations in both devices for the six conditions was the main variable used for validation. Excellent concordance between RombergLab and clinical approved force platform was obtained (intra-class correlation coefficient =0.94). A Bland and Altman graphic concordance plot was also obtained. The source code used to develop RombergLab was published in open source terms.

Open core control software for surgical robots.

PubMed

Arata, Jumpei; Kozuka, Hiroaki; Kim, Hyung Wook; Takesue, Naoyuki; Vladimirov, B; Sakaguchi, Masamichi; Tokuda, Junichi; Hata, Nobuhiko; Chinzei, Kiyoyuki; Fujimoto, Hideo

2010-05-01

In these days, patients and doctors in operation room are surrounded by many medical devices as resulting from recent advancement of medical technology. However, these cutting-edge medical devices are working independently and not collaborating with each other, even though the collaborations between these devices such as navigation systems and medical imaging devices are becoming very important for accomplishing complex surgical tasks (such as a tumor removal procedure while checking the tumor location in neurosurgery). On the other hand, several surgical robots have been commercialized, and are becoming common. However, these surgical robots are not open for collaborations with external medical devices in these days. A cutting-edge "intelligent surgical robot" will be possible in collaborating with surgical robots, various kinds of sensors, navigation system and so on. On the other hand, most of the academic software developments for surgical robots are "home-made" in their research institutions and not open to the public. Therefore, open source control software for surgical robots can be beneficial in this field. From these perspectives, we developed Open Core Control software for surgical robots to overcome these challenges. In general, control softwares have hardware dependencies based on actuators, sensors and various kinds of internal devices. Therefore, these control softwares cannot be used on different types of robots without modifications. However, the structure of the Open Core Control software can be reused for various types of robots by abstracting hardware dependent parts. In addition, network connectivity is crucial for collaboration between advanced medical devices. The OpenIGTLink is adopted in Interface class which plays a role to communicate with external medical devices. At the same time, it is essential to maintain the stable operation within the asynchronous data transactions through network. In the Open Core Control software, several techniques for this purpose were introduced. Virtual fixture is well known technique as a "force guide" for supporting operators to perform precise manipulation by using a master-slave robot. The virtual fixture for precise and safety surgery was implemented on the system to demonstrate an idea of high-level collaboration between a surgical robot and a navigation system. The extension of virtual fixture is not a part of the Open Core Control system, however, the function such as virtual fixture cannot be realized without a tight collaboration between cutting-edge medical devices. By using the virtual fixture, operators can pre-define an accessible area on the navigation system, and the area information can be transferred to the robot. In this manner, the surgical console generates the reflection force when the operator tries to get out from the pre-defined accessible area during surgery. The Open Core Control software was implemented on a surgical master-slave robot and stable operation was observed in a motion test. The tip of the surgical robot was displayed on a navigation system by connecting the surgical robot with a 3D position sensor through the OpenIGTLink. The accessible area was pre-defined before the operation, and the virtual fixture was displayed as a "force guide" on the surgical console. In addition, the system showed stable performance in a duration test with network disturbance. In this paper, a design of the Open Core Control software for surgical robots and the implementation of virtual fixture were described. The Open Core Control software was implemented on a surgical robot system and showed stable performance in high-level collaboration works. The Open Core Control software is developed to be a widely used platform of surgical robots. Safety issues are essential for control software of these complex medical devices. It is important to follow the global specifications such as a FDA requirement "General Principles of Software Validation" or IEC62304. For following these regulations, it is important to develop a self-test environment. Therefore, a test environment is now under development to test various interference in operation room such as a noise of electric knife by considering safety and test environment regulations such as ISO13849 and IEC60508. The Open Core Control software is currently being developed software in open-source manner and available on the Internet. A communization of software interface is becoming a major trend in this field. Based on this perspective, the Open Core Control software can be expected to bring contributions in this field.

The GenABEL Project for statistical genomics

PubMed Central

Karssen, Lennart C.; van Duijn, Cornelia M.; Aulchenko, Yurii S.

2016-01-01

Development of free/libre open source software is usually done by a community of people with an interest in the tool. For scientific software, however, this is less often the case. Most scientific software is written by only a few authors, often a student working on a thesis. Once the paper describing the tool has been published, the tool is no longer developed further and is left to its own device. Here we describe the broad, multidisciplinary community we formed around a set of tools for statistical genomics. The GenABEL project for statistical omics actively promotes open interdisciplinary development of statistical methodology and its implementation in efficient and user-friendly software under an open source licence. The software tools developed withing the project collectively make up the GenABEL suite, which currently consists of eleven tools. The open framework of the project actively encourages involvement of the community in all stages, from formulation of methodological ideas to application of software to specific data sets. A web forum is used to channel user questions and discussions, further promoting the use of the GenABEL suite. Developer discussions take place on a dedicated mailing list, and development is further supported by robust development practices including use of public version control, code review and continuous integration. Use of this open science model attracts contributions from users and developers outside the “core team”, facilitating agile statistical omics methodology development and fast dissemination. PMID:27347381

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

PubMed

Ciobanu, O

2009-01-01

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

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

PubMed Central

Busby, Ben; Lesko, Matthew; Federer, Lisa

2016-01-01

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

On the Prospects and Concerns of Integrating Open Source Software Environment in Software Engineering Education

ERIC Educational Resources Information Center

Kamthan, Pankaj

2007-01-01

Open Source Software (OSS) has introduced a new dimension in software community. As the development and use of OSS becomes prominent, the question of its integration in education arises. In this paper, the following practices fundamental to projects and processes in software engineering are examined from an OSS perspective: project management;…

"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.

Open Source, Openness, and Higher Education

ERIC Educational Resources Information Center

Wiley, David

2006-01-01

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

Achieving Better Buying Power for Mobile Open Architecture Software Systems Through Diverse Acquisition Scenarios

DTIC Science & Technology

2016-04-30

software (OSS) and proprietary (CSS) software elements or remote services (Scacchi, 2002, 2010), eventually including recent efforts to support Web ...specific platforms, including those operating on secured Web /mobile devices.  Common Development Technology provides AC development tools and common...transition to OA systems and OSS software elements, specifically for Web and Mobile devices within the realm of C3CB. OA, Open APIs, OSS, and CSS OA

The case for open-source software in drug discovery.

PubMed

DeLano, Warren L

2005-02-01

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

Entrepreneurial model based technology creative industries sector software through the use of free open source software for Universitas Pendidikan Indonesia students

NASA Astrophysics Data System (ADS)

Hasan, B.; Hasbullah; Purnama, W.; Hery, A.

2016-04-01

Creative industry development areas of software by using Free Open Source Software (FOSS) is expected to be one of the solutions to foster new entrepreneurs of the students who can open job opportunities and contribute to economic development in Indonesia. This study aims to create entrepreneurial coaching model based on the creative industries by utilizing FOSS software field as well as provide understanding and fostering entrepreneurial creative industries based field software for students of Universitas Pendidikan Indonesia. This activity phase begins with identifying entrepreneurs or business software technology that will be developed, training and mentoring, apprenticeship process at industrial partners, creation of business plans and monitoring and evaluation. This activity involves 30 UPI student which has the motivation to self-employment and have competence in the field of information technology. The results and outcomes expected from these activities is the birth of a number of new entrepreneurs from the students engaged in the software industry both software in the world of commerce (e-commerce) and education/learning (e-learning/LMS) and games.

Open Source Software in Medium Size Organizations: Key Factors for Adoption

ERIC Educational Resources Information Center

Solomon, Jerry T.

2010-01-01

For-profit organizations are constantly evaluating new technologies to gain competitive advantage. One such technology, application software, has changed significantly over the past 25 years with the introduction of Open Source Software (OSS). In contrast to commercial software that is developed by private companies and sold to organizations, OSS…

Open high-level data formats and software for gamma-ray astronomy

NASA Astrophysics Data System (ADS)

Deil, Christoph; Boisson, Catherine; Kosack, Karl; Perkins, Jeremy; King, Johannes; Eger, Peter; Mayer, Michael; Wood, Matthew; Zabalza, Victor; Knödlseder, Jürgen; Hassan, Tarek; Mohrmann, Lars; Ziegler, Alexander; Khelifi, Bruno; Dorner, Daniela; Maier, Gernot; Pedaletti, Giovanna; Rosado, Jaime; Contreras, José Luis; Lefaucheur, Julien; Brügge, Kai; Servillat, Mathieu; Terrier, Régis; Walter, Roland; Lombardi, Saverio

2017-01-01

In gamma-ray astronomy, a variety of data formats and proprietary software have been traditionally used, often developed for one specific mission or experiment. Especially for ground-based imaging atmospheric Cherenkov telescopes (IACTs), data and software are mostly private to the collaborations operating the telescopes. However, there is a general movement in science towards the use of open data and software. In addition, the next-generation IACT instrument, the Cherenkov Telescope Array (CTA), will be operated as an open observatory. We have created a Github organisation at https://github.com/open-gamma-ray-astro where we are developing high-level data format specifications. A public mailing list was set up at https://lists.nasa.gov/mailman/listinfo/open-gamma-ray-astro and a first face-to-face meeting on the IACT high-level data model and formats took place in April 2016 in Meudon (France). This open multi-mission effort will help to accelerate the development of open data formats and open-source software for gamma-ray astronomy, leading to synergies in the development of analysis codes and eventually better scientific results (reproducible, multi-mission). This write-up presents this effort for the first time, explaining the motivation and context, the available resources and process we use, as well as the status and planned next steps for the data format specifications. We hope that it will stimulate feedback and future contributions from the gamma-ray astronomy community.

Developing Open Source Software To Advance High End Computing. Report to the President.

ERIC Educational Resources Information Center

National Coordination Office for Information Technology Research and Development, Arlington, VA.

This is part of a series of reports to the President and Congress developed by the President's Information Technology Advisory Committee (PITAC) on key contemporary issues in information technology. This report defines open source software, explains PITAC's interest in this model, describes the process used to investigate issues in open source…

Open Source Software Development

DTIC Science & Technology

2011-01-01

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

Lessons learned in transitioning to an open systems environment

NASA Technical Reports Server (NTRS)

Boland, Dillard E.; Green, David S.; Steger, Warren L.

1994-01-01

Software development organizations, both commercial and governmental, are undergoing rapid change spurred by developments in the computing industry. To stay competitive, these organizations must adopt new technologies, skills, and practices quickly. Yet even for an organization with a well-developed set of software engineering models and processes, transitioning to a new technology can be expensive and risky. Current industry trends are leading away from traditional mainframe environments and toward the workstation-based, open systems world. This paper presents the experiences of software engineers on three recent projects that pioneered open systems development for NASA's Flight Dynamics Division of the Goddard Space Flight Center (GSFC).

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.

Open-source meteor detection software for low-cost single-board computers

NASA Astrophysics Data System (ADS)

Vida, D.; Zubović, D.; Šegon, D.; Gural, P.; Cupec, R.

2016-01-01

This work aims to overcome the current price threshold of meteor stations which can sometimes deter meteor enthusiasts from owning one. In recent years small card-sized computers became widely available and are used for numerous applications. To utilize such computers for meteor work, software which can run on them is needed. In this paper we present a detailed description of newly-developed open-source software for fireball and meteor detection optimized for running on low-cost single board computers. Furthermore, an update on the development of automated open-source software which will handle video capture, fireball and meteor detection, astrometry and photometry is given.

User Driven Development of Software Tools for Open Data Discovery and Exploration

NASA Astrophysics Data System (ADS)

Schlobinski, Sascha; Keppel, Frank; Dihe, Pascal; Boot, Gerben; Falkenroth, Esa

2016-04-01

The use of open data in research faces challenges not restricted to inherent properties such as data quality, resolution of open data sets. Often Open data is catalogued insufficiently or fragmented. Software tools that support the effective discovery including the assessment of the data's appropriateness for research have shortcomings such as the lack of essential functionalities like support for data provenance. We believe that one of the reasons is the neglect of real end users requirements in the development process of aforementioned software tools. In the context of the FP7 Switch-On project we have pro-actively engaged the relevant user user community to collaboratively develop a means to publish, find and bind open data relevant for hydrologic research. Implementing key concepts of data discovery and exploration we have used state of the art web technologies to provide an interactive software tool that is easy to use yet powerful enough to satisfy the data discovery and access requirements of the hydrological research community.

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

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics.

PubMed

Bonnal, Raoul J P; Aerts, Jan; Githinji, George; Goto, Naohisa; MacLean, Dan; Miller, Chase A; Mishima, Hiroyuki; Pagani, Massimiliano; Ramirez-Gonzalez, Ricardo; Smant, Geert; Strozzi, Francesco; Syme, Rob; Vos, Rutger; Wennblom, Trevor J; Woodcroft, Ben J; Katayama, Toshiaki; Prins, Pjotr

2012-04-01

Biogem provides a software development environment for the Ruby programming language, which encourages community-based software development for bioinformatics while lowering the barrier to entry and encouraging best practices. Biogem, with its targeted modular and decentralized approach, software generator, tools and tight web integration, is an improved general model for scaling up collaborative open source software development in bioinformatics. Biogem and modules are free and are OSS. Biogem runs on all systems that support recent versions of Ruby, including Linux, Mac OS X and Windows. Further information at http://www.biogems.info. A tutorial is available at http://www.biogems.info/howto.html bonnal@ingm.org.

Open core control software for surgical robots

PubMed Central

Kozuka, Hiroaki; Kim, Hyung Wook; Takesue, Naoyuki; Vladimirov, B.; Sakaguchi, Masamichi; Tokuda, Junichi; Hata, Nobuhiko; Chinzei, Kiyoyuki; Fujimoto, Hideo

2010-01-01

Object In these days, patients and doctors in operation room are surrounded by many medical devices as resulting from recent advancement of medical technology. However, these cutting-edge medical devices are working independently and not collaborating with each other, even though the collaborations between these devices such as navigation systems and medical imaging devices are becoming very important for accomplishing complex surgical tasks (such as a tumor removal procedure while checking the tumor location in neurosurgery). On the other hand, several surgical robots have been commercialized, and are becoming common. However, these surgical robots are not open for collaborations with external medical devices in these days. A cutting-edge “intelligent surgical robot” will be possible in collaborating with surgical robots, various kinds of sensors, navigation system and so on. On the other hand, most of the academic software developments for surgical robots are “home-made” in their research institutions and not open to the public. Therefore, open source control software for surgical robots can be beneficial in this field. From these perspectives, we developed Open Core Control software for surgical robots to overcome these challenges. Materials and methods In general, control softwares have hardware dependencies based on actuators, sensors and various kinds of internal devices. Therefore, these control softwares cannot be used on different types of robots without modifications. However, the structure of the Open Core Control software can be reused for various types of robots by abstracting hardware dependent parts. In addition, network connectivity is crucial for collaboration between advanced medical devices. The OpenIGTLink is adopted in Interface class which plays a role to communicate with external medical devices. At the same time, it is essential to maintain the stable operation within the asynchronous data transactions through network. In the Open Core Control software, several techniques for this purpose were introduced. Virtual fixture is well known technique as a “force guide” for supporting operators to perform precise manipulation by using a master–slave robot. The virtual fixture for precise and safety surgery was implemented on the system to demonstrate an idea of high-level collaboration between a surgical robot and a navigation system. The extension of virtual fixture is not a part of the Open Core Control system, however, the function such as virtual fixture cannot be realized without a tight collaboration between cutting-edge medical devices. By using the virtual fixture, operators can pre-define an accessible area on the navigation system, and the area information can be transferred to the robot. In this manner, the surgical console generates the reflection force when the operator tries to get out from the pre-defined accessible area during surgery. Results The Open Core Control software was implemented on a surgical master–slave robot and stable operation was observed in a motion test. The tip of the surgical robot was displayed on a navigation system by connecting the surgical robot with a 3D position sensor through the OpenIGTLink. The accessible area was pre-defined before the operation, and the virtual fixture was displayed as a “force guide” on the surgical console. In addition, the system showed stable performance in a duration test with network disturbance. Conclusion In this paper, a design of the Open Core Control software for surgical robots and the implementation of virtual fixture were described. The Open Core Control software was implemented on a surgical robot system and showed stable performance in high-level collaboration works. The Open Core Control software is developed to be a widely used platform of surgical robots. Safety issues are essential for control software of these complex medical devices. It is important to follow the global specifications such as a FDA requirement “General Principles of Software Validation” or IEC62304. For following these regulations, it is important to develop a self-test environment. Therefore, a test environment is now under development to test various interference in operation room such as a noise of electric knife by considering safety and test environment regulations such as ISO13849 and IEC60508. The Open Core Control software is currently being developed software in open-source manner and available on the Internet. A communization of software interface is becoming a major trend in this field. Based on this perspective, the Open Core Control software can be expected to bring contributions in this field. PMID:20033506

Embracing Open Software Development in Solar Physics

NASA Astrophysics Data System (ADS)

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

2012-12-01

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

Whole earth modeling: developing and disseminating scientific software for computational geophysics.

NASA Astrophysics Data System (ADS)

Kellogg, L. H.

2016-12-01

Historically, a great deal of specialized scientific software for modeling and data analysis has been developed by individual researchers or small groups of scientists working on their own specific research problems. As the magnitude of available data and computer power has increased, so has the complexity of scientific problems addressed by computational methods, creating both a need to sustain existing scientific software, and expand its development to take advantage of new algorithms, new software approaches, and new computational hardware. To that end, communities like the Computational Infrastructure for Geodynamics (CIG) have been established to support the use of best practices in scientific computing for solid earth geophysics research and teaching. Working as a scientific community enables computational geophysicists to take advantage of technological developments, improve the accuracy and performance of software, build on prior software development, and collaborate more readily. The CIG community, and others, have adopted an open-source development model, in which code is developed and disseminated by the community in an open fashion, using version control and software repositories like Git. One emerging issue is how to adequately identify and credit the intellectual contributions involved in creating open source scientific software. The traditional method of disseminating scientific ideas, peer reviewed publication, was not designed for review or crediting scientific software, although emerging publication strategies such software journals are attempting to address the need. We are piloting an integrated approach in which authors are identified and credited as scientific software is developed and run. Successful software citation requires integration with the scholarly publication and indexing mechanisms as well, to assign credit, ensure discoverability, and provide provenance for software.

Open Source Software Development Experiences on the Students' Resumes: Do They Count?--Insights from the Employers' Perspectives

ERIC Educational Resources Information Center

Long, Ju

2009-01-01

Open Source Software (OSS) is a major force in today's Information Technology (IT) landscape. Companies are increasingly using OSS in mission-critical applications. The transparency of the OSS technology itself with openly available source codes makes it ideal for students to participate in the OSS project development. OSS can provide unique…

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

NASA Astrophysics Data System (ADS)

Frigeri, A.

2012-12-01

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

Science and Software

NASA Astrophysics Data System (ADS)

Zelt, C. A.

2017-12-01

Earth science attempts to understand how the earth works. This research often depends on software for modeling, processing, inverting or imaging. Freely sharing open-source software is essential to prevent reinventing the wheel and allows software to be improved and applied in ways the original author may never have envisioned. For young scientists, releasing software can increase their name ID when applying for jobs and funding, and create opportunities for collaborations when scientists who collect data want the software's creator to be involved in their project. However, we frequently hear scientists say software is a tool, it's not science. Creating software that implements a new or better way of earth modeling or geophysical processing, inverting or imaging should be viewed as earth science. Creating software for things like data visualization, format conversion, storage, or transmission, or programming to enhance computational performance, may be viewed as computer science. The former, ideally with an application to real data, can be published in earth science journals, the latter possibly in computer science journals. Citations in either case should accurately reflect the impact of the software on the community. Funding agencies need to support more software development and open-source releasing, and the community should give more high-profile awards for developing impactful open-source software. Funding support and community recognition for software development can have far reaching benefits when the software is used in foreseen and unforeseen ways, potentially for years after the original investment in the software development. For funding, an open-source release that is well documented should be required, with example input and output files. Appropriate funding will provide the incentive and time to release user-friendly software, and minimize the need for others to duplicate the effort. All funded software should be available through a single web site, ideally maintained by someone in a funded position. Perhaps the biggest challenge is the reality that researches who use software, as opposed to develop software, are more attractive university hires because they are more likely to be "big picture" scientists that publish in the highest profile journals, although sometimes the two go together.

Open source molecular modeling.

PubMed

Pirhadi, Somayeh; Sunseri, Jocelyn; Koes, David Ryan

2016-09-01

The success of molecular modeling and computational chemistry efforts are, by definition, dependent on quality software applications. Open source software development provides many advantages to users of modeling applications, not the least of which is that the software is free and completely extendable. In this review we categorize, enumerate, and describe available open source software packages for molecular modeling and computational chemistry. An updated online version of this catalog can be found at https://opensourcemolecularmodeling.github.io. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

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

NASA Astrophysics Data System (ADS)

Vinay, S.; Downs, R. R.

2012-12-01

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

Open Source Software and the Intellectual Commons.

ERIC Educational Resources Information Center

Dorman, David

2002-01-01

Discusses the Open Source Software method of software development and its relationship to control over information content. Topics include digital library resources; reference services; preservation; the legal and economic status of information; technical standards; access to digital data; control of information use; and copyright and patent laws.…

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

NASA Astrophysics Data System (ADS)

Melton, R.; Thomas, J.

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

Develop Direct Geo-referencing System Based on Open Source Software and Hardware Platform

NASA Astrophysics Data System (ADS)

Liu, H. S.; Liao, H. M.

2015-08-01

Direct geo-referencing system uses the technology of remote sensing to quickly grasp images, GPS tracks, and camera position. These data allows the construction of large volumes of images with geographic coordinates. So that users can be measured directly on the images. In order to properly calculate positioning, all the sensor signals must be synchronized. Traditional aerial photography use Position and Orientation System (POS) to integrate image, coordinates and camera position. However, it is very expensive. And users could not use the result immediately because the position information does not embed into image. To considerations of economy and efficiency, this study aims to develop a direct geo-referencing system based on open source software and hardware platform. After using Arduino microcontroller board to integrate the signals, we then can calculate positioning with open source software OpenCV. In the end, we use open source panorama browser, panini, and integrate all these to open source GIS software, Quantum GIS. A wholesome collection of data - a data processing system could be constructed.

Web accessibility and open source software.

PubMed

Obrenović, Zeljko

2009-07-01

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

Using Open Source Software in Visual Simulation Development

DTIC Science & Technology

2005-09-01

increased the use of the technology in training activities. Using open source/free software tools in the process can expand these possibilities...resulting in even greater cost reduction and allowing the flexibility needed in a training environment. This thesis presents a configuration and architecture...to be used when developing training visual simulations using both personal computers and open source tools. Aspects of the requirements needed in a

Anatomy of BioJS, an open source community for the life sciences.

PubMed

Yachdav, Guy; Goldberg, Tatyana; Wilzbach, Sebastian; Dao, David; Shih, Iris; Choudhary, Saket; Crouch, Steve; Franz, Max; García, Alexander; García, Leyla J; Grüning, Björn A; Inupakutika, Devasena; Sillitoe, Ian; Thanki, Anil S; Vieira, Bruno; Villaveces, José M; Schneider, Maria V; Lewis, Suzanna; Pettifer, Steve; Rost, Burkhard; Corpas, Manuel

2015-07-08

BioJS is an open source software project that develops visualization tools for different types of biological data. Here we report on the factors that influenced the growth of the BioJS user and developer community, and outline our strategy for building on this growth. The lessons we have learned on BioJS may also be relevant to other open source software projects.

Development of Automated Procedures to Generate Reference Building Models for ASHRAE Standard 90.1 and India’s Building Energy Code and Implementation in OpenStudio

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

Parker, Andrew; Haves, Philip; Jegi, Subhash

This paper describes a software system for automatically generating a reference (baseline) building energy model from the proposed (as-designed) building energy model. This system is built using the OpenStudio Software Development Kit (SDK) and is designed to operate on building energy models in the OpenStudio file format.

Communal Resources in Open Source Software Development

ERIC Educational Resources Information Center

Spaeth, Sebastian; Haefliger, Stefan; von Krogh, Georg; Renzl, Birgit

2008-01-01

Introduction: Virtual communities play an important role in innovation. The paper focuses on the particular form of collective action in virtual communities underlying as Open Source software development projects. Method: Building on resource mobilization theory and private-collective innovation, we propose a theory of collective action in…

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

CrossTalk: The Journal of Defense Software Engineering. Volume 24, Number 6. November/December 2011

DTIC Science & Technology

2011-11-01

Software Development.” Software Quality Professional Journal, American Society for Quality (ASQ), (March 2010) 4-14. 3. Nair, Gopalakrishnan T.R...Inspection Performance Metric”. Software Quality Professional Journal, American Society for Quality (ASQ), Volume 13, Issue 2, (March 2011) 14-26...the discovery process and are marketed by compa- nies such as Black Duck Software, OpenLogic, Palamida, and Protecode, among others.7 A number of open

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

PubMed Central

2012-01-01

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

The open-source movement: an introduction for forestry professionals

Treesearch

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

2005-01-01

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

[GNU Pattern: open source pattern hunter for biological sequences based on SPLASH algorithm].

PubMed

Xu, Ying; Li, Yi-xue; Kong, Xiang-yin

2005-06-01

To construct a high performance open source software engine based on IBM SPLASH algorithm for later research on pattern discovery. Gpat, which is based on SPLASH algorithm, was developed by using open source software. GNU Pattern (Gpat) software was developped, which efficiently implemented the core part of SPLASH algorithm. Full source code of Gpat was also available for other researchers to modify the program under the GNU license. Gpat is a successful implementation of SPLASH algorithm and can be used as a basic framework for later research on pattern recognition in biological sequences.

Software Productivity of Field Experiments Using the Mobile Agents Open Architecture with Workflow Interoperability

NASA Technical Reports Server (NTRS)

Clancey, William J.; Lowry, Michael R.; Nado, Robert Allen; Sierhuis, Maarten

2011-01-01

We analyzed a series of ten systematically developed surface exploration systems that integrated a variety of hardware and software components. Design, development, and testing data suggest that incremental buildup of an exploration system for long-duration capabilities is facilitated by an open architecture with appropriate-level APIs, specifically designed to facilitate integration of new components. This improves software productivity by reducing changes required for reconfiguring an existing system.

Digital beacon receiver for ionospheric TEC measurement developed with GNU Radio

NASA Astrophysics Data System (ADS)

Yamamoto, M.

2008-11-01

A simple digital receiver named GNU Radio Beacon Receiver (GRBR) was developed for the satellite-ground beacon experiment to measure the ionospheric total electron content (TEC). The open-source software toolkit for the software defined radio, GNU Radio, is utilized to realize the basic function of the receiver and perform fast signal processing. The software is written in Python for a LINUX PC. The open-source hardware called Universal Software Radio Peripheral (USRP), which best matches the GNU Radio, is used as a front-end to acquire the satellite beacon signals of 150 and 400 MHz. The first experiment was successful as results from GRBR showed very good agreement to those from the co-located analog beacon receiver. Detailed design information and software codes are open at the URL http://www.rish.kyoto-u.ac.jp/digitalbeacon/.

Applying Open Source Software in a Development Context: Expectations and Experiences. A Case Study of a University in Uganda

ERIC Educational Resources Information Center

van Reijswoud, Victor; Mulo, Emmanuel

2006-01-01

Over recent years the issue of free and open source software (FOSS) for development in less developed countries (LDCs) has received increasing attention. In the beginning the benefits of FOSS for lower developed countries was only stressed by small groups of idealists like Richard Stallman. Now, however, it is moving into the hands of large…

Clinical software development for the Web: lessons learned from the BOADICEA project

PubMed Central

2012-01-01

Background In the past 20 years, society has witnessed the following landmark scientific advances: (i) the sequencing of the human genome, (ii) the distribution of software by the open source movement, and (iii) the invention of the World Wide Web. Together, these advances have provided a new impetus for clinical software development: developers now translate the products of human genomic research into clinical software tools; they use open-source programs to build them; and they use the Web to deliver them. Whilst this open-source component-based approach has undoubtedly made clinical software development easier, clinical software projects are still hampered by problems that traditionally accompany the software process. This study describes the development of the BOADICEA Web Application, a computer program used by clinical geneticists to assess risks to patients with a family history of breast and ovarian cancer. The key challenge of the BOADICEA Web Application project was to deliver a program that was safe, secure and easy for healthcare professionals to use. We focus on the software process, problems faced, and lessons learned. Our key objectives are: (i) to highlight key clinical software development issues; (ii) to demonstrate how software engineering tools and techniques can facilitate clinical software development for the benefit of individuals who lack software engineering expertise; and (iii) to provide a clinical software development case report that can be used as a basis for discussion at the start of future projects. Results We developed the BOADICEA Web Application using an evolutionary software process. Our approach to Web implementation was conservative and we used conventional software engineering tools and techniques. The principal software development activities were: requirements, design, implementation, testing, documentation and maintenance. The BOADICEA Web Application has now been widely adopted by clinical geneticists and researchers. BOADICEA Web Application version 1 was released for general use in November 2007. By May 2010, we had > 1200 registered users based in the UK, USA, Canada, South America, Europe, Africa, Middle East, SE Asia, Australia and New Zealand. Conclusions We found that an evolutionary software process was effective when we developed the BOADICEA Web Application. The key clinical software development issues identified during the BOADICEA Web Application project were: software reliability, Web security, clinical data protection and user feedback. PMID:22490389

Clinical software development for the Web: lessons learned from the BOADICEA project.

PubMed

Cunningham, Alex P; Antoniou, Antonis C; Easton, Douglas F

2012-04-10

In the past 20 years, society has witnessed the following landmark scientific advances: (i) the sequencing of the human genome, (ii) the distribution of software by the open source movement, and (iii) the invention of the World Wide Web. Together, these advances have provided a new impetus for clinical software development: developers now translate the products of human genomic research into clinical software tools; they use open-source programs to build them; and they use the Web to deliver them. Whilst this open-source component-based approach has undoubtedly made clinical software development easier, clinical software projects are still hampered by problems that traditionally accompany the software process. This study describes the development of the BOADICEA Web Application, a computer program used by clinical geneticists to assess risks to patients with a family history of breast and ovarian cancer. The key challenge of the BOADICEA Web Application project was to deliver a program that was safe, secure and easy for healthcare professionals to use. We focus on the software process, problems faced, and lessons learned. Our key objectives are: (i) to highlight key clinical software development issues; (ii) to demonstrate how software engineering tools and techniques can facilitate clinical software development for the benefit of individuals who lack software engineering expertise; and (iii) to provide a clinical software development case report that can be used as a basis for discussion at the start of future projects. We developed the BOADICEA Web Application using an evolutionary software process. Our approach to Web implementation was conservative and we used conventional software engineering tools and techniques. The principal software development activities were: requirements, design, implementation, testing, documentation and maintenance. The BOADICEA Web Application has now been widely adopted by clinical geneticists and researchers. BOADICEA Web Application version 1 was released for general use in November 2007. By May 2010, we had > 1200 registered users based in the UK, USA, Canada, South America, Europe, Africa, Middle East, SE Asia, Australia and New Zealand. We found that an evolutionary software process was effective when we developed the BOADICEA Web Application. The key clinical software development issues identified during the BOADICEA Web Application project were: software reliability, Web security, clinical data protection and user feedback.

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

PubMed

Ratib, Osman; Rosset, Antoine; Heuberger, Joris

2011-05-01

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

Open Source Software and Design-Based Research Symbiosis in Developing 3D Virtual Learning Environments: Examples from the iSocial Project

ERIC Educational Resources Information Center

Schmidt, Matthew; Galyen, Krista; Laffey, James; Babiuch, Ryan; Schmidt, Carla

2014-01-01

Design-based research (DBR) and open source software are both acknowledged as potentially productive ways for advancing learning technologies. These approaches have practical benefits for the design and development process and for building and leveraging community to augment and sustain design and development. This report presents a case study of…

Open-Source Software in Computational Research: A Case Study

DOE PAGES

Syamlal, Madhava; O'Brien, Thomas J.; Benyahia, Sofiane; ...

2008-01-01

A case study of open-source (OS) development of the computational research software MFIX, used for multiphase computational fluid dynamics simulations, is presented here. The verification and validation steps required for constructing modern computational software and the advantages of OS development in those steps are discussed. The infrastructure used for enabling the OS development of MFIX is described. The impact of OS development on computational research and education in gas-solids flow, as well as the dissemination of information to other areas such as geophysical and volcanology research, is demonstrated. This study shows that the advantages of OS development were realized inmore » the case of MFIX: verification by many users, which enhances software quality; the use of software as a means for accumulating and exchanging information; the facilitation of peer review of the results of computational research.« less

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

PubMed

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

2014-01-01

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

Matlab-Excel Interface for OpenDSS

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

The software allows users of the OpenDSS grid modeling software to access their load flow models using a GUI interface developed in MATLAB. The circuit definitions are entered into a Microsoft Excel spreadsheet which makes circuit creation and editing a much simpler process than the basic text-based editors used in the native OpenDSS interface. Plot tools have been developed which can be accessed through a MATLAB GUI once the desired parameters have been simulated.

Bioconductor: open software development for computational biology and bioinformatics

PubMed Central

Gentleman, Robert C; Carey, Vincent J; Bates, Douglas M; Bolstad, Ben; Dettling, Marcel; Dudoit, Sandrine; Ellis, Byron; Gautier, Laurent; Ge, Yongchao; Gentry, Jeff; Hornik, Kurt; Hothorn, Torsten; Huber, Wolfgang; Iacus, Stefano; Irizarry, Rafael; Leisch, Friedrich; Li, Cheng; Maechler, Martin; Rossini, Anthony J; Sawitzki, Gunther; Smith, Colin; Smyth, Gordon; Tierney, Luke; Yang, Jean YH; Zhang, Jianhua

2004-01-01

The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples. PMID:15461798

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.

3D reconstruction software comparison for short sequences

NASA Astrophysics Data System (ADS)

Strupczewski, Adam; Czupryński, BłaŻej

2014-11-01

Large scale multiview reconstruction is recently a very popular area of research. There are many open source tools that can be downloaded and run on a personal computer. However, there are few, if any, comparisons between all the available software in terms of accuracy on small datasets that a single user can create. The typical datasets for testing of the software are archeological sites or cities, comprising thousands of images. This paper presents a comparison of currently available open source multiview reconstruction software for small datasets. It also compares the open source solutions with a simple structure from motion pipeline developed by the authors from scratch with the use of OpenCV and Eigen libraries.

OpenROCS: a software tool to control robotic observatories

NASA Astrophysics Data System (ADS)

Colomé, Josep; Sanz, Josep; Vilardell, Francesc; Ribas, Ignasi; Gil, Pere

2012-09-01

We present the Open Robotic Observatory Control System (OpenROCS), an open source software platform developed for the robotic control of telescopes. It acts as a software infrastructure that executes all the necessary processes to implement responses to the system events that appear in the routine and non-routine operations associated to data-flow and housekeeping control. The OpenROCS software design and implementation provides a high flexibility to be adapted to different observatory configurations and event-action specifications. It is based on an abstract model that is independent of the specific hardware or software and is highly configurable. Interfaces to the system components are defined in a simple manner to achieve this goal. We give a detailed description of the version 2.0 of this software, based on a modular architecture developed in PHP and XML configuration files, and using standard communication protocols to interface with applications for hardware monitoring and control, environment monitoring, scheduling of tasks, image processing and data quality control. We provide two examples of how it is used as the core element of the control system in two robotic observatories: the Joan Oró Telescope at the Montsec Astronomical Observatory (Catalonia, Spain) and the SuperWASP Qatar Telescope at the Roque de los Muchachos Observatory (Canary Islands, Spain).

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

NASA Astrophysics Data System (ADS)

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

2009-12-01

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

The 2015 Bioinformatics Open Source Conference (BOSC 2015).

PubMed

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

2016-02-01

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

The Open AUC Project.

PubMed

Cölfen, Helmut; Laue, Thomas M; Wohlleben, Wendel; Schilling, Kristian; Karabudak, Engin; Langhorst, Bradley W; Brookes, Emre; Dubbs, Bruce; Zollars, Dan; Rocco, Mattia; Demeler, Borries

2010-02-01

Progress in analytical ultracentrifugation (AUC) has been hindered by obstructions to hardware innovation and by software incompatibility. In this paper, we announce and outline the Open AUC Project. The goals of the Open AUC Project are to stimulate AUC innovation by improving instrumentation, detectors, acquisition and analysis software, and collaborative tools. These improvements are needed for the next generation of AUC-based research. The Open AUC Project combines on-going work from several different groups. A new base instrument is described, one that is designed from the ground up to be an analytical ultracentrifuge. This machine offers an open architecture, hardware standards, and application programming interfaces for detector developers. All software will use the GNU Public License to assure that intellectual property is available in open source format. The Open AUC strategy facilitates collaborations, encourages sharing, and eliminates the chronic impediments that have plagued AUC innovation for the last 20 years. This ultracentrifuge will be equipped with multiple and interchangeable optical tracks so that state-of-the-art electronics and improved detectors will be available for a variety of optical systems. The instrument will be complemented by a new rotor, enhanced data acquisition and analysis software, as well as collaboration software. Described here are the instrument, the modular software components, and a standardized database that will encourage and ease integration of data analysis and interpretation software.

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

NASA Astrophysics Data System (ADS)

Hameed, Saji; Realini, Eugenio; Ishida, Shinya

2016-04-01

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

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

The TJO-OAdM robotic observatory: OpenROCS and dome control

NASA Astrophysics Data System (ADS)

Colomé, Josep; Francisco, Xavier; Ribas, Ignasi; Casteels, Kevin; Martín, Jonatan

2010-07-01

The Telescope Joan Oró at the Montsec Astronomical Observatory (TJO - OAdM) is a small-class observatory working in completely unattended control. There are key problems to solve when a robotic control is envisaged, both on hardware and software issues. We present the OpenROCS (ROCS stands for Robotic Observatory Control System), an open source platform developed for the robotic control of the TJO - OAdM and similar astronomical observatories. It is a complex software architecture, composed of several applications for hardware control, event handling, environment monitoring, target scheduling, image reduction pipeline, etc. The code is developed in Java, C++, Python and Perl. The software infrastructure used is based on the Internet Communications Engine (Ice), an object-oriented middleware that provides object-oriented remote procedure call, grid computing, and publish/subscribe functionality. We also describe the subsystem in charge of the dome control: several hardware and software elements developed to specially protect the system at this identified single point of failure. It integrates a redundant control and a rain detector signal for alarm triggering and it responds autonomously in case communication with any of the control elements is lost (watchdog functionality). The self-developed control software suite (OpenROCS) and dome control system have proven to be highly reliable.

Journal of Open Source Software (JOSS): design and first-year review

NASA Astrophysics Data System (ADS)

Smith, Arfon M.

2018-01-01

JOSS is a free and open-access journal that publishes articles describing research software across all disciplines. It has the dual goals of improving the quality of the software submitted and providing a mechanism for research software developers to receive credit. While designed to work within the current merit system of science, JOSS addresses the dearth of rewards for key contributions to science made in the form of software. JOSS publishes articles that encapsulate scholarship contained in the software itself, and its rigorous peer review targets the software components: functionality, documentation, tests, continuous integration, and the license. A JOSS article contains an abstract describing the purpose and functionality of the software, references, and a link to the software archive. JOSS published more than 100 articles in its first year, many from the scientific python ecosystem (including a number of articles related to astronomy and astrophysics). JOSS is a sponsored project of the nonprofit organization NumFOCUS and is an affiliate of the Open Source Initiative.In this presentation, I'll describes the motivation, design, and progress of the Journal of Open Source Software (JOSS) and how it compares to other avenues for publishing research software in astronomy.

Ensemble: an Architecture for Mission-Operations Software

NASA Technical Reports Server (NTRS)

Norris, Jeffrey; Powell, Mark; Fox, Jason; Rabe, Kenneth; Shu, IHsiang; McCurdy, Michael; Vera, Alonso

2008-01-01

Ensemble is the name of an open architecture for, and a methodology for the development of, spacecraft mission operations software. Ensemble is also potentially applicable to the development of non-spacecraft mission-operations- type software. Ensemble capitalizes on the strengths of the open-source Eclipse software and its architecture to address several issues that have arisen repeatedly in the development of mission-operations software: Heretofore, mission-operations application programs have been developed in disparate programming environments and integrated during the final stages of development of missions. The programs have been poorly integrated, and it has been costly to develop, test, and deploy them. Users of each program have been forced to interact with several different graphical user interfaces (GUIs). Also, the strategy typically used in integrating the programs has yielded serial chains of operational software tools of such a nature that during use of a given tool, it has not been possible to gain access to the capabilities afforded by other tools. In contrast, the Ensemble approach offers a low-risk path towards tighter integration of mission-operations software tools.

A Requirements-Based Exploration of Open-Source Software Development Projects--Towards a Natural Language Processing Software Analysis Framework

ERIC Educational Resources Information Center

Vlas, Radu Eduard

2012-01-01

Open source projects do have requirements; they are, however, mostly informal, text descriptions found in requests, forums, and other correspondence. Understanding such requirements provides insight into the nature of open source projects. Unfortunately, manual analysis of natural language requirements is time-consuming, and for large projects,…

Open Architecture SDR for Space

NASA Technical Reports Server (NTRS)

Smith, Carl; Long, Chris; Liebetreu, John; Reinhart, Richard C.

2005-01-01

This paper describes an open-architecture SDR (software defined radio) infrastructure that is suitable for space-based operations (Space-SDR). SDR technologies will endow space and planetary exploration systems with dramatically increased capability, reduced power consumption, and significantly less mass than conventional systems, at costs reduced by vigorous competition, hardware commonality, dense integration, reduced obsolescence, interoperability, and software re-use. Significant progress has been recorded on developments like the Joint Tactical Radio System (JSTRS) Software Communication Architecture (SCA), which is oriented toward reconfigurable radios for defense forces operating in multiple theaters of engagement. The JTRS-SCA presents a consistent software interface for waveform development, and facilitates interoperability, waveform portability, software re-use, and technology evolution.

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

PubMed

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

2007-11-01

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

USE OF COMPUTER-AIDED PROCESS ENGINEERING TOOL IN POLLUTION PREVENTION

EPA Science Inventory

Computer-Aided Process Engineering has become established in industry as a design tool. With the establishment of the CAPE-OPEN software specifications for process simulation environments. CAPE-OPEN provides a set of "middleware" standards that enable software developers to acces...

Embracing Open Source for NASA's Earth Science Data Systems

NASA Technical Reports Server (NTRS)

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

2017-01-01

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

OpenSatKit Enables Quick Startup for CubeSat Missions

NASA Technical Reports Server (NTRS)

McComas, David; Melton, Ryan

2017-01-01

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

Open source tools for ATR development and performance evaluation

NASA Astrophysics Data System (ADS)

Baumann, James M.; Dilsavor, Ronald L.; Stubbles, James; Mossing, John C.

2002-07-01

Early in almost every engineering project, a decision must be made about tools; should I buy off-the-shelf tools or should I develop my own. Either choice can involve significant cost and risk. Off-the-shelf tools may be readily available, but they can be expensive to purchase and to maintain licenses, and may not be flexible enough to satisfy all project requirements. On the other hand, developing new tools permits great flexibility, but it can be time- (and budget-) consuming, and the end product still may not work as intended. Open source software has the advantages of both approaches without many of the pitfalls. This paper examines the concept of open source software, including its history, unique culture, and informal yet closely followed conventions. These characteristics influence the quality and quantity of software available, and ultimately its suitability for serious ATR development work. We give an example where Python, an open source scripting language, and OpenEV, a viewing and analysis tool for geospatial data, have been incorporated into ATR performance evaluation projects. While this case highlights the successful use of open source tools, we also offer important insight into risks associated with this approach.

The Computational Infrastructure for Geodynamics: An Example of Software Curation and Citation in the Geodynamics Community

NASA Astrophysics Data System (ADS)

Hwang, L.; Kellogg, L. H.

2017-12-01

Curation of software promotes discoverability and accessibility and works hand in hand with scholarly citation to ascribe value to, and provide recognition for software development. To meet this challenge, the Computational Infrastructure for Geodynamics (CIG) maintains a community repository built on custom and open tools to promote discovery, access, identification, credit, and provenance of research software for the geodynamics community. CIG (geodynamics.org) originated from recognition of the tremendous effort required to develop sound software and the need to reduce duplication of effort and to sustain community codes. CIG curates software across 6 domains and has developed and follows software best practices that include establishing test cases, documentation, and a citable publication for each software package. CIG software landing web pages provide access to current and past releases; many are also accessible through the CIG community repository on github. CIG has now developed abc - attribution builder for citation to enable software users to give credit to software developers. abc uses zenodo as an archive and as the mechanism to obtain a unique identifier (DOI) for scientific software. To assemble the metadata, we searched the software's documentation and research publications and then requested the primary developers to verify. In this process, we have learned that each development community approaches software attribution differently. The metadata gathered is based on guidelines established by groups such as FORCE11 and OntoSoft. The rollout of abc is gradual as developers are forward-looking, rarely willing to go back and archive prior releases in zenodo. Going forward all actively developed packages will utilize the zenodo and github integration to automate the archival process when a new release is issued. How to handle legacy software, multi-authored libraries, and assigning roles to software remain open issues.

The 2015 Bioinformatics Open Source Conference (BOSC 2015)

PubMed Central

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

2016-01-01

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

NASA's Earth Imagery Service as Open Source Software

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

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

NASA Astrophysics Data System (ADS)

Ames, D. P.

2013-12-01

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

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

PubMed

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

2016-12-01

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

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

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

PubMed

Benson, Tim

2016-07-04

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

Listening to the student voice to improve educational software.

PubMed

van Wyk, Mari; van Ryneveld, Linda

2017-01-01

Academics often develop software for teaching and learning purposes with the best of intentions, only to be disappointed by the low acceptance rate of the software by their students once it is implemented. In this study, the focus is on software that was designed to enable veterinary students to record their clinical skills. A pilot of the software clearly showed that the program had not been received as well as had been anticipated, and therefore the researchers used a group interview and a questionnaire with closed-ended and open-ended questions to obtain the students' feedback. The open-ended questions were analysed with conceptual content analysis, and themes were identified. Students made valuable suggestions about what they regarded as important considerations when a new software program is introduced. The most important lesson learnt was that students cannot always predict their needs accurately if they are asked for input prior to the development of software. For that reason student input should be obtained on a continuous and regular basis throughout the design and development phases.

COTS-based OO-component approach for software inter-operability and reuse (software systems engineering methodology)

NASA Technical Reports Server (NTRS)

Yin, J.; Oyaki, A.; Hwang, C.; Hung, C.

2000-01-01

The purpose of this research and study paper is to provide a summary description and results of rapid development accomplishments at NASA/JPL in the area of advanced distributed computing technology using a Commercial-Off--The-Shelf (COTS)-based object oriented component approach to open inter-operable software development and software reuse.

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

Lehe, Remi

Many simulation software produce data in the form of a set of field values or of a set of particle positions. (one such example is that of particle-in-cell codes, which produce data on the electromagnetic fields that they simulate.) However, each particular software uses its own particular format and layout, for the output data. This makes it difficult to compare the results of different simulation software, or to have a common visualization tool for these results. However, a standardized layout for fields and particles has recently been developed: the openPMD format ( HYPERLINK "http://www.openpmd.org/"www.openpmd.org) This format is open- source, andmore » specifies a standard way in which field data and particle data should be written. The openPMD format is already implemented in the particle-in-cell code Warp (developed at LBL) and in PIConGPU (developed at HZDR, Germany). In this context, the proposed software (openPMD-viewer) is a Python package, which allows to access and visualize any data which has been formatted according to the openPMD standard. This package contains two main components: - a Python API, which allows to read and extract the data from a openPMD file, so as to be able to work with it within the Python environment. (e.g. plot the data and reprocess it with particular Python functions) - a graphical interface, which works with the ipython notebook, and allows to quickly visualize the data and browse through a set of openPMD files. The proposed software will be typically used when analyzing the results of numerical simulations. It will be useful to quickly extract scientific meaning from a set of numerical data.« less

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

NASA Technical Reports Server (NTRS)

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

2016-01-01

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

World Reaction to Virtual Space

NASA Technical Reports Server (NTRS)

1999-01-01

DRaW Computing developed virtual reality software for the International Space Station. Open Worlds, as the software has been named, can be made to support Java scripting and virtual reality hardware devices. Open Worlds permits the use of VRML script nodes to add virtual reality capabilities to the user's applications.

Understanding How the "Open" of Open Source Software (OSS) Will Improve Global Health Security.

PubMed

Hahn, Erin; Blazes, David; Lewis, Sheri

2016-01-01

Improving global health security will require bold action in all corners of the world, particularly in developing settings, where poverty often contributes to an increase in emerging infectious diseases. In order to mitigate the impact of emerging pandemic threats, enhanced disease surveillance is needed to improve early detection and rapid response to outbreaks. However, the technology to facilitate this surveillance is often unattainable because of high costs, software and hardware maintenance needs, limited technical competence among public health officials, and internet connectivity challenges experienced in the field. One potential solution is to leverage open source software, a concept that is unfortunately often misunderstood. This article describes the principles and characteristics of open source software and how it may be applied to solve global health security challenges.

Building CHAOS: An Operating System for Livermore Linux Clusters

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

Garlick, J E; Dunlap, C M

2003-02-21

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

75 FR 10439 - Cognitive Radio Technologies and Software Defined Radios

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-08

... Technologies and Software Defined Radios AGENCY: Federal Communications Commission. ACTION: Final rule. SUMMARY... concerning the use of open source software to implement security features in software defined radios (SDRs... ongoing technical developments in cognitive and software defined radio (SDR) technologies. 2. On April 20...

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

PubMed

Massaut, Jacques; Reper, Pascal

2008-01-01

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

The image-guided surgery toolkit IGSTK: an open source C++ software toolkit.

PubMed

Enquobahrie, Andinet; Cheng, Patrick; Gary, Kevin; Ibanez, Luis; Gobbi, David; Lindseth, Frank; Yaniv, Ziv; Aylward, Stephen; Jomier, Julien; Cleary, Kevin

2007-11-01

This paper presents an overview of the image-guided surgery toolkit (IGSTK). IGSTK is an open source C++ software library that provides the basic components needed to develop image-guided surgery applications. It is intended for fast prototyping and development of image-guided surgery applications. The toolkit was developed through a collaboration between academic and industry partners. Because IGSTK was designed for safety-critical applications, the development team has adopted lightweight software processes that emphasizes safety and robustness while, at the same time, supporting geographically separated developers. A software process that is philosophically similar to agile software methods was adopted emphasizing iterative, incremental, and test-driven development principles. The guiding principle in the architecture design of IGSTK is patient safety. The IGSTK team implemented a component-based architecture and used state machine software design methodologies to improve the reliability and safety of the components. Every IGSTK component has a well-defined set of features that are governed by state machines. The state machine ensures that the component is always in a valid state and that all state transitions are valid and meaningful. Realizing that the continued success and viability of an open source toolkit depends on a strong user community, the IGSTK team is following several key strategies to build an active user community. These include maintaining a users and developers' mailing list, providing documentation (application programming interface reference document and book), presenting demonstration applications, and delivering tutorial sessions at relevant scientific conferences.

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

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

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

NASA Astrophysics Data System (ADS)

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

2009-12-01

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

Student’s Entrepreneur Model Development in Creative Industry through Utilization of Web Development Software and Educational Game

NASA Astrophysics Data System (ADS)

Hasan, B.; Hasbullah, H.; Elvyanti, S.; Purnama, W.

2018-02-01

The creative industry is the utilization of creativity, skill and talent of individuals to create wealth and jobs by generating and exploiting creativity power of individual. In the field of design, utilization of information technology can spur creative industry, development of creative industry design will accommodate a lot of creative energy that can pour their ideas and creativity without limitations. Open Source software is a trend in the field of information technology has developed since the 1990s. Examples of applications developed by the Open Source approach is the Apache web services, Linux and Android Operating System, the MySQL database. This community service activities based entrepreneurship aims to: 1). give an idea about the profile of the UPI student’s knowledge of entrepreneurship about the business based creative industries in software by using web software development and educational game 2) create a model for fostering entrepreneurship based on the creative industries in software by leveraging web development and educational games, 3) conduct training and guidance on UPI students who want to develop business in the field of creative industries engaged in the software industry . PKM-based entrepreneurship activity was attended by about 35 students DPTE FPTK UPI had entrepreneurial high interest and competence in information technology. Outcome generated from PKM entrepreneurship is the emergence of entrepreneurs from the students who are interested in the creative industry in the field of software which is able to open up business opportunities for themselves and others. Another outcome of this entrepreneurship PKM activity is the publication of articles or scientific publications in journals of national/international indexed.

Ad Hoc Networking for Unmanned Ground Vehicles: Design and Evaluation at Command, Control, Communications, Intelligence, Surveillance and Reconnaissance On-the-Move

DTIC Science & Technology

2006-11-01

software components used in the ad hoc nodes for the C4ISR OTM experiment were OLSRD, an open-source proactive MANET routing software, and OpenVPN , an...developed by Mike Baker (openwrt.org). 6OpenVPN is a trademark of OpenVPN Solutions LLC. 6 Secure communications in the MANET are achieved with...encryption provided by Wired Equivalent Privacy (WEP) and OpenVPN . The WEP protocol, which is part of the IEEE 802.11 wireless networking standard

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

PubMed

Stajich, Jason E; Lapp, Hilmar

2006-09-01

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

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

NASA Astrophysics Data System (ADS)

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

2014-01-01

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

Enabling cost-effective multimodal trip planners through open transit data.

DOT National Transportation Integrated Search

2011-05-01

This study examined whether multimodal trip planners can be developed using opensource software and open data sources. : OpenStreetMap (OSM), maintained by the nonprofit OpenStreetMap Foundation, is an open, freely available international : rep...

Enabling cost-effective multimodal trip planners through open transit data.

DOT National Transportation Integrated Search

2011-05-01

This study examined whether multimodal trip planners can be developed using opensource software and open data sources. OpenStreetMap (OSM), maintained by the nonprofit OpenStreetMap Foundation, is an open, freely available international reposit...

Weather forecasting with open source software

NASA Astrophysics Data System (ADS)

Rautenhaus, Marc; Dörnbrack, Andreas

2013-04-01

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

Noninvasive Fetal ECG: the PhysioNet/Computing in Cardiology Challenge 2013.

PubMed

Silva, Ikaro; Behar, Joachim; Sameni, Reza; Zhu, Tingting; Oster, Julien; Clifford, Gari D; Moody, George B

2013-03-01

The PhysioNet/CinC 2013 Challenge aimed to stimulate rapid development and improvement of software for estimating fetal heart rate (FHR), fetal interbeat intervals (FRR), and fetal QT intervals (FQT), from multichannel recordings made using electrodes placed on the mother's abdomen. For the challenge, five data collections from a variety of sources were used to compile a large standardized database, which was divided into training, open test, and hidden test subsets. Gold-standard fetal QRS and QT interval annotations were developed using a novel crowd-sourcing framework. The challenge organizers used the hidden test subset to evaluate 91 open-source software entries submitted by 53 international teams of participants in three challenge events, estimating FHR, FRR, and FQT using the hidden test subset, which was not available for study by participants. Two additional events required only user-submitted QRS annotations to evaluate FHR and FRR estimation accuracy using the open test subset available to participants. The challenge yielded a total of 91 open-source software entries. The best of these achieved average estimation errors of 187bpm 2 for FHR, 20.9 ms for FRR, and 152.7 ms for FQT. The open data sets, scoring software, and open-source entries are available at PhysioNet for researchers interested on working on these problems.

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

NASA Astrophysics Data System (ADS)

Behrends, Knut; Conze, Ronald

2013-04-01

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

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.

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

NASA Technical Reports Server (NTRS)

Schlesinger, Adam

2017-01-01

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

Open source approaches to health information systems in Kenya.

PubMed

Drury, Peter; Dahlman, Bruce

2005-01-01

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

An Assessment of Educational Benefits from the OpenOrbiter Space Program

ERIC Educational Resources Information Center

Straub, Jeremy; Whalen, David

2013-01-01

This paper analyzes the educational impact of the OpenOrbiter Small Spacecraft Development Initiative, a CubeSat development program underway at the University of North Dakota. OpenOrbiter includes traditional STEM activities (e.g., spacecraft engineering, software development); it also incorporates students from non-STEM disciplines not generally…

75 FR 11918 - Hewlett Pachard Company, Business Critical Systems, Mission Critical Business Software Division...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-12

... Pachard Company, Business Critical Systems, Mission Critical Business Software Division, Openvms Operating... Business Software Division, Openvms Operating System Development Group, Including an Employee Operating Out... Company, Business Critical Systems, Mission Critical Business Software Division, OpenVMS Operating System...

Software Development Life Cycle Security Issues

NASA Astrophysics Data System (ADS)

Kaur, Daljit; Kaur, Parminder

2011-12-01

Security is now-a-days one of the major problems because of many reasons. Security is now-a-days one of the major problems because of many reasons. The main cause is that software can't withstand security attacks because of vulnerabilities in it which are caused by defective specifications design and implementation. We have conducted a survey asking software developers, project managers and other people in software development about their security awareness and implementation in Software Development Life Cycle (SDLC). The survey was open to participation for three weeks and this paper explains the survey results.

Free and open-source software application for the evaluation of coronary computed tomography angiography images.

PubMed

Hadlich, Marcelo Souza; Oliveira, Gláucia Maria Moraes; Feijóo, Raúl A; Azevedo, Clerio F; Tura, Bernardo Rangel; Ziemer, Paulo Gustavo Portela; Blanco, Pablo Javier; Pina, Gustavo; Meira, Márcio; Souza e Silva, Nelson Albuquerque de

2012-10-01

The standardization of images used in Medicine in 1993 was performed using the DICOM (Digital Imaging and Communications in Medicine) standard. Several tests use this standard and it is increasingly necessary to design software applications capable of handling this type of image; however, these software applications are not usually free and open-source, and this fact hinders their adjustment to most diverse interests. To develop and validate a free and open-source software application capable of handling DICOM coronary computed tomography angiography images. We developed and tested the ImageLab software in the evaluation of 100 tests randomly selected from a database. We carried out 600 tests divided between two observers using ImageLab and another software sold with Philips Brilliance computed tomography appliances in the evaluation of coronary lesions and plaques around the left main coronary artery (LMCA) and the anterior descending artery (ADA). To evaluate intraobserver, interobserver and intersoftware agreements, we used simple and kappa statistics agreements. The agreements observed between software applications were generally classified as substantial or almost perfect in most comparisons. The ImageLab software agreed with the Philips software in the evaluation of coronary computed tomography angiography tests, especially in patients without lesions, with lesions < 50% in the LMCA and < 70% in the ADA. The agreement for lesions > 70% in the ADA was lower, but this is also observed when the anatomical reference standard is used.

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.

Listening to the student voice to improve educational software

PubMed Central

van Wyk, Mari; van Ryneveld, Linda

2017-01-01

ABSTRACT Academics often develop software for teaching and learning purposes with the best of intentions, only to be disappointed by the low acceptance rate of the software by their students once it is implemented. In this study, the focus is on software that was designed to enable veterinary students to record their clinical skills. A pilot of the software clearly showed that the program had not been received as well as had been anticipated, and therefore the researchers used a group interview and a questionnaire with closed-ended and open-ended questions to obtain the students’ feedback. The open-ended questions were analysed with conceptual content analysis, and themes were identified. Students made valuable suggestions about what they regarded as important considerations when a new software program is introduced. The most important lesson learnt was that students cannot always predict their needs accurately if they are asked for input prior to the development of software. For that reason student input should be obtained on a continuous and regular basis throughout the design and development phases. PMID:28678678

Four simple recommendations to encourage best practices in research software

PubMed Central

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

2017-01-01

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

Four simple recommendations to encourage best practices in research software.

PubMed

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

2017-01-01

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

The Use of Open Source Software in the Global Land Ice Measurements From Space (GLIMS) Project, and the Relevance to Institutional Cooperation

Treesearch

Christopher W. Helm

2006-01-01

GLIMS is a NASA funded project that utilizes Open-Source Software to achieve its goal of creating a globally complete inventory of glaciers. The participation of many international institutions and the development of on-line mapping applications to provide access to glacial data have both been enhanced by Open-Source GIS capabilities and play a crucial role in the...

Scientific Software - the role of best practices and recommendations

NASA Astrophysics Data System (ADS)

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

2017-04-01

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

An open source platform for multi-scale spatially distributed simulations of microbial ecosystems

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

Segre, Daniel

2014-08-14

The goal of this project was to develop a tool for facilitating simulation, validation and discovery of multiscale dynamical processes in microbial ecosystems. This led to the development of an open-source software platform for Computation Of Microbial Ecosystems in Time and Space (COMETS). COMETS performs spatially distributed time-dependent flux balance based simulations of microbial metabolism. Our plan involved building the software platform itself, calibrating and testing it through comparison with experimental data, and integrating simulations and experiments to address important open questions on the evolution and dynamics of cross-feeding interactions between microbial species.

Nurturing reliable and robust open-source scientific software

NASA Astrophysics Data System (ADS)

Uieda, L.; Wessel, P.

2017-12-01

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

GiPSi:a framework for open source/open architecture software development for organ-level surgical simulation.

PubMed

Cavuşoğlu, M Cenk; Göktekin, Tolga G; Tendick, Frank

2006-04-01

This paper presents the architectural details of an evolving open source/open architecture software framework for developing organ-level surgical simulations. Our goal is to facilitate shared development of reusable models, to accommodate heterogeneous models of computation, and to provide a framework for interfacing multiple heterogeneous models. The framework provides an application programming interface for interfacing dynamic models defined over spatial domains. It is specifically designed to be independent of the specifics of the modeling methods used, and therefore facilitates seamless integration of heterogeneous models and processes. Furthermore, each model has separate geometries for visualization, simulation, and interfacing, allowing the model developer to choose the most natural geometric representation for each case. Input/output interfaces for visualization and haptics for real-time interactive applications have also been provided.

A Quantitative Analysis of Open Source Software's Acceptability as Production-Quality Code

ERIC Educational Resources Information Center

Fischer, Michael

2011-01-01

The difficulty in writing defect-free software has been long acknowledged both by academia and industry. A constant battle occurs as developers seek to craft software that works within aggressive business schedules and deadlines. Many tools and techniques are used in attempt to manage these software projects. Software metrics are a tool that has…

PD5: a general purpose library for primer design software.

PubMed

Riley, Michael C; Aubrey, Wayne; Young, Michael; Clare, Amanda

2013-01-01

Complex PCR applications for large genome-scale projects require fast, reliable and often highly sophisticated primer design software applications. Presently, such applications use pipelining methods to utilise many third party applications and this involves file parsing, interfacing and data conversion, which is slow and prone to error. A fully integrated suite of software tools for primer design would considerably improve the development time, the processing speed, and the reliability of bespoke primer design software applications. The PD5 software library is an open-source collection of classes and utilities, providing a complete collection of software building blocks for primer design and analysis. It is written in object-oriented C(++) with an emphasis on classes suitable for efficient and rapid development of bespoke primer design programs. The modular design of the software library simplifies the development of specific applications and also integration with existing third party software where necessary. We demonstrate several applications created using this software library that have already proved to be effective, but we view the project as a dynamic environment for building primer design software and it is open for future development by the bioinformatics community. Therefore, the PD5 software library is published under the terms of the GNU General Public License, which guarantee access to source-code and allow redistribution and modification. The PD5 software library is downloadable from Google Code and the accompanying Wiki includes instructions and examples: http://code.google.com/p/primer-design.

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…

Data-Driven Software Framework for Web-Based ISS Telescience

NASA Technical Reports Server (NTRS)

Tso, Kam S.

2005-01-01

Software that enables authorized users to monitor and control scientific payloads aboard the International Space Station (ISS) from diverse terrestrial locations equipped with Internet connections is undergoing development. This software reflects a data-driven approach to distributed operations. A Web-based software framework leverages prior developments in Java and Extensible Markup Language (XML) to create portable code and portable data, to which one can gain access via Web-browser software on almost any common computer. Open-source software is used extensively to minimize cost; the framework also accommodates enterprise-class server software to satisfy needs for high performance and security. To accommodate the diversity of ISS experiments and users, the framework emphasizes openness and extensibility. Users can take advantage of available viewer software to create their own client programs according to their particular preferences, and can upload these programs for custom processing of data, generation of views, and planning of experiments. The same software system, possibly augmented with a subset of data and additional software tools, could be used for public outreach by enabling public users to replay telescience experiments, conduct their experiments with simulated payloads, and create their own client programs and other custom software.

OpenMx: An Open Source Extended Structural Equation Modeling Framework

ERIC Educational Resources Information Center

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

2011-01-01

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

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.

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

NASA Astrophysics Data System (ADS)

Babin, B. L.; Hu, L.

2008-12-01

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

Open Radio Communications Architecture Core Framework V1.1.0 Volume 1 Software Users Manual

DTIC Science & Technology

2005-02-01

on a PC utilizing the KDE desktop that comes with Red Hat Linux . The default desktop for most Red Hat Linux installations is the GNOME desktop. The...SCA) v2.2. The software was designed for a desktop computer running the Linux operating system (OS). It was developed in C++, uses ACE/TAO for CORBA...middleware, Xerces for the XML parser, and Red Hat Linux for the Operating System. The software is referred to as, Open Radio Communication

An object oriented implementation of the Yeadon human inertia model

PubMed Central

Dembia, Christopher; Moore, Jason K.; Hubbard, Mont

2015-01-01

We present an open source software implementation of a popular mathematical method developed by M.R. Yeadon for calculating the body and segment inertia parameters of a human body. The software is written in a high level open source language and provides three interfaces for manipulating the data and the model: a Python API, a command-line user interface, and a graphical user interface. Thus the software can fit into various data processing pipelines and requires only simple geometrical measures as input. PMID:25717365

An object oriented implementation of the Yeadon human inertia model.

PubMed

Dembia, Christopher; Moore, Jason K; Hubbard, Mont

2014-01-01

We present an open source software implementation of a popular mathematical method developed by M.R. Yeadon for calculating the body and segment inertia parameters of a human body. The software is written in a high level open source language and provides three interfaces for manipulating the data and the model: a Python API, a command-line user interface, and a graphical user interface. Thus the software can fit into various data processing pipelines and requires only simple geometrical measures as input.

CellProfiler and KNIME: open source tools for high content screening.

PubMed

Stöter, Martin; Niederlein, Antje; Barsacchi, Rico; Meyenhofer, Felix; Brandl, Holger; Bickle, Marc

2013-01-01

High content screening (HCS) has established itself in the world of the pharmaceutical industry as an essential tool for drug discovery and drug development. HCS is currently starting to enter the academic world and might become a widely used technology. Given the diversity of problems tackled in academic research, HCS could experience some profound changes in the future, mainly with more imaging modalities and smart microscopes being developed. One of the limitations in the establishment of HCS in academia is flexibility and cost. Flexibility is important to be able to adapt the HCS setup to accommodate the multiple different assays typical of academia. Many cost factors cannot be avoided, but the costs of the software packages necessary to analyze large datasets can be reduced by using Open Source software. We present and discuss the Open Source software CellProfiler for image analysis and KNIME for data analysis and data mining that provide software solutions which increase flexibility and keep costs low.

Basic to Advanced InSAR Processing: GMTSAR

NASA Astrophysics Data System (ADS)

Sandwell, D. T.; Xu, X.; Baker, S.; Hogrelius, A.; Mellors, R. J.; Tong, X.; Wei, M.; Wessel, P.

2017-12-01

Monitoring crustal deformation using InSAR is becoming a standard technique for the science and application communities. Optimal use of the new data streams from Sentinel-1 and NISAR will require open software tools as well as education on the strengths and limitations of the InSAR methods. Over the past decade we have developed freely available, open-source software for processing InSAR data. The software relies on the Generic Mapping Tools (GMT) for the back-end data analysis and display and is thus called GMTSAR. With startup funding from NSF, we accelerated the development of GMTSAR to include more satellite data sources and provide better integration and distribution with GMT. In addition, with support from UNAVCO we have offered 6 GMTSAR short courses to educate mostly novice InSAR users. Currently, the software is used by hundreds of scientists and engineers around the world to study deformation at more than 4300 different sites. The most challenging aspect of the recent software development was the transition from image alignment using the cross-correlation method to a completely new alignment algorithm that uses only the precise orbital information to geometrically align images to an accuracy of better than 7 cm. This development was needed to process a new data type that is being acquired by the Sentinel-1A/B satellites. This combination of software and open data is transforming radar interferometry from a research tool into a fully operational time series analysis tool. Over the next 5 years we are planning to continue to broaden the user base through: improved software delivery methods; code hardening; better integration with data archives; support for high level products being developed for NISAR; and continued education and outreach.

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

NASA Astrophysics Data System (ADS)

Engel, P.; Schweimler, B.

2016-04-01

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

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

ERIC Educational Resources Information Center

Wang, Shuo; Wang, Jing; Gao, Yanjing

2017-01-01

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

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

PubMed

Paton, C; Karopka, T

2017-08-01

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

Model driven development of clinical information sytems using openEHR.

PubMed

Atalag, Koray; Yang, Hong Yul; Tempero, Ewan; Warren, Jim

2011-01-01

openEHR and the recent international standard (ISO 13606) defined a model driven software development methodology for health information systems. However there is little evidence in the literature describing implementation; especially for desktop clinical applications. This paper presents an implementation pathway using .Net/C# technology for Microsoft Windows desktop platforms. An endoscopy reporting application driven by openEHR Archetypes and Templates has been developed. A set of novel GUI directives has been defined and presented which guides the automatic graphical user interface generator to render widgets properly. We also reveal the development steps and important design decisions; from modelling to the final software product. This might provide guidance for other developers and form evidence required for the adoption of these standards for vendors and national programs alike.

A Clustering-Based Approach to Enriching Code Foraging Environment.

PubMed

Niu, Nan; Jin, Xiaoyu; Niu, Zhendong; Cheng, Jing-Ru C; Li, Ling; Kataev, Mikhail Yu

2016-09-01

Developers often spend valuable time navigating and seeking relevant code in software maintenance. Currently, there is a lack of theoretical foundations to guide tool design and evaluation to best shape the code base to developers. This paper contributes a unified code navigation theory in light of the optimal food-foraging principles. We further develop a novel framework for automatically assessing the foraging mechanisms in the context of program investigation. We use the framework to examine to what extent the clustering of software entities affects code foraging. Our quantitative analysis of long-lived open-source projects suggests that clustering enriches the software environment and improves foraging efficiency. Our qualitative inquiry reveals concrete insights into real developer's behavior. Our research opens the avenue toward building a new set of ecologically valid code navigation tools.

HydroDesktop: An Open Source GIS-Based Platform for Hydrologic Data Discovery, Visualization, and Analysis

NASA Astrophysics Data System (ADS)

Ames, D. P.; Kadlec, J.; Cao, Y.; Grover, D.; Horsburgh, J. S.; Whiteaker, T.; Goodall, J. L.; Valentine, D. W.

2010-12-01

A growing number of hydrologic information servers are being deployed by government agencies, university networks, and individual researchers using the Consortium of Universities for the Advancement of Hydrologic Science, Inc. (CUAHSI) Hydrologic Information System (HIS). The CUAHSI HIS Project has developed a standard software stack, called HydroServer, for publishing hydrologic observations data. It includes the Observations Data Model (ODM) database and Water Data Service web services, which together enable publication of data on the Internet in a standard format called Water Markup Language (WaterML). Metadata describing available datasets hosted on these servers is compiled within a central metadata catalog called HIS Central at the San Diego Supercomputer Center and is searchable through a set of predefined web services based queries. Together, these servers and central catalog service comprise a federated HIS of a scale and comprehensiveness never previously available. This presentation will briefly review/introduce the CUAHSI HIS system with special focus on a new HIS software tool called "HydroDesktop" and the open source software development web portal, www.HydroDesktop.org, which supports community development and maintenance of the software. HydroDesktop is a client-side, desktop software application that acts as a search and discovery tool for exploring the distributed network of HydroServers, downloading specific data series, visualizing and summarizing data series and exporting these to formats needed for analysis by external software. HydroDesktop is based on the open source DotSpatial GIS developer toolkit which provides it with map-based data interaction and visualization, and a plug-in interface that can be used by third party developers and researchers to easily extend the software using Microsoft .NET programming languages. HydroDesktop plug-ins that are presently available or currently under development within the project and by third party collaborators include functions for data search and discovery, extensive graphing, data editing and export, HydroServer exploration, integration with the OpenMI workflow and modeling system, and an interface for data analysis through the R statistical package.

A Generic Software Architecture For Prognostics

NASA Technical Reports Server (NTRS)

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

2017-01-01

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

Integrating HCI Specialists into Open Source Software Development Projects

NASA Astrophysics Data System (ADS)

Hedberg, Henrik; Iivari, Netta

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

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

NASA Astrophysics Data System (ADS)

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

2012-12-01

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

AKM in Open Source Communities

NASA Astrophysics Data System (ADS)

Stamelos, Ioannis; Kakarontzas, George

Previous chapters in this book have dealt with Architecture Knowledge Management in traditional Closed Source Software (CSS) projects. This chapterwill attempt to examine the ways that knowledge is shared among participants in Free Libre Open Source Software (FLOSS 1) projects and how architectural knowledge is managed w.r.t. CSS. FLOSS projects are organized and developed in a fundamentally different way than CSS projects. FLOSS projects simply do not develop code as CSS projects do. As a consequence, their knowledge management mechanisms are also based on different concepts and tools.

Orchestrating high-throughput genomic analysis with Bioconductor

PubMed Central

Huber, Wolfgang; Carey, Vincent J.; Gentleman, Robert; Anders, Simon; Carlson, Marc; Carvalho, Benilton S.; Bravo, Hector Corrada; Davis, Sean; Gatto, Laurent; Girke, Thomas; Gottardo, Raphael; Hahne, Florian; Hansen, Kasper D.; Irizarry, Rafael A.; Lawrence, Michael; Love, Michael I.; MacDonald, James; Obenchain, Valerie; Oleś, Andrzej K.; Pagès, Hervé; Reyes, Alejandro; Shannon, Paul; Smyth, Gordon K.; Tenenbaum, Dan; Waldron, Levi; Morgan, Martin

2015-01-01

Bioconductor is an open-source, open-development software project for the analysis and comprehension of high-throughput data in genomics and molecular biology. The project aims to enable interdisciplinary research, collaboration and rapid development of scientific software. Based on the statistical programming language R, Bioconductor comprises 934 interoperable packages contributed by a large, diverse community of scientists. Packages cover a range of bioinformatic and statistical applications. They undergo formal initial review and continuous automated testing. We present an overview for prospective users and contributors. PMID:25633503

Software Assurance: Five Essential Considerations for Acquisition Officials

DTIC Science & Technology

2007-05-01

May 2007 www.stsc.hill.af.mil 17 2 • address security concerns in the software development life cycle ( SDLC )? • Are there formal software quality...What threat modeling process, if any, is used when designing the software ? What analysis, design, and construction tools are used by your software design...the-shelf (COTS), government off-the-shelf (GOTS), open- source, embedded, and legacy software . Attackers exploit unintentional vulnerabil- ities or

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

NASA Astrophysics Data System (ADS)

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

2013-12-01

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

[Example of product development by industry and research solidarity].

PubMed

Seki, Masayoshi

2014-01-01

When the industrial firms develop the product, the research result from research institutions is used or to reflect the ideas from users on the developed product would be significant in order to improve the product. To state the software product which developed jointly as an example to describe the adopted development technique and its result, and to consider the modality of the industry solidarity seen from the company side and joint development. The software development methods have the merit and demerit and necessary to choose the optimal development technique by the system which develops. We have been jointly developed the dose distribution browsing software. As the software development method, we adopted the prototype model. In order to display the dose distribution information, it is necessary to load four objects which are CT-Image, Structure Set, RT-Plan, and RT-Dose, are displayed in a composite manner. The prototype model which is the development technique was adopted by this joint development was optimal especially to develop the dose distribution browsing software. In a prototype model, since the detail design was created based on the program source code after the program was finally completed, there was merit on the period shortening of document written and consist in design and implementation. This software eventually opened to the public as an open source. Based on this developed prototype software, the release version of the dose distribution browsing software was developed. Developing this type of novelty software, it normally takes two to three years, but since the joint development was adopted, it shortens the development period to one year. Shortening the development period was able to hold down to the minimum development cost for a company and thus, this will be reflected to the product price. The specialists make requests on the product from user's point of view are important, but increase in specialists as professionals for product development will increase the expectations to develop a product to meet the users demand.

Reflecting Indigenous Culture in Educational Software Design.

ERIC Educational Resources Information Center

Fleer, Marilyn

1989-01-01

Discusses research on Australian Aboriginal cognition which relates to the development of appropriate educational software. Describes "Tinja," a software program using familiar content and experiences, Aboriginal characters and cultural values, extensive graphics and animation, peer and group work, and open-ended design to help young…

Software Cost-Estimation Model

NASA Technical Reports Server (NTRS)

Tausworthe, R. C.

1985-01-01

Software Cost Estimation Model SOFTCOST provides automated resource and schedule model for software development. Combines several cost models found in open literature into one comprehensive set of algorithms. Compensates for nearly fifty implementation factors relative to size of task, inherited baseline, organizational and system environment and difficulty of task.

The Computational Infrastructure for Geodynamics as a Community of Practice

NASA Astrophysics Data System (ADS)

Hwang, L.; Kellogg, L. H.

2016-12-01

Computational Infrastructure for Geodynamics (CIG), geodynamics.org, originated in 2005 out of community recognition that the efforts of individual or small groups of researchers to develop scientifically-sound software is impossible to sustain, duplicates effort, and makes it difficult for scientists to adopt state-of-the art computational methods that promote new discovery. As a community of practice, participants in CIG share an interest in computational modeling in geodynamics and work together on open source software to build the capacity to support complex, extensible, scalable, interoperable, reliable, and reusable software in an effort to increase the return on investment in scientific software development and increase the quality of the resulting software. The group interacts regularly to learn from each other and better their practices formally through webinar series, workshops, and tutorials and informally through listservs and hackathons. Over the past decade, we have learned that successful scientific software development requires at a minimum: collaboration between domain-expert researchers, software developers and computational scientists; clearly identified and committed lead developer(s); well-defined scientific and computational goals that are regularly evaluated and updated; well-defined benchmarks and testing throughout development; attention throughout development to usability and extensibility; understanding and evaluation of the complexity of dependent libraries; and managed user expectations through education, training, and support. CIG's code donation standards provide the basis for recently formalized best practices in software development (geodynamics.org/cig/dev/best-practices/). Best practices include use of version control; widely used, open source software libraries; extensive test suites; portable configuration and build systems; extensive documentation internal and external to the code; and structured, human readable input formats.

Improving Software Sustainability: Lessons Learned from Profiles in Science.

PubMed

Gallagher, Marie E

2013-01-01

The Profiles in Science® digital library features digitized surrogates of historical items selected from the archival collections of the U.S. National Library of Medicine as well as collaborating institutions. In addition, it contains a database of descriptive, technical and administrative metadata. It also contains various software components that allow creation of the metadata, management of the digital items, and access to the items and metadata through the Profiles in Science Web site [1]. The choices made building the digital library were designed to maximize the sustainability and long-term survival of all of the components of the digital library [2]. For example, selecting standard and open digital file formats rather than proprietary formats increases the sustainability of the digital files [3]. Correspondingly, using non-proprietary software may improve the sustainability of the software--either through in-house expertise or through the open source community. Limiting our digital library software exclusively to open source software or to software developed in-house has not been feasible. For example, we have used proprietary operating systems, scanning software, a search engine, and office productivity software. We did this when either lack of essential capabilities or the cost-benefit trade-off favored using proprietary software. We also did so knowing that in the future we would need to replace or upgrade some of our proprietary software, analogous to migrating from an obsolete digital file format to a new format as the technological landscape changes. Since our digital library's start in 1998, all of its software has been upgraded or replaced, but the digitized items have not yet required migration to other formats. Technological changes that compelled us to replace proprietary software included the cost of product licensing, product support, incompatibility with other software, prohibited use due to evolving security policies, and product abandonment. Sometimes these changes happen on short notice, so we continually monitor our library's software for signs of endangerment. We have attempted to replace proprietary software with suitable in-house or open source software. When the replacement involves a standalone piece of software with a nearly equivalent version, such as replacing a commercial HTTP server with an open source HTTP server, the replacement is straightforward. Recently we replaced software that functioned not only as our search engine but also as the backbone of the architecture of our Web site. In this paper, we describe the lessons learned and the pros and cons of replacing this software with open source software.

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

PubMed

Desai, Trunil S; Srivastava, Shireesh

2018-01-01

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

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

PubMed Central

Desai, Trunil S.

2018-01-01

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

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

NASA Technical Reports Server (NTRS)

Stensrud, Kjell C.; Hamm, Dustin

2007-01-01

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

Towards easing the configuration and new team member accommodation for open source software based portals

NASA Astrophysics Data System (ADS)

Fu, L.; West, P.; Zednik, S.; Fox, P. A.

2013-12-01

For simple portals such as vocabulary based services, which contain small amounts of data and require only hyper-textual representation, it is often an overkill to adopt the whole software stack of database, middleware and front end, or to use a general Web development framework as the starting point of development. Directly combining open source software is a much more favorable approach. However, our experience with the Coastal and Marine Spatial Planning Vocabulary (CMSPV) service portal shows that there are still issues such as system configuration and accommodating a new team member that need to be handled carefully. In this contribution, we share our experience in the context of the CMSPV portal, and focus on the tools and mechanisms we've developed to ease the configuration job and the incorporation process of new project members. We discuss the configuration issues that arise when we don't have complete control over how the software in use is configured and need to follow existing configuration styles that may not be well documented, especially when multiple pieces of such software need to work together as a combined system. As for the CMSPV portal, it is built on two pieces of open source software that are still under rapid development: a Fuseki data server and Epimorphics Linked Data API (ELDA) front end. Both lack mature documentation and tutorials. We developed comparison and labeling tools to ease the problem of system configuration. Another problem that slowed down the project is that project members came and went during the development process, so new members needed to start with a partially configured system and incomplete documentation left by old members. We developed documentation/tutorial maintenance mechanisms based on our comparison and labeling tools to make it easier for the new members to be incorporated into the project. These tools and mechanisms also provided benefit to other projects that reused the software components from the CMSPV system.

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

NASA Technical Reports Server (NTRS)

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

2006-01-01

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

Open source pipeline for ESPaDOnS reduction and analysis

NASA Astrophysics Data System (ADS)

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

2012-09-01

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

Sustaining Open Source Communities through Hackathons - An Example from the ASPECT Community

NASA Astrophysics Data System (ADS)

Heister, T.; Hwang, L.; Bangerth, W.; Kellogg, L. H.

2016-12-01

The ecosystem surrounding a successful scientific open source software package combines both social and technical aspects. Much thought has been given to the technology side of writing sustainable software for large infrastructure projects and software libraries, but less about building the human capacity to perpetuate scientific software used in computational modeling. One effective format for building capacity is regular multi-day hackathons. Scientific hackathons bring together a group of science domain users and scientific software contributors to make progress on a specific software package. Innovation comes through the chance to work with established and new collaborations. Especially in the domain sciences with small communities, hackathons give geographically distributed scientists an opportunity to connect face-to-face. They foster lively discussions amongst scientists with different expertise, promote new collaborations, and increase transparency in both the technical and scientific aspects of code development. ASPECT is an open source, parallel, extensible finite element code to simulate thermal convection, that began development in 2011 under the Computational Infrastructure for Geodynamics. ASPECT hackathons for the past 3 years have grown the number of authors to >50, training new code maintainers in the process. Hackathons begin with leaders establishing project-specific conventions for development, demonstrating the workflow for code contributions, and reviewing relevant technical skills. Each hackathon expands the developer community. Over 20 scientists add >6,000 lines of code during the >1 week event. Participants grow comfortable contributing to the repository and over half continue to contribute afterwards. A high return rate of participants ensures continuity and stability of the group as well as mentoring for novice members. We hope to build other software communities on this model, but anticipate each to bring their own unique challenges.

The SCEC/UseIT Intern Program: Creating Open-Source Visualization Software Using Diverse Resources

NASA Astrophysics Data System (ADS)

Francoeur, H.; Callaghan, S.; Perry, S.; Jordan, T.

2004-12-01

The Southern California Earthquake Center undergraduate IT intern program (SCEC UseIT) conducts IT research to benefit collaborative earth science research. Through this program, interns have developed real-time, interactive, 3D visualization software using open-source tools. Dubbed LA3D, a distribution of this software is now in use by the seismic community. LA3D enables the user to interactively view Southern California datasets and models of importance to earthquake scientists, such as faults, earthquakes, fault blocks, digital elevation models, and seismic hazard maps. LA3D is now being extended to support visualizations anywhere on the planet. The new software, called SCEC-VIDEO (Virtual Interactive Display of Earth Objects), makes use of a modular, plugin-based software architecture which supports easy development and integration of new data sets. Currently SCEC-VIDEO is in beta testing, with a full open-source release slated for the future. Both LA3D and SCEC-VIDEO were developed using a wide variety of software technologies. These, which included relational databases, web services, software management technologies, and 3-D graphics in Java, were necessary to integrate the heterogeneous array of data sources which comprise our software. Currently the interns are working to integrate new technologies and larger data sets to increase software functionality and value. In addition, both LA3D and SCEC-VIDEO allow the user to script and create movies. Thus program interns with computer science backgrounds have been writing software while interns with other interests, such as cinema, geology, and education, have been making movies that have proved of great use in scientific talks, media interviews, and education. Thus, SCEC UseIT incorporates a wide variety of scientific and human resources to create products of value to the scientific and outreach communities. The program plans to continue with its interdisciplinary approach, increasing the relevance of the software and expanding its use in the scientific community.

OpenComet: An automated tool for comet assay image analysis

PubMed Central

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

2014-01-01

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

OpenComet: an automated tool for comet assay image analysis.

PubMed

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

2014-01-01

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

The Azimuth Project: an Open-Access Educational Resource

NASA Astrophysics Data System (ADS)

Baez, J. C.

2012-12-01

The Azimuth Project is an online collaboration of scientists, engineers and programmers who are volunteering their time to do something about a wide range of environmental problems. The project has several aspects: 1) a wiki designed to make reliable, sourced information easy to find and accessible to a technically literate nonexperts, 2) a blog featuring expository articles and news items, 3) a project to write programs that explain basic concepts of climate physics and illustrate principles of good open-source software design, and 4) a project to develop mathematical tools for studying complex networked systems. We discuss the progress so far and some preliminary lessons. For example, enlisting the help of experts outside academia highlights the problems with pay-walled journals and the benefits of open access, as well as differences between how software development is done commercially, in the free software community, and in academe.

CymeR: cytometry analysis using KNIME, docker and R

PubMed Central

Muchmore, B.; Alarcón-Riquelme, M.E.

2017-01-01

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

CymeR: cytometry analysis using KNIME, docker and R.

PubMed

Muchmore, B; Alarcón-Riquelme, M E

2017-03-01

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

SPLASSH: Open source software for camera-based high-speed, multispectral in-vivo optical image acquisition

PubMed Central

Sun, Ryan; Bouchard, Matthew B.; Hillman, Elizabeth M. C.

2010-01-01

Camera-based in-vivo optical imaging can provide detailed images of living tissue that reveal structure, function, and disease. High-speed, high resolution imaging can reveal dynamic events such as changes in blood flow and responses to stimulation. Despite these benefits, commercially available scientific cameras rarely include software that is suitable for in-vivo imaging applications, making this highly versatile form of optical imaging challenging and time-consuming to implement. To address this issue, we have developed a novel, open-source software package to control high-speed, multispectral optical imaging systems. The software integrates a number of modular functions through a custom graphical user interface (GUI) and provides extensive control over a wide range of inexpensive IEEE 1394 Firewire cameras. Multispectral illumination can be incorporated through the use of off-the-shelf light emitting diodes which the software synchronizes to image acquisition via a programmed microcontroller, allowing arbitrary high-speed illumination sequences. The complete software suite is available for free download. Here we describe the software’s framework and provide details to guide users with development of this and similar software. PMID:21258475

Human factors for capacity building: lessons learned from the OpenMRS implementers network.

PubMed

Seebregts, C J; Mamlin, B W; Biondich, P G; Fraser, H S F; Wolfe, B A; Jazayeri, D; Miranda, J; Blaya, J; Sinha, C; Bailey, C T; Kanter, A S

2010-01-01

The overall objective of this project was to investigate ways to strengthen the OpenMRS community by (i) developing capacity and implementing a network focusing specifically on the needs of OpenMRS implementers, (ii) strengthening community-driven aspects of OpenMRS and providing a dedicated forum for implementation-specific issues, and; (iii) providing regional support for OpenMRS implementations as well as mentorship and training. The methods used included (i) face-to-face networking using meetings and workshops; (ii) online collaboration tools, peer support and mentorship programmes; (iii) capacity and community development programmes, and; (iv) community outreach programmes. The community-driven approach, combined with a few simple interventions, has been a key factor in the growth and success of the OpenMRS Implementers Network. It has contributed to implementations in at least twenty-three different countries using basic online tools; and provided mentorship and peer support through an annual meeting, workshops and an internship program. The OpenMRS Implementers Network has formed collaborations with several other open source networks and is evolving regional OpenMRS Centres of Excellence to provide localized support for OpenMRS development and implementation. These initiatives are increasing the range of functionality and sustainability of open source software in the health domain, resulting in improved adoption and enterprise-readiness. Social organization and capacity development activities are important in growing a successful community-driven open source software model.

Computational Infrastructure for Geodynamics (CIG)

NASA Astrophysics Data System (ADS)

Gurnis, M.; Kellogg, L. H.; Bloxham, J.; Hager, B. H.; Spiegelman, M.; Willett, S.; Wysession, M. E.; Aivazis, M.

2004-12-01

Solid earth geophysicists have a long tradition of writing scientific software to address a wide range of problems. In particular, computer simulations came into wide use in geophysics during the decade after the plate tectonic revolution. Solution schemes and numerical algorithms that developed in other areas of science, most notably engineering, fluid mechanics, and physics, were adapted with considerable success to geophysics. This software has largely been the product of individual efforts and although this approach has proven successful, its strength for solving problems of interest is now starting to show its limitations as we try to share codes and algorithms or when we want to recombine codes in novel ways to produce new science. With funding from the NSF, the US community has embarked on a Computational Infrastructure for Geodynamics (CIG) that will develop, support, and disseminate community-accessible software for the greater geodynamics community from model developers to end-users. The software is being developed for problems involving mantle and core dynamics, crustal and earthquake dynamics, magma migration, seismology, and other related topics. With a high level of community participation, CIG is leveraging state-of-the-art scientific computing into a suite of open-source tools and codes. The infrastructure that we are now starting to develop will consist of: (a) a coordinated effort to develop reusable, well-documented and open-source geodynamics software; (b) the basic building blocks - an infrastructure layer - of software by which state-of-the-art modeling codes can be quickly assembled; (c) extension of existing software frameworks to interlink multiple codes and data through a superstructure layer; (d) strategic partnerships with the larger world of computational science and geoinformatics; and (e) specialized training and workshops for both the geodynamics and broader Earth science communities. The CIG initiative has already started to leverage and develop long-term strategic partnerships with open source development efforts within the larger thrusts of scientific computing and geoinformatics. These strategic partnerships are essential as the frontier has moved into multi-scale and multi-physics problems in which many investigators now want to use simulation software for data interpretation, data assimilation, and hypothesis testing.

Terra Harvest software architecture

NASA Astrophysics Data System (ADS)

Humeniuk, Dave; Klawon, Kevin

2012-06-01

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

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

PubMed

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

2016-03-01

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

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

PubMed Central

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

2016-01-01

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

Launching GUPPI: the Green Bank Ultimate Pulsar Processing Instrument

NASA Astrophysics Data System (ADS)

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

2008-08-01

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

Inequalities in Open Source Software Development: Analysis of Contributor's Commits in Apache Software Foundation Projects.

PubMed

Chełkowski, Tadeusz; Gloor, Peter; Jemielniak, Dariusz

2016-01-01

While researchers are becoming increasingly interested in studying OSS phenomenon, there is still a small number of studies analyzing larger samples of projects investigating the structure of activities among OSS developers. The significant amount of information that has been gathered in the publicly available open-source software repositories and mailing-list archives offers an opportunity to analyze projects structures and participant involvement. In this article, using on commits data from 263 Apache projects repositories (nearly all), we show that although OSS development is often described as collaborative, but it in fact predominantly relies on radically solitary input and individual, non-collaborative contributions. We also show, in the first published study of this magnitude, that the engagement of contributors is based on a power-law distribution.

Inequalities in Open Source Software Development: Analysis of Contributor’s Commits in Apache Software Foundation Projects

PubMed Central

2016-01-01

While researchers are becoming increasingly interested in studying OSS phenomenon, there is still a small number of studies analyzing larger samples of projects investigating the structure of activities among OSS developers. The significant amount of information that has been gathered in the publicly available open-source software repositories and mailing-list archives offers an opportunity to analyze projects structures and participant involvement. In this article, using on commits data from 263 Apache projects repositories (nearly all), we show that although OSS development is often described as collaborative, but it in fact predominantly relies on radically solitary input and individual, non-collaborative contributions. We also show, in the first published study of this magnitude, that the engagement of contributors is based on a power-law distribution. PMID:27096157

FieldTrip: Open source software for advanced analysis of MEG, EEG, and invasive electrophysiological data.

PubMed

Oostenveld, Robert; Fries, Pascal; Maris, Eric; Schoffelen, Jan-Mathijs

2011-01-01

This paper describes FieldTrip, an open source software package that we developed for the analysis of MEG, EEG, and other electrophysiological data. The software is implemented as a MATLAB toolbox and includes a complete set of consistent and user-friendly high-level functions that allow experimental neuroscientists to analyze experimental data. It includes algorithms for simple and advanced analysis, such as time-frequency analysis using multitapers, source reconstruction using dipoles, distributed sources and beamformers, connectivity analysis, and nonparametric statistical permutation tests at the channel and source level. The implementation as toolbox allows the user to perform elaborate and structured analyses of large data sets using the MATLAB command line and batch scripting. Furthermore, users and developers can easily extend the functionality and implement new algorithms. The modular design facilitates the reuse in other software packages.

Rapid sample classification using an open port sampling interface coupled with liquid introduction atmospheric pressure ionization mass spectrometry

DOE PAGES

Van Berkel, Gary J.; Kertesz, Vilmos

2016-11-15

An “Open Access”-like mass spectrometric platform to fully utilize the simplicity of the manual open port sampling interface for rapid characterization of unprocessed samples by liquid introduction atmospheric pressure ionization mass spectrometry has been lacking. The in-house developed integrated software with a simple, small and relatively low-cost mass spectrometry system introduced here fills this void. Software was developed to operate the mass spectrometer, to collect and process mass spectrometric data files, to build a database and to classify samples using such a database. These tasks were accomplished via the vendorprovided software libraries. Sample classification based on spectral comparison utilized themore » spectral contrast angle method. As a result, using the developed software platform near real-time sample classification is exemplified using a series of commercially available blue ink rollerball pens and vegetable oils. In the case of the inks, full scan positive and negative ion ESI mass spectra were both used for database generation and sample classification. For the vegetable oils, full scan positive ion mode APCI mass spectra were recorded. The overall accuracy of the employed spectral contrast angle statistical model was 95.3% and 98% in case of the inks and oils, respectively, using leave-one-out cross-validation. In conclusion, this work illustrates that an open port sampling interface/mass spectrometer combination, with appropriate instrument control and data processing software, is a viable direct liquid extraction sampling and analysis system suitable for the non-expert user and near real-time sample classification via database matching.« less

Rapid sample classification using an open port sampling interface coupled with liquid introduction atmospheric pressure ionization mass spectrometry

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

Van Berkel, Gary J.; Kertesz, Vilmos

An “Open Access”-like mass spectrometric platform to fully utilize the simplicity of the manual open port sampling interface for rapid characterization of unprocessed samples by liquid introduction atmospheric pressure ionization mass spectrometry has been lacking. The in-house developed integrated software with a simple, small and relatively low-cost mass spectrometry system introduced here fills this void. Software was developed to operate the mass spectrometer, to collect and process mass spectrometric data files, to build a database and to classify samples using such a database. These tasks were accomplished via the vendorprovided software libraries. Sample classification based on spectral comparison utilized themore » spectral contrast angle method. As a result, using the developed software platform near real-time sample classification is exemplified using a series of commercially available blue ink rollerball pens and vegetable oils. In the case of the inks, full scan positive and negative ion ESI mass spectra were both used for database generation and sample classification. For the vegetable oils, full scan positive ion mode APCI mass spectra were recorded. The overall accuracy of the employed spectral contrast angle statistical model was 95.3% and 98% in case of the inks and oils, respectively, using leave-one-out cross-validation. In conclusion, this work illustrates that an open port sampling interface/mass spectrometer combination, with appropriate instrument control and data processing software, is a viable direct liquid extraction sampling and analysis system suitable for the non-expert user and near real-time sample classification via database matching.« less

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

PubMed

Rosset, Antoine; Spadola, Luca; Ratib, Osman

2004-09-01

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

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

ERIC Educational Resources Information Center

Krishnamurthy, M.

2008-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2010-12-01

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

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

PubMed Central

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

2015-01-01

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

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.

ObsPy: Establishing and maintaining an open-source community package

NASA Astrophysics Data System (ADS)

Krischer, L.; Megies, T.; Barsch, R.

2017-12-01

Python's ecosystem evolved into one of the most powerful and productive research environment across disciplines. ObsPy (https://obspy.org) is a fully community driven, open-source project dedicated to provide a bridge for seismology into that ecosystem. It does so by offering Read and write support for essentially every commonly used data format in seismology, Integrated access to the largest data centers, web services, and real-time data streams, A powerful signal processing toolbox tuned to the specific needs of seismologists, and Utility functionality like travel time calculations, geodetic functions, and data visualizations. ObsPy has been in constant unfunded development for more than eight years and is developed and used by scientists around the world with successful applications in all branches of seismology. By now around 70 people directly contributed code to ObsPy and we aim to make it a self-sustaining community project.This contributions focusses on several meta aspects of open-source software in science, in particular how we experienced them. During the panel we would like to discuss obvious questions like long-term sustainability with very limited to no funding, insufficient computer science training in many sciences, and gaining hard scientific credits for software development, but also the following questions: How to best deal with the fact that a lot of scientific software is very specialized thus usually solves a complex problem but at the same time can only ever reach a limited pool of developers and users by virtue of it being so specialized? Therefore the "many eyes on the code" approach to develop and improve open-source software only applies in a limited fashion. An initial publication for a significant new scientific software package is fairly straightforward. How to on-board and motivate potential new contributors when they can no longer be lured by a potential co-authorship? When is spending significant time and effort on reusable scientific open-source development a reasonable choice for young researchers? The effort to go from purpose tailored code for a single application resulting in a scientific publication is significantly less compared to generalising and engineering it well enough so it can be used by others.

Current trends for customized biomedical software tools.

PubMed

Khan, Haseeb Ahmad

2017-01-01

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

Pilot Study of an Open-source Image Analysis Software for Automated Screening of Conventional Cervical Smears.

PubMed

Sanyal, Parikshit; Ganguli, Prosenjit; Barui, Sanghita; Deb, Prabal

2018-01-01

The Pap stained cervical smear is a screening tool for cervical cancer. Commercial systems are used for automated screening of liquid based cervical smears. However, there is no image analysis software used for conventional cervical smears. The aim of this study was to develop and test the diagnostic accuracy of a software for analysis of conventional smears. The software was developed using Python programming language and open source libraries. It was standardized with images from Bethesda Interobserver Reproducibility Project. One hundred and thirty images from smears which were reported Negative for Intraepithelial Lesion or Malignancy (NILM), and 45 images where some abnormality has been reported, were collected from the archives of the hospital. The software was then tested on the images. The software was able to segregate images based on overall nuclear: cytoplasmic ratio, coefficient of variation (CV) in nuclear size, nuclear membrane irregularity, and clustering. 68.88% of abnormal images were flagged by the software, as well as 19.23% of NILM images. The major difficulties faced were segmentation of overlapping cell clusters and separation of neutrophils. The software shows potential as a screening tool for conventional cervical smears; however, further refinement in technique is required.

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.

Evaluation of the OpenCL AES Kernel using the Intel FPGA SDK for OpenCL

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

Jin, Zheming; Yoshii, Kazutomo; Finkel, Hal

The OpenCL standard is an open programming model for accelerating algorithms on heterogeneous computing system. OpenCL extends the C-based programming language for developing portable codes on different platforms such as CPU, Graphics processing units (GPUs), Digital Signal Processors (DSPs) and Field Programmable Gate Arrays (FPGAs). The Intel FPGA SDK for OpenCL is a suite of tools that allows developers to abstract away the complex FPGA-based development flow for a high-level software development flow. Users can focus on the design of hardware-accelerated kernel functions in OpenCL and then direct the tools to generate the low-level FPGA implementations. The approach makes themore » FPGA-based development more accessible to software users as the needs for hybrid computing using CPUs and FPGAs are increasing. It can also significantly reduce the hardware development time as users can evaluate different ideas with high-level language without deep FPGA domain knowledge. In this report, we evaluate the performance of the kernel using the Intel FPGA SDK for OpenCL and Nallatech 385A FPGA board. Compared to the M506 module, the board provides more hardware resources for a larger design exploration space. The kernel performance is measured with the compute kernel throughput, an upper bound to the FPGA throughput. The report presents the experimental results in details. The Appendix lists the kernel source code.« less

Software for MR image overlay guided needle insertions: the clinical translation process

NASA Astrophysics Data System (ADS)

Ungi, Tamas; U-Thainual, Paweena; Fritz, Jan; Iordachita, Iulian I.; Flammang, Aaron J.; Carrino, John A.; Fichtinger, Gabor

2013-03-01

PURPOSE: Needle guidance software using augmented reality image overlay was translated from the experimental phase to support preclinical and clinical studies. Major functional and structural changes were needed to meet clinical requirements. We present the process applied to fulfill these requirements, and selected features that may be applied in the translational phase of other image-guided surgical navigation systems. METHODS: We used an agile software development process for rapid adaptation to unforeseen clinical requests. The process is based on iterations of operating room test sessions, feedback discussions, and software development sprints. The open-source application framework of 3D Slicer and the NA-MIC kit provided sufficient flexibility and stable software foundations for this work. RESULTS: All requirements were addressed in a process with 19 operating room test iterations. Most features developed in this phase were related to workflow simplification and operator feedback. CONCLUSION: Efficient and affordable modifications were facilitated by an open source application framework and frequent clinical feedback sessions. Results of cadaver experiments show that software requirements were successfully solved after a limited number of operating room tests.

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

NASA Astrophysics Data System (ADS)

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

2017-04-01

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

Leveraging OpenStudio's Application Programming Interfaces: Preprint

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

Long, N.; Ball, B.; Goldwasser, D.

2013-11-01

OpenStudio development efforts have been focused on providing Application Programming Interfaces (APIs) where users are able to extend OpenStudio without the need to compile the open source libraries. This paper will discuss the basic purposes and functionalities of the core libraries that have been wrapped with APIs including the Building Model, Results Processing, Advanced Analysis, UncertaintyQuantification, and Data Interoperability through Translators. Several building energy modeling applications have been produced using OpenStudio's API and Software Development Kits (SDK) including the United States Department of Energy's Asset ScoreCalculator, a mobile-based audit tool, an energy design assistance reporting protocol, and a portfolio scalemore » incentive optimization analysismethodology. Each of these software applications will be discussed briefly and will describe how the APIs were leveraged for various uses including high-level modeling, data transformations from detailed building audits, error checking/quality assurance of models, and use of high-performance computing for mass simulations.« less

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

NASA Technical Reports Server (NTRS)

Johnson, Sandra; Eddy, Wesley

2016-01-01

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

Open Crowdsourcing: Leveraging Community Software Developers for IT Projects

ERIC Educational Resources Information Center

Phair, Derek

2012-01-01

This qualitative exploratory single-case study was designed to examine and understand the use of volunteer community participants as software developers and other project related roles, such as testers, in completing a web-based application project by a non-profit organization. This study analyzed the strategic decision to engage crowd…

Alone Together: A Socio-Technical Theory of Motivation, Coordination and Collaboration Technologies in Organizing for Free and Open Source Software Development

ERIC Educational Resources Information Center

Howison, James

2009-01-01

This dissertation presents evidence that the production of Free and Open Source Software (FLOSS) is far more alone than together; it is far more often individual work done "in company" than it is teamwork. When tasks appear too large for an individual they are more likely to be deferred until they are easier rather than be undertaken through…

Survivability as a Tool for Evaluating Open Source Software

DTIC Science & Technology

2015-06-01

the thesis limited the program development, so it is only able to process project issues (bugs or feature requests), which is an important metric for...Ideally, these insights may provide an analytic framework to generate guidance for decision makers that may support the inclusion of OSS to more...refine their efforts to build quality software and to strengthen their software development communities. 1.4 Research Questions This thesis addresses

Towards an Open, Distributed Software Architecture for UxS Operations

NASA Technical Reports Server (NTRS)

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

2015-01-01

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

Challenges of the Open Source Component Marketplace in the Industry

NASA Astrophysics Data System (ADS)

Ayala, Claudia; Hauge, Øyvind; Conradi, Reidar; Franch, Xavier; Li, Jingyue; Velle, Ketil Sandanger

The reuse of Open Source Software components available on the Internet is playing a major role in the development of Component Based Software Systems. Nevertheless, the special nature of the OSS marketplace has taken the “classical” concept of software reuse based on centralized repositories to a completely different arena based on massive reuse over Internet. In this paper we provide an overview of the actual state of the OSS marketplace, and report preliminary findings about how companies interact with this marketplace to reuse OSS components. Such data was gathered from interviews in software companies in Spain and Norway. Based on these results we identify some challenges aimed to improve the industrial reuse of OSS components.

Software for Real-Time Analysis of Subsonic Test Shot Accuracy

DTIC Science & Technology

2014-03-01

used the C++ programming language, the Open Source Computer Vision ( OpenCV ®) software library, and Microsoft Windows® Application Programming...video for comparison through OpenCV image analysis tools. Based on the comparison, the software then computed the coordinates of each shot relative to...DWB researchers wanted to use the Open Source Computer Vision ( OpenCV ) software library for capturing and analyzing frames of video. OpenCV contains

Establishing a Professional Development Network around Dynamic Mathematics Software in England

ERIC Educational Resources Information Center

Lavicza, Zsolt; Hohenwarter, Markus; Jones, Keith; Lu, Allison; Dawes, Mark

2010-01-01

In this paper, we will outline some results of an NCETM (National Centre for Excellence in the Teaching of Mathematics) funded project that aimed to establish a professional development network with an open-source mathematical software--GeoGebra--in England. During the past few years a large international user and developer community has formed…

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

PubMed Central

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

2011-01-01

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

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

PubMed

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

2011-01-01

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

The development and technology transfer of software engineering technology at NASA. Johnson Space Center

NASA Technical Reports Server (NTRS)

Pitman, C. L.; Erb, D. M.; Izygon, M. E.; Fridge, E. M., III; Roush, G. B.; Braley, D. M.; Savely, R. T.

1992-01-01

The United State's big space projects of the next decades, such as Space Station and the Human Exploration Initiative, will need the development of many millions of lines of mission critical software. NASA-Johnson (JSC) is identifying and developing some of the Computer Aided Software Engineering (CASE) technology that NASA will need to build these future software systems. The goal is to improve the quality and the productivity of large software development projects. New trends are outlined in CASE technology and how the Software Technology Branch (STB) at JSC is endeavoring to provide some of these CASE solutions for NASA is described. Key software technology components include knowledge-based systems, software reusability, user interface technology, reengineering environments, management systems for the software development process, software cost models, repository technology, and open, integrated CASE environment frameworks. The paper presents the status and long-term expectations for CASE products. The STB's Reengineering Application Project (REAP), Advanced Software Development Workstation (ASDW) project, and software development cost model (COSTMODL) project are then discussed. Some of the general difficulties of technology transfer are introduced, and a process developed by STB for CASE technology insertion is described.

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

DOE PAGES

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

2013-02-06

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

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

PubMed

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

2014-02-01

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

Open source software to control Bioflo bioreactors.

PubMed

Burdge, David A; Libourel, Igor G L

2014-01-01

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

Open Source Software to Control Bioflo Bioreactors

PubMed Central

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

2014-01-01

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

Space Station Software Recommendations

NASA Technical Reports Server (NTRS)

Voigt, S. (Editor)

1985-01-01

Four panels of invited experts and NASA representatives focused on the following topics: software management, software development environment, languages, and software standards. Each panel deliberated in private, held two open sessions with audience participation, and developed recommendations for the NASA Space Station Program. The major thrusts of the recommendations were as follows: (1) The software management plan should establish policies, responsibilities, and decision points for software acquisition; (2) NASA should furnish a uniform modular software support environment and require its use for all space station software acquired (or developed); (3) The language Ada should be selected for space station software, and NASA should begin to address issues related to the effective use of Ada; and (4) The space station software standards should be selected (based upon existing standards where possible), and an organization should be identified to promulgate and enforce them. These and related recommendations are described in detail in the conference proceedings.

Architecture for Survivable System Processing (ASSP)

NASA Astrophysics Data System (ADS)

Wood, Richard J.

1991-11-01

The Architecture for Survivable System Processing (ASSP) Program is a multi-phase effort to implement Department of Defense (DOD) and commercially developed high-tech hardware, software, and architectures for reliable space avionics and ground based systems. System configuration options provide processing capabilities to address Time Dependent Processing (TDP), Object Dependent Processing (ODP), and Mission Dependent Processing (MDP) requirements through Open System Architecture (OSA) alternatives that allow for the enhancement, incorporation, and capitalization of a broad range of development assets. High technology developments in hardware, software, and networking models, address technology challenges of long processor life times, fault tolerance, reliability, throughput, memories, radiation hardening, size, weight, power (SWAP) and security. Hardware and software design, development, and implementation focus on the interconnectivity/interoperability of an open system architecture and is being developed to apply new technology into practical OSA components. To insure for widely acceptable architecture capable of interfacing with various commercial and military components, this program provides for regular interactions with standardization working groups (e.g.) the International Standards Organization (ISO), American National Standards Institute (ANSI), Society of Automotive Engineers (SAE), and Institute of Electrical and Electronic Engineers (IEEE). Selection of a viable open architecture is based on the widely accepted standards that implement the ISO/OSI Reference Model.

Calculating the Mean Amplitude of Glycemic Excursions from Continuous Glucose Data Using an Open-Code Programmable Algorithm Based on the Integer Nonlinear Method.

PubMed

Yu, Xuefei; Lin, Liangzhuo; Shen, Jie; Chen, Zhi; Jian, Jun; Li, Bin; Xin, Sherman Xuegang

2018-01-01

The mean amplitude of glycemic excursions (MAGE) is an essential index for glycemic variability assessment, which is treated as a key reference for blood glucose controlling at clinic. However, the traditional "ruler and pencil" manual method for the calculation of MAGE is time-consuming and prone to error due to the huge data size, making the development of robust computer-aided program an urgent requirement. Although several software products are available instead of manual calculation, poor agreement among them is reported. Therefore, more studies are required in this field. In this paper, we developed a mathematical algorithm based on integer nonlinear programming. Following the proposed mathematical method, an open-code computer program named MAGECAA v1.0 was developed and validated. The results of the statistical analysis indicated that the developed program was robust compared to the manual method. The agreement among the developed program and currently available popular software is satisfied, indicating that the worry about the disagreement among different software products is not necessary. The open-code programmable algorithm is an extra resource for those peers who are interested in the related study on methodology in the future.

Architecture for Survivable System Processing (ASSP)

NASA Technical Reports Server (NTRS)

Wood, Richard J.

1991-01-01

The Architecture for Survivable System Processing (ASSP) Program is a multi-phase effort to implement Department of Defense (DOD) and commercially developed high-tech hardware, software, and architectures for reliable space avionics and ground based systems. System configuration options provide processing capabilities to address Time Dependent Processing (TDP), Object Dependent Processing (ODP), and Mission Dependent Processing (MDP) requirements through Open System Architecture (OSA) alternatives that allow for the enhancement, incorporation, and capitalization of a broad range of development assets. High technology developments in hardware, software, and networking models, address technology challenges of long processor life times, fault tolerance, reliability, throughput, memories, radiation hardening, size, weight, power (SWAP) and security. Hardware and software design, development, and implementation focus on the interconnectivity/interoperability of an open system architecture and is being developed to apply new technology into practical OSA components. To insure for widely acceptable architecture capable of interfacing with various commercial and military components, this program provides for regular interactions with standardization working groups (e.g.) the International Standards Organization (ISO), American National Standards Institute (ANSI), Society of Automotive Engineers (SAE), and Institute of Electrical and Electronic Engineers (IEEE). Selection of a viable open architecture is based on the widely accepted standards that implement the ISO/OSI Reference Model.

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.

FieldTrip: Open Source Software for Advanced Analysis of MEG, EEG, and Invasive Electrophysiological Data

PubMed Central

Oostenveld, Robert; Fries, Pascal; Maris, Eric; Schoffelen, Jan-Mathijs

2011-01-01

This paper describes FieldTrip, an open source software package that we developed for the analysis of MEG, EEG, and other electrophysiological data. The software is implemented as a MATLAB toolbox and includes a complete set of consistent and user-friendly high-level functions that allow experimental neuroscientists to analyze experimental data. It includes algorithms for simple and advanced analysis, such as time-frequency analysis using multitapers, source reconstruction using dipoles, distributed sources and beamformers, connectivity analysis, and nonparametric statistical permutation tests at the channel and source level. The implementation as toolbox allows the user to perform elaborate and structured analyses of large data sets using the MATLAB command line and batch scripting. Furthermore, users and developers can easily extend the functionality and implement new algorithms. The modular design facilitates the reuse in other software packages. PMID:21253357

The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology.

PubMed

Galdzicki, Michal; Clancy, Kevin P; Oberortner, Ernst; Pocock, Matthew; Quinn, Jacqueline Y; Rodriguez, Cesar A; Roehner, Nicholas; Wilson, Mandy L; Adam, Laura; Anderson, J Christopher; Bartley, Bryan A; Beal, Jacob; Chandran, Deepak; Chen, Joanna; Densmore, Douglas; Endy, Drew; Grünberg, Raik; Hallinan, Jennifer; Hillson, Nathan J; Johnson, Jeffrey D; Kuchinsky, Allan; Lux, Matthew; Misirli, Goksel; Peccoud, Jean; Plahar, Hector A; Sirin, Evren; Stan, Guy-Bart; Villalobos, Alan; Wipat, Anil; Gennari, John H; Myers, Chris J; Sauro, Herbert M

2014-06-01

The re-use of previously validated designs is critical to the evolution of synthetic biology from a research discipline to an engineering practice. Here we describe the Synthetic Biology Open Language (SBOL), a proposed data standard for exchanging designs within the synthetic biology community. SBOL represents synthetic biology designs in a community-driven, formalized format for exchange between software tools, research groups and commercial service providers. The SBOL Developers Group has implemented SBOL as an XML/RDF serialization and provides software libraries and specification documentation to help developers implement SBOL in their own software. We describe early successes, including a demonstration of the utility of SBOL for information exchange between several different software tools and repositories from both academic and industrial partners. As a community-driven standard, SBOL will be updated as synthetic biology evolves to provide specific capabilities for different aspects of the synthetic biology workflow.

Open University Environmental Education and Training.

ERIC Educational Resources Information Center

Blackmore, Christine

1996-01-01

Describes the approach to environmental education courses at Open University. Includes broad course content, team teaching approach, and philosophy of reorienting education towards sustainable development. Course material for open learning includes self-contained study packs as well as course texts, video, audio, and computer software. Nonformal…

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

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

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

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

Data Mining Meets HCI: Making Sense of Large Graphs

DTIC Science & Technology

2012-07-01

graph algo- rithms, won the Open Source Software World Challenge, Silver Award. We have released Pegasus as free , open-source software, downloaded by...METIS [77], spectral clustering [108], and the parameter- free “Cross-associations” (CA) [26]. Belief Propagation can also be used for clus- tering, as...number of tools have been developed to support “ landscape ” views of information. These include WebBook and Web- Forager [23], which use a book metaphor

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

PubMed

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

2015-02-01

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

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

DTIC Science & Technology

2007-04-01

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

A Stigmergy Approach for Open Source Software Developer Community Simulation

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

Cui, Xiaohui; Beaver, Justin M; Potok, Thomas E

2009-01-01

The stigmergy collaboration approach provides a hypothesized explanation about how online groups work together. In this research, we presented a stigmergy approach for building an agent based open source software (OSS) developer community collaboration simulation. We used group of actors who collaborate on OSS projects as our frame of reference and investigated how the choices actors make in contribution their work on the projects determinate the global status of the whole OSS projects. In our simulation, the forum posts and project codes served as the digital pheromone and the modified Pierre-Paul Grasse pheromone model is used for computing developer agentmore » behaviors selection probability.« less

Rapid sample classification using an open port sampling interface coupled with liquid introduction atmospheric pressure ionization mass spectrometry.

PubMed

Van Berkel, Gary J; Kertesz, Vilmos

2017-02-15

An "Open Access"-like mass spectrometric platform to fully utilize the simplicity of the manual open port sampling interface for rapid characterization of unprocessed samples by liquid introduction atmospheric pressure ionization mass spectrometry has been lacking. The in-house developed integrated software with a simple, small and relatively low-cost mass spectrometry system introduced here fills this void. Software was developed to operate the mass spectrometer, to collect and process mass spectrometric data files, to build a database and to classify samples using such a database. These tasks were accomplished via the vendor-provided software libraries. Sample classification based on spectral comparison utilized the spectral contrast angle method. Using the developed software platform near real-time sample classification is exemplified using a series of commercially available blue ink rollerball pens and vegetable oils. In the case of the inks, full scan positive and negative ion ESI mass spectra were both used for database generation and sample classification. For the vegetable oils, full scan positive ion mode APCI mass spectra were recorded. The overall accuracy of the employed spectral contrast angle statistical model was 95.3% and 98% in case of the inks and oils, respectively, using leave-one-out cross-validation. This work illustrates that an open port sampling interface/mass spectrometer combination, with appropriate instrument control and data processing software, is a viable direct liquid extraction sampling and analysis system suitable for the non-expert user and near real-time sample classification via database matching. Published in 2016. This article is a U.S. Government work and is in the public domain in the USA. Published in 2016. This article is a U.S. Government work and is in the public domain in the USA.

The ORT Open Tech Robotics and Automation Literacy Course.

ERIC Educational Resources Information Center

Sharon, Dan; And Others

1987-01-01

Presents an overview of a course on robotics and automation developed by the Organization for Rehabilitation through Training (ORT) to be offered through an open learning environment in the United Kingdom. Highlights include hardware and software requirements, an educational model, design principles, and future developments. (LRW)

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

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

A Virtual World Workshop Environment for Learning Agile Software Development Techniques

ERIC Educational Resources Information Center

Parsons, David; Stockdale, Rosemary

2012-01-01

Multi-User Virtual Environments (MUVEs) are the subject of increasing interest for educators and trainers. This article reports on a longitudinal project that seeks to establish a virtual agile software development workshop hosted in the Open Wonderland MUVE, designed to help learners to understand the basic principles of some core agile software…

TOWARD DEVELOPMENT OF A COMMON SOFTWARE APPLICATION PROGRAMMING INTERFACE (API) FOR UNCERTAINTY, SENSITIVITY, AND PARAMETER ESTIMATION METHODS AND TOOLS

EPA Science Inventory

The final session of the workshop considered the subject of software technology and how it might be better constructed to support those who develop, evaluate, and apply multimedia environmental models. Two invited presentations were featured along with an extended open discussio...

Dimensional Error in Rapid Prototyping with Open Source Software and Low-cost 3D-printer

PubMed Central

Andrade-Delgado, Laura; Telich-Tarriba, Jose E.; Fuente-del-Campo, Antonio; Altamirano-Arcos, Carlos A.

2018-01-01

Summary: Rapid prototyping models (RPMs) had been extensively used in craniofacial and maxillofacial surgery, especially in areas such as orthognathic surgery, posttraumatic or oncological reconstructions, and implantology. Economic limitations are higher in developing countries such as Mexico, where resources dedicated to health care are limited, therefore limiting the use of RPM to few selected centers. This article aims to determine the dimensional error of a low-cost fused deposition modeling 3D printer (Tronxy P802MA, Shenzhen, Tronxy Technology Co), with Open source software. An ordinary dry human mandible was scanned with a computed tomography device. The data were processed with open software to build a rapid prototype with a fused deposition machine. Linear measurements were performed to find the mean absolute and relative difference. The mean absolute and relative difference was 0.65 mm and 1.96%, respectively (P = 0.96). Low-cost FDM machines and Open Source Software are excellent options to manufacture RPM, with the benefit of low cost and a similar relative error than other more expensive technologies. PMID:29464171

Dimensional Error in Rapid Prototyping with Open Source Software and Low-cost 3D-printer.

PubMed

Rendón-Medina, Marco A; Andrade-Delgado, Laura; Telich-Tarriba, Jose E; Fuente-Del-Campo, Antonio; Altamirano-Arcos, Carlos A

2018-01-01

Rapid prototyping models (RPMs) had been extensively used in craniofacial and maxillofacial surgery, especially in areas such as orthognathic surgery, posttraumatic or oncological reconstructions, and implantology. Economic limitations are higher in developing countries such as Mexico, where resources dedicated to health care are limited, therefore limiting the use of RPM to few selected centers. This article aims to determine the dimensional error of a low-cost fused deposition modeling 3D printer (Tronxy P802MA, Shenzhen, Tronxy Technology Co), with Open source software. An ordinary dry human mandible was scanned with a computed tomography device. The data were processed with open software to build a rapid prototype with a fused deposition machine. Linear measurements were performed to find the mean absolute and relative difference. The mean absolute and relative difference was 0.65 mm and 1.96%, respectively ( P = 0.96). Low-cost FDM machines and Open Source Software are excellent options to manufacture RPM, with the benefit of low cost and a similar relative error than other more expensive technologies.

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.

Design and Implementation of a Modern Automatic Deformation Monitoring System

NASA Astrophysics Data System (ADS)

Engel, Philipp; Schweimler, Björn

2016-03-01

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

The Medical Imaging Interaction Toolkit: challenges and advances : 10 years of open-source development.

PubMed

Nolden, Marco; Zelzer, Sascha; Seitel, Alexander; Wald, Diana; Müller, Michael; Franz, Alfred M; Maleike, Daniel; Fangerau, Markus; Baumhauer, Matthias; Maier-Hein, Lena; Maier-Hein, Klaus H; Meinzer, Hans-Peter; Wolf, Ivo

2013-07-01

The Medical Imaging Interaction Toolkit (MITK) has been available as open-source software for almost 10 years now. In this period the requirements of software systems in the medical image processing domain have become increasingly complex. The aim of this paper is to show how MITK evolved into a software system that is able to cover all steps of a clinical workflow including data retrieval, image analysis, diagnosis, treatment planning, intervention support, and treatment control. MITK provides modularization and extensibility on different levels. In addition to the original toolkit, a module system, micro services for small, system-wide features, a service-oriented architecture based on the Open Services Gateway initiative (OSGi) standard, and an extensible and configurable application framework allow MITK to be used, extended and deployed as needed. A refined software process was implemented to deliver high-quality software, ease the fulfillment of regulatory requirements, and enable teamwork in mixed-competence teams. MITK has been applied by a worldwide community and integrated into a variety of solutions, either at the toolkit level or as an application framework with custom extensions. The MITK Workbench has been released as a highly extensible and customizable end-user application. Optional support for tool tracking, image-guided therapy, diffusion imaging as well as various external packages (e.g. CTK, DCMTK, OpenCV, SOFA, Python) is available. MITK has also been used in several FDA/CE-certified applications, which demonstrates the high-quality software and rigorous development process. MITK provides a versatile platform with a high degree of modularization and interoperability and is well suited to meet the challenging tasks of today's and tomorrow's clinically motivated research.

OpenStructure: a flexible software framework for computational structural biology.

PubMed

Biasini, Marco; Mariani, Valerio; Haas, Jürgen; Scheuber, Stefan; Schenk, Andreas D; Schwede, Torsten; Philippsen, Ansgar

2010-10-15

Developers of new methods in computational structural biology are often hampered in their research by incompatible software tools and non-standardized data formats. To address this problem, we have developed OpenStructure as a modular open source platform to provide a powerful, yet flexible general working environment for structural bioinformatics. OpenStructure consists primarily of a set of libraries written in C++ with a cleanly designed application programmer interface. All functionality can be accessed directly in C++ or in a Python layer, meeting both the requirements for high efficiency and ease of use. Powerful selection queries and the notion of entity views to represent these selections greatly facilitate the development and implementation of algorithms on structural data. The modular integration of computational core methods with powerful visualization tools makes OpenStructure an ideal working and development environment. Several applications, such as the latest versions of IPLT and QMean, have been implemented based on OpenStructure-demonstrating its value for the development of next-generation structural biology algorithms. Source code licensed under the GNU lesser general public license and binaries for MacOS X, Linux and Windows are available for download at http://www.openstructure.org. torsten.schwede@unibas.ch Supplementary data are available at Bioinformatics online.

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

PubMed Central

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

2015-01-01

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

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

PubMed

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

2015-01-01

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

Defense Acquisitions: DOD Efforts to Adopt Open Systems for Its Unmanned Aircraft Systems Have Progressed Slowly

DTIC Science & Technology

2013-07-01

applications introduced by third-party developers to connect to the Android operating system through an open software interface. This allows customers...Definition Multimedia Interface have been developed to address the need for standards for high-definition televisions and computer monitors. Perhaps

The Core Flight System (cFS) Community: Providing Low Cost Solutions for Small Spacecraft

NASA Technical Reports Server (NTRS)

McComas, David; Wilmot, Jonathan; Cudmore, Alan

2016-01-01

In February 2015 the NASA Goddard Space Flight Center (GSFC) completed the open source release of the entire Core Flight Software (cFS) suite. After the open source release a multi-NASA center Configuration Control Board (CCB) was established that has managed multiple cFS product releases. The cFS was developed and is being maintained in compliance with the NASA Class B software development process requirements and the open source release includes all Class B artifacts. The cFS is currently running on three operational science spacecraft and is being used on multiple spacecraft and instrument development efforts. While the cFS itself is a viable flight software (FSW) solution, we have discovered that the cFS community is a continuous source of innovation and growth that provides products and tools that serve the entire FSW lifecycle and future mission needs. This paper summarizes the current state of the cFS community, the key FSW technologies being pursued, the development/verification tools and opportunities for the small satellite community to become engaged. The cFS is a proven high quality and cost-effective solution for small satellites with constrained budgets.

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

PubMed

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

2014-10-01

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

An efficient approach to the deployment of complex open source information systems

PubMed Central

Cong, Truong Van Chi; Groeneveld, Eildert

2011-01-01

Complex open source information systems are usually implemented as component-based software to inherit the available functionality of existing software packages developed by third parties. Consequently, the deployment of these systems not only requires the installation of operating system, application framework and the configuration of services but also needs to resolve the dependencies among components. The problem becomes more challenging when the application must be installed and used on different platforms such as Linux and Windows. To address this, an efficient approach using the virtualization technology is suggested and discussed in this paper. The approach has been applied in our project to deploy a web-based integrated information system in molecular genetics labs. It is a low-cost solution to benefit both software developers and end-users. PMID:22102770

An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics

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

Taylor, Ronald C.

Bioinformatics researchers are increasingly confronted with analysis of ultra large-scale data sets, a problem that will only increase at an alarming rate in coming years. Recent developments in open source software, that is, the Hadoop project and associated software, provide a foundation for scaling to petabyte scale data warehouses on Linux clusters, providing fault-tolerant parallelized analysis on such data using a programming style named MapReduce. An overview is given of the current usage within the bioinformatics community of Hadoop, a top-level Apache Software Foundation project, and of associated open source software projects. The concepts behind Hadoop and the associated HBasemore » project are defined, and current bioinformatics software that employ Hadoop is described. The focus is on next-generation sequencing, as the leading application area to date.« less

Generation of a Database of Laboratory Laser-Induced Breakdown Spectroscopy (LIBS) Spectra and Associated Analysis Software

NASA Astrophysics Data System (ADS)

Anderson, R. B.; Clegg, S. M.; Graff, T.; Morris, R. V.; Laura, J.

2015-06-01

We describe plans to generate a database of LIBS spectra of planetary analog materials and develop free, open-source software to enable the planetary community to analyze LIBS (and other spectral) data.

Open Source 2010: Reflections on 2007

ERIC Educational Resources Information Center

Wheeler, Brad

2007-01-01

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

Efficacy of a Virtual Teaching Assistant in an Open Laboratory Environment for Electric Circuits

ERIC Educational Resources Information Center

Saleheen, Firdous; Wang, Zicong; Picone, Joseph; Butz, Brian P.; Won, Chang-Hee

2018-01-01

In order to provide an on-demand, open electrical engineering laboratory, we developed an innovative software-based Virtual Open Laboratory Teaching Assistant (VOLTA). This web-based virtual assistant provides laboratory instructions, equipment usage videos, circuit simulation assistance, and hardware implementation diagnostics. VOLTA allows…

RINGMesh: A programming library for developing mesh-based geomodeling applications

NASA Astrophysics Data System (ADS)

Pellerin, Jeanne; Botella, Arnaud; Bonneau, François; Mazuyer, Antoine; Chauvin, Benjamin; Lévy, Bruno; Caumon, Guillaume

2017-07-01

RINGMesh is a C++ open-source programming library for manipulating discretized geological models. It is designed to ease the development of applications and workflows that use discretized 3D models. It is neither a geomodeler, nor a meshing software. RINGMesh implements functionalities to read discretized surface-based or volumetric structural models and to check their validity. The models can be then exported in various file formats. RINGMesh provides data structures to represent geological structural models, either defined by their discretized boundary surfaces, and/or by discretized volumes. A programming interface allows to develop of new geomodeling methods, and to plug in external software. The goal of RINGMesh is to help researchers to focus on the implementation of their specific method rather than on tedious tasks common to many applications. The documented code is open-source and distributed under the modified BSD license. It is available at https://www.ring-team.org/index.php/software/ringmesh.

Free for All: Open Source Software

ERIC Educational Resources Information Center

Schneider, Karen

2008-01-01

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

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

PubMed

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

2007-11-01

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

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.

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

DTIC Science & Technology

2016-01-06

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

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

PubMed Central

2011-01-01

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

OPM: The Open Porous Media Initiative

NASA Astrophysics Data System (ADS)

Flemisch, B.; Flornes, K. M.; Lie, K.; Rasmussen, A.

2011-12-01

The principal objective of the Open Porous Media (OPM) initiative is to develop a simulation suite that is capable of modeling industrially and scientifically relevant flow and transport processes in porous media and bridge the gap between the different application areas of porous media modeling, including reservoir mechanics, CO2 sequestration, biological systems, and product development of engineered media. The OPM initiative will provide a long-lasting, efficient, and well-maintained open-source software for flow and transport in porous media built on modern software principles. The suite is released under the GNU General Public License (GPL). Our motivation is to provide a means to unite industry and public research on simulation of flow and transport in porous media. For academic users, we seek to provide a software infrastructure that facilitates testing of new ideas on models with industry-standard complexity, while at the same time giving the researcher control over discretization and solvers. Similarly, we aim to accelerate the technology transfer from academic institutions to professional companies by making new research results available as free software of professional standard. The OPM initiative is currently supported by six research groups in Norway and Germany and funded by existing grants from public research agencies as well as from Statoil Petroleum and Total E&P Norge. However, a full-scale development of the OPM initiative requires substantially more funding and involvement of more research groups and potential end users. In this talk, we will provide an overview of the current activities in the OPM initiative. Special emphasis will be given to the demonstration of the synergies achieved by combining the strengths of individual open-source software components. In particular, a new fully implicit solver developed within the DUNE-based simulator DuMux could be enhanced by the ability to read industry-standard Eclipse input files and to run on grids given in corner-point format. Examples taken from the SPE comparative solution projects and CO2 sequestration benchmarks illustrate the current capabilities of the simulation suite.

Experiences Supporting the Lunar Reconnaissance Orbiter Camera: the Devops Model

NASA Astrophysics Data System (ADS)

Licht, A.; Estes, N. M.; Bowman-Cisnesros, E.; Hanger, C. D.

2013-12-01

Introduction: The Lunar Reconnaissance Orbiter Camera (LROC) Science Operations Center (SOC) is responsible for instrument targeting, product processing, and archiving [1]. The LROC SOC maintains over 1,000,000 observations with over 300 TB of released data. Processing challenges compound with the acquisition of over 400 Gbits of observations daily creating the need for a robust, efficient, and reliable suite of specialized software. Development Environment: The LROC SOC's software development methodology has evolved over time. Today, the development team operates in close cooperation with the systems administration team in a model known in the IT industry as DevOps. The DevOps model enables a highly productive development environment that facilitates accomplishment of key goals within tight schedules[2]. The LROC SOC DevOps model incorporates industry best practices including prototyping, continuous integration, unit testing, code coverage analysis, version control, and utilizing existing open source software. Scientists and researchers at LROC often prototype algorithms and scripts in a high-level language such as MATLAB or IDL. After the prototype is functionally complete the solution is implemented as production ready software by the developers. Following this process ensures that all controls and requirements set by the LROC SOC DevOps team are met. The LROC SOC also strives to enhance the efficiency of the operations staff by way of weekly presentations and informal mentoring. Many small scripting tasks are assigned to the cognizant operations personnel (end users), allowing for the DevOps team to focus on more complex and mission critical tasks. In addition to leveraging open source software the LROC SOC has also contributed to the open source community by releasing Lunaserv [3]. Findings: The DevOps software model very efficiently provides smooth software releases and maintains team momentum. Scientists prototyping their work has proven to be very efficient as developers do not need to spend time iterating over small changes. Instead, these changes are realized in early prototypes and implemented before the task is seen by developers. The development practices followed by the LROC SOC DevOps team help facilitate a high level of software quality that is necessary for LROC SOC operations. Application to the Scientific Community: There is no replacement for having software developed by professional developers. While it is beneficial for scientists to write software, this activity should be seen as prototyping, which is then made production ready by professional developers. When constructed properly, even a small development team has the ability to increase the rate of software development for a research group while creating more efficient, reliable, and maintainable products. This strategy allows scientists to accomplish more, focusing on teamwork, rather than software development, which may not be their primary focus. 1. Robinson et al. (2010) Space Sci. Rev. 150, 81-124 2. DeGrandis. (2011) Cutter IT Journal. Vol 24, No. 8, 34-39 3. Estes, N.M.; Hanger, C.D.; Licht, A.A.; Bowman-Cisneros, E.; Lunaserv Web Map Service: History, Implementation Details, Development, and Uses, http://adsabs.harvard.edu/abs/2013LPICo1719.2609E.

Architecting for Large Scale Agile Software Development: A Risk-Driven Approach

DTIC Science & Technology

2013-05-01

addressed aspect of scale in agile software development. Practices such as Scrum of Scrums are meant to address orchestration of multiple development...owner, Scrum master) have differing responsibilities from the roles in the existing phase-based waterfall program structures. Such differences may... Scrum . Communication with both internal and external stakeholders must be open and documentation should not be used as a substitute for communication

PC Scene Generation

NASA Astrophysics Data System (ADS)

Buford, James A., Jr.; Cosby, David; Bunfield, Dennis H.; Mayhall, Anthony J.; Trimble, Darian E.

2007-04-01

AMRDEC has successfully tested hardware and software for Real-Time Scene Generation for IR and SAL Sensors on COTS PC based hardware and video cards. AMRDEC personnel worked with nVidia and Concurrent Computer Corporation to develop a Scene Generation system capable of frame rates of at least 120Hz while frame locked to an external source (such as a missile seeker) with no dropped frames. Latency measurements and image validation were performed using COTS and in-house developed hardware and software. Software for the Scene Generation system was developed using OpenSceneGraph.

RSEIS and RFOC: Seismic Analysis in R

NASA Astrophysics Data System (ADS)

Lees, J. M.

2015-12-01

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

Open source cardiology electronic health record development for DIGICARDIAC implementation

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

Open Architecture Standard for NASA's Software-Defined Space Telecommunications Radio Systems

NASA Technical Reports Server (NTRS)

Reinhart, Richard C.; Johnson, Sandra K.; Kacpura, Thomas J.; Hall, Charles S.; Smith, Carl R.; Liebetreu, John

2008-01-01

NASA is developing an architecture standard for software-defined radios used in space- and ground-based platforms to enable commonality among radio developments to enhance capability and services while reducing mission and programmatic risk. Transceivers (or transponders) with functionality primarily defined in software (e.g., firmware) have the ability to change their functional behavior through software alone. This radio architecture standard offers value by employing common waveform software interfaces, method of instantiation, operation, and testing among different compliant hardware and software products. These common interfaces within the architecture abstract application software from the underlying hardware to enable technology insertion independently at either the software or hardware layer. This paper presents the initial Space Telecommunications Radio System (STRS) Architecture for NASA missions to provide the desired software abstraction and flexibility while minimizing the resources necessary to support the architecture.

Acquiring Data by Mining the Past: Pairing Communities with Environmental Monitoring Methods through Open Online Collaborative Replication

NASA Astrophysics Data System (ADS)

Lippincott, M.; Lewis, E. S.; Gehrke, G. E.; Wise, A.; Pyle, S.; Sinatra, V.; Bland, G.; Bydlowski, D.; Henry, A.; Gilberts, P. A.

2016-12-01

Community groups are interested in low-cost sensors to monitor their environment. However, many new commercial sensors are unknown devices without peer-reviewed evaluations of data quality or pathways to regulatory acceptance, and the time to achieve these outcomes may be beyond a community's patience and attention. Rather than developing a device from scratch or validating a new commercial product, a workflow is presented whereby existing technologies, especially those that are out of patent, are replicated through open online collaboration between communities affected by environmental pollution, volunteers, academic institutions, and existing open hardware and open source software projects. Technology case studies will be presented, focusing primarily on a passive PM monitor based on the UNC Passive Monitor. Stages of the project will be detailed moving from identifying community needs, reviewing existing technology, partnership development, technology replication, IP review and licensing, data quality assurance (in process), and field evaluation with community partners (in process), with special attention to partnership development and technology review. We have leveraged open hardware and open source software to lower the cost and access barriers of existing technologies for PM10-2.5 and other atmospheric measures that have already been validated through peer review. Existing validation of and regulatory familiarity with a technology enables a rapid pathway towards collecting data, shortening the time it takes for communities to leverage data in environmental management decisions. Online collaboration requires rigorous documentation that aids in spreading research methods and promoting deep engagement by interested community researchers outside academia. At the same time, careful choice of technology and the use of small-scale fabrication through laser cutting, 3D printing, and open, shared repositories of plans and software enables educational engagement that broadens a project's reach.

Final Report. Center for Scalable Application Development Software

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

Mellor-Crummey, John

2014-10-26

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

An Inexpensive, Open-Source USB Arduino Data Acquisition Device for Chemical Instrumentation.

PubMed

Grinias, James P; Whitfield, Jason T; Guetschow, Erik D; Kennedy, Robert T

2016-07-12

Many research and teaching labs rely on USB data acquisition devices to collect voltage signals from instrumentation. However, these devices can be cost-prohibitive (especially when large numbers are needed for teaching labs) and require software to be developed for operation. In this article, we describe the development and use of an open-source USB data acquisition device (with 16-bit acquisition resolution) built using simple electronic components and an Arduino Uno that costs under $50. Additionally, open-source software written in Python is included so that data can be acquired using nearly any PC or Mac computer with a simple USB connection. Use of the device was demonstrated for a sophomore-level analytical experiment using GC and a CE-UV separation on an instrument used for research purposes.

Open Source in Higher Education: Towards an Understanding of Networked Universities

ERIC Educational Resources Information Center

Quint-Rapoport, Mia

2012-01-01

This article addresses the question of understanding more about networked universities by looking at open source software developers working in academic contexts. It sketches their identities and work as an emerging professional community that both relies upon and develops digitally mediated networks and contributes to the progress of academic…

openECA Platform and Analytics Alpha Test Results

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

Robertson, Russell

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

openECA Platform and Analytics Beta Demonstration Results

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

Robertson, Russell

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

Development and Deployment of the OpenMRS-Ebola Electronic Health Record System for an Ebola Treatment Center in Sierra Leone

PubMed Central

Jazayeri, Darius; Teich, Jonathan M; Ball, Ellen; Nankubuge, Patricia Alexandra; Rwebembera, Job; Wing, Kevin; Sesay, Alieu Amara; Kanter, Andrew S; Ramos, Glauber D; Walton, David; Cummings, Rachael; Checchi, Francesco; Fraser, Hamish S

2017-01-01

Background Stringent infection control requirements at Ebola treatment centers (ETCs), which are specialized facilities for isolating and treating Ebola patients, create substantial challenges for recording and reviewing patient information. During the 2014-2016 West African Ebola epidemic, paper-based data collection systems at ETCs compromised the quality, quantity, and confidentiality of patient data. Electronic health record (EHR) systems have the potential to address such problems, with benefits for patient care, surveillance, and research. However, no suitable software was available for deployment when large-scale ETCs opened as the epidemic escalated in 2014. Objective We present our work on rapidly developing and deploying OpenMRS-Ebola, an EHR system for the Kerry Town ETC in Sierra Leone. We describe our experience, lessons learned, and recommendations for future health emergencies. Methods We used the OpenMRS platform and Agile software development approaches to build OpenMRS-Ebola. Key features of our work included daily communications between the development team and ground-based operations team, iterative processes, and phased development and implementation. We made design decisions based on the restrictions of the ETC environment and regular user feedback. To evaluate the system, we conducted predeployment user questionnaires and compared the EHR records with duplicate paper records. Results We successfully built OpenMRS-Ebola, a modular stand-alone EHR system with a tablet-based application for infectious patient wards and a desktop-based application for noninfectious areas. OpenMRS-Ebola supports patient tracking (registration, bed allocation, and discharge); recording of vital signs and symptoms; medication and intravenous fluid ordering and monitoring; laboratory results; clinician notes; and data export. It displays relevant patient information to clinicians in infectious and noninfectious zones. We implemented phase 1 (patient tracking; drug ordering and monitoring) after 2.5 months of full-time development. OpenMRS-Ebola was used for 112 patient registrations, 569 prescription orders, and 971 medication administration recordings. We were unable to fully implement phases 2 and 3 as the ETC closed because of a decrease in new Ebola cases. The phase 1 evaluation suggested that OpenMRS-Ebola worked well in the context of the rollout, and the user feedback was positive. Conclusions To our knowledge, OpenMRS-Ebola is the most comprehensive adaptable clinical EHR built for a low-resource setting health emergency. It is designed to address the main challenges of data collection in highly infectious environments that require robust infection prevention and control measures and it is interoperable with other electronic health systems. Although we built and deployed OpenMRS-Ebola more rapidly than typical software, our work highlights the challenges of having to develop an appropriate system during an emergency rather than being able to rapidly adapt an existing one. Lessons learned from this and previous emergencies should be used to ensure that a set of well-designed, easy-to-use, pretested health software is ready for quick deployment in future. PMID:28827211

Continuous integration for concurrent MOOSE framework and application development on GitHub

DOE PAGES

Slaughter, Andrew E.; Peterson, John W.; Gaston, Derek R.; ...

2015-11-20

For the past several years, Idaho National Laboratory’s MOOSE framework team has employed modern software engineering techniques (continuous integration, joint application/framework source code repos- itories, automated regression testing, etc.) in developing closed-source multiphysics simulation software (Gaston et al., Journal of Open Research Software vol. 2, article e10, 2014). In March 2014, the MOOSE framework was released under an open source license on GitHub, significantly expanding and diversifying the pool of current active and potential future contributors on the project. Despite this recent growth, the same philosophy of concurrent framework and application development continues to guide the project’s development roadmap. Severalmore » specific practices, including techniques for managing multiple repositories, conducting automated regression testing, and implementing a cascading build process are discussed in this short paper. Furthermore, special attention is given to describing the manner in which these practices naturally synergize with the GitHub API and GitHub-specific features such as issue tracking, Pull Requests, and project forks.« less

Continuous integration for concurrent MOOSE framework and application development on GitHub

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

Slaughter, Andrew E.; Peterson, John W.; Gaston, Derek R.

For the past several years, Idaho National Laboratory’s MOOSE framework team has employed modern software engineering techniques (continuous integration, joint application/framework source code repos- itories, automated regression testing, etc.) in developing closed-source multiphysics simulation software (Gaston et al., Journal of Open Research Software vol. 2, article e10, 2014). In March 2014, the MOOSE framework was released under an open source license on GitHub, significantly expanding and diversifying the pool of current active and potential future contributors on the project. Despite this recent growth, the same philosophy of concurrent framework and application development continues to guide the project’s development roadmap. Severalmore » specific practices, including techniques for managing multiple repositories, conducting automated regression testing, and implementing a cascading build process are discussed in this short paper. Furthermore, special attention is given to describing the manner in which these practices naturally synergize with the GitHub API and GitHub-specific features such as issue tracking, Pull Requests, and project forks.« less

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

PubMed

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

2017-05-01

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

Ensemble Eclipse: A Process for Prefab Development Environment for the Ensemble Project

NASA Technical Reports Server (NTRS)

Wallick, Michael N.; Mittman, David S.; Shams, Khawaja, S.; Bachmann, Andrew G.; Ludowise, Melissa

2013-01-01

This software simplifies the process of having to set up an Eclipse IDE programming environment for the members of the cross-NASA center project, Ensemble. It achieves this by assembling all the necessary add-ons and custom tools/preferences. This software is unique in that it allows developers in the Ensemble Project (approximately 20 to 40 at any time) across multiple NASA centers to set up a development environment almost instantly and work on Ensemble software. The software automatically has the source code repositories and other vital information and settings included. The Eclipse IDE is an open-source development framework. The NASA (Ensemble-specific) version of the software includes Ensemble-specific plug-ins as well as settings for the Ensemble project. This software saves developers the time and hassle of setting up a programming environment, making sure that everything is set up in the correct manner for Ensemble development. Existing software (i.e., standard Eclipse) requires an intensive setup process that is both time-consuming and error prone. This software is built once by a single user and tested, allowing other developers to simply download and use the software

Realizing the Living Paper using the ProvONE Model for Reproducible Research

NASA Astrophysics Data System (ADS)

Jones, M. B.; Jones, C. S.; Ludäscher, B.; Missier, P.; Walker, L.; Slaughter, P.; Schildhauer, M.; Cuevas-Vicenttín, V.

2015-12-01

Science has advanced through traditional publications that codify research results as a permenant part of the scientific record. But because publications are static and atomic, researchers can only cite and reference a whole work when building on prior work of colleagues. The open source software model has demonstrated a new approach in which strong version control in an open environment can nurture an open ecosystem of software. Developers now commonly fork and extend software giving proper credit, with less repetition, and with confidence in the relationship to original software. Through initiatives like 'Beyond the PDF', an analogous model has been imagined for open science, in which software, data, analyses, and derived products become first class objects within a publishing ecosystem that has evolved to be finer-grained and is realized through a web of linked open data. We have prototyped a Living Paper concept by developing the ProvONE provenance model for scientific workflows, with prototype deployments in DataONE. ProvONE promotes transparency and openness by describing the authenticity, origin, structure, and processing history of research artifacts and by detailing the steps in computational workflows that produce derived products. To realize the Living Paper, we decompose scientific papers into their constituent products and publish these as compound objects in the DataONE federation of archival repositories. Each individual finding and sub-product of a reseach project (such as a derived data table, a workflow or script, a figure, an image, or a finding) can be independently stored, versioned, and cited. ProvONE provenance traces link these fine-grained products within and across versions of a paper, and across related papers that extend an original analysis. This allows for open scientific publishing in which researchers extend and modify findings, creating a dynamic, evolving web of results that collectively represent the scientific enterprise. The Living Paper provides detailed metadata for properly interpreting and verifying individual research findings, for tracing the origin of ideas, for launching new lines of inquiry, and for implementing transitive credit for research and engineering.

IGT-Open: An open-source, computerized version of the Iowa Gambling Task.

PubMed

Dancy, Christopher L; Ritter, Frank E

2017-06-01

The Iowa Gambling Task (IGT) is commonly used to understand the processes involved in decision-making. Though the task was originally run without a computer, using a computerized version of the task has become typical. These computerized versions of the IGT are useful, because they can make the task more standardized across studies and allow for the task to be used in environments where a physical version of the task may be difficult or impossible to use (e.g., while collecting brain imaging data). Though these computerized versions of the IGT have been useful for experimentation, having multiple software implementations of the task could present reliability issues. We present an open-source software version of the Iowa Gambling Task (called IGT-Open) that allows for millisecond visual presentation accuracy and is freely available to be used and modified. This software has been used to collect data from human subjects and also has been used to run model-based simulations with computational process models developed to run in the ACT-R architecture.

Statistics of software vulnerability detection in certification testing

NASA Astrophysics Data System (ADS)

Barabanov, A. V.; Markov, A. S.; Tsirlov, V. L.

2018-05-01

The paper discusses practical aspects of introduction of the methods to detect software vulnerability in the day-to-day activities of the accredited testing laboratory. It presents the approval results of the vulnerability detection methods as part of the study of the open source software and the software that is a test object of the certification tests under information security requirements, including software for communication networks. Results of the study showing the allocation of identified vulnerabilities by types of attacks, country of origin, programming languages used in the development, methods for detecting vulnerability, etc. are given. The experience of foreign information security certification systems related to the detection of certified software vulnerabilities is analyzed. The main conclusion based on the study is the need to implement practices for developing secure software in the development life cycle processes. The conclusions and recommendations for the testing laboratories on the implementation of the vulnerability analysis methods are laid down.

Open-Source as a strategy for operational software - the case of Enki

NASA Astrophysics Data System (ADS)

Kolberg, Sjur; Bruland, Oddbjørn

2014-05-01

Since 2002, SINTEF Energy has been developing what is now known as the Enki modelling system. This development has been financed by Norway's largest hydropower producer Statkraft, motivated by a desire for distributed hydrological models in operational use. As the owner of the source code, Statkraft has recently decided on Open Source as a strategy for further development, and for migration from an R&D context to operational use. A current cooperation project is currently carried out between SINTEF Energy, 7 large Norwegian hydropower producers including Statkraft, three universities and one software company. Of course, the most immediate task is that of software maturing. A more important challenge, however, is one of gaining experience within the operational hydropower industry. A transition from lumped to distributed models is likely to also require revision of measurement program, calibration strategy, use of GIS and modern data sources like weather radar and satellite imagery. On the other hand, map based visualisations enable a richer information exchange between hydrologic forecasters and power market traders. The operating context of a distributed hydrology model within hydropower planning is far from settled. Being both a modelling framework and a library of plugin-routines to build models from, Enki supports the flexibility needed in this situation. Recent development has separated the core from the user interface, paving the way for a scripting API, cross-platform compilation, and front-end programs serving different degrees of flexibility, robustness and security. The open source strategy invites anyone to use Enki and to develop and contribute new modules. Once tested, the same modules are available for the operational versions of the program. A core challenge is to offer rigid testing procedures and mechanisms to reject routines in an operational setting, without limiting the experimentation with new modules. The Open Source strategy also has implications for building and maintaining competence around the source code and the advanced hydrological and statistical routines in Enki. Originally developed by hydrologists, the Enki code is now approaching a state where maintenance requires a background in professional software development. Without the advantage of proprietary source code, both hydrologic improvements and software maintenance depend on donations or development support on a case-to-case basis, a situation well known within the open source community. It remains to see whether these mechanisms suffice to keep Enki at the maintenance level required by the hydropower sector. ENKI is available from www.opensource-enki.org.

Software Writing Skills for Your Research - Lessons Learned from Workshops in the Geosciences

NASA Astrophysics Data System (ADS)

Hammitzsch, Martin

2016-04-01

Findings presented in scientific papers are based on data and software. Once in a while they come along with data - but not commonly with software. However, the software used to gain findings plays a crucial role in the scientific work. Nevertheless, software is rarely seen publishable. Thus researchers may not reproduce the findings without the software which is in conflict with the principle of reproducibility in sciences. For both, the writing of publishable software and the reproducibility issue, the quality of software is of utmost importance. For many programming scientists the treatment of source code, e.g. with code design, version control, documentation, and testing is associated with additional work that is not covered in the primary research task. This includes the adoption of processes following the software development life cycle. However, the adoption of software engineering rules and best practices has to be recognized and accepted as part of the scientific performance. Most scientists have little incentive to improve code and do not publish code because software engineering habits are rarely practised by researchers or students. Software engineering skills are not passed on to followers as for paper writing skill. Thus it is often felt that the software or code produced is not publishable. The quality of software and its source code has a decisive influence on the quality of research results obtained and their traceability. So establishing best practices from software engineering to serve scientific needs is crucial for the success of scientific software. Even though scientists use existing software and code, i.e., from open source software repositories, only few contribute their code back into the repositories. So writing and opening code for Open Science means that subsequent users are able to run the code, e.g. by the provision of sufficient documentation, sample data sets, tests and comments which in turn can be proven by adequate and qualified reviews. This assumes that scientist learn to write and release code and software as they learn to write and publish papers. Having this in mind, software could be valued and assessed as a contribution to science. But this requires the relevant skills that can be passed to colleagues and followers. Therefore, the GFZ German Research Centre for Geosciences performed three workshops in 2015 to address the passing of software writing skills to young scientists, the next generation of researchers in the Earth, planetary and space sciences. Experiences in running these workshops and the lessons learned will be summarized in this presentation. The workshops have received support and funding by Software Carpentry, a volunteer organization whose goal is to make scientists more productive, and their work more reliable, by teaching them basic computing skills, and by FOSTER (Facilitate Open Science Training for European Research), a two-year, EU-Funded (FP7) project, whose goal to produce a European-wide training programme that will help to incorporate Open Access approaches into existing research methodologies and to integrate Open Science principles and practice in the current research workflow by targeting the young researchers and other stakeholders.

Mobile Inquiry Learning in Sweden: Development Insights on Interoperability, Extensibility and Sustainability of the LETS GO Software System

ERIC Educational Resources Information Center

Vogel, Bahtijar; Kurti, Arianit; Milrad, Marcelo; Johansson, Emil; Müller, Maximilian

2014-01-01

This paper presents the overall lifecycle and evolution of a software system we have developed in relation to the "Learning Ecology through Science with Global Outcomes" (LETS GO) research project. One of the aims of the project is to support "open inquiry learning" using mobile science collaboratories that provide open…

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

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

Development of RT-components for the M-3 Strawberry Harvesting Robot

NASA Astrophysics Data System (ADS)

Yamashita, Tomoki; Tanaka, Motomasa; Yamamoto, Satoshi; Hayashi, Shigehiko; Saito, Sadafumi; Sugano, Shigeki

We are now developing the strawberry harvest robot called “M-3” prototype robot system under the 4th urgent project of MAFF. In order to develop the control software of the M-3 robot more efficiently, we innovated the RT-middleware “OpenRTM-aist” software platform. In this system, we developed 9 kind of RT-Components (RTC): Robot task sequence player RTC, Proxy RTC for image processing software, DC motor controller RTC, Arm kinematics RTC, and so on. In this paper, we discuss advantages of RT-middleware developing system and problems about operating the RTC-configured robotic system by end-users.

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

NASA Astrophysics Data System (ADS)

Delipetrev, Blagoj

2016-04-01

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

Open source EMR software: profiling, insights and hands-on analysis.

PubMed

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

2014-11-01

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

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

PubMed

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

2015-03-01

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

mdFoam+: Advanced molecular dynamics in OpenFOAM

NASA Astrophysics Data System (ADS)

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

2018-03-01

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

Transforming High School Classrooms with Free/Open Source Software: "It's Time for an Open Source Software Revolution"

ERIC Educational Resources Information Center

Pfaffman, Jay

2008-01-01

Free/Open Source Software (FOSS) applications meet many of the software needs of high school science classrooms. In spite of the availability and quality of FOSS tools, they remain unknown to many teachers and utilized by fewer still. In a world where most software has restrictions on copying and use, FOSS is an anomaly, free to use and to…

OpenNFT: An open-source Python/Matlab framework for real-time fMRI neurofeedback training based on activity, connectivity and multivariate pattern analysis.

PubMed

Koush, Yury; Ashburner, John; Prilepin, Evgeny; Sladky, Ronald; Zeidman, Peter; Bibikov, Sergei; Scharnowski, Frank; Nikonorov, Artem; De Ville, Dimitri Van

2017-08-01

Neurofeedback based on real-time functional magnetic resonance imaging (rt-fMRI) is a novel and rapidly developing research field. It allows for training of voluntary control over localized brain activity and connectivity and has demonstrated promising clinical applications. Because of the rapid technical developments of MRI techniques and the availability of high-performance computing, new methodological advances in rt-fMRI neurofeedback become possible. Here we outline the core components of a novel open-source neurofeedback framework, termed Open NeuroFeedback Training (OpenNFT), which efficiently integrates these new developments. This framework is implemented using Python and Matlab source code to allow for diverse functionality, high modularity, and rapid extendibility of the software depending on the user's needs. In addition, it provides an easy interface to the functionality of Statistical Parametric Mapping (SPM) that is also open-source and one of the most widely used fMRI data analysis software. We demonstrate the functionality of our new framework by describing case studies that include neurofeedback protocols based on brain activity levels, effective connectivity models, and pattern classification approaches. This open-source initiative provides a suitable framework to actively engage in the development of novel neurofeedback approaches, so that local methodological developments can be easily made accessible to a wider range of users. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Guide to NavyFOAM V1.0

DTIC Science & Technology

2011-04-01

NavyFOAM has been developed using an open-source CFD software tool-kit ( OpenFOAM ) that draws heavily upon object-oriented programming. The...numerical methods and the physical models in the original version of OpenFOAM have been upgraded in an effort to improve accuracy and robustness of...computational fluid dynamics OpenFOAM , Object Oriented Programming (OOP) (CFD), NavyFOAM, 16. SECURITY CLASSIFICATION OF: a. REPORT UNCLASSIFIED b

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

NASA Astrophysics Data System (ADS)

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

2012-12-01

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

Are Earth System model software engineering practices fit for purpose? A case study.

NASA Astrophysics Data System (ADS)

Easterbrook, S. M.; Johns, T. C.

2009-04-01

We present some analysis and conclusions from a case study of the culture and practices of scientists at the Met Office and Hadley Centre working on the development of software for climate and Earth System models using the MetUM infrastructure. The study examined how scientists think about software correctness, prioritize their requirements in making changes, and develop a shared understanding of the resulting models. We conclude that highly customized techniques driven strongly by scientific research goals have evolved for verification and validation of such models. In a formal software engineering context these represents costly, but invaluable, software integration tests with considerable benefits. The software engineering practices seen also exhibit recognisable features of both agile and open source software development projects - self-organisation of teams consistent with a meritocracy rather than top-down organisation, extensive use of informal communication channels, and software developers who are generally also users and science domain experts. We draw some general conclusions on whether these practices work well, and what new software engineering challenges may lie ahead as Earth System models become ever more complex and petascale computing becomes the norm.

Open source Modeling and optimization tools for Planning

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

Peles, S.

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

Nipype: a flexible, lightweight and extensible neuroimaging data processing framework in python.

PubMed

Gorgolewski, Krzysztof; Burns, Christopher D; Madison, Cindee; Clark, Dav; Halchenko, Yaroslav O; Waskom, Michael L; Ghosh, Satrajit S

2011-01-01

Current neuroimaging software offer users an incredible opportunity to analyze their data in different ways, with different underlying assumptions. Several sophisticated software packages (e.g., AFNI, BrainVoyager, FSL, FreeSurfer, Nipy, R, SPM) are used to process and analyze large and often diverse (highly multi-dimensional) data. However, this heterogeneous collection of specialized applications creates several issues that hinder replicable, efficient, and optimal use of neuroimaging analysis approaches: (1) No uniform access to neuroimaging analysis software and usage information; (2) No framework for comparative algorithm development and dissemination; (3) Personnel turnover in laboratories often limits methodological continuity and training new personnel takes time; (4) Neuroimaging software packages do not address computational efficiency; and (5) Methods sections in journal articles are inadequate for reproducing results. To address these issues, we present Nipype (Neuroimaging in Python: Pipelines and Interfaces; http://nipy.org/nipype), an open-source, community-developed, software package, and scriptable library. Nipype solves the issues by providing Interfaces to existing neuroimaging software with uniform usage semantics and by facilitating interaction between these packages using Workflows. Nipype provides an environment that encourages interactive exploration of algorithms, eases the design of Workflows within and between packages, allows rapid comparative development of algorithms and reduces the learning curve necessary to use different packages. Nipype supports both local and remote execution on multi-core machines and clusters, without additional scripting. Nipype is Berkeley Software Distribution licensed, allowing anyone unrestricted usage. An open, community-driven development philosophy allows the software to quickly adapt and address the varied needs of the evolving neuroimaging community, especially in the context of increasing demand for reproducible research.

Nipype: A Flexible, Lightweight and Extensible Neuroimaging Data Processing Framework in Python

PubMed Central

Gorgolewski, Krzysztof; Burns, Christopher D.; Madison, Cindee; Clark, Dav; Halchenko, Yaroslav O.; Waskom, Michael L.; Ghosh, Satrajit S.

2011-01-01

Current neuroimaging software offer users an incredible opportunity to analyze their data in different ways, with different underlying assumptions. Several sophisticated software packages (e.g., AFNI, BrainVoyager, FSL, FreeSurfer, Nipy, R, SPM) are used to process and analyze large and often diverse (highly multi-dimensional) data. However, this heterogeneous collection of specialized applications creates several issues that hinder replicable, efficient, and optimal use of neuroimaging analysis approaches: (1) No uniform access to neuroimaging analysis software and usage information; (2) No framework for comparative algorithm development and dissemination; (3) Personnel turnover in laboratories often limits methodological continuity and training new personnel takes time; (4) Neuroimaging software packages do not address computational efficiency; and (5) Methods sections in journal articles are inadequate for reproducing results. To address these issues, we present Nipype (Neuroimaging in Python: Pipelines and Interfaces; http://nipy.org/nipype), an open-source, community-developed, software package, and scriptable library. Nipype solves the issues by providing Interfaces to existing neuroimaging software with uniform usage semantics and by facilitating interaction between these packages using Workflows. Nipype provides an environment that encourages interactive exploration of algorithms, eases the design of Workflows within and between packages, allows rapid comparative development of algorithms and reduces the learning curve necessary to use different packages. Nipype supports both local and remote execution on multi-core machines and clusters, without additional scripting. Nipype is Berkeley Software Distribution licensed, allowing anyone unrestricted usage. An open, community-driven development philosophy allows the software to quickly adapt and address the varied needs of the evolving neuroimaging community, especially in the context of increasing demand for reproducible research. PMID:21897815

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

PubMed

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

2016-10-01

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

An Analysis of Open Source Security Software Products Downloads

ERIC Educational Resources Information Center

Barta, Brian J.

2014-01-01

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

Post-processing open-source software for the CBCT monitoring of periapical lesions healing following endodontic treatment: technical report of two cases.

PubMed

Villoria, Eduardo M; Lenzi, Antônio R; Soares, Rodrigo V; Souki, Bernardo Q; Sigurdsson, Asgeir; Marques, Alexandre P; Fidel, Sandra R

2017-01-01

To describe the use of open-source software for the post-processing of CBCT imaging for the assessment of periapical lesions development after endodontic treatment. CBCT scans were retrieved from endodontic records of two patients. Three-dimensional virtual models, voxel counting, volumetric measurement (mm 3 ) and mean intensity of the periapical lesion were performed with ITK-SNAP v. 3.0 software. Three-dimensional models of the lesions were aligned and overlapped through the MeshLab software, which performed an automatic recording of the anatomical structures, based on the best fit. Qualitative and quantitative analyses of the changes in lesions size after treatment were performed with the 3DMeshMetric software. The ITK-SNAP v. 3.0 showed the smaller value corresponding to the voxel count and the volume of the lesion segmented in yellow, indicating reduction in volume of the lesion after the treatment. A higher value of the mean intensity of the segmented image in yellow was also observed, which suggested new bone formation. Colour mapping and "point value" tool allowed the visualization of the reduction of periapical lesions in several regions. Researchers and clinicians in the monitoring of endodontic periapical lesions have the opportunity to use open-source software.

Raven-II: an open platform for surgical robotics research.

PubMed

Hannaford, Blake; Rosen, Jacob; Friedman, Diana W; King, Hawkeye; Roan, Phillip; Cheng, Lei; Glozman, Daniel; Ma, Ji; Kosari, Sina Nia; White, Lee

2013-04-01

The Raven-II is a platform for collaborative research on advances in surgical robotics. Seven universities have begun research using this platform. The Raven-II system has two 3-DOF spherical positioning mechanisms capable of attaching interchangeable four DOF instruments. The Raven-II software is based on open standards such as Linux and ROS to maximally facilitate software development. The mechanism is robust enough for repeated experiments and animal surgery experiments, but is not engineered to sufficient safety standards for human use. Mechanisms in place for interaction among the user community and dissemination of results include an electronic forum, an online software SVN repository, and meetings and workshops at major robotics conferences.

Spatial Dmbs Architecture for a Free and Open Source Bim

NASA Astrophysics Data System (ADS)

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

2017-08-01

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

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

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

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

Demonstrating High-Accuracy Orbital Access Using Open-Source Tools

NASA Technical Reports Server (NTRS)

Gilbertson, Christian; Welch, Bryan

2017-01-01

Orbit propagation is fundamental to almost every space-based analysis. Currently, many system analysts use commercial software to predict the future positions of orbiting satellites. This is one of many capabilities that can replicated, with great accuracy, without using expensive, proprietary software. NASAs SCaN (Space Communication and Navigation) Center for Engineering, Networks, Integration, and Communications (SCENIC) project plans to provide its analysis capabilities using a combination of internal and open-source software, allowing for a much greater measure of customization and flexibility, while reducing recurring software license costs. MATLAB and the open-source Orbit Determination Toolbox created by Goddard Space Flight Center (GSFC) were utilized to develop tools with the capability to propagate orbits, perform line-of-sight (LOS) availability analyses, and visualize the results. The developed programs are modular and can be applied for mission planning and viability analysis in a variety of Solar System applications. The tools can perform 2 and N-body orbit propagation, find inter-satellite and satellite to ground station LOS access (accounting for intermediate oblate spheroid body blocking, geometric restrictions of the antenna field-of-view (FOV), and relativistic corrections), and create animations of planetary movement, satellite orbits, and LOS accesses. The code is the basis for SCENICs broad analysis capabilities including dynamic link analysis, dilution-of-precision navigation analysis, and orbital availability calculations.

Experimental research control software system

NASA Astrophysics Data System (ADS)

Cohn, I. A.; Kovalenko, A. G.; Vystavkin, A. N.

2014-05-01

A software system, intended for automation of a small scale research, has been developed. The software allows one to control equipment, acquire and process data by means of simple scripts. The main purpose of that development is to increase experiment automation easiness, thus significantly reducing experimental setup automation efforts. In particular, minimal programming skills are required and supervisors have no reviewing troubles. Interactions between scripts and equipment are managed automatically, thus allowing to run multiple scripts simultaneously. Unlike well-known data acquisition commercial software systems, the control is performed by an imperative scripting language. This approach eases complex control and data acquisition algorithms implementation. A modular interface library performs interaction with external interfaces. While most widely used interfaces are already implemented, a simple framework is developed for fast implementations of new software and hardware interfaces. While the software is in continuous development with new features being implemented, it is already used in our laboratory for automation of a helium-3 cryostat control and data acquisition. The software is open source and distributed under Gnu Public License.

A Padawan Programmer's Guide to Developing Software Libraries.

PubMed

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

2017-11-22

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

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

ERIC Educational Resources Information Center

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

2008-01-01

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

Open Technology Development: Roadmap Plan

DTIC Science & Technology

2006-04-01

65 RECOMMENDATION 1: APPROVE AND FUND AN OTD STRIKE TEAM................. 67 Senior Leadership...negotiated, rather than an innate property of the product. Software’s replicability also means it can be incorporated into other software systems without...to leverage an open code development model, DoD would provide the market incentives to increase the agility and competitiveness of the industrial

SimVascular: An Open Source Pipeline for Cardiovascular Simulation.

PubMed

Updegrove, Adam; Wilson, Nathan M; Merkow, Jameson; Lan, Hongzhi; Marsden, Alison L; Shadden, Shawn C

2017-03-01

Patient-specific cardiovascular simulation has become a paradigm in cardiovascular research and is emerging as a powerful tool in basic, translational and clinical research. In this paper we discuss the recent development of a fully open-source SimVascular software package, which provides a complete pipeline from medical image data segmentation to patient-specific blood flow simulation and analysis. This package serves as a research tool for cardiovascular modeling and simulation, and has contributed to numerous advances in personalized medicine, surgical planning and medical device design. The SimVascular software has recently been refactored and expanded to enhance functionality, usability, efficiency and accuracy of image-based patient-specific modeling tools. Moreover, SimVascular previously required several licensed components that hindered new user adoption and code management and our recent developments have replaced these commercial components to create a fully open source pipeline. These developments foster advances in cardiovascular modeling research, increased collaboration, standardization of methods, and a growing developer community.

A generic open-source software framework supporting scenario simulations in bioterrorist crises.

PubMed

Falenski, Alexander; Filter, Matthias; Thöns, Christian; Weiser, Armin A; Wigger, Jan-Frederik; Davis, Matthew; Douglas, Judith V; Edlund, Stefan; Hu, Kun; Kaufman, James H; Appel, Bernd; Käsbohrer, Annemarie

2013-09-01

Since the 2001 anthrax attack in the United States, awareness of threats originating from bioterrorism has grown. This led internationally to increased research efforts to improve knowledge of and approaches to protecting human and animal populations against the threat from such attacks. A collaborative effort in this context is the extension of the open-source Spatiotemporal Epidemiological Modeler (STEM) simulation and modeling software for agro- or bioterrorist crisis scenarios. STEM, originally designed to enable community-driven public health disease models and simulations, was extended with new features that enable integration of proprietary data as well as visualization of agent spread along supply and production chains. STEM now provides a fully developed open-source software infrastructure supporting critical modeling tasks such as ad hoc model generation, parameter estimation, simulation of scenario evolution, estimation of effects of mitigation or management measures, and documentation. This open-source software resource can be used free of charge. Additionally, STEM provides critical features like built-in worldwide data on administrative boundaries, transportation networks, or environmental conditions (eg, rainfall, temperature, elevation, vegetation). Users can easily combine their own confidential data with built-in public data to create customized models of desired resolution. STEM also supports collaborative and joint efforts in crisis situations by extended import and export functionalities. In this article we demonstrate specifically those new software features implemented to accomplish STEM application in agro- or bioterrorist crisis scenarios.

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

PubMed

Wenig, Philip; Odermatt, Juergen

2010-07-30

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

ProteoWizard: open source software for rapid proteomics tools development.

PubMed

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

2008-11-01

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

CellAnimation: an open source MATLAB framework for microscopy assays.

PubMed

Georgescu, Walter; Wikswo, John P; Quaranta, Vito

2012-01-01

Advances in microscopy technology have led to the creation of high-throughput microscopes that are capable of generating several hundred gigabytes of images in a few days. Analyzing such wealth of data manually is nearly impossible and requires an automated approach. There are at present a number of open-source and commercial software packages that allow the user to apply algorithms of different degrees of sophistication to the images and extract desired metrics. However, the types of metrics that can be extracted are severely limited by the specific image processing algorithms that the application implements, and by the expertise of the user. In most commercial software, code unavailability prevents implementation by the end user of newly developed algorithms better suited for a particular type of imaging assay. While it is possible to implement new algorithms in open-source software, rewiring an image processing application requires a high degree of expertise. To obviate these limitations, we have developed an open-source high-throughput application that allows implementation of different biological assays such as cell tracking or ancestry recording, through the use of small, relatively simple image processing modules connected into sophisticated imaging pipelines. By connecting modules, non-expert users can apply the particular combination of well-established and novel algorithms developed by us and others that are best suited for each individual assay type. In addition, our data exploration and visualization modules make it easy to discover or select specific cell phenotypes from a heterogeneous population. CellAnimation is distributed under the Creative Commons Attribution-NonCommercial 3.0 Unported license (http://creativecommons.org/licenses/by-nc/3.0/). CellAnimationsource code and documentation may be downloaded from www.vanderbilt.edu/viibre/software/documents/CellAnimation.zip. Sample data are available at www.vanderbilt.edu/viibre/software/documents/movies.zip. walter.georgescu@vanderbilt.edu Supplementary data available at Bioinformatics online.

Frameworks Coordinate Scientific Data Management

NASA Technical Reports Server (NTRS)

2012-01-01

Jet Propulsion Laboratory computer scientists developed a unique software framework to help NASA manage its massive amounts of science data. Through a partnership with the Apache Software Foundation of Forest Hill, Maryland, the technology is now available as an open-source solution and is in use by cancer researchers and pediatric hospitals.

Undergraduate Research Opportunities in OSS

NASA Astrophysics Data System (ADS)

Boldyreff, Cornelia; Capiluppi, Andrea; Knowles, Thomas; Munro, James

Using Open Source Software (OSS) in undergraduate teaching in universities is now commonplace. Students use OSS applications and systems in their courses on programming, operating systems, DBMS, web development to name but a few. Studying OSS projects from both a product and a process view also forms part of the software engineering curriculum at various universities. Many students have taken part in OSS projects as well as developers.

Reconfigurable Software for Mission Operations

NASA Technical Reports Server (NTRS)

Trimble, Jay

2014-01-01

We developed software that provides flexibility to mission organizations through modularity and composability. Modularity enables removal and addition of functionality through the installation of plug-ins. Composability enables users to assemble software from pre-built reusable objects, thus reducing or eliminating the walls associated with traditional application architectures and enabling unique combinations of functionality. We have used composable objects to reduce display build time, create workflows, and build scenarios to test concepts for lunar roving operations. The software is open source, and may be downloaded from https:github.comnasamct.

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

NASA Astrophysics Data System (ADS)

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

2011-06-01

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

Fostering successful scientific software communities

NASA Astrophysics Data System (ADS)

Bangerth, W.; Heister, T.; Hwang, L.; Kellogg, L. H.

2016-12-01

Developing sustainable open source software packages for the sciences appears at first to be primarily a technical challenge: How can one create stable and robust algorithms, appropriate software designs, sufficient documentation, quality assurance strategies such as continuous integration and test suites, or backward compatibility approaches that yield high-quality software usable not only by the authors, but also the broader community of scientists? However, our experience from almost two decades of leading the development of the deal.II software library (http://www.dealii.org, a widely-used finite element package) and the ASPECT code (http://aspect.dealii.org, used to simulate convection in the Earth's mantle) has taught us that technical aspects are not the most difficult ones in scientific open source software. Rather, it is the social challenge of building and maintaining a community of users and developers interested in answering questions on user forums, contributing code, and jointly finding solutions to common technical and non-technical challenges. These problems are posed in an environment where project leaders typically have no resources to reward the majority of contributors, where very few people are specifically paid for the work they do on the project, and with frequent turnover of contributors as project members rotate into and out of jobs. In particular, much software work is done by graduate students who may become fluent enough in a software only a year or two before they leave academia. We will discuss strategies we have found do and do not work in maintaining and growing communities around the scientific software projects we lead. Specifically, we will discuss the management style necessary to keep contributors engaged, ways to give credit where credit is due, and structuring documentation to decrease reliance on forums and thereby allow user communities to grow without straining those who answer questions.

Reusable Software and Open Data Incorporate Ecological Understanding To Optimize Agriculture and Improveme Crops.

NASA Astrophysics Data System (ADS)

LeBauer, D.

2015-12-01

Humans need a secure and sustainable food supply, and science can help. We have an opportunity to transform agriculture by combining knowledge of organisms and ecosystems to engineer ecosystems that sustainably produce food, fuel, and other services. The challenge is that the information we have. Measurements, theories, and laws found in publications, notebooks, measurements, software, and human brains are difficult to combine. We homogenize, encode, and automate the synthesis of data and mechanistic understanding in a way that links understanding at different scales and across domains. This allows extrapolation, prediction, and assessment. Reusable components allow automated construction of new knowledge that can be used to assess, predict, and optimize agro-ecosystems. Developing reusable software and open-access databases is hard, and examples will illustrate how we use the Predictive Ecosystem Analyzer (PEcAn, pecanproject.org), the Biofuel Ecophysiological Traits and Yields database (BETYdb, betydb.org), and ecophysiological crop models to predict crop yield, decide which crops to plant, and which traits can be selected for the next generation of data driven crop improvement. A next step is to automate the use of sensors mounted on robots, drones, and tractors to assess plants in the field. The TERRA Reference Phenotyping Platform (TERRA-Ref, terraref.github.io) will provide an open access database and computing platform on which researchers can use and develop tools that use sensor data to assess and manage agricultural and other terrestrial ecosystems. TERRA-Ref will adopt existing standards and develop modular software components and common interfaces, in collaboration with researchers from iPlant, NEON, AgMIP, USDA, rOpenSci, ARPA-E, many scientists and industry partners. Our goal is to advance science by enabling efficient use, reuse, exchange, and creation of knowledge.

Proposal for a CLIPS software library

NASA Technical Reports Server (NTRS)

Porter, Ken

1991-01-01

This paper is a proposal to create a software library for the C Language Integrated Production System (CLIPS) expert system shell developed by NASA. Many innovative ideas for extending CLIPS were presented at the First CLIPS Users Conference, including useful user and database interfaces. CLIPS developers would benefit from a software library of reusable code. The CLIPS Users Group should establish a software library-- a course of action to make that happen is proposed. Open discussion to revise this library concept is essential, since only a group effort is likely to succeed. A response form intended to solicit opinions and support from the CLIPS community is included.

Adaptive optics system for the IRSOL solar observatory

NASA Astrophysics Data System (ADS)

Ramelli, Renzo; Bucher, Roberto; Rossini, Leopoldo; Bianda, Michele; Balemi, Silvano

2010-07-01

We present a low cost adaptive optics system developed for the solar observatory at Istituto Ricerche Solari Locarno (IRSOL), Switzerland. The Shack-Hartmann Wavefront Sensor is based on a Dalsa CCD camera with 256 pixels × 256 pixels working at 1kHz. The wavefront compensation is obtained by a deformable mirror with 37 actuators and a Tip-Tilt mirror. A real time control software has been developed on a RTAI-Linux PC. Scicos/Scilab based software has been realized for an online analysis of the system behavior. The software is completely open source.

Achieving Better Buying Power through Acquisition of Open Architecture Software Systems for Web-Based and Mobile Devices

DTIC Science & Technology

2015-05-01

Achieving Better Buying Power through Acquisition of Open Architecture Software Systems for Web-Based and Mobile Devices Walt Scacchi and Thomas...2015 to 00-00-2015 4. TITLE AND SUBTITLE Achieving Better Buying Power through Acquisition of Open Architecture Software Systems for Web-Based and...architecture (OA) software systems  Emerging challenges in achieving Better Buying Power (BBP) via OA software systems for Web- based and Mobile devices

Digital Image Correlation from Commercial to FOS Software: a Mature Technique for Full-Field Displacement Measurements

NASA Astrophysics Data System (ADS)

Belloni, V.; Ravanelli, R.; Nascetti, A.; Di Rita, M.; Mattei, D.; Crespi, M.

2018-05-01

In the last few decades, there has been a growing interest in studying non-contact methods for full-field displacement and strain measurement. Among such techniques, Digital Image Correlation (DIC) has received particular attention, thanks to its ability to provide these information by comparing digital images of a sample surface before and after deformation. The method is now commonly adopted in the field of civil, mechanical and aerospace engineering and different companies and some research groups implemented 2D and 3D DIC software. In this work a review on DIC software status is given at first. Moreover, a free and open source 2D DIC software is presented, named py2DIC and developed in Python at the Geodesy and Geomatics Division of DICEA of the University of Rome "La Sapienza"; its potentialities were evaluated by processing the images captured during tensile tests performed in the Structural Engineering Lab of the University of Rome "La Sapienza" and comparing them to those obtained using the commercial software Vic-2D developed by Correlated Solutions Inc, USA. The agreement of these results at one hundredth of millimetre level demonstrate the possibility to use this open source software as a valuable 2D DIC tool to measure full-field displacements on the investigated sample surface.

Demonstrating the Open Data Repository's Data Publisher: The CheMin Database

NASA Astrophysics Data System (ADS)

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

2018-04-01

The Open Data Repository's Data Publisher aims to provide an easy-to-use software tool that will allow researchers to create and publish database templates and related data. The CheMin Database developed using this framework is shown as an example.

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

NASA Astrophysics Data System (ADS)

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

2012-07-01

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

OpenStreetMap Collaborative Prototype, Phase 1

USGS Publications Warehouse

Wolf, Eric B.; Matthews, Greg D.; McNinch, Kevin; Poore, Barbara S.

2011-01-01

Phase One of the OpenStreetMap Collaborative Prototype (OSMCP) attempts to determine if the open source software developed for the OpenStreetMap (OSM, http://www.openstreetmap.org) can be used for data contributions and improvements that meet or exceed the requirements for integration into The National Map (http://www.nationalmap.gov). OpenStreetMap Collaborative Prototype Phase One focused on road data aggregated at the state level by the Kansas Data Access and Support Center (DASC). Road data from the DASC were loaded into a system hosted by the U.S. Geological Survey (USGS) National Geospatial Technical Operations Center (NGTOC) in Rolla, Missouri. U.S. Geological Survey editing specifications were developed by NGTOC personnel (J. Walters and G. Matthews, USGS, unpub. report, 2010). Interstate and U.S. Highways in the dataset were edited to the specifications by NGTOC personnel while State roads were edited by DASC personnel. Resulting data were successfully improved to meet standards for The National Map once the system and specifications were in place. The OSM software proved effective in providing a usable platform for collaborative data editing

Investigating Advances in the Acquisition of Secure Systems Based on Open Architecture, Open Source Software, and Software Product Lines

DTIC Science & Technology

2012-01-27

example is found in games converted to serve a purpose other than entertainment , such as the development and use of games for science, technology, and...These play-session histories can then be further modded via video editing or remixing with other media (e.g., adding music ) to better enable cinematic...available OSS (e.g., the Linux Kernel on the Sony PS3 game console2) that game system hackers seek to undo. Finally, games are one of the most commonly

Software Attribution for Geoscience Applications in the Computational Infrastructure for Geodynamics

NASA Astrophysics Data System (ADS)

Hwang, L.; Dumit, J.; Fish, A.; Soito, L.; Kellogg, L. H.; Smith, M.

2015-12-01

Scientific software is largely developed by individual scientists and represents a significant intellectual contribution to the field. As the scientific culture and funding agencies move towards an expectation that software be open-source, there is a corresponding need for mechanisms to cite software, both to provide credit and recognition to developers, and to aid in discoverability of software and scientific reproducibility. We assess the geodynamic modeling community's current citation practices by examining more than 300 predominantly self-reported publications utilizing scientific software in the past 5 years that is available through the Computational Infrastructure for Geodynamics (CIG). Preliminary results indicate that authors cite and attribute software either through citing (in rank order) peer-reviewed scientific publications, a user's manual, and/or a paper describing the software code. Attributions maybe found directly in the text, in acknowledgements, in figure captions, or in footnotes. What is considered citable varies widely. Citations predominantly lack software version numbers or persistent identifiers to find the software package. Versioning may be implied through reference to a versioned user manual. Authors sometimes report code features used and whether they have modified the code. As an open-source community, CIG requests that researchers contribute their modifications to the repository. However, such modifications may not be contributed back to a repository code branch, decreasing the chances of discoverability and reproducibility. Survey results through CIG's Software Attribution for Geoscience Applications (SAGA) project suggest that lack of knowledge, tools, and workflows to cite codes are barriers to effectively implement the emerging citation norms. Generated on-demand attributions on software landing pages and a prototype extensible plug-in to automatically generate attributions in codes are the first steps towards reproducibility.

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

PubMed

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

2014-01-01

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

The 2006 NESCent Phyloinformatics Hackathon: A Field Report

PubMed Central

Lapp, Hilmar; Bala, Sendu; Balhoff, James P.; Bouck, Amy; Goto, Naohisa; Holder, Mark; Holland, Richard; Holloway, Alisha; Katayama, Toshiaki; Lewis, Paul O.; Mackey, Aaron J.; Osborne, Brian I.; Piel, William H.; Kosakovsky Pond, Sergei L.; Poon, Art F.Y.; Qiu, Wei-Gang; Stajich, Jason E.; Stoltzfus, Arlin; Thierer, Tobias; Vilella, Albert J.; Vos, Rutger A.; Zmasek, Christian M.; Zwickl, Derrick J.; Vision, Todd J.

2007-01-01

In December, 2006, a group of 26 software developers from some of the most widely used life science programming toolkits and phylogenetic software projects converged on Durham, North Carolina, for a Phyloinformatics Hackathon, an intense five-day collaborative software coding event sponsored by the National Evolutionary Synthesis Center (NESCent). The goal was to help researchers to integrate multiple phylogenetic software tools into automated workflows. Participants addressed deficiencies in interoperability between programs by implementing “glue code” and improving support for phylogenetic data exchange standards (particularly NEXUS) across the toolkits. The work was guided by use-cases compiled in advance by both developers and users, and the code was documented as it was developed. The resulting software is freely available for both users and developers through incorporation into the distributions of several widely-used open-source toolkits. We explain the motivation for the hackathon, how it was organized, and discuss some of the outcomes and lessons learned. We conclude that hackathons are an effective mode of solving problems in software interoperability and usability, and are underutilized in scientific software development.

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

PubMed

Evans, Nicholas G; Selgelid, Michael J

2015-08-01

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

The Research and Implementation of MUSER CLEAN Algorithm Based on OpenCL

NASA Astrophysics Data System (ADS)

Feng, Y.; Chen, K.; Deng, H.; Wang, F.; Mei, Y.; Wei, S. L.; Dai, W.; Yang, Q. P.; Liu, Y. B.; Wu, J. P.

2017-03-01

It's urgent to carry out high-performance data processing with a single machine in the development of astronomical software. However, due to the different configuration of the machine, traditional programming techniques such as multi-threading, and CUDA (Compute Unified Device Architecture)+GPU (Graphic Processing Unit) have obvious limitations in portability and seamlessness between different operation systems. The OpenCL (Open Computing Language) used in the development of MUSER (MingantU SpEctral Radioheliograph) data processing system is introduced. And the Högbom CLEAN algorithm is re-implemented into parallel CLEAN algorithm by the Python language and PyOpenCL extended package. The experimental results show that the CLEAN algorithm based on OpenCL has approximately equally operating efficiency compared with the former CLEAN algorithm based on CUDA. More important, the data processing in merely CPU (Central Processing Unit) environment of this system can also achieve high performance, which has solved the problem of environmental dependence of CUDA+GPU. Overall, the research improves the adaptability of the system with emphasis on performance of MUSER image clean computing. In the meanwhile, the realization of OpenCL in MUSER proves its availability in scientific data processing. In view of the high-performance computing features of OpenCL in heterogeneous environment, it will probably become the preferred technology in the future high-performance astronomical software development.

a Framework for AN Open Source Geospatial Certification Model

NASA Astrophysics Data System (ADS)

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

2016-06-01

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

Evaluation of CHO Benchmarks on the Arria 10 FPGA using Intel FPGA SDK for OpenCL

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

Jin, Zheming; Yoshii, Kazutomo; Finkel, Hal

The OpenCL standard is an open programming model for accelerating algorithms on heterogeneous computing system. OpenCL extends the C-based programming language for developing portable codes on different platforms such as CPU, Graphics processing units (GPUs), Digital Signal Processors (DSPs) and Field Programmable Gate Arrays (FPGAs). The Intel FPGA SDK for OpenCL is a suite of tools that allows developers to abstract away the complex FPGA-based development flow for a high-level software development flow. Users can focus on the design of hardware-accelerated kernel functions in OpenCL and then direct the tools to generate the low-level FPGA implementations. The approach makes themore » FPGA-based development more accessible to software users as the needs for hybrid computing using CPUs and FPGAs are increasing. It can also significantly reduce the hardware development time as users can evaluate different ideas with high-level language without deep FPGA domain knowledge. Benchmarking of OpenCL-based framework is an effective way for analyzing the performance of system by studying the execution of the benchmark applications. CHO is a suite of benchmark applications that provides support for OpenCL [1]. The authors presented CHO as an OpenCL port of the CHStone benchmark. Using Altera OpenCL (AOCL) compiler to synthesize the benchmark applications, they listed the resource usage and performance of each kernel that can be successfully synthesized by the compiler. In this report, we evaluate the resource usage and performance of the CHO benchmark applications using the Intel FPGA SDK for OpenCL and Nallatech 385A FPGA board that features an Arria 10 FPGA device. The focus of the report is to have a better understanding of the resource usage and performance of the kernel implementations using Arria-10 FPGA devices compared to Stratix-5 FPGA devices. In addition, we also gain knowledge about the limitations of the current compiler when it fails to synthesize a benchmark application.« less

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

Chamana, Manohar; Prabakar, Kumaraguru; Palmintier, Bryan

A software process is developed to convert distribution network models from a quasi-static time-series tool (OpenDSS) to a real-time dynamic phasor simulator (ePHASORSIM). The description of this process in this paper would be helpful for researchers who intend to perform similar conversions. The converter could be utilized directly by users of real-time simulators who intend to perform software-in-the-loop or hardware-in-the-loop tests on large distribution test feeders for a range of use cases, including testing functions of advanced distribution management systems against a simulated distribution system. In the future, the developers intend to release the conversion tool as open source tomore » enable use by others.« less

Open source libraries and frameworks for biological data visualisation: a guide for developers.

PubMed

Wang, Rui; Perez-Riverol, Yasset; Hermjakob, Henning; Vizcaíno, Juan Antonio

2015-04-01

Recent advances in high-throughput experimental techniques have led to an exponential increase in both the size and the complexity of the data sets commonly studied in biology. Data visualisation is increasingly used as the key to unlock this data, going from hypothesis generation to model evaluation and tool implementation. It is becoming more and more the heart of bioinformatics workflows, enabling scientists to reason and communicate more effectively. In parallel, there has been a corresponding trend towards the development of related software, which has triggered the maturation of different visualisation libraries and frameworks. For bioinformaticians, scientific programmers and software developers, the main challenge is to pick out the most fitting one(s) to create clear, meaningful and integrated data visualisation for their particular use cases. In this review, we introduce a collection of open source or free to use libraries and frameworks for creating data visualisation, covering the generation of a wide variety of charts and graphs. We will focus on software written in Java, JavaScript or Python. We truly believe this software offers the potential to turn tedious data into exciting visual stories. © 2014 The Authors. PROTEOMICS published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Open source libraries and frameworks for biological data visualisation: A guide for developers

PubMed Central

Wang, Rui; Perez-Riverol, Yasset; Hermjakob, Henning; Vizcaíno, Juan Antonio

2015-01-01

Recent advances in high-throughput experimental techniques have led to an exponential increase in both the size and the complexity of the data sets commonly studied in biology. Data visualisation is increasingly used as the key to unlock this data, going from hypothesis generation to model evaluation and tool implementation. It is becoming more and more the heart of bioinformatics workflows, enabling scientists to reason and communicate more effectively. In parallel, there has been a corresponding trend towards the development of related software, which has triggered the maturation of different visualisation libraries and frameworks. For bioinformaticians, scientific programmers and software developers, the main challenge is to pick out the most fitting one(s) to create clear, meaningful and integrated data visualisation for their particular use cases. In this review, we introduce a collection of open source or free to use libraries and frameworks for creating data visualisation, covering the generation of a wide variety of charts and graphs. We will focus on software written in Java, JavaScript or Python. We truly believe this software offers the potential to turn tedious data into exciting visual stories. PMID:25475079

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

Jin, Zheming; Yoshii, Kazutomo; Finkel, Hal

Open Computing Language (OpenCL) is a high-level language that enables software programmers to explore Field Programmable Gate Arrays (FPGAs) for application acceleration. The Intel FPGA software development kit (SDK) for OpenCL allows a user to specify applications at a high level and explore the performance of low-level hardware acceleration. In this report, we present the FPGA performance and power consumption results of the single-precision floating-point vector add OpenCL kernel using the Intel FPGA SDK for OpenCL on the Nallatech 385A FPGA board. The board features an Arria 10 FPGA. We evaluate the FPGA implementations using the compute unit duplication andmore » kernel vectorization optimization techniques. On the Nallatech 385A FPGA board, the maximum compute kernel bandwidth we achieve is 25.8 GB/s, approximately 76% of the peak memory bandwidth. The power consumption of the FPGA device when running the kernels ranges from 29W to 42W.« less

Reconfigurable Transceiver and Software-Defined Radio Architecture and Technology Evaluated for NASA Space Communications

NASA Technical Reports Server (NTRS)

Reinhart, Richard C.; Kacpura, Thomas J.

2004-01-01

The NASA Glenn Research Center is investigating the development and suitability of a software-based open-architecture for space-based reconfigurable transceivers (RTs) and software-defined radios (SDRs). The main objectives of this project are to enable advanced operations and reduce mission costs. SDRs are becoming more common because of the capabilities of reconfigurable digital signal processing technologies such as field programmable gate arrays and digital signal processors, which place radio functions in firmware and software that were traditionally performed with analog hardware components. Features of interest of this communications architecture include nonproprietary open standards and application programming interfaces to enable software reuse and portability, independent hardware and software development, and hardware and software functional separation. The goals for RT and SDR technologies for NASA space missions include prelaunch and on-orbit frequency and waveform reconfigurability and programmability, high data rate capability, and overall communications and processing flexibility. These operational advances over current state-of-art transceivers will be provided to reduce the power, mass, and cost of RTs and SDRs for space communications. The open architecture for NASA communications will support existing (legacy) communications needs and capabilities while providing a path to more capable, advanced waveform development and mission concepts (e.g., ad hoc constellations with self-healing networks and high-rate science data return). A study was completed to assess the state of the art in RT architectures, implementations, and technologies. In-house researchers conducted literature searches and analysis, interviewed Government and industry contacts, and solicited information and white papers from industry on space-qualifiable RTs and SDRs and their associated technologies for space-based NASA applications. The white papers were evaluated, compiled, and used to assess RT and SDR system architectures and core technology elements to determine an appropriate investment strategy to advance these technologies to meet future mission needs. The use of these radios in the space environment represents a challenge because of the space radiation suitability of the components, which drastically reduces the processing capability. The radios available for space are considered to be RTs (as opposed to SDRs), which are digitally programmable radios with selectable changes from an architecture combining analog and digital components. The limited flexibility of this design contrasts against the desire to have a power-efficient solution and open architecture.

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

PubMed Central

2017-01-01

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

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

PubMed

Tchantchaleishvili, Vakhtang; Schmitto, Jan D

2011-10-22

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

Comparison of 3D reconstruction of mandible for pre-operative planning using commercial and open-source software

NASA Astrophysics Data System (ADS)

Abdullah, Johari Yap; Omar, Marzuki; Pritam, Helmi Mohd Hadi; Husein, Adam; Rajion, Zainul Ahmad

2016-12-01

3D printing of mandible is important for pre-operative planning, diagnostic purposes, as well as for education and training. Currently, the processing of CT data is routinely performed with commercial software which increases the cost of operation and patient management for a small clinical setting. Usage of open-source software as an alternative to commercial software for 3D reconstruction of the mandible from CT data is scarce. The aim of this study is to compare two methods of 3D reconstruction of the mandible using commercial Materialise Mimics software and open-source Medical Imaging Interaction Toolkit (MITK) software. Head CT images with a slice thickness of 1 mm and a matrix of 512x512 pixels each were retrieved from the server located at the Radiology Department of Hospital Universiti Sains Malaysia. The CT data were analysed and the 3D models of mandible were reconstructed using both commercial Materialise Mimics and open-source MITK software. Both virtual 3D models were saved in STL format and exported to 3matic and MeshLab software for morphometric and image analyses. Both models were compared using Wilcoxon Signed Rank Test and Hausdorff Distance. No significant differences were obtained between the 3D models of the mandible produced using Mimics and MITK software. The 3D model of the mandible produced using MITK open-source software is comparable to the commercial MIMICS software. Therefore, open-source software could be used in clinical setting for pre-operative planning to minimise the operational cost.

Leaf-GP: an open and automated software application for measuring growth phenotypes for arabidopsis and wheat.

PubMed

Zhou, Ji; Applegate, Christopher; Alonso, Albor Dobon; Reynolds, Daniel; Orford, Simon; Mackiewicz, Michal; Griffiths, Simon; Penfield, Steven; Pullen, Nick

2017-01-01

Plants demonstrate dynamic growth phenotypes that are determined by genetic and environmental factors. Phenotypic analysis of growth features over time is a key approach to understand how plants interact with environmental change as well as respond to different treatments. Although the importance of measuring dynamic growth traits is widely recognised, available open software tools are limited in terms of batch image processing, multiple traits analyses, software usability and cross-referencing results between experiments, making automated phenotypic analysis problematic. Here, we present Leaf-GP (Growth Phenotypes), an easy-to-use and open software application that can be executed on different computing platforms. To facilitate diverse scientific communities, we provide three software versions, including a graphic user interface (GUI) for personal computer (PC) users, a command-line interface for high-performance computer (HPC) users, and a well-commented interactive Jupyter Notebook (also known as the iPython Notebook) for computational biologists and computer scientists. The software is capable of extracting multiple growth traits automatically from large image datasets. We have utilised it in Arabidopsis thaliana and wheat ( Triticum aestivum ) growth studies at the Norwich Research Park (NRP, UK). By quantifying a number of growth phenotypes over time, we have identified diverse plant growth patterns between different genotypes under several experimental conditions. As Leaf-GP has been evaluated with noisy image series acquired by different imaging devices (e.g. smartphones and digital cameras) and still produced reliable biological outputs, we therefore believe that our automated analysis workflow and customised computer vision based feature extraction software implementation can facilitate a broader plant research community for their growth and development studies. Furthermore, because we implemented Leaf-GP based on open Python-based computer vision, image analysis and machine learning libraries, we believe that our software not only can contribute to biological research, but also demonstrates how to utilise existing open numeric and scientific libraries (e.g. Scikit-image, OpenCV, SciPy and Scikit-learn) to build sound plant phenomics analytic solutions, in a efficient and effective way. Leaf-GP is a sophisticated software application that provides three approaches to quantify growth phenotypes from large image series. We demonstrate its usefulness and high accuracy based on two biological applications: (1) the quantification of growth traits for Arabidopsis genotypes under two temperature conditions; and (2) measuring wheat growth in the glasshouse over time. The software is easy-to-use and cross-platform, which can be executed on Mac OS, Windows and HPC, with open Python-based scientific libraries preinstalled. Our work presents the advancement of how to integrate computer vision, image analysis, machine learning and software engineering in plant phenomics software implementation. To serve the plant research community, our modulated source code, detailed comments, executables (.exe for Windows; .app for Mac), and experimental results are freely available at https://github.com/Crop-Phenomics-Group/Leaf-GP/releases.

Opening Up "Open Systems": Moving toward True Interoperability among Library Software. DataResearch Automation Guide Series, Number One.

ERIC Educational Resources Information Center

Data Research Associates, Inc., St. Louis, MO.

The topic of open systems as it relates to the needs of libraries to establish interoperability between dissimilar computer systems can be clarified by an understanding of the background and evolution of the issue. The International Standards Organization developed a model to link dissimilar computers, and this model has evolved into consensus…

Xtreme Learning Control: Examples of the Open Source Movement's Impact on Our Educational Practice in a University Setting.

ERIC Educational Resources Information Center

Dunlap, Joanna C.; Wilson, Brent G.; Young, David L.

This paper describes how Open Source philosophy, a movement that has developed in opposition to the proprietary software industry, has influenced educational practice in the pursuit of scholarly freedom and authentic learning activities for students and educators. This paper provides a brief overview of the Open Source movement, and describes…

Open system environment procurement

NASA Technical Reports Server (NTRS)

Fisher, Gary

1994-01-01

Relationships between the request for procurement (RFP) process and open system environment (OSE) standards are described. A guide was prepared to help Federal agency personnel overcome problems in writing an adequate statement of work and developing realistic evaluation criteria when transitioning to an OSE. The guide contains appropriate decision points and transition strategies for developing applications that are affordable, scalable and interoperable across a broad range of computing environments. While useful, the guide does not eliminate the requirement that agencies posses in-depth expertise in software development, communications, and database technology in order to evaluate open systems.

Open source IPSEC software in manned and unmanned space missions

NASA Astrophysics Data System (ADS)

Edwards, Jacob

Network security is a major topic of research because cyber attackers pose a threat to national security. Securing ground-space communications for NASA missions is important because attackers could endanger mission success and human lives. This thesis describes how an open source IPsec software package was used to create a secure and reliable channel for ground-space communications. A cost efficient, reproducible hardware testbed was also created to simulate ground-space communications. The testbed enables simulation of low-bandwidth and high latency communications links to experiment how the open source IPsec software reacts to these network constraints. Test cases were built that allowed for validation of the testbed and the open source IPsec software. The test cases also simulate using an IPsec connection from mission control ground routers to points of interest in outer space. Tested open source IPsec software did not meet all the requirements. Software changes were suggested to meet requirements.

Open Source Hbim for Cultural Heritage: a Project Proposal

NASA Astrophysics Data System (ADS)

Diara, F.; Rinaudo, F.

2018-05-01

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

Current Practice in Software Development for Computational Neuroscience and How to Improve It

PubMed Central

Gewaltig, Marc-Oliver; Cannon, Robert

2014-01-01

Almost all research work in computational neuroscience involves software. As researchers try to understand ever more complex systems, there is a continual need for software with new capabilities. Because of the wide range of questions being investigated, new software is often developed rapidly by individuals or small groups. In these cases, it can be hard to demonstrate that the software gives the right results. Software developers are often open about the code they produce and willing to share it, but there is little appreciation among potential users of the great diversity of software development practices and end results, and how this affects the suitability of software tools for use in research projects. To help clarify these issues, we have reviewed a range of software tools and asked how the culture and practice of software development affects their validity and trustworthiness. We identified four key questions that can be used to categorize software projects and correlate them with the type of product that results. The first question addresses what is being produced. The other three concern why, how, and by whom the work is done. The answers to these questions show strong correlations with the nature of the software being produced, and its suitability for particular purposes. Based on our findings, we suggest ways in which current software development practice in computational neuroscience can be improved and propose checklists to help developers, reviewers, and scientists to assess the quality of software and whether particular pieces of software are ready for use in research. PMID:24465191

Current practice in software development for computational neuroscience and how to improve it.

PubMed

Gewaltig, Marc-Oliver; Cannon, Robert

2014-01-01

Almost all research work in computational neuroscience involves software. As researchers try to understand ever more complex systems, there is a continual need for software with new capabilities. Because of the wide range of questions being investigated, new software is often developed rapidly by individuals or small groups. In these cases, it can be hard to demonstrate that the software gives the right results. Software developers are often open about the code they produce and willing to share it, but there is little appreciation among potential users of the great diversity of software development practices and end results, and how this affects the suitability of software tools for use in research projects. To help clarify these issues, we have reviewed a range of software tools and asked how the culture and practice of software development affects their validity and trustworthiness. We identified four key questions that can be used to categorize software projects and correlate them with the type of product that results. The first question addresses what is being produced. The other three concern why, how, and by whom the work is done. The answers to these questions show strong correlations with the nature of the software being produced, and its suitability for particular purposes. Based on our findings, we suggest ways in which current software development practice in computational neuroscience can be improved and propose checklists to help developers, reviewers, and scientists to assess the quality of software and whether particular pieces of software are ready for use in research.

OpenMEEG: opensource software for quasistatic bioelectromagnetics.

PubMed

Gramfort, Alexandre; Papadopoulo, Théodore; Olivi, Emmanuel; Clerc, Maureen

2010-09-06

Interpreting and controlling bioelectromagnetic phenomena require realistic physiological models and accurate numerical solvers. A semi-realistic model often used in practise is the piecewise constant conductivity model, for which only the interfaces have to be meshed. This simplified model makes it possible to use Boundary Element Methods. Unfortunately, most Boundary Element solutions are confronted with accuracy issues when the conductivity ratio between neighboring tissues is high, as for instance the scalp/skull conductivity ratio in electro-encephalography. To overcome this difficulty, we proposed a new method called the symmetric BEM, which is implemented in the OpenMEEG software. The aim of this paper is to present OpenMEEG, both from the theoretical and the practical point of view, and to compare its performances with other competing software packages. We have run a benchmark study in the field of electro- and magneto-encephalography, in order to compare the accuracy of OpenMEEG with other freely distributed forward solvers. We considered spherical models, for which analytical solutions exist, and we designed randomized meshes to assess the variability of the accuracy. Two measures were used to characterize the accuracy. the Relative Difference Measure and the Magnitude ratio. The comparisons were run, either with a constant number of mesh nodes, or a constant number of unknowns across methods. Computing times were also compared. We observed more pronounced differences in accuracy in electroencephalography than in magnetoencephalography. The methods could be classified in three categories: the linear collocation methods, that run very fast but with low accuracy, the linear collocation methods with isolated skull approach for which the accuracy is improved, and OpenMEEG that clearly outperforms the others. As far as speed is concerned, OpenMEEG is on par with the other methods for a constant number of unknowns, and is hence faster for a prescribed accuracy level. This study clearly shows that OpenMEEG represents the state of the art for forward computations. Moreover, our software development strategies have made it handy to use and to integrate with other packages. The bioelectromagnetic research community should therefore be able to benefit from OpenMEEG with a limited development effort.

OpenMEEG: opensource software for quasistatic bioelectromagnetics

PubMed Central

2010-01-01

Background Interpreting and controlling bioelectromagnetic phenomena require realistic physiological models and accurate numerical solvers. A semi-realistic model often used in practise is the piecewise constant conductivity model, for which only the interfaces have to be meshed. This simplified model makes it possible to use Boundary Element Methods. Unfortunately, most Boundary Element solutions are confronted with accuracy issues when the conductivity ratio between neighboring tissues is high, as for instance the scalp/skull conductivity ratio in electro-encephalography. To overcome this difficulty, we proposed a new method called the symmetric BEM, which is implemented in the OpenMEEG software. The aim of this paper is to present OpenMEEG, both from the theoretical and the practical point of view, and to compare its performances with other competing software packages. Methods We have run a benchmark study in the field of electro- and magneto-encephalography, in order to compare the accuracy of OpenMEEG with other freely distributed forward solvers. We considered spherical models, for which analytical solutions exist, and we designed randomized meshes to assess the variability of the accuracy. Two measures were used to characterize the accuracy. the Relative Difference Measure and the Magnitude ratio. The comparisons were run, either with a constant number of mesh nodes, or a constant number of unknowns across methods. Computing times were also compared. Results We observed more pronounced differences in accuracy in electroencephalography than in magnetoencephalography. The methods could be classified in three categories: the linear collocation methods, that run very fast but with low accuracy, the linear collocation methods with isolated skull approach for which the accuracy is improved, and OpenMEEG that clearly outperforms the others. As far as speed is concerned, OpenMEEG is on par with the other methods for a constant number of unknowns, and is hence faster for a prescribed accuracy level. Conclusions This study clearly shows that OpenMEEG represents the state of the art for forward computations. Moreover, our software development strategies have made it handy to use and to integrate with other packages. The bioelectromagnetic research community should therefore be able to benefit from OpenMEEG with a limited development effort. PMID:20819204

pyam: Python Implementation of YaM

NASA Technical Reports Server (NTRS)

Myint, Steven; Jain, Abhinandan

2012-01-01

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

World Wind Tools Reveal Environmental Change

NASA Technical Reports Server (NTRS)

2012-01-01

Originally developed under NASA's Learning Technologies program as a tool to engage and inspire students, World Wind software was released under the NASA Open Source Agreement license. Honolulu, Hawaii based Intelesense Technologies is one of the companies currently making use of the technology for environmental, public health, and other monitoring applications for nonprofit organizations and Government agencies. The company saved about $1 million in development costs by using the NASA software.

Open systems storage platforms

NASA Technical Reports Server (NTRS)

Collins, Kirby

1992-01-01

The building blocks for an open storage system includes a system platform, a selection of storage devices and interfaces, system software, and storage applications CONVEX storage systems are based on the DS Series Data Server systems. These systems are a variant of the C3200 supercomputer with expanded I/O capabilities. These systems support a variety of medium and high speed interfaces to networks and peripherals. System software is provided in the form of ConvexOS, a POSIX compliant derivative of 4.3BSD UNIX. Storage applications include products such as UNITREE and EMASS. With the DS Series of storage systems, Convex has developed a set of products which provide open system solutions for storage management applications. The systems are highly modular, assembled from off the shelf components with industry standard interfaces. The C Series system architecture provides a stable base, with the performance and reliability of a general purpose platform. This combination of a proven system architecture with a variety of choices in peripherals and application software allows wide flexibility in configurations, and delivers the benefits of open systems to the mass storage world.

Analyzing huge pathology images with open source software.

PubMed

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

2013-06-06

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

Analyzing huge pathology images with open source software

PubMed Central

2013-01-01

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

Developing Digital Competences Using an Educational Software. A Pedagogical Research

ERIC Educational Resources Information Center

Magdas, Ioana; Bontea, Timea

2011-01-01

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

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

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-05

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

Open Scenario Study, Phase II Report: Assessment and Development of Approaches for Satisfying Unclassified Scenario Needs

DTIC Science & Technology

2010-01-01

interface, another providing the application logic (a program used to manipulate the data), and a server running Microsoft SQL Server or Oracle RDBMS... Oracle ) • Mysql (Open Source) • Other What application server software will be needed? • Application Server • CGI PHP/Perl (Open Source...are used throughout DoD and serve a variety of functions. While DoD has a codified and institutionalized process for the development of a common set

Sensor Open System Architecture (SOSA) evolution for collaborative standards development

NASA Astrophysics Data System (ADS)

Collier, Charles Patrick; Lipkin, Ilya; Davidson, Steven A.; Baldwin, Rusty; Orlovsky, Michael C.; Ibrahim, Tim

2017-04-01

The Sensor Open System Architecture (SOSA) is a C4ISR-focused technical and economic collaborative effort between the Air Force, Navy, Army, the Department of Defense (DoD), Industry, and other Governmental agencies to develop (and incorporate) a technical Open Systems Architecture standard in order to maximize C4ISR sub-system, system, and platform affordability, re-configurability, and hardware/software/firmware re-use. The SOSA effort will effectively create an operational and technical framework for the integration of disparate payloads into C4ISR systems; with a focus on the development of a modular decomposition (defining functions and behaviors) and associated key interfaces (physical and logical) for common multi-purpose architecture for radar, EO/IR, SIGINT, EW, and Communications. SOSA addresses hardware, software, and mechanical/electrical interfaces. The modular decomposition will produce a set of re-useable components, interfaces, and sub-systems that engender reusable capabilities. This, in effect, creates a realistic and affordable ecosystem enabling mission effectiveness through systematic re-use of all available re-composed hardware, software, and electrical/mechanical base components and interfaces. To this end, SOSA will leverage existing standards as much as possible and evolve the SOSA architecture through modification, reuse, and enhancements to achieve C4ISR goals. This paper will present accomplishments over the first year of SOSA initiative.

Software and electronic developments for TUG - T60 robotic telescope

NASA Astrophysics Data System (ADS)

Parmaksizoglu, M.; Dindar, M.; Kirbiyik, H.; Helhel, S.

2014-12-01

A robotic telescope is a telescope that can make observations without hands-on human control. Its low level behavior is automatic and computer-controlled. Robotic telescopes usually run under the control of a scheduler, which provides high-level control by selecting astronomical targets for observation. TUBITAK National Observatory (TUG) T60 Robotic Telescope is controlled by open source OCAAS software, formally named TALON. This study introduces the improvements on TALON software, new electronic and mechanic designs. The designs and software improvements were implemented in the T60 telescope control software and tested on the real system successfully.

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

ERIC Educational Resources Information Center

Guhlin, Miguel

2007-01-01

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

WE-D-9A-06: Open Source Monitor Calibration and Quality Control Software for Enterprise Display Management

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

Bevins, N; Vanderhoek, M; Lang, S

2014-06-15

Purpose: Medical display monitor calibration and quality control present challenges to medical physicists. The purpose of this work is to demonstrate and share experiences with an open source package that allows for both initial monitor setup and routine performance evaluation. Methods: A software package, pacsDisplay, has been developed over the last decade to aid in the calibration of all monitors within the radiology group in our health system. The software is used to calibrate monitors to follow the DICOM Grayscale Standard Display Function (GSDF) via lookup tables installed on the workstation. Additional functionality facilitates periodic evaluations of both primary andmore » secondary medical monitors to ensure satisfactory performance. This software is installed on all radiology workstations, and can also be run as a stand-alone tool from a USB disk. Recently, a database has been developed to store and centralize the monitor performance data and to provide long-term trends for compliance with internal standards and various accrediting organizations. Results: Implementation and utilization of pacsDisplay has resulted in improved monitor performance across the health system. Monitor testing is now performed at regular intervals and the software is being used across multiple imaging modalities. Monitor performance characteristics such as maximum and minimum luminance, ambient luminance and illuminance, color tracking, and GSDF conformity are loaded into a centralized database for system performance comparisons. Compliance reports for organizations such as MQSA, ACR, and TJC are generated automatically and stored in the same database. Conclusion: An open source software solution has simplified and improved the standardization of displays within our health system. This work serves as an example method for calibrating and testing monitors within an enterprise health system.« less

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

The plpdfa software is a product of an LDRD project at LLNL entitked "Adaptive Sampling for Very High Throughput Data Streams" (tracking number 11-ERD-035). This software was developed by a graduate student summer intern, Chris Challis, who worked under project PI Dan Merl furing the summer of 2011. The software the source code is implementing is a statistical analysis technique for clustering and classification of text-valued data. The method had been previously published by the PI in the open literature.

Comparing Acquisition Strategies: Open Architecture versus Product Lines

DTIC Science & Technology

2010-04-30

software • New SOW language for accepting software deliveries – Enables third-party reuse • Additional SOW language regarding conducting software code walkthroughs and for using integrated development environments ...change the business environment must be the primary factor that drives the technical approach. Accordingly, there are business case decisions to be...elements of a system design should be made available to the customer to observe throughout the design process. Electronic access to the design environment

Technology Transfer Challenges for High-Assurance Software Engineering Tools

NASA Technical Reports Server (NTRS)

Koga, Dennis (Technical Monitor); Penix, John; Markosian, Lawrence Z.

2003-01-01

In this paper, we describe our experience with the challenges thar we are currently facing in our effort to develop advanced software verification and validation tools. We categorize these challenges into several areas: cost benefits modeling, tool usability, customer application domain, and organizational issues. We provide examples of challenges in each area and identrfj, open research issues in areas which limit our ability to transfer high-assurance software engineering tools into practice.

A view of software management issues

NASA Technical Reports Server (NTRS)

Manley, J. H.

1985-01-01

The Software Development Environment (SDE) Panel addressed key programmatic, scope, and structural issues raised by its members and the general audience regarding the proposed software development environment for the Space Station program. The general team approach taken by this group led to a consensus on 18 recommendations to NASA mangament regarding the acquisition and definition of the SDE. This approach was keyed by the initial issues presentation given to the general audience. Additional issues (for a total of 23) were developed by the panelists in their first closed session from which key areas were selected and discussed in open session. These discussions led to key recommendations which are summarized and described.

Development and realization of the open fault diagnosis system based on XPE

NASA Astrophysics Data System (ADS)

Deng, Hui; Wang, TaiYong; He, HuiLong; Xu, YongGang; Zeng, JuXiang

2005-12-01

To make the complex mechanical equipment work in good service, the technology for realizing an embedded open system is introduced systematically, including open hardware configuration, customized embedded operation system and open software structure. The ETX technology is adopted in this system, integrating the CPU main-board functions, and achieving the quick, real-time signal acquisition and intelligent data analysis with applying DSP and CPLD data acquisition card. Under the open configuration, the signal bus mode such as PCI, ISA and PC/104 can be selected and the styles of the signals can be chosen too. In addition, through customizing XPE system, adopting the EWF (Enhanced Write Filter), and realizing the open system authentically, the stability of the system is enhanced. Multi-thread and multi-task programming techniques are adopted in the software programming process. Interconnecting with the remote fault diagnosis center via the net interface, cooperative diagnosis is conducted and the intelligent degree of the fault diagnosis is improved.

77 FR 20489 - Open Season for Membership to the Electronic Tax Administration Advisory Committee (ETAAC)

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-04

... returns, (3) tax software developers, (4) large and small business, (5) employers and payroll service... DEPARTMENT OF THE TREASURY Internal Revenue Service Open Season for Membership to the Electronic Tax Administration Advisory Committee (ETAAC) AGENCY: Internal Revenue Service (IRS), Treasury. ACTION...

78 FR 10693 - Open Season for Membership to the Electronic Tax Administration Advisory Committee (ETAAC)

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-14

... returns, (3) tax software developers, (4) large and small business, (5) employers and payroll service... DEPARTMENT OF THE TREASURY Internal Revenue Service Open Season for Membership to the Electronic Tax Administration Advisory Committee (ETAAC) AGENCY: Internal Revenue Service (IRS), Treasury. ACTION...

Development of a new software for analyzing 3-D fracture network

NASA Astrophysics Data System (ADS)

Um, Jeong-Gi; Noh, Young-Hwan; Choi, Yosoon

2014-05-01

A new software is presented to analyze fracture network in 3-D. Recently, we completed the software package based on information given in EGU2013. The software consists of several modules that play roles in management of borehole data, stochastic modelling of fracture network, construction of analysis domain, visualization of fracture geometry in 3-D, calculation of equivalent pipes and production of cross-section diagrams. Intel Parallel Studio XE 2013, Visual Studio.NET 2010 and the open source VTK library were utilized as development tools to efficiently implement the modules and the graphical user interface of the software. A case study was performed to analyze 3-D fracture network system at the Upper Devonian Grosmont Formation in Alberta, Canada. The results have suggested that the developed software is effective in modelling and visualizing 3-D fracture network system, and can provide useful information to tackle the geomechanical problems related to strength, deformability and hydraulic behaviours of the fractured rock masses. This presentation describes the concept and details of the development and implementation of the software.

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

PubMed Central

2011-01-01

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

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

PubMed

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

2014-04-05

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

A novel method for automated tracking and quantification of adult zebrafish behaviour during anxiety.

PubMed

Nema, Shubham; Hasan, Whidul; Bhargava, Anamika; Bhargava, Yogesh

2016-09-15

Behavioural neuroscience relies on software driven methods for behavioural assessment, but the field lacks cost-effective, robust, open source software for behavioural analysis. Here we propose a novel method which we called as ZebraTrack. It includes cost-effective imaging setup for distraction-free behavioural acquisition, automated tracking using open-source ImageJ software and workflow for extraction of behavioural endpoints. Our ImageJ algorithm is capable of providing control to users at key steps while maintaining automation in tracking without the need for the installation of external plugins. We have validated this method by testing novelty induced anxiety behaviour in adult zebrafish. Our results, in agreement with established findings, showed that during state-anxiety, zebrafish showed reduced distance travelled, increased thigmotaxis and freezing events. Furthermore, we proposed a method to represent both spatial and temporal distribution of choice-based behaviour which is currently not possible to represent using simple videograms. ZebraTrack method is simple and economical, yet robust enough to give results comparable with those obtained from costly proprietary software like Ethovision XT. We have developed and validated a novel cost-effective method for behavioural analysis of adult zebrafish using open-source ImageJ software. Copyright © 2016 Elsevier B.V. All rights reserved.

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

PubMed Central

Ackerman, Michael J.; Yoo, Terry S.

2003-01-01

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

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

PubMed

Solomon, Robert W

2009-06-01

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

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

PubMed Central

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

2014-01-01

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

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

PubMed

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

2014-01-01

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

openBEB: open biological experiment browser for correlative measurements

PubMed Central

2014-01-01

Background New experimental methods must be developed to study interaction networks in systems biology. To reduce biological noise, individual subjects, such as single cells, should be analyzed using high throughput approaches. The measurement of several correlative physical properties would further improve data consistency. Accordingly, a considerable quantity of data must be acquired, correlated, catalogued and stored in a database for subsequent analysis. Results We have developed openBEB (open Biological Experiment Browser), a software framework for data acquisition, coordination, annotation and synchronization with database solutions such as openBIS. OpenBEB consists of two main parts: A core program and a plug-in manager. Whereas the data-type independent core of openBEB maintains a local container of raw-data and metadata and provides annotation and data management tools, all data-specific tasks are performed by plug-ins. The open architecture of openBEB enables the fast integration of plug-ins, e.g., for data acquisition or visualization. A macro-interpreter allows the automation and coordination of the different modules. An update and deployment mechanism keeps the core program, the plug-ins and the metadata definition files in sync with a central repository. Conclusions The versatility, the simple deployment and update mechanism, and the scalability in terms of module integration offered by openBEB make this software interesting for a large scientific community. OpenBEB targets three types of researcher, ideally working closely together: (i) Engineers and scientists developing new methods and instruments, e.g., for systems-biology, (ii) scientists performing biological experiments, (iii) theoreticians and mathematicians analyzing data. The design of openBEB enables the rapid development of plug-ins, which will inherently benefit from the “house keeping” abilities of the core program. We report the use of openBEB to combine live cell microscopy, microfluidic control and visual proteomics. In this example, measurements from diverse complementary techniques are combined and correlated. PMID:24666611

The Five 'R's' for Developing Trusted Software Frameworks to increase confidence in, and maximise reuse of, Open Source Software.

NASA Astrophysics Data System (ADS)

Fraser, Ryan; Gross, Lutz; Wyborn, Lesley; Evans, Ben; Klump, Jens

2015-04-01

Recent investments in HPC, cloud and Petascale data stores, have dramatically increased the scale and resolution that earth science challenges can now be tackled. These new infrastructures are highly parallelised and to fully utilise them and access the large volumes of earth science data now available, a new approach to software stack engineering needs to be developed. The size, complexity and cost of the new infrastructures mean any software deployed has to be reliable, trusted and reusable. Increasingly software is available via open source repositories, but these usually only enable code to be discovered and downloaded. As a user it is hard for a scientist to judge the suitability and quality of individual codes: rarely is there information on how and where codes can be run, what the critical dependencies are, and in particular, on the version requirements and licensing of the underlying software stack. A trusted software framework is proposed to enable reliable software to be discovered, accessed and then deployed on multiple hardware environments. More specifically, this framework will enable those who generate the software, and those who fund the development of software, to gain credit for the effort, IP, time and dollars spent, and facilitate quantification of the impact of individual codes. For scientific users, the framework delivers reviewed and benchmarked scientific software with mechanisms to reproduce results. The trusted framework will have five separate, but connected components: Register, Review, Reference, Run, and Repeat. 1) The Register component will facilitate discovery of relevant software from multiple open source code repositories. The registration process of the code should include information about licensing, hardware environments it can be run on, define appropriate validation (testing) procedures and list the critical dependencies. 2) The Review component is targeting on the verification of the software typically against a set of benchmark cases. This will be achieved by linking the code in the software framework to peer review forums such as Mozilla Science or appropriate Journals (e.g. Geoscientific Model Development Journal) to assist users to know which codes to trust. 3) Referencing will be accomplished by linking the Software Framework to groups such as Figshare or ImpactStory that help disseminate and measure the impact of scientific research, including program code. 4) The Run component will draw on information supplied in the registration process, benchmark cases described in the review and relevant information to instantiate the scientific code on the selected environment. 5) The Repeat component will tap into existing Provenance Workflow engines that will automatically capture information that relate to a particular run of that software, including identification of all input and output artefacts, and all elements and transactions within that workflow. The proposed trusted software framework will enable users to rapidly discover and access reliable code, reduce the time to deploy it and greatly facilitate sharing, reuse and reinstallation of code. Properly designed it could enable an ability to scale out to massively parallel systems and be accessed nationally/ internationally for multiple use cases, including Supercomputer centres, cloud facilities, and local computers.

SCA Waveform Development for Space Telemetry

NASA Technical Reports Server (NTRS)

Mortensen, Dale J.; Kifle, Multi; Hall, C. Steve; Quinn, Todd M.

2004-01-01

The NASA Glenn Research Center is investigating and developing suitable reconfigurable radio architectures for future NASA missions. This effort is examining software-based open-architectures for space based transceivers, as well as common hardware platform architectures. The Joint Tactical Radio System's (JTRS) Software Communications Architecture (SCA) is a candidate for the software approach, but may need modifications or adaptations for use in space. An in-house SCA compliant waveform development focuses on increasing understanding of software defined radio architectures and more specifically the JTRS SCA. Space requirements put a premium on size, mass, and power. This waveform development effort is key to evaluating tradeoffs with the SCA for space applications. Existing NASA telemetry links, as well as Space Exploration Initiative scenarios, are the basis for defining the waveform requirements. Modeling and simulations are being developed to determine signal processing requirements associated with a waveform and a mission-specific computational burden. Implementation of the waveform on a laboratory software defined radio platform is proceeding in an iterative fashion. Parallel top-down and bottom-up design approaches are employed.

Agile Acceptance Test–Driven Development of Clinical Decision Support Advisories: Feasibility of Using Open Source Software

PubMed Central

Baldwin, Krystal L; Kannan, Vaishnavi; Flahaven, Emily L; Parks, Cassandra J; Ott, Jason M; Willett, Duwayne L

2018-01-01

Background Moving to electronic health records (EHRs) confers substantial benefits but risks unintended consequences. Modern EHRs consist of complex software code with extensive local configurability options, which can introduce defects. Defects in clinical decision support (CDS) tools are surprisingly common. Feasible approaches to prevent and detect defects in EHR configuration, including CDS tools, are needed. In complex software systems, use of test–driven development and automated regression testing promotes reliability. Test–driven development encourages modular, testable design and expanding regression test coverage. Automated regression test suites improve software quality, providing a “safety net” for future software modifications. Each automated acceptance test serves multiple purposes, as requirements (prior to build), acceptance testing (on completion of build), regression testing (once live), and “living” design documentation. Rapid-cycle development or “agile” methods are being successfully applied to CDS development. The agile practice of automated test–driven development is not widely adopted, perhaps because most EHR software code is vendor-developed. However, key CDS advisory configuration design decisions and rules stored in the EHR may prove amenable to automated testing as “executable requirements.” Objective We aimed to establish feasibility of acceptance test–driven development of clinical decision support advisories in a commonly used EHR, using an open source automated acceptance testing framework (FitNesse). Methods Acceptance tests were initially constructed as spreadsheet tables to facilitate clinical review. Each table specified one aspect of the CDS advisory’s expected behavior. Table contents were then imported into a test suite in FitNesse, which queried the EHR database to automate testing. Tests and corresponding CDS configuration were migrated together from the development environment to production, with tests becoming part of the production regression test suite. Results We used test–driven development to construct a new CDS tool advising Emergency Department nurses to perform a swallowing assessment prior to administering oral medication to a patient with suspected stroke. Test tables specified desired behavior for (1) applicable clinical settings, (2) triggering action, (3) rule logic, (4) user interface, and (5) system actions in response to user input. Automated test suite results for the “executable requirements” are shown prior to building the CDS alert, during build, and after successful build. Conclusions Automated acceptance test–driven development and continuous regression testing of CDS configuration in a commercial EHR proves feasible with open source software. Automated test–driven development offers one potential contribution to achieving high-reliability EHR configuration. Vetting acceptance tests with clinicians elicits their input on crucial configuration details early during initial CDS design and iteratively during rapid-cycle optimization. PMID:29653922

Agile Acceptance Test-Driven Development of Clinical Decision Support Advisories: Feasibility of Using Open Source Software.

PubMed

Basit, Mujeeb A; Baldwin, Krystal L; Kannan, Vaishnavi; Flahaven, Emily L; Parks, Cassandra J; Ott, Jason M; Willett, Duwayne L

2018-04-13

Moving to electronic health records (EHRs) confers substantial benefits but risks unintended consequences. Modern EHRs consist of complex software code with extensive local configurability options, which can introduce defects. Defects in clinical decision support (CDS) tools are surprisingly common. Feasible approaches to prevent and detect defects in EHR configuration, including CDS tools, are needed. In complex software systems, use of test-driven development and automated regression testing promotes reliability. Test-driven development encourages modular, testable design and expanding regression test coverage. Automated regression test suites improve software quality, providing a "safety net" for future software modifications. Each automated acceptance test serves multiple purposes, as requirements (prior to build), acceptance testing (on completion of build), regression testing (once live), and "living" design documentation. Rapid-cycle development or "agile" methods are being successfully applied to CDS development. The agile practice of automated test-driven development is not widely adopted, perhaps because most EHR software code is vendor-developed. However, key CDS advisory configuration design decisions and rules stored in the EHR may prove amenable to automated testing as "executable requirements." We aimed to establish feasibility of acceptance test-driven development of clinical decision support advisories in a commonly used EHR, using an open source automated acceptance testing framework (FitNesse). Acceptance tests were initially constructed as spreadsheet tables to facilitate clinical review. Each table specified one aspect of the CDS advisory's expected behavior. Table contents were then imported into a test suite in FitNesse, which queried the EHR database to automate testing. Tests and corresponding CDS configuration were migrated together from the development environment to production, with tests becoming part of the production regression test suite. We used test-driven development to construct a new CDS tool advising Emergency Department nurses to perform a swallowing assessment prior to administering oral medication to a patient with suspected stroke. Test tables specified desired behavior for (1) applicable clinical settings, (2) triggering action, (3) rule logic, (4) user interface, and (5) system actions in response to user input. Automated test suite results for the "executable requirements" are shown prior to building the CDS alert, during build, and after successful build. Automated acceptance test-driven development and continuous regression testing of CDS configuration in a commercial EHR proves feasible with open source software. Automated test-driven development offers one potential contribution to achieving high-reliability EHR configuration. Vetting acceptance tests with clinicians elicits their input on crucial configuration details early during initial CDS design and iteratively during rapid-cycle optimization. ©Mujeeb A Basit, Krystal L Baldwin, Vaishnavi Kannan, Emily L Flahaven, Cassandra J Parks, Jason M Ott, Duwayne L Willett. Originally published in JMIR Medical Informatics (http://medinform.jmir.org), 13.04.2018.

Mobile Care (Moca) for Remote Diagnosis and Screening

PubMed Central

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

2010-01-01

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

Investigating the application of AOP methodology in development of Financial Accounting Software using Eclipse-AJDT Environment

NASA Astrophysics Data System (ADS)

Sharma, Amita; Sarangdevot, S. S.

2010-11-01

Aspect-Oriented Programming (AOP) methodology has been investigated in development of real world business application software—Financial Accounting Software. Eclipse-AJDT environment has been used as open source enhanced IDE support for programming in AOP language—Aspect J. Crosscutting concerns have been identified and modularized as aspects. This reduces the complexity of the design considerably due to elimination of code scattering and tangling. Improvement in modularity, quality and performance is achieved. The study concludes that AOP methodology in Eclipse-AJDT environment offers powerful support for modular design and implementation of real world quality business software.

Near-infrared face recognition utilizing open CV software

NASA Astrophysics Data System (ADS)

Sellami, Louiza; Ngo, Hau; Fowler, Chris J.; Kearney, Liam M.

2014-06-01

Commercially available hardware, freely available algorithms, and authors' developed software are synergized successfully to detect and recognize subjects in an environment without visible light. This project integrates three major components: an illumination device operating in near infrared (NIR) spectrum, a NIR capable camera and a software algorithm capable of performing image manipulation, facial detection and recognition. Focusing our efforts in the near infrared spectrum allows the low budget system to operate covertly while still allowing for accurate face recognition. In doing so a valuable function has been developed which presents potential benefits in future civilian and military security and surveillance operations.

Canary: An NLP Platform for Clinicians and Researchers.

PubMed

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

2017-05-03

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

Development and validation of open-source software for DNA mixture interpretation based on a quantitative continuous model

PubMed Central

Manabe, Sho; Morimoto, Chie; Hamano, Yuya; Fujimoto, Shuntaro

2017-01-01

In criminal investigations, forensic scientists need to evaluate DNA mixtures. The estimation of the number of contributors and evaluation of the contribution of a person of interest (POI) from these samples are challenging. In this study, we developed a new open-source software “Kongoh” for interpreting DNA mixture based on a quantitative continuous model. The model uses quantitative information of peak heights in the DNA profile and considers the effect of artifacts and allelic drop-out. By using this software, the likelihoods of 1–4 persons’ contributions are calculated, and the most optimal number of contributors is automatically determined; this differs from other open-source software. Therefore, we can eliminate the need to manually determine the number of contributors before the analysis. Kongoh also considers allele- or locus-specific effects of biological parameters based on the experimental data. We then validated Kongoh by calculating the likelihood ratio (LR) of a POI’s contribution in true contributors and non-contributors by using 2–4 person mixtures analyzed through a 15 short tandem repeat typing system. Most LR values obtained from Kongoh during true-contributor testing strongly supported the POI’s contribution even for small amounts or degraded DNA samples. Kongoh correctly rejected a false hypothesis in the non-contributor testing, generated reproducible LR values, and demonstrated higher accuracy of the estimated number of contributors than another software based on the quantitative continuous model. Therefore, Kongoh is useful in accurately interpreting DNA evidence like mixtures and small amounts or degraded DNA samples. PMID:29149210

Development and validation of open-source software for DNA mixture interpretation based on a quantitative continuous model.

PubMed

Manabe, Sho; Morimoto, Chie; Hamano, Yuya; Fujimoto, Shuntaro; Tamaki, Keiji

2017-01-01

In criminal investigations, forensic scientists need to evaluate DNA mixtures. The estimation of the number of contributors and evaluation of the contribution of a person of interest (POI) from these samples are challenging. In this study, we developed a new open-source software "Kongoh" for interpreting DNA mixture based on a quantitative continuous model. The model uses quantitative information of peak heights in the DNA profile and considers the effect of artifacts and allelic drop-out. By using this software, the likelihoods of 1-4 persons' contributions are calculated, and the most optimal number of contributors is automatically determined; this differs from other open-source software. Therefore, we can eliminate the need to manually determine the number of contributors before the analysis. Kongoh also considers allele- or locus-specific effects of biological parameters based on the experimental data. We then validated Kongoh by calculating the likelihood ratio (LR) of a POI's contribution in true contributors and non-contributors by using 2-4 person mixtures analyzed through a 15 short tandem repeat typing system. Most LR values obtained from Kongoh during true-contributor testing strongly supported the POI's contribution even for small amounts or degraded DNA samples. Kongoh correctly rejected a false hypothesis in the non-contributor testing, generated reproducible LR values, and demonstrated higher accuracy of the estimated number of contributors than another software based on the quantitative continuous model. Therefore, Kongoh is useful in accurately interpreting DNA evidence like mixtures and small amounts or degraded DNA samples.

New software for 3D fracture network analysis and visualization

NASA Astrophysics Data System (ADS)

Song, J.; Noh, Y.; Choi, Y.; Um, J.; Hwang, S.

2013-12-01

This study presents new software to perform analysis and visualization of the fracture network system in 3D. The developed software modules for the analysis and visualization, such as BOUNDARY, DISK3D, FNTWK3D, CSECT and BDM, have been developed using Microsoft Visual Basic.NET and Visualization TookKit (VTK) open-source library. Two case studies revealed that each module plays a role in construction of analysis domain, visualization of fracture geometry in 3D, calculation of equivalent pipes, production of cross-section map and management of borehole data, respectively. The developed software for analysis and visualization of the 3D fractured rock mass can be used to tackle the geomechanical problems related to strength, deformability and hydraulic behaviors of the fractured rock masses.

FermiLib v0.1

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

MCCLEAN, JARROD; HANER, THOMAS; STEIGER, DAMIAN

FermiLib is an open source software package designed to facilitate the development and testing of algorithms for simulations of fermionic systems on quantum computers. Fermionic simulations represent an important application of early quantum devices with a lot of potential high value targets, such as quantum chemistry for the development of new catalysts. This software strives to provide a link between the required domain expertise in specific fermionic applications and quantum computing to enable more users to directly interface with, and develop for, these applications. It is an extensible Python library designed to interface with the high performance quantum simulator, ProjectQ,more » as well as application specific software such as PSI4 from the domain of quantum chemistry. Such software is key to enabling effective user facilities in quantum computation research.« less

Driving Innovation in Health Systems through an Apps-Based Information Economy

PubMed Central

Mandel, Joshua C.; Kohane, Isaac S.

2015-01-01

Healthcare data will soon be accessible using standard, open software interfaces. Here, we describe how these interfaces could lead to improved healthcare by facilitating the development of software applications (apps) that can be shared across physicians, health care organizations, translational researchers, and patients. We provide recommendations for next steps and resources for the myriad stakeholders. If challenges related to efficacy, accuracy, utility, safety, privacy, and security can be met, this emerging apps model for health information technology will open up the point of care for innovation and connect patients at home to their healthcare data. PMID:26339683

ibex: An open infrastructure software platform to facilitate collaborative work in radiomics

PubMed Central

Zhang, Lifei; Fried, David V.; Fave, Xenia J.; Hunter, Luke A.; Court, Laurence E.

2015-01-01

Purpose: Radiomics, which is the high-throughput extraction and analysis of quantitative image features, has been shown to have considerable potential to quantify the tumor phenotype. However, at present, a lack of software infrastructure has impeded the development of radiomics and its applications. Therefore, the authors developed the imaging biomarker explorer (ibex), an open infrastructure software platform that flexibly supports common radiomics workflow tasks such as multimodality image data import and review, development of feature extraction algorithms, model validation, and consistent data sharing among multiple institutions. Methods: The ibex software package was developed using the matlab and c/c++ programming languages. The software architecture deploys the modern model-view-controller, unit testing, and function handle programming concepts to isolate each quantitative imaging analysis task, to validate if their relevant data and algorithms are fit for use, and to plug in new modules. On one hand, ibex is self-contained and ready to use: it has implemented common data importers, common image filters, and common feature extraction algorithms. On the other hand, ibex provides an integrated development environment on top of matlab and c/c++, so users are not limited to its built-in functions. In the ibex developer studio, users can plug in, debug, and test new algorithms, extending ibex’s functionality. ibex also supports quality assurance for data and feature algorithms: image data, regions of interest, and feature algorithm-related data can be reviewed, validated, and/or modified. More importantly, two key elements in collaborative workflows, the consistency of data sharing and the reproducibility of calculation result, are embedded in the ibex workflow: image data, feature algorithms, and model validation including newly developed ones from different users can be easily and consistently shared so that results can be more easily reproduced between institutions. Results: Researchers with a variety of technical skill levels, including radiation oncologists, physicists, and computer scientists, have found the ibex software to be intuitive, powerful, and easy to use. ibex can be run at any computer with the windows operating system and 1GB RAM. The authors fully validated the implementation of all importers, preprocessing algorithms, and feature extraction algorithms. Windows version 1.0 beta of stand-alone ibex and ibex’s source code can be downloaded. Conclusions: The authors successfully implemented ibex, an open infrastructure software platform that streamlines common radiomics workflow tasks. Its transparency, flexibility, and portability can greatly accelerate the pace of radiomics research and pave the way toward successful clinical translation. PMID:25735289

IBEX: an open infrastructure software platform to facilitate collaborative work in radiomics.

PubMed

Zhang, Lifei; Fried, David V; Fave, Xenia J; Hunter, Luke A; Yang, Jinzhong; Court, Laurence E

2015-03-01

Radiomics, which is the high-throughput extraction and analysis of quantitative image features, has been shown to have considerable potential to quantify the tumor phenotype. However, at present, a lack of software infrastructure has impeded the development of radiomics and its applications. Therefore, the authors developed the imaging biomarker explorer (IBEX), an open infrastructure software platform that flexibly supports common radiomics workflow tasks such as multimodality image data import and review, development of feature extraction algorithms, model validation, and consistent data sharing among multiple institutions. The IBEX software package was developed using the MATLAB and c/c++ programming languages. The software architecture deploys the modern model-view-controller, unit testing, and function handle programming concepts to isolate each quantitative imaging analysis task, to validate if their relevant data and algorithms are fit for use, and to plug in new modules. On one hand, IBEX is self-contained and ready to use: it has implemented common data importers, common image filters, and common feature extraction algorithms. On the other hand, IBEX provides an integrated development environment on top of MATLAB and c/c++, so users are not limited to its built-in functions. In the IBEX developer studio, users can plug in, debug, and test new algorithms, extending IBEX's functionality. IBEX also supports quality assurance for data and feature algorithms: image data, regions of interest, and feature algorithm-related data can be reviewed, validated, and/or modified. More importantly, two key elements in collaborative workflows, the consistency of data sharing and the reproducibility of calculation result, are embedded in the IBEX workflow: image data, feature algorithms, and model validation including newly developed ones from different users can be easily and consistently shared so that results can be more easily reproduced between institutions. Researchers with a variety of technical skill levels, including radiation oncologists, physicists, and computer scientists, have found the IBEX software to be intuitive, powerful, and easy to use. IBEX can be run at any computer with the windows operating system and 1GB RAM. The authors fully validated the implementation of all importers, preprocessing algorithms, and feature extraction algorithms. Windows version 1.0 beta of stand-alone IBEX and IBEX's source code can be downloaded. The authors successfully implemented IBEX, an open infrastructure software platform that streamlines common radiomics workflow tasks. Its transparency, flexibility, and portability can greatly accelerate the pace of radiomics research and pave the way toward successful clinical translation.

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

PubMed

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

2017-02-24

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

Clarity: An Open Source Manager for Laboratory Automation

PubMed Central

Delaney, Nigel F.; Echenique, José Rojas; Marx, Christopher J.

2013-01-01

Software to manage automated laboratories interfaces with hardware instruments, gives users a way to specify experimental protocols, and schedules activities to avoid hardware conflicts. In addition to these basics, modern laboratories need software that can run multiple different protocols in parallel and that can be easily extended to interface with a constantly growing diversity of techniques and instruments. We present Clarity: a laboratory automation manager that is hardware agnostic, portable, extensible and open source. Clarity provides critical features including remote monitoring, robust error reporting by phone or email, and full state recovery in the event of a system crash. We discuss the basic organization of Clarity; demonstrate an example of its implementation for the automated analysis of bacterial growth; and describe how the program can be extended to manage new hardware. Clarity is mature; well documented; actively developed; written in C# for the Common Language Infrastructure; and is free and open source software. These advantages set Clarity apart from currently available laboratory automation programs. PMID:23032169

Thermal Tracker: The Secret Lives of Bats and Birds Revealed

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

None

Offshore wind developers and stakeholders can accelerate the sustainable, widespread deployment of offshore wind using a new open-source software program, called ThermalTracker. Researchers can now collect the data they need to better understand the potential effects of offshore wind turbines on bird and bat populations. This plug and play software can be used with any standard desktop computer, thermal camera, and statistical software to identify species and behaviors of animals in offshore locations.

Baseliner: an open source, interactive tool for processing sap flux data from thermal dissipation probes.

Treesearch

Andrew C. Oishi; David Hawthorne; Ram Oren

2016-01-01

Estimating transpiration from woody plants using thermal dissipation sap flux sensors requires careful data processing. Currently, researchers accomplish this using spreadsheets, or by personally writing scripts for statistical software programs (e.g., R, SAS). We developed the Baseliner software to help establish a standardized protocol for processing sap...

From, by, and for the OSSD: Software Engineering Education Using an Open Source Software Approach

ERIC Educational Resources Information Center

Huang, Kun; Dong, Yifei; Ge, Xun

2006-01-01

Computing is a complex, multidisciplinary field that requires a range of professional proficiencies. Computing students are expected to develop in-depth knowledge and skills, integrate and apply their knowledge flexibly to solve complex problems, and work successfully in teams. However, many students who graduate with degrees in computing fail to…

Introducing Dynamic Mathematics Software to Secondary School Teachers: The Case of GeoGebra

ERIC Educational Resources Information Center

Hohenwarter, Judith; Hohenwarter, Markus; Lavicza, Zsolt

2009-01-01

This paper describes a study aimed to identify most common impediments related to the introduction of an open-source mathematical software package GeoGebra. We report on the analysis of data collected during a three-week professional development programme organised for middle and high school teachers in Florida. The study identified challenges…

The ALMA common software: dispatch from the trenches

NASA Astrophysics Data System (ADS)

Schwarz, J.; Sommer, H.; Jeram, B.; Sekoranja, M.; Chiozzi, G.; Grimstrup, A.; Caproni, A.; Paredes, C.; Allaert, E.; Harrington, S.; Turolla, S.; Cirami, R.

2008-07-01

The ALMA Common Software (ACS) provides both an application framework and CORBA-based middleware for the distributed software system of the Atacama Large Millimeter Array. Building upon open-source tools such as the JacORB, TAO and OmniORB ORBs, ACS supports the development of component-based software in any of three languages: Java, C++ and Python. Now in its seventh major release, ACS has matured, both in its feature set as well as in its reliability and performance. However, it is only recently that the ALMA observatory's hardware and application software has reached a level at which it can exploit and challenge the infrastructure that ACS provides. In particular, the availability of an Antenna Test Facility(ATF) at the site of the Very Large Array in New Mexico has enabled us to exercise and test the still evolving end-to-end ALMA software under realistic conditions. The major focus of ACS, consequently, has shifted from the development of new features to consideration of how best to use those that already exist. Configuration details which could be neglected for the purpose of running unit tests or skeletal end-to-end simulations have turned out to be sensitive levers for achieving satisfactory performance in a real-world environment. Surprising behavior in some open-source tools has required us to choose between patching code that we did not write or addressing its deficiencies by implementing workarounds in our own software. We will discuss these and other aspects of our recent experience at the ATF and in simulation.

A Digital Repository and Execution Platform for Interactive Scholarly Publications in Neuroscience.

PubMed

Hodge, Victoria; Jessop, Mark; Fletcher, Martyn; Weeks, Michael; Turner, Aaron; Jackson, Tom; Ingram, Colin; Smith, Leslie; Austin, Jim

2016-01-01

The CARMEN Virtual Laboratory (VL) is a cloud-based platform which allows neuroscientists to store, share, develop, execute, reproduce and publicise their work. This paper describes new functionality in the CARMEN VL: an interactive publications repository. This new facility allows users to link data and software to publications. This enables other users to examine data and software associated with the publication and execute the associated software within the VL using the same data as the authors used in the publication. The cloud-based architecture and SaaS (Software as a Service) framework allows vast data sets to be uploaded and analysed using software services. Thus, this new interactive publications facility allows others to build on research results through reuse. This aligns with recent developments by funding agencies, institutions, and publishers with a move to open access research. Open access provides reproducibility and verification of research resources and results. Publications and their associated data and software will be assured of long-term preservation and curation in the repository. Further, analysing research data and the evaluations described in publications frequently requires a number of execution stages many of which are iterative. The VL provides a scientific workflow environment to combine software services into a processing tree. These workflows can also be associated with publications and executed by users. The VL also provides a secure environment where users can decide the access rights for each resource to ensure copyright and privacy restrictions are met.

Analysis of Cisco Open Network Environment (ONE) OpenFlow Controller Implementation

DTIC Science & Technology

2014-08-01

Software - Defined Networking ( SDN ), when fully realized, offer many improvements over the current rigid and...functionalities like handshake, connection setup, switch management, and security. 15. SUBJECT TERMS OpenFlow, software - defined networking , Cisco ONE, SDN ...innovating packet-forwarding technologies. Network device roles are strictly defined with little or no flexibility. In Software - Defined Networks ( SDNs ),

Development and Deployment of the OpenMRS-Ebola Electronic Health Record System for an Ebola Treatment Center in Sierra Leone.

PubMed

Oza, Shefali; Jazayeri, Darius; Teich, Jonathan M; Ball, Ellen; Nankubuge, Patricia Alexandra; Rwebembera, Job; Wing, Kevin; Sesay, Alieu Amara; Kanter, Andrew S; Ramos, Glauber D; Walton, David; Cummings, Rachael; Checchi, Francesco; Fraser, Hamish S

2017-08-21

Stringent infection control requirements at Ebola treatment centers (ETCs), which are specialized facilities for isolating and treating Ebola patients, create substantial challenges for recording and reviewing patient information. During the 2014-2016 West African Ebola epidemic, paper-based data collection systems at ETCs compromised the quality, quantity, and confidentiality of patient data. Electronic health record (EHR) systems have the potential to address such problems, with benefits for patient care, surveillance, and research. However, no suitable software was available for deployment when large-scale ETCs opened as the epidemic escalated in 2014. We present our work on rapidly developing and deploying OpenMRS-Ebola, an EHR system for the Kerry Town ETC in Sierra Leone. We describe our experience, lessons learned, and recommendations for future health emergencies. We used the OpenMRS platform and Agile software development approaches to build OpenMRS-Ebola. Key features of our work included daily communications between the development team and ground-based operations team, iterative processes, and phased development and implementation. We made design decisions based on the restrictions of the ETC environment and regular user feedback. To evaluate the system, we conducted predeployment user questionnaires and compared the EHR records with duplicate paper records. We successfully built OpenMRS-Ebola, a modular stand-alone EHR system with a tablet-based application for infectious patient wards and a desktop-based application for noninfectious areas. OpenMRS-Ebola supports patient tracking (registration, bed allocation, and discharge); recording of vital signs and symptoms; medication and intravenous fluid ordering and monitoring; laboratory results; clinician notes; and data export. It displays relevant patient information to clinicians in infectious and noninfectious zones. We implemented phase 1 (patient tracking; drug ordering and monitoring) after 2.5 months of full-time development. OpenMRS-Ebola was used for 112 patient registrations, 569 prescription orders, and 971 medication administration recordings. We were unable to fully implement phases 2 and 3 as the ETC closed because of a decrease in new Ebola cases. The phase 1 evaluation suggested that OpenMRS-Ebola worked well in the context of the rollout, and the user feedback was positive. To our knowledge, OpenMRS-Ebola is the most comprehensive adaptable clinical EHR built for a low-resource setting health emergency. It is designed to address the main challenges of data collection in highly infectious environments that require robust infection prevention and control measures and it is interoperable with other electronic health systems. Although we built and deployed OpenMRS-Ebola more rapidly than typical software, our work highlights the challenges of having to develop an appropriate system during an emergency rather than being able to rapidly adapt an existing one. Lessons learned from this and previous emergencies should be used to ensure that a set of well-designed, easy-to-use, pretested health software is ready for quick deployment in future. ©Shefali Oza, Darius Jazayeri, Jonathan M Teich, Ellen Ball, Patricia Alexandra Nankubuge, Job Rwebembera, Kevin Wing, Alieu Amara Sesay, Andrew S Kanter, Glauber D Ramos, David Walton, Rachael Cummings, Francesco Checchi, Hamish S Fraser. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 21.08.2017.

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

NASA Astrophysics Data System (ADS)

Konnik, Mikhail V.; Welsh, James

2012-09-01

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

Software for real-time localization of baleen whale calls using directional sonobuoys: A case study on Antarctic blue whales.

PubMed

Miller, Brian S; Calderan, Susannah; Gillespie, Douglas; Weatherup, Graham; Leaper, Russell; Collins, Kym; Double, Michael C

2016-03-01

Directional frequency analysis and recording (DIFAR) sonobuoys can allow real-time acoustic localization of baleen whales for underwater tracking and remote sensing, but limited availability of hardware and software has prevented wider usage. These software limitations were addressed by developing a module in the open-source software PAMGuard. A case study is presented demonstrating that this software provides greater efficiency and accessibility than previous methods for detecting, localizing, and tracking Antarctic blue whales in real time. Additionally, this software can easily be extended to track other low and mid frequency sounds including those from other cetaceans, pinnipeds, icebergs, shipping, and seismic airguns.

A multi-center study benchmarks software tools for label-free proteome quantification

PubMed Central

Gillet, Ludovic C; Bernhardt, Oliver M.; MacLean, Brendan; Röst, Hannes L.; Tate, Stephen A.; Tsou, Chih-Chiang; Reiter, Lukas; Distler, Ute; Rosenberger, George; Perez-Riverol, Yasset; Nesvizhskii, Alexey I.; Aebersold, Ruedi; Tenzer, Stefan

2016-01-01

The consistent and accurate quantification of proteins by mass spectrometry (MS)-based proteomics depends on the performance of instruments, acquisition methods and data analysis software. In collaboration with the software developers, we evaluated OpenSWATH, SWATH2.0, Skyline, Spectronaut and DIA-Umpire, five of the most widely used software methods for processing data from SWATH-MS (sequential window acquisition of all theoretical fragment ion spectra), a method that uses data-independent acquisition (DIA) for label-free protein quantification. We analyzed high-complexity test datasets from hybrid proteome samples of defined quantitative composition acquired on two different MS instruments using different SWATH isolation windows setups. For consistent evaluation we developed LFQbench, an R-package to calculate metrics of precision and accuracy in label-free quantitative MS, and report the identification performance, robustness and specificity of each software tool. Our reference datasets enabled developers to improve their software tools. After optimization, all tools provided highly convergent identification and reliable quantification performance, underscoring their robustness for label-free quantitative proteomics. PMID:27701404

A multicenter study benchmarks software tools for label-free proteome quantification.

PubMed

Navarro, Pedro; Kuharev, Jörg; Gillet, Ludovic C; Bernhardt, Oliver M; MacLean, Brendan; Röst, Hannes L; Tate, Stephen A; Tsou, Chih-Chiang; Reiter, Lukas; Distler, Ute; Rosenberger, George; Perez-Riverol, Yasset; Nesvizhskii, Alexey I; Aebersold, Ruedi; Tenzer, Stefan

2016-11-01

Consistent and accurate quantification of proteins by mass spectrometry (MS)-based proteomics depends on the performance of instruments, acquisition methods and data analysis software. In collaboration with the software developers, we evaluated OpenSWATH, SWATH 2.0, Skyline, Spectronaut and DIA-Umpire, five of the most widely used software methods for processing data from sequential window acquisition of all theoretical fragment-ion spectra (SWATH)-MS, which uses data-independent acquisition (DIA) for label-free protein quantification. We analyzed high-complexity test data sets from hybrid proteome samples of defined quantitative composition acquired on two different MS instruments using different SWATH isolation-window setups. For consistent evaluation, we developed LFQbench, an R package, to calculate metrics of precision and accuracy in label-free quantitative MS and report the identification performance, robustness and specificity of each software tool. Our reference data sets enabled developers to improve their software tools. After optimization, all tools provided highly convergent identification and reliable quantification performance, underscoring their robustness for label-free quantitative proteomics.

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

PubMed Central

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

2014-01-01

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

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

PubMed

Rijnbeek, Mark; Steinbeck, Christoph

2009-10-22

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

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

NASA Technical Reports Server (NTRS)

Hughes, Steven P.

2007-01-01

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

Coupled RipCAS-DFLOW (CoRD) Software and Data Management System for Reproducible Floodplain Vegetation Succession Modeling

NASA Astrophysics Data System (ADS)

Turner, M. A.; Miller, S.; Gregory, A.; Cadol, D. D.; Stone, M. C.; Sheneman, L.

2016-12-01

We present the Coupled RipCAS-DFLOW (CoRD) modeling system created to encapsulate the workflow to analyze the effects of stream flooding on vegetation succession. CoRD provides an intuitive command-line and web interface to run DFLOW and RipCAS in succession over many years automatically, which is a challenge because, for our application, DFLOW must be run on a supercomputing cluster via the PBS job scheduler. RipCAS is a vegetation succession model, and DFLOW is a 2D open channel flow model. Data adaptors have been developed to seamlessly connect DFLOW output data to be RipCAS inputs, and vice-versa. CoRD provides automated statistical analysis and visualization, plus automatic syncing of input and output files and model run metadata to the hydrological data management system HydroShare using its excellent Python REST client. This combination of technologies and data management techniques allows the results to be shared with collaborators and eventually published. Perhaps most importantly, it allows results to be easily reproduced via either the command-line or web user interface. This system is a result of collaboration between software developers and hydrologists participating in the Western Consortium for Watershed Analysis, Visualization, and Exploration (WC-WAVE). Because of the computing-intensive nature of this particular workflow, including automating job submission/monitoring and data adaptors, software engineering expertise is required. However, the hydrologists provide the software developers with a purpose and ensure a useful, intuitive tool is developed. Our hydrologists contribute software, too: RipCAS was developed from scratch by hydrologists on the team as a specialized, open-source version of the Computer Aided Simulation Model for Instream Flow and Riparia (CASiMiR) vegetation model; our hydrologists running DFLOW provided numerous examples and help with the supercomputing system. This project is written in Python, a popular language in the geosciences and a good beginner programming language, and is completely open source. It can be accessed at https://github.com/VirtualWatershed/CoRD with documentation available at http://virtualwatershed.github.io/CoRD. These facts enable continued development and use beyond the involvement of the current authors.

XSEOS: An Open Software for Chemical Engineering Thermodynamics

ERIC Educational Resources Information Center

Castier, Marcelo

2008-01-01

An Excel add-in--XSEOS--that implements several excess Gibbs free energy models and equations of state has been developed for educational use. Several traditional and modern thermodynamic models are available in the package with a user-friendly interface. XSEOS has open code, is freely available, and should be useful for instructors and students…

Panel: Governance in Open Source Projects and Communities

NASA Astrophysics Data System (ADS)

Bolici, Francesco; de Laat, Paul; Ljungberg, Jan; Pontiggia, Andrea; Rossi Lamastra, Cristina

“Although considerable research has been devoted to the growth and expansion of open source communities and the comparison between the efficiency of corporate structures and community structures in the field of software development, rather less attention has been paid to their governance structures (control, monitoring, supervision)” (Lattemann and Stieglitz 2005).

SWMM5 Application Programming Interface and PySWMM: A ...

EPA Pesticide Factsheets

In support of the OpenWaterAnalytics open source initiative, the PySWMM project encompasses the development of a Python interfacing wrapper to SWMM5 with parallel ongoing development of the USEPA Stormwater Management Model (SWMM5) application programming interface (API). ... The purpose of this work is to increase the utility of the SWMM dll by creating a Toolkit API for accessing its functionality. The utility of the Toolkit is further enhanced with a wrapper to allow access from the Python scripting language. This work is being prosecuted as part of an Open Source development strategy and is being performed by volunteer software developers.

Implementation of highly parallel and large scale GW calculations within the OpenAtom software

NASA Astrophysics Data System (ADS)

Ismail-Beigi, Sohrab

The need to describe electronic excitations with better accuracy than provided by band structures produced by Density Functional Theory (DFT) has been a long-term enterprise for the computational condensed matter and materials theory communities. In some cases, appropriate theoretical frameworks have existed for some time but have been difficult to apply widely due to computational cost. For example, the GW approximation incorporates a great deal of important non-local and dynamical electronic interaction effects but has been too computationally expensive for routine use in large materials simulations. OpenAtom is an open source massively parallel ab initiodensity functional software package based on plane waves and pseudopotentials (http://charm.cs.uiuc.edu/OpenAtom/) that takes advantage of the Charm + + parallel framework. At present, it is developed via a three-way collaboration, funded by an NSF SI2-SSI grant (ACI-1339804), between Yale (Ismail-Beigi), IBM T. J. Watson (Glenn Martyna) and the University of Illinois at Urbana Champaign (Laxmikant Kale). We will describe the project and our current approach towards implementing large scale GW calculations with OpenAtom. Potential applications of large scale parallel GW software for problems involving electronic excitations in semiconductor and/or metal oxide systems will be also be pointed out.

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

PubMed

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

2012-10-01

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

caGrid 1.0 : an enterprise Grid infrastructure for biomedical research.

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

Oster, S.; Langella, S.; Hastings, S.

To develop software infrastructure that will provide support for discovery, characterization, integrated access, and management of diverse and disparate collections of information sources, analysis methods, and applications in biomedical research. Design: An enterprise Grid software infrastructure, called caGrid version 1.0 (caGrid 1.0), has been developed as the core Grid architecture of the NCI-sponsored cancer Biomedical Informatics Grid (caBIG{trademark}) program. It is designed to support a wide range of use cases in basic, translational, and clinical research, including (1) discovery, (2) integrated and large-scale data analysis, and (3) coordinated study. Measurements: The caGrid is built as a Grid software infrastructure andmore » leverages Grid computing technologies and the Web Services Resource Framework standards. It provides a set of core services, toolkits for the development and deployment of new community provided services, and application programming interfaces for building client applications. Results: The caGrid 1.0 was released to the caBIG community in December 2006. It is built on open source components and caGrid source code is publicly and freely available under a liberal open source license. The core software, associated tools, and documentation can be downloaded from the following URL: .« less

An Open Service Provider Concept for Enterprise Complex Automation

NASA Astrophysics Data System (ADS)

Ivaschenko, A. V.; Sitnikov, P. V.; Tanonykhina, M. O.

2017-01-01

The paper introduces a solution for IT services representation and management in the integrated information space of distributed enterprises. It is proposed to develop an Open Service Provider as a software platform for interaction between IT services providers and their users. Implementation of the proposed concept and approach is illustrated by an after-sales customer support system for a large manufacturing corporation delivered by SEC “Open Code”.

Multimedia courseware in an open-systems environment: a DoD strategy

NASA Astrophysics Data System (ADS)

Welsch, Lawrence A.

1991-03-01

The federal government is about to invest billions of dollars to develop multimedia training materials for delivery on computer-based interactive training systems. Acquisition of a variety of computers and peripheral devices hosting various operating systems and suites of authoring system software will be necessary to facilitate the development of this courseware. There is no single source that will satisfy all needs. Although high-performance, low-cost interactive training hardware is available, the products have proprietary software interfaces. Because the interfaces are proprietary, expensive reprogramming is usually required to adapt such software products to other platforms. This costly reprogramming could be eliminated by adopting standard software interfaces. DoD's Portable Courseware Project (PORTCO) is typical of projects worldwide that require standard software interfaces. This paper articulates the strategy whereby PORTCO leverages the open systems movement and the new realities of information technology. These realities encompass changes in the pace at which new technology becomes available, changes in organizational goals and philosophy, new roles of vendors and users, changes in the procurement process, and acceleration toward open system environments. The PORTCO strategy is applicable to all projects and systems that require open systems to achieve mission objectives. The federal goal is to facilitate the creation of an environment in which high quality portable courseware is available as commercial off-the-shelf products and is competitively supplied by a variety of vendors. In order to achieve this goal a system architecture incorporating standards to meet the users' needs must be established. The Request for Architecture (RFA) developed cooperatively by DoD and the National Institute of Standards and Technology (NIST) will generate the PORTCO systems architecture. This architecture must freely integrate the courseware and authoring software from the lower levels of machine architecture and systems service implementation. In addition, the systems architecture will establish how the application-specific technologies relate to other technologies. Further, a computer-based interactive training applications profile must be developed. This profile, along with the systems architecture derived as a result of the RFA, provides the basis for identifying the needed standards. NIST will then accelerate the development of these standards using, but not restricted to, existing standards activities within established standards forums. The federal multimedia courseware effort has adopted the Interactive Multimedia Association (INA) Recommended Practices for Interactive Video Portability as the baseline for the migration of computer-based interactive training systems to an open systems environment based upon international standards. The PORTCO strategy includes an evolutionary migration to a standards-based, Open System Environments (OSE). An important aspect of this migration strategy is to move to open systems via stepwise evolution rather than via quantum leaps. Another area of concern is that of infrastructure issues, such as maintaining and supporting the technologies required for computer-based interactive training. The federal multimedia initiative will use the RFA-based architecture to differentiate between those technologies that can be maintained and supported by existing infrastructure mechanisms and those that require new mechanisms. Existing infrastructure mechanisms will be used and where infrastructure mechanisms do not exist, the approach will be to place high priority on establishing the appropriate mechanisms. Establishing an infrastructure mechanism is a nontrivial task requiring sustained investment of resources.

Open source tools for fluorescent imaging.

PubMed

Hamilton, Nicholas A

2012-01-01

As microscopy becomes increasingly automated and imaging expands in the spatial and time dimensions, quantitative analysis tools for fluorescent imaging are becoming critical to remove both bottlenecks in throughput as well as fully extract and exploit the information contained in the imaging. In recent years there has been a flurry of activity in the development of bio-image analysis tools and methods with the result that there are now many high-quality, well-documented, and well-supported open source bio-image analysis projects with large user bases that cover essentially every aspect from image capture to publication. These open source solutions are now providing a viable alternative to commercial solutions. More importantly, they are forming an interoperable and interconnected network of tools that allow data and analysis methods to be shared between many of the major projects. Just as researchers build on, transmit, and verify knowledge through publication, open source analysis methods and software are creating a foundation that can be built upon, transmitted, and verified. Here we describe many of the major projects, their capabilities, and features. We also give an overview of the current state of open source software for fluorescent microscopy analysis and the many reasons to use and develop open source methods. Copyright © 2012 Elsevier Inc. All rights reserved.

Political Economy, the Internet and FL/OSS Development

NASA Astrophysics Data System (ADS)

Mansell, Robin; Berdou, Evangelia

Despite the growing amount of research on Free/Libre/Open Source Software (FL/OSS) development, there is little insight into how structural factors associated with institutions influence the patterns of software developer activity in this area. This article examines some of the dynamics of the development of this type of software and the extent to which these dynamics are associated with features of the gift economy as is frequently suggested in the literature. Drawing on an empirical analysis of contributors to the GNOME FL/OSS project, we suggest that greater attention should be given to the emergence of a mixed economy in which features of the exchange economy come to the fore with implications for the power relationships among those contributing to FL/OSS.

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

Looking toward the Future: A Case Study of Open Source Software in the Humanities

ERIC Educational Resources Information Center

Quamen, Harvey

2006-01-01

In this article Harvey Quamen examines how the philosophy of open source software might be of particular benefit to humanities scholars in the near future--particularly for academic journals with limited financial resources. To this end he provides a case study in which he describes his use of open source technology (MySQL database software and…

Creating a Rackspace and NASA Nebula compatible cloud using the OpenStack project (Invited)

NASA Astrophysics Data System (ADS)

Clark, R.

2010-12-01

NASA and Rackspace have both provided technology to the OpenStack that allows anyone to create a private Infrastructure as a Service (IaaS) cloud using open source software and commodity hardware. OpenStack is designed and developed completely in the open and with an open governance process. NASA donated Nova, which powers the compute portion of NASA Nebula Cloud Computing Platform, and Rackspace donated Swift, which powers Rackspace Cloud Files. The project is now in continuous development by NASA, Rackspace, and hundreds of other participants. When you create a private cloud using Openstack, you will have the ability to easily interact with your private cloud, a government cloud, and an ecosystem of public cloud providers, using the same API.

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.

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

PubMed

Fichou, Dimitri; Morlock, Gertrud E

2018-07-27

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

NASA Operational Simulator for Small Satellites: Tools for Software Based Validation and Verification of Small Satellites

NASA Technical Reports Server (NTRS)

Grubb, Matt

2016-01-01

The NASA Operational Simulator for Small Satellites (NOS3) is a suite of tools to aid in areas such as software development, integration test (IT), mission operations training, verification and validation (VV), and software systems check-out. NOS3 provides a software development environment, a multi-target build system, an operator interface-ground station, dynamics and environment simulations, and software-based hardware models. NOS3 enables the development of flight software (FSW) early in the project life cycle, when access to hardware is typically not available. For small satellites there are extensive lead times on many of the commercial-off-the-shelf (COTS) components as well as limited funding for engineering test units (ETU). Considering the difficulty of providing a hardware test-bed to each developer tester, hardware models are modeled based upon characteristic data or manufacturers data sheets for each individual component. The fidelity of each hardware models is such that FSW executes unaware that physical hardware is not present. This allows binaries to be compiled for both the simulation environment, and the flight computer, without changing the FSW source code. For hardware models that provide data dependent on the environment, such as a GPS receiver or magnetometer, an open-source tool from NASA GSFC (42 Spacecraft Simulation) is used to provide the necessary data. The underlying infrastructure used to transfer messages between FSW and the hardware models can also be used to monitor, intercept, and inject messages, which has proven to be beneficial for VV of larger missions such as James Webb Space Telescope (JWST). As hardware is procured, drivers can be added to the environment to enable hardware-in-the-loop (HWIL) testing. When strict time synchronization is not vital, any number of combinations of hardware components and software-based models can be tested. The open-source operator interface used in NOS3 is COSMOS from Ball Aerospace. For testing, plug-ins are implemented in COSMOS to control the NOS3 simulations, while the command and telemetry tools available in COSMOS are used to communicate with FSW. NOS3 is actively being used for FSW development and component testing of the Simulation-to-Flight 1 (STF-1) CubeSat. As NOS3 matures, hardware models have been added for common CubeSat components such as Novatel GPS receivers, ClydeSpace electrical power systems and batteries, ISISpace antenna systems, etc. In the future, NASA IVV plans to distribute NOS3 to other CubeSat developers and release the suite to the open-source community.

Using Selection Pressure as an Asset to Develop Reusable, Adaptable Software Systems

NASA Technical Reports Server (NTRS)

Berrick, Stephen; Lynnes, Christopher

2007-01-01

The Goddard Earth Sciences Data and Information Services Center (GES DISC) at NASA has over the years developed and honed several reusable architectural components for supporting large-scale data centers with a large customer base. These include a processing system (S4PM) and an archive system (S4PA) based upon a workflow engine called the Simple Scalable Script based Science Processor (S4P) and an online data visualization and analysis system (Giovanni). These subsystems are currently reused internally in a variety of combinations to implement customized data management on behalf of instrument science teams and other science investigators. Some of these subsystems (S4P and S4PM) have also been reused by other data centers for operational science processing. Our experience has been that development and utilization of robust interoperable and reusable software systems can actually flourish in environments defined by heterogeneous commodity hardware systems the emphasis on value-added customer service and the continual goal for achieving higher cost efficiencies. The repeated internal reuse that is fostered by such an environment encourages and even forces changes to the software that make it more reusable and adaptable. Allowing and even encouraging such selective pressures to software development has been a key factor In the success of S4P and S4PM which are now available to the open source community under the NASA Open source Agreement

OpenCluster: A Flexible Distributed Computing Framework for Astronomical Data Processing

NASA Astrophysics Data System (ADS)

Wei, Shoulin; Wang, Feng; Deng, Hui; Liu, Cuiyin; Dai, Wei; Liang, Bo; Mei, Ying; Shi, Congming; Liu, Yingbo; Wu, Jingping

2017-02-01

The volume of data generated by modern astronomical telescopes is extremely large and rapidly growing. However, current high-performance data processing architectures/frameworks are not well suited for astronomers because of their limitations and programming difficulties. In this paper, we therefore present OpenCluster, an open-source distributed computing framework to support rapidly developing high-performance processing pipelines of astronomical big data. We first detail the OpenCluster design principles and implementations and present the APIs facilitated by the framework. We then demonstrate a case in which OpenCluster is used to resolve complex data processing problems for developing a pipeline for the Mingantu Ultrawide Spectral Radioheliograph. Finally, we present our OpenCluster performance evaluation. Overall, OpenCluster provides not only high fault tolerance and simple programming interfaces, but also a flexible means of scaling up the number of interacting entities. OpenCluster thereby provides an easily integrated distributed computing framework for quickly developing a high-performance data processing system of astronomical telescopes and for significantly reducing software development expenses.

Open-source, small-animal magnetic resonance-guided focused ultrasound system.

PubMed

Poorman, Megan E; Chaplin, Vandiver L; Wilkens, Ken; Dockery, Mary D; Giorgio, Todd D; Grissom, William A; Caskey, Charles F

2016-01-01

MR-guided focused ultrasound or high-intensity focused ultrasound (MRgFUS/MRgHIFU) is a non-invasive therapeutic modality with many potential applications in areas such as cancer therapy, drug delivery, and blood-brain barrier opening. However, the large financial costs involved in developing preclinical MRgFUS systems represent a barrier to research groups interested in developing new techniques and applications. We aim to mitigate these challenges by detailing a validated, open-source preclinical MRgFUS system capable of delivering thermal and mechanical FUS in a quantifiable and repeatable manner under real-time MRI guidance. A hardware and software package was developed that includes closed-loop feedback controlled thermometry code and CAD drawings for a therapy table designed for a preclinical MRI scanner. For thermal treatments, the modular software uses a proportional integral derivative controller to maintain a precise focal temperature rise in the target given input from MR phase images obtained concurrently. The software computes the required voltage output and transmits it to a FUS transducer that is embedded in the delivery table within the magnet bore. The delivery table holds the FUS transducer, a small animal and its monitoring equipment, and a transmit/receive RF coil. The transducer is coupled to the animal via a water bath and is translatable in two dimensions from outside the magnet. The transducer is driven by a waveform generator and amplifier controlled by real-time software in Matlab. MR acoustic radiation force imaging is also implemented to confirm the position of the focus for mechanical and thermal treatments. The system was validated in tissue-mimicking phantoms and in vivo during murine tumor hyperthermia treatments. Sonications were successfully controlled over a range of temperatures and thermal doses for up to 20 min with minimal temperature overshoot. MR thermometry was validated with an optical temperature probe, and focus visualization was achieved with acoustic radiation force imaging. We developed an MRgFUS platform for small-animal treatments that robustly delivers accurate, precise, and controllable sonications over extended time periods. This system is an open source and could increase the availability of low-cost small-animal systems to interdisciplinary researchers seeking to develop new MRgFUS applications and technology.

Comparison/Validation Study of Lattice Boltzmann and Navier Stokes for Various Benchmark Applications: Report 1 in Discrete Nano-Scale Mechanics and Simulations Series

DTIC Science & Technology

2014-09-15

solver, OpenFOAM version 2.1.‡ In particular, the incompressible laminar flow equations (Eq. 6-8) were solved in conjunction with the pressure im- plicit...central differencing and upwinding schemes, respectively. Since the OpenFOAM code is inherently transient, steady-state conditions were ob- tained...collaborative effort between Kitware and Los Alamos National Laboratory. ‡ OpenFOAM is a free, open-source computational fluid dynamics software developed

Research on infrared small-target tracking technology under complex background

NASA Astrophysics Data System (ADS)

Liu, Lei; Wang, Xin; Chen, Jilu; Pan, Tao

2012-10-01

In this paper, some basic principles and the implementing flow charts of a series of algorithms for target tracking are described. On the foundation of above works, a moving target tracking software base on the OpenCV is developed by the software developing platform MFC. Three kinds of tracking algorithms are integrated in this software. These two tracking algorithms are Kalman Filter tracking method and Camshift tracking method. In order to explain the software clearly, the framework and the function are described in this paper. At last, the implementing processes and results are analyzed, and those algorithms for tracking targets are evaluated from the two aspects of subjective and objective. This paper is very significant in the application of the infrared target tracking technology.

Streamlined sign-out of capillary protein electrophoresis using middleware and an open-source macro application.

PubMed

Mathur, Gagan; Haugen, Thomas H; Davis, Scott L; Krasowski, Matthew D

2014-01-01

Interfacing of clinical laboratory instruments with the laboratory information system (LIS) via "middleware" software is increasingly common. Our clinical laboratory implemented capillary electrophoresis using a Sebia(®) Capillarys-2™ (Norcross, GA, USA) instrument for serum and urine protein electrophoresis. Using Data Innovations Instrument Manager, an interface was established with the LIS (Cerner) that allowed for bi-directional transmission of numeric data. However, the text of the interpretive pathology report was not properly transferred. To reduce manual effort and possibility for error in text data transfer, we developed scripts in AutoHotkey, a free, open-source macro-creation and automation software utility. Scripts were written to create macros that automated mouse and key strokes. The scripts retrieve the specimen accession number, capture user input text, and insert the text interpretation in the correct patient record in the desired format. The scripts accurately and precisely transfer narrative interpretation into the LIS. Combined with bar-code reading by the electrophoresis instrument, the scripts transfer data efficiently to the correct patient record. In addition, the AutoHotKey script automated repetitive key strokes required for manual entry into the LIS, making protein electrophoresis sign-out easier to learn and faster to use by the pathology residents. Scripts allow for either preliminary verification by residents or final sign-out by the attending pathologist. Using the open-source AutoHotKey software, we successfully improved the transfer of text data between capillary electrophoresis software and the LIS. The use of open-source software tools should not be overlooked as tools to improve interfacing of laboratory instruments.

A Brief Assessment of LC2IEDM, MIST and Web Services for use in Naval Tactical Data Management

DTIC Science & Technology

2004-07-01

server software, messaging between the client and server, and a database. The MIST database is implemented in an open source DBMS named PostGreSQL ... PostGreSQL had its beginnings at the University of California, Berkley, in 1986 [11]. The development of PostGreSQL has since evolved into a...contact history from the database. DRDC Atlantic TM 2004-148 9 Request Software Request Software Server Side Response from service

Reference software implementation for GIFTS ground data processing

NASA Astrophysics Data System (ADS)

Garcia, R. K.; Howell, H. B.; Knuteson, R. O.; Martin, G. D.; Olson, E. R.; Smuga-Otto, M. J.

2006-08-01

Future satellite weather instruments such as high spectral resolution imaging interferometers pose a challenge to the atmospheric science and software development communities due to the immense data volumes they will generate. An open-source, scalable reference software implementation demonstrating the calibration of radiance products from an imaging interferometer, the Geosynchronous Imaging Fourier Transform Spectrometer1 (GIFTS), is presented. This paper covers essential design principles laid out in summary system diagrams, lessons learned during implementation and preliminary test results from the GIFTS Information Processing System (GIPS) prototype.

Challenges of Implementing Free and Open Source Software (FOSS): Evidence from the Indian Educational Setting

ERIC Educational Resources Information Center

Thankachan, Briju; Moore, David Richard

2017-01-01

The use of Free and Open Source Software (FOSS), a subset of Information and Communication Technology (ICT), can reduce the cost of purchasing software. Despite the benefit in the initial purchase price of software, deploying software requires total cost that goes beyond the initial purchase price. Total cost is a silent issue of FOSS and can only…

How Is Open Source Special?

ERIC Educational Resources Information Center

Kapor, Mitchell

2005-01-01

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

Promoting Science Software Best Practices: A Scientist's Perspective (Invited)

NASA Astrophysics Data System (ADS)

Blanton, B. O.

2013-12-01

Software is at the core of most modern scientific activities, and as societal awareness of, and impacts from, extreme weather, disasters, and climate and global change continue to increase, the roles that scientific software play in analyses and decision-making are brought more to the forefront. Reproducibility of research results (particularly those that enter into the decision-making arena) and open access to the software is essential for scientific and scientists' credibility. This has been highlighted in a recent article by Joppa et al (Troubling Trends in Scientific Software Use, Science Magazine, May 2013) that describes reasons for particular software being chosen by scientists, including that the "developer is well-respected" and on "recommendation from a close colleague". This reliance on recommendation, Joppa et al conclude, is fraught with risks to both sciences and scientists. Scientists must frequently take software for granted, assuming that it performs as expected and advertised and that the software itself has been validated and results verified. This is largely due to the manner in which much software is written and developed; in an ad hoc manner, with an inconsistent funding stream, and with little application of core software engineering best practices. Insufficient documentation, limited test cases, and code unavailability are significant barriers to informed and intelligent science software usage. This situation is exacerbated when the scientist becomes the software developer out of necessity due to resource constraints. Adoption of, and adherence to, best practices in scientific software development will substantially increase intelligent software usage and promote a sustainable evolution of the science as encoded in the software. We describe a typical scientist's perspective on using and developing scientific software in the context of storm surge research and forecasting applications that have real-time objectives and regulatory constraints. This include perspectives on what scientists/users of software can contribute back to the software development process and examples of successful scientist/developer interactions, and the competition between "getting it done" and "getting it done right".

Supporting Trust in Globally Distributed Software Teams: The Impact of Visualized Collaborative Traces on Perceived Trustworthiness

ERIC Educational Resources Information Center

Trainer, Erik Harrison

2012-01-01

Trust plays an important role in collaborations because it creates an environment in which people can openly exchange ideas and information with one another and engineer innovative solutions together with less perceived risk. The rise in globally distributed software development has created an environment in which workers are likely to have less…

Guidance and Control Software Project Data - Volume 2: Development Documents

NASA Technical Reports Server (NTRS)

Hayhurst, Kelly J. (Editor)

2008-01-01

The Guidance and Control Software (GCS) project was the last in a series of software reliability studies conducted at Langley Research Center between 1977 and 1994. The technical results of the GCS project were recorded after the experiment was completed. Some of the support documentation produced as part of the experiment, however, is serving an unexpected role far beyond its original project context. Some of the software used as part of the GCS project was developed to conform to the RTCA/DO-178B software standard, "Software Considerations in Airborne Systems and Equipment Certification," used in the civil aviation industry. That standard requires extensive documentation throughout the software development life cycle, including plans, software requirements, design and source code, verification cases and results, and configuration management and quality control data. The project documentation that includes this information is open for public scrutiny without the legal or safety implications associated with comparable data from an avionics manufacturer. This public availability has afforded an opportunity to use the GCS project documents for DO-178B training. This report provides a brief overview of the GCS project, describes the 4-volume set of documents and the role they are playing in training, and includes the development documents from the GCS project. Volume 2 contains three appendices: A. Guidance and Control Software Development Specification; B. Design Description for the Pluto Implementation of the Guidance and Control Software; and C. Source Code for the Pluto Implementation of the Guidance and Control Software

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

USGS Publications Warehouse

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

2012-01-01

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

An Inverse Modeling Plugin for HydroDesktop using the Method of Anchored Distributions (MAD)

NASA Astrophysics Data System (ADS)

Ames, D. P.; Osorio, C.; Over, M. W.; Rubin, Y.

2011-12-01

The CUAHSI Hydrologic Information System (HIS) software stack is based on an open and extensible architecture that facilitates the addition of new functions and capabilities at both the server side (using HydroServer) and the client side (using HydroDesktop). The HydroDesktop client plugin architecture is used here to expose a new scripting based plugin that makes use of the R statistics software as a means for conducting inverse modeling using the Method of Anchored Distributions (MAD). MAD is a Bayesian inversion technique for conditioning computational model parameters on relevant field observations yielding probabilistic distributions of the model parameters, related to the spatial random variable of interest, by assimilating multi-type and multi-scale data. The implementation of a desktop software tool for using the MAD technique is expected to significantly lower the barrier to use of inverse modeling in education, research, and resource management. The HydroDesktop MAD plugin is being developed following a community-based, open-source approach that will help both its adoption and long term sustainability as a user tool. This presentation will briefly introduce MAD, HydroDesktop, and the MAD plugin and software development effort.

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

NASA Astrophysics Data System (ADS)

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

2012-12-01

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

FROMS3D: New Software for 3-D Visualization of Fracture Network System in Fractured Rock Masses

NASA Astrophysics Data System (ADS)

Noh, Y. H.; Um, J. G.; Choi, Y.

2014-12-01

A new software (FROMS3D) is presented to visualize fracture network system in 3-D. The software consists of several modules that play roles in management of borehole and field fracture data, fracture network modelling, visualization of fracture geometry in 3-D and calculation and visualization of intersections and equivalent pipes between fractures. Intel Parallel Studio XE 2013, Visual Studio.NET 2010 and the open source VTK library were utilized as development tools to efficiently implement the modules and the graphical user interface of the software. The results have suggested that the developed software is effective in visualizing 3-D fracture network system, and can provide useful information to tackle the engineering geological problems related to strength, deformability and hydraulic behaviors of the fractured rock masses.

Simplified Deployment of Health Informatics Applications by Providing Docker Images.

PubMed

Löbe, Matthias; Ganslandt, Thomas; Lotzmann, Lydia; Mate, Sebastian; Christoph, Jan; Baum, Benjamin; Sariyar, Murat; Wu, Jie; Stäubert, Sebastian

2016-01-01

Due to the specific needs of biomedical researchers, in-house development of software is widespread. A common problem is to maintain and enhance software after the funded project has ended. Even if many tools are made open source, only a couple of projects manage to attract a user basis large enough to ensure sustainability. Reasons for this include complex installation and configuration of biomedical software as well as an ambiguous terminology of the features provided; all of which make evaluation of software laborious. Docker is a para-virtualization technology based on Linux containers that eases deployment of applications and facilitates evaluation. We investigated a suite of software developments funded by a large umbrella organization for networked medical research within the last 10 years and created Docker containers for a number of applications to support utilization and dissemination.

An open CAM system for dentistry on the basis of China-made 5-axis simultaneous contouring CNC machine tool and industrial CAM software.

PubMed

Lu, Li; Liu, Shusheng; Shi, Shenggen; Yang, Jianzhong

2011-10-01

China-made 5-axis simultaneous contouring CNC machine tool and domestically developed industrial computer-aided manufacture (CAM) technology were used for full crown fabrication and measurement of crown accuracy, with an attempt to establish an open CAM system for dental processing and to promote the introduction of domestic dental computer-aided design (CAD)/CAM system. Commercially available scanning equipment was used to make a basic digital tooth model after preparation of crown, and CAD software that comes with the scanning device was employed to design the crown by using domestic industrial CAM software to process the crown data in order to generate a solid model for machining purpose, and then China-made 5-axis simultaneous contouring CNC machine tool was used to complete machining of the whole crown and the internal accuracy of the crown internal was measured by using 3D-MicroCT. The results showed that China-made 5-axis simultaneous contouring CNC machine tool in combination with domestic industrial CAM technology can be used for crown making and the crown was well positioned in die. The internal accuracy was successfully measured by using 3D-MicroCT. It is concluded that an open CAM system for dentistry on the basis of China-made 5-axis simultaneous contouring CNC machine tool and domestic industrial CAM software has been established, and development of the system will promote the introduction of domestically-produced dental CAD/CAM system.

An Open Hardware seismic data recorder - a solid basis for citizen science

NASA Astrophysics Data System (ADS)

Mertl, Stefan

2015-04-01

"Ruwai" is a 24-Bit Open Hardware seismic data recorder. It is built up of four stackable printed circuit boards fitting the Arduino Mega 2560 microcontroller prototyping platform. An interface to the BeagleBone Black single-board computer enables extensive data storage, -processing and networking capabilities. The four printed circuit boards provide a uBlox Lea-6T GPS module and real-time clock (GPS Timing shield), an Texas Instruments ADS1274 24-Bit analog to digital converter (ADC main shield), an analog input section with a Texas Instruments PGA281 programmable gain amplifier and an analog anti-aliasing filter (ADC analog interface pga) and the power conditioning based on 9-36V DC input (power supply shield). The Arduino Mega 2560 is used for controlling the hardware components, timestamping sampled data using the GPS timing information and transmitting the data to the BeagleBone Black single-board computer. The BeagleBone Black provides local data storage, wireless mesh networking using the optimized link state routing daemon and differential GNSS positioning using the RTKLIB software. The complete hardware and software is published under free software - or open hardware licenses and only free software (e.g. KiCad) was used for the development to facilitate the reusability of the design and increases the sustainability of the project. "Ruwai" was developed within the framework of the "Community Environmental Observation Network (CEON)" (http://www.mertl-research.at/ceon/) which was supported by the Internet Foundation Austria (IPA) within the NetIdee 2013 call.

Bridging the Particle Physics and Big Data Worlds

NASA Astrophysics Data System (ADS)

Pivarski, James

2017-09-01

For decades, particle physicists have developed custom software because the scale and complexity of our problems were unique. In recent years, however, the ``big data'' industry has begun to tackle similar problems, and has developed some novel solutions. Incorporating scientific Python libraries, Spark, TensorFlow, and machine learning tools into the physics software stack can improve abstraction, reliability, and in some cases performance. Perhaps more importantly, it can free physicists to concentrate on domain-specific problems. Building bridges isn't always easy, however. Physics software and open-source software from industry differ in many incidental ways and a few fundamental ways. I will show work from the DIANA-HEP project to streamline data flow from ROOT to Numpy and Spark, to incorporate ideas of functional programming into histogram aggregation, and to develop real-time, query-style manipulations of particle data.

Lessons Learned through the Development and Publication of AstroImageJ

NASA Astrophysics Data System (ADS)

Collins, Karen

2018-01-01

As lead author of the scientific image processing software package AstroImageJ (AIJ), I will discuss the reasoning behind why we decided to release AIJ to the public, and the lessons we learned related to the development, publication, distribution, and support of AIJ. I will also summarize the AIJ code language selection, code documentation and testing approaches, code distribution, update, and support facilities used, and the code citation and licensing decisions. Since AIJ was initially developed as part of my graduate research and was my first scientific open source software publication, many of my experiences and difficulties encountered may parallel those of others new to scientific software publication. Finally, I will discuss the benefits and disadvantages of releasing scientific software that I now recognize after having AIJ in the public domain for more than five years.

PsyToolkit: a software package for programming psychological experiments using Linux.

PubMed

Stoet, Gijsbert

2010-11-01

PsyToolkit is a set of software tools for programming psychological experiments on Linux computers. Given that PsyToolkit is freely available under the Gnu Public License, open source, and designed such that it can easily be modified and extended for individual needs, it is suitable not only for technically oriented Linux users, but also for students, researchers on small budgets, and universities in developing countries. The software includes a high-level scripting language, a library for the programming language C, and a questionnaire presenter. The software easily integrates with other open source tools, such as the statistical software package R. PsyToolkit is designed to work with external hardware (including IoLab and Cedrus response keyboards and two common digital input/output boards) and to support millisecond timing precision. Four in-depth examples explain the basic functionality of PsyToolkit. Example 1 demonstrates a stimulus-response compatibility experiment. Example 2 demonstrates a novel mouse-controlled visual search experiment. Example 3 shows how to control light emitting diodes using PsyToolkit, and Example 4 shows how to build a light-detection sensor. The last two examples explain the electronic hardware setup such that they can even be used with other software packages.

Graphic representations: keys to disclose the codex of nature

NASA Astrophysics Data System (ADS)

Caramelo, Liliana; Gonçalves, Norberto; Pereira, Mário; Soares, Armando; Naia, Marco

2010-05-01

Undergraduate and university level students present some difficulties to understand and interpret many of the geosciences concepts, in particular those represented by vector and scalar fields. Our experience reveals that these difficulties are associated with a lack in the development of their abstraction and mental picturing abilities. On the other hand, these students have easy access to communication and information technology software which can be used to built graphic representations of experimental data, time series and vector and scalar fields. This transformation allows an easiest extraction, interpretation and summary of the most important characteristics in the data. There is already commercial and open source software with graphical tools that can be used for this purpose but commercial software packs with user friendly interfaces but their price is not negligible. Open source software can circumvent this difficulty even if, in general, their graphical user interface hasn't reached the desirable level of the commercial ones. We will show a simple procedure to generate an image from the data that characterizes the generation of the suitable images illustrating the key concepts in study, using a freeware code, exactly as it is presented to the students in our open teaching sessions to the general student community. Our experience demonstrated that the students are very enthusiastic using this approach. Furthermore, the use of this software can easily be adopted by teachers and students of secondary schools as part of curricular activities.

Open Source and Design Thinking at NASA: A Vision for Future Software

NASA Technical Reports Server (NTRS)

Trimble, Jay

2017-01-01

NASA Mission Control Software for the Visualization of data has historically been closed, accessible only to small groups of flight controllers, often bound to a specific mission discipline such as flight dynamics, health and status or mission planning. Open Mission Control Technologies (MCT) provides new capability for NASA mission controllers and, by being fully open source, opens up NASA software for the visualization of mission data to broader communities inside and outside of NASA. Open MCT is the product of a design thinking process within NASA, using participatory design and design sprints to build a product that serves users.

Analysis of High-Throughput ELISA Microarray Data

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

White, Amanda M.; Daly, Don S.; Zangar, Richard C.

Our research group develops analytical methods and software for the high-throughput analysis of quantitative enzyme-linked immunosorbent assay (ELISA) microarrays. ELISA microarrays differ from DNA microarrays in several fundamental aspects and most algorithms for analysis of DNA microarray data are not applicable to ELISA microarrays. In this review, we provide an overview of the steps involved in ELISA microarray data analysis and how the statistically sound algorithms we have developed provide an integrated software suite to address the needs of each data-processing step. The algorithms discussed are available in a set of open-source software tools (http://www.pnl.gov/statistics/ProMAT).

Organizing Community-Based Data Standards: Lessons from Developing a Successful Open Standard in Systems Biology

NASA Astrophysics Data System (ADS)

Hucka, M.

2015-09-01

In common with many fields, including astronomy, a vast number of software tools for computational modeling and simulation are available today in systems biology. This wealth of resources is a boon to researchers, but it also presents interoperability problems. Despite working with different software tools, researchers want to disseminate their work widely as well as reuse and extend the models of other researchers. This situation led in the year 2000 to an effort to create a tool-independent, machine-readable file format for representing models: SBML, the Systems Biology Markup Language. SBML has since become the de facto standard for its purpose. Its success and general approach has inspired and influenced other community-oriented standardization efforts in systems biology. Open standards are essential for the progress of science in all fields, but it is often difficult for academic researchers to organize successful community-based standards. I draw on personal experiences from the development of SBML and summarize some of the lessons learned, in the hope that this may be useful to other groups seeking to develop open standards in a community-oriented fashion.

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

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

Conversion and Validation of Distribution System Model from a QSTS-Based Tool to a Real-Time Dynamic Phasor Simulator

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

Chamana, Manohar; Prabakar, Kumaraguru; Palmintier, Bryan

A software process is developed to convert distribution network models from a quasi-static time-series tool (OpenDSS) to a real-time dynamic phasor simulator (ePHASORSIM). The description of this process in this paper would be helpful for researchers who intend to perform similar conversions. The converter could be utilized directly by users of real-time simulators who intend to perform software-in-the-loop or hardware-in-the-loop tests on large distribution test feeders for a range of use cases, including testing functions of advanced distribution management systems against a simulated distribution system. In the future, the developers intend to release the conversion tool as open source tomore » enable use by others.« less

Conversion and Validation of Distribution System Model from a QSTS-Based Tool to a Real-Time Dynamic Phasor Simulator: Preprint

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

Chamana, Manohar; Prabakar, Kumaraguru; Palmintier, Bryan

A software process is developed to convert distribution network models from a quasi-static time-series tool (OpenDSS) to a real-time dynamic phasor simulator (ePHASORSIM). The description of this process in this paper would be helpful for researchers who intend to perform similar conversions. The converter could be utilized directly by users of real-time simulators who intend to perform software-in-the-loop or hardware-in-the-loop tests on large distribution test feeders for a range of use cases, including testing functions of advanced distribution management systems against a simulated distribution system. In the future, the developers intend to release the conversion tool as open source tomore » enable use by others.« less

The Ensemble Canon

NASA Technical Reports Server (NTRS)

MIittman, David S

2011-01-01

Ensemble is an open architecture for the development, integration, and deployment of mission operations software. Fundamentally, it is an adaptation of the Eclipse Rich Client Platform (RCP), a widespread, stable, and supported framework for component-based application development. By capitalizing on the maturity and availability of the Eclipse RCP, Ensemble offers a low-risk, politically neutral path towards a tighter integration of operations tools. The Ensemble project is a highly successful, ongoing collaboration among NASA Centers. Since 2004, the Ensemble project has supported the development of mission operations software for NASA's Exploration Systems, Science, and Space Operations Directorates.

RGG: A general GUI Framework for R scripts

PubMed Central

Visne, Ilhami; Dilaveroglu, Erkan; Vierlinger, Klemens; Lauss, Martin; Yildiz, Ahmet; Weinhaeusel, Andreas; Noehammer, Christa; Leisch, Friedrich; Kriegner, Albert

2009-01-01

Background R is the leading open source statistics software with a vast number of biostatistical and bioinformatical analysis packages. To exploit the advantages of R, extensive scripting/programming skills are required. Results We have developed a software tool called R GUI Generator (RGG) which enables the easy generation of Graphical User Interfaces (GUIs) for the programming language R by adding a few Extensible Markup Language (XML) – tags. RGG consists of an XML-based GUI definition language and a Java-based GUI engine. GUIs are generated in runtime from defined GUI tags that are embedded into the R script. User-GUI input is returned to the R code and replaces the XML-tags. RGG files can be developed using any text editor. The current version of RGG is available as a stand-alone software (RGGRunner) and as a plug-in for JGR. Conclusion RGG is a general GUI framework for R that has the potential to introduce R statistics (R packages, built-in functions and scripts) to users with limited programming skills and helps to bridge the gap between R developers and GUI-dependent users. RGG aims to abstract the GUI development from individual GUI toolkits by using an XML-based GUI definition language. Thus RGG can be easily integrated in any software. The RGG project further includes the development of a web-based repository for RGG-GUIs. RGG is an open source project licensed under the Lesser General Public License (LGPL) and can be downloaded freely at PMID:19254356

Free/Libre Open Source Software Implementation in Schools: Evidence from the Field and Implications for the Future

ERIC Educational Resources Information Center

Lin, Yu-Wei; Zini, Enrico

2008-01-01

This empirical paper shows how free/libre open source software (FLOSS) contributes to mutual and collaborative learning in an educational environment. Unlike proprietary software, FLOSS allows extensive customisation of software to support the needs of local users better. This also allows users to participate more proactively in the development…

Shaping Software Engineering Curricula Using Open Source Communities: A Case Study

ERIC Educational Resources Information Center

Bowring, James; Burke, Quinn

2016-01-01

This paper documents four years of a novel approach to teaching a two-course sequence in software engineering as part of the ABET-accredited computer science curriculum at the College of Charleston. This approach is team-based and centers on learning software engineering in the context of open source software projects. In the first course, teams…

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…

Instrumentino: An Open-Source Software for Scientific Instruments.

PubMed

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

2015-01-01

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

Hybrid Optimization Parallel Search PACKage

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

2009-11-10

HOPSPACK is open source software for solving optimization problems without derivatives. Application problems may have a fully nonlinear objective function, bound constraints, and linear and nonlinear constraints. Problem variables may be continuous, integer-valued, or a mixture of both. The software provides a framework that supports any derivative-free type of solver algorithm. Through the framework, solvers request parallel function evaluation, which may use MPI (multiple machines) or multithreading (multiple processors/cores on one machine). The framework provides a Cache and Pending Cache of saved evaluations that reduces execution time and facilitates restarts. Solvers can dynamically create other algorithms to solve subproblems, amore » useful technique for handling multiple start points and integer-valued variables. HOPSPACK ships with the Generating Set Search (GSS) algorithm, developed at Sandia as part of the APPSPACK open source software project.« less

Four aspects to make science open "by design" and not as an after-thought.

PubMed

Halchenko, Yaroslav O; Hanke, Michael

2015-01-01

Unrestricted dissemination of methodological developments in neuroimaging became the propelling force in advancing our understanding of brain function. However, despite such a rich legacy, it remains not uncommon to encounter software and datasets that are distributed under unnecessarily restricted terms, or that violate terms of third-party products (software or data). With this brief correspondence we would like to recapitulate four important aspects of scientific research practice, which should be taken into consideration as early as possible in the course of any project. Keeping these in check will help neuroimaging to stay at the forefront of the open science movement.

Design and Evaluation of an Open Web Platform Cartography Lab Curriculum

ERIC Educational Resources Information Center

Sack, Carl M.; Roth, Robert E.

2017-01-01

Recent shifts in web map technology away from proprietary software and toward development on the Open Web Platform have increased the number and complexity of technical skills needed to do cartography on the Web. Web-based cartography curricula likewise must be adapted to prepare geography, cartography, and GIS students with the skills needed to…

Delivering Savings with Open Architecture and Product Lines

DTIC Science & Technology

2011-04-30

p.m. Chair: Christopher Deegan , Executive Director, Program Executive Office for Integrated Warfare Systems Delivering Savings with Open...Architectures Walt Scacchi and Thomas Alspaugh, Institute for Software Research Christopher Deegan —Executive Director, Program Executive Officer...Integrated Warfare Systems (PEO IWS). Mr. Deegan directs the development, acquisition, and fleet support of 150 combat weapon system programs managed by 350

Introducing a new open source GIS user interface for the SWAT model

USDA-ARS?s Scientific Manuscript database

The Soil and Water Assessment Tool (SWAT) model is a robust watershed modelling tool. It typically uses the ArcSWAT interface to create its inputs. ArcSWAT is public domain software which works in the licensed ArcGIS environment. The aim of this paper was to develop an open source user interface ...

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

General guidelines for biomedical software development

PubMed Central

Silva, Luis Bastiao; Jimenez, Rafael C.; Blomberg, Niklas; Luis Oliveira, José

2017-01-01

Most bioinformatics tools available today were not written by professional software developers, but by people that wanted to solve their own problems, using computational solutions and spending the minimum time and effort possible, since these were just the means to an end. Consequently, a vast number of software applications are currently available, hindering the task of identifying the utility and quality of each. At the same time, this situation has hindered regular adoption of these tools in clinical practice. Typically, they are not sufficiently developed to be used by most clinical researchers and practitioners. To address these issues, it is necessary to re-think how biomedical applications are built and adopt new strategies that ensure quality, efficiency, robustness, correctness and reusability of software components. We also need to engage end-users during the development process to ensure that applications fit their needs. In this review, we present a set of guidelines to support biomedical software development, with an explanation of how they can be implemented and what kind of open-source tools can be used for each specific topic. PMID:28443186

Agile Methods for Open Source Safety-Critical Software

PubMed Central

Enquobahrie, Andinet; Ibanez, Luis; Cheng, Patrick; Yaniv, Ziv; Cleary, Kevin; Kokoori, Shylaja; Muffih, Benjamin; Heidenreich, John

2011-01-01

The introduction of software technology in a life-dependent environment requires the development team to execute a process that ensures a high level of software reliability and correctness. Despite their popularity, agile methods are generally assumed to be inappropriate as a process family in these environments due to their lack of emphasis on documentation, traceability, and other formal techniques. Agile methods, notably Scrum, favor empirical process control, or small constant adjustments in a tight feedback loop. This paper challenges the assumption that agile methods are inappropriate for safety-critical software development. Agile methods are flexible enough to encourage the right amount of ceremony; therefore if safety-critical systems require greater emphasis on activities like formal specification and requirements management, then an agile process will include these as necessary activities. Furthermore, agile methods focus more on continuous process management and code-level quality than classic software engineering process models. We present our experiences on the image-guided surgical toolkit (IGSTK) project as a backdrop. IGSTK is an open source software project employing agile practices since 2004. We started with the assumption that a lighter process is better, focused on evolving code, and only adding process elements as the need arose. IGSTK has been adopted by teaching hospitals and research labs, and used for clinical trials. Agile methods have matured since the academic community suggested they are not suitable for safety-critical systems almost a decade ago, we present our experiences as a case study for renewing the discussion. PMID:21799545

Agile Methods for Open Source Safety-Critical Software.

PubMed

Gary, Kevin; Enquobahrie, Andinet; Ibanez, Luis; Cheng, Patrick; Yaniv, Ziv; Cleary, Kevin; Kokoori, Shylaja; Muffih, Benjamin; Heidenreich, John

2011-08-01

The introduction of software technology in a life-dependent environment requires the development team to execute a process that ensures a high level of software reliability and correctness. Despite their popularity, agile methods are generally assumed to be inappropriate as a process family in these environments due to their lack of emphasis on documentation, traceability, and other formal techniques. Agile methods, notably Scrum, favor empirical process control, or small constant adjustments in a tight feedback loop. This paper challenges the assumption that agile methods are inappropriate for safety-critical software development. Agile methods are flexible enough to encourage the rightamount of ceremony; therefore if safety-critical systems require greater emphasis on activities like formal specification and requirements management, then an agile process will include these as necessary activities. Furthermore, agile methods focus more on continuous process management and code-level quality than classic software engineering process models. We present our experiences on the image-guided surgical toolkit (IGSTK) project as a backdrop. IGSTK is an open source software project employing agile practices since 2004. We started with the assumption that a lighter process is better, focused on evolving code, and only adding process elements as the need arose. IGSTK has been adopted by teaching hospitals and research labs, and used for clinical trials. Agile methods have matured since the academic community suggested they are not suitable for safety-critical systems almost a decade ago, we present our experiences as a case study for renewing the discussion.

Stereo Vision Inside Tire

DTIC Science & Technology

2015-08-21

using the Open Computer Vision ( OpenCV ) libraries [6] for computer vision and the Qt library [7] for the user interface. The software has the...depth. The software application calibrates the cameras using the plane based calibration model from the OpenCV calib3D module and allows the...6] OpenCV . 2015. OpenCV Open Source Computer Vision. [Online]. Available at: opencv.org [Accessed]: 09/01/2015. [7] Qt. 2015. Qt Project home

A Roadmap for using Agile Development in a Traditional System

NASA Technical Reports Server (NTRS)

Streiffert, Barbara; Starbird, Thomas

2006-01-01

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

Managing Digital Archives Using Open Source Software Tools

NASA Astrophysics Data System (ADS)

Barve, S.; Dongare, S.

2007-10-01

This paper describes the use of open source software tools such as MySQL and PHP for creating database-backed websites. Such websites offer many advantages over ones built from static HTML pages. This paper will discuss how OSS tools are used and their benefits, and after the successful implementation of these tools how the library took the initiative in implementing an institutional repository using DSpace open source software.

Achieving Better Buying Power through Acquisition of Open Architecture Software Systems for Web and Mobile Devices

DTIC Science & Technology

2016-02-22

SPONSORED REPORT SERIES Achieving Better Buying Power through Acquisition of Open Architecture Software Systems for Web and Mobile Devices 22...ACQUISITION RESEARCH PROGRAM SPONSORED REPORT SERIES Achieving Better Buying Power through Acquisition of Open Architecture Software Systems for Web ...Policy Naval Postgraduate School Executive Summary Many people within large enterprises rely on up to four Web -based or mobile devices for their

A framework for integration of scientific applications into the OpenTopography workflow

NASA Astrophysics Data System (ADS)

Nandigam, V.; Crosby, C.; Baru, C.

2012-12-01

The NSF-funded OpenTopography facility provides online access to Earth science-oriented high-resolution LIDAR topography data, online processing tools, and derivative products. The underlying cyberinfrastructure employs a multi-tier service oriented architecture that is comprised of an infrastructure tier, a processing services tier, and an application tier. The infrastructure tier consists of storage, compute resources as well as supporting databases. The services tier consists of the set of processing routines each deployed as a Web service. The applications tier provides client interfaces to the system. (e.g. Portal). We propose a "pluggable" infrastructure design that will allow new scientific algorithms and processing routines developed and maintained by the community to be integrated into the OpenTopography system so that the wider earth science community can benefit from its availability. All core components in OpenTopography are available as Web services using a customized open-source Opal toolkit. The Opal toolkit provides mechanisms to manage and track job submissions, with the help of a back-end database. It allows monitoring of job and system status by providing charting tools. All core components in OpenTopography have been developed, maintained and wrapped as Web services using Opal by OpenTopography developers. However, as the scientific community develops new processing and analysis approaches this integration approach is not scalable efficiently. Most of the new scientific applications will have their own active development teams performing regular updates, maintenance and other improvements. It would be optimal to have the application co-located where its developers can continue to actively work on it while still making it accessible within the OpenTopography workflow for processing capabilities. We will utilize a software framework for remote integration of these scientific applications into the OpenTopography system. This will be accomplished by virtually extending the OpenTopography service over the various infrastructures running these scientific applications and processing routines. This involves packaging and distributing a customized instance of the Opal toolkit that will wrap the software application as an OPAL-based web service and integrate it into the OpenTopography framework. We plan to make this as automated as possible. A structured specification of service inputs and outputs along with metadata annotations encoded in XML can be utilized to automate the generation of user interfaces, with appropriate tools tips and user help features, and generation of other internal software. The OpenTopography Opal toolkit will also include the customizations that will enable security authentication, authorization and the ability to write application usage and job statistics back to the OpenTopography databases. This usage information could then be reported to the original service providers and used for auditing and performance improvements. This pluggable framework will enable the application developers to continue to work on enhancing their application while making the latest iteration available in a timely manner to the earth sciences community. This will also help us establish an overall framework that other scientific application providers will also be able to use going forward.

Research and Deployment a Hospital Open Software Platform for e-Health on the Grid System at VAST/IAMI

NASA Astrophysics Data System (ADS)

van Tuyet, Dao; Tuan, Ngo Anh; van Lang, Tran

Grid computing has been an increasing topic in recent years. It attracts the attention of many scientists from many fields. As a result, many Grid systems have been built for serving people's demands. At present, many tools for developing the Grid systems such as Globus, gLite, Unicore still developed incessantly. Especially, gLite - the Grid Middleware - was developed by the Europe Community scientific in recent years. Constant growth of Grid technology opened the way for new opportunities in term of information and data exchange in a secure and collaborative context. These new opportunities can be exploited to offer physicians new telemedicine services in order to improve their collaborative capacities. Our platform gives physicians an easy method to use telemedicine environment to manage and share patient's information (such as electronic medical record, images formatted DICOM) between remote locations. This paper presents the Grid Infrastructure based on gLite; some main components of gLite; the challenge scenario in which new applications can be developed to improve collaborative work between scientists; the process of deploying Hospital Open software Platform for E-health (HOPE) on the Grid.

Singularity: Scientific containers for mobility of compute.

PubMed

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

2017-01-01

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

Singularity: Scientific containers for mobility of compute

PubMed Central

Kurtzer, Gregory M.; Bauer, Michael W.

2017-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2015-12-01

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