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

Treesearch

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

2017-01-01

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

48 CFR 619.811-1 - Sole source.

Code of Federal Regulations, 2011 CFR

2011-10-01

... contracting activity shall include SBA's requirement number on the award document. (4) A single award document... sign the contract as a third party. The 8(a) contractor's signature shall be placed on the award... and open competition. (2) The contracting officer shall insert FAR 52.219-14, Limitations on...

48 CFR 619.811-1 - Sole source.

Code of Federal Regulations, 2010 CFR

2010-10-01

... contracting activity shall include SBA's requirement number on the award document. (4) A single award document... sign the contract as a third party. The 8(a) contractor's signature shall be placed on the award... and open competition. (2) The contracting officer shall insert FAR 52.219-14, Limitations on...

LaTeX for Agricultural Extension Professionals

USDA-ARS?s Scientific Manuscript database

LaTeX is a free open source document preparation system for professional quality documents and presentation materials. Extension professionals, trying to reach their audience though various forms of printed and online resources, can benefit from the vast potential of LaTeX. Using LaTeX empowers the ...

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

PubMed

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

2015-04-21

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

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

PubMed Central

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

2015-01-01

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

No Permit Needed for Emergency-Related Opening Burning on Tribal Lands

EPA Pesticide Factsheets

This document may be of assistance in applying the New Source Review (NSR) air permitting regulations including the Prevention of Significant Deterioration (PSD) requirements. This document is part of the NSR Policy and Guidance Database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Consideration of Fugitives in Open-Air Cattle Operations

EPA Pesticide Factsheets

This document may be of assistance in applying the New Source Review (NSR) air permitting regulations including the Prevention of Significant Deterioration (PSD) requirements. This document is part of the NSR Policy and Guidance Database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

jTraML: an open source Java API for TraML, the PSI standard for sharing SRM transitions.

PubMed

Helsens, Kenny; Brusniak, Mi-Youn; Deutsch, Eric; Moritz, Robert L; Martens, Lennart

2011-11-04

We here present jTraML, a Java API for the Proteomics Standards Initiative TraML data standard. The library provides fully functional classes for all elements specified in the TraML XSD document, as well as convenient methods to construct controlled vocabulary-based instances required to define SRM transitions. The use of jTraML is demonstrated via a two-way conversion tool between TraML documents and vendor specific files, facilitating the adoption process of this new community standard. The library is released as open source under the permissive Apache2 license and can be downloaded from http://jtraml.googlecode.com . TraML files can also be converted online at http://iomics.ugent.be/jtraml .

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.

Opening the black box: evaluation of nutrient nonpoint source management for estuarine watersheds

EPA Science Inventory

Over the last 40 years, there have been significant improvements in water quality and ecosystem condition in estuaries stressed by nutrient enrichment. However, documented improvements have been largely attributed to reductions in point sources. In contrast, improvement of coasta...

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.

M2Lite: An Open-source, Light-weight, Pluggable and Fast Proteome Discoverer MSF to mzIdentML Tool.

PubMed

Aiyetan, Paul; Zhang, Bai; Chen, Lily; Zhang, Zhen; Zhang, Hui

2014-04-28

Proteome Discoverer is one of many tools used for protein database search and peptide to spectrum assignment in mass spectrometry-based proteomics. However, the inadequacy of conversion tools makes it challenging to compare and integrate its results to those of other analytical tools. Here we present M2Lite, an open-source, light-weight, easily pluggable and fast conversion tool. M2Lite converts proteome discoverer derived MSF files to the proteomics community defined standard - the mzIdentML file format. M2Lite's source code is available as open-source at https://bitbucket.org/paiyetan/m2lite/src and its compiled binaries and documentation can be freely downloaded at https://bitbucket.org/paiyetan/m2lite/downloads.

NoSQL: collection document and cloud by using a dynamic web query form

NASA Astrophysics Data System (ADS)

Abdalla, Hemn B.; Lin, Jinzhao; Li, Guoquan

2015-07-01

Mongo-DB (from "humongous") is an open-source document database and the leading NoSQL database. A NoSQL (Not Only SQL, next generation databases, being non-relational, deal, open-source and horizontally scalable) presenting a mechanism for storage and retrieval of documents. Previously, we stored and retrieved the data using the SQL queries. Here, we use the MonogoDB that means we are not utilizing the MySQL and SQL queries. Directly importing the documents into our Drives, retrieving the documents on that drive by not applying the SQL queries, using the IO BufferReader and Writer, BufferReader for importing our type of document files to my folder (Drive). For retrieving the document files, the usage is BufferWriter from the particular folder (or) Drive. In this sense, providing the security for those storing files for what purpose means if we store the documents in our local folder means all or views that file and modified that file. So preventing that file, we are furnishing the security. The original document files will be changed to another format like in this paper; Binary format is used. Our documents will be converting to the binary format after that direct storing in one of our folder, that time the storage space will provide the private key for accessing that file. Wherever any user tries to discover the Document files means that file data are in the binary format, the document's file owner simply views that original format using that personal key from receive the secret key from the cloud.

Public Data Set: Impedance of an Intense Plasma-Cathode Electron Source for Tokamak Plasma Startup

DOE Data Explorer

Hinson, Edward T. [University of Wisconsin-Madison] (ORCID:000000019713140X); Barr, Jayson L. [University of Wisconsin-Madison] (ORCID:0000000177685931); Bongard, Michael W. [University of Wisconsin-Madison] (ORCID:0000000231609746); Burke, Marcus G. [University of Wisconsin-Madison] (ORCID:0000000176193724); Fonck, Raymond J. [University of Wisconsin-Madison] (ORCID:0000000294386762); Perry, Justin M. [University of Wisconsin-Madison] (ORCID:0000000171228609)

2016-05-31

This data set contains openly-documented, machine readable digital research data corresponding to figures published in E.T. Hinson et al., 'Impedance of an Intense Plasma-Cathode Electron Source for Tokamak Plasma Startup,' Physics of Plasmas 23, 052515 (2016).

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

PubMed

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

2016-02-15

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

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).

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

PubMed

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

2018-05-08

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

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.

A Far Cry from School History: Massive Online Open Courses as a Generative Source for Historical Research

ERIC Educational Resources Information Center

Gallagher, Silvia; Wallace, Ciaran

2016-01-01

Current research into Massive Online Open Courses (MOOCs) has neglected the potential of using learner comments for discipline-specific analysis. This article explores how MOOCs, within the historical discipline, can be used to generate, investigate, and document personal narratives, and argues that they serve as a rich platform for historical…

78 FR 80376 - Federal Acquisition Regulation; Prioritizing Sources of Supplies and Services for Use by the...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-12-31

... that use of FSS is not mandatory. Rather, as part of good market research, agencies are encouraged to... of their market research before considering open market sources. Comment: One respondent recommended...'s needs. Response: This type of documentation may be appropriate as part of the market research...

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

PubMed

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

2015-06-01

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

Extracting and connecting chemical structures from text sources using chemicalize.org.

PubMed

Southan, Christopher; Stracz, Andras

2013-04-23

Exploring bioactive chemistry requires navigating between structures and data from a variety of text-based sources. While PubChem currently includes approximately 16 million document-extracted structures (15 million from patents) the extent of public inter-document and document-to-database links is still well below any estimated total, especially for journal articles. A major expansion in access to text-entombed chemistry is enabled by chemicalize.org. This on-line resource can process IUPAC names, SMILES, InChI strings, CAS numbers and drug names from pasted text, PDFs or URLs to generate structures, calculate properties and launch searches. Here, we explore its utility for answering questions related to chemical structures in documents and where these overlap with database records. These aspects are illustrated using a common theme of Dipeptidyl Peptidase 4 (DPPIV) inhibitors. Full-text open URL sources facilitated the download of over 1400 structures from a DPPIV patent and the alignment of specific examples with IC50 data. Uploading the SMILES to PubChem revealed extensive linking to patents and papers, including prior submissions from chemicalize.org as submitting source. A DPPIV medicinal chemistry paper was completely extracted and structures were aligned to the activity results table, as well as linked to other documents via PubChem. In both cases, key structures with data were partitioned from common chemistry by dividing them into individual new PDFs for conversion. Over 500 structures were also extracted from a batch of PubMed abstracts related to DPPIV inhibition. The drug structures could be stepped through each text occurrence and included some converted MeSH-only IUPAC names not linked in PubChem. Performing set intersections proved effective for detecting compounds-in-common between documents and merged extractions. This work demonstrates the utility of chemicalize.org for the exploration of chemical structure connectivity between documents and databases, including structure searches in PubChem, InChIKey searches in Google and the chemicalize.org archive. It has the flexibility to extract text from any internal, external or Web source. It synergizes with other open tools and the application is undergoing continued development. It should thus facilitate progress in medicinal chemistry, chemical biology and other bioactive chemistry domains.

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.

scikit-image: image processing in Python.

PubMed

van der Walt, Stéfan; Schönberger, Johannes L; Nunez-Iglesias, Juan; Boulogne, François; Warner, Joshua D; Yager, Neil; Gouillart, Emmanuelle; Yu, Tony

2014-01-01

scikit-image is an image processing library that implements algorithms and utilities for use in research, education and industry applications. It is released under the liberal Modified BSD open source license, provides a well-documented API in the Python programming language, and is developed by an active, international team of collaborators. In this paper we highlight the advantages of open source to achieve the goals of the scikit-image library, and we showcase several real-world image processing applications that use scikit-image. More information can be found on the project homepage, http://scikit-image.org.

SuML: A Survey Markup Language for Generalized Survey Encoding

PubMed Central

Barclay, MW; Lober, WB; Karras, BT

2002-01-01

There is a need in clinical and research settings for a sophisticated, generalized, web based survey tool that supports complex logic, separation of content and presentation, and computable guidelines. There are many commercial and open source survey packages available that provide simple logic; few provide sophistication beyond “goto” statements; none support the use of guidelines. These tools are driven by databases, static web pages, and structured documents using markup languages such as eXtensible Markup Language (XML). We propose a generalized, guideline aware language and an implementation architecture using open source standards.

An Evolving Worldview: Making Open Source Easy

NASA Technical Reports Server (NTRS)

Rice, Zachary

2017-01-01

NASA Worldview is an interactive interface for browsing full-resolution, global satellite imagery. Worldview supports an open data policy so that academia, private industries and the general public can use NASA's satellite data to address Earth science related issues. Worldview was open sourced in 2014. By shifting to an open source approach, the Worldview application has evolved to better serve end-users. Project developers are able to have discussions with end-users and community developers to understand issues and develop new features. New developers are able to track upcoming features, collaborate on them and make their own contributions. Getting new developers to contribute to the project has been one of the most important and difficult aspects of open sourcing Worldview. A focus has been made on making the installation of Worldview simple to reduce the initial learning curve and make contributing code easy. One way we have addressed this is through a simplified setup process. Our setup documentation includes a set of prerequisites and a set of straight forward commands to clone, configure, install and run. This presentation will emphasis our focus to simplify and standardize Worldview's open source code so more people are able to contribute. The more people who contribute, the better the application will become over time.

FreeSASA: An open source C library for solvent accessible surface area calculations.

PubMed

Mitternacht, Simon

2016-01-01

Calculating solvent accessible surface areas (SASA) is a run-of-the-mill calculation in structural biology. Although there are many programs available for this calculation, there are no free-standing, open-source tools designed for easy tool-chain integration. FreeSASA is an open source C library for SASA calculations that provides both command-line and Python interfaces in addition to its C API. The library implements both Lee and Richards' and Shrake and Rupley's approximations, and is highly configurable to allow the user to control molecular parameters, accuracy and output granularity. It only depends on standard C libraries and should therefore be easy to compile and install on any platform. The library is well-documented, stable and efficient. The command-line interface can easily replace closed source legacy programs, with comparable or better accuracy and speed, and with some added functionality.

Physics 30 Program Machine-Scorable Open-Ended Questions: Unit 2: Electric and Magnetic Forces. Diploma Examinations Program.

ERIC Educational Resources Information Center

Alberta Dept. of Education, Edmonton.

This document outlines the use of machine-scorable open-ended questions for the evaluation of Physics 30 in Alberta. Contents include: (1) an introduction to the questions; (2) sample instruction sheet; (3) fifteen sample items; (4) item information including the key, difficulty, and source of each item; (5) solutions to items having multiple…

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments.

PubMed

MacLean, Brendan; Tomazela, Daniela M; Shulman, Nicholas; Chambers, Matthew; Finney, Gregory L; Frewen, Barbara; Kern, Randall; Tabb, David L; Liebler, Daniel C; MacCoss, Michael J

2010-04-01

Skyline is a Windows client application for targeted proteomics method creation and quantitative data analysis. It is open source and freely available for academic and commercial use. The Skyline user interface simplifies the development of mass spectrometer methods and the analysis of data from targeted proteomics experiments performed using selected reaction monitoring (SRM). Skyline supports using and creating MS/MS spectral libraries from a wide variety of sources to choose SRM filters and verify results based on previously observed ion trap data. Skyline exports transition lists to and imports the native output files from Agilent, Applied Biosystems, Thermo Fisher Scientific and Waters triple quadrupole instruments, seamlessly connecting mass spectrometer output back to the experimental design document. The fast and compact Skyline file format is easily shared, even for experiments requiring many sample injections. A rich array of graphs displays results and provides powerful tools for inspecting data integrity as data are acquired, helping instrument operators to identify problems early. The Skyline dynamic report designer exports tabular data from the Skyline document model for in-depth analysis with common statistical tools. Single-click, self-updating web installation is available at http://proteome.gs.washington.edu/software/skyline. This web site also provides access to instructional videos, a support board, an issues list and a link to the source code project.

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

OpenEIS. Developer Guide

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

Lutes, Robert G.; Neubauer, Casey C.; Haack, Jereme N.

2015-03-31

The Department of Energy’s (DOE’s) Building Technologies Office (BTO) is supporting the development of an open-source software tool for analyzing building energy and operational data: OpenEIS (open energy information system). This tool addresses the problems of both owners of building data and developers of tools to analyze this data. Building owners and managers have data but lack the tools to analyze it while tool developers lack data in a common format to ease development of reusable data analysis tools. This document is intended for developers of applications and explains the mechanisms for building analysis applications, accessing data, and displaying datamore » using a visualization from the included library. A brief introduction to the visualizations can be used as a jumping off point for developers familiar with JavaScript to produce their own. Several example applications are included which can be used along with this document to implement algorithms for performing energy data analysis.« less

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

PubMed

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

2013-08-02

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

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

PubMed Central

2013-01-01

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

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

PubMed

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

2014-02-07

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

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.

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

PubMed Central

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

2014-01-01

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

Improving the Product Documentation Process of a Small Software Company

NASA Astrophysics Data System (ADS)

Valtanen, Anu; Ahonen, Jarmo J.; Savolainen, Paula

Documentation is an important part of the software process, even though it is often neglected in software companies. The eternal question is how much documentation is enough. In this article, we present a practical implementation of lightweight product documentation process resulting from SPI efforts in a small company. Small companies’ financial and human resources are often limited. The documentation process described here, offers a template for creating adequate documentation consuming minimal amount of resources. The key element of the documentation process is an open source web-based bugtracking system that was customized to be used as a documentation tool. The use of the tool enables iterative and well structured documentation. The solution best serves the needs of a small company with off-the-shelf software products and striving for SPI.

scikit-image: image processing in Python

PubMed Central

Schönberger, Johannes L.; Nunez-Iglesias, Juan; Boulogne, François; Warner, Joshua D.; Yager, Neil; Gouillart, Emmanuelle; Yu, Tony

2014-01-01

scikit-image is an image processing library that implements algorithms and utilities for use in research, education and industry applications. It is released under the liberal Modified BSD open source license, provides a well-documented API in the Python programming language, and is developed by an active, international team of collaborators. In this paper we highlight the advantages of open source to achieve the goals of the scikit-image library, and we showcase several real-world image processing applications that use scikit-image. More information can be found on the project homepage, http://scikit-image.org. PMID:25024921

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

PubMed

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

2013-04-01

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

Psynteract: A flexible, cross-platform, open framework for interactive experiments.

PubMed

Henninger, Felix; Kieslich, Pascal J; Hilbig, Benjamin E

2017-10-01

We introduce a novel platform for interactive studies, that is, any form of study in which participants' experiences depend not only on their own responses, but also on those of other participants who complete the same study in parallel, for example a prisoner's dilemma or an ultimatum game. The software thus especially serves the rapidly growing field of strategic interaction research within psychology and behavioral economics. In contrast to all available software packages, our platform does not handle stimulus display and response collection itself. Instead, we provide a mechanism to extend existing experimental software to incorporate interactive functionality. This approach allows us to draw upon the capabilities already available, such as accuracy of temporal measurement, integration with auxiliary hardware such as eye-trackers or (neuro-)physiological apparatus, and recent advances in experimental software, for example capturing response dynamics through mouse-tracking. Through integration with OpenSesame, an open-source graphical experiment builder, studies can be assembled via a drag-and-drop interface requiring little or no further programming skills. In addition, by using the same communication mechanism across software packages, we also enable interoperability between systems. Our source code, which provides support for all major operating systems and several popular experimental packages, can be freely used and distributed under an open source license. The communication protocols underlying its functionality are also well documented and easily adapted to further platforms. Code and documentation are available at https://github.com/psynteract/ .

Open Source Tools for Seismicity Analysis

NASA Astrophysics Data System (ADS)

Powers, P.

2010-12-01

The spatio-temporal analysis of seismicity plays an important role in earthquake forecasting and is integral to research on earthquake interactions and triggering. For instance, the third version of the Uniform California Earthquake Rupture Forecast (UCERF), currently under development, will use Epidemic Type Aftershock Sequences (ETAS) as a model for earthquake triggering. UCERF will be a "living" model and therefore requires robust, tested, and well-documented ETAS algorithms to ensure transparency and reproducibility. Likewise, as earthquake aftershock sequences unfold, real-time access to high quality hypocenter data makes it possible to monitor the temporal variability of statistical properties such as the parameters of the Omori Law and the Gutenberg Richter b-value. Such statistical properties are valuable as they provide a measure of how much a particular sequence deviates from expected behavior and can be used when assigning probabilities of aftershock occurrence. To address these demands and provide public access to standard methods employed in statistical seismology, we present well-documented, open-source JavaScript and Java software libraries for the on- and off-line analysis of seismicity. The Javascript classes facilitate web-based asynchronous access to earthquake catalog data and provide a framework for in-browser display, analysis, and manipulation of catalog statistics; implementations of this framework will be made available on the USGS Earthquake Hazards website. The Java classes, in addition to providing tools for seismicity analysis, provide tools for modeling seismicity and generating synthetic catalogs. These tools are extensible and will be released as part of the open-source OpenSHA Commons library.

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments

PubMed Central

MacLean, Brendan; Tomazela, Daniela M.; Shulman, Nicholas; Chambers, Matthew; Finney, Gregory L.; Frewen, Barbara; Kern, Randall; Tabb, David L.; Liebler, Daniel C.; MacCoss, Michael J.

2010-01-01

Summary: Skyline is a Windows client application for targeted proteomics method creation and quantitative data analysis. It is open source and freely available for academic and commercial use. The Skyline user interface simplifies the development of mass spectrometer methods and the analysis of data from targeted proteomics experiments performed using selected reaction monitoring (SRM). Skyline supports using and creating MS/MS spectral libraries from a wide variety of sources to choose SRM filters and verify results based on previously observed ion trap data. Skyline exports transition lists to and imports the native output files from Agilent, Applied Biosystems, Thermo Fisher Scientific and Waters triple quadrupole instruments, seamlessly connecting mass spectrometer output back to the experimental design document. The fast and compact Skyline file format is easily shared, even for experiments requiring many sample injections. A rich array of graphs displays results and provides powerful tools for inspecting data integrity as data are acquired, helping instrument operators to identify problems early. The Skyline dynamic report designer exports tabular data from the Skyline document model for in-depth analysis with common statistical tools. Availability: Single-click, self-updating web installation is available at http://proteome.gs.washington.edu/software/skyline. This web site also provides access to instructional videos, a support board, an issues list and a link to the source code project. Contact: brendanx@u.washington.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:20147306

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.

InChI in the wild: an assessment of InChIKey searching in Google

PubMed Central

2013-01-01

While chemical databases can be queried using the InChI string and InChIKey (IK) the latter was designed for open-web searching. It is becoming increasingly effective for this since more sources enhance crawling of their websites by the Googlebot and consequent IK indexing. Searchers who use Google as an adjunct to database access may be less familiar with the advantages of using the IK as explored in this review. As an example, the IK for atorvastatin retrieves ~200 low-redundancy links from a Google search in 0.3 of a second. These include most major databases and a very low false-positive rate. Results encompass less familiar but potentially useful sources and can be extended to isomer capture by using just the skeleton layer of the IK. Google Advanced Search can be used to filter large result sets. Image searching with the IK is also effective and complementary to open-web queries. Results can be particularly useful for less-common structures as exemplified by a major metabolite of atorvastatin giving only three hits. Testing also demonstrated document-to-document and document-to-database joins via structure matching. The necessary generation of an IK from chemical names can be accomplished using open tools and resources for patents, papers, abstracts or other text sources. Active global sharing of local IK-linked information can be accomplished via surfacing in open laboratory notebooks, blogs, Twitter, figshare and other routes. While information-rich chemistry (e.g. approved drugs) can exhibit swamping and redundancy effects, the much smaller IK result sets for link-poor structures become a transformative first-pass option. The IK indexing has therefore turned Google into a de-facto open global chemical information hub by merging links to most significant sources, including over 50 million PubChem and ChemSpider records. The simplicity, specificity and speed of matching make it a useful option for biologists or others less familiar with chemical searching. However, compared to rigorously maintained major databases, users need to be circumspect about the consistency of Google results and provenance of retrieved links. In addition, community engagement may be necessary to ameliorate possible future degradation of utility. PMID:23399051

Panorama: A Targeted Proteomics Knowledge Base

PubMed Central

2015-01-01

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

Using soft-hard fusion for misinformation detection and pattern of life analysis in OSINT

NASA Astrophysics Data System (ADS)

Levchuk, Georgiy; Shabarekh, Charlotte

2017-05-01

Today's battlefields are shifting to "denied areas", where the use of U.S. Military air and ground assets is limited. To succeed, the U.S. intelligence analysts increasingly rely on available open-source intelligence (OSINT) which is fraught with inconsistencies, biased reporting and fake news. Analysts need automated tools for retrieval of information from OSINT sources, and these solutions must identify and resolve conflicting and deceptive information. In this paper, we present a misinformation detection model (MDM) which converts text to attributed knowledge graphs and runs graph-based analytics to identify misinformation. At the core of our solution is identification of knowledge conflicts in the fused multi-source knowledge graph, and semi-supervised learning to compute locally consistent reliability and credibility scores for the documents and sources, respectively. We present validation of proposed method using an open source dataset constructed from the online investigations of MH17 downing in Eastern Ukraine.

An Analysis of the Computer Security Ramifications of Weakened Asymmetric Cryptographic Algorithms

DTIC Science & Technology

2012-06-01

OpenVPN (Yonan). TLS (and by extension SSL) obviously rely on encryption to provide the confidentiality, integrity and authentication services it...Secure Shell (SSH) Transport Layer Protocol.” IETF, Jan. 2006. <tools.ietf.org/html/rfc4253> Yonan, James, and Mattock. " OpenVPN ." SourceForge...11 May 2012. <http://sourceforge.net/projects/ openvpn /> 92 REPORT DOCUMENTATION PAGE Form Approved OMB No. 074-0188 The public reporting

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

PubMed

Wang, Anliang; Yan, Xiaolong; Wei, Zhijun

2018-04-27

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

An Evolving Worldview: Making Open Source Easy

NASA Astrophysics Data System (ADS)

Rice, Z.

2017-12-01

NASA Worldview is an interactive interface for browsing full-resolution, global satellite imagery. Worldview supports an open data policy so that academia, private industries and the general public can use NASA's satellite data to address Earth science related issues. Worldview was open sourced in 2014. By shifting to an open source approach, the Worldview application has evolved to better serve end-users. Project developers are able to have discussions with end-users and community developers to understand issues and develop new features. Community developers are able to track upcoming features, collaborate on them and make their own contributions. Developers who discover issues are able to address those issues and submit a fix. This reduces the time it takes for a project developer to reproduce an issue or develop a new feature. Getting new developers to contribute to the project has been one of the most important and difficult aspects of open sourcing Worldview. After witnessing potential outside contributors struggle, a focus has been made on making the installation of Worldview simple to reduce the initial learning curve and make contributing code easy. One way we have addressed this is through a simplified setup process. Our setup documentation includes a set of prerequisites and a set of straightforward commands to clone, configure, install and run. This presentation will emphasize our focus to simplify and standardize Worldview's open source code so that more people are able to contribute. The more people who contribute, the better the application will become over time.

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

EPA Pesticide Factsheets

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

Special population planner 4 : an open source release.

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

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

2008-01-01

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

OpenSWPC: an open-source integrated parallel simulation code for modeling seismic wave propagation in 3D heterogeneous viscoelastic media

NASA Astrophysics Data System (ADS)

Maeda, Takuto; Takemura, Shunsuke; Furumura, Takashi

2017-07-01

We have developed an open-source software package, Open-source Seismic Wave Propagation Code (OpenSWPC), for parallel numerical simulations of seismic wave propagation in 3D and 2D (P-SV and SH) viscoelastic media based on the finite difference method in local-to-regional scales. This code is equipped with a frequency-independent attenuation model based on the generalized Zener body and an efficient perfectly matched layer for absorbing boundary condition. A hybrid-style programming using OpenMP and the Message Passing Interface (MPI) is adopted for efficient parallel computation. OpenSWPC has wide applicability for seismological studies and great portability to allowing excellent performance from PC clusters to supercomputers. Without modifying the code, users can conduct seismic wave propagation simulations using their own velocity structure models and the necessary source representations by specifying them in an input parameter file. The code has various modes for different types of velocity structure model input and different source representations such as single force, moment tensor and plane-wave incidence, which can easily be selected via the input parameters. Widely used binary data formats, the Network Common Data Form (NetCDF) and the Seismic Analysis Code (SAC) are adopted for the input of the heterogeneous structure model and the outputs of the simulation results, so users can easily handle the input/output datasets. All codes are written in Fortran 2003 and are available with detailed documents in a public repository.[Figure not available: see fulltext.

WorldWide Telescope: A Newly Open Source Astronomy Visualization System

NASA Astrophysics Data System (ADS)

Fay, Jonathan; Roberts, Douglas A.

2016-01-01

After eight years of development by Microsoft Research, WorldWide Telescope (WWT) was made an open source project at the end of June 2015. WWT was motivated by the desire to put new surveys of objects, such as the Sloan Digital Sky Survey in the context of the night sky. The development of WWT under Microsoft started with the creation of a Windows desktop client that is widely used in various education, outreach and research projects. Using this, users can explore the data built into WWT as well as data that is loaded in. Beyond exploration, WWT can be used to create tours that present various datasets a narrative format.In the past two years, the team developed a collection of web controls, including an HTML5 web client, which contains much of the functionality of the Windows desktop client. The project under Microsoft has deep connections with several user communities such as education through the WWT Ambassadors program, http://wwtambassadors.org/ and with planetariums and museums such as the Adler Planetarium. WWT can also support research, including using WWT to visualize the Bones of the Milky Way and rich connections between WWT and the Astrophysical Data Systems (ADS, http://labs.adsabs.harvard.edu/adsabs/). One important new research connection is the use of WWT to create dynamic and potentially interactive supplements to journal articles, which have been created in 2015.Now WWT is an open source community lead project. The source code is available in GitHub (https://github.com/WorldWideTelescope). There is significant developer documentation on the website (http://worldwidetelescope.org/Developers/) and an extensive developer workshops (http://wwtworkshops.org/?tribe_events=wwt-developer-workshop) has taken place in the fall of 2015.Now that WWT is open source anyone who has the interest in the project can be a contributor. As important as helping out with coding, the project needs people interested in documentation, testing, training and other roles.

Modular Integrated Stackable Layers (MISL) 1.1 Design Specification. Design Guideline Document

NASA Technical Reports Server (NTRS)

Yim, Hester J.

2012-01-01

This document establishes the design guideline of the Modular Instrumentation Data Acquisition (MI-DAQ) system in utilization of several designs available in EV. The MI- DAQ provides the options to the customers depending on their system requirements i.e. a 28V interface power supply, a low power battery operated system, a low power microcontroller, a higher performance microcontroller, a USB interface, a Ethernet interface, a wireless communication, various sensor interfaces, etc. Depending on customer's requirements, the each functional board can be stacked up from a bottom level of power supply to a higher level of stack to provide user interfaces. The stack up of boards are accomplished by a predefined and standardized power bus and data bus connections which are included in this document along with other physical and electrical guidelines. This guideline also provides information for a new design options. This specification is the product of a collaboration between NASA/JSC/EV and Texas A&M University. The goal of the collaboration is to open source the specification and allow outside entities to design, build, and market modules that are compatible with the specification. NASA has designed and is using numerous modules that are compatible to this specification. A limited number of these modules will also be released as open source designs to support the collaboration. The released designs are listed in the Applicable Documents.

Using OpenOffice as a Portable Interface to JAVA-Based Applications

NASA Astrophysics Data System (ADS)

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

2004-07-01

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

GridAPPS-D

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

2017-03-28

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

Earth System Documentation (ES-DOC) Preparation for CMIP6

NASA Astrophysics Data System (ADS)

Denvil, S.; Murphy, S.; Greenslade, M. A.; Lawrence, B.; Guilyardi, E.; Pascoe, C.; Treshanksy, A.; Elkington, M.; Hibling, E.; Hassell, D.

2015-12-01

During the course of 2015 the Earth System Documentation (ES-DOC) project began its preparations for CMIP6 (Coupled Model Inter-comparison Project 6) by further extending the ES-DOC tooling ecosystem in support of Earth System Model (ESM) documentation creation, search, viewing & comparison. The ES-DOC online questionnaire, the ES-DOC desktop notebook, and the ES-DOC python toolkit will serve as multiple complementary pathways to generating CMIP6 documentation. It is envisaged that institutes will leverage these tools at different points of the CMIP6 lifecycle. Institutes will be particularly interested to know that the documentation burden will be either streamlined or completely automated.As all the tools are tightly integrated with the ES-DOC web-service, institutes can be confident that the latency between documentation creation & publishing will be reduced to a minimum. Published documents will be viewable with the online ES-DOC Viewer (accessible via citable URL's). Model inter-comparison scenarios will be supported using the ES-DOC online Comparator tool. The Comparator is being extended to:• Support comparison of both Model descriptions & Simulation runs;• Greatly streamline the effort involved in compiling official tables.The entire ES-DOC ecosystem is open source and built upon open standards such as the Common Information Model (CIM) (versions 1 and 2).

Review assessment support in Open Journal System using TextRank

NASA Astrophysics Data System (ADS)

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

2017-01-01

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

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

Postgraduate Students as OER Capacitators

ERIC Educational Resources Information Center

King, Thomas William

2017-01-01

A comprehensive theoretical, legal and practical basis for OER has been developed over the past fifteen years, supported by the expansion of open source curation platforms and the work of advocacy groups and international bodies. OER's potential has been sufficiently documented; the question remains how best to support, integrate and normalise OER…

SpectraFox: A free open-source data management and analysis tool for scanning probe microscopy and spectroscopy

NASA Astrophysics Data System (ADS)

Ruby, Michael

In the last decades scanning probe microscopy and spectroscopy have become well-established tools in nanotechnology and surface science. This opened the market for many commercial manufacturers, each with different hardware and software standards. Besides the advantage of a wide variety of available hardware, the diversity may software-wise complicate the data exchange between scientists, and the data analysis for groups working with hardware developed by different manufacturers. Not only the file format differs between manufacturers, but also the data often requires further numerical treatment before publication. SpectraFox is an open-source and independent tool which manages, processes, and evaluates scanning probe spectroscopy and microscopy data. It aims at simplifying the documentation in parallel to measurement, and it provides solid evaluation tools for a large number of data.

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

DTIC Science & Technology

2012-05-28

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

Performing Quantitative Imaging Acquisition, Analysis and Visualization Using the Best of Open Source and Commercial Software Solutions.

PubMed

Shenoy, Shailesh M

2016-07-01

A challenge in any imaging laboratory, especially one that uses modern techniques, is to achieve a sustainable and productive balance between using open source and commercial software to perform quantitative image acquisition, analysis and visualization. In addition to considering the expense of software licensing, one must consider factors such as the quality and usefulness of the software's support, training and documentation. Also, one must consider the reproducibility with which multiple people generate results using the same software to perform the same analysis, how one may distribute their methods to the community using the software and the potential for achieving automation to improve productivity.

OntoMaton: a bioportal powered ontology widget for Google Spreadsheets.

PubMed

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

2013-02-15

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

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.

a Semi-Automated Point Cloud Processing Methodology for 3d Cultural Heritage Documentation

NASA Astrophysics Data System (ADS)

Kıvılcım, C. Ö.; Duran, Z.

2016-06-01

The preliminary phase in any architectural heritage project is to obtain metric measurements and documentation of the building and its individual elements. On the other hand, conventional measurement techniques require tremendous resources and lengthy project completion times for architectural surveys and 3D model production. Over the past two decades, the widespread use of laser scanning and digital photogrammetry have significantly altered the heritage documentation process. Furthermore, advances in these technologies have enabled robust data collection and reduced user workload for generating various levels of products, from single buildings to expansive cityscapes. More recently, the use of procedural modelling methods and BIM relevant applications for historic building documentation purposes has become an active area of research, however fully automated systems in cultural heritage documentation still remains open. In this paper, we present a semi-automated methodology, for 3D façade modelling of cultural heritage assets based on parametric and procedural modelling techniques and using airborne and terrestrial laser scanning data. We present the contribution of our methodology, which we implemented in an open source software environment using the example project of a 16th century early classical era Ottoman structure, Sinan the Architect's Şehzade Mosque in Istanbul, Turkey.

The Victor C++ library for protein representation and advanced manipulation.

PubMed

Hirsh, Layla; Piovesan, Damiano; Giollo, Manuel; Ferrari, Carlo; Tosatto, Silvio C E

2015-04-01

Protein sequence and structure representation and manipulation require dedicated software libraries to support methods of increasing complexity. Here, we describe the VIrtual Constrution TOol for pRoteins (Victor) C++ library, an open source platform dedicated to enabling inexperienced users to develop advanced tools and gathering contributions from the community. The provided application examples cover statistical energy potentials, profile-profile sequence alignments and ab initio loop modeling. Victor was used over the last 15 years in several publications and optimized for efficiency. It is provided as a GitHub repository with source files and unit tests, plus extensive online documentation, including a Wiki with help files and tutorials, examples and Doxygen documentation. The C++ library and online documentation, distributed under a GPL license are available from URL: http://protein.bio.unipd.it/victor/. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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.

Infrastructure for Multiphysics Software Integration in High Performance Computing-Aided Science and Engineering

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

Campbell, Michael T.; Safdari, Masoud; Kress, Jessica E.

The project described in this report constructed and exercised an innovative multiphysics coupling toolkit called the Illinois Rocstar MultiPhysics Application Coupling Toolkit (IMPACT). IMPACT is an open source, flexible, natively parallel infrastructure for coupling multiple uniphysics simulation codes into multiphysics computational systems. IMPACT works with codes written in several high-performance-computing (HPC) programming languages, and is designed from the beginning for HPC multiphysics code development. It is designed to be minimally invasive to the individual physics codes being integrated, and has few requirements on those physics codes for integration. The goal of IMPACT is to provide the support needed to enablemore » coupling existing tools together in unique and innovative ways to produce powerful new multiphysics technologies without extensive modification and rewrite of the physics packages being integrated. There are three major outcomes from this project: 1) construction, testing, application, and open-source release of the IMPACT infrastructure, 2) production of example open-source multiphysics tools using IMPACT, and 3) identification and engagement of interested organizations in the tools and applications resulting from the project. This last outcome represents the incipient development of a user community and application echosystem being built using IMPACT. Multiphysics coupling standardization can only come from organizations working together to define needs and processes that span the space of necessary multiphysics outcomes, which Illinois Rocstar plans to continue driving toward. The IMPACT system, including source code, documentation, and test problems are all now available through the public gitHUB.org system to anyone interested in multiphysics code coupling. Many of the basic documents explaining use and architecture of IMPACT are also attached as appendices to this document. Online HTML documentation is available through the gitHUB site. There are over 100 unit tests provided that run through the Illinois Rocstar Application Development (IRAD) lightweight testing infrastructure that is also supplied along with IMPACT. The package as a whole provides an excellent base for developing high-quality multiphysics applications using modern software development practices. To facilitate understanding how to utilize IMPACT effectively, two multiphysics systems have been developed and are available open-source through gitHUB. The simpler of the two systems, named ElmerFoamFSI in the repository, is a multiphysics, fluid-structure-interaction (FSI) coupling of the solid mechanics package Elmer with a fluid dynamics module from OpenFOAM. This coupling illustrates how to combine software packages that are unrelated by either author or architecture and combine them into a robust, parallel multiphysics system. A more complex multiphysics tool is the Illinois Rocstar Rocstar Multiphysics code that was rebuilt during the project around IMPACT. Rocstar Multiphysics was already an HPC multiphysics tool, but now that it has been rearchitected around IMPACT, it can be readily expanded to capture new and different physics in the future. In fact, during this project, the Elmer and OpenFOAM tools were also coupled into Rocstar Multiphysics and demonstrated. The full Rocstar Multiphysics codebase is also available on gitHUB, and licensed for any organization to use as they wish. Finally, the new IMPACT product is already being used in several multiphysics code coupling projects for the Air Force, NASA and the Missile Defense Agency, and initial work on expansion of the IMPACT-enabled Rocstar Multiphysics has begun in support of a commercial company. These initiatives promise to expand the interest and reach of IMPACT and Rocstar Multiphysics, ultimately leading to the envisioned standardization and consortium of users that was one of the goals of this project.« less

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

NASA Technical Reports Server (NTRS)

Conway, Darrel J.; Hughes, Steven P.

2010-01-01

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

Drug interaction databases in medical literature: transparency of ownership, funding, classification algorithms, level of documentation, and staff qualifications. A systematic review.

PubMed

Kongsholm, Gertrud Gansmo; Nielsen, Anna Katrine Toft; Damkier, Per

2015-11-01

It is well documented that drug-drug interaction databases (DIDs) differ substantially with respect to classification of drug-drug interactions (DDIs). The aim of this study was to study online available transparency of ownership, funding, information, classifications, staff training, and underlying documentation of the five most commonly used open access English language-based online DIDs and the three most commonly used subscription English language-based online DIDs in the literature. We conducted a systematic literature search to identify the five most commonly used open access and the three most commonly used subscription DIDs in the medical literature. The following parameters were assessed for each of the databases: Ownership, classification of interactions, primary information sources, and staff qualification. We compared the overall proportion of yes/no answers from open access databases and subscription databases by Fisher's exact test-both prior to and after requesting missing information. Among open access DIDs, 20/60 items could be verified from the webpage directly compared to 24/36 for the subscription DIDs (p = 0.0028). Following personal request, these numbers rose to 22/60 and 30/36, respectively (p < 0.0001). For items within the "classification of interaction" domain, proportions were 3/25 versus 11/15 available from the webpage (P = 0.0001) and 3/25 versus 15/15 (p < 0.0001) available upon personal request. Available information on online available transparency of ownership, funding, information, classifications, staff training, and underlying documentation varies substantially among various DIDs. Open access DIDs had a statistically lower score on parameters assessed.

ToxicDocs (www.ToxicDocs.org): from history buried in stacks of paper to open, searchable archives online.

PubMed

Rosner, David; Markowitz, Gerald; Chowkwanyun, Merlin

2018-02-01

As a result of a legal mechanism called discovery, the authors accumulated millions of internal corporate and trade association documents related to the introduction of new products and chemicals into workplaces and commerce. What did these private entities discuss among themselves and with their experts? The plethora of documents, both a blessing and a curse, opened new sources and interesting questions about corporate and regulatory histories. But they also posed an almost insurmountable challenge to historians. Thus emerged ToxicDocs, possible only with a technological innovation known as "Big Data." That refers to the sheer volume of new digital data and to the computational power to analyze them. Users will be able to identify what firms knew (or did not know) about the dangers of toxic substances in their products-and when. The database opens many areas to inquiry including environmental studies, business history, government regulation, and public policy. ToxicDocs will remain a resource free and open to all, anywhere in the world.

Enhancements of nonpoint source monitoring of volatile organic compounds in ground water

USGS Publications Warehouse

Lapham, W.W.; Moran, M.J.; Zogorski, J.S.

2000-01-01

The U.S. Geological Survey (USGS) has compiled a national retrospective data set of analyses of volatile organic compounds (VOCs) in ground water of the United States. The data are from Federal, State, and local nonpoint-source monitoring programs, collected between 1985–95. This data set is being used to augment data collected by the USGS National Water-Quality Assessment (NAWQA) Program to ascertain the occurrence of VOCs in ground water nationwide. Eleven attributes of the retrospective data set were evaluated to determine the suitability of the data to augment NAWQA data in answering occurrence questions of varying complexity. These 11 attributes are the VOC analyte list and the associated reporting levels for each VOC, well type, well-casing material, type of openings in the interval (screened interval or open hole), well depth, depth to the top and bottom of the open interval(s), depth to water level in the well, aquifer type (confined or unconfined), and aquifer lithology. VOCs frequently analyzed included solvents, industrial reagents, and refrigerants, but other VOCs of current interest were not frequently analyzed. About 70 percent of the sampled wells have the type of well documented in the data set, and about 74 percent have well depth documented. However, the data set generally lacks documentation of other characteristics, such as well-casing material, information about the screened or open interval(s), depth to water level in the well, and aquifer type and lithology. For example, only about 20 percent of the wells include information on depth to water level in the well and only about 14 percent of the wells include information about aquifer type. The three most important enhancements to VOC data collected in nonpoint-source monitoring programs for use in a national assessment of VOC occurrence in ground water would be an expanded VOC analyte list, recording the reporting level for each analyte for every analysis, and recording key ancillary information about each well. These enhancements would greatly increase the usefulness of VOC data in addressing complex occurrence questions, such as those that seek to explain the reasons for VOC occurrence and nonoccurrence in ground water of the United States.

Pyteomics--a Python framework for exploratory data analysis and rapid software prototyping in proteomics.

PubMed

Goloborodko, Anton A; Levitsky, Lev I; Ivanov, Mark V; Gorshkov, Mikhail V

2013-02-01

Pyteomics is a cross-platform, open-source Python library providing a rich set of tools for MS-based proteomics. It provides modules for reading LC-MS/MS data, search engine output, protein sequence databases, theoretical prediction of retention times, electrochemical properties of polypeptides, mass and m/z calculations, and sequence parsing. Pyteomics is available under Apache license; release versions are available at the Python Package Index http://pypi.python.org/pyteomics, the source code repository at http://hg.theorchromo.ru/pyteomics, documentation at http://packages.python.org/pyteomics. Pyteomics.biolccc documentation is available at http://packages.python.org/pyteomics.biolccc/. Questions on installation and usage can be addressed to pyteomics mailing list: pyteomics@googlegroups.com.

Implementing a Dynamic Database-Driven Course Using LAMP

ERIC Educational Resources Information Center

Laverty, Joseph Packy; Wood, David; Turchek, John

2011-01-01

This paper documents the formulation of a database driven open source architecture web development course. The design of a web-based curriculum faces many challenges: a) relative emphasis of client and server-side technologies, b) choice of a server-side language, and c) the cost and efficient delivery of a dynamic web development, database-driven…

Introducing Text Analytics as a Graduate Business School Course

ERIC Educational Resources Information Center

Edgington, Theresa M.

2011-01-01

Text analytics refers to the process of analyzing unstructured data from documented sources, including open-ended surveys, blogs, and other types of web dialog. Text analytics has enveloped the concept of text mining, an analysis approach influenced heavily from data mining. While text mining has been covered extensively in various computer…

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

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

LSST communications middleware implementation

NASA Astrophysics Data System (ADS)

Mills, Dave; Schumacher, German; Lotz, Paul

2016-07-01

The LSST communications middleware is based on a set of software abstractions; which provide standard interfaces for common communications services. The observatory requires communication between diverse subsystems, implemented by different contractors, and comprehensive archiving of subsystem status data. The Service Abstraction Layer (SAL) is implemented using open source packages that implement open standards of DDS (Data Distribution Service1) for data communication, and SQL (Standard Query Language) for database access. For every subsystem, abstractions for each of the Telemetry datastreams, along with Command/Response and Events, have been agreed with the appropriate component vendor (such as Dome, TMA, Hexapod), and captured in ICD's (Interface Control Documents).The OpenSplice (Prismtech) Community Edition of DDS provides an LGPL licensed distribution which may be freely redistributed. The availability of the full source code provides assurances that the project will be able to maintain it over the full 10 year survey, independent of the fortunes of the original providers.

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.

gadfly: A pandas-based Framework for Analyzing GADGET Simulation Data

NASA Astrophysics Data System (ADS)

Hummel, Jacob A.

2016-11-01

We present the first public release (v0.1) of the open-source gadget Dataframe Library: gadfly. The aim of this package is to leverage the capabilities of the broader python scientific computing ecosystem by providing tools for analyzing simulation data from the astrophysical simulation codes gadget and gizmo using pandas, a thoroughly documented, open-source library providing high-performance, easy-to-use data structures that is quickly becoming the standard for data analysis in python. Gadfly is a framework for analyzing particle-based simulation data stored in the HDF5 format using pandas DataFrames. The package enables efficient memory management, includes utilities for unit handling, coordinate transformations, and parallel batch processing, and provides highly optimized routines for visualizing smoothed-particle hydrodynamics data sets.

pyNS: an open-source framework for 0D haemodynamic modelling.

PubMed

Manini, Simone; Antiga, Luca; Botti, Lorenzo; Remuzzi, Andrea

2015-06-01

A number of computational approaches have been proposed for the simulation of haemodynamics and vascular wall dynamics in complex vascular networks. Among them, 0D pulse wave propagation methods allow to efficiently model flow and pressure distributions and wall displacements throughout vascular networks at low computational costs. Although several techniques are documented in literature, the availability of open-source computational tools is still limited. We here present python Network Solver, a modular solver framework for 0D problems released under a BSD license as part of the archToolkit ( http://archtk.github.com ). As an application, we describe patient-specific models of the systemic circulation and detailed upper extremity for use in the prediction of maturation after surgical creation of vascular access for haemodialysis.

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.

PV_LIB Toolbox v. 1.3

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

2015-12-09

PV_LIB comprises a library of Matlab? code for modeling photovoltaic (PV) systems. Included are functions to compute solar position and to estimate irradiance in the PV system's plane of array, cell temperature, PV module electrical output, and conversion from DC to AC power. Also included are functions that aid in determining parameters for module performance models from module characterization testing. PV_LIB is open source code primarily intended for research and academic purposes. All algorithms are documented in openly available literature with the appropriate references included in comments within the code.

Building integrated business environments: analysing open-source ESB

NASA Astrophysics Data System (ADS)

Martínez-Carreras, M. A.; García Jimenez, F. J.; Gómez Skarmeta, A. F.

2015-05-01

Integration and interoperability are two concepts that have gained significant prominence in the business field, providing tools which enable enterprise application integration (EAI). In this sense, enterprise service bus (ESB) has played a crucial role as the underpinning technology for creating integrated environments in which companies may connect all their legacy-applications. However, the potential of these technologies remains unknown and some important features are not used to develop suitable business environments. The aim of this paper is to describe and detail the elements for building the next generation of integrated business environments (IBE) and to analyse the features of ESBs as the core of this infrastructure. For this purpose, we evaluate how well-known open-source ESB products fulfil these needs. Moreover, we introduce a scenario in which the collaborative system 'Alfresco' is integrated in the business infrastructure. Finally, we provide a comparison of the different open-source ESBs available for IBE requirements. According to this study, Fuse ESB provides the best results, considering features such as support for a wide variety of standards and specifications, documentation and implementation, security, advanced business trends, ease of integration and performance.

Using Open Source to Give Patrons What They Want

ERIC Educational Resources Information Center

De Groff, Amy Begg

2008-01-01

Librarians role as partners in education is to instruct customers on how to find information. Their purpose is to get information to customers. Often, that takes the form of delivering a book. Sometimes, it is accomplished by typing a URL into a web browser, reading text, and copying some of it into a text document for manipulation and…

Cleaning Up the Seas. UNEP Environment Brief No. 5.

ERIC Educational Resources Information Center

United Nations Environment Programme, Nairobi (Kenya).

While the open oceans remain relatively unpolluted, many coastal areas are suffering from oil, sewage, industrial wastes, and agricultural run-off. This document presents some of the key facts related to these kinds of water pollution. It focuses on the major sources of contamination in the world's seas, and provides an overview of how these…

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

NASA Astrophysics Data System (ADS)

Zaghi, S.

2014-07-01

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

An open annotation ontology for science on web 3.0

PubMed Central

2011-01-01

Background There is currently a gap between the rich and expressive collection of published biomedical ontologies, and the natural language expression of biomedical papers consumed on a daily basis by scientific researchers. The purpose of this paper is to provide an open, shareable structure for dynamic integration of biomedical domain ontologies with the scientific document, in the form of an Annotation Ontology (AO), thus closing this gap and enabling application of formal biomedical ontologies directly to the literature as it emerges. Methods Initial requirements for AO were elicited by analysis of integration needs between biomedical web communities, and of needs for representing and integrating results of biomedical text mining. Analysis of strengths and weaknesses of previous efforts in this area was also performed. A series of increasingly refined annotation tools were then developed along with a metadata model in OWL, and deployed for feedback and additional requirements the ontology to users at a major pharmaceutical company and a major academic center. Further requirements and critiques of the model were also elicited through discussions with many colleagues and incorporated into the work. Results This paper presents Annotation Ontology (AO), an open ontology in OWL-DL for annotating scientific documents on the web. AO supports both human and algorithmic content annotation. It enables “stand-off” or independent metadata anchored to specific positions in a web document by any one of several methods. In AO, the document may be annotated but is not required to be under update control of the annotator. AO contains a provenance model to support versioning, and a set model for specifying groups and containers of annotation. AO is freely available under open source license at http://purl.org/ao/, and extensive documentation including screencasts is available on AO’s Google Code page: http://code.google.com/p/annotation-ontology/ . Conclusions The Annotation Ontology meets critical requirements for an open, freely shareable model in OWL, of annotation metadata created against scientific documents on the Web. We believe AO can become a very useful common model for annotation metadata on Web documents, and will enable biomedical domain ontologies to be used quite widely to annotate the scientific literature. Potential collaborators and those with new relevant use cases are invited to contact the authors. PMID:21624159

An open annotation ontology for science on web 3.0.

PubMed

Ciccarese, Paolo; Ocana, Marco; Garcia Castro, Leyla Jael; Das, Sudeshna; Clark, Tim

2011-05-17

There is currently a gap between the rich and expressive collection of published biomedical ontologies, and the natural language expression of biomedical papers consumed on a daily basis by scientific researchers. The purpose of this paper is to provide an open, shareable structure for dynamic integration of biomedical domain ontologies with the scientific document, in the form of an Annotation Ontology (AO), thus closing this gap and enabling application of formal biomedical ontologies directly to the literature as it emerges. Initial requirements for AO were elicited by analysis of integration needs between biomedical web communities, and of needs for representing and integrating results of biomedical text mining. Analysis of strengths and weaknesses of previous efforts in this area was also performed. A series of increasingly refined annotation tools were then developed along with a metadata model in OWL, and deployed for feedback and additional requirements the ontology to users at a major pharmaceutical company and a major academic center. Further requirements and critiques of the model were also elicited through discussions with many colleagues and incorporated into the work. This paper presents Annotation Ontology (AO), an open ontology in OWL-DL for annotating scientific documents on the web. AO supports both human and algorithmic content annotation. It enables "stand-off" or independent metadata anchored to specific positions in a web document by any one of several methods. In AO, the document may be annotated but is not required to be under update control of the annotator. AO contains a provenance model to support versioning, and a set model for specifying groups and containers of annotation. AO is freely available under open source license at http://purl.org/ao/, and extensive documentation including screencasts is available on AO's Google Code page: http://code.google.com/p/annotation-ontology/ . The Annotation Ontology meets critical requirements for an open, freely shareable model in OWL, of annotation metadata created against scientific documents on the Web. We believe AO can become a very useful common model for annotation metadata on Web documents, and will enable biomedical domain ontologies to be used quite widely to annotate the scientific literature. Potential collaborators and those with new relevant use cases are invited to contact the authors.

PV_LIB Toolbox

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

2012-09-11

While an organized source of reference information on PV performance modeling is certainly valuable, there is nothing to match the availability of actual examples of modeling algorithms being used in practice. To meet this need, Sandia has developed a PV performance modeling toolbox (PV_LIB) for Matlab. It contains a set of well-documented, open source functions and example scripts showing the functions being used in practical examples. This toolbox is meant to help make the multi-step process of modeling a PV system more transparent and provide the means for model users to validate and understand the models they use and ormore » develop. It is fully integrated into Matlab's help and documentation utilities. The PV_LIB Toolbox provides more than 30 functions that are sorted into four categories« less

Electronic Health Record Application Support Service Enablers.

PubMed

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

2015-08-01

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

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.

The Computable Catchment: An executable document for model-data software sharing, reproducibility and interactive visualization

NASA Astrophysics Data System (ADS)

Gil, Y.; Duffy, C.

2015-12-01

This paper proposes the concept of a "Computable Catchment" which is used to develop a collaborative platform for watershed modeling and data analysis. The object of the research is a sharable, executable document similar to a pdf, but one that includes documentation of the underlying theoretical concepts, interactive computational/numerical resources, linkage to essential data repositories and the ability for interactive model-data visualization and analysis. The executable document for each catchment is stored in the cloud with automatic provisioning and a unique identifier allowing collaborative model and data enhancements for historical hydroclimatic reconstruction and/or future landuse or climate change scenarios to be easily reconstructed or extended. The Computable Catchment adopts metadata standards for naming all variables in the model and the data. The a-priori or initial data is derived from national data sources for soils, hydrogeology, climate, and land cover available from the www.hydroterre.psu.edu data service (Leonard and Duffy, 2015). The executable document is based on Wolfram CDF or Computable Document Format with an interactive open-source reader accessible by any modern computing platform. The CDF file and contents can be uploaded to a website or simply shared as a normal document maintaining all interactive features of the model and data. The Computable Catchment concept represents one application for Geoscience Papers of the Future representing an extensible document that combines theory, models, data and analysis that are digitally shared, documented and reused among research collaborators, students, educators and decision makers.

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.

ePCR: an R-package for survival and time-to-event prediction in advanced prostate cancer, applied to real-world patient cohorts.

PubMed

Laajala, Teemu D; Murtojärvi, Mika; Virkki, Arho; Aittokallio, Tero

2018-06-15

Prognostic models are widely used in clinical decision-making, such as risk stratification and tailoring treatment strategies, with the aim to improve patient outcomes while reducing overall healthcare costs. While prognostic models have been adopted into clinical use, benchmarking their performance has been difficult due to lack of open clinical datasets. The recent DREAM 9.5 Prostate Cancer Challenge carried out an extensive benchmarking of prognostic models for metastatic Castration-Resistant Prostate Cancer (mCRPC), based on multiple cohorts of open clinical trial data. We make available an open-source implementation of the top-performing model, ePCR, along with an extended toolbox for its further re-use and development, and demonstrate how to best apply the implemented model to real-world data cohorts of advanced prostate cancer patients. The open-source R-package ePCR and its reference documentation are available at the Central R Archive Network (CRAN): https://CRAN.R-project.org/package=ePCR. R-vignette provides step-by-step examples for the ePCR usage. Supplementary data are available at Bioinformatics online.

76 FR 52669 - Report on the Performance of Drug and Biologics Firms in Conducting Postmarketing Requirements...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-08-23

...\\ Number of open PMRs 526 149. On-schedule open PMRs (see 477 (91%) 131 (88%). table 2 of this document). Off-schedule open PMRs (see 49 (9%) 18 (12%). table 3 of this document). Number of open PMCs \\2\\........ 473 307. On-schedule open PMCs (see 399 (84%) 236 (77%). table 4 of this document). Off-schedule open...

Taking advantage of continuity of care documents to populate a research repository.

PubMed

Klann, Jeffrey G; Mendis, Michael; Phillips, Lori C; Goodson, Alyssa P; Rocha, Beatriz H; Goldberg, Howard S; Wattanasin, Nich; Murphy, Shawn N

2015-03-01

Clinical data warehouses have accelerated clinical research, but even with available open source tools, there is a high barrier to entry due to the complexity of normalizing and importing data. The Office of the National Coordinator for Health Information Technology's Meaningful Use Incentive Program now requires that electronic health record systems produce standardized consolidated clinical document architecture (C-CDA) documents. Here, we leverage this data source to create a low volume standards based import pipeline for the Informatics for Integrating Biology and the Bedside (i2b2) clinical research platform. We validate this approach by creating a small repository at Partners Healthcare automatically from C-CDA documents. We designed an i2b2 extension to import C-CDAs into i2b2. It is extensible to other sites with variances in C-CDA format without requiring custom code. We also designed new ontology structures for querying the imported data. We implemented our methodology at Partners Healthcare, where we developed an adapter to retrieve C-CDAs from Enterprise Services. Our current implementation supports demographics, encounters, problems, and medications. We imported approximately 17 000 clinical observations on 145 patients into i2b2 in about 24 min. We were able to perform i2b2 cohort finding queries and view patient information through SMART apps on the imported data. This low volume import approach can serve small practices with local access to C-CDAs and will allow patient registries to import patient supplied C-CDAs. These components will soon be available open source on the i2b2 wiki. Our approach will lower barriers to entry in implementing i2b2 where informatics expertise or data access are limited. © The Author 2014. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

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.

Design and Development of an Institutional Repository at the Indian Institute of Technology Kharagpur

ERIC Educational Resources Information Center

Sutradhar, B.

2006-01-01

Purpose: To describe how an institutional repository (IR) was set up, using open source software, at the Indian Institute of Technology (IIT) in Kharagpur. Members of the IIT can publish their research documents in the IR for online access as well as digital preservation. Material in this IR includes instructional materials, records, data sets,…

Missed Opportunity? Was Iran s Green Movement an Unconventional Warfare Option?

DTIC Science & Technology

2014-12-12

leadership. Speeches , reports, websites, and foreign documents constituted the majority of usable research. The author assumed accurate translation of...expanding economic influence. The RAND Corporation’s study compiled research from the OpenSource website, scholarly reports, and translated speeches ...constructed from Mir Houssein Mousavi’s speeches . Although difficult to accredit, the manifesto echoed Green Movement leadership ideologies. This work

Dynamic mobility applications open source application development portal task 6.1a : architecture and high-level design task 6.1b : list of requirements included in initial architecture and high-level design.

DOT National Transportation Integrated Search

2016-10-12

This document offers a detailed discussion of the systems functionality that was planned to be implemented. However, following the Agile Development methodology, during the course of system development, diligent decisions were made based on the la...

Tangible interactive system for document browsing and visualisation of multimedia data

NASA Astrophysics Data System (ADS)

Rytsar, Yuriy; Voloshynovskiy, Sviatoslav; Koval, Oleksiy; Deguillaume, Frederic; Topak, Emre; Startchik, Sergei; Pun, Thierry

2006-01-01

In this paper we introduce and develop a framework for document interactive navigation in multimodal databases. First, we analyze the main open issues of existing multimodal interfaces and then discuss two applications that include interaction with documents in several human environments, i.e., the so-called smart rooms. Second, we propose a system set-up dedicated to the efficient navigation in the printed documents. This set-up is based on the fusion of data from several modalities that include images and text. Both modalities can be used as cover data for hidden indexes using data-hiding technologies as well as source data for robust visual hashing. The particularities of the proposed robust visual hashing are described in the paper. Finally, we address two practical applications of smart rooms for tourism and education and demonstrate the advantages of the proposed solution.

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

NASA Astrophysics Data System (ADS)

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

2016-08-01

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

Biopython: freely available Python tools for computational molecular biology and bioinformatics.

PubMed

Cock, Peter J A; Antao, Tiago; Chang, Jeffrey T; Chapman, Brad A; Cox, Cymon J; Dalke, Andrew; Friedberg, Iddo; Hamelryck, Thomas; Kauff, Frank; Wilczynski, Bartek; de Hoon, Michiel J L

2009-06-01

The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning. Biopython is freely available, with documentation and source code at (www.biopython.org) under the Biopython license.

Cytoscape.js: a graph theory library for visualisation and analysis.

PubMed

Franz, Max; Lopes, Christian T; Huck, Gerardo; Dong, Yue; Sumer, Onur; Bader, Gary D

2016-01-15

Cytoscape.js is an open-source JavaScript-based graph library. Its most common use case is as a visualization software component, so it can be used to render interactive graphs in a web browser. It also can be used in a headless manner, useful for graph operations on a server, such as Node.js. Cytoscape.js is implemented in JavaScript. Documentation, downloads and source code are available at http://js.cytoscape.org. gary.bader@utoronto.ca. © The Author 2015. Published by Oxford University Press.

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

PubMed

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

2018-04-05

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

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

PubMed

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

2014-12-01

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

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

PubMed

Helmus, Jonathan J; Jaroniec, Christopher P

2013-04-01

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

JBioWH: an open-source Java framework for bioinformatics data integration

PubMed Central

Vera, Roberto; Perez-Riverol, Yasset; Perez, Sonia; Ligeti, Balázs; Kertész-Farkas, Attila; Pongor, Sándor

2013-01-01

The Java BioWareHouse (JBioWH) project is an open-source platform-independent programming framework that allows a user to build his/her own integrated database from the most popular data sources. JBioWH can be used for intensive querying of multiple data sources and the creation of streamlined task-specific data sets on local PCs. JBioWH is based on a MySQL relational database scheme and includes JAVA API parser functions for retrieving data from 20 public databases (e.g. NCBI, KEGG, etc.). It also includes a client desktop application for (non-programmer) users to query data. In addition, JBioWH can be tailored for use in specific circumstances, including the handling of massive queries for high-throughput analyses or CPU intensive calculations. The framework is provided with complete documentation and application examples and it can be downloaded from the Project Web site at http://code.google.com/p/jbiowh. A MySQL server is available for demonstration purposes at hydrax.icgeb.trieste.it:3307. Database URL: http://code.google.com/p/jbiowh PMID:23846595

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

PubMed Central

Helmus, Jonathan J.; Jaroniec, Christopher P.

2013-01-01

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

JBioWH: an open-source Java framework for bioinformatics data integration.

PubMed

Vera, Roberto; Perez-Riverol, Yasset; Perez, Sonia; Ligeti, Balázs; Kertész-Farkas, Attila; Pongor, Sándor

2013-01-01

The Java BioWareHouse (JBioWH) project is an open-source platform-independent programming framework that allows a user to build his/her own integrated database from the most popular data sources. JBioWH can be used for intensive querying of multiple data sources and the creation of streamlined task-specific data sets on local PCs. JBioWH is based on a MySQL relational database scheme and includes JAVA API parser functions for retrieving data from 20 public databases (e.g. NCBI, KEGG, etc.). It also includes a client desktop application for (non-programmer) users to query data. In addition, JBioWH can be tailored for use in specific circumstances, including the handling of massive queries for high-throughput analyses or CPU intensive calculations. The framework is provided with complete documentation and application examples and it can be downloaded from the Project Web site at http://code.google.com/p/jbiowh. A MySQL server is available for demonstration purposes at hydrax.icgeb.trieste.it:3307. Database URL: http://code.google.com/p/jbiowh.

A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature.

PubMed

Hart, Reece K; Rico, Rudolph; Hare, Emily; Garcia, John; Westbrook, Jody; Fusaro, Vincent A

2015-01-15

Biological sequence variants are commonly represented in scientific literature, clinical reports and databases of variation using the mutation nomenclature guidelines endorsed by the Human Genome Variation Society (HGVS). Despite the widespread use of the standard, no freely available and comprehensive programming libraries are available. Here we report an open-source and easy-to-use Python library that facilitates the parsing, manipulation, formatting and validation of variants according to the HGVS specification. The current implementation focuses on the subset of the HGVS recommendations that precisely describe sequence-level variation relevant to the application of high-throughput sequencing to clinical diagnostics. The package is released under the Apache 2.0 open-source license. Source code, documentation and issue tracking are available at http://bitbucket.org/hgvs/hgvs/. Python packages are available at PyPI (https://pypi.python.org/pypi/hgvs). Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature

PubMed Central

Hart, Reece K.; Rico, Rudolph; Hare, Emily; Garcia, John; Westbrook, Jody; Fusaro, Vincent A.

2015-01-01

Summary: Biological sequence variants are commonly represented in scientific literature, clinical reports and databases of variation using the mutation nomenclature guidelines endorsed by the Human Genome Variation Society (HGVS). Despite the widespread use of the standard, no freely available and comprehensive programming libraries are available. Here we report an open-source and easy-to-use Python library that facilitates the parsing, manipulation, formatting and validation of variants according to the HGVS specification. The current implementation focuses on the subset of the HGVS recommendations that precisely describe sequence-level variation relevant to the application of high-throughput sequencing to clinical diagnostics. Availability and implementation: The package is released under the Apache 2.0 open-source license. Source code, documentation and issue tracking are available at http://bitbucket.org/hgvs/hgvs/. Python packages are available at PyPI (https://pypi.python.org/pypi/hgvs). Contact: reecehart@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25273102

DATA-MEAns: an open source tool for the classification and management of neural ensemble recordings.

PubMed

Bonomini, María P; Ferrandez, José M; Bolea, Jose Angel; Fernandez, Eduardo

2005-10-30

The number of laboratories using techniques that allow to acquire simultaneous recordings of as many units as possible is considerably increasing. However, the development of tools used to analyse this multi-neuronal activity is generally lagging behind the development of the tools used to acquire these data. Moreover, the data exchange between research groups using different multielectrode acquisition systems is hindered by commercial constraints such as exclusive file structures, high priced licenses and hard policies on intellectual rights. This paper presents a free open-source software for the classification and management of neural ensemble data. The main goal is to provide a graphical user interface that links the experimental data to a basic set of routines for analysis, visualization and classification in a consistent framework. To facilitate the adaptation and extension as well as the addition of new routines, tools and algorithms for data analysis, the source code and documentation are freely available.

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

Complication rates of open transvesical prostatectomy according to the Clavien-Dindo classification system.

PubMed

Oranusi, C K; Nwofor, Ame; Oranusi, I O

2012-01-01

Traditional open prostatectomies either transvesical or retropubic remains the reference standard for managing benign prostatic enlargement in some centers, especially in developing countries. The comparison of complication rates between the various types of open prostatectomies is usually a source of significant debate among urologists, most times with conflicting results. The Clavien-Dindo classification system is an excellent attempt at standardization of reporting complications associated with surgeries. We reviewed retrospectively the records of patients who had open transvesical prostatectomy (TVP) in three specialist urology centers in Anambra state, Southeast Nigeria, over a period of 5 years (January 2004-December 2009), with the aim of documenting medical and surgical complications arising from open TVP. These complications were then categorized according to the Clavien-Dindo system. A total of 362 patients had open TVP over the period under review. Of this number, 145 had documented evidence of complications. The mean age of the patients was 66.3 years (SD 9.4 years; range 49-96 years). The mean follow-up period was 27.8 months (SD 12.6 months; range 6-33 months). The overall complication rate for open TVP in this study was 40.1% (145/362). Complication rates for grades i, id, ii, iiia, and iiib were 0.8%, 0.6%, 35.1%, 0.6%, and 3.0%, respectively. Most complications of open TVP occur in the early postoperative period. Open TVP still remains a valid surgical option in contemporary environment where advanced techniques for transurethral resection of the prostate and laparoscopic prostatectomy are unavailable. Most complications occur in the early postoperative period, with bleeding requiring several units of blood transfusion accounting for the commonest complication. This should be explained to patients during the preoperative counselling.

Parallelization of interpolation, solar radiation and water flow simulation modules in GRASS GIS using OpenMP

NASA Astrophysics Data System (ADS)

Hofierka, Jaroslav; Lacko, Michal; Zubal, Stanislav

2017-10-01

In this paper, we describe the parallelization of three complex and computationally intensive modules of GRASS GIS using the OpenMP application programming interface for multi-core computers. These include the v.surf.rst module for spatial interpolation, the r.sun module for solar radiation modeling and the r.sim.water module for water flow simulation. We briefly describe the functionality of the modules and parallelization approaches used in the modules. Our approach includes the analysis of the module's functionality, identification of source code segments suitable for parallelization and proper application of OpenMP parallelization code to create efficient threads processing the subtasks. We document the efficiency of the solutions using the airborne laser scanning data representing land surface in the test area and derived high-resolution digital terrain model grids. We discuss the performance speed-up and parallelization efficiency depending on the number of processor threads. The study showed a substantial increase in computation speeds on a standard multi-core computer while maintaining the accuracy of results in comparison to the output from original modules. The presented parallelization approach showed the simplicity and efficiency of the parallelization of open-source GRASS GIS modules using OpenMP, leading to an increased performance of this geospatial software on standard multi-core computers.

Plenario: An Open Data Discovery and Exploration Platform for Urban Science

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

Catlett, Charlie; Malik, Tanu; Goldstein, Brett J.

2014-12-01

The past decade has seen the widespread release of open data concerning city services, conditions, and activities by government bodies and public institutions of all sizes. Hundreds of open data portals now host thousands of datasets of many different types. These new data sources represent enormous po- tential for improved understanding of urban dynamics and processes—and, ultimately, for more livable, efficient, and prosperous communities. However, those who seek to realize this potential quickly discover that discovering and applying those data relevant to any particular question can be extraordinarily dif- ficult, due to decentralized storage, heterogeneous formats, and poor documentation. Inmore » this context, we introduce Plenario, a platform designed to automating time-consuming tasks associated with the discovery, exploration, and application of open city data—and, in so doing, reduce barriers to data use for researchers, policymakers, service providers, journalists, and members of the general public. Key innovations include a geospatial data warehouse that allows data from many sources to be registered into a common spatial and temporal frame; simple and intuitive interfaces that permit rapid discovery and exploration of data subsets pertaining to a particular area and time, regardless of type and source; easy export of such data subsets for further analysis; a user-configurable data ingest framework for automated importing and periodic updating of new datasets into the data warehouse; cloud hosting for elastic scaling and rapid creation of new Plenario instances; and an open source implementation to enable community contributions. We describe here the architecture and implementation of the Plenario platform, discuss lessons learned from its use by several communities, and outline plans for future work.« less

Dealing with extreme data diversity: extraction and fusion from the growing types of document formats

NASA Astrophysics Data System (ADS)

David, Peter; Hansen, Nichole; Nolan, James J.; Alcocer, Pedro

2015-05-01

The growth in text data available online is accompanied by a growth in the diversity of available documents. Corpora with extreme heterogeneity in terms of file formats, document organization, page layout, text style, and content are common. The absence of meaningful metadata describing the structure of online and open-source data leads to text extraction results that contain no information about document structure and are cluttered with page headers and footers, web navigation controls, advertisements, and other items that are typically considered noise. We describe an approach to document structure and metadata recovery that uses visual analysis of documents to infer the communicative intent of the author. Our algorithm identifies the components of documents such as titles, headings, and body content, based on their appearance. Because it operates on an image of a document, our technique can be applied to any type of document, including scanned images. Our approach to document structure recovery considers a finer-grained set of component types than prior approaches. In this initial work, we show that a machine learning approach to document structure recovery using a feature set based on the geometry and appearance of images of documents achieves a 60% greater F1- score than a baseline random classifier.

Software Tools for In-Situ Documentation of Built Heritage

NASA Astrophysics Data System (ADS)

Smars, P.

2013-07-01

The paper presents open source software tools developed by the author to facilitate in-situ documentation of architectural and archæological heritage. The design choices are exposed and related to a general issue in conservation and documentation: taking decisions about a valuable object under threat . The questions of level of objectivity is central to the three steps of this process. It is our belief that in-situ documentation has to be favoured in this demanding context, full of potential discoveries. The very powerful surveying techniques in rapid development nowadays enhance our vision but often tend to bring back a critical part of the documentation process to the office. The software presented facilitate a direct treatment of the data on the site. Emphasis is given to flexibility, interoperability and simplicity. Key features of the software are listed and illustrated with examples (3D model of Gothic vaults, analysis of the shape of a column, deformation of a wall, direct interaction with AutoCAD).

Open Source Patient-Controlled Analgesic Pump Requirements Documentation

PubMed Central

Larson, Brian R.; Hatcliff, John; Chalin, Patrice

2014-01-01

The dynamic nature of the medical domain is driving a need for continuous innovation and improvement in techniques for developing and assuring medical devices. Unfortunately, research in academia and communication between academics, industrial engineers, and regulatory authorities is hampered by the lack of realistic non-proprietary development artifacts for medical devices. In this paper, we give an overview of a detailed requirements document for a Patient-Controlled Analgesic (PCA) pump developed under the US NSF’s Food and Drug Administration (FDA) Scholar-in-Residence (SIR) program. This 60+ page document follows the methodology outlined in the US Federal Aviation Administrations (FAA) Requirements Engineering Management Handbook (REMH) and includes a domain overview, use cases, statements of safety & security requirements, and formal top-level system architectural description. Based on previous experience with release of a requirements document for a cardiac pacemaker that spawned a number of research and pedagogical activities, we believe that the described PCA requirements document can be an important research enabler within the formal methods and software engineering communities. PMID:24931440

Bridging the Gap between HL7 CDA and HL7 FHIR: A JSON Based Mapping.

PubMed

Rinner, Christoph; Duftschmid, Georg

2016-01-01

The Austrian electronic health record (EHR) system ELGA went live in December 2016. It is a document oriented EHR system and is based on the HL7 Clinical Document Architecture (CDA). The HL7 Fast Healthcare Interoperability Resources (FHIR) is a relatively new standard that combines the advantages of HL7 messages and CDA Documents. In order to offer easier access to information stored in ELGA we present a method based on adapted FHIR resources to map CDA documents to FHIR resources. A proof-of-concept tool using Java, the open-source FHIR framework HAPI-FHIR and publicly available FHIR servers was created to evaluate the presented mapping. In contrast to other approaches the close resemblance of the mapping file to the FHIR specification allows existing FHIR infrastructure to be reused. In order to reduce information overload and facilitate the access to CDA documents, FHIR could offer a standardized way to query CDA data on a fine granular base in Austria.

The Earth System (ES-DOC) Project

NASA Astrophysics Data System (ADS)

Greenslade, Mark; Murphy, Sylvia; Treshansky, Allyn; DeLuca, Cecilia; Guilyardi, Eric; Denvil, Sebastien

2014-05-01

ESSI1.3 New Paradigms, Modelling, and International Collaboration Strategies for Earth System Sciences Earth System Documentation (ES-DOC) is an international project supplying tools & services in support of earth system documentation creation, analysis and dissemination. It is nurturing a sustainable standards based documentation eco-system that aims to become an integral part of the next generation of exa-scale dataset archives. ES-DOC leverages open source software and places end-user narratives at the heart of all it does. ES-DOC has initially focused upon nurturing the Earth System Model (ESM) documentation eco-system. Within this context ES-DOC leverages emerging documentation standards and supports the following projects: Coupled Model Inter-comparison Project Phase 5 (CMIP5); Dynamical Core Model Inter-comparison Project (DCMIP); National Climate Predictions and Projections Platforms Quantitative Evaluation of Downscaling Workshop. This presentation will introduce the project to a wider audience and demonstrate the range of tools and services currently available for use. It will also demonstrate how international collaborative efforts are essential to the success of ES-DOC.

3Dmol.js: molecular visualization with WebGL.

PubMed

Rego, Nicholas; Koes, David

2015-04-15

3Dmol.js is a modern, object-oriented JavaScript library that uses the latest web technologies to provide interactive, hardware-accelerated three-dimensional representations of molecular data without the need to install browser plugins or Java. 3Dmol.js provides a full featured API for developers as well as a straightforward declarative interface that lets users easily share and embed molecular data in websites. 3Dmol.js is distributed under the permissive BSD open source license. Source code and documentation can be found at http://3Dmol.csb.pitt.edu dkoes@pitt.edu. © The Author 2014. Published by Oxford University Press.

Check-Cases for Verification of 6-Degree-of-Freedom Flight Vehicle Simulations. Volume 2; Appendices

NASA Technical Reports Server (NTRS)

Murri, Daniel G.; Jackson, E. Bruce; Shelton, Robert O.

2015-01-01

This NASA Engineering and Safety Center (NESC) assessment was established to develop a set of time histories for the flight behavior of increasingly complex example aerospacecraft that could be used to partially validate various simulation frameworks. The assessment was conducted by representatives from several NASA Centers and an open-source simulation project. This document contains details on models, implementation, and results.

The Virtual Collaboration Environment: New Media for Crisis Response

DTIC Science & Technology

2011-05-01

openvce.net/forum-alternative-platforms and http://openvce.net/more), the open-source Drupal ®-based Proceedings of the 8th International ISCRAM... Drupal is a widely used modular content management system, with an active development community of its own. It provides a user management system and...authoring text documents (a facility felt to be lacking at the time in Drupal ). This wiki feature has itself been supplemented with experimental

Database of historically documented springs and spring flow measurements in Texas

USGS Publications Warehouse

Heitmuller, Franklin T.; Reece, Brian D.

2003-01-01

Springs are naturally occurring features that convey excess ground water to the land surface; they represent a transition from ground water to surface water. Water issues through one opening, multiple openings, or numerous seeps in the rock or soil. The database of this report provides information about springs and spring flow in Texas including spring names, identification numbers, location, and, if available, water source and use. This database does not include every spring in Texas, but is limited to an aggregation of selected digital and hard-copy data of the U.S. Geological Survey (USGS), the Texas Water Development Board (TWDB), and Capitol Environmental Services.

Research Notes - Openness and Evolvability - Documentation Quality Assessment

DTIC Science & Technology

2016-08-01

UNCLASSIFIED UNCLASSIFIED Notes – Openness and Evolvability – Documentation Quality Assessment Michael Haddy* and Adam Sbrana...Methods and Processes. This set of Research Notes focusses on Documentation Quality Assessment. This work was undertaken from the late 1990s to 2007...1 2. DOCUMENTATION QUALITY ASSESSMENT ......................................................... 1 2.1 Documentation Quality Assessment

PlasmaPy: beginning a community developed Python package for plasma physics

NASA Astrophysics Data System (ADS)

Murphy, Nicholas A.; Huang, Yi-Min; PlasmaPy Collaboration

2016-10-01

In recent years, researchers in several disciplines have collaborated on community-developed open source Python packages such as Astropy, SunPy, and SpacePy. These packages provide core functionality, common frameworks for data analysis and visualization, and educational tools. We propose that our community begins the development of PlasmaPy: a new open source core Python package for plasma physics. PlasmaPy could include commonly used functions in plasma physics, easy-to-use plasma simulation codes, Grad-Shafranov solvers, eigenmode solvers, and tools to analyze both simulations and experiments. The development will include modern programming practices such as version control, embedding documentation in the code, unit tests, and avoiding premature optimization. We will describe early code development on PlasmaPy, and discuss plans moving forward. The success of PlasmaPy depends on active community involvement and a welcoming and inclusive environment, so anyone interested in joining this collaboration should contact the authors.

CHRONOS architecture: Experiences with an open-source services-oriented architecture for geoinformatics

USGS Publications Warehouse

Fils, D.; Cervato, C.; Reed, J.; Diver, P.; Tang, X.; Bohling, G.; Greer, D.

2009-01-01

CHRONOS's purpose is to transform Earth history research by seamlessly integrating stratigraphic databases and tools into a virtual on-line stratigraphic record. In this paper, we describe the various components of CHRONOS's distributed data system, including the encoding of semantic and descriptive data into a service-based architecture. We give examples of how we have integrated well-tested resources available from the open-source and geoinformatic communities, like the GeoSciML schema and the simple knowledge organization system (SKOS), into the services-oriented architecture to encode timescale and phylogenetic synonymy data. We also describe on-going efforts to use geospatially enhanced data syndication and informally including semantic information by embedding it directly into the XHTML Document Object Model (DOM). XHTML DOM allows machine-discoverable descriptive data such as licensing and citation information to be incorporated directly into data sets retrieved by users. ?? 2008 Elsevier Ltd. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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

2015-02-01

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

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.

Observations and Thermochemical Calculations for Hot-Jupiter Atmospheres

NASA Astrophysics Data System (ADS)

Blecic, Jasmina; Harrington, Joseph; Bowman, M. Oliver; Cubillos, Patricio; Stemm, Madison

2015-01-01

I present Spitzer eclipse observations for WASP-14b and WASP-43b, an open source tool for thermochemical equilibrium calculations, and components of an open source tool for atmospheric parameter retrieval from spectroscopic data. WASP-14b is a planet that receives high irradiation from its host star, yet, although theory does not predict it, the planet hosts a thermal inversion. The WASP-43b eclipses have signal-to-noise ratios of ~25, one of the largest among exoplanets. To assess these planets' atmospheric composition and thermal structure, we developed an open-source Bayesian Atmospheric Radiative Transfer (BART) code. My dissertation tasks included developing a Thermochemical Equilibrium Abundances (TEA) code, implementing the eclipse geometry calculation in BART's radiative transfer module, and generating parameterized pressure and temperature profiles so the radiative-transfer module can be driven by the statistical module.To initialize the radiative-transfer calculation in BART, TEA calculates the equilibrium abundances of gaseous molecular species at a given temperature and pressure. It uses the Gibbs-free-energy minimization method with an iterative Lagrangian optimization scheme. Given elemental abundances, TEA calculates molecular abundances for a particular temperature and pressure or a list of temperature-pressure pairs. The code is tested against the original method developed by White at al. (1958), the analytic method developed by Burrows and Sharp (1999), and the Newton-Raphson method implemented in the open-source Chemical Equilibrium with Applications (CEA) code. TEA, written in Python, is modular, documented, and available to the community via the open-source development site GitHub.com.Support for this work was provided by NASA Headquarters under the NASA Earth and Space Science Fellowship Program, grant NNX12AL83H, by NASA through an award issued by JPL/Caltech, and through the Science Mission Directorate's Planetary Atmospheres Program, grant NNX12AI69G.

A Nursing Intelligence System to Support Secondary Use of Nursing Routine Data

PubMed Central

Rauchegger, F.; Ammenwerth, E.

2015-01-01

Summary Background Nursing care is facing exponential growth of information from nursing documentation. This amount of electronically available data collected routinely opens up new opportunities for secondary use. Objectives To present a case study of a nursing intelligence system for reusing routinely collected nursing documentation data for multiple purposes, including quality management of nursing care. Methods The SPIRIT framework for systematically planning the reuse of clinical routine data was leveraged to design a nursing intelligence system which then was implemented using open source tools in a large university hospital group following the spiral model of software engineering. Results The nursing intelligence system is in routine use now and updated regularly, and includes over 40 million data sets. It allows the outcome and quality analysis of data related to the nursing process. Conclusions Following a systematic approach for planning and designing a solution for reusing routine care data appeared to be successful. The resulting nursing intelligence system is useful in practice now, but remains malleable for future changes. PMID:26171085

ERPLAB: an open-source toolbox for the analysis of event-related potentials

PubMed Central

Lopez-Calderon, Javier; Luck, Steven J.

2014-01-01

ERPLAB toolbox is a freely available, open-source toolbox for processing and analyzing event-related potential (ERP) data in the MATLAB environment. ERPLAB is closely integrated with EEGLAB, a popular open-source toolbox that provides many EEG preprocessing steps and an excellent user interface design. ERPLAB adds to EEGLAB’s EEG processing functions, providing additional tools for filtering, artifact detection, re-referencing, and sorting of events, among others. ERPLAB also provides robust tools for averaging EEG segments together to create averaged ERPs, for creating difference waves and other recombinations of ERP waveforms through algebraic expressions, for filtering and re-referencing the averaged ERPs, for plotting ERP waveforms and scalp maps, and for quantifying several types of amplitudes and latencies. ERPLAB’s tools can be accessed either from an easy-to-learn graphical user interface or from MATLAB scripts, and a command history function makes it easy for users with no programming experience to write scripts. Consequently, ERPLAB provides both ease of use and virtually unlimited power and flexibility, making it appropriate for the analysis of both simple and complex ERP experiments. Several forms of documentation are available, including a detailed user’s guide, a step-by-step tutorial, a scripting guide, and a set of video-based demonstrations. PMID:24782741

ERPLAB: an open-source toolbox for the analysis of event-related potentials.

PubMed

Lopez-Calderon, Javier; Luck, Steven J

2014-01-01

ERPLAB toolbox is a freely available, open-source toolbox for processing and analyzing event-related potential (ERP) data in the MATLAB environment. ERPLAB is closely integrated with EEGLAB, a popular open-source toolbox that provides many EEG preprocessing steps and an excellent user interface design. ERPLAB adds to EEGLAB's EEG processing functions, providing additional tools for filtering, artifact detection, re-referencing, and sorting of events, among others. ERPLAB also provides robust tools for averaging EEG segments together to create averaged ERPs, for creating difference waves and other recombinations of ERP waveforms through algebraic expressions, for filtering and re-referencing the averaged ERPs, for plotting ERP waveforms and scalp maps, and for quantifying several types of amplitudes and latencies. ERPLAB's tools can be accessed either from an easy-to-learn graphical user interface or from MATLAB scripts, and a command history function makes it easy for users with no programming experience to write scripts. Consequently, ERPLAB provides both ease of use and virtually unlimited power and flexibility, making it appropriate for the analysis of both simple and complex ERP experiments. Several forms of documentation are available, including a detailed user's guide, a step-by-step tutorial, a scripting guide, and a set of video-based demonstrations.

76 FR 4659 - Science Advisory Board Staff Office; Notification of a Public Teleconference of the Science...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-26

...://yosemite.epa.gov/sab/ sabproduct.nsf/fedrgstr--activities/ FL%20Estuaries%20TSD?OpenDocument'' should read ``http:// yosemite.epa.gov/sab/sabproduct.nsf/fedrgstr--activites/ FL%20Estuaries%20TSD?OpenDocument.'' 2.../sabproduct.nsf/fedrgstr--activities/ FL%20Estuaries%20TSD?OpenDocument'' should read ``http:// yosemite.epa...

Massively Scalable Near Duplicate Detection in Streams of Documents using MDSH

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

Bogen, Paul Logasa; Symons, Christopher T; McKenzie, Amber T

2013-01-01

In a world where large-scale text collections are not only becoming ubiquitous but also are growing at increasing rates, near duplicate documents are becoming a growing concern that has the potential to hinder many different information filtering tasks. While others have tried to address this problem, prior techniques have only been used on limited collection sizes and static cases. We will briefly describe the problem in the context of Open Source Intelligence (OSINT) along with our additional constraints for performance. In this work we propose two variations on Multi-dimensional Spectral Hash (MDSH) tailored for working on extremely large, growing setsmore » of text documents. We analyze the memory and runtime characteristics of our techniques and provide an informal analysis of the quality of the near-duplicate clusters produced by our techniques.« less

CWA 15793 2011 Planning and Implementation Tool

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

Gross, Alan; Nail, George

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

Laying the Groundwork for Enterprise-Wide Medical Language Processing Services: Architecture and Process

PubMed Central

Chen, Elizabeth S.; Maloney, Francine L.; Shilmayster, Eugene; Goldberg, Howard S.

2009-01-01

A systematic and standard process for capturing information within free-text clinical documents could facilitate opportunities for improving quality and safety of patient care, enhancing decision support, and advancing data warehousing across an enterprise setting. At Partners HealthCare System, the Medical Language Processing (MLP) services project was initiated to establish a component-based architectural model and processes to facilitate putting MLP functionality into production for enterprise consumption, promote sharing of components, and encourage reuse. Key objectives included exploring the use of an open-source framework called the Unstructured Information Management Architecture (UIMA) and leveraging existing MLP-related efforts, terminology, and document standards. This paper describes early experiences in defining the infrastructure and standards for extracting, encoding, and structuring clinical observations from a variety of clinical documents to serve enterprise-wide needs. PMID:20351830

Laying the groundwork for enterprise-wide medical language processing services: architecture and process.

PubMed

Chen, Elizabeth S; Maloney, Francine L; Shilmayster, Eugene; Goldberg, Howard S

2009-11-14

A systematic and standard process for capturing information within free-text clinical documents could facilitate opportunities for improving quality and safety of patient care, enhancing decision support, and advancing data warehousing across an enterprise setting. At Partners HealthCare System, the Medical Language Processing (MLP) services project was initiated to establish a component-based architectural model and processes to facilitate putting MLP functionality into production for enterprise consumption, promote sharing of components, and encourage reuse. Key objectives included exploring the use of an open-source framework called the Unstructured Information Management Architecture (UIMA) and leveraging existing MLP-related efforts, terminology, and document standards. This paper describes early experiences in defining the infrastructure and standards for extracting, encoding, and structuring clinical observations from a variety of clinical documents to serve enterprise-wide needs.

SemMat: Federated Semantic Services Platform for Open materials Science and Engineering

DTIC Science & Technology

2017-01-01

identified the following two important tasks to remedy the data heterogeneity challenge to promote data integration: (1) creating the semantic...sourced from the structural and bio -materials domains. For structural materials data, we reviewed and used MIL-HDBK-5J [11] and MIL-HDBK-17. Furthermore...documents about composite materials provided by our domain expert. Based on the suggestions given by domain experts in bio -materials, the following

Next Steps in Syria

DTIC Science & Technology

2014-01-01

military intervention.2 Press sources document the presence of the Islamic Revolutionary Guard Corps ( IRGC ) from the Quds Force fighting with Syrian and...speech in mid-September to commanders of the IRGC , Ruhani wel- comed a possible deal between Washington and Moscow to reduce Syria’s chemical weap...ons stockpile and warned the IRGC , with units fighting openly in Syria, not to get involved in politics.6 Iran does not want to see a Saudi “victory

Proceedings of the Very Low Frequency (VLF) Ambient Noise Workshop Held in Stennis, Mississippi on 20-21 September 1988

DTIC Science & Technology

1988-12-01

20-21 September 1988 (This document contains the unclassified presentations only.) DTIC Ronad A by&S"LECTE 0 iCompiled W.y: Ronald A. Wagstaff 0140...7 IV* Summary........................11 V. Presentations ................................... 37 "Opening Remarks," R. Wagstaff ............... 39...34Influence of Noise Source Distributions and Propagation Mechanisms on Noise Field Directionality," M. Bradley/R. Wagstaff ...... 51 "Distant Storm

openECA Detailed Design Document

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

Robertson, Russell

This document describes the functional and non-functional requirements for: The openECA platform The included analytic systems that will: Validate the operational readiness and performance of the openECA platform Provide out-of-box value to those that implement the openECA platform with an initial collection of analytics

MpTheory Java library: a multi-platform Java library for systems biology based on the Metabolic P theory.

PubMed

Marchetti, Luca; Manca, Vincenzo

2015-04-15

MpTheory Java library is an open-source project collecting a set of objects and algorithms for modeling observed dynamics by means of the Metabolic P (MP) theory, that is, a mathematical theory introduced in 2004 for modeling biological dynamics. By means of the library, it is possible to model biological systems both at continuous and at discrete time. Moreover, the library comprises a set of regression algorithms for inferring MP models starting from time series of observations. To enhance the modeling experience, beside a pure Java usage, the library can be directly used within the most popular computing environments, such as MATLAB, GNU Octave, Mathematica and R. The library is open-source and licensed under the GNU Lesser General Public License (LGPL) Version 3.0. Source code, binaries and complete documentation are available at http://mptheory.scienze.univr.it. luca.marchetti@univr.it, marchetti@cosbi.eu Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Getting more out of biomedical documents with GATE's full lifecycle open source text analytics.

PubMed

Cunningham, Hamish; Tablan, Valentin; Roberts, Angus; Bontcheva, Kalina

2013-01-01

This software article describes the GATE family of open source text analysis tools and processes. GATE is one of the most widely used systems of its type with yearly download rates of tens of thousands and many active users in both academic and industrial contexts. In this paper we report three examples of GATE-based systems operating in the life sciences and in medicine. First, in genome-wide association studies which have contributed to discovery of a head and neck cancer mutation association. Second, medical records analysis which has significantly increased the statistical power of treatment/outcome models in the UK's largest psychiatric patient cohort. Third, richer constructs in drug-related searching. We also explore the ways in which the GATE family supports the various stages of the lifecycle present in our examples. We conclude that the deployment of text mining for document abstraction or rich search and navigation is best thought of as a process, and that with the right computational tools and data collection strategies this process can be made defined and repeatable. The GATE research programme is now 20 years old and has grown from its roots as a specialist development tool for text processing to become a rather comprehensive ecosystem, bringing together software developers, language engineers and research staff from diverse fields. GATE now has a strong claim to cover a uniquely wide range of the lifecycle of text analysis systems. It forms a focal point for the integration and reuse of advances that have been made by many people (the majority outside of the authors' own group) who work in text processing for biomedicine and other areas. GATE is available online <1> under GNU open source licences and runs on all major operating systems. Support is available from an active user and developer community and also on a commercial basis.

Getting More Out of Biomedical Documents with GATE's Full Lifecycle Open Source Text Analytics

PubMed Central

Cunningham, Hamish; Tablan, Valentin; Roberts, Angus; Bontcheva, Kalina

2013-01-01

This software article describes the GATE family of open source text analysis tools and processes. GATE is one of the most widely used systems of its type with yearly download rates of tens of thousands and many active users in both academic and industrial contexts. In this paper we report three examples of GATE-based systems operating in the life sciences and in medicine. First, in genome-wide association studies which have contributed to discovery of a head and neck cancer mutation association. Second, medical records analysis which has significantly increased the statistical power of treatment/outcome models in the UK's largest psychiatric patient cohort. Third, richer constructs in drug-related searching. We also explore the ways in which the GATE family supports the various stages of the lifecycle present in our examples. We conclude that the deployment of text mining for document abstraction or rich search and navigation is best thought of as a process, and that with the right computational tools and data collection strategies this process can be made defined and repeatable. The GATE research programme is now 20 years old and has grown from its roots as a specialist development tool for text processing to become a rather comprehensive ecosystem, bringing together software developers, language engineers and research staff from diverse fields. GATE now has a strong claim to cover a uniquely wide range of the lifecycle of text analysis systems. It forms a focal point for the integration and reuse of advances that have been made by many people (the majority outside of the authors' own group) who work in text processing for biomedicine and other areas. GATE is available online <1> under GNU open source licences and runs on all major operating systems. Support is available from an active user and developer community and also on a commercial basis. PMID:23408875

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

NASA Astrophysics Data System (ADS)

Salih, S. A.; Ismail, S.

2017-12-01

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

The OpenPicoAmp: an open-source planar lipid bilayer amplifier for hands-on learning of neuroscience.

PubMed

Shlyonsky, Vadim; Dupuis, Freddy; Gall, David

2014-01-01

Understanding the electrical biophysical properties of the cell membrane can be difficult for neuroscience students as it relies solely on lectures of theoretical models without practical hands on experiments. To address this issue, we developed an open-source lipid bilayer amplifier, the OpenPicoAmp, which is appropriate for use in introductory courses in biophysics or neurosciences at the undergraduate level, dealing with the electrical properties of the cell membrane. The amplifier is designed using the common lithographic printed circuit board fabrication process and off-the-shelf electronic components. In addition, we propose a specific design for experimental chambers allowing the insertion of a commercially available polytetrafluoroethylene film. We provide a complete documentation allowing to build the amplifier and the experimental chamber. The students hand-out giving step-by step instructions to perform a recording is also included. Our experimental setup can be used in basic experiments in which students monitor the bilayer formation by capacitance measurement and record unitary currents produced by ionic channels like gramicidin A dimers. Used in combination with a low-cost data acquisition board this system provides a complete solution for hands-on lessons, therefore improving the effectiveness in teaching basic neurosciences or biophysics.

The OpenPicoAmp: An Open-Source Planar Lipid Bilayer Amplifier for Hands-On Learning of Neuroscience

PubMed Central

Shlyonsky, Vadim; Dupuis, Freddy; Gall, David

2014-01-01

Understanding the electrical biophysical properties of the cell membrane can be difficult for neuroscience students as it relies solely on lectures of theoretical models without practical hands on experiments. To address this issue, we developed an open-source lipid bilayer amplifier, the OpenPicoAmp, which is appropriate for use in introductory courses in biophysics or neurosciences at the undergraduate level, dealing with the electrical properties of the cell membrane. The amplifier is designed using the common lithographic printed circuit board fabrication process and off-the-shelf electronic components. In addition, we propose a specific design for experimental chambers allowing the insertion of a commercially available polytetrafluoroethylene film. We provide a complete documentation allowing to build the amplifier and the experimental chamber. The students hand-out giving step-by step instructions to perform a recording is also included. Our experimental setup can be used in basic experiments in which students monitor the bilayer formation by capacitance measurement and record unitary currents produced by ionic channels like gramicidin A dimers. Used in combination with a low-cost data acquisition board this system provides a complete solution for hands-on lessons, therefore improving the effectiveness in teaching basic neurosciences or biophysics. PMID:25251830

The Role of Citizen Science in Risk Mitigation and Disaster Response: A Case Study of 2015 Nepalese Earthquake Using OpenStreetMap

NASA Astrophysics Data System (ADS)

Rieger, C.; Byrne, J. M.

2015-12-01

Citizen science includes networks of ordinary people acting as sensors, observing and recording information for science. OpenStreetMap is one such sensor network which empowers citizens to collaboratively produce a global picture from free geographic information. The success of this open source software is extended by the development of freely used open databases for the user community. Participating citizens do not require a high level of skill. Final results are processed by professionals following quality assurance protocols before map information is released. OpenStreetMap is not only the cheapest source of timely maps in many cases but also often the only source. This is particularly true in developing countries. Emergency responses to the recent earthquake in Nepal illustrates the value for rapidly updated geographical information. This includes emergency management, damage assessment, post-disaster response, and future risk mitigation. Local disaster conditions (landslides, road closings, bridge failures, etc.) were documented for local aid workers by citizen scientists working remotely. Satellites and drones provide digital imagery of the disaster zone and OpenStreetMap participants shared the data from locations around the globe. For the Nepal earthquake, OpenStreetMap provided a team of volunteers on the ground through their Humanitarian OpenStreetMap Team (HOT) which contribute data to the disaster response through smartphones and laptops. This, combined with global citizen science efforts, provided immediate geographically useful maps to assist aid workers, including the Red Cross and Canadian DART Team, and the Nepalese government. As of August 2014, almost 1.7 million users provided over 2.5 billion edits to the OpenStreetMap map database. Due to the increased usage of smartphones, GPS-enabled devices, and the growing participation in citizen science projects, data gathering is proving an effective way to contribute as a global citizen. This paper aims to describe the significance of citizen participation in the case of the Nepal earthquake using OpenStreetMap to respond to disasters as well as its role in future risk mitigation.

GALE: a generic open source extensible adaptation engine

NASA Astrophysics Data System (ADS)

De Bra, Paul; Knutov, Evgeny; Smits, David; Stash, Natalia; Ramos, Vinicius F. C.

2013-06-01

This paper motivates and describes GALE, the Generic Adaptation Language and Engine that came out of the GRAPPLE EU FP7 project. The main focus of the paper is the extensible nature of GALE. The purpose of this description is to illustrate how a single core adaptation engine can be used for different types of adaptation, applied to different types of information items and documents. We illustrate the adaptive functionality on some examples of hypermedia documents. In April 2012, David Smits defended the world's first adaptive PhD thesis on this topic. The thesis, available for download and direct adaptive access at http://gale.win.tue.nl/thesis, shows that a single source of information can serve different audiences and at the same time also allows more freedom of navigation than is possible in any paper or static hypermedia document. The same can be done for course texts, hyperfiction, encyclopedia, museum, or other cultural heritage websites, etc. We explain how to add functionality to GALE if desired, to adapt the system's behavior to whatever the application requires. This stresses our main objective: to provide a technological base for adaptive (hypermedia) system researchers on which they can build extensions for the specific research they have in mind.

Amanzi: An Open-Source Multi-process Simulator for Environmental Applications

NASA Astrophysics Data System (ADS)

Moulton, J. D.; Molins, S.; Johnson, J. N.; Coon, E.; Lipnikov, K.; Day, M.; Barker, E.

2014-12-01

The Advanced Simulation Capabililty for Environmental Management (ASCEM) program is developing an approach and open-source tool suite for standardized risk and performance assessments at legacy nuclear waste sites. These assessments begin with simplified models, and add geometric and geologic complexity as understanding is gained. The Platform toolsets (Akuna) generates these conceptual models and Amanzi provides the computational engine to perform the simulations, returning the results for analysis and visualization. In this presentation we highlight key elements of the design, algorithms and implementations used in Amanzi. In particular, the hierarchical and modular design is aligned with the coupled processes being sumulated, and naturally supports a wide range of model complexity. This design leverages a dynamic data manager and the synergy of two graphs (one from the high-level perspective of the models the other from the dependencies of the variables in the model) to enable this flexible model configuration at run time. Moreover, to model sites with complex hydrostratigraphy, as well as engineered systems, we are developing a dual unstructured/structured capability. Recently, these capabilities have been collected in a framework named Arcos, and efforts have begun to improve interoperability between the unstructured and structured AMR approaches in Amanzi. To leverage a range of biogeochemistry capability from the community (e.g., CrunchFlow, PFLOTRAN, etc.), a biogeochemistry interface library was developed called Alquimia. To ensure that Amanzi is truly an open-source community code we require a completely open-source tool chain for our development. We will comment on elements of this tool chain, including the testing and documentation development tools such as docutils, and Sphinx. Finally, we will show simulation results from our phased demonstrations, including the geochemically complex Savannah River F-Area seepage basins.

Plenario: A Spatio-Temporal Platform for Discovery and Exploration of Urban Science Data

NASA Astrophysics Data System (ADS)

Engler, W. H.; Malik, T.; Catlett, C.; Foster, I.; Goldstein, B.

2015-12-01

The past decade has seen the widespread release of open data concerning city services, conditions, and activities by government bodies and public institutions of all sizes. Hundreds of open data portals now host thousands of datasets of many different types. These new data sources represent enormous potential for improved understanding of urban dynamics and processes—and, ultimately, for more livable, efficient, and prosperous communities. However, those who seek to realize this potential quickly discover that discovering and applying those data relevant to any particular question can be extraordinarily difficult, due to decentralized storage, heterogeneous formats, and poor documentation. In this context, we introduce Plenario, a platform designed to automating time-consuming tasks associated with the discovery, exploration, and application of open city data—and, in so doing, reduce barriers to data use for researchers, policymakers, service providers, journalists, and members of the general public. Key innovations include a geospatial data warehouse that allows data from many sources to be registered into a common spatial and temporal frame; simple and intuitive interfaces that permit rapid discovery and exploration of data subsets pertaining to a particular area and time, regardless of type and source; easy export of such data subsets for further analysis; a user-configurable data ingest framework for automated importing and periodic updating of new datasets into the data warehouse; cloud hosting for elastic scaling and rapid creation of new Plenario instances; and an open source implementation to enable community contributions. We describe here the architecture and implementation of the Plenario platform, discuss lessons learned from its use by several communities, and outline plans for future work.

Visualization, documentation, analysis, and communication of large scale gene regulatory networks

PubMed Central

Longabaugh, William J.R.; Davidson, Eric H.; Bolouri, Hamid

2009-01-01

Summary Genetic regulatory networks (GRNs) are complex, large-scale, and spatially and temporally distributed. These characteristics impose challenging demands on computational GRN modeling tools, and there is a need for custom modeling tools. In this paper, we report on our ongoing development of BioTapestry, an open source, freely available computational tool designed specifically for GRN modeling. We also outline our future development plans, and give some examples of current applications of BioTapestry. PMID:18757046

GRIP Collaboration Portal: Information Management for a Hurricane Field Campaign

NASA Astrophysics Data System (ADS)

Conover, H.; Kulkarni, A.; Garrett, M.; Smith, T.; Goodman, H. M.

2010-12-01

NASA’s Genesis and Rapid Intensification Processes (GRIP) experiment, carried out in August and September of 2010, was a complex operation, involving three aircraft and their crews based at different airports, a dozen instrument teams, mission scientists, weather forecasters, project coordinators and a variety of other participants. In addition, GRIP was coordinated with concurrent airborne missions: NOAA’s IFEX and then NSF-funded PREDICT. The GRIP Collaboration Portal was developed to facilitate communication within and between the different teams and serve as an information repository for the field campaign, providing a single access point for project documents, plans, weather forecasts, flight reports and quicklook data. The portal was developed using the Drupal open source content management framework. This presentation will cover both technology and participation issues. Specific examples include: Drupal’s large and diverse open source developer community is an advantage in that we were able to reuse many modules rather than develop capabilities from scratch, but integrating multiple modules developed by many people adds to the overall complexity of the site. Many of the communication capabilities provided by the site, such as discussion forums and blogs, were not used. Participants were diligent about posting necessary documents, but the favored communication method remained email. Drupal's developer-friendly nature allowed for quick development of the customized functionality needed to accommodate the rapidly changing requirements of GRIP experiment. DC-8 Overflight of Hurricane Earl during GRIP Mission

The Earth System Documentation (ES-DOC) project

NASA Astrophysics Data System (ADS)

Murphy, S.; Greenslade, M. A.; Treshansky, A.; DeLuca, C.; Guilyardi, E.; Denvil, S.

2013-12-01

Earth System Documentation (ES-DOC) is an international project supplying high quality tools and services in support of Earth system documentation creation, analysis and dissemination. It is nurturing a sustainable standards based documentation ecosystem that aims to become an integral part of the next generation of exa-scale dataset archives. ES-DOC leverages open source software, and applies a software development methodology that places end-user narratives at the heart of all it does. ES-DOC has initially focused upon nurturing the Earth System Model (ESM) documentation eco-system. Within this context ES-DOC leverages the emerging Common Information Model (CIM) metadata standard, which has supported the following projects: ** Coupled Model Inter-comparison Project Phase 5 (CMIP5); ** Dynamical Core Model Inter-comparison Project (DCMIP-2012); ** National Climate Predictions and Projections Platforms (NCPP) Quantitative Evaluation of Downscaling Workshop (QED-2013). This presentation will introduce the project to a wider audience and will demonstrate the current production level capabilities of the eco-system: ** An ESM documentation Viewer embeddable into any website; ** An ESM Questionnaire configurable on a project by project basis; ** An ESM comparison tool reusable across projects; ** An ESM visualization tool reusable across projects; ** A search engine for speedily accessing published documentation; ** Libraries for streamlining document creation, validation and publishing pipelines.

Development of an information retrieval tool for biomedical patents.

PubMed

Alves, Tiago; Rodrigues, Rúben; Costa, Hugo; Rocha, Miguel

2018-06-01

The volume of biomedical literature has been increasing in the last years. Patent documents have also followed this trend, being important sources of biomedical knowledge, technical details and curated data, which are put together along the granting process. The field of Biomedical text mining (BioTM) has been creating solutions for the problems posed by the unstructured nature of natural language, which makes the search of information a challenging task. Several BioTM techniques can be applied to patents. From those, Information Retrieval (IR) includes processes where relevant data are obtained from collections of documents. In this work, the main goal was to build a patent pipeline addressing IR tasks over patent repositories to make these documents amenable to BioTM tasks. The pipeline was developed within @Note2, an open-source computational framework for BioTM, adding a number of modules to the core libraries, including patent metadata and full text retrieval, PDF to text conversion and optical character recognition. Also, user interfaces were developed for the main operations materialized in a new @Note2 plug-in. The integration of these tools in @Note2 opens opportunities to run BioTM tools over patent texts, including tasks from Information Extraction, such as Named Entity Recognition or Relation Extraction. We demonstrated the pipeline's main functions with a case study, using an available benchmark dataset from BioCreative challenges. Also, we show the use of the plug-in with a user query related to the production of vanillin. This work makes available all the relevant content from patents to the scientific community, decreasing drastically the time required for this task, and provides graphical interfaces to ease the use of these tools. Copyright © 2018 Elsevier B.V. All rights reserved.

Cluster-lensing: A Python Package for Galaxy Clusters and Miscentering

NASA Astrophysics Data System (ADS)

Ford, Jes; VanderPlas, Jake

2016-12-01

We describe a new open source package for calculating properties of galaxy clusters, including Navarro, Frenk, and White halo profiles with and without the effects of cluster miscentering. This pure-Python package, cluster-lensing, provides well-documented and easy-to-use classes and functions for calculating cluster scaling relations, including mass-richness and mass-concentration relations from the literature, as well as the surface mass density {{Σ }}(R) and differential surface mass density {{Δ }}{{Σ }}(R) profiles, probed by weak lensing magnification and shear. Galaxy cluster miscentering is especially a concern for stacked weak lensing shear studies of galaxy clusters, where offsets between the assumed and the true underlying matter distribution can lead to a significant bias in the mass estimates if not accounted for. This software has been developed and released in a public GitHub repository, and is licensed under the permissive MIT license. The cluster-lensing package is archived on Zenodo. Full documentation, source code, and installation instructions are available at http://jesford.github.io/cluster-lensing/.

Increasing the value of geospatial informatics with open approaches for Big Data

NASA Astrophysics Data System (ADS)

Percivall, G.; Bermudez, L. E.

2017-12-01

Open approaches to big data provide geoscientists with new capabilities to address problems of unmatched size and complexity. Consensus approaches for Big Geo Data have been addressed in multiple international workshops and testbeds organized by the Open Geospatial Consortium (OGC) in the past year. Participants came from government (NASA, ESA, USGS, NOAA, DOE); research (ORNL, NCSA, IU, JPL, CRIM, RENCI); industry (ESRI, Digital Globe, IBM, rasdaman); standards (JTC 1/NIST); and open source software communities. Results from the workshops and testbeds are documented in Testbed reports and a White Paper published by the OGC. The White Paper identifies the following set of use cases: Collection and Ingest: Remote sensed data processing; Data stream processing Prepare and Structure: SQL and NoSQL databases; Data linking; Feature identification Analytics and Visualization: Spatial-temporal analytics; Machine Learning; Data Exploration Modeling and Prediction: Integrated environmental models; Urban 4D models. Open implementations were developed in the Arctic Spatial Data Pilot using Discrete Global Grid Systems (DGGS) and in Testbeds using WPS and ESGF to publish climate predictions. Further development activities to advance open implementations of Big Geo Data include the following: Open Cloud Computing: Avoid vendor lock-in through API interoperability and Application portability. Open Source Extensions: Implement geospatial data representations in projects from Apache, Location Tech, and OSGeo. Investigate parallelization strategies for N-Dimensional spatial data. Geospatial Data Representations: Schemas to improve processing and analysis using geospatial concepts: Features, Coverages, DGGS. Use geospatial encodings like NetCDF and GeoPackge. Big Linked Geodata: Use linked data methods scaled to big geodata. Analysis Ready Data: Support "Download as last resort" and "Analytics as a service". Promote elements common to "datacubes."

Integrated protocol for reliable and fast quantification and documentation of electrophoresis gels.

PubMed

Rehbein, Peter; Schwalbe, Harald

2015-06-01

Quantitative analysis of electrophoresis gels is an important part in molecular cloning, as well as in protein expression and purification. Parallel quantifications in yield and purity can be most conveniently obtained from densitometric analysis. This communication reports a comprehensive, reliable and simple protocol for gel quantification and documentation, applicable for single samples and with special features for protein expression screens. As major component of the protocol, the fully annotated code of a proprietary open source computer program for semi-automatic densitometric quantification of digitized electrophoresis gels is disclosed. The program ("GelQuant") is implemented for the C-based macro-language of the widespread integrated development environment of IGOR Pro. Copyright © 2014 Elsevier Inc. All rights reserved.

Sleep: An Open-Source Python Software for Visualization, Analysis, and Staging of Sleep Data

PubMed Central

Combrisson, Etienne; Vallat, Raphael; Eichenlaub, Jean-Baptiste; O'Reilly, Christian; Lajnef, Tarek; Guillot, Aymeric; Ruby, Perrine M.; Jerbi, Karim

2017-01-01

We introduce Sleep, a new Python open-source graphical user interface (GUI) dedicated to visualization, scoring and analyses of sleep data. Among its most prominent features are: (1) Dynamic display of polysomnographic data, spectrogram, hypnogram and topographic maps with several customizable parameters, (2) Implementation of several automatic detection of sleep features such as spindles, K-complexes, slow waves, and rapid eye movements (REM), (3) Implementation of practical signal processing tools such as re-referencing or filtering, and (4) Display of main descriptive statistics including publication-ready tables and figures. The software package supports loading and reading raw EEG data from standard file formats such as European Data Format, in addition to a range of commercial data formats. Most importantly, Sleep is built on top of the VisPy library, which provides GPU-based fast and high-level visualization. As a result, it is capable of efficiently handling and displaying large sleep datasets. Sleep is freely available (http://visbrain.org/sleep) and comes with sample datasets and an extensive documentation. Novel functionalities will continue to be added and open-science community efforts are expected to enhance the capacities of this module. PMID:28983246

Sleep: An Open-Source Python Software for Visualization, Analysis, and Staging of Sleep Data.

PubMed

Combrisson, Etienne; Vallat, Raphael; Eichenlaub, Jean-Baptiste; O'Reilly, Christian; Lajnef, Tarek; Guillot, Aymeric; Ruby, Perrine M; Jerbi, Karim

2017-01-01

We introduce Sleep, a new Python open-source graphical user interface (GUI) dedicated to visualization, scoring and analyses of sleep data. Among its most prominent features are: (1) Dynamic display of polysomnographic data, spectrogram, hypnogram and topographic maps with several customizable parameters, (2) Implementation of several automatic detection of sleep features such as spindles, K-complexes, slow waves, and rapid eye movements (REM), (3) Implementation of practical signal processing tools such as re-referencing or filtering, and (4) Display of main descriptive statistics including publication-ready tables and figures. The software package supports loading and reading raw EEG data from standard file formats such as European Data Format, in addition to a range of commercial data formats. Most importantly, Sleep is built on top of the VisPy library, which provides GPU-based fast and high-level visualization. As a result, it is capable of efficiently handling and displaying large sleep datasets. Sleep is freely available (http://visbrain.org/sleep) and comes with sample datasets and an extensive documentation. Novel functionalities will continue to be added and open-science community efforts are expected to enhance the capacities of this module.

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

NASA Astrophysics Data System (ADS)

Strassmann, Kuno M.; Joos, Fortunat

2018-05-01

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

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

PubMed

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

2007-02-09

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

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

PubMed

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

2011-03-08

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

Low-Level Waste Regulation: Putting Principles Into Practice - 13297 - The Richard S. Hodes, M.D., Honor Lecture Award

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

Kennedy, James E.

2013-07-01

In carrying out its mission to ensure the safe use of radioactive materials for beneficial civilian purposes while protecting people and the environment, the U.S. Nuclear Regulatory Commission (NRC) adheres to its Principles of Good Regulation. The Principles-Independence, Openness, Efficiency, Clarity, and Reliability-apply to the agency as a whole in its decision-making and to the individual conduct of NRC employees. This paper describes the application of the Principles in a real-life staff activity, a guidance document used in the NRC's low-level radioactive waste (LLW) program, the Concentration Averaging and Encapsulation Branch Technical Position (CA BTP). The staff's process to revisemore » the document, as well as the final content of the document, were influenced by following the Principles. For example, consistent with the Openness Principle, the staff conducted a number of outreach activities and received many comments on three drafts of the document. Stakeholder comments affected the final staff positions in some cases. The revised CA BTP, once implemented, is expected to improve management and disposal of LLW in the United States. Its positions have an improved nexus to health and safety; are more performance-based than previously, thus providing licensees with options for how they achieve the required outcome of protecting an inadvertent human intruder into a disposal facility; and provide for disposal of more sealed radioactive sources, which are a potential threat to national security. (author)« less

ProDaMa: an open source Python library to generate protein structure datasets.

PubMed

Armano, Giuliano; Manconi, Andrea

2009-10-02

The huge difference between the number of known sequences and known tertiary structures has justified the use of automated methods for protein analysis. Although a general methodology to solve these problems has not been yet devised, researchers are engaged in developing more accurate techniques and algorithms whose training plays a relevant role in determining their performance. From this perspective, particular importance is given to the training data used in experiments, and researchers are often engaged in the generation of specialized datasets that meet their requirements. To facilitate the task of generating specialized datasets we devised and implemented ProDaMa, an open source Python library than provides classes for retrieving, organizing, updating, analyzing, and filtering protein data. ProDaMa has been used to generate specialized datasets useful for secondary structure prediction and to develop a collaborative web application aimed at generating and sharing protein structure datasets. The library, the related database, and the documentation are freely available at the URL http://iasc.diee.unica.it/prodama.

TEA: A Code Calculating Thermochemical Equilibrium Abundances

NASA Astrophysics Data System (ADS)

Blecic, Jasmina; Harrington, Joseph; Bowman, M. Oliver

2016-07-01

We present an open-source Thermochemical Equilibrium Abundances (TEA) code that calculates the abundances of gaseous molecular species. The code is based on the methodology of White et al. and Eriksson. It applies Gibbs free-energy minimization using an iterative, Lagrangian optimization scheme. Given elemental abundances, TEA calculates molecular abundances for a particular temperature and pressure or a list of temperature-pressure pairs. We tested the code against the method of Burrows & Sharp, the free thermochemical equilibrium code Chemical Equilibrium with Applications (CEA), and the example given by Burrows & Sharp. Using their thermodynamic data, TEA reproduces their final abundances, but with higher precision. We also applied the TEA abundance calculations to models of several hot-Jupiter exoplanets, producing expected results. TEA is written in Python in a modular format. There is a start guide, a user manual, and a code document in addition to this theory paper. TEA is available under a reproducible-research, open-source license via https://github.com/dzesmin/TEA.

What makes computational open source software libraries successful?

NASA Astrophysics Data System (ADS)

Bangerth, Wolfgang; Heister, Timo

2013-01-01

Software is the backbone of scientific computing. Yet, while we regularly publish detailed accounts about the results of scientific software, and while there is a general sense of which numerical methods work well, our community is largely unaware of best practices in writing the large-scale, open source scientific software upon which our discipline rests. This is particularly apparent in the commonly held view that writing successful software packages is largely the result of simply ‘being a good programmer’ when in fact there are many other factors involved, for example the social skill of community building. In this paper, we consider what we have found to be the necessary ingredients for successful scientific software projects and, in particular, for software libraries upon which the vast majority of scientific codes are built today. In particular, we discuss the roles of code, documentation, communities, project management and licenses. We also briefly comment on the impact on academic careers of engaging in software projects.

TEA: A CODE CALCULATING THERMOCHEMICAL EQUILIBRIUM ABUNDANCES

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

Blecic, Jasmina; Harrington, Joseph; Bowman, M. Oliver, E-mail: jasmina@physics.ucf.edu

2016-07-01

We present an open-source Thermochemical Equilibrium Abundances (TEA) code that calculates the abundances of gaseous molecular species. The code is based on the methodology of White et al. and Eriksson. It applies Gibbs free-energy minimization using an iterative, Lagrangian optimization scheme. Given elemental abundances, TEA calculates molecular abundances for a particular temperature and pressure or a list of temperature–pressure pairs. We tested the code against the method of Burrows and Sharp, the free thermochemical equilibrium code Chemical Equilibrium with Applications (CEA), and the example given by Burrows and Sharp. Using their thermodynamic data, TEA reproduces their final abundances, but withmore » higher precision. We also applied the TEA abundance calculations to models of several hot-Jupiter exoplanets, producing expected results. TEA is written in Python in a modular format. There is a start guide, a user manual, and a code document in addition to this theory paper. TEA is available under a reproducible-research, open-source license via https://github.com/dzesmin/TEA.« less

The impact of cigarette pack shape, size and opening: evidence from tobacco company documents.

PubMed

Kotnowski, Kathy; Hammond, David

2013-09-01

To use tobacco industry documents on cigarette pack shape, size and openings to identify industry findings on associations with brand imagery, product attributes, consumer perceptions and behaviour. Internal tobacco industry research and marketing documents obtained through court disclosure contained in the Legacy Tobacco Documents Library were searched using keywords related to pack shapes, sizes and opening methods. The search identified 66 documents related to consumer research and marketing plans on pack shape, size and openings, drawn from 1973 to 2002. Industry research consistently found that packs that deviated from the traditional flip-top box projected impressions of 'modern', 'elegant' and 'unique' brand imagery. Alternative pack shape and openings were identified as an effective means to communicate product attributes, particularly with regard to premium quality and smooth taste. Consumer studies consistently found that pack shape, size and opening style influenced perceptions of reduced product harm, and were often used to communicate a 'lighter' product. Slim, rounded, oval and booklet packs were found to be particularly appealing among young adults, and several studies demonstrated increased purchase interest for tobacco products presented in novel packaging shape or opening. Evidence from consumer tracking reports and company presentations indicate that pack innovations in shape or opening method increased market share of brands. Consumer research by the tobacco industry between 1973 and 2002 found that variations in packaging shape, size and opening method could influence brand appeal and risk perceptions and increase cigarette sales. © 2013 Society for the Study of Addiction.

Kauai Test Facility hazards assessment document

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

Swihart, A

1995-05-01

The Department of Energy Order 55003A requires facility-specific hazards assessment be prepared, maintained, and used for emergency planning purposes. This hazards assessment document describes the chemical and radiological hazards associated with the Kauai Test Facility, Barking Sands, Kauai, Hawaii. The Kauai Test Facility`s chemical and radiological inventories were screened according to potential airborne impact to onsite and offsite individuals. The air dispersion model, ALOHA, estimated pollutant concentrations downwind from the source of a release, taking into consideration the toxicological and physical characteristics of the release site, the atmospheric conditions, and the circumstances of the release. The greatest distance to themore » Early Severe Health Effects threshold is 4.2 kilometers. The highest emergency classification is a General Emergency at the {open_quotes}Main Complex{close_quotes} and a Site Area Emergency at the Kokole Point Launch Site. The Emergency Planning Zone for the {open_quotes}Main Complex{close_quotes} is 5 kilometers. The Emergency Planning Zone for the Kokole Point Launch Site is the Pacific Missile Range Facility`s site boundary.« less

The Experiment Factory: Standardizing Behavioral Experiments.

PubMed

Sochat, Vanessa V; Eisenberg, Ian W; Enkavi, A Zeynep; Li, Jamie; Bissett, Patrick G; Poldrack, Russell A

2016-01-01

The administration of behavioral and experimental paradigms for psychology research is hindered by lack of a coordinated effort to develop and deploy standardized paradigms. While several frameworks (Mason and Suri, 2011; McDonnell et al., 2012; de Leeuw, 2015; Lange et al., 2015) have provided infrastructure and methods for individual research groups to develop paradigms, missing is a coordinated effort to develop paradigms linked with a system to easily deploy them. This disorganization leads to redundancy in development, divergent implementations of conceptually identical tasks, disorganized and error-prone code lacking documentation, and difficulty in replication. The ongoing reproducibility crisis in psychology and neuroscience research (Baker, 2015; Open Science Collaboration, 2015) highlights the urgency of this challenge: reproducible research in behavioral psychology is conditional on deployment of equivalent experiments. A large, accessible repository of experiments for researchers to develop collaboratively is most efficiently accomplished through an open source framework. Here we present the Experiment Factory, an open source framework for the development and deployment of web-based experiments. The modular infrastructure includes experiments, virtual machines for local or cloud deployment, and an application to drive these components and provide developers with functions and tools for further extension. We release this infrastructure with a deployment (http://www.expfactory.org) that researchers are currently using to run a set of over 80 standardized web-based experiments on Amazon Mechanical Turk. By providing open source tools for both deployment and development, this novel infrastructure holds promise to bring reproducibility to the administration of experiments, and accelerate scientific progress by providing a shared community resource of psychological paradigms.

The Experiment Factory: Standardizing Behavioral Experiments

PubMed Central

Sochat, Vanessa V.; Eisenberg, Ian W.; Enkavi, A. Zeynep; Li, Jamie; Bissett, Patrick G.; Poldrack, Russell A.

2016-01-01

The administration of behavioral and experimental paradigms for psychology research is hindered by lack of a coordinated effort to develop and deploy standardized paradigms. While several frameworks (Mason and Suri, 2011; McDonnell et al., 2012; de Leeuw, 2015; Lange et al., 2015) have provided infrastructure and methods for individual research groups to develop paradigms, missing is a coordinated effort to develop paradigms linked with a system to easily deploy them. This disorganization leads to redundancy in development, divergent implementations of conceptually identical tasks, disorganized and error-prone code lacking documentation, and difficulty in replication. The ongoing reproducibility crisis in psychology and neuroscience research (Baker, 2015; Open Science Collaboration, 2015) highlights the urgency of this challenge: reproducible research in behavioral psychology is conditional on deployment of equivalent experiments. A large, accessible repository of experiments for researchers to develop collaboratively is most efficiently accomplished through an open source framework. Here we present the Experiment Factory, an open source framework for the development and deployment of web-based experiments. The modular infrastructure includes experiments, virtual machines for local or cloud deployment, and an application to drive these components and provide developers with functions and tools for further extension. We release this infrastructure with a deployment (http://www.expfactory.org) that researchers are currently using to run a set of over 80 standardized web-based experiments on Amazon Mechanical Turk. By providing open source tools for both deployment and development, this novel infrastructure holds promise to bring reproducibility to the administration of experiments, and accelerate scientific progress by providing a shared community resource of psychological paradigms. PMID:27199843

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.

ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level

PubMed Central

Rocca-Serra, Philippe; Brandizi, Marco; Maguire, Eamonn; Sklyar, Nataliya; Taylor, Chris; Begley, Kimberly; Field, Dawn; Harris, Stephen; Hide, Winston; Hofmann, Oliver; Neumann, Steffen; Sterk, Peter; Tong, Weida; Sansone, Susanna-Assunta

2010-01-01

Summary: The first open source software suite for experimentalists and curators that (i) assists in the annotation and local management of experimental metadata from high-throughput studies employing one or a combination of omics and other technologies; (ii) empowers users to uptake community-defined checklists and ontologies; and (iii) facilitates submission to international public repositories. Availability and Implementation: Software, documentation, case studies and implementations at http://www.isa-tools.org Contact: isatools@googlegroups.com PMID:20679334

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

Open Data and Open Science for better Research in the Geo and Space Domain

NASA Astrophysics Data System (ADS)

Ritschel, B.; Seelus, C.; Neher, G.; Iyemori, T.; Koyama, Y.; Yatagai, A. I.; Murayama, Y.; King, T. A.; Hughes, S.; Fung, S. F.; Galkin, I. A.; Hapgood, M. A.; Belehaki, A.

2015-12-01

Main open data principles had been worked out in the run-up and finally adopted in the Open Data Charta at the G8 summit in Lough Erne, Northern Ireland in June 2013. Important principles are also valid for science data, such as Open Data by Default, Quality and Quantity, Useable by All, Releasing Data for Improved Governance, Releasing Data for Innovation. There is also an explicit relationship to such areas of high values as earth observation, education and geospatial data. The European union implementation plan of the Open Data Charta identifies among other things objectives such as making data available in an open format, enabling semantic interoperability, ensuring quality, documentation and where appropriate reconciliation across different data sources, implementing software solutionsallowing easy management, publication or visualization of datasets and simplifying clearance of intellectual property rights.Open Science is not just a list of already for a longer time known principles but stands for a lot of initiatives and projects around a better handling of scientific data and openly shared scientific knowledge. It is also about transparency in methodology and collection of data, availability and reuse of scientific data, public accessibility to scientific communication and using of social media to facility scientific collaboration. Some projects are concentrating on open sharing of free and open source software and even further hardware in kind of processing capabilities. In addition question about the mashup of data and publication and an open peer review process are addressed.Following the principles of open data and open science the newest results of the collaboration efforts in mashing up the data servers related to the Japanese IUGONET, the European Union ESPAS and the GFZ ISDC semantic Web projects will be presented here. The semantic Web based approach for the mashup is focusing on the design and implementation of a common but still distributed data catalog based on semantical interoperability including the transparent access to data in relational data bases. References: https://www.gov.uk/government/uploads/system/uploads/attachment_data/file/207772/Open_Data_Charter.pdfhttp://www.openscience.org/blog/wp-content/uploads/2013/06/OpenSciencePoster.pdf

Biopython: freely available Python tools for computational molecular biology and bioinformatics

PubMed Central

Cock, Peter J. A.; Antao, Tiago; Chang, Jeffrey T.; Chapman, Brad A.; Cox, Cymon J.; Dalke, Andrew; Friedberg, Iddo; Hamelryck, Thomas; Kauff, Frank; Wilczynski, Bartek; de Hoon, Michiel J. L.

2009-01-01

Summary: The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning. Availability: Biopython is freely available, with documentation and source code at www.biopython.org under the Biopython license. Contact: All queries should be directed to the Biopython mailing lists, see www.biopython.org/wiki/_Mailing_listspeter.cock@scri.ac.uk. PMID:19304878

FRETBursts: An Open Source Toolkit for Analysis of Freely-Diffusing Single-Molecule FRET

PubMed Central

Lerner, Eitan; Chung, SangYoon; Weiss, Shimon; Michalet, Xavier

2016-01-01

Single-molecule Förster Resonance Energy Transfer (smFRET) allows probing intermolecular interactions and conformational changes in biomacromolecules, and represents an invaluable tool for studying cellular processes at the molecular scale. smFRET experiments can detect the distance between two fluorescent labels (donor and acceptor) in the 3-10 nm range. In the commonly employed confocal geometry, molecules are free to diffuse in solution. When a molecule traverses the excitation volume, it emits a burst of photons, which can be detected by single-photon avalanche diode (SPAD) detectors. The intensities of donor and acceptor fluorescence can then be related to the distance between the two fluorophores. While recent years have seen a growing number of contributions proposing improvements or new techniques in smFRET data analysis, rarely have those publications been accompanied by software implementation. In particular, despite the widespread application of smFRET, no complete software package for smFRET burst analysis is freely available to date. In this paper, we introduce FRETBursts, an open source software for analysis of freely-diffusing smFRET data. FRETBursts allows executing all the fundamental steps of smFRET bursts analysis using state-of-the-art as well as novel techniques, while providing an open, robust and well-documented implementation. Therefore, FRETBursts represents an ideal platform for comparison and development of new methods in burst analysis. We employ modern software engineering principles in order to minimize bugs and facilitate long-term maintainability. Furthermore, we place a strong focus on reproducibility by relying on Jupyter notebooks for FRETBursts execution. Notebooks are executable documents capturing all the steps of the analysis (including data files, input parameters, and results) and can be easily shared to replicate complete smFRET analyzes. Notebooks allow beginners to execute complex workflows and advanced users to customize the analysis for their own needs. By bundling analysis description, code and results in a single document, FRETBursts allows to seamless share analysis workflows and results, encourages reproducibility and facilitates collaboration among researchers in the single-molecule community. PMID:27532626

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

PubMed

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

2017-03-01

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

dsmcFoam+: An OpenFOAM based direct simulation Monte Carlo solver

NASA Astrophysics Data System (ADS)

White, C.; Borg, M. K.; Scanlon, T. J.; Longshaw, S. M.; John, B.; Emerson, D. R.; Reese, J. M.

2018-03-01

dsmcFoam+ is a direct simulation Monte Carlo (DSMC) solver for rarefied gas dynamics, implemented within the OpenFOAM software framework, and parallelised with MPI. It is open-source and released under the GNU General Public License in a publicly available software repository that includes detailed documentation and tutorial DSMC gas flow cases. This release of the code includes many features not found in standard dsmcFoam, such as molecular vibrational and electronic energy modes, chemical reactions, and subsonic pressure boundary conditions. Since dsmcFoam+ is designed entirely within OpenFOAM's C++ object-oriented framework, it benefits from a number of key features: the code emphasises extensibility and flexibility so it is aimed first and foremost as a research tool for DSMC, allowing new models and test cases to be developed and tested rapidly. All DSMC cases are as straightforward as setting up any standard OpenFOAM case, as dsmcFoam+ relies upon the standard 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 a DSMC simulation is not typical of most OpenFOAM applications. We show that dsmcFoam+ compares well to other well-known DSMC codes and to analytical solutions in terms of benchmark results.

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.

jqcML: an open-source java API for mass spectrometry quality control data in the qcML format.

PubMed

Bittremieux, Wout; Kelchtermans, Pieter; Valkenborg, Dirk; Martens, Lennart; Laukens, Kris

2014-07-03

The awareness that systematic quality control is an essential factor to enable the growth of proteomics into a mature analytical discipline has increased over the past few years. To this aim, a controlled vocabulary and document structure have recently been proposed by Walzer et al. to store and disseminate quality-control metrics for mass-spectrometry-based proteomics experiments, called qcML. To facilitate the adoption of this standardized quality control routine, we introduce jqcML, a Java application programming interface (API) for the qcML data format. First, jqcML provides a complete object model to represent qcML data. Second, jqcML provides the ability to read, write, and work in a uniform manner with qcML data from different sources, including the XML-based qcML file format and the relational database qcDB. Interaction with the XML-based file format is obtained through the Java Architecture for XML Binding (JAXB), while generic database functionality is obtained by the Java Persistence API (JPA). jqcML is released as open-source software under the permissive Apache 2.0 license and can be downloaded from https://bitbucket.org/proteinspector/jqcml .

An Open-source Community Web Site To Support Ground-Water Model Testing

NASA Astrophysics Data System (ADS)

Kraemer, S. R.; Bakker, M.; Craig, J. R.

2007-12-01

A community wiki wiki web site has been created as a resource to support ground-water model development and testing. The Groundwater Gourmet wiki is a repository for user supplied analytical and numerical recipes, howtos, and examples. Members are encouraged to submit analytical solutions, including source code and documentation. A diversity of code snippets are sought in a variety of languages, including Fortran, C, C++, Matlab, Python. In the spirit of a wiki, all contributions may be edited and altered by other users, and open source licensing is promoted. Community accepted contributions are graduated into the library of analytic solutions and organized into either a Strack (Groundwater Mechanics, 1989) or Bruggeman (Analytical Solutions of Geohydrological Problems, 1999) classification. The examples section of the wiki are meant to include laboratory experiments (e.g., Hele Shaw), classical benchmark problems (e.g., Henry Problem), and controlled field experiments (e.g., Borden landfill and Cape Cod tracer tests). Although this work was reviewed by EPA and approved for publication, it may not necessarily reflect official Agency policy. Mention of trade names or commercial products does not constitute endorsement or recommendation for use.

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

PubMed Central

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

2015-01-01

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

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

PubMed

Haarbrandt, Birger; Tute, Erik; Marschollek, Michael

2016-10-01

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

Toward a Wireless Open Source Instrument: Functional Near-infrared Spectroscopy in Mobile Neuroergonomics and BCI Applications

PubMed Central

von Lühmann, Alexander; Herff, Christian; Heger, Dominic; Schultz, Tanja

2015-01-01

Brain-Computer Interfaces (BCIs) and neuroergonomics research have high requirements regarding robustness and mobility. Additionally, fast applicability and customization are desired. Functional Near-Infrared Spectroscopy (fNIRS) is an increasingly established technology with a potential to satisfy these conditions. EEG acquisition technology, currently one of the main modalities used for mobile brain activity assessment, is widely spread and open for access and thus easily customizable. fNIRS technology on the other hand has either to be bought as a predefined commercial solution or developed from scratch using published literature. To help reducing time and effort of future custom designs for research purposes, we present our approach toward an open source multichannel stand-alone fNIRS instrument for mobile NIRS-based neuroimaging, neuroergonomics and BCI/BMI applications. The instrument is low-cost, miniaturized, wireless and modular and openly documented on www.opennirs.org. It provides features such as scalable channel number, configurable regulated light intensities, programmable gain and lock-in amplification. In this paper, the system concept, hardware, software and mechanical implementation of the lightweight stand-alone instrument are presented and the evaluation and verification results of the instrument's hardware and physiological fNIRS functionality are described. Its capability to measure brain activity is demonstrated by qualitative signal assessments and a quantitative mental arithmetic based BCI study with 12 subjects. PMID:26617510

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

PubMed

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

2015-01-01

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

MzJava: An open source library for mass spectrometry data processing.

PubMed

Horlacher, Oliver; Nikitin, Frederic; Alocci, Davide; Mariethoz, Julien; Müller, Markus; Lisacek, Frederique

2015-11-03

Mass spectrometry (MS) is a widely used and evolving technique for the high-throughput identification of molecules in biological samples. The need for sharing and reuse of code among bioinformaticians working with MS data prompted the design and implementation of MzJava, an open-source Java Application Programming Interface (API) for MS related data processing. MzJava provides data structures and algorithms for representing and processing mass spectra and their associated biological molecules, such as metabolites, glycans and peptides. MzJava includes functionality to perform mass calculation, peak processing (e.g. centroiding, filtering, transforming), spectrum alignment and clustering, protein digestion, fragmentation of peptides and glycans as well as scoring functions for spectrum-spectrum and peptide/glycan-spectrum matches. For data import and export MzJava implements readers and writers for commonly used data formats. For many classes support for the Hadoop MapReduce (hadoop.apache.org) and Apache Spark (spark.apache.org) frameworks for cluster computing was implemented. The library has been developed applying best practices of software engineering. To ensure that MzJava contains code that is correct and easy to use the library's API was carefully designed and thoroughly tested. MzJava is an open-source project distributed under the AGPL v3.0 licence. MzJava requires Java 1.7 or higher. Binaries, source code and documentation can be downloaded from http://mzjava.expasy.org and https://bitbucket.org/sib-pig/mzjava. This article is part of a Special Issue entitled: Computational Proteomics. Copyright © 2015 Elsevier B.V. All rights reserved.

Information Management Systems for Monitoring and Documenting World Heritage - the Silk Roads Chris

NASA Astrophysics Data System (ADS)

Vileikis, O.; Serruys, E.; Dumont, B.; van Balen, K.; Santana Quinterod, M.; de Maeyer, P.; Tigny, V.

2012-07-01

This paper discusses the application of Information Management Systems (IMS) for documenting and monitoring World Heritage (WH) properties. The application of IMS in WH can support all stakeholders involved in conservation, and management of cultural heritage by more easily inventorying, mining and exchanging information from multiple sources based on international standards. Moreover, IMS could assist in detecting damages and preparing management strategies to mitigate risks, and slowing down the deterioration of the integrity of WH properties. The case study of the Silk Roads Cultural Heritage Resource Information System (CHRIS), a Belgian Federal Science Policy Office funded project, illustrates the capabilities of IMS in the context of the nomination of the Central Asian Silk Roads on the WH List. This multi-lingual, web-based IMS will act as a collaborative platform allowing for the completion of improved transnational nomination dossiers and subsequent monitoring activities with all necessary baseline information to easily verify consistency and quality of the proposal. The Silk Roads CHRIS Geospatial Content Management System uses open source technologies and allows to georeference data from different scales and sources including data from field recording methods and combine it with historical and heritage features documented through various means such as textual descriptions, documents, photographs, 3D models or videos. Moreover, tailored maps can also be generated by overlaying a selection of available layers and then be exported to support the nomination dossier. Finally, by using this innovative information and decision support system, the State Parties and other interested stakeholders will have access to a complete nomination dossier and could therefore respond more effectively to hazards and disaster phenomena.

Mapping the literature of pediatric nursing: update and implications for library services

PubMed Central

Watwood, Carol L.

2016-01-01

Objective The purpose of this study was to identify core journals and other types of literature cited in four major pediatric nursing journals and to characterize coverage of these resources in major bibliographic databases. The study was part of the “Mapping the Literature of Nursing Project” of the Medical Library Association's Nursing and Allied Health Resource Section. It updates a similar analysis published in 2006 and determines whether citation patterns have changed over time. Methods Cited references from articles published in 4 pediatric nursing journals between 2011 and 2013 were collected. Cited journal titles were ranked according to number of times cited and analyzed according to Bradford's Law of Scattering and the 80/20 rule to identify the most frequently cited journals. Five databases were surveyed to assess the coverage of the most-often-cited journals. The most frequently cited non-journal sources were also identified. Results Journals were the most frequently cited sources, followed by books, government documents, Internet resources, and miscellaneous resources. Most cited sources were cited within ten years of their publication, which was particularly true for government documents and Internet resources. Scopus had complete coverage of the most frequently cited journals, whereas PubMed had nearly complete coverage. Conclusions Compared with the 2006 study, the list of top-cited journals referenced by pediatric nursing researchers has remained relatively stable, but the number of cited journal titles has increased. Book citations have declined, and Internet and government document references have increased. These findings suggest that librarians should retain subscriptions to frequently cited journal titles, provide efficient document delivery of articles from infrequently used journals, de-emphasize but not eliminate books, and connect patrons with useful open-access Internet resources. PMID:27822148

Mapping the literature of pediatric nursing: update and implications for library services.

PubMed

Watwood, Carol L

2016-10-01

The purpose of this study was to identify core journals and other types of literature cited in four major pediatric nursing journals and to characterize coverage of these resources in major bibliographic databases. The study was part of the "Mapping the Literature of Nursing Project" of the Medical Library Association's Nursing and Allied Health Resource Section. It updates a similar analysis published in 2006 and determines whether citation patterns have changed over time. Cited references from articles published in 4 pediatric nursing journals between 2011 and 2013 were collected. Cited journal titles were ranked according to number of times cited and analyzed according to Bradford's Law of Scattering and the 80/20 rule to identify the most frequently cited journals. Five databases were surveyed to assess the coverage of the most-often-cited journals. The most frequently cited non-journal sources were also identified. Journals were the most frequently cited sources, followed by books, government documents, Internet resources, and miscellaneous resources. Most cited sources were cited within ten years of their publication, which was particularly true for government documents and Internet resources. Scopus had complete coverage of the most frequently cited journals, whereas PubMed had nearly complete coverage. Compared with the 2006 study, the list of top-cited journals referenced by pediatric nursing researchers has remained relatively stable, but the number of cited journal titles has increased. Book citations have declined, and Internet and government document references have increased. These findings suggest that librarians should retain subscriptions to frequently cited journal titles, provide efficient document delivery of articles from infrequently used journals, de-emphasize but not eliminate books, and connect patrons with useful open-access Internet resources.

75 FR 41102 - Energy Conservation Program: Re-Opening of the Public Comment Period for Commercial Refrigeration...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-15

... Conservation Program: Re-Opening of the Public Comment Period for Commercial Refrigeration Equipment AGENCY... document for commercial refrigeration equipment and provide notice of a public meeting. The NOPM provided... the framework document for commercial refrigeration equipment is to be re-opened from July 15, 2010 to...

Using Feedback from Data Consumers to Capture Quality Information on Environmental Research Data

NASA Astrophysics Data System (ADS)

Devaraju, A.; Klump, J. F.

2015-12-01

Data quality information is essential to facilitate reuse of Earth science data. Recorded quality information must be sufficient for other researchers to select suitable data sets for their analysis and confirm the results and conclusions. In the research data ecosystem, several entities are responsible for data quality. Data producers (researchers and agencies) play a major role in this aspect as they often include validation checks or data cleaning as part of their work. It is possible that the quality information is not supplied with published data sets; if it is available, the descriptions might be incomplete, ambiguous or address specific quality aspects. Data repositories have built infrastructures to share data, but not all of them assess data quality. They normally provide guidelines of documenting quality information. Some suggests that scholarly and data journals should take a role in ensuring data quality by involving reviewers to assess data sets used in articles, and incorporating data quality criteria in the author guidelines. However, this mechanism primarily addresses data sets submitted to journals. We believe that data consumers will complement existing entities to assess and document the quality of published data sets. This has been adopted in crowd-source platforms such as Zooniverse, OpenStreetMap, Wikipedia, Mechanical Turk and Tomnod. This paper presents a framework designed based on open source tools to capture and share data users' feedback on the application and assessment of research data. The framework comprises a browser plug-in, a web service and a data model such that feedback can be easily reported, retrieved and searched. The feedback records are also made available as Linked Data to promote integration with other sources on the Web. Vocabularies from Dublin Core and PROV-O are used to clarify the source and attribution of feedback. The application of the framework is illustrated with the CSIRO's Data Access Portal.

Using the General Mission Analysis Tool (GMAT)

NASA Technical Reports Server (NTRS)

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

2017-01-01

This is a software tutorial and presentation demonstrating the application of the General Mission Analysis Tool (GMAT). These slides will be used to accompany the demonstration. The demonstration discusses GMAT basics, then presents a detailed example of GMAT application to the Transiting Exoplanet Survey Satellite (TESS) mission. This talk is a combination of existing presentations and material; system user guide and technical documentation; a GMAT basics and overview, and technical presentations from the TESS projects on their application of GMAT to critical mission design. The GMAT basics slides are taken from the open source training material. The TESS slides are a streamlined version of the CDR package provided by the project with SBU and ITAR data removed by the TESS project. Slides for navigation and optimal control are borrowed from system documentation and training material.

Evaluation of the free, open source software WordPress as electronic portfolio system in undergraduate medical education.

PubMed

Avila, Javier; Sostmann, Kai; Breckwoldt, Jan; Peters, Harm

2016-06-03

Electronic portfolios (ePortfolios) are used to document and support learning activities. E-portfolios with mobile capabilities allow even more flexibility. However, the development or acquisition of ePortfolio software is often costly, and at the same time, commercially available systems may not sufficiently fit the institution's needs. The aim of this study was to design and evaluate an ePortfolio system with mobile capabilities using a commercially free and open source software solution. We created an online ePortfolio environment using the blogging software WordPress based on reported capability features of such software by a qualitative weight and sum method. Technical implementation and usability were evaluated by 25 medical students during their clinical training by quantitative and qualitative means using online questionnaires and focus groups. The WordPress ePortfolio environment allowed students a broad spectrum of activities - often documented via mobile devices - like collection of multimedia evidences, posting reflections, messaging, web publishing, ePortfolio searches, collaborative learning, knowledge management in a content management system including a wiki and RSS feeds, and the use of aid tools for studying. The students' experience with WordPress revealed a few technical problems, and this report provides workarounds. The WordPress ePortfolio was rated positively by the students as a content management system (67 % of the students), for exchange with other students (74 %), as a note pad for reflections (53 %) and for its potential as an information source for assessment (48 %) and exchange with a mentor (68 %). On the negative side, 74 % of the students in this pilot study did not find it easy to get started with the system, and 63 % rated the ePortfolio as not being user-friendly. Qualitative analysis indicated a need for more introductory information and training. It is possible to build an advanced ePortfolio system with mobile capabilities with the free and open source software WordPress. This allows institutions without proprietary software to build a sophisticated ePortfolio system adapted to their needs with relatively few resources. The implementation of WordPress should be accompanied by introductory courses in the use of the software and its apps in order to facilitate its usability.

18 CFR 35.9 - Requirements for filing rate schedules, tariffs or service agreements.

Code of Federal Regulations, 2010 CFR

2010-04-01

... entire document except as provided in paragraphs (b) and (c) of this section. (b) Open Access...) OATT and other open access documents filed by Independent System Operators or Regional Transmission...

18 CFR 35.9 - Requirements for filing rate schedules, tariffs or service agreements.

Code of Federal Regulations, 2011 CFR

2011-04-01

... entire document except as provided in paragraphs (b) and (c) of this section. (b) Open Access...) OATT and other open access documents filed by Independent System Operators or Regional Transmission...

WebProtégé: a collaborative Web-based platform for editing biomedical ontologies.

PubMed

Horridge, Matthew; Tudorache, Tania; Nuylas, Csongor; Vendetti, Jennifer; Noy, Natalya F; Musen, Mark A

2014-08-15

WebProtégé is an open-source Web application for editing OWL 2 ontologies. It contains several features to aid collaboration, including support for the discussion of issues, change notification and revision-based change tracking. WebProtégé also features a simple user interface, which is geared towards editing the kinds of class descriptions and annotations that are prevalent throughout biomedical ontologies. Moreover, it is possible to configure the user interface using views that are optimized for editing Open Biomedical Ontology (OBO) class descriptions and metadata. Some of these views are shown in the Supplementary Material and can be seen in WebProtégé itself by configuring the project as an OBO project. WebProtégé is freely available for use on the Web at http://webprotege.stanford.edu. It is implemented in Java and JavaScript using the OWL API and the Google Web Toolkit. All major browsers are supported. For users who do not wish to host their ontologies on the Stanford servers, WebProtégé is available as a Web app that can be run locally using a Servlet container such as Tomcat. Binaries, source code and documentation are available under an open-source license at http://protegewiki.stanford.edu/wiki/WebProtege. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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

PubMed

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

2006-11-13

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

Actionable, long-term stable and semantic web compatible identifiers for access to biological collection objects

PubMed Central

Hyam, Roger; Hagedorn, Gregor; Chagnoux, Simon; Röpert, Dominik; Casino, Ana; Droege, Gabi; Glöckler, Falko; Gödderz, Karsten; Groom, Quentin; Hoffmann, Jana; Holleman, Ayco; Kempa, Matúš; Koivula, Hanna; Marhold, Karol; Nicolson, Nicky; Smith, Vincent S.; Triebel, Dagmar

2017-01-01

With biodiversity research activities being increasingly shifted to the web, the need for a system of persistent and stable identifiers for physical collection objects becomes increasingly pressing. The Consortium of European Taxonomic Facilities agreed on a common system of HTTP-URI-based stable identifiers which is now rolled out to its member organizations. The system follows Linked Open Data principles and implements redirection mechanisms to human-readable and machine-readable representations of specimens facilitating seamless integration into the growing semantic web. The implementation of stable identifiers across collection organizations is supported with open source provider software scripts, best practices documentations and recommendations for RDF metadata elements facilitating harmonized access to collection information in web portals. Database URL: http://cetaf.org/cetaf-stable-identifiers PMID:28365724

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

Code of Federal Regulations, 2010 CFR

2010-07-01

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

"Pleiades Visions" for organ solo: A composition supported by documented research

NASA Astrophysics Data System (ADS)

Whitehouse, Matthew Robert

Pleiades Visions is a three-movement work for organ solo inspired by indigenous music and mythology associated with the Pleiades (Seven Sisters) star cluster. Three cultural groups are represented in Pleiades Visions. The first movement, entitled "Uluru," draws from Australian Aboriginal music and mythology. The second movement, entitled "...life on other worlds," is based loosely on a Quechan (Yuman) Indian song. The concluding movement, entitled "Mauna Kea," is inspired by the opening lines of the Kumulipo, a creation chant of the Native Hawaiian culture. The source material for Pleiades Visions was identified through research incorporating techniques from the fields of cultural astronomy and ethnomusicology. This research represents a new line of inquiry for both fields. This document situates Pleiades Visions in the context of the organ literature, and suggests that Pleiades Visions might be the first organ work with a cultural astronomy inspiration. It also describes the research undergirding Pleiades Visions, demonstrates the manner in which that research informed the composition of the work, and addresses issues surrounding the use of indigenous source material in a culturally sensitive manner.

a Heritage Inventory for Documenting Endangered Archaeology in the Middle East and North Africa

NASA Astrophysics Data System (ADS)

Sheldrick, N.; Zerbini, A.

2017-08-01

The heritage of the Middle East and North Africa is under growing threat from a variety of factors, including agricultural expansion, urban development, looting, and conflict. Recording and documenting this heritage is therefore a key priority to aid heritage practitioners tasked with protecting sites and evaluating their condition on the ground. The Endangered Archaeology in the Middle East and North Africa (EAMENA) project has developed a methodology for the identification, documentation, analysis, and monitoring of sites across the region to aid heritage professionals in these efforts. The project uses remote sensing techniques along with traditional archaeological research and prospection methods to collect data, which are stored and managed in a custom-designed database adapted from open-source Arches v.3 software, using CIDOC CRM standards and controlled vocabularies. In addition to these activities, the EAMENA project has initiated an international conference series and training workshops to support and establish partnerships with heritage professionals and institutions across the region.

In Search of Social Translucence: An Audit Log Analysis of Handoff Documentation Views and Updates.

PubMed

Jiang, Silis Y; Hum, R Stanley; Vawdrey, David; Mamykina, Lena

2015-01-01

Communication and information sharing are critical parts of teamwork in the hospital; however, achieving open and fluid communication can be challenging. Finding specific patient information within documentation can be difficult. Recent studies on handoff documentation tools show that resident handoff notes are increasingly used as an alternative information source by non-physician clinicians. Previous findings also show that residents have become aware of this unintended use. This study investigated the alignment of resident note updating patterns and team note viewing patterns based on usage log data of handoff notes. Qualitative interviews with clinicians were used to triangulate findings based on the log analysis. The study found that notes that were frequently updated were viewed significantly more frequently than notes updated less often (p < 2.2 × 10(-16)). Almost 44% of all notes had aligned frequency of views and updates. The considerable percentage (56%) of mismatched note utilization suggests an opportunity for improvement.

MSAViewer: interactive JavaScript visualization of multiple sequence alignments.

PubMed

Yachdav, Guy; Wilzbach, Sebastian; Rauscher, Benedikt; Sheridan, Robert; Sillitoe, Ian; Procter, James; Lewis, Suzanna E; Rost, Burkhard; Goldberg, Tatyana

2016-11-15

The MSAViewer is a quick and easy visualization and analysis JavaScript component for Multiple Sequence Alignment data of any size. Core features include interactive navigation through the alignment, application of popular color schemes, sorting, selecting and filtering. The MSAViewer is 'web ready': written entirely in JavaScript, compatible with modern web browsers and does not require any specialized software. The MSAViewer is part of the BioJS collection of components. The MSAViewer is released as open source software under the Boost Software License 1.0. Documentation, source code and the viewer are available at http://msa.biojs.net/Supplementary information: Supplementary data are available at Bioinformatics online. msa@bio.sh. © The Author 2016. Published by Oxford University Press.

ProtVista: visualization of protein sequence annotations.

PubMed

Watkins, Xavier; Garcia, Leyla J; Pundir, Sangya; Martin, Maria J

2017-07-01

ProtVista is a comprehensive visualization tool for the graphical representation of protein sequence features in the UniProt Knowledgebase, experimental proteomics and variation public datasets. The complexity and relationships in this wealth of data pose a challenge in interpretation. Integrative visualization approaches such as provided by ProtVista are thus essential for researchers to understand the data and, for instance, discover patterns affecting function and disease associations. ProtVista is a JavaScript component released as an open source project under the Apache 2 License. Documentation and source code are available at http://ebi-uniprot.github.io/ProtVista/ . martin@ebi.ac.uk. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

MSAViewer: interactive JavaScript visualization of multiple sequence alignments

PubMed Central

Yachdav, Guy; Wilzbach, Sebastian; Rauscher, Benedikt; Sheridan, Robert; Sillitoe, Ian; Procter, James; Lewis, Suzanna E.; Rost, Burkhard; Goldberg, Tatyana

2016-01-01

Summary: The MSAViewer is a quick and easy visualization and analysis JavaScript component for Multiple Sequence Alignment data of any size. Core features include interactive navigation through the alignment, application of popular color schemes, sorting, selecting and filtering. The MSAViewer is ‘web ready’: written entirely in JavaScript, compatible with modern web browsers and does not require any specialized software. The MSAViewer is part of the BioJS collection of components. Availability and Implementation: The MSAViewer is released as open source software under the Boost Software License 1.0. Documentation, source code and the viewer are available at http://msa.biojs.net/. Supplementary information: Supplementary data are available at Bioinformatics online. Contact: msa@bio.sh PMID:27412096

nodeGame: Real-time, synchronous, online experiments in the browser.

PubMed

Balietti, Stefano

2017-10-01

nodeGame is a free, open-source JavaScript/ HTML5 framework for conducting synchronous experiments online and in the lab directly in the browser window. It is specifically designed to support behavioral research along three dimensions: (i) larger group sizes, (ii) real-time (but also discrete time) experiments, and (iii) batches of simultaneous experiments. nodeGame has a modular source code, and defines an API (application programming interface) through which experimenters can create new strategic environments and configure the platform. With zero-install, nodeGame can run on a great variety of devices, from desktop computers to laptops, smartphones, and tablets. The current version of the software is 3.0, and extensive documentation is available on the wiki pages at http://nodegame.org .

Impact of problem finding on the quality of authentic open inquiry science research projects

NASA Astrophysics Data System (ADS)

Labanca, Frank

2008-11-01

Problem finding is a creative process whereby individuals develop original ideas for study. Secondary science students who successfully participate in authentic, novel, open inquiry studies must engage in problem finding to determine viable and suitable topics. This study examined problem finding strategies employed by students who successfully completed and presented the results of their open inquiry research at the 2007 Connecticut Science Fair and the 2007 International Science and Engineering Fair. A multicase qualitative study was framed through the lenses of creativity, inquiry strategies, and situated cognition learning theory. Data were triangulated by methods (interviews, document analysis, surveys) and sources (students, teachers, mentors, fair directors, documents). The data demonstrated that the quality of student projects was directly impacted by the quality of their problem finding. Effective problem finding was a result of students using resources from previous, specialized experiences. They had a positive self-concept and a temperament for both the creative and logical perspectives of science research. Successful problem finding was derived from an idiosyncratic, nonlinear, and flexible use and understanding of inquiry. Finally, problem finding was influenced and assisted by the community of practicing scientists, with whom the students had an exceptional ability to communicate effectively. As a result, there appears to be a juxtaposition of creative and logical/analytical thought for open inquiry that may not be present in other forms of inquiry. Instructional strategies are suggested for teachers of science research students to improve the quality of problem finding for their students and their subsequent research projects.

An assessment of transient hydraulics phenomena and its characterization

NASA Technical Reports Server (NTRS)

Mortimer, R. W.

1974-01-01

A systematic search of the open literature was performed with the purpose of identifying the causes, effects, and characterization (modelling and solution techniques) of transient hydraulics phenomena. The governing partial differential equations are presented which were found to be used most often in the literature. Detail survey sheets are shown which contain the type of hydraulics problem, the cause, the modelling, the solution technique utilized, and experimental verification used for each paper. References and source documents are listed and a discussion of the purpose and accomplishments of the study is presented.

Improved document image segmentation algorithm using multiresolution morphology

NASA Astrophysics Data System (ADS)

Bukhari, Syed Saqib; Shafait, Faisal; Breuel, Thomas M.

2011-01-01

Page segmentation into text and non-text elements is an essential preprocessing step before optical character recognition (OCR) operation. In case of poor segmentation, an OCR classification engine produces garbage characters due to the presence of non-text elements. This paper describes modifications to the text/non-text segmentation algorithm presented by Bloomberg,1 which is also available in his open-source Leptonica library.2The modifications result in significant improvements and achieved better segmentation accuracy than the original algorithm for UW-III, UNLV, ICDAR 2009 page segmentation competition test images and circuit diagram datasets.

The Einstein Dossiers: Science and Politics - Einstein's Berlin Period with an Appendix on Einstein's FBI File

NASA Astrophysics Data System (ADS)

Grundmann, Siegfried

In 1919 the Prussian Ministry of Science, Arts and Culture opened a dossier on "Einstein's Theory of Relativity." It was rediscovered by the author in 1961 and is used in conjunction with numerous other subsequently identified 'Einstein' files as the basis of this fascinating book. In particular, the author carefully scrutinizes Einstein's FBI file from 1950-55 against mostly unpublished material from European including Soviet sources and presents hitherto unknown documentation on Einstein's alleged contacts with the German Communist Party and the Comintern.

Multidisciplinary Analysis and Optimization Generation 1 and Next Steps

NASA Technical Reports Server (NTRS)

Naiman, Cynthia Gutierrez

2008-01-01

The Multidisciplinary Analysis & Optimization Working Group (MDAO WG) of the Systems Analysis Design & Optimization (SAD&O) discipline in the Fundamental Aeronautics Program s Subsonic Fixed Wing (SFW) project completed three major milestones during Fiscal Year (FY)08: "Requirements Definition" Milestone (1/31/08); "GEN 1 Integrated Multi-disciplinary Toolset" (Annual Performance Goal) (6/30/08); and "Define Architecture & Interfaces for Next Generation Open Source MDAO Framework" Milestone (9/30/08). Details of all three milestones are explained including documentation available, potential partner collaborations, and next steps in FY09.

Muscle: a source of progenitor cells for bone fracture healing.

PubMed

Henrotin, Yves

2011-12-22

Bone repair failure is a major complication of open fracture, leading to non-union of broken bone extremities and movement at the fracture site. This results in a serious disability for patients. The role played by the periosteum and bone marrow progenitors in bone repair is now well documented. In contrast, limited information is available on the role played by myogenic progenitor cells in bone repair. In a recent article published in BMC Musculoskeletal Disorders, Liu et al. compared the presence of myogenic progenitor (MyoD lineage cells) in closed and open fractures. They showed that myogenic progenitors are present in open, but not closed fractures, suggesting that muscle satellite cells may colonize the fracture site in the absence of intact periosteum. Interestingly, these progenitors sequentially expressed a chondrogenic and, thereafter, an osteoblastic phenotype, suggestive of a functional role in the repair process. This finding opens up new perspectives for the research of orthopedic surgical methods, which could maximize myogenic progenitor access and mobilization to augment bone repair. Please see related article: http://www.biomedcentral.com/1471-2474/12/288.

Fairbanks International Airport, Transportation & Public Facilities, State

Science.gov Websites

, Alaska 99709 Phone: (907) 474-2500 Fax: (907) 474-2513 Email FAI Hours of Operation: FAI is open 24 hours a day. Passenger screening checkpoints are open: 4:00 a.m. to 2:00 a.m. daily, including holidays PDF document FAI to Host Open House at La Quinta Inn & Suites PDF document FAI Helps Combat Opioid

OpenFDA: an innovative platform providing access to a wealth of FDA's publicly available data.

PubMed

Kass-Hout, Taha A; Xu, Zhiheng; Mohebbi, Matthew; Nelsen, Hans; Baker, Adam; Levine, Jonathan; Johanson, Elaine; Bright, Roselie A

2016-05-01

The objective of openFDA is to facilitate access and use of big important Food and Drug Administration public datasets by developers, researchers, and the public through harmonization of data across disparate FDA datasets provided via application programming interfaces (APIs). Using cutting-edge technologies deployed on FDA's new public cloud computing infrastructure, openFDA provides open data for easier, faster (over 300 requests per second per process), and better access to FDA datasets; open source code and documentation shared on GitHub for open community contributions of examples, apps and ideas; and infrastructure that can be adopted for other public health big data challenges. Since its launch on June 2, 2014, openFDA has developed four APIs for drug and device adverse events, recall information for all FDA-regulated products, and drug labeling. There have been more than 20 million API calls (more than half from outside the United States), 6000 registered users, 20,000 connected Internet Protocol addresses, and dozens of new software (mobile or web) apps developed. A case study demonstrates a use of openFDA data to understand an apparent association of a drug with an adverse event. With easier and faster access to these datasets, consumers worldwide can learn more about FDA-regulated products. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved.

OpenFDA: an innovative platform providing access to a wealth of FDA’s publicly available data

PubMed Central

Kass-Hout, Taha A; Mohebbi, Matthew; Nelsen, Hans; Baker, Adam; Levine, Jonathan; Johanson, Elaine; Bright, Roselie A

2016-01-01

Objective The objective of openFDA is to facilitate access and use of big important Food and Drug Administration public datasets by developers, researchers, and the public through harmonization of data across disparate FDA datasets provided via application programming interfaces (APIs). Materials and Methods Using cutting-edge technologies deployed on FDA’s new public cloud computing infrastructure, openFDA provides open data for easier, faster (over 300 requests per second per process), and better access to FDA datasets; open source code and documentation shared on GitHub for open community contributions of examples, apps and ideas; and infrastructure that can be adopted for other public health big data challenges. Results Since its launch on June 2, 2014, openFDA has developed four APIs for drug and device adverse events, recall information for all FDA-regulated products, and drug labeling. There have been more than 20 million API calls (more than half from outside the United States), 6000 registered users, 20,000 connected Internet Protocol addresses, and dozens of new software (mobile or web) apps developed. A case study demonstrates a use of openFDA data to understand an apparent association of a drug with an adverse event. Conclusion With easier and faster access to these datasets, consumers worldwide can learn more about FDA-regulated products. PMID:26644398

PlasmaPy: initial development of a Python package for plasma physics

NASA Astrophysics Data System (ADS)

Murphy, Nicholas; Leonard, Andrew J.; Stańczak, Dominik; Haggerty, Colby C.; Parashar, Tulasi N.; Huang, Yu-Min; PlasmaPy Community

2017-10-01

We report on initial development of PlasmaPy: an open source community-driven Python package for plasma physics. PlasmaPy seeks to provide core functionality that is needed for the formation of a fully open source Python ecosystem for plasma physics. PlasmaPy prioritizes code readability, consistency, and maintainability while using best practices for scientific computing such as version control, continuous integration testing, embedding documentation in code, and code review. We discuss our current and planned capabilities, including features presently under development. The development roadmap includes features such as fluid and particle simulation capabilities, a Grad-Shafranov solver, a dispersion relation solver, atomic data retrieval methods, and tools to analyze simulations and experiments. We describe several ways to contribute to PlasmaPy. PlasmaPy has a code of conduct and is being developed under a BSD license, with a version 0.1 release planned for 2018. The success of PlasmaPy depends on active community involvement, so anyone interested in contributing to this project should contact the authors. This work was partially supported by the U.S. Department of Energy.

Mocking the weak lensing universe: The LensTools Python computing package

NASA Astrophysics Data System (ADS)

Petri, A.

2016-10-01

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

Graph-based word sense disambiguation of biomedical documents.

PubMed

Agirre, Eneko; Soroa, Aitor; Stevenson, Mark

2010-11-15

Word Sense Disambiguation (WSD), automatically identifying the meaning of ambiguous words in context, is an important stage of text processing. This article presents a graph-based approach to WSD in the biomedical domain. The method is unsupervised and does not require any labeled training data. It makes use of knowledge from the Unified Medical Language System (UMLS) Metathesaurus which is represented as a graph. A state-of-the-art algorithm, Personalized PageRank, is used to perform WSD. When evaluated on the NLM-WSD dataset, the algorithm outperforms other methods that rely on the UMLS Metathesaurus alone. The WSD system is open source licensed and available from http://ixa2.si.ehu.es/ukb/. The UMLS, MetaMap program and NLM-WSD corpus are available from the National Library of Medicine https://www.nlm.nih.gov/research/umls/, http://mmtx.nlm.nih.gov and http://wsd.nlm.nih.gov. Software to convert the NLM-WSD corpus into a format that can be used by our WSD system is available from http://www.dcs.shef.ac.uk/∼marks/biomedical_wsd under open source license.

Integrating personalized medical test contents with XML and XSL-FO.

PubMed

Toddenroth, Dennis; Dugas, Martin; Frankewitsch, Thomas

2011-03-01

In 2004 the adoption of a modular curriculum at the medical faculty in Muenster led to the introduction of centralized examinations based on multiple-choice questions (MCQs). We report on how organizational challenges of realizing faculty-wide personalized tests were addressed by implementation of a specialized software module to automatically generate test sheets from individual test registrations and MCQ contents. Key steps of the presented method for preparing personalized test sheets are (1) the compilation of relevant item contents and graphical media from a relational database with database queries, (2) the creation of Extensible Markup Language (XML) intermediates, and (3) the transformation into paginated documents. The software module by use of an open source print formatter consistently produced high-quality test sheets, while the blending of vectorized textual contents and pixel graphics resulted in efficient output file sizes. Concomitantly the module permitted an individual randomization of item sequences to prevent illicit collusion. The automatic generation of personalized MCQ test sheets is feasible using freely available open source software libraries, and can be efficiently deployed on a faculty-wide scale.

Chaste: An Open Source C++ Library for Computational Physiology and Biology

PubMed Central

Mirams, Gary R.; Arthurs, Christopher J.; Bernabeu, Miguel O.; Bordas, Rafel; Cooper, Jonathan; Corrias, Alberto; Davit, Yohan; Dunn, Sara-Jane; Fletcher, Alexander G.; Harvey, Daniel G.; Marsh, Megan E.; Osborne, James M.; Pathmanathan, Pras; Pitt-Francis, Joe; Southern, James; Zemzemi, Nejib; Gavaghan, David J.

2013-01-01

Chaste — Cancer, Heart And Soft Tissue Environment — is an open source C++ library for the computational simulation of mathematical models developed for physiology and biology. Code development has been driven by two initial applications: cardiac electrophysiology and cancer development. A large number of cardiac electrophysiology studies have been enabled and performed, including high-performance computational investigations of defibrillation on realistic human cardiac geometries. New models for the initiation and growth of tumours have been developed. In particular, cell-based simulations have provided novel insight into the role of stem cells in the colorectal crypt. Chaste is constantly evolving and is now being applied to a far wider range of problems. The code provides modules for handling common scientific computing components, such as meshes and solvers for ordinary and partial differential equations (ODEs/PDEs). Re-use of these components avoids the need for researchers to ‘re-invent the wheel’ with each new project, accelerating the rate of progress in new applications. Chaste is developed using industrially-derived techniques, in particular test-driven development, to ensure code quality, re-use and reliability. In this article we provide examples that illustrate the types of problems Chaste can be used to solve, which can be run on a desktop computer. We highlight some scientific studies that have used or are using Chaste, and the insights they have provided. The source code, both for specific releases and the development version, is available to download under an open source Berkeley Software Distribution (BSD) licence at http://www.cs.ox.ac.uk/chaste, together with details of a mailing list and links to documentation and tutorials. PMID:23516352

Use of Electronic Health Records in sub-Saharan Africa: Progress and challenges

PubMed Central

Akanbi, Maxwell O.; Ocheke, Amaka N.; Agaba, Patricia A.; Daniyam, Comfort A.; Agaba, Emmanuel I.; Okeke, Edith N.; Ukoli, Christiana O.

2012-01-01

Background The Electronic Health Record (EHR) is a key component of medical informatics that is increasingly being utilized in industrialized nations to improve healthcare. There is limited information on the use of EHR in sub-Saharan Africa. This paper reviews availability of EHRs in sub-Saharan Africa. Methods Searches were performed on PubMed and Google Scholar databases using the terms ‘Electronic Health Records OR Electronic Medical Records OR e-Health and Africa’. References from identified publications were reviewed. Inclusion criterion was documented use of EHR in Africa. Results The search yielded 147 publications of which 21papers from 15 sub-Saharan African countries documented the use of EHR in Africa and were reviewed. About 91% reported use of Open Source healthcare software, with OpenMRS being the most widely used. Most reports were from HIV related health centers. Barriers to adoption of EHRs include high cost of procurement and maintenance, poor network infrastructure and lack of comfort among health workers with electronic medical records. Conclusion There has been an increase in the use of EHRs in sub-Saharan Africa, largely driven by utilization by HIV treatment programs. Penetration is still however very low. PMID:25243111

Mass spectrometer output file format mzML.

PubMed

Deutsch, Eric W

2010-01-01

Mass spectrometry is an important technique for analyzing proteins and other biomolecular compounds in biological samples. Each of the vendors of these mass spectrometers uses a different proprietary binary output file format, which has hindered data sharing and the development of open source software for downstream analysis. The solution has been to develop, with the full participation of academic researchers as well as software and hardware vendors, an open XML-based format for encoding mass spectrometer output files, and then to write software to use this format for archiving, sharing, and processing. This chapter presents the various components and information available for this format, mzML. In addition to the XML schema that defines the file structure, a controlled vocabulary provides clear terms and definitions for the spectral metadata, and a semantic validation rules mapping file allows the mzML semantic validator to insure that an mzML document complies with one of several levels of requirements. Complete documentation and example files insure that the format may be uniformly implemented. At the time of release, there already existed several implementations of the format and vendors have committed to supporting the format in their products.

The Emergence of Open-Source Software in China

ERIC Educational Resources Information Center

Pan, Guohua; Bonk, Curtis J.

2007-01-01

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

A Study of Clinically Related Open Source Software Projects

PubMed Central

Hogarth, Michael A.; Turner, Stuart

2005-01-01

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

Mapping DICOM to OpenDocument format

NASA Astrophysics Data System (ADS)

Yu, Cong; Yao, Zhihong

2009-02-01

In order to enhance the readability, extensibility and sharing of DICOM files, we have introduced XML into DICOM file system (SPIE Volume 5748)[1] and the multilayer tree structure into DICOM (SPIE Volume 6145)[2]. In this paper, we proposed mapping DICOM to ODF(OpenDocument Format), for it is also based on XML. As a result, the new format realizes the separation of content(including text content and image) and display style. Meanwhile, since OpenDocument files take the format of a ZIP compressed archive, the new kind of DICOM files can benefit from ZIP's lossless compression to reduce file size. Moreover, this open format can also guarantee long-term access to data without legal or technical barriers, making medical images accessible to various fields.

CosmoQuest Transient Tracker: Opensource Photometry & Astrometry software

NASA Astrophysics Data System (ADS)

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

2018-01-01

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

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.

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…

SlicerRT: radiation therapy research toolkit for 3D Slicer.

PubMed

Pinter, Csaba; Lasso, Andras; Wang, An; Jaffray, David; Fichtinger, Gabor

2012-10-01

Interest in adaptive radiation therapy research is constantly growing, but software tools available for researchers are mostly either expensive, closed proprietary applications, or free open-source packages with limited scope, extensibility, reliability, or user support. To address these limitations, we propose SlicerRT, a customizable, free, and open-source radiation therapy research toolkit. SlicerRT aspires to be an open-source toolkit for RT research, providing fast computations, convenient workflows for researchers, and a general image-guided therapy infrastructure to assist clinical translation of experimental therapeutic approaches. It is a medium into which RT researchers can integrate their methods and algorithms, and conduct comparative testing. SlicerRT was implemented as an extension for the widely used 3D Slicer medical image visualization and analysis application platform. SlicerRT provides functionality specifically designed for radiation therapy research, in addition to the powerful tools that 3D Slicer offers for visualization, registration, segmentation, and data management. The feature set of SlicerRT was defined through consensus discussions with a large pool of RT researchers, including both radiation oncologists and medical physicists. The development processes used were similar to those of 3D Slicer to ensure software quality. Standardized mechanisms of 3D Slicer were applied for documentation, distribution, and user support. The testing and validation environment was configured to automatically launch a regression test upon each software change and to perform comparison with ground truth results provided by other RT applications. Modules have been created for importing and loading DICOM-RT data, computing and displaying dose volume histograms, creating accumulated dose volumes, comparing dose volumes, and visualizing isodose lines and surfaces. The effectiveness of using 3D Slicer with the proposed SlicerRT extension for radiation therapy research was demonstrated on multiple use cases. A new open-source software toolkit has been developed for radiation therapy research. SlicerRT can import treatment plans from various sources into 3D Slicer for visualization, analysis, comparison, and processing. The provided algorithms are extensively tested and they are accessible through a convenient graphical user interface as well as a flexible application programming interface.

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

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

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

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

Fieldwork online: a GIS-based electronic learning environment for supervising fieldwork

NASA Astrophysics Data System (ADS)

Alberti, Koko; Marra, Wouter; Baarsma, Rein; Karssenberg, Derek

2016-04-01

Fieldwork comes in many forms: individual research projects in unique places, large groups of students on organized fieldtrips, and everything in between those extremes. Supervising students in often distant places can be a logistical challenge and requires a significant time investment of their supervisors. We developed an online application for remote supervision of students on fieldwork. In our fieldworkonline webapp, which is accessible through a web browser, students can upload their field data in the form of a spreadsheet with coordinates (in a system of choice) and data-fields. Field data can be any combination of quantitative or qualitative data, and can contain references to photos or other documents uploaded to the app. The student's data is converted to a map with data-points that contain all the data-fields and links to photos and documents associated with that location. Supervisors can review the data of their students and provide feedback on observations, or geo-referenced feedback on the map. Similarly, students can ask geo-referenced questions to their supervisors. Furthermore, supervisors can choose different basemaps or upload their own. Fieldwork online is a useful tool for supervising students at a distant location in the field and is most suitable for first-order feedback on students' observations, can be used to guide students to interesting locations, and allows for short discussions on phenomena observed in the field. We seek user that like to use this system, we are able to provide support and add new features if needed. The website is built and controlled using Flask, an open-source Python Framework. The maps are generated and controlled using MapServer and OpenLayers, and the database is built in PostgreSQL with PostGIS support. Fieldworkonline and all tools used to create it are open-source. Experience fieldworkonline at our demo during this session, or online at fieldworkonline.geo.uu.nl (username: EGU2016, password: Vienna).

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

PubMed

Rosenberg, David M; Horn, Charles C

2016-08-01

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

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

PubMed Central

2016-01-01

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

Cargo Movement Operations System (CMOS) Requirements Traceability Matrix, Version 3 Increment II

DTIC Science & Technology

1990-12-17

above SCs should be documented. CMOS PMO ACCEPTS COMMENT: YES [ ] NO [ ] ERCI ACCEPTS COMMENT: YES [ ] NO [ ] COMMENT DISPOSITION: COMMENT STATUS: OPEN...These two documents should be in agreement with each other. CMOS PMO ACCEPTS COMMENT: YES [ ] NO [ ] ERCI ACCEPTS COMMENT: YES [ ] NO [ ] COMMENT DISPOSITION...completeness, they should be documented. CMOS PMO ACCEPTS COMMENT: YES [ ] NO [ ] ERCI ACCEPTS COMMENT: YES [ ] NO [ ] COMMENT DISPOSITION: COMMENT STATUS: OPEN

CTF Theory Manual

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

Avramova, Maria N.; Salko, Robert K.

Coolant-Boiling in Rod Arrays|Two Fluids (COBRA-TF) is a thermal/ hydraulic (T/H) simulation code designed for light water reactor (LWR) vessel analysis. It uses a two-fluid, three-field (i.e. fluid film, fluid drops, and vapor) modeling approach. Both sub-channel and 3D Cartesian forms of 9 conservation equations are available for LWR modeling. The code was originally developed by Pacific Northwest Laboratory in 1980 and had been used and modified by several institutions over the last few decades. COBRA-TF also found use at the Pennsylvania State University (PSU) by the Reactor Dynamics and Fuel Management Group (RDFMG) and has been improved, updated, andmore » subsequently re-branded as CTF. As part of the improvement process, it was necessary to generate sufficient documentation for the open-source code which had lacked such material upon being adopted by RDFMG. This document serves mainly as a theory manual for CTF, detailing the many two-phase heat transfer, drag, and important accident scenario models contained in the code as well as the numerical solution process utilized. Coding of the models is also discussed, all with consideration for updates that have been made when transitioning from COBRA-TF to CTF. Further documentation outside of this manual is also available at RDFMG which focus on code input deck generation and source code global variable and module listings.« less

The Earth System Documentation (ES-DOC) Software Process

NASA Astrophysics Data System (ADS)

Greenslade, M. A.; Murphy, S.; Treshansky, A.; DeLuca, C.; Guilyardi, E.; Denvil, S.

2013-12-01

Earth System Documentation (ES-DOC) is an international project supplying high-quality tools & services in support of earth system documentation creation, analysis and dissemination. It is nurturing a sustainable standards based documentation eco-system that aims to become an integral part of the next generation of exa-scale dataset archives. ES-DOC leverages open source software, and applies a software development methodology that places end-user narratives at the heart of all it does. ES-DOC has initially focused upon nurturing the Earth System Model (ESM) documentation eco-system and currently supporting the following projects: * Coupled Model Inter-comparison Project Phase 5 (CMIP5); * Dynamical Core Model Inter-comparison Project (DCMIP); * National Climate Predictions and Projections Platforms Quantitative Evaluation of Downscaling Workshop. This talk will demonstrate that ES-DOC implements a relatively mature software development process. Taking a pragmatic Agile process as inspiration, ES-DOC: * Iteratively develops and releases working software; * Captures user requirements via a narrative based approach; * Uses online collaboration tools (e.g. Earth System CoG) to manage progress; * Prototypes applications to validate their feasibility; * Leverages meta-programming techniques where appropriate; * Automates testing whenever sensibly feasible; * Streamlines complex deployments to a single command; * Extensively leverages GitHub and Pivotal Tracker; * Enforces strict separation of the UI from underlying API's; * Conducts code reviews.

The successes and challenges of open-source biopharmaceutical innovation.

PubMed

Allarakhia, Minna

2014-05-01

Increasingly, open-source-based alliances seek to provide broad access to data, research-based tools, preclinical samples and downstream compounds. The challenge is how to create value from open-source biopharmaceutical innovation. This value creation may occur via transparency and usage of data across the biopharmaceutical value chain as stakeholders move dynamically between open source and open innovation. In this article, several examples are used to trace the evolution of biopharmaceutical open-source initiatives. The article specifically discusses the technological challenges associated with the integration and standardization of big data; the human capacity development challenges associated with skill development around big data usage; and the data-material access challenge associated with data and material access and usage rights, particularly as the boundary between open source and open innovation becomes more fluid. It is the author's opinion that the assessment of when and how value creation will occur, through open-source biopharmaceutical innovation, is paramount. The key is to determine the metrics of value creation and the necessary technological, educational and legal frameworks to support the downstream outcomes of now big data-based open-source initiatives. The continued focus on the early-stage value creation is not advisable. Instead, it would be more advisable to adopt an approach where stakeholders transform open-source initiatives into open-source discovery, crowdsourcing and open product development partnerships on the same platform.

43 CFR 2091.07 - Principles.

Code of Federal Regulations, 2011 CFR

2011-10-01

... OF THE INTERIOR LAND RESOURCE MANAGEMENT (2000) SPECIAL LAWS AND RULES Segregation and Opening of... the Geothermal Steam Act, if so specified in the document that segregates the lands. The segregation... are required when the opening date is not specified in the document creating the segregation, or when...

Health Physics Positions Data Base: Revision 1

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

Kerr, G.D.; Borges, T.; Stafford, R.S.

1994-02-01

The Health Physics Positions (HPPOS) Data Base of the Nuclear Regulatory Commission (NRC) is a collection of NRC staff positions on a wide range of topics involving radiation protection (health physics). It consists of 328 documents in the form of letters, memoranda, and excerpts from technical reports. The HPPOS Data Base was developed by the NRC Headquarters and Regional Offices to help ensure uniformity in inspections, enforcement, and licensing actions. Staff members of the Oak Ridge National Laboratory (ORNL) have assisted the NRC staff in summarizing the documents during the preparation of this NUREG report. These summaries are also beingmore » made available as a {open_quotes}stand alone{close_quotes} software package for IBM and IBM-compatible personal computers. The software package for this report is called HPPOS Version 2.0. A variety of indexing schemes were used to increase the usefulness of the NUREG report and its associated software. The software package and the summaries in the report are written in the context of the {open_quotes}new{close_quotes} 10 CFR Part 20 ({section}{section}20.1001--20.2401). The purpose of this NUREG report is to allow interested individuals to familiarize themselves with the contents of the HPPOS Data Base and with the basis of many NRC decisions and regulations. The HPPOS summaries and original documents are intended to serve as a source of information for radiation protection programs at nuclear research and power reactors, nuclear medicine, and other industries that either process or use nuclear materials.« less

Concepts and Technologies for a Comprehensive Information System for Historical Research and Heritage Documentation

NASA Astrophysics Data System (ADS)

Henze, F.; Magdalinski, N.; Schwarzbach, F.; Schulze, A.; Gerth, Ph.; Schäfer, F.

2013-07-01

Information systems play an important role in historical research as well as in heritage documentation. As part of a joint research project of the German Archaeological Institute, the Brandenburg University of Technology Cottbus and the Dresden University of Applied Sciences a web-based documentation system is currently being developed, which can easily be adapted to the needs of different projects with individual scientific concepts, methods and questions. Based on open source and standardized technologies it will focus on open and well-documented interfaces to ease the dissemination and re-use of its content via web-services and to communicate with desktop applications for further evaluation and analysis. Core of the system is a generic data model that represents a wide range of topics and methods of archaeological work. By the provision of a concerted amount of initial themes and attributes a cross project analysis of research data will be possible. The development of enhanced search and retrieval functionalities will simplify the processing and handling of large heterogeneous data sets. To achieve a high degree of interoperability with existing external data, systems and applications, standardized interfaces will be integrated. The analysis of spatial data shall be possible through the integration of web-based GIS functions. As an extension to this, customized functions for storage, processing and provision of 3D geo data are being developed. As part of the contribution system requirements and concepts will be presented and discussed. A particular focus will be on introducing the generic data model and the derived database schema. The research work on enhanced search and retrieval capabilities will be illustrated by prototypical developments, as well as concepts and first implementations for an integrated 2D/3D Web-GIS.

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

PubMed Central

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

2006-01-01

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

Soil and nutrient retention in winter-flooded ricefields with implications for watershed management

USGS Publications Warehouse

Manley, S.W.; Kaminski, R.M.; Rodrigue, P.B.; Dewey, J.C.; Schoenholtz, S.H.; Gerard, P.D.; Reinecke, K.J.

2009-01-01

The ability of water resources to support aquatic life and human needs depends, in part, on reducing nonpoint source pollution amid contemporary agricultural practices. Winter retention of shallow water on rice and other agricultural fields is an accepted management practice for wildlife conservation; however, soil and water conservation benefits are not well documented. We evaluated the ability of four post-harvest ricefield treatment combinations (stubble-flooded, stubble-open, disked-flooded and disked-open) to abate nonpoint source exports into watersheds of the Mississippi Alluvial Valley. Total suspended solid exports were 1,121 kg ha-1 (1,000 lb ac-1) from disked-open fields where rice stubble was disked after harvest and fields were allowed to drain, compared with 35 kg ha-1 (31 lb ac-1) from stubble-flooded fields where stubble was left standing after harvest and fields captured rainfall from November 1 to March 1. Estimates of total suspended solid exports from ricefields based on Landsat imagery and USDA crop data are 0.43 and 0.40 Mg km-2 day-1 in the Big Sunflower and L'Anguille watersheds, respectively. Estimated reductions in total suspended solid exports from ricefields into the Big Sunflower and L'Anguille water-sheds range from 26% to 64% under hypothetical scenarios in which 65% to 100% of the rice production area is managed to capture winter rainfall. Winter ricefield management reduced nonpoint source export by decreasing concentrations of solids and nutrients in, and reducing runoff volume from, ricefields in the Mississippi Alluvial Valley.

One-dimensional statistical parametric mapping in Python.

PubMed

Pataky, Todd C

2012-01-01

Statistical parametric mapping (SPM) is a topological methodology for detecting field changes in smooth n-dimensional continua. Many classes of biomechanical data are smooth and contained within discrete bounds and as such are well suited to SPM analyses. The current paper accompanies release of 'SPM1D', a free and open-source Python package for conducting SPM analyses on a set of registered 1D curves. Three example applications are presented: (i) kinematics, (ii) ground reaction forces and (iii) contact pressure distribution in probabilistic finite element modelling. In addition to offering a high-level interface to a variety of common statistical tests like t tests, regression and ANOVA, SPM1D also emphasises fundamental concepts of SPM theory through stand-alone example scripts. Source code and documentation are available at: www.tpataky.net/spm1d/.

ESS++: a C++ objected-oriented algorithm for Bayesian stochastic search model exploration

PubMed Central

Bottolo, Leonardo; Langley, Sarah R.; Petretto, Enrico; Tiret, Laurence; Tregouet, David; Richardson, Sylvia

2011-01-01

Summary: ESS++ is a C++ implementation of a fully Bayesian variable selection approach for single and multiple response linear regression. ESS++ works well both when the number of observations is larger than the number of predictors and in the ‘large p, small n’ case. In the current version, ESS++ can handle several hundred observations, thousands of predictors and a few responses simultaneously. The core engine of ESS++ for the selection of relevant predictors is based on Evolutionary Monte Carlo. Our implementation is open source, allowing community-based alterations and improvements. Availability: C++ source code and documentation including compilation instructions are available under GNU licence at http://bgx.org.uk/software/ESS.html. Contact: l.bottolo@imperial.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:21233165

Itzï (version 17.1): an open-source, distributed GIS model for dynamic flood simulation

NASA Astrophysics Data System (ADS)

Guillaume Courty, Laurent; Pedrozo-Acuña, Adrián; Bates, Paul David

2017-05-01

Worldwide, floods are acknowledged as one of the most destructive hazards. In human-dominated environments, their negative impacts are ascribed not only to the increase in frequency and intensity of floods but also to a strong feedback between the hydrological cycle and anthropogenic development. In order to advance a more comprehensive understanding of this complex interaction, this paper presents the development of a new open-source tool named Itzï that enables the 2-D numerical modelling of rainfall-runoff processes and surface flows integrated with the open-source geographic information system (GIS) software known as GRASS. Therefore, it takes advantage of the ability given by GIS environments to handle datasets with variations in both temporal and spatial resolutions. Furthermore, the presented numerical tool can handle datasets from different sources with varied spatial resolutions, facilitating the preparation and management of input and forcing data. This ability reduces the preprocessing time usually required by other models. Itzï uses a simplified form of the shallow water equations, the damped partial inertia equation, for the resolution of surface flows, and the Green-Ampt model for the infiltration. The source code is now publicly available online, along with complete documentation. The numerical model is verified against three different tests cases: firstly, a comparison with an analytic solution of the shallow water equations is introduced; secondly, a hypothetical flooding event in an urban area is implemented, where results are compared to those from an established model using a similar approach; and lastly, the reproduction of a real inundation event that occurred in the city of Kingston upon Hull, UK, in June 2007, is presented. The numerical approach proved its ability at reproducing the analytic and synthetic test cases. Moreover, simulation results of the real flood event showed its suitability at identifying areas affected by flooding, which were verified against those recorded after the event by local authorities.

Open for Business

ERIC Educational Resources Information Center

Voyles, Bennett

2007-01-01

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

Transparent ICD and DRG coding using information technology: linking and associating information sources with the eXtensible Markup Language.

PubMed

Hoelzer, Simon; Schweiger, Ralf K; Dudeck, Joachim

2003-01-01

With the introduction of ICD-10 as the standard for diagnostics, it becomes necessary to develop an electronic representation of its complete content, inherent semantics, and coding rules. The authors' design relates to the current efforts by the CEN/TC 251 to establish a European standard for hierarchical classification systems in health care. The authors have developed an electronic representation of ICD-10 with the eXtensible Markup Language (XML) that facilitates integration into current information systems and coding software, taking different languages and versions into account. In this context, XML provides a complete processing framework of related technologies and standard tools that helps develop interoperable applications. XML provides semantic markup. It allows domain-specific definition of tags and hierarchical document structure. The idea of linking and thus combining information from different sources is a valuable feature of XML. In addition, XML topic maps are used to describe relationships between different sources, or "semantically associated" parts of these sources. The issue of achieving a standardized medical vocabulary becomes more and more important with the stepwise implementation of diagnostically related groups, for example. The aim of the authors' work is to provide a transparent and open infrastructure that can be used to support clinical coding and to develop further software applications. The authors are assuming that a comprehensive representation of the content, structure, inherent semantics, and layout of medical classification systems can be achieved through a document-oriented approach.

Transparent ICD and DRG Coding Using Information Technology: Linking and Associating Information Sources with the eXtensible Markup Language

PubMed Central

Hoelzer, Simon; Schweiger, Ralf K.; Dudeck, Joachim

2003-01-01

With the introduction of ICD-10 as the standard for diagnostics, it becomes necessary to develop an electronic representation of its complete content, inherent semantics, and coding rules. The authors' design relates to the current efforts by the CEN/TC 251 to establish a European standard for hierarchical classification systems in health care. The authors have developed an electronic representation of ICD-10 with the eXtensible Markup Language (XML) that facilitates integration into current information systems and coding software, taking different languages and versions into account. In this context, XML provides a complete processing framework of related technologies and standard tools that helps develop interoperable applications. XML provides semantic markup. It allows domain-specific definition of tags and hierarchical document structure. The idea of linking and thus combining information from different sources is a valuable feature of XML. In addition, XML topic maps are used to describe relationships between different sources, or “semantically associated” parts of these sources. The issue of achieving a standardized medical vocabulary becomes more and more important with the stepwise implementation of diagnostically related groups, for example. The aim of the authors' work is to provide a transparent and open infrastructure that can be used to support clinical coding and to develop further software applications. The authors are assuming that a comprehensive representation of the content, structure, inherent semantics, and layout of medical classification systems can be achieved through a document-oriented approach. PMID:12807813

The Commercial Open Source Business Model

NASA Astrophysics Data System (ADS)

Riehle, Dirk

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

Provenance of upper Triassic sandstone, southwest Iberia (Alentejo and Algarve basins): tracing variability in the sources

NASA Astrophysics Data System (ADS)

Pereira, M. F.; Ribeiro, C.; Gama, C.; Drost, K.; Chichorro, M.; Vilallonga, F.; Hofmann, M.; Linnemann, U.

2017-01-01

Laser ablation ICP-MS U-Pb analyses have been conducted on detrital zircon of Upper Triassic sandstone from the Alentejo and Algarve basins in southwest Iberia. The predominance of Neoproterozoic, Devonian, Paleoproterozoic and Carboniferous detrital zircon ages confirms previous studies that indicate the locus of the sediment source of the late Triassic Alentejo Basin in the pre-Mesozoic basement of the South Portuguese and Ossa-Morena zones. Suitable sources for the Upper Triassic Algarve sandstone are the Upper Devonian-Lower Carboniferous of the South Portuguese Zone (Phyllite-Quartzite and Tercenas formations) and the Meguma Terrane (present-day in Nova Scotia). Spatial variations of the sediment sources of both Upper Triassic basins suggest a more complex history of drainage than previously documented involving other source rocks located outside present-day Iberia. The two Triassic basins were isolated from each other with the detrital transport being controlled by two independent drainage systems. This study is important for the reconstruction of the late Triassic paleogeography in a place where, later, the opening of the Central Atlantic Ocean took place separating Europe from North America.

A suite of R packages for web-enabled modeling and analysis of surface waters

NASA Astrophysics Data System (ADS)

Read, J. S.; Winslow, L. A.; Nüst, D.; De Cicco, L.; Walker, J. I.

2014-12-01

Researchers often create redundant methods for downloading, manipulating, and analyzing data from online resources. Moreover, the reproducibility of science can be hampered by complicated and voluminous data, lack of time for documentation and long-term maintenance of software, and fear of exposing programming skills. The combination of these factors can encourage unshared one-off programmatic solutions instead of openly provided reusable methods. Federal and academic researchers in the water resources and informatics domains have collaborated to address these issues. The result of this collaboration is a suite of modular R packages that can be used independently or as elements in reproducible analytical workflows. These documented and freely available R packages were designed to fill basic needs for the effective use of water data: the retrieval of time-series and spatial data from web resources (dataRetrieval, geoknife), performing quality assurance and quality control checks of these data with robust statistical methods (sensorQC), the creation of useful data derivatives (including physically- and biologically-relevant indices; GDopp, LakeMetabolizer), and the execution and evaluation of models (glmtools, rLakeAnalyzer). Here, we share details and recommendations for the collaborative coding process, and highlight the benefits of an open-source tool development pattern with a popular programming language in the water resources discipline (such as R). We provide examples of reproducible science driven by large volumes of web-available data using these tools, explore benefits of accessing packages as standardized web processing services (WPS) and present a working platform that allows domain experts to publish scientific algorithms in a service-oriented architecture (WPS4R). We assert that in the era of open data, tools that leverage these data should also be freely shared, transparent, and developed in an open innovation environment.

MDSplus quality improvement project

DOE PAGES

Fredian, Thomas W.; Stillerman, Joshua; Manduchi, Gabriele; ...

2016-05-31

MDSplus is a data acquisition and analysis system used worldwide predominantly in the fusion research community. Development began 29 years ago on the OpenVMS operating system. Since that time there have been many new features added and the code has been ported to many different operating systems. There have been contributions to the MDSplus development from the fusion community in the way of feature suggestions, feature implementations, documentation and porting to different operating systems. The bulk of the development and support of MDSplus, however, has been provided by a relatively small core developer group of three or four members. Givenmore » the size of the development team and the large number of users much more effort was focused on providing new features for the community than on keeping the underlying code and documentation up to date with the evolving software development standards. To ensure that MDSplus will continue to provide the needs of the community in the future, the MDSplus development team along with other members of the MDSplus user community has commenced on a major quality improvement project. The planned improvements include changes to software build scripts to better use GNU Autoconf and Automake tools, refactoring many of the source code modules using new language features available in modern compilers, using GNU MinGW-w64 to create MS Windows distributions, migrating to a more modern source code management system, improvement of source documentation as well as improvements to the www.mdsplus.org web site documentation and layout, and the addition of more comprehensive test suites to apply to MDSplus code builds prior to releasing installation kits to the community. This paper should lead to a much more robust product and establish a framework to maintain stability as more enhancements and features are added. Finally, this paper will describe these efforts that are either in progress or planned for the near future.« less

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

PubMed

Matter, Ulrich; Stutzer, Alois

2015-01-01

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

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

PubMed

Taylor, Stephen; Noble, Roger

2014-09-15

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

Calibrated Blade-Element/Momentum Theory Aerodynamic Model of the MARIN Stock Wind Turbine: Preprint

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

Goupee, A.; Kimball, R.; de Ridder, E. J.

2015-04-02

In this paper, a calibrated blade-element/momentum theory aerodynamic model of the MARIN stock wind turbine is developed and documented. The model is created using open-source software and calibrated to closely emulate experimental data obtained by the DeepCwind Consortium using a genetic algorithm optimization routine. The provided model will be useful for those interested in validating interested in validating floating wind turbine numerical simulators that rely on experiments utilizing the MARIN stock wind turbine—for example, the International Energy Agency Wind Task 30’s Offshore Code Comparison Collaboration Continued, with Correlation project.

MetExploreViz: web component for interactive metabolic network visualization.

PubMed

Chazalviel, Maxime; Frainay, Clément; Poupin, Nathalie; Vinson, Florence; Merlet, Benjamin; Gloaguen, Yoann; Cottret, Ludovic; Jourdan, Fabien

2017-09-15

MetExploreViz is an open source web component that can be easily embedded in any web site. It provides features dedicated to the visualization of metabolic networks and pathways and thus offers a flexible solution to analyze omics data in a biochemical context. Documentation and link to GIT code repository (GPL 3.0 license)are available at this URL: http://metexplore.toulouse.inra.fr/metexploreViz/doc /. Tutorial is available at this URL. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

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

NASA Astrophysics Data System (ADS)

Udell, C.; Selker, J. S.

2017-12-01

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

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.

Improving PHENIX search with Solr, Nutch and Drupal.

NASA Astrophysics Data System (ADS)

Morrison, Dave; Sourikova, Irina

2012-12-01

During its 20 years of R&D, construction and operation the PHENIX experiment at the Relativistic Heavy Ion Collider (RHIC) has accumulated large amounts of proprietary collaboration data that is hosted on many servers around the world and is not open for commercial search engines for indexing and searching. The legacy search infrastructure did not scale well with the fast growing PHENIX document base and produced results inadequate in both precision and recall. After considering the possible alternatives that would provide an aggregated, fast, full text search of a variety of data sources and file formats we decided to use Nutch [1] as a web crawler and Solr [2] as a search engine. To present XML-based Solr search results in a user-friendly format we use Drupal [3] as a web interface to Solr. We describe the experience of building a federated search for a heterogeneous collection of 10 million PHENIX documents with Nutch, Solr and Drupal.

An Overview of R in Health Decision Sciences.

PubMed

Jalal, Hawre; Pechlivanoglou, Petros; Krijkamp, Eline; Alarid-Escudero, Fernando; Enns, Eva; Hunink, M G Myriam

2017-10-01

As the complexity of health decision science applications increases, high-level programming languages are increasingly adopted for statistical analyses and numerical computations. These programming languages facilitate sophisticated modeling, model documentation, and analysis reproducibility. Among the high-level programming languages, the statistical programming framework R is gaining increased recognition. R is freely available, cross-platform compatible, and open source. A large community of users who have generated an extensive collection of well-documented packages and functions supports it. These functions facilitate applications of health decision science methodology as well as the visualization and communication of results. Although R's popularity is increasing among health decision scientists, methodological extensions of R in the field of decision analysis remain isolated. The purpose of this article is to provide an overview of existing R functionality that is applicable to the various stages of decision analysis, including model design, input parameter estimation, and analysis of model outputs.

Towards Image Documentation of Grave Coverings and Epitaphs for Exhibition Purposes

NASA Astrophysics Data System (ADS)

Pomaska, G.; Dementiev, N.

2015-08-01

Epitaphs and memorials as immovable items in sacred spaces provide with their inscriptions valuable documents of history. Today not only photography or photos are suitable as presentation material for cultural assets in museums. Computer vision and photogrammetry provide methods for recording, 3D modelling, rendering under artificial light conditions as well as further options for analysis and investigation of artistry. For exhibition purposes epitaphs have been recorded by the structure from motion method. A comparison of different kinds of SFM software distributions could be worked out. The suitability of open source software in the mesh processing chain from modelling up to displaying on computer monitors should be answered. Raspberry Pi, a computer in SoC technology works as a media server under Linux applying Python scripts. Will the little computer meet the requirements for a museum and is the handling comfortable enough for staff and visitors? This contribution reports about the case study.

Cultural Heritage Reconstruction from Historical Photographs and Videos

NASA Astrophysics Data System (ADS)

Condorelli, F.; Rinaudo, F.

2018-05-01

Historical archives save invaluable treasures and play a critical role in the conservation of Cultural Heritage. Old photographs and videos, which have survived over time and stored in these archives, preserve traces of architecture and urban transformation and, in many cases, are the only evidence of buildings that no longer exist. They are a precious source of enormous informative potential in Cultural Heritage documentation and save invaluable treasures. Thanks to photogrammetric techniques it is possible to extract metric information from these sources useful for 3D virtual reconstructions of monuments and historic buildings. This paper explores the ways to search for, classify and group historical data by considering their possible use in metric documentation and aims to provide an overview of criticality and open issues of the methodologies that could be used to process these data. A practical example is described and presented as a case study. The video "Torino 1928", an old movie dating from the 1930s, was processed for reconstructing the temporary pavilions of the "Exposition" held in Turin in 1928. Despite the initial concerns relating to processing this kind of data, the experimental methodology used in this research has allowed to reach a quality of results of acceptable standard.

Open-Source Data and the Study of Homicide.

PubMed

Parkin, William S; Gruenewald, Jeff

2015-07-20

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

Ensuring the Environmental and Industrial Safety in Solid Mineral Deposit Surface Mining

NASA Astrophysics Data System (ADS)

Trubetskoy, Kliment; Rylnikova, Marina; Esina, Ekaterina

2017-11-01

The growing environmental pressure of mineral deposit surface mining and severization of industrial safety requirements dictate the necessity of refining the regulatory framework governing safe and efficient development of underground resources. The applicable regulatory documentation governing the procedure of ore open-pit wall and bench stability design for the stage of pit reaching its final boundary was issued several decades ago. Over recent decades, mining and geomechanical conditions have changed significantly in surface mining operations, numerous new software packages and computer developments have appeared, opportunities of experimental methods of source data collection and processing, grounding of the permissible parameters of open pit walls have changed dramatically, and, thus, methods of risk assessment have been perfected [10-13]. IPKON RAS, with the support of the Federal Service for Environmental Supervision, assumed the role of the initiator of the project for the development of Federal norms and regulations of industrial safety "Rules for ensuring the stability of walls and benches of open pits, open-cast mines and spoil banks", which contribute to the improvement of economic efficiency and safety of mineral deposit surface mining and enhancement of the competitiveness of Russian mines at the international level that is very important in the current situation.

Understanding Lustre Internals

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

Wang, Feiyi; Oral, H Sarp; Shipman, Galen M

2009-04-01

Lustre was initiated and funded, almost a decade ago, by the U.S. Department of Energy (DoE) Office of Science and National Nuclear Security Administration laboratories to address the need for an open source, highly-scalable, high-performance parallel filesystem on by then present and future supercomputing platforms. Throughout the last decade, it was deployed over numerous medium-to-large-scale supercomputing platforms and clusters, and it performed and met the expectations of the Lustre user community. As it stands at the time of writing this document, according to the Top500 list, 15 of the top 30 supercomputers in the world use Lustre filesystem. This reportmore » aims to present a streamlined overview on how Lustre works internally at reasonable details including relevant data structures, APIs, protocols and algorithms involved for Lustre version 1.6 source code base. More importantly, it tries to explain how various components interconnect with each other and function as a system. Portions of this report are based on discussions with Oak Ridge National Laboratory Lustre Center of Excellence team members and portions of it are based on our own understanding of how the code works. We, as the authors team bare all responsibilities for all errors and omissions in this document. We can only hope it helps current and future Lustre users and Lustre code developers as much as it helped us understanding the Lustre source code and its internal workings.« less

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…

Minimizing the risks created by an emissions inventory

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

Oppenfeld, R.R. von; Evans, D.M.; Vamos, J.C.

Emissions inventories are required under the federal Clean Air Act ({open_quotes}Act{close_quotes}). Sources must identify emissions points and the types of air pollutants emitted, and quantify by measurement, modeling, or estimation the amount of each pollutant. The emissions inventory is an information gathering tool, providing regulatory agencies and the public with an overview of pollutants that may be emitted. Emission inventories are not reports of precise measurements of emissions and may be misunderstood, misinterpreted or misused. The emissions inventory and the underlying documentation are potential evidence in enforcement actions under the Act and other federal and state environmental laws. Readily availablemore » to the public, emission inventories may also be used in citizen suits, toxic tort actions and other types of civil actions for damages. Practical as well as legal mechanisms allow regulated entities to minimize the possibility that an emissions inventory or its underlying documentation will be a {open_quotes}smoking gun.{close_quotes} Practical tools include use of qualifying or disclaimer language in the final inventory. The inventory effort can be planned and executed to minimize the risk of misuse and to bring the effort within privileges, such as the self-evaluative privilege, statutory audit privileges, the attorney-client privilege or the attorney work product privilege.« less

Protecting the pipeline of science: openness, scientific methods and the lessons from ticagrelor and the PLATO trial.

PubMed

Coats, Andrew J Stewart; Nijjer, Sukhjinder S; Francis, Darrel P

2014-10-20

Ticagrelor, a potent antiplatelet, has been shown to be beneficial in patients with acute coronary syndromes in a randomised controlled trial published in a highly ranked peer reviewed journal. Accordingly it has entered guidelines and has been approved for clinical use by authorities. However, there remains a controversy regarding aspects of the PLATO trial, which are not immediately apparent from the peer-reviewed publications. A number of publications have sought to highlight potential discrepancies, using data available in publicly published documents from the US Food and Drug Administration (FDA) leading to disagreement regarding the value of open science and data sharing. We reflect upon potential sources of bias present in even rigorously performed randomised controlled trials, on whether peer review can establish the presence of bias and the need to constantly challenge and question even accepted data. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Performance of Reynolds Averaged Navier-Stokes Models in Predicting Separated Flows: Study of the Hump Flow Model Problem

NASA Technical Reports Server (NTRS)

Cappelli, Daniele; Mansour, Nagi N.

2012-01-01

Separation can be seen in most aerodynamic flows, but accurate prediction of separated flows is still a challenging problem for computational fluid dynamics (CFD) tools. The behavior of several Reynolds Averaged Navier-Stokes (RANS) models in predicting the separated ow over a wall-mounted hump is studied. The strengths and weaknesses of the most popular RANS models (Spalart-Allmaras, k-epsilon, k-omega, k-omega-SST) are evaluated using the open source software OpenFOAM. The hump ow modeled in this work has been documented in the 2004 CFD Validation Workshop on Synthetic Jets and Turbulent Separation Control. Only the baseline case is treated; the slot flow control cases are not considered in this paper. Particular attention is given to predicting the size of the recirculation bubble, the position of the reattachment point, and the velocity profiles downstream of the hump.

Open access resources for genome-wide association mapping in rice

PubMed Central

McCouch, Susan R.; Wright, Mark H.; Tung, Chih-Wei; Maron, Lyza G.; McNally, Kenneth L.; Fitzgerald, Melissa; Singh, Namrata; DeClerck, Genevieve; Agosto-Perez, Francisco; Korniliev, Pavel; Greenberg, Anthony J.; Naredo, Ma. Elizabeth B.; Mercado, Sheila Mae Q.; Harrington, Sandra E.; Shi, Yuxin; Branchini, Darcy A.; Kuser-Falcão, Paula R.; Leung, Hei; Ebana, Kowaru; Yano, Masahiro; Eizenga, Georgia; McClung, Anna; Mezey, Jason

2016-01-01

Increasing food production is essential to meet the demands of a growing human population, with its rising income levels and nutritional expectations. To address the demand, plant breeders seek new sources of genetic variation to enhance the productivity, sustainability and resilience of crop varieties. Here we launch a high-resolution, open-access research platform to facilitate genome-wide association mapping in rice, a staple food crop. The platform provides an immortal collection of diverse germplasm, a high-density single-nucleotide polymorphism data set tailored for gene discovery, well-documented analytical strategies, and a suite of bioinformatics resources to facilitate biological interpretation. Using grain length, we demonstrate the power and resolution of our new high-density rice array, the accompanying genotypic data set, and an expanded diversity panel for detecting major and minor effect QTLs and subpopulation-specific alleles, with immediate implications for rice improvement. PMID:26842267

A low-cost programmable pulse generator for physiology and behavior

PubMed Central

Sanders, Joshua I.; Kepecs, Adam

2014-01-01

Precisely timed experimental manipulations of the brain and its sensory environment are often employed to reveal principles of brain function. While complex and reliable pulse trains for temporal stimulus control can be generated with commercial instruments, contemporary options remain expensive and proprietary. We have developed Pulse Pal, an open source device that allows users to create and trigger software-defined trains of voltage pulses with high temporal precision. Here we describe Pulse Pal’s circuitry and firmware, and characterize its precision and reliability. In addition, we supply online documentation with instructions for assembling, testing and installing Pulse Pal. While the device can be operated as a stand-alone instrument, we also provide application programming interfaces in several programming languages. As an inexpensive, flexible and open solution for temporal control, we anticipate that Pulse Pal will be used to address a wide range of instrumentation timing challenges in neuroscience research. PMID:25566051

The semantic measures library and toolkit: fast computation of semantic similarity and relatedness using biomedical ontologies.

PubMed

Harispe, Sébastien; Ranwez, Sylvie; Janaqi, Stefan; Montmain, Jacky

2014-03-01

The semantic measures library and toolkit are robust open-source and easy to use software solutions dedicated to semantic measures. They can be used for large-scale computations and analyses of semantic similarities between terms/concepts defined in terminologies and ontologies. The comparison of entities (e.g. genes) annotated by concepts is also supported. A large collection of measures is available. Not limited to a specific application context, the library and the toolkit can be used with various controlled vocabularies and ontology specifications (e.g. Open Biomedical Ontology, Resource Description Framework). The project targets both designers and practitioners of semantic measures providing a JAVA library, as well as a command-line tool that can be used on personal computers or computer clusters. Downloads, documentation, tutorials, evaluation and support are available at http://www.semantic-measures-library.org.

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

PubMed

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

2011-09-28

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

Method and system of filtering and recommending documents

DOEpatents

Patton, Robert M.; Potok, Thomas E.

2016-02-09

Disclosed is a method and system for discovering documents using a computer and providing a small set of the most relevant documents to the attention of a human observer. Using the method, the computer obtains a seed document from the user and generates a seed document vector using term frequency-inverse corpus frequency weighting. A keyword index for a plurality of source documents can be compared with the weighted terms of the seed document vector. The comparison is then filtered to reduce the number of documents, which define an initial subset of the source documents. Initial subset vectors are generated and compared to the seed document vector to obtain a similarity value for each comparison. Based on the similarity value, the method then recommends one or more of the source documents.

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.

Digital data collection in paleoanthropology.

PubMed

Reed, Denné; Barr, W Andrew; Mcpherron, Shannon P; Bobe, René; Geraads, Denis; Wynn, Jonathan G; Alemseged, Zeresenay

2015-01-01

Understanding patterns of human evolution across space and time requires synthesizing data collected by independent research teams, and this effort is part of a larger trend to develop cyber infrastructure and e-science initiatives. At present, paleoanthropology cannot easily answer basic questions about the total number of fossils and artifacts that have been discovered, or exactly how those items were collected. In this paper, we examine the methodological challenges to data integration, with the hope that mitigating the technical obstacles will further promote data sharing. At a minimum, data integration efforts must document what data exist and how the data were collected (discovery), after which we can begin standardizing data collection practices with the aim of achieving combined analyses (synthesis). This paper outlines a digital data collection system for paleoanthropology. We review the relevant data management principles for a general audience and supplement this with technical details drawn from over 15 years of paleontological and archeological field experience in Africa and Europe. The system outlined here emphasizes free open-source software (FOSS) solutions that work on multiple computer platforms; it builds on recent advances in open-source geospatial software and mobile computing. © 2015 Wiley Periodicals, Inc.

icoshift: A versatile tool for the rapid alignment of 1D NMR spectra

NASA Astrophysics Data System (ADS)

Savorani, F.; Tomasi, G.; Engelsen, S. B.

2010-02-01

The increasing scientific and industrial interest towards metabonomics takes advantage from the high qualitative and quantitative information level of nuclear magnetic resonance (NMR) spectroscopy. However, several chemical and physical factors can affect the absolute and the relative position of an NMR signal and it is not always possible or desirable to eliminate these effects a priori. To remove misalignment of NMR signals a posteriori, several algorithms have been proposed in the literature. The icoshift program presented here is an open source and highly efficient program designed for solving signal alignment problems in metabonomic NMR data analysis. The icoshift algorithm is based on correlation shifting of spectral intervals and employs an FFT engine that aligns all spectra simultaneously. The algorithm is demonstrated to be faster than similar methods found in the literature making full-resolution alignment of large datasets feasible and thus avoiding down-sampling steps such as binning. The algorithm uses missing values as a filling alternative in order to avoid spectral artifacts at the segment boundaries. The algorithm is made open source and the Matlab code including documentation can be downloaded from www.models.life.ku.dk.

ERDDAP: Reducing Data Friction with an Open Source Data Platform

NASA Astrophysics Data System (ADS)

O'Brien, K.

2017-12-01

Data friction is not just an issue facing interdisciplinary research. Often times, even within disciplines, significant data friction can exist. Issues of differing formats, limited metadata and non-existent machine-to-machine data access are all issues that exist within disciplines and make it that much harder for successful interdisciplinary cooperation. Therefore, reducing data friction within disciplines is crucial first step in providing better overall collaboration. ERDDAP, an open source data platform developed at NOAA's Southwest Fisheries Center, is well poised to improve data useability and understanding and reduce data friction, both in single and multi-disciplinary research. By virtue of its ability to integrate data of varying formats and provide RESTful-based user access to data and metadata, use of ERDDAP has grown substantially throughout the ocean data community. ERDDAP also supports standards such as the DAP data protocol, the Climate and Forecast (CF) metadata conventions and the Bagit document standard for data archival. In this presentation, we will discuss the advantages of using ERDDAP as a data platform. We will also show specific use cases where utilizing ERDDAP has reduced friction within a single discipline (physical oceanography) and improved interdisciplinary collaboration as well.

The TimeStudio Project: An open source scientific workflow system for the behavioral and brain sciences.

PubMed

Nyström, Pär; Falck-Ytter, Terje; Gredebäck, Gustaf

2016-06-01

This article describes a new open source scientific workflow system, the TimeStudio Project, dedicated to the behavioral and brain sciences. The program is written in MATLAB and features a graphical user interface for the dynamic pipelining of computer algorithms developed as TimeStudio plugins. TimeStudio includes both a set of general plugins (for reading data files, modifying data structures, visualizing data structures, etc.) and a set of plugins specifically developed for the analysis of event-related eyetracking data as a proof of concept. It is possible to create custom plugins to integrate new or existing MATLAB code anywhere in a workflow, making TimeStudio a flexible workbench for organizing and performing a wide range of analyses. The system also features an integrated sharing and archiving tool for TimeStudio workflows, which can be used to share workflows both during the data analysis phase and after scientific publication. TimeStudio thus facilitates the reproduction and replication of scientific studies, increases the transparency of analyses, and reduces individual researchers' analysis workload. The project website ( http://timestudioproject.com ) contains the latest releases of TimeStudio, together with documentation and user forums.

Sybil--efficient constraint-based modelling in R.

PubMed

Gelius-Dietrich, Gabriel; Desouki, Abdelmoneim Amer; Fritzemeier, Claus Jonathan; Lercher, Martin J

2013-11-13

Constraint-based analyses of metabolic networks are widely used to simulate the properties of genome-scale metabolic networks. Publicly available implementations tend to be slow, impeding large scale analyses such as the genome-wide computation of pairwise gene knock-outs, or the automated search for model improvements. Furthermore, available implementations cannot easily be extended or adapted by users. Here, we present sybil, an open source software library for constraint-based analyses in R; R is a free, platform-independent environment for statistical computing and graphics that is widely used in bioinformatics. Among other functions, sybil currently provides efficient methods for flux-balance analysis (FBA), MOMA, and ROOM that are about ten times faster than previous implementations when calculating the effect of whole-genome single gene deletions in silico on a complete E. coli metabolic model. Due to the object-oriented architecture of sybil, users can easily build analysis pipelines in R or even implement their own constraint-based algorithms. Based on its highly efficient communication with different mathematical optimisation programs, sybil facilitates the exploration of high-dimensional optimisation problems on small time scales. Sybil and all its dependencies are open source. Sybil and its documentation are available for download from the comprehensive R archive network (CRAN).

Standard Generalized Markup Language for self-defining structured reports.

PubMed

Kahn, C E

1999-01-01

Structured reporting is the process of using standardized data elements and predetermined data-entry formats to record observations. The Standard Generalized Markup Language (SGML; International Standards Organization (ISO) 8879:1986)--an open, internationally accepted standard for document interchange was used to encode medical observations acquired in an Internet-based structured reporting system. The resulting report is self-documenting: it includes a definition of its allowable data fields and values encoded as a report-specific SGML document type definition (DTD). The data-entry forms, DTD, and report document instances are based on report specifications written in a simple, SGML-based language designed for that purpose. Reporting concepts can be linked with those of external vocabularies such as the Unified Medical Language System (UMLS) Metathesaurus. The use of open standards such as SGML is an important step in the creation of open, universally comprehensible structured reports.

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.

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

Biological Diversity in the Patent System

PubMed Central

Oldham, Paul; Hall, Stephen; Forero, Oscar

2013-01-01

Biological diversity in the patent system is an enduring focus of controversy but empirical analysis of the presence of biodiversity in the patent system has been limited. To address this problem we text mined 11 million patent documents for 6 million Latin species names from the Global Names Index (GNI) established by the Global Biodiversity Information Facility (GBIF) and Encyclopedia of Life (EOL). We identified 76,274 full Latin species names from 23,882 genera in 767,955 patent documents. 25,595 species appeared in the claims section of 136,880 patent documents. This reveals that human innovative activity involving biodiversity in the patent system focuses on approximately 4% of taxonomically described species and between 0.8–1% of predicted global species. In this article we identify the major features of the patent landscape for biological diversity by focusing on key areas including pharmaceuticals, neglected diseases, traditional medicines, genetic engineering, foods, biocides, marine genetic resources and Antarctica. We conclude that the narrow focus of human innovative activity and ownership of genetic resources is unlikely to be in the long term interest of humanity. We argue that a broader spectrum of biodiversity needs to be opened up to research and development based on the principles of equitable benefit-sharing, respect for the objectives of the Convention on Biological Diversity, human rights and ethics. Finally, we argue that alternative models of innovation, such as open source and commons models, are required to open up biodiversity for research that addresses actual and neglected areas of human need. The research aims to inform the implementation of the 2010 Nagoya Protocol on Access to Genetic Resources and the Equitable Sharing of Benefits Arising from their Utilization and international debates directed to the governance of genetic resources. Our research also aims to inform debates under the Intergovernmental Committee on Intellectual Property and Genetic Resources, Traditional Knowledge and Folklore at the World Intellectual Property Organization. PMID:24265714

Cf-252 Characterization Documents

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

Feldman, Alexander

2014-03-14

Six documents were written by Vance and Associates under contract to the Off-Site Source Recovery Project of Los Alamos National Laboratory. These Six documents provided the basis for characterization of Californium-252 sealed sources and for the packaging and manifesting of this material for disposal at the Waste Isolation Pilot Project. The Six documents are: 1. VA-OSR-10, Development of radionuclide distributions for Cf-252 sealed sources. 2. VA-OSR-11, Uncertainty analysis for Cf-252 sealed sources. 3. VA-OSR-12, To determine the radionuclides in the waste drums containing Cf-252 sealed source waste that are required to be reported under the requirements of the WIPP WACmore » and the TRAMPAC. 4. VA-OSR-13, Development of the spreadsheet for the radiological calculations for the characterization of Cf-252 sources. 5. VA-OSR-14, Relative importance of neutron-induced fission in Cf-252 sources. 6. VA-OSR-15, Determine upper bound of decay product inventories from a drum of Cf-252 sources. These six documents provide the technical basis for the characterization of Cf-252 sources and will be part of the AK documentation required for submittal to the Central Characterization Project (CCP) of WIPP.« less

Polar Domain Discovery with Sparkler

NASA Astrophysics Data System (ADS)

Duerr, R.; Khalsa, S. J. S.; Mattmann, C. A.; Ottilingam, N. K.; Singh, K.; Lopez, L. A.

2017-12-01

The scientific web is vast and ever growing. It encompasses millions of textual, scientific and multimedia documents describing research in a multitude of scientific streams. Most of these documents are hidden behind forms which require user action to retrieve and thus can't be directly accessed by content crawlers. These documents are hosted on web servers across the world, most often on outdated hardware and network infrastructure. Hence it is difficult and time-consuming to aggregate documents from the scientific web, especially those relevant to a specific domain. Thus generating meaningful domain-specific insights is currently difficult. We present an automated discovery system (Figure 1) using Sparkler, an open-source, extensible, horizontally scalable crawler which facilitates high throughput and focused crawling of documents pertinent to a particular domain such as information about polar regions. With this set of highly domain relevant documents, we show that it is possible to answer analytical questions about that domain. Our domain discovery algorithm leverages prior domain knowledge to reach out to commercial/scientific search engines to generate seed URLs. Subject matter experts then annotate these seed URLs manually on a scale from highly relevant to irrelevant. We leverage this annotated dataset to train a machine learning model which predicts the `domain relevance' of a given document. We extend Sparkler with this model to focus crawling on documents relevant to that domain. Sparkler avoids disruption of service by 1) partitioning URLs by hostname such that every node gets a different host to crawl and by 2) inserting delays between subsequent requests. With an NSF-funded supercomputer Wrangler, we scaled our domain discovery pipeline to crawl about 200k polar specific documents from the scientific web, within a day.

CDAPubMed: a browser extension to retrieve EHR-based biomedical literature.

PubMed

Perez-Rey, David; Jimenez-Castellanos, Ana; Garcia-Remesal, Miguel; Crespo, Jose; Maojo, Victor

2012-04-05

Over the last few decades, the ever-increasing output of scientific publications has led to new challenges to keep up to date with the literature. In the biomedical area, this growth has introduced new requirements for professionals, e.g., physicians, who have to locate the exact papers that they need for their clinical and research work amongst a huge number of publications. Against this backdrop, novel information retrieval methods are even more necessary. While web search engines are widespread in many areas, facilitating access to all kinds of information, additional tools are required to automatically link information retrieved from these engines to specific biomedical applications. In the case of clinical environments, this also means considering aspects such as patient data security and confidentiality or structured contents, e.g., electronic health records (EHRs). In this scenario, we have developed a new tool to facilitate query building to retrieve scientific literature related to EHRs. We have developed CDAPubMed, an open-source web browser extension to integrate EHR features in biomedical literature retrieval approaches. Clinical users can use CDAPubMed to: (i) load patient clinical documents, i.e., EHRs based on the Health Level 7-Clinical Document Architecture Standard (HL7-CDA), (ii) identify relevant terms for scientific literature search in these documents, i.e., Medical Subject Headings (MeSH), automatically driven by the CDAPubMed configuration, which advanced users can optimize to adapt to each specific situation, and (iii) generate and launch literature search queries to a major search engine, i.e., PubMed, to retrieve citations related to the EHR under examination. CDAPubMed is a platform-independent tool designed to facilitate literature searching using keywords contained in specific EHRs. CDAPubMed is visually integrated, as an extension of a widespread web browser, within the standard PubMed interface. It has been tested on a public dataset of HL7-CDA documents, returning significantly fewer citations since queries are focused on characteristics identified within the EHR. For instance, compared with more than 200,000 citations retrieved by breast neoplasm, fewer than ten citations were retrieved when ten patient features were added using CDAPubMed. This is an open source tool that can be freely used for non-profit purposes and integrated with other existing systems.

CDAPubMed: a browser extension to retrieve EHR-based biomedical literature

PubMed Central

2012-01-01

Background Over the last few decades, the ever-increasing output of scientific publications has led to new challenges to keep up to date with the literature. In the biomedical area, this growth has introduced new requirements for professionals, e.g., physicians, who have to locate the exact papers that they need for their clinical and research work amongst a huge number of publications. Against this backdrop, novel information retrieval methods are even more necessary. While web search engines are widespread in many areas, facilitating access to all kinds of information, additional tools are required to automatically link information retrieved from these engines to specific biomedical applications. In the case of clinical environments, this also means considering aspects such as patient data security and confidentiality or structured contents, e.g., electronic health records (EHRs). In this scenario, we have developed a new tool to facilitate query building to retrieve scientific literature related to EHRs. Results We have developed CDAPubMed, an open-source web browser extension to integrate EHR features in biomedical literature retrieval approaches. Clinical users can use CDAPubMed to: (i) load patient clinical documents, i.e., EHRs based on the Health Level 7-Clinical Document Architecture Standard (HL7-CDA), (ii) identify relevant terms for scientific literature search in these documents, i.e., Medical Subject Headings (MeSH), automatically driven by the CDAPubMed configuration, which advanced users can optimize to adapt to each specific situation, and (iii) generate and launch literature search queries to a major search engine, i.e., PubMed, to retrieve citations related to the EHR under examination. Conclusions CDAPubMed is a platform-independent tool designed to facilitate literature searching using keywords contained in specific EHRs. CDAPubMed is visually integrated, as an extension of a widespread web browser, within the standard PubMed interface. It has been tested on a public dataset of HL7-CDA documents, returning significantly fewer citations since queries are focused on characteristics identified within the EHR. For instance, compared with more than 200,000 citations retrieved by breast neoplasm, fewer than ten citations were retrieved when ten patient features were added using CDAPubMed. This is an open source tool that can be freely used for non-profit purposes and integrated with other existing systems. PMID:22480327

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.

Modelling of Operative Report Documents for Data Integration into an openEHR-Based Enterprise Data Warehouse.

PubMed

Haarbrandt, Birger; Wilschko, Andreas; Marschollek, Michael

2016-01-01

In order to integrate operative report documents from two operating room management systems into a data warehouse, we investigated the application of the two-level modelling approach of openEHR to create a shared data model. Based on the systems' analyses, a template consisting of 13 archetypes has been developed. Of these 13 archetypes, 3 have been obtained from the international archetype repository of the openEHR foundation. The remaining 10 archetypes have been newly created. The template was evaluated by an application system expert and through conducting a first test mapping of real-world data from one of the systems. The evaluation showed that by using the two-level modelling approach of openEHR, we succeeded to represent an integrated and shared information model for operative report documents. More research is needed to learn about the limitations of this approach in other data integration scenarios.

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

NASA Astrophysics Data System (ADS)

Slaughter, A.; Johnson, M.

2017-12-01

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

CoNekT: an open-source framework for comparative genomic and transcriptomic network analyses.

PubMed

Proost, Sebastian; Mutwil, Marek

2018-05-01

The recent accumulation of gene expression data in the form of RNA sequencing creates unprecedented opportunities to study gene regulation and function. Furthermore, comparative analysis of the expression data from multiple species can elucidate which functional gene modules are conserved across species, allowing the study of the evolution of these modules. However, performing such comparative analyses on raw data is not feasible for many biologists. Here, we present CoNekT (Co-expression Network Toolkit), an open source web server, that contains user-friendly tools and interactive visualizations for comparative analyses of gene expression data and co-expression networks. These tools allow analysis and cross-species comparison of (i) gene expression profiles; (ii) co-expression networks; (iii) co-expressed clusters involved in specific biological processes; (iv) tissue-specific gene expression; and (v) expression profiles of gene families. To demonstrate these features, we constructed CoNekT-Plants for green alga, seed plants and flowering plants (Picea abies, Chlamydomonas reinhardtii, Vitis vinifera, Arabidopsis thaliana, Oryza sativa, Zea mays and Solanum lycopersicum) and thus provide a web-tool with the broadest available collection of plant phyla. CoNekT-Plants is freely available from http://conekt.plant.tools, while the CoNekT source code and documentation can be found at https://github.molgen.mpg.de/proost/CoNekT/.

Design Support System for Open Distance Learning Student Teamwork

NASA Astrophysics Data System (ADS)

Putranto, A.; Pradipto, Y. D.

2017-01-01

Open distance learning students in doing team assignment, they seldom face to some problems such as student fell unfair in numbers of workload contribution, instructors also do not know which students do more work than others. So there are some questions ie: how to connect between instructor, team members, and working documents. Methods will be used are first, analyzing current condition and last by designing systems to connect between instructor, team members, and document. The expected result is support systems for open distance learning student teamwork.

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

PubMed

Giancarlo, R; Scaturro, D; Utro, F

2015-02-01

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

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.

Open-source hardware for medical devices

PubMed Central

2016-01-01

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

Open-source hardware for medical devices.

PubMed

Niezen, Gerrit; Eslambolchilar, Parisa; Thimbleby, Harold

2016-04-01

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

The case for open-source software in drug discovery.

PubMed

DeLano, Warren L

2005-02-01

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

Direct solar energy conversion for large scale terrestrial use

NASA Technical Reports Server (NTRS)

Boeer, K. W.; Meakin, J. D.

1975-01-01

Various techniques to increase the open circuit voltage are being explored. It had been previously observed that cells made on CdS deposited from a single source gave a consistently higher V sub oc. Further tests have now shown that this effect may in fact relate to differences in source and substrate temperatures. The resulting differences in CdS structure and crystallinity are being documented. Deposits of mixed CdS and ZnS are being produced and will be initially made into cells using the conventional barriering technique. Analysis of I-V characteristics at temperatures between 25 and 110 C is being perfected to provide nondestructive analysis of the Cu2S. Changes due to vacuum heat treatments and exposure to oxygen are also being monitored by the same technique. Detailed spectral response measurements are being made.

A System for Information Management in BioMedical Studies—SIMBioMS

PubMed Central

Krestyaninova, Maria; Zarins, Andris; Viksna, Juris; Kurbatova, Natalja; Rucevskis, Peteris; Neogi, Sudeshna Guha; Gostev, Mike; Perheentupa, Teemu; Knuuttila, Juha; Barrett, Amy; Lappalainen, Ilkka; Rung, Johan; Podnieks, Karlis; Sarkans, Ugis; McCarthy, Mark I; Brazma, Alvis

2009-01-01

Summary: SIMBioMS is a web-based open source software system for managing data and information in biomedical studies. It provides a solution for the collection, storage, management and retrieval of information about research subjects and biomedical samples, as well as experimental data obtained using a range of high-throughput technologies, including gene expression, genotyping, proteomics and metabonomics. The system can easily be customized and has proven to be successful in several large-scale multi-site collaborative projects. It is compatible with emerging functional genomics data standards and provides data import and export in accepted standard formats. Protocols for transferring data to durable archives at the European Bioinformatics Institute have been implemented. Availability: The source code, documentation and initialization scripts are available at http://simbioms.org. Contact: support@simbioms.org; mariak@ebi.ac.uk PMID:19633095

HALE UAS Concept of Operations. Version 3.0

NASA Technical Reports Server (NTRS)

2006-01-01

This document is a system level Concept of Operations (CONOPS) from the perspective of future High Altitude Long Endurance (HALE) Unmanned Aircraft Systems (UAS) service providers and National Airspace System (NAS) users. It describes current systems (existing UAS), describes HALE UAS functions and operations to be performed (via sample missions), and offers insight into the user s environment (i.e., the UAS as a system of systems). It is intended to be a source document for NAS UAS operational requirements, and provides a construct for government agencies to use in guiding their regulatory decisions, architecture requirements, and investment strategies. Although it does not describe the technical capabilities of a specific HALE UAS system (which do, and will vary widely), it is intended to aid in requirements capture and to be used as input to the functional requirements and analysis process. The document provides a basis for development of functional requirements and operational guidelines to achieve unrestricted access into the NAS. This document is an FY06 update to the FY05 Access 5 Project-approved Concept of Operations document previously published in the Public Domain on the Access 5 open website. This version is recommended to be approved for public release also. The updates are a reorganization of materials from the previous version with the addition of an updated set of operational requirements, inclusion of sample mission scenarios, and identification of roles and responsibilities of interfaces within flight phases.

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

NASA Astrophysics Data System (ADS)

Johansson, Björn; Sudzina, Frantisek

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

78 FR 17942 - Draft of SWGDOC Standard for Indentation Examinations

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-25

..., Office of Justice Programs, National Institute of Justice, Scientific Working Group for Forensic Document... Indentation Examinations''. The opportunity to provide comments on this document is open to forensic document...

SUSHI: an exquisite recipe for fully documented, reproducible and reusable NGS data analysis.

PubMed

Hatakeyama, Masaomi; Opitz, Lennart; Russo, Giancarlo; Qi, Weihong; Schlapbach, Ralph; Rehrauer, Hubert

2016-06-02

Next generation sequencing (NGS) produces massive datasets consisting of billions of reads and up to thousands of samples. Subsequent bioinformatic analysis is typically done with the help of open source tools, where each application performs a single step towards the final result. This situation leaves the bioinformaticians with the tasks to combine the tools, manage the data files and meta-information, document the analysis, and ensure reproducibility. We present SUSHI, an agile data analysis framework that relieves bioinformaticians from the administrative challenges of their data analysis. SUSHI lets users build reproducible data analysis workflows from individual applications and manages the input data, the parameters, meta-information with user-driven semantics, and the job scripts. As distinguishing features, SUSHI provides an expert command line interface as well as a convenient web interface to run bioinformatics tools. SUSHI datasets are self-contained and self-documented on the file system. This makes them fully reproducible and ready to be shared. With the associated meta-information being formatted as plain text tables, the datasets can be readily further analyzed and interpreted outside SUSHI. SUSHI provides an exquisite recipe for analysing NGS data. By following the SUSHI recipe, SUSHI makes data analysis straightforward and takes care of documentation and administration tasks. Thus, the user can fully dedicate his time to the analysis itself. SUSHI is suitable for use by bioinformaticians as well as life science researchers. It is targeted for, but by no means constrained to, NGS data analysis. Our SUSHI instance is in productive use and has served as data analysis interface for more than 1000 data analysis projects. SUSHI source code as well as a demo server are freely available.

Developing open-source codes for electromagnetic geophysics using industry support

NASA Astrophysics Data System (ADS)

Key, K.

2017-12-01

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

76 FR 60754 - Preserving the Open Internet

Federal Register 2010, 2011, 2012, 2013, 2014

2011-09-30

...-201] Preserving the Open Internet AGENCY: Federal Communications Commission. ACTION: Final rule..., 2011, a document establishing rules to preserve the open Internet. Inadvertently the wrong paragraph... alleging violations of the open Internet rules. Federal Communications Commission. Matt Warner, Attorney...

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

ERIC Educational Resources Information Center

Wang, Jing

2013-01-01

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

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

ERIC Educational Resources Information Center

Kisworo, Marsudi Wahyu

2016-01-01

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

An Analysis of Open Source Security Software Products Downloads

ERIC Educational Resources Information Center

Barta, Brian J.

2014-01-01

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

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

NASA Astrophysics Data System (ADS)

Wang, Lei; Zhang, Dandan

2017-06-01

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

Innovating to enhance clinical data management using non-commercial and open source solutions across a multi-center network supporting inpatient pediatric care and research in Kenya

PubMed Central

Tuti, Timothy; Bitok, Michael; Paton, Chris; Makone, Boniface; Malla, Lucas; Muinga, Naomi; Gathara, David; English, Mike

2016-01-01

Objective To share approaches and innovations adopted to deliver a relatively inexpensive clinical data management (CDM) framework within a low-income setting that aims to deliver quality pediatric data useful for supporting research, strengthening the information culture and informing improvement efforts in local clinical practice. Materials and methods The authors implemented a CDM framework to support a Clinical Information Network (CIN) using Research Electronic Data Capture (REDCap), a noncommercial software solution designed for rapid development and deployment of electronic data capture tools. It was used for collection of standardized data from case records of multiple hospitals’ pediatric wards. R, an open-source statistical language, was used for data quality enhancement, analysis, and report generation for the hospitals. Results In the first year of CIN, the authors have developed innovative solutions to support the implementation of a secure, rapid pediatric data collection system spanning 14 hospital sites with stringent data quality checks. Data have been collated on over 37 000 admission episodes, with considerable improvement in clinical documentation of admissions observed. Using meta-programming techniques in R, coupled with branching logic, randomization, data lookup, and Application Programming Interface (API) features offered by REDCap, CDM tasks were configured and automated to ensure quality data was delivered for clinical improvement and research use. Conclusion A low-cost clinically focused but geographically dispersed quality CDM (Clinical Data Management) in a long-term, multi-site, and real world context can be achieved and sustained and challenges can be overcome through thoughtful design and implementation of open-source tools for handling data and supporting research. PMID:26063746

Innovating to enhance clinical data management using non-commercial and open source solutions across a multi-center network supporting inpatient pediatric care and research in Kenya.

PubMed

Tuti, Timothy; Bitok, Michael; Paton, Chris; Makone, Boniface; Malla, Lucas; Muinga, Naomi; Gathara, David; English, Mike

2016-01-01

To share approaches and innovations adopted to deliver a relatively inexpensive clinical data management (CDM) framework within a low-income setting that aims to deliver quality pediatric data useful for supporting research, strengthening the information culture and informing improvement efforts in local clinical practice. The authors implemented a CDM framework to support a Clinical Information Network (CIN) using Research Electronic Data Capture (REDCap), a noncommercial software solution designed for rapid development and deployment of electronic data capture tools. It was used for collection of standardized data from case records of multiple hospitals' pediatric wards. R, an open-source statistical language, was used for data quality enhancement, analysis, and report generation for the hospitals. In the first year of CIN, the authors have developed innovative solutions to support the implementation of a secure, rapid pediatric data collection system spanning 14 hospital sites with stringent data quality checks. Data have been collated on over 37 000 admission episodes, with considerable improvement in clinical documentation of admissions observed. Using meta-programming techniques in R, coupled with branching logic, randomization, data lookup, and Application Programming Interface (API) features offered by REDCap, CDM tasks were configured and automated to ensure quality data was delivered for clinical improvement and research use. A low-cost clinically focused but geographically dispersed quality CDM (Clinical Data Management) in a long-term, multi-site, and real world context can be achieved and sustained and challenges can be overcome through thoughtful design and implementation of open-source tools for handling data and supporting research. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association.

Online molecular image repository and analysis system: A multicenter collaborative open-source infrastructure for molecular imaging research and application.

PubMed

Rahman, Mahabubur; Watabe, Hiroshi

2018-05-01

Molecular imaging serves as an important tool for researchers and clinicians to visualize and investigate complex biochemical phenomena using specialized instruments; these instruments are either used individually or in combination with targeted imaging agents to obtain images related to specific diseases with high sensitivity, specificity, and signal-to-noise ratios. However, molecular imaging, which is a multidisciplinary research field, faces several challenges, including the integration of imaging informatics with bioinformatics and medical informatics, requirement of reliable and robust image analysis algorithms, effective quality control of imaging facilities, and those related to individualized disease mapping, data sharing, software architecture, and knowledge management. As a cost-effective and open-source approach to address these challenges related to molecular imaging, we develop a flexible, transparent, and secure infrastructure, named MIRA, which stands for Molecular Imaging Repository and Analysis, primarily using the Python programming language, and a MySQL relational database system deployed on a Linux server. MIRA is designed with a centralized image archiving infrastructure and information database so that a multicenter collaborative informatics platform can be built. The capability of dealing with metadata, image file format normalization, and storing and viewing different types of documents and multimedia files make MIRA considerably flexible. With features like logging, auditing, commenting, sharing, and searching, MIRA is useful as an Electronic Laboratory Notebook for effective knowledge management. In addition, the centralized approach for MIRA facilitates on-the-fly access to all its features remotely through any web browser. Furthermore, the open-source approach provides the opportunity for sustainable continued development. MIRA offers an infrastructure that can be used as cross-boundary collaborative MI research platform for the rapid achievement in cancer diagnosis and therapeutics. Copyright © 2018 Elsevier Ltd. All rights reserved.

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

PubMed Central

2011-01-01

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

The 2017 Bioinformatics Open Source Conference (BOSC)

PubMed Central

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

2017-01-01

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

The 2017 Bioinformatics Open Source Conference (BOSC).

PubMed

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

2017-01-01

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

The Efficient Utilization of Open Source Information

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

Baty, Samuel R.

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

Guidance and Control Software Project Data - Volume 1: Planning 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 planning documents from the GCS project. Volume 1 contains five appendices: A. Plan for Software Aspects of Certification for the Guidance and Control Software Project; B. Software Development Standards for the Guidance and Control Software Project; C. Software Verification Plan for the Guidance and Control Software Project; D. Software Configuration Management Plan for the Guidance and Control Software Project; and E. Software Quality Assurance Activities.

Guidance and Control Software Project Data - Volume 3: Verification 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 verification documents from the GCS project. Volume 3 contains four appendices: A. Software Verification Cases and Procedures for the Guidance and Control Software Project; B. Software Verification Results for the Pluto Implementation of the Guidance and Control Software; C. Review Records for the Pluto Implementation of the Guidance and Control Software; and D. Test Results Logs for the Pluto Implementation of the Guidance and Control Software.

NPTFit: A Code Package for Non-Poissonian Template Fitting

NASA Astrophysics Data System (ADS)

Mishra-Sharma, Siddharth; Rodd, Nicholas L.; Safdi, Benjamin R.

2017-06-01

We present NPTFit, an open-source code package, written in Python and Cython, for performing non-Poissonian template fits (NPTFs). The NPTF is a recently developed statistical procedure for characterizing the contribution of unresolved point sources (PSs) to astrophysical data sets. The NPTF was first applied to Fermi gamma-ray data to provide evidence that the excess of ˜GeV gamma-rays observed in the inner regions of the Milky Way likely arises from a population of sub-threshold point sources, and the NPTF has since found additional applications studying sub-threshold extragalactic sources at high Galactic latitudes. The NPTF generalizes traditional astrophysical template fits to allow for the ability to search for populations of unresolved PSs that may follow a given spatial distribution. NPTFit builds upon the framework of the fluctuation analyses developed in X-ray astronomy, thus it likely has applications beyond those demonstrated with gamma-ray data. The NPTFit package utilizes novel computational methods to perform the NPTF efficiently. The code is available at http://github.com/bsafdi/NPTFit and up-to-date and extensive documentation may be found at http://nptfit.readthedocs.io.

Technical structure of the global nanoscience and nanotechnology literature

NASA Astrophysics Data System (ADS)

Kostoff, Ronald N.; Koytcheff, Raymond G.; Lau, Clifford G. Y.

2007-10-01

Text mining was used to extract technical intelligence from the open source global nanotechnology and nanoscience research literature. An extensive nanotechnology/nanoscience-focused query was applied to the Science Citation Index/Social Science Citation Index (SCI/SSCI) databases. The nanotechnology/nanoscience research literature technical structure (taxonomy) was obtained using computational linguistics/document clustering and factor analysis. The infrastructure (prolific authors, key journals/institutions/countries, most cited authors/journals/documents) for each of the clusters generated by the document clustering algorithm was obtained using bibliometrics. Another novel addition was the use of phrase auto-correlation maps to show technical thrust areas based on phrase co-occurrence in Abstracts, and the use of phrase-phrase cross-correlation maps to show technical thrust areas based on phrase relations due to the sharing of common co-occurring phrases. The ˜400 most cited nanotechnology papers since 1991 were grouped, and their characteristics generated. Whereas the main analysis provided technical thrusts of all nanotechnology papers retrieved, analysis of the most cited papers allowed their characteristics to be displayed. Finally, most cited papers from selected time periods were extracted, along with all publications from those time periods, and the institutions and countries were compared based on their representation in the most cited documents list relative to their representation in the most publications list.

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.

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…

Development of an open metadata schema for prospective clinical research (openPCR) in China.

PubMed

Xu, W; Guan, Z; Sun, J; Wang, Z; Geng, Y

2014-01-01

In China, deployment of electronic data capture (EDC) and clinical data management system (CDMS) for clinical research (CR) is in its very early stage, and about 90% of clinical studies collected and submitted clinical data manually. This work aims to build an open metadata schema for Prospective Clinical Research (openPCR) in China based on openEHR archetypes, in order to help Chinese researchers easily create specific data entry templates for registration, study design and clinical data collection. Singapore Framework for Dublin Core Application Profiles (DCAP) is used to develop openPCR and four steps such as defining the core functional requirements and deducing the core metadata items, developing archetype models, defining metadata terms and creating archetype records, and finally developing implementation syntax are followed. The core functional requirements are divided into three categories: requirements for research registration, requirements for trial design, and requirements for case report form (CRF). 74 metadata items are identified and their Chinese authority names are created. The minimum metadata set of openPCR includes 3 documents, 6 sections, 26 top level data groups, 32 lower data groups and 74 data elements. The top level container in openPCR is composed of public document, internal document and clinical document archetypes. A hierarchical structure of openPCR is established according to Data Structure of Electronic Health Record Architecture and Data Standard of China (Chinese EHR Standard). Metadata attributes are grouped into six parts: identification, definition, representation, relation, usage guides, and administration. OpenPCR is an open metadata schema based on research registration standards, standards of the Clinical Data Interchange Standards Consortium (CDISC) and Chinese healthcare related standards, and is to be publicly available throughout China. It considers future integration of EHR and CR by adopting data structure and data terms in Chinese EHR Standard. Archetypes in openPCR are modularity models and can be separated, recombined, and reused. The authors recommend that the method to develop openPCR can be referenced by other countries when designing metadata schema of clinical research. In the next steps, openPCR should be used in a number of CR projects to test its applicability and to continuously improve its coverage. Besides, metadata schema for research protocol can be developed to structurize and standardize protocol, and syntactical interoperability of openPCR with other related standards can be considered.

The Emergence of Open-Source Software in North America

ERIC Educational Resources Information Center

Pan, Guohua; Bonk, Curtis J.

2007-01-01

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

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.

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

NASA Astrophysics Data System (ADS)

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

2012-04-01

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

The tissue microarray data exchange specification: A community-based, open source tool for sharing tissue microarray data

PubMed Central

Berman, Jules J; Edgerton, Mary E; Friedman, Bruce A

2003-01-01

Background Tissue Microarrays (TMAs) allow researchers to examine hundreds of small tissue samples on a single glass slide. The information held in a single TMA slide may easily involve Gigabytes of data. To benefit from TMA technology, the scientific community needs an open source TMA data exchange specification that will convey all of the data in a TMA experiment in a format that is understandable to both humans and computers. A data exchange specification for TMAs allows researchers to submit their data to journals and to public data repositories and to share or merge data from different laboratories. In May 2001, the Association of Pathology Informatics (API) hosted the first in a series of four workshops, co-sponsored by the National Cancer Institute, to develop an open, community-supported TMA data exchange specification. Methods A draft tissue microarray data exchange specification was developed through workshop meetings. The first workshop confirmed community support for the effort and urged the creation of an open XML-based specification. This was to evolve in steps with approval for each step coming from the stakeholders in the user community during open workshops. By the fourth workshop, held October, 2002, a set of Common Data Elements (CDEs) was established as well as a basic strategy for organizing TMA data in self-describing XML documents. Results The TMA data exchange specification is a well-formed XML document with four required sections: 1) Header, containing the specification Dublin Core identifiers, 2) Block, describing the paraffin-embedded array of tissues, 3)Slide, describing the glass slides produced from the Block, and 4) Core, containing all data related to the individual tissue samples contained in the array. Eighty CDEs, conforming to the ISO-11179 specification for data elements constitute XML tags used in the TMA data exchange specification. A set of six simple semantic rules describe the complete data exchange specification. Anyone using the data exchange specification can validate their TMA files using a software implementation written in Perl and distributed as a supplemental file with this publication. Conclusion The TMA data exchange specification is now available in a draft form with community-approved Common Data Elements and a community-approved general file format and data structure. The specification can be freely used by the scientific community. Efforts sponsored by the Association for Pathology Informatics to refine the draft TMA data exchange specification are expected to continue for at least two more years. The interested public is invited to participate in these open efforts. Information on future workshops will be posted at (API we site). PMID:12769826

6 CFR 37.31 - Source document retention.

Code of Federal Regulations, 2014 CFR

2014-01-01

... keep digital images of source documents must retain the images for a minimum of ten years. (4) States... using digital imaging to retain source documents must store the images as follows: (1) Photo images must be stored in the Joint Photographic Experts Group (JPEG) 2000 standard for image compression, or a...

6 CFR 37.31 - Source document retention.

Code of Federal Regulations, 2012 CFR

2012-01-01

... keep digital images of source documents must retain the images for a minimum of ten years. (4) States... using digital imaging to retain source documents must store the images as follows: (1) Photo images must be stored in the Joint Photographic Experts Group (JPEG) 2000 standard for image compression, or a...

6 CFR 37.31 - Source document retention.

Code of Federal Regulations, 2010 CFR

2010-01-01

... keep digital images of source documents must retain the images for a minimum of ten years. (4) States... using digital imaging to retain source documents must store the images as follows: (1) Photo images must be stored in the Joint Photographic Experts Group (JPEG) 2000 standard for image compression, or a...

6 CFR 37.31 - Source document retention.

Code of Federal Regulations, 2011 CFR

2011-01-01

... keep digital images of source documents must retain the images for a minimum of ten years. (4) States... using digital imaging to retain source documents must store the images as follows: (1) Photo images must be stored in the Joint Photographic Experts Group (JPEG) 2000 standard for image compression, or a...

6 CFR 37.31 - Source document retention.

Code of Federal Regulations, 2013 CFR

2013-01-01

... keep digital images of source documents must retain the images for a minimum of ten years. (4) States... using digital imaging to retain source documents must store the images as follows: (1) Photo images must be stored in the Joint Photographic Experts Group (JPEG) 2000 standard for image compression, or a...

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

Guidance and Control Software Project Data - Volume 4: Configuration Management and Quality Assurance 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 configuration management and quality assurance documents from the GCS project. Volume 4 contains six appendices: A. Software Accomplishment Summary for the Guidance and Control Software Project; B. Software Configuration Index for the Guidance and Control Software Project; C. Configuration Management Records for the Guidance and Control Software Project; D. Software Quality Assurance Records for the Guidance and Control Software Project; E. Problem Report for the Pluto Implementation of the Guidance and Control Software Project; and F. Support Documentation Change Reports for the Guidance and Control Software Project.

76 FR 1173 - Draft Guidance for Industry on Electronic Source Documentation in Clinical Investigations...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-07

...] Draft Guidance for Industry on Electronic Source Documentation in Clinical Investigations; Availability... Documentation in Clinical Investigations.'' This document provides guidance to sponsors, contract research organizations (CROs), data management centers, and clinical investigators on capturing, using, and archiving...

Genes2WordCloud: a quick way to identify biological themes from gene lists and free text.

PubMed

Baroukh, Caroline; Jenkins, Sherry L; Dannenfelser, Ruth; Ma'ayan, Avi

2011-10-13

Word-clouds recently emerged on the web as a solution for quickly summarizing text by maximizing the display of most relevant terms about a specific topic in the minimum amount of space. As biologists are faced with the daunting amount of new research data commonly presented in textual formats, word-clouds can be used to summarize and represent biological and/or biomedical content for various applications. Genes2WordCloud is a web application that enables users to quickly identify biological themes from gene lists and research relevant text by constructing and displaying word-clouds. It provides users with several different options and ideas for the sources that can be used to generate a word-cloud. Different options for rendering and coloring the word-clouds give users the flexibility to quickly generate customized word-clouds of their choice. Genes2WordCloud is a word-cloud generator and a word-cloud viewer that is based on WordCram implemented using Java, Processing, AJAX, mySQL, and PHP. Text is fetched from several sources and then processed to extract the most relevant terms with their computed weights based on word frequencies. Genes2WordCloud is freely available for use online; it is open source software and is available for installation on any web-site along with supporting documentation at http://www.maayanlab.net/G2W. Genes2WordCloud provides a useful way to summarize and visualize large amounts of textual biological data or to find biological themes from several different sources. The open source availability of the software enables users to implement customized word-clouds on their own web-sites and desktop applications.

Genes2WordCloud: a quick way to identify biological themes from gene lists and free text

PubMed Central

2011-01-01

Background Word-clouds recently emerged on the web as a solution for quickly summarizing text by maximizing the display of most relevant terms about a specific topic in the minimum amount of space. As biologists are faced with the daunting amount of new research data commonly presented in textual formats, word-clouds can be used to summarize and represent biological and/or biomedical content for various applications. Results Genes2WordCloud is a web application that enables users to quickly identify biological themes from gene lists and research relevant text by constructing and displaying word-clouds. It provides users with several different options and ideas for the sources that can be used to generate a word-cloud. Different options for rendering and coloring the word-clouds give users the flexibility to quickly generate customized word-clouds of their choice. Methods Genes2WordCloud is a word-cloud generator and a word-cloud viewer that is based on WordCram implemented using Java, Processing, AJAX, mySQL, and PHP. Text is fetched from several sources and then processed to extract the most relevant terms with their computed weights based on word frequencies. Genes2WordCloud is freely available for use online; it is open source software and is available for installation on any web-site along with supporting documentation at http://www.maayanlab.net/G2W. Conclusions Genes2WordCloud provides a useful way to summarize and visualize large amounts of textual biological data or to find biological themes from several different sources. The open source availability of the software enables users to implement customized word-clouds on their own web-sites and desktop applications. PMID:21995939

Improved Software Testing for Open Architecture

DTIC Science & Technology

2010-04-30

2.5 4.2 28 7  Boston  Whaler  36  6.78 2.5 4 30 8  Zodiac   23  4.7  6.25  4.5  32  5  Wave Runner  44  3.66  6.25  4.4  47  15  The data in Table 1...30 April 2010 bu`bomq=colj=qeb Report Documentation Page Form ApprovedOMB No. 0704-0188 Public reporting burden for the collection of information is...estimated to average 1 hour per response, including the time for reviewing instructions, searching existing data sources, gathering and maintaining

Photogrammetric Archaeological Survey with UAV

NASA Astrophysics Data System (ADS)

Mouget, A.; Lucet, G.

2014-05-01

This document describes a way to obtain various photogrammetric products from aerial photograph using a drone. The aim of the project was to develop a methodology to obtain information for the study of the architecture of pre-Columbian archaeological sites in Mexico combining the manoeuvrability and low cost of a drone with the accuracy of the results of the open source photogrammetric MicMac software. It presents the UAV and the camera used, explains how to manipulate it to carry out stereoscopic photographs, the flight and camera parameters chosen, the treatments performed to obtain orthophotos and 3D models with a centimetric resolution, and finally outlines the quality of the results.

Further Development of Verification Check-Cases for Six- Degree-of-Freedom Flight Vehicle Simulations

NASA Technical Reports Server (NTRS)

Jackson, E. Bruce; Madden, Michael M.; Shelton, Robert; Jackson, A. A.; Castro, Manuel P.; Noble, Deleena M.; Zimmerman, Curtis J.; Shidner, Jeremy D.; White, Joseph P.; Dutta, Doumyo;

ConKit: a python interface to contact predictions.

PubMed

Simkovic, Felix; Thomas, Jens M H; Rigden, Daniel J

2017-07-15

Recent advances in protein residue contact prediction algorithms have led to the emergence of many new methods and a variety of file formats. We present ConKit , an open source, modular and extensible Python interface which allows facile conversion between formats and provides an interface to analyses of sequence alignments and sets of contact predictions. ConKit is available via the Python Package Index. The documentation can be found at http://www.conkit.org . ConKit is licensed under the BSD 3-Clause. hlfsimko@liverpool.ac.uk or drigden@liverpool.ac.uk. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Thermo-msf-parser: an open source Java library to parse and visualize Thermo Proteome Discoverer msf files.

PubMed

Colaert, Niklaas; Barsnes, Harald; Vaudel, Marc; Helsens, Kenny; Timmerman, Evy; Sickmann, Albert; Gevaert, Kris; Martens, Lennart

2011-08-05

The Thermo Proteome Discoverer program integrates both peptide identification and quantification into a single workflow for peptide-centric proteomics. Furthermore, its close integration with Thermo mass spectrometers has made it increasingly popular in the field. Here, we present a Java library to parse the msf files that constitute the output of Proteome Discoverer. The parser is also implemented as a graphical user interface allowing convenient access to the information found in the msf files, and in Rover, a program to analyze and validate quantitative proteomics information. All code, binaries, and documentation is freely available at http://thermo-msf-parser.googlecode.com.

NetProt: Complex-based Feature Selection.

PubMed

Goh, Wilson Wen Bin; Wong, Limsoon

2017-08-04

Protein complex-based feature selection (PCBFS) provides unparalleled reproducibility with high phenotypic relevance on proteomics data. Currently, there are five PCBFS paradigms, but not all representative methods have been implemented or made readily available. To allow general users to take advantage of these methods, we developed the R-package NetProt, which provides implementations of representative feature-selection methods. NetProt also provides methods for generating simulated differential data and generating pseudocomplexes for complex-based performance benchmarking. The NetProt open source R package is available for download from https://github.com/gohwils/NetProt/releases/ , and online documentation is available at http://rpubs.com/gohwils/204259 .

magnum.fe: A micromagnetic finite-element simulation code based on FEniCS

NASA Astrophysics Data System (ADS)

Abert, Claas; Exl, Lukas; Bruckner, Florian; Drews, André; Suess, Dieter

2013-11-01

We have developed a finite-element micromagnetic simulation code based on the FEniCS package called magnum.fe. Here we describe the numerical methods that are applied as well as their implementation with FEniCS. We apply a transformation method for the solution of the demagnetization-field problem. A semi-implicit weak formulation is used for the integration of the Landau-Lifshitz-Gilbert equation. Numerical experiments show the validity of simulation results. magnum.fe is open source and well documented. The broad feature range of the FEniCS package makes magnum.fe a good choice for the implementation of novel micromagnetic finite-element algorithms.

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

PubMed

Deibel, Eric

2014-01-01

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

Building a multi-scaled geospatial temporal ecology database from disparate data sources: fostering open science and data reuse.

PubMed

Soranno, Patricia A; Bissell, Edward G; Cheruvelil, Kendra S; Christel, Samuel T; Collins, Sarah M; Fergus, C Emi; Filstrup, Christopher T; Lapierre, Jean-Francois; Lottig, Noah R; Oliver, Samantha K; Scott, Caren E; Smith, Nicole J; Stopyak, Scott; Yuan, Shuai; Bremigan, Mary Tate; Downing, John A; Gries, Corinna; Henry, Emily N; Skaff, Nick K; Stanley, Emily H; Stow, Craig A; Tan, Pang-Ning; Wagner, Tyler; Webster, Katherine E

2015-01-01

Although there are considerable site-based data for individual or groups of ecosystems, these datasets are widely scattered, have different data formats and conventions, and often have limited accessibility. At the broader scale, national datasets exist for a large number of geospatial features of land, water, and air that are needed to fully understand variation among these ecosystems. However, such datasets originate from different sources and have different spatial and temporal resolutions. By taking an open-science perspective and by combining site-based ecosystem datasets and national geospatial datasets, science gains the ability to ask important research questions related to grand environmental challenges that operate at broad scales. Documentation of such complicated database integration efforts, through peer-reviewed papers, is recommended to foster reproducibility and future use of the integrated database. Here, we describe the major steps, challenges, and considerations in building an integrated database of lake ecosystems, called LAGOS (LAke multi-scaled GeOSpatial and temporal database), that was developed at the sub-continental study extent of 17 US states (1,800,000 km(2)). LAGOS includes two modules: LAGOSGEO, with geospatial data on every lake with surface area larger than 4 ha in the study extent (~50,000 lakes), including climate, atmospheric deposition, land use/cover, hydrology, geology, and topography measured across a range of spatial and temporal extents; and LAGOSLIMNO, with lake water quality data compiled from ~100 individual datasets for a subset of lakes in the study extent (~10,000 lakes). Procedures for the integration of datasets included: creating a flexible database design; authoring and integrating metadata; documenting data provenance; quantifying spatial measures of geographic data; quality-controlling integrated and derived data; and extensively documenting the database. Our procedures make a large, complex, and integrated database reproducible and extensible, allowing users to ask new research questions with the existing database or through the addition of new data. The largest challenge of this task was the heterogeneity of the data, formats, and metadata. Many steps of data integration need manual input from experts in diverse fields, requiring close collaboration.

Building a multi-scaled geospatial temporal ecology database from disparate data sources: Fostering open science through data reuse

USGS Publications Warehouse

Soranno, Patricia A.; Bissell, E.G.; Cheruvelil, Kendra S.; Christel, Samuel T.; Collins, Sarah M.; Fergus, C. Emi; Filstrup, Christopher T.; Lapierre, Jean-Francois; Lotting, Noah R.; Oliver, Samantha K.; Scott, Caren E.; Smith, Nicole J.; Stopyak, Scott; Yuan, Shuai; Bremigan, Mary Tate; Downing, John A.; Gries, Corinna; Henry, Emily N.; Skaff, Nick K.; Stanley, Emily H.; Stow, Craig A.; Tan, Pang-Ning; Wagner, Tyler; Webster, Katherine E.

2015-01-01

Although there are considerable site-based data for individual or groups of ecosystems, these datasets are widely scattered, have different data formats and conventions, and often have limited accessibility. At the broader scale, national datasets exist for a large number of geospatial features of land, water, and air that are needed to fully understand variation among these ecosystems. However, such datasets originate from different sources and have different spatial and temporal resolutions. By taking an open-science perspective and by combining site-based ecosystem datasets and national geospatial datasets, science gains the ability to ask important research questions related to grand environmental challenges that operate at broad scales. Documentation of such complicated database integration efforts, through peer-reviewed papers, is recommended to foster reproducibility and future use of the integrated database. Here, we describe the major steps, challenges, and considerations in building an integrated database of lake ecosystems, called LAGOS (LAke multi-scaled GeOSpatial and temporal database), that was developed at the sub-continental study extent of 17 US states (1,800,000 km2). LAGOS includes two modules: LAGOSGEO, with geospatial data on every lake with surface area larger than 4 ha in the study extent (~50,000 lakes), including climate, atmospheric deposition, land use/cover, hydrology, geology, and topography measured across a range of spatial and temporal extents; and LAGOSLIMNO, with lake water quality data compiled from ~100 individual datasets for a subset of lakes in the study extent (~10,000 lakes). Procedures for the integration of datasets included: creating a flexible database design; authoring and integrating metadata; documenting data provenance; quantifying spatial measures of geographic data; quality-controlling integrated and derived data; and extensively documenting the database. Our procedures make a large, complex, and integrated database reproducible and extensible, allowing users to ask new research questions with the existing database or through the addition of new data. The largest challenge of this task was the heterogeneity of the data, formats, and metadata. Many steps of data integration need manual input from experts in diverse fields, requiring close collaboration.

Final Report for ALCC Allocation: Predictive Simulation of Complex Flow in Wind Farms

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

Barone, Matthew F.; Ananthan, Shreyas; Churchfield, Matt

This report documents work performed using ALCC computing resources granted under a proposal submitted in February 2016, with the resource allocation period spanning the period July 2016 through June 2017. The award allocation was 10.7 million processor-hours at the National Energy Research Scientific Computing Center. The simulations performed were in support of two projects: the Atmosphere to Electrons (A2e) project, supported by the DOE EERE office; and the Exascale Computing Project (ECP), supported by the DOE Office of Science. The project team for both efforts consists of staff scientists and postdocs from Sandia National Laboratories and the National Renewable Energymore » Laboratory. At the heart of these projects is the open-source computational-fluid-dynamics (CFD) code, Nalu. Nalu solves the low-Mach-number Navier-Stokes equations using an unstructured- grid discretization. Nalu leverages the open-source Trilinos solver library and the Sierra Toolkit (STK) for parallelization and I/O. This report documents baseline computational performance of the Nalu code on problems of direct relevance to the wind plant physics application - namely, Large Eddy Simulation (LES) of an atmospheric boundary layer (ABL) flow and wall-modeled LES of a flow past a static wind turbine rotor blade. Parallel performance of Nalu and its constituent solver routines residing in the Trilinos library has been assessed previously under various campaigns. However, both Nalu and Trilinos have been, and remain, in active development and resources have not been available previously to rigorously track code performance over time. With the initiation of the ECP, it is important to establish and document baseline code performance on the problems of interest. This will allow the project team to identify and target any deficiencies in performance, as well as highlight any performance bottlenecks as we exercise the code on a greater variety of platforms and at larger scales. The current study is rather modest in scale, examining performance on problem sizes of O(100 million) elements and core counts up to 8k cores. This will be expanded as more computational resources become available to the projects.« less

Open Learning in the Community. A Collection of Conference Papers (Lancaster, England, March 1988).

ERIC Educational Resources Information Center

Hodgson, Vivien, Ed.; And Others

The 18 papers presented at the conference reported in this document are grouped into four major sections. The first section, on the nature of open learning, includes "How Open Is Open Learning?" (H. Temple); "Open Learning and Community" (I. Cunningham); "Are We Really Open--With Our Learners and Ourselves?" (W. J. K.…

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

ERIC Educational Resources Information Center

Hirst, Tony

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

Free for All: Open Source Software

ERIC Educational Resources Information Center

Schneider, Karen

2008-01-01

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

Contaminants of emerging concern in the open sea waters of the Western Mediterranean.

PubMed

Brumovský, Miroslav; Bečanová, Jitka; Kohoutek, Jiří; Borghini, Mireno; Nizzetto, Luca

2017-10-01

Pollution by chemical substances is of concern for the maintenance of healthy and sustainable aquatic environments. While the occurrence and fate of numerous emerging contaminants, especially pharmaceuticals, is well documented in freshwater, their occurrence and behavior in coastal and marine waters is much less studied and understood. This study investigates the occurrence of 58 chemicals in the open surface water of the Western Mediterranean Sea for the first time. 70 samples in total were collected in 10 different sampling areas. 3 pesticides, 11 pharmaceuticals and personal care products and 2 artificial sweeteners were detected at sub-ng to ng/L levels. Among them, the herbicide terbuthylazine, the pharmaceuticals caffeine, carbamazepine, naproxen and paracetamol, the antibiotic sulfamethoxazole, the antibacterial triclocarban and the two artificial sweeteners acesulfame and saccharin were detected in all samples. The compound detected at the highest concentration was saccharin (up to 5.23 ng/L). Generally small spatial differences among individual sampling areas point to a diffuse character of sources which are likely dominated by WWTP effluents and runoffs from agricultural areas or even, at least for pharmaceuticals and artificial food additives, from offshore sources such as ferries and cruising ships. The implications of the ubiquitous presence in the open sea of chemicals that are bio-active or toxic at low doses on photosynthetic organisms and/or bacteria (i.e., terbuthylazine, sulfamethoxazole or triclocarban) deserve scientific attention, especially concerning possible subtle impacts from chronic exposure of pelagic microorganisms. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

PubMed Central

2015-01-01

Digital data from the political sphere is abundant, omnipresent, and more and more directly accessible through the Internet. Project Vote Smart (PVS) is a prominent example of this big public data and covers various aspects of U.S. politics in astonishing detail. Despite the vast potential of PVS’ data for political science, economics, and sociology, it is hardly used in empirical research. The systematic compilation of semi-structured data can be complicated and time consuming as the data format is not designed for conventional scientific research. This paper presents a new tool that makes the data easily accessible to a broad scientific community. We provide the software called pvsR as an add-on to the R programming environment for statistical computing. This open source interface (OSI) serves as a direct link between a statistical analysis and the large PVS database. The free and open code is expected to substantially reduce the cost of research with PVS’ new big public data in a vast variety of possible applications. We discuss its advantages vis-à-vis traditional methods of data generation as well as already existing interfaces. The validity of the library is documented based on an illustration involving female representation in local politics. In addition, pvsR facilitates the replication of research with PVS data at low costs, including the pre-processing of data. Similar OSIs are recommended for other big public databases. PMID:26132154

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

PubMed

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

2007-01-01

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

MOLGENIS/connect: a system for semi-automatic integration of heterogeneous phenotype data with applications in biobanks.

PubMed

Pang, Chao; van Enckevort, David; de Haan, Mark; Kelpin, Fleur; Jetten, Jonathan; Hendriksen, Dennis; de Boer, Tommy; Charbon, Bart; Winder, Erwin; van der Velde, K Joeri; Doiron, Dany; Fortier, Isabel; Hillege, Hans; Swertz, Morris A

2016-07-15

While the size and number of biobanks, patient registries and other data collections are increasing, biomedical researchers still often need to pool data for statistical power, a task that requires time-intensive retrospective integration. To address this challenge, we developed MOLGENIS/connect, a semi-automatic system to find, match and pool data from different sources. The system shortlists relevant source attributes from thousands of candidates using ontology-based query expansion to overcome variations in terminology. Then it generates algorithms that transform source attributes to a common target DataSchema. These include unit conversion, categorical value matching and complex conversion patterns (e.g. calculation of BMI). In comparison to human-experts, MOLGENIS/connect was able to auto-generate 27% of the algorithms perfectly, with an additional 46% needing only minor editing, representing a reduction in the human effort and expertise needed to pool data. Source code, binaries and documentation are available as open-source under LGPLv3 from http://github.com/molgenis/molgenis and www.molgenis.org/connect : m.a.swertz@rug.nl Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

MOLGENIS/connect: a system for semi-automatic integration of heterogeneous phenotype data with applications in biobanks

PubMed Central

Pang, Chao; van Enckevort, David; de Haan, Mark; Kelpin, Fleur; Jetten, Jonathan; Hendriksen, Dennis; de Boer, Tommy; Charbon, Bart; Winder, Erwin; van der Velde, K. Joeri; Doiron, Dany; Fortier, Isabel; Hillege, Hans

2016-01-01

Motivation: While the size and number of biobanks, patient registries and other data collections are increasing, biomedical researchers still often need to pool data for statistical power, a task that requires time-intensive retrospective integration. Results: To address this challenge, we developed MOLGENIS/connect, a semi-automatic system to find, match and pool data from different sources. The system shortlists relevant source attributes from thousands of candidates using ontology-based query expansion to overcome variations in terminology. Then it generates algorithms that transform source attributes to a common target DataSchema. These include unit conversion, categorical value matching and complex conversion patterns (e.g. calculation of BMI). In comparison to human-experts, MOLGENIS/connect was able to auto-generate 27% of the algorithms perfectly, with an additional 46% needing only minor editing, representing a reduction in the human effort and expertise needed to pool data. Availability and Implementation: Source code, binaries and documentation are available as open-source under LGPLv3 from http://github.com/molgenis/molgenis and www.molgenis.org/connect. Contact: m.a.swertz@rug.nl Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27153686

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

ERIC Educational Resources Information Center

Committee for Economic Development, 2006

2006-01-01

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

caGrid 1.0: An Enterprise Grid Infrastructure for Biomedical Research

PubMed Central

Oster, Scott; Langella, Stephen; Hastings, Shannon; Ervin, David; Madduri, Ravi; Phillips, Joshua; Kurc, Tahsin; Siebenlist, Frank; Covitz, Peter; Shanbhag, Krishnakant; Foster, Ian; Saltz, Joel

2008-01-01

Objective 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™) 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 and 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: https://cabig.nci.nih.gov/workspaces/Architecture/caGrid. Conclusions While caGrid 1.0 is designed to address use cases in cancer research, the requirements associated with discovery, analysis and integration of large scale data, and coordinated studies are common in other biomedical fields. In this respect, caGrid 1.0 is the realization of a framework that can benefit the entire biomedical community. PMID:18096909

caGrid 1.0: an enterprise Grid infrastructure for biomedical research.

PubMed

Oster, Scott; Langella, Stephen; Hastings, Shannon; Ervin, David; Madduri, Ravi; Phillips, Joshua; Kurc, Tahsin; Siebenlist, Frank; Covitz, Peter; Shanbhag, Krishnakant; Foster, Ian; Saltz, Joel

2008-01-01

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. 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) 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. The caGrid is built as a Grid software infrastructure and 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. 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: https://cabig.nci.nih.gov/workspaces/Architecture/caGrid. While caGrid 1.0 is designed to address use cases in cancer research, the requirements associated with discovery, analysis and integration of large scale data, and coordinated studies are common in other biomedical fields. In this respect, caGrid 1.0 is the realization of a framework that can benefit the entire biomedical community.

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

Guidance Determining Applicability of New Major Source Regulations in the Granting of Construction Permits to Sources of Air Emissions

EPA Pesticide Factsheets

This document may be of assistance in applying the New Source Review (NSR) air permitting regulations including the Prevention of Significant Deterioration (PSD) requirements. This document is part of the NSR Policy and Guidance Database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Forensic document analysis using scanning microscopy

NASA Astrophysics Data System (ADS)

Shaffer, Douglas K.

2009-05-01

The authentication and identification of the source of a printed document(s) can be important in forensic investigations involving a wide range of fraudulent materials, including counterfeit currency, travel and identity documents, business and personal checks, money orders, prescription labels, travelers checks, medical records, financial documents and threatening correspondence. The physical and chemical characterization of document materials - including paper, writing inks and printed media - is becoming increasingly relevant for law enforcement agencies, with the availability of a wide variety of sophisticated commercial printers and copiers which are capable of producing fraudulent documents of extremely high print quality, rendering these difficult to distinguish from genuine documents. This paper describes various applications and analytical methodologies using scanning electron miscoscopy/energy dispersive (x-ray) spectroscopy (SEM/EDS) and related technologies for the characterization of fraudulent documents, and illustrates how their morphological and chemical profiles can be compared to (1) authenticate and (2) link forensic documents with a common source(s) in their production history.

Open Textbook Proof-of-Concept via Connexions

ERIC Educational Resources Information Center

Baker, Judy; Thierstein, Joel; Fletcher, Kathi; Kaur, Manpreet; Emmons, Jonathan

2009-01-01

To address the high cost of textbooks, Rice University's Connexions and the Community College Open Textbook Project (CCOTP) collaborated to develop a proof-of-concept free and open textbook. The proof-of-concept served to document a workflow process that would support adoption of open textbooks. Open textbooks provide faculty and students with a…

The 2016 Bioinformatics Open Source Conference (BOSC).

PubMed

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

2016-01-01

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

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

ERIC Educational Resources Information Center

Villano, Matt

2006-01-01

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

EMISSIONS OF ORGANIC AIR TOXICS FROM OPEN ...

EPA Pesticide Factsheets

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

SFO-Project: The New Generation of Sharable, Editable and Open-Access CFD Tutorials

NASA Astrophysics Data System (ADS)

Javaherchi, Teymour; Javaherchi, Ardeshir; Aliseda, Alberto

2016-11-01

One of the most common approaches to develop a Computational Fluid Dynamic (CFD) simulation for a new case study of interest is to search for the most similar, previously developed and validated CFD simulation among other works. A simple search would result into a pool of written/visual tutorials. However, users should spend significant amount of time and effort to find the most correct, compatible and valid tutorial in this pool and further modify it toward their simulation of interest. SFO is an open-source project with the core idea of saving the above-mentioned time and effort. This is done via documenting/sharing scientific and methodological approaches to develop CFD simulations for a wide spectrum of fundamental and industrial case studies in three different CFD solvers; STAR-CCM +, FLUENT and Open FOAM (SFO). All of the steps and required files of these tutorials are accessible and editable under the common roof of Github (a web-based Git repository hosting service). In this presentation we will present the current library of 20 + developed CFD tutorials, discuss the idea and benefit of using them, their educational values and explain how the next generation of open-access and live resource of CFD tutorials can be built further hand-in-hand within our community.

Running an open experiment: transparency and reproducibility in soil and ecosystem science

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

Bond-Lamberty, Benjamin; Smith, Ashly P.; Bailey, Vanessa L.

Researchers in soil and ecosystem science, and almost every other field, are being pushed--by funders, journals, governments, and their peers--to increase transparency and reproducibility of their work. A key part of this effort is a move towards open data as a way to fight post-publication data loss, improve data and code quality, enable powerful meta- and cross-disciplinary analyses, and increase trust in, and the efficiency of, publicly-funded research. Many scientists however lack experience in, and may be unsure of the benefits of, making their data and fully-reproducible analyses publicly available. Here we describe a recent "open experiment", in which wemore » documented every aspect of a soil incubation online, making all raw data, scripts, diagnostics, final analyses, and manuscripts available in real time. We found that using tools such as version control, issue tracking, and open-source statistical software improved data integrity, accelerated our team's communication and productivity, and ensured transparency. There are many avenues to improve scientific reproducibility and data availability, of which is this only one example, and it is not an approach suited for every experiment or situation. Nonetheless, we encourage the communities in our respective fields to consider its advantages, and to lead rather than follow with respect to scientific reproducibility, transparency, and data availability.« less

Running an open experiment: transparency and reproducibility in soil and ecosystem science

NASA Astrophysics Data System (ADS)

Bond-Lamberty, Ben; Peyton Smith, A.; Bailey, Vanessa

2016-08-01

Researchers in soil and ecosystem science, and almost every other field, are being pushed—by funders, journals, governments, and their peers—to increase transparency and reproducibility of their work. A key part of this effort is a move towards open data as a way to fight post-publication data loss, improve data and code quality, enable powerful meta- and cross-disciplinary analyses, and increase trust in, and the efficiency of, publicly-funded research. Many scientists however lack experience in, and may be unsure of the benefits of, making their data and fully-reproducible analyses publicly available. Here we describe a recent ‘open experiment’, in which we documented every aspect of a soil incubation online, making all raw data, scripts, diagnostics, final analyses, and manuscripts available in real time. We found that using tools such as version control, issue tracking, and open-source statistical software improved data integrity, accelerated our team’s communication and productivity, and ensured transparency. There are many avenues to improve scientific reproducibility and data availability, of which is this only one example, and it is not an approach suited for every experiment or situation. Nonetheless, we encourage the communities in our respective fields to consider its advantages, and to lead rather than follow with respect to scientific reproducibility, transparency, and data availability.

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

PubMed

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

2014-05-01

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

Galaxy Portal: interacting with the galaxy platform through mobile devices.

PubMed

Børnich, Claus; Grytten, Ivar; Hovig, Eivind; Paulsen, Jonas; Čech, Martin; Sandve, Geir Kjetil

2016-06-01

: We present Galaxy Portal app, an open source interface to the Galaxy system through smart phones and tablets. The Galaxy Portal provides convenient and efficient monitoring of job completion, as well as opportunities for inspection of results and execution history. In addition to being useful to the Galaxy community, we believe that the app also exemplifies a useful way of exploiting mobile interfaces for research/high-performance computing resources in general. The source is freely available under a GPL license on GitHub, along with user documentation and pre-compiled binaries and instructions for several platforms: https://github.com/Tarostar/QMLGalaxyPortal It is available for iOS version 7 (and newer) through the Apple App Store, and for Android through Google Play for version 4.1 (API 16) or newer. geirksa@ifi.uio.no. © The Author 2016. Published by Oxford University Press.

ImgLib2--generic image processing in Java.

PubMed

Pietzsch, Tobias; Preibisch, Stephan; Tomancák, Pavel; Saalfeld, Stephan

2012-11-15

ImgLib2 is an open-source Java library for n-dimensional data representation and manipulation with focus on image processing. It aims at minimizing code duplication by cleanly separating pixel-algebra, data access and data representation in memory. Algorithms can be implemented for classes of pixel types and generic access patterns by which they become independent of the specific dimensionality, pixel type and data representation. ImgLib2 illustrates that an elegant high-level programming interface can be achieved without sacrificing performance. It provides efficient implementations of common data types, storage layouts and algorithms. It is the data model underlying ImageJ2, the KNIME Image Processing toolbox and an increasing number of Fiji-Plugins. ImgLib2 is licensed under BSD. Documentation and source code are available at http://imglib2.net and in a public repository at https://github.com/imagej/imglib. Supplementary data are available at Bioinformatics Online. saalfeld@mpi-cbg.de

Microsoft Biology Initiative: .NET Bioinformatics Platform and Tools

PubMed Central

Diaz Acosta, B.

2011-01-01

The Microsoft Biology Initiative (MBI) is an effort in Microsoft Research to bring new technology and tools to the area of bioinformatics and biology. This initiative is comprised of two primary components, the Microsoft Biology Foundation (MBF) and the Microsoft Biology Tools (MBT). MBF is a language-neutral bioinformatics toolkit built as an extension to the Microsoft .NET Framework—initially aimed at the area of Genomics research. Currently, it implements a range of parsers for common bioinformatics file formats; a range of algorithms for manipulating DNA, RNA, and protein sequences; and a set of connectors to biological web services such as NCBI BLAST. MBF is available under an open source license, and executables, source code, demo applications, documentation and training materials are freely downloadable from http://research.microsoft.com/bio. MBT is a collection of tools that enable biology and bioinformatics researchers to be more productive in making scientific discoveries.

BioCIDER: a Contextualisation InDEx for biological Resources discovery

PubMed Central

Horro, Carlos; Cook, Martin; Attwood, Teresa K.; Brazas, Michelle D.; Hancock, John M.; Palagi, Patricia; Corpas, Manuel; Jimenez, Rafael

2017-01-01

Abstract Summary The vast, uncoordinated proliferation of bioinformatics resources (databases, software tools, training materials etc.) makes it difficult for users to find them. To facilitate their discovery, various services are being developed to collect such resources into registries. We have developed BioCIDER, which, rather like online shopping ‘recommendations’, provides a contextualization index to help identify biological resources relevant to the content of the sites in which it is embedded. Availability and Implementation BioCIDER (www.biocider.org) is an open-source platform. Documentation is available online (https://goo.gl/Klc51G), and source code is freely available via GitHub (https://github.com/BioCIDER). The BioJS widget that enables websites to embed contextualization is available from the BioJS registry (http://biojs.io/). All code is released under an MIT licence. Contact carlos.horro@earlham.ac.uk or rafael.jimenez@elixir-europe.org or manuel@repositive.io PMID:28407033

Anchoring historical sequences using a new source of astro-chronological tie-points

NASA Astrophysics Data System (ADS)

Dee, Michael W.; Pope, Benjamin J. S.

2016-08-01

The discovery of past spikes in atmospheric radiocarbon activity, caused by major solar energetic particle events, has opened up new possibilities for high-precision chronometry. The two spikes, or Miyake Events, have now been widely identified in tree-rings that grew in the years 775 and 994 CE. Furthermore, all other plant material that grew in these years would also have incorporated the anomalously high concentrations of radiocarbon. Crucially, some plant-based artefacts, such as papyrus documents, timber beams and linen garments, can also be allocated to specific positions within long, currently unfixed, historical sequences. Thus, Miyake Events represent a new source of tie-points that could provide the means for anchoring early chronologies to the absolute timescale. Here, we explore this possibility, outlining the most expeditious approaches, the current challenges and obstacles, and how they might best be overcome.

BioRuby: bioinformatics software for the Ruby programming language.

PubMed

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

2010-10-15

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

SED-ED, a workflow editor for computational biology experiments written in SED-ML.

PubMed

Adams, Richard R

2012-04-15

The simulation experiment description markup language (SED-ML) is a new community data standard to encode computational biology experiments in a computer-readable XML format. Its widespread adoption will require the development of software support to work with SED-ML files. Here, we describe a software tool, SED-ED, to view, edit, validate and annotate SED-ML documents while shielding end-users from the underlying XML representation. SED-ED supports modellers who wish to create, understand and further develop a simulation description provided in SED-ML format. SED-ED is available as a standalone Java application, as an Eclipse plug-in and as an SBSI (www.sbsi.ed.ac.uk) plug-in, all under an MIT open-source license. Source code is at https://sed-ed-sedmleditor.googlecode.com/svn. The application itself is available from https://sourceforge.net/projects/jlibsedml/files/SED-ED/.

Open Scenario Study: IDA Open Scenario Repository User’s Manual

DTIC Science & Technology

2010-01-01

Thomason, Study Co-Lead Zachary S. Rabold, Sub-Task Lead Ylli Bajraktari Rachel D. Dubin Mary Catherine Flythe Open Scenario Study: IDA Open Scenario... Bajraktari Rachel D. Dubin Mary Catherine Flythe Open Scenario Study: IDA Open Scenario Repository User’s Manual iii Preface This document reports the...vii Appendices A. Identifying Scenario Components...........................................................A-1 B . Acronyms

ASaiM: a Galaxy-based framework to analyze microbiota data.

PubMed

Batut, Bérénice; Gravouil, Kévin; Defois, Clémence; Hiltemann, Saskia; Brugère, Jean-François; Peyretaillade, Eric; Peyret, Pierre

2018-05-22

New generations of sequencing platforms coupled to numerous bioinformatics tools has led to rapid technological progress in metagenomics and metatranscriptomics to investigate complex microorganism communities. Nevertheless, a combination of different bioinformatic tools remains necessary to draw conclusions out of microbiota studies. Modular and user-friendly tools would greatly improve such studies. We therefore developed ASaiM, an Open-Source Galaxy-based framework dedicated to microbiota data analyses. ASaiM provides an extensive collection of tools to assemble, extract, explore and visualize microbiota information from raw metataxonomic, metagenomic or metatranscriptomic sequences. To guide the analyses, several customizable workflows are included and are supported by tutorials and Galaxy interactive tours, which guide users through the analyses step by step. ASaiM is implemented as a Galaxy Docker flavour. It is scalable to thousands of datasets, but also can be used on a normal PC. The associated source code is available under Apache 2 license at https://github.com/ASaiM/framework and documentation can be found online (http://asaim.readthedocs.io). Based on the Galaxy framework, ASaiM offers a sophisticated environment with a variety of tools, workflows, documentation and training to scientists working on complex microorganism communities. It makes analysis and exploration analyses of microbiota data easy, quick, transparent, reproducible and shareable.

Cargo Movement Operations System (CMOS) Final System Segment Design Document Increment II, (ChaNge 02)

DTIC Science & Technology

1990-11-07

present, the documents are in conflict with each other. CMOS PMO ACCEPTS COMMENT: YES [ ] NO [ ] ERCI ACCEPTS COMMENT: YES [ ] NO [ ] COMMENT DISPOSITION...NO [ ] ERCI ACCEPTS COMMENT: YES [ ] NO [ ] COMMENT DISPOSITION: COMMENT STATUS: OPEN [ ] CLOSED [ ] p ORIGINATOR CONTROL NUMBER: SSDD-0003 PROGRAM...ERCI ACCEPTS COMMENT: YES [ ] NO [ ] COMMENT DISPOSITION: COMMENT STATUS: OPEN [ ] CLOSED [1 ORIGINATOR CONTROL NUMBER: SSDD-0005 PROGRAM OFFICE

Open-Source 3D-Printable Optics Equipment

PubMed Central

Zhang, Chenlong; Anzalone, Nicholas C.; Faria, Rodrigo P.; Pearce, Joshua M.

2013-01-01

Just as the power of the open-source design paradigm has driven down the cost of software to the point that it is accessible to most people, the rise of open-source hardware is poised to drive down the cost of doing experimental science to expand access to everyone. To assist in this aim, this paper introduces a library of open-source 3-D-printable optics components. This library operates as a flexible, low-cost public-domain tool set for developing both research and teaching optics hardware. First, the use of parametric open-source designs using an open-source computer aided design package is described to customize the optics hardware for any application. Second, details are provided on the use of open-source 3-D printers (additive layer manufacturing) to fabricate the primary mechanical components, which are then combined to construct complex optics-related devices. Third, the use of the open-source electronics prototyping platform are illustrated as control for optical experimental apparatuses. This study demonstrates an open-source optical library, which significantly reduces the costs associated with much optical equipment, while also enabling relatively easily adapted customizable designs. The cost reductions in general are over 97%, with some components representing only 1% of the current commercial investment for optical products of similar function. The results of this study make its clear that this method of scientific hardware development enables a much broader audience to participate in optical experimentation both as research and teaching platforms than previous proprietary methods. PMID:23544104

Open-source 3D-printable optics equipment.

PubMed

Zhang, Chenlong; Anzalone, Nicholas C; Faria, Rodrigo P; Pearce, Joshua M

2013-01-01

Just as the power of the open-source design paradigm has driven down the cost of software to the point that it is accessible to most people, the rise of open-source hardware is poised to drive down the cost of doing experimental science to expand access to everyone. To assist in this aim, this paper introduces a library of open-source 3-D-printable optics components. This library operates as a flexible, low-cost public-domain tool set for developing both research and teaching optics hardware. First, the use of parametric open-source designs using an open-source computer aided design package is described to customize the optics hardware for any application. Second, details are provided on the use of open-source 3-D printers (additive layer manufacturing) to fabricate the primary mechanical components, which are then combined to construct complex optics-related devices. Third, the use of the open-source electronics prototyping platform are illustrated as control for optical experimental apparatuses. This study demonstrates an open-source optical library, which significantly reduces the costs associated with much optical equipment, while also enabling relatively easily adapted customizable designs. The cost reductions in general are over 97%, with some components representing only 1% of the current commercial investment for optical products of similar function. The results of this study make its clear that this method of scientific hardware development enables a much broader audience to participate in optical experimentation both as research and teaching platforms than previous proprietary methods.

Tarjetas v.1.2015.7.23

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

Burchard, Ross L.; Pierson, Kathleen P.; Trumbo, Derek

Tarjetas is used to generate requirements from source documents. These source documents are in a hierarchical XML format that have been produced from PDF documents processed through the “Reframe” software package. The software includes the ability to create Topics and associate text Snippets with those topics. Requirements are then generated and text Snippets with their associated Topics are referenced to the requirement. The software maintains traceability from the requirement ultimately to the source document that produced the snippet

PDF text classification to leverage information extraction from publication reports.

PubMed

Bui, Duy Duc An; Del Fiol, Guilherme; Jonnalagadda, Siddhartha

2016-06-01

Data extraction from original study reports is a time-consuming, error-prone process in systematic review development. Information extraction (IE) systems have the potential to assist humans in the extraction task, however majority of IE systems were not designed to work on Portable Document Format (PDF) document, an important and common extraction source for systematic review. In a PDF document, narrative content is often mixed with publication metadata or semi-structured text, which add challenges to the underlining natural language processing algorithm. Our goal is to categorize PDF texts for strategic use by IE systems. We used an open-source tool to extract raw texts from a PDF document and developed a text classification algorithm that follows a multi-pass sieve framework to automatically classify PDF text snippets (for brevity, texts) into TITLE, ABSTRACT, BODYTEXT, SEMISTRUCTURE, and METADATA categories. To validate the algorithm, we developed a gold standard of PDF reports that were included in the development of previous systematic reviews by the Cochrane Collaboration. In a two-step procedure, we evaluated (1) classification performance, and compared it with machine learning classifier, and (2) the effects of the algorithm on an IE system that extracts clinical outcome mentions. The multi-pass sieve algorithm achieved an accuracy of 92.6%, which was 9.7% (p<0.001) higher than the best performing machine learning classifier that used a logistic regression algorithm. F-measure improvements were observed in the classification of TITLE (+15.6%), ABSTRACT (+54.2%), BODYTEXT (+3.7%), SEMISTRUCTURE (+34%), and MEDADATA (+14.2%). In addition, use of the algorithm to filter semi-structured texts and publication metadata improved performance of the outcome extraction system (F-measure +4.1%, p=0.002). It also reduced of number of sentences to be processed by 44.9% (p<0.001), which corresponds to a processing time reduction of 50% (p=0.005). The rule-based multi-pass sieve framework can be used effectively in categorizing texts extracted from PDF documents. Text classification is an important prerequisite step to leverage information extraction from PDF documents. Copyright © 2016 Elsevier Inc. All rights reserved.

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

EPA Science Inventory

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

Volcanic Hazard Maps; the results and progress made by the IAVCEI Hazard Map working group

NASA Astrophysics Data System (ADS)

Calder, Eliza; Lindsay, Jan; Wright, Heather

2017-04-01

The IAVCEI Commission on Volcanic Hazards and Risk set up a working group on Hazard Maps in 2014. Since then, the group has led or co-organised three major workshops, and organized two thematic conference sessions. In particular we have initiated a series of workshops, named the "State of the Hazard Map" which we plan to continue (the first was held at COV8 (State of the Hazard Map 1) and second at COV9 (State of the Hazard Map 2) and the third will be held at IAVCEI General Assembly in Portland. The broad aim of these activities is to work towards an IAVCEI-endorsed considerations or guidelines document for volcanic hazard map generation. The workshops have brought together people from around the world working on volcanic hazard maps, and have had four primary objectives: 1) to review (and collect further data on) the diverse variety of methods and rationales currently used to develop maps; 2) to openly discuss approaches and experiences regarding how hazard maps are interpreted and used by different groups; 3) to discuss and prepare the IAVCEI Guidelines document; and lastly, 4) Discuss options for finalizing, publishing and disseminating the Guidelines document (e.g. wiki, report, open-source publication). This presentation will provide an update of the results and outcomes of those initiatives. This includes brief outcomes of the reviews undertaken, a survey that has been constructed in order to gather additional data, the planned structure for the guidelines documents and a summary of the key findings to date. The majority of the participants of these activities so far have come from volcano observatories or geological surveys, as these institutions commonly have primary responsibility for making operational hazard map. It is important however that others in the scientific community that work on quantification of volcanic hazard contribute to these guidelines. We therefore invite interested parties to become involved.

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

PubMed Central

Ackerman, Michael J.; Yoo, Terry S.

2003-01-01

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

a Low-Cost Panoramic Camera for the 3d Documentation of Contaminated Crime Scenes

NASA Astrophysics Data System (ADS)

Abate, D.; Toschi, I.; Sturdy-Colls, C.; Remondino, F.

2017-11-01

Crime scene documentation is a fundamental task which has to be undertaken in a fast, accurate and reliable way, highlighting evidence which can be further used for ensuring justice for victims and for guaranteeing the successful prosecution of perpetrators. The main focus of this paper is on the documentation of a typical crime scene and on the rapid recording of any possible contamination that could have influenced its original appearance. A 3D reconstruction of the environment is first generated by processing panoramas acquired with the low-cost Ricoh Theta 360 camera, and further analysed to highlight potentials and limits of this emerging and consumer-grade technology. Then, a methodology is proposed for the rapid recording of changes occurring between the original and the contaminated crime scene. The approach is based on an automatic 3D feature-based data registration, followed by a cloud-to-cloud distance computation, given as input the 3D point clouds generated before and after e.g. the misplacement of evidence. All the algorithms adopted for panoramas pre-processing, photogrammetric 3D reconstruction, 3D geometry registration and analysis, are presented and currently available in open-source or low-cost software solutions.

Sensor Placement Optimization using Chama

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

Klise, Katherine A.; Nicholson, Bethany L.; Laird, Carl Damon

Continuous or regularly scheduled monitoring has the potential to quickly identify changes in the environment. However, even with low - cost sensors, only a limited number of sensors can be deployed. The physical placement of these sensors, along with the sensor technology and operating conditions, can have a large impact on the performance of a monitoring strategy. Chama is an open source Python package which includes mixed - integer, stochastic programming formulations to determine sensor locations and technology that maximize monitoring effectiveness. The methods in Chama are general and can be applied to a wide range of applications. Chama ismore » currently being used to design sensor networks to monitor airborne pollutants and to monitor water quality in water distribution systems. The following documentation includes installation instructions and examples, description of software features, and software license. The software is intended to be used by regulatory agencies, industry, and the research community. It is assumed that the reader is familiar with the Python Programming Language. References are included for addit ional background on software components. Online documentation, hosted at http://chama.readthedocs.io/, will be updated as new features are added. The online version includes API documentation .« less

Who has used internal company documents for biomedical and public health research and where did they find them?

PubMed

Wieland, L Susan; Rutkow, Lainie; Vedula, S Swaroop; Kaufmann, Christopher N; Rosman, Lori M; Twose, Claire; Mahendraratnam, Nirosha; Dickersin, Kay

2014-01-01

To describe the sources of internal company documents used in public health and healthcare research. We searched PubMed and Embase for articles using internal company documents to address a research question about a health-related topic. Our primary interest was where authors obtained internal company documents for their research. We also extracted information on type of company, type of research question, type of internal documents, and funding source. Our searches identified 9,305 citations of which 357 were eligible. Scanning of reference lists and consultation with colleagues identified 4 additional articles, resulting in 361 included articles. Most articles examined internal tobacco company documents (325/361; 90%). Articles using documents from pharmaceutical companies (20/361; 6%) were the next most common. Tobacco articles used documents from repositories; pharmaceutical documents were from a range of sources. Most included articles relied upon internal company documents obtained through litigation (350/361; 97%). The research questions posed were primarily about company strategies to promote or position the company and its products (326/361; 90%). Most articles (346/361; 96%) used information from miscellaneous documents such as memos or letters, or from unspecified types of documents. When explicit information about study funding was provided (290/361 articles), the most common source was the US-based National Cancer Institute. We developed an alternative and more sensitive search targeted at identifying additional research articles using internal pharmaceutical company documents, but the search retrieved an impractical number of citations for review. Internal company documents provide an excellent source of information on health topics (e.g., corporate behavior, study data) exemplified by articles based on tobacco industry documents. Pharmaceutical and other industry documents appear to have been less used for research, indicating a need for funding for this type of research and well-indexed and curated repositories to provide researchers with ready access to the documents.

Who Has Used Internal Company Documents for Biomedical and Public Health Research and Where Did They Find Them?

PubMed Central

Wieland, L. Susan; Rutkow, Lainie; Vedula, S. Swaroop; Kaufmann, Christopher N.; Rosman, Lori M.; Twose, Claire; Mahendraratnam, Nirosha; Dickersin, Kay

2014-01-01

Objective To describe the sources of internal company documents used in public health and healthcare research. Methods We searched PubMed and Embase for articles using internal company documents to address a research question about a health-related topic. Our primary interest was where authors obtained internal company documents for their research. We also extracted information on type of company, type of research question, type of internal documents, and funding source. Results Our searches identified 9,305 citations of which 357 were eligible. Scanning of reference lists and consultation with colleagues identified 4 additional articles, resulting in 361 included articles. Most articles examined internal tobacco company documents (325/361; 90%). Articles using documents from pharmaceutical companies (20/361; 6%) were the next most common. Tobacco articles used documents from repositories; pharmaceutical documents were from a range of sources. Most included articles relied upon internal company documents obtained through litigation (350/361; 97%). The research questions posed were primarily about company strategies to promote or position the company and its products (326/361; 90%). Most articles (346/361; 96%) used information from miscellaneous documents such as memos or letters, or from unspecified types of documents. When explicit information about study funding was provided (290/361 articles), the most common source was the US-based National Cancer Institute. We developed an alternative and more sensitive search targeted at identifying additional research articles using internal pharmaceutical company documents, but the search retrieved an impractical number of citations for review. Conclusions Internal company documents provide an excellent source of information on health topics (e.g., corporate behavior, study data) exemplified by articles based on tobacco industry documents. Pharmaceutical and other industry documents appear to have been less used for research, indicating a need for funding for this type of research and well-indexed and curated repositories to provide researchers with ready access to the documents. PMID:24800999

Implementing the EuroFIR Document and Data Repositories as accessible resources of food composition information.

PubMed

Unwin, Ian; Jansen-van der Vliet, Martine; Westenbrink, Susanne; Presser, Karl; Infanger, Esther; Porubska, Janka; Roe, Mark; Finglas, Paul

2016-02-15

The EuroFIR Document and Data Repositories are being developed as accessible collections of source documents, including grey literature, and the food composition data reported in them. These Repositories will contain source information available to food composition database compilers when selecting their nutritional data. The Document Repository was implemented as searchable bibliographic records in the Europe PubMed Central database, which links to the documents online. The Data Repository will contain original data from source documents in the Document Repository. Testing confirmed the FoodCASE food database management system as a suitable tool for the input, documentation and quality assessment of Data Repository information. Data management requirements for the input and documentation of reported analytical results were established, including record identification and method documentation specifications. Document access and data preparation using the Repositories will provide information resources for compilers, eliminating duplicated work and supporting unambiguous referencing of data contributing to their compiled data. Copyright © 2014 Elsevier Ltd. All rights reserved.

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

Major Source Determinations for Military Installations under the Air Toxics, New Source Review, and Title V Operating Permit Programs of the Clean Air Act (Act)

EPA Pesticide Factsheets

This document may be of assistance in applying the New Source Review (NSR) air permitting regulations including the Prevention of Significant Deterioration (PSD) requirements. This document is part of the NSR Policy and Guidance Database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

77 FR 75554 - Drawbridge Operation Regulation; Apalachicola River, FL

Federal Register 2010, 2011, 2012, 2013, 2014

2012-12-21

... documented decrease in the number of requests for openings in the last three years. In 2010, the bridge opened 12 times for the passage of vessels. Eight of those openings were for either a United States Coast... opened four times for the passage of vessels. Three of those openings were for either a USCG vessel or...

A standardized SOA for clinical data interchange in a cardiac telemonitoring environment.

PubMed

Gazzarata, Roberta; Vergari, Fabio; Cinotti, Tullio Salmon; Giacomini, Mauro

2014-11-01

Care of chronic cardiac patients requires information interchange between patients' homes, clinical environments, and the electronic health record. Standards are emerging to support clinical information collection, exchange and management and to overcome information fragmentation and actors delocalization. Heterogeneity of information sources at patients' homes calls for open solutions to collect and accommodate multidomain information, including environmental data. Based on the experience gained in a European Research Program, this paper presents an integrated and open approach for clinical data interchange in cardiac telemonitoring applications. This interchange is supported by the use of standards following the indications provided by the national authorities of the countries involved. Taking into account the requirements provided by the medical staff involved in the project, the authors designed and implemented a prototypal middleware, based on a service-oriented architecture approach, to give a structured and robust tool to congestive heart failure patients for their personalized telemonitoring. The middleware is represented by a health record management service, whose interface is compliant to the healthcare services specification project Retrieve, Locate and Update Service standard (Level 0), which allows communication between the agents involved through the exchange of Clinical Document Architecture Release 2 documents. Three performance tests were carried out and showed that the prototype completely fulfilled all requirements indicated by the medical staff; however, certain aspects, such as authentication, security and scalability, should be deeply analyzed within a future engineering phase.

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…

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.

Nasalance and nasality at experimental velopharyngeal openings in palatal prosthesis: a case study

PubMed Central

LIMA-GREGIO, Aveliny Mantovan; MARINO, Viviane Cristina de Castro; PEGORARO-KROOK, Maria Inês; BARBOSA, Plinio Almeida; AFERRI, Homero Carneiro; DUTKA, Jeniffer de Cassia Rillo

2011-01-01

The use of prosthetic devices for correction of velopharyngeal insufficiency (VPI) is an alternative treatment for patients with conditions that preclude surgery and for those individuals with a hypofunctional velopharynx (HV) with a poor prognosis for the surgical repair of VPI. Understanding the role and measuring the outcome of prosthetic treatment of velopharyngeal dysfunction requires the use of tools that allow for documenting pre- and post-treatment outcomes. Experimental openings in speech bulbs have been used for simulating VPI in studies documenting changes in aerodynamic, acoustic and kinematics aspects of speech associated with the use of palatal prosthetic devices. The use of nasometry to document changes in speech associated with experimental openings in speech bulbs, however, has not been described in the literature. Objective This single-subject study investigated nasalance and nasality at the presence of experimental openings drilled through the speech bulb of a patient with HV. Material and Methods Nasometric recordings of the word "pato" were obtained under 4 velopharyngeal conditions: no-opening (control condition), no speech bulb, speech bulb with a 20 mm2 opening, and speech bulb with 30 mm2 opening. Five speech-language pathologists performed auditory-perceptual ratings while the subject read an oral passage under all conditions. Results Kruskal-Wallis test showed significant difference among conditions (p=0.0002), with Scheffé post hoc test indicating difference from the no-opening condition. Conclusion The changes in nasalance observed after drilling holes of known sizes in a speech bulb suggest that nasometry reflect changes in transfer of sound energy related to different sizes of velopharyngeal opening. PMID:22230996

Hgis and Archive Researches: a Tool for the Study of the Ancient Mill Channel of Cesena (italy)

NASA Astrophysics Data System (ADS)

Bitelli, G.; Bartolini, F.; Gatta, G.

2016-06-01

The present study aims to demonstrate the usefulness of GIS to support archive searches and historical studies (e.g. related to industrial archaeology), in the case of an ancient channel for mill powering near Cesena (Emilia-Romagna, Italy), whose history is weaved together with the history of the Compagnia dei Molini di Cesena mill company, the most ancient limited company in Italy. Several historical maps (about 40 sheets in total) inherent the studied area and 80 archive documents (drawings, photos, specifications, administrative acts, newspaper articles), over a period of more than 600 years, were collected. Once digitized, historical maps were analysed, georeferenced and mosaicked where necessary. Subsequently, in all the maps the channel with its four mills and the Savio river were vectorized. All the additional archive documents were digitized, catalogued and stored. Using the QGIS open source platform, a Historical GIS was created, encompassing the current cartographic base and all historical maps, with their vectorized elements; each archive document was linked to the proper historical map, so that the document can be immediately retrieved and visualized. In such a HGIS, the maps form the base for a spatial and temporal navigation, facilitated by a specific interface; the external documents linked to them complete the description of the represented elements. This simple and interactive tool offers a new approach to archive searches, as it allows reconstruction in space and time of the evolution of the ancient channel and the history of this important mill company.

Standardized access, display, and retrieval of medical video

NASA Astrophysics Data System (ADS)

Bellaire, Gunter; Steines, Daniel; Graschew, Georgi; Thiel, Andreas; Bernarding, Johannes; Tolxdorff, Thomas; Schlag, Peter M.

1999-05-01

The system presented here enhances documentation and data- secured, second-opinion facilities by integrating video sequences into DICOM 3.0. We present an implementation for a medical video server extended by a DICOM interface. Security mechanisms conforming with DICOM are integrated to enable secure internet access. Digital video documents of diagnostic and therapeutic procedures should be examined regarding the clip length and size necessary for second opinion and manageable with today's hardware. Image sources relevant for this paper include 3D laparoscope, 3D surgical microscope, 3D open surgery camera, synthetic video, and monoscopic endoscopes, etc. The global DICOM video concept and three special workplaces of distinct applications are described. Additionally, an approach is presented to analyze the motion of the endoscopic camera for future automatic video-cutting. Digital stereoscopic video sequences are especially in demand for surgery . Therefore DSVS are also integrated into the DICOM video concept. Results are presented describing the suitability of stereoscopic display techniques for the operating room.

ProtocolNavigator: emulation-based software for the design, documentation and reproduction biological experiments.

PubMed

Khan, Imtiaz A; Fraser, Adam; Bray, Mark-Anthony; Smith, Paul J; White, Nick S; Carpenter, Anne E; Errington, Rachel J

2014-12-01

Experimental reproducibility is fundamental to the progress of science. Irreproducible research decreases the efficiency of basic biological research and drug discovery and impedes experimental data reuse. A major contributing factor to irreproducibility is difficulty in interpreting complex experimental methodologies and designs from written text and in assessing variations among different experiments. Current bioinformatics initiatives either are focused on computational research reproducibility (i.e. data analysis) or laboratory information management systems. Here, we present a software tool, ProtocolNavigator, which addresses the largely overlooked challenges of interpretation and assessment. It provides a biologist-friendly open-source emulation-based tool for designing, documenting and reproducing biological experiments. ProtocolNavigator was implemented in Python 2.7, using the wx module to build the graphical user interface. It is a platform-independent software and freely available from http://protocolnavigator.org/index.html under the GPL v2 license. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

A python framework for environmental model uncertainty analysis

USGS Publications Warehouse

White, Jeremy; Fienen, Michael N.; Doherty, John E.

2016-01-01

We have developed pyEMU, a python framework for Environmental Modeling Uncertainty analyses, open-source tool that is non-intrusive, easy-to-use, computationally efficient, and scalable to highly-parameterized inverse problems. The framework implements several types of linear (first-order, second-moment (FOSM)) and non-linear uncertainty analyses. The FOSM-based analyses can also be completed prior to parameter estimation to help inform important modeling decisions, such as parameterization and objective function formulation. Complete workflows for several types of FOSM-based and non-linear analyses are documented in example notebooks implemented using Jupyter that are available in the online pyEMU repository. Example workflows include basic parameter and forecast analyses, data worth analyses, and error-variance analyses, as well as usage of parameter ensemble generation and management capabilities. These workflows document the necessary steps and provides insights into the results, with the goal of educating users not only in how to apply pyEMU, but also in the underlying theory of applied uncertainty quantification.

Cameo: A Python Library for Computer Aided Metabolic Engineering and Optimization of Cell Factories.

PubMed

Cardoso, João G R; Jensen, Kristian; Lieven, Christian; Lærke Hansen, Anne Sofie; Galkina, Svetlana; Beber, Moritz; Özdemir, Emre; Herrgård, Markus J; Redestig, Henning; Sonnenschein, Nikolaus

2018-04-20

Computational systems biology methods enable rational design of cell factories on a genome-scale and thus accelerate the engineering of cells for the production of valuable chemicals and proteins. Unfortunately, the majority of these methods' implementations are either not published, rely on proprietary software, or do not provide documented interfaces, which has precluded their mainstream adoption in the field. In this work we present cameo, a platform-independent software that enables in silico design of cell factories and targets both experienced modelers as well as users new to the field. It is written in Python and implements state-of-the-art methods for enumerating and prioritizing knockout, knock-in, overexpression, and down-regulation strategies and combinations thereof. Cameo is an open source software project and is freely available under the Apache License 2.0. A dedicated Web site including documentation, examples, and installation instructions can be found at http://cameo.bio . Users can also give cameo a try at http://try.cameo.bio .

A GPU accelerated PDF transparency engine

NASA Astrophysics Data System (ADS)

Recker, John; Lin, I.-Jong; Tastl, Ingeborg

2011-01-01

As commercial printing presses become faster, cheaper and more efficient, so too must the Raster Image Processors (RIP) that prepare data for them to print. Digital press RIPs, however, have been challenged to on the one hand meet the ever increasing print performance of the latest digital presses, and on the other hand process increasingly complex documents with transparent layers and embedded ICC profiles. This paper explores the challenges encountered when implementing a GPU accelerated driver for the open source Ghostscript Adobe PostScript and PDF language interpreter targeted at accelerating PDF transparency for high speed commercial presses. It further describes our solution, including an image memory manager for tiling input and output images and documents, a PDF compatible multiple image layer blending engine, and a GPU accelerated ICC v4 compatible color transformation engine. The result, we believe, is the foundation for a scalable, efficient, distributed RIP system that can meet current and future RIP requirements for a wide range of commercial digital presses.

ARX - A Comprehensive Tool for Anonymizing Biomedical Data

PubMed Central

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

2014-01-01

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

Big-BOE: Fusing Spanish Official Gazette with Big Data Technology.

PubMed

Basanta-Val, Pablo; Sánchez-Fernández, Luis

2018-06-01

The proliferation of new data sources, stemmed from the adoption of open-data schemes, in combination with an increasing computing capacity causes the inception of new type of analytics that process Internet of things with low-cost engines to speed up data processing using parallel computing. In this context, the article presents an initiative, called BIG-Boletín Oficial del Estado (BOE), designed to process the Spanish official government gazette (BOE) with state-of-the-art processing engines, to reduce computation time and to offer additional speed up for big data analysts. The goal of including a big data infrastructure is to be able to process different BOE documents in parallel with specific analytics, to search for several issues in different documents. The application infrastructure processing engine is described from an architectural perspective and from performance, showing evidence on how this type of infrastructure improves the performance of different types of simple analytics as several machines cooperate.

HKHC Community Dashboard: design, development, and function of a Web-based performance monitoring system.

PubMed

Bors, Philip A; Kemner, Allison; Fulton, John; Stachecki, Jessica; Brennan, Laura K

2015-01-01

As part of Robert Wood Johnson Foundation's Healthy Kids, Healthy Communities (HKHC) national grant program, a technical assistance team designed the HKHC Community Dashboard, an online progress documentation and networking system. The Dashboard was central to HKHC's multimethod program evaluation and became a communication interface for grantees and technical assistance providers. The Dashboard was designed through an iterative process of identifying needs and priorities; designing the user experience, technical development, and usability testing; and applying visual design. The system was created with an open-source content management system and support for building an online community of users. The site developer trained technical assistance providers at the national program office and evaluators, who subsequently trained all 49 grantees. Evaluators provided support for Dashboard users and populated the site with the bulk of its uploaded tools and resource documents. The system tracked progress through an interactive work plan template, regular documentation by local staff and partners, and data coding and analysis by the evaluation team. Other features included the ability to broadcast information to Dashboard users via e-mail, event calendars, discussion forums, private messaging, a resource clearinghouse, a technical assistance diary, and real-time progress reports. The average number of Dashboard posts was 694 per grantee during the grant period. Technical assistance providers and grantees uploaded a total of 1304 resource documents. The Dashboard functions with the highest grantee satisfaction were its interfaces for sharing and progress documentation. A majority of Dashboard users (69%) indicated a preference for continued access to the Dashboard's uploaded resource documents. The Dashboard was a useful and innovative tool for participatory evaluation of a large national grant program. While progress documentation added some burden to local project staff, the system proved to be a useful resource-sharing technology.

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…

FOUNTAIN: A JAVA open-source package to assist large sequencing projects

PubMed Central

Buerstedde, Jean-Marie; Prill, Florian

2001-01-01

Background Better automation, lower cost per reaction and a heightened interest in comparative genomics has led to a dramatic increase in DNA sequencing activities. Although the large sequencing projects of specialized centers are supported by in-house bioinformatics groups, many smaller laboratories face difficulties managing the appropriate processing and storage of their sequencing output. The challenges include documentation of clones, templates and sequencing reactions, and the storage, annotation and analysis of the large number of generated sequences. Results We describe here a new program, named FOUNTAIN, for the management of large sequencing projects . FOUNTAIN uses the JAVA computer language and data storage in a relational database. Starting with a collection of sequencing objects (clones), the program generates and stores information related to the different stages of the sequencing project using a web browser interface for user input. The generated sequences are subsequently imported and annotated based on BLAST searches against the public databases. In addition, simple algorithms to cluster sequences and determine putative polymorphic positions are implemented. Conclusions A simple, but flexible and scalable software package is presented to facilitate data generation and storage for large sequencing projects. Open source and largely platform and database independent, we wish FOUNTAIN to be improved and extended in a community effort. PMID:11591214

MetaDB a Data Processing Workflow in Untargeted MS-Based Metabolomics Experiments.

PubMed

Franceschi, Pietro; Mylonas, Roman; Shahaf, Nir; Scholz, Matthias; Arapitsas, Panagiotis; Masuero, Domenico; Weingart, Georg; Carlin, Silvia; Vrhovsek, Urska; Mattivi, Fulvio; Wehrens, Ron

2014-01-01

Due to their sensitivity and speed, mass-spectrometry based analytical technologies are widely used to in metabolomics to characterize biological phenomena. To address issues like metadata organization, quality assessment, data processing, data storage, and, finally, submission to public repositories, bioinformatic pipelines of a non-interactive nature are often employed, complementing the interactive software used for initial inspection and visualization of the data. These pipelines often are created as open-source software allowing the complete and exhaustive documentation of each step, ensuring the reproducibility of the analysis of extensive and often expensive experiments. In this paper, we will review the major steps which constitute such a data processing pipeline, discussing them in the context of an open-source software for untargeted MS-based metabolomics experiments recently developed at our institute. The software has been developed by integrating our metaMS R package with a user-friendly web-based application written in Grails. MetaMS takes care of data pre-processing and annotation, while the interface deals with the creation of the sample lists, the organization of the data storage, and the generation of survey plots for quality assessment. Experimental and biological metadata are stored in the ISA-Tab format making the proposed pipeline fully integrated with the Metabolights framework.

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

NASA Astrophysics Data System (ADS)

Hearin, Andrew

2016-03-01

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

Supporting Indonesia's National Forest Monitoring System with LiDAR Observations

NASA Astrophysics Data System (ADS)

Hagen, S. C.

2015-12-01

Scientists at Applied GeoSolutions, Jet Propulsion Laboratory, Winrock International, and the University of New Hampshire are working with the government of Indonesia to enhance the National Forest Monitoring System in Kalimantan, Indonesia. The establishment of a reliable, transparent, and comprehensive NFMS has been limited by a dearth of relevant data that are accurate, low-cost, and spatially resolved at subnational scales. In this NASA funded project, we are developing, evaluating, and validating several critical components of a NFMS in Kalimantan, Indonesia, focusing on the use of LiDAR and radar imagery for improved carbon stock and forest degradation information. Applied GeoSolutions and the University of New Hampshire have developed an Open Source Software package to process large amounts LiDAR data quickly, easily, and accurately. The Open Source project is called lidar2dems and includes the classification of raw LAS point clouds and the creation of Digital Terrain Models (DTMs), Digital Surface Models (DSMs), and Canopy Height Models (CHMs). Preliminary estimates of forest structure and forest damage from logging from these data sets support the idea that comprehensive, well documented, freely available software for processing LiDAR data can enable countries such as Indonesia to cost effectively monitor their forests with high precision.

LakeMetabolizer: An R package for estimating lake metabolism from free-water oxygen using diverse statistical models

USGS Publications Warehouse

Winslow, Luke; Zwart, Jacob A.; Batt, Ryan D.; Dugan, Hilary; Woolway, R. Iestyn; Corman, Jessica; Hanson, Paul C.; Read, Jordan S.

2016-01-01

Metabolism is a fundamental process in ecosystems that crosses multiple scales of organization from individual organisms to whole ecosystems. To improve sharing and reuse of published metabolism models, we developed LakeMetabolizer, an R package for estimating lake metabolism from in situ time series of dissolved oxygen, water temperature, and, optionally, additional environmental variables. LakeMetabolizer implements 5 different metabolism models with diverse statistical underpinnings: bookkeeping, ordinary least squares, maximum likelihood, Kalman filter, and Bayesian. Each of these 5 metabolism models can be combined with 1 of 7 models for computing the coefficient of gas exchange across the air–water interface (k). LakeMetabolizer also features a variety of supporting functions that compute conversions and implement calculations commonly applied to raw data prior to estimating metabolism (e.g., oxygen saturation and optical conversion models). These tools have been organized into an R package that contains example data, example use-cases, and function documentation. The release package version is available on the Comprehensive R Archive Network (CRAN), and the full open-source GPL-licensed code is freely available for examination and extension online. With this unified, open-source, and freely available package, we hope to improve access and facilitate the application of metabolism in studies and management of lentic ecosystems.

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.

Establishing Consensus Turbulence Statistics for Hot Subsonic Jets

NASA Technical Reports Server (NTRS)

Bridges, James; Werner, Mark P.

2010-01-01

Many tasks in fluids engineering require knowledge of the turbulence in jets. There is a strong, although fragmented, literature base for low order statistics, such as jet spread and other meanvelocity field characteristics. Some sources, particularly for low speed cold jets, also provide turbulence intensities that are required for validating Reynolds-averaged Navier-Stokes (RANS) Computational Fluid Dynamics (CFD) codes. There are far fewer sources for jet spectra and for space-time correlations of turbulent velocity required for aeroacoustics applications, although there have been many singular publications with various unique statistics, such as Proper Orthogonal Decomposition, designed to uncover an underlying low-order dynamical description of turbulent jet flow. As the complexity of the statistic increases, the number of flows for which the data has been categorized and assembled decreases, making it difficult to systematically validate prediction codes that require high-level statistics over a broad range of jet flow conditions. For several years, researchers at NASA have worked on developing and validating jet noise prediction codes. One such class of codes, loosely called CFD-based or statistical methods, uses RANS CFD to predict jet mean and turbulent intensities in velocity and temperature. These flow quantities serve as the input to the acoustic source models and flow-sound interaction calculations that yield predictions of far-field jet noise. To develop this capability, a catalog of turbulent jet flows has been created with statistics ranging from mean velocity to space-time correlations of Reynolds stresses. The present document aims to document this catalog and to assess the accuracies of the data, e.g. establish uncertainties for the data. This paper covers the following five tasks: Document acquisition and processing procedures used to create the particle image velocimetry (PIV) datasets. Compare PIV data with hotwire and laser Doppler velocimetry (LDV) data published in the open literature. Compare different datasets acquired at roughly the same flow conditions to establish uncertainties. Create a consensus dataset for a range of hot jet flows, including uncertainty bands. Analyze this consensus dataset for self-consistency and compare jet characteristics to those of the open literature. One final objective fulfilled by this work was the demonstration of a universal scaling for the jet flow fields, at least within the region of interest to aeroacoustics. The potential core length and the spread rate of the half-velocity radius were used to collapse of the mean and turbulent velocity fields over the first 20 jet diameters in a highly satisfying manner.

Seismic characteristics of tensile fracture growth induced by hydraulic fracturing

NASA Astrophysics Data System (ADS)

Eaton, D. W. S.; Van der Baan, M.; Boroumand, N.

2014-12-01

Hydraulic fracturing is a process of injecting high-pressure slurry into a rockmass to enhance its permeability. Variants of this process are used for unconventional oil and gas development, engineered geothermal systems and block-cave mining; similar processes occur within volcanic systems. Opening of hydraulic fractures is well documented by mineback trials and tiltmeter monitoring and is a physical requirement to accommodate the volume of injected fluid. Numerous microseismic monitoring investigations acquired in the audio-frequency band are interpreted to show a prevalence of shear-dominated failure mechanisms surrounding the tensile fracture. Moreover, the radiated seismic energy in the audio-frequency band appears to be a miniscule fraction (<< 1%) of the net injected energy, i.e., the integral of the product of fluid pressure and injection rate. We use a simple penny-shaped crack model as a predictive framework to describe seismic characteristics of tensile opening during hydraulic fracturing. This model provides a useful scaling relation that links seismic moment to effective fluid pressure within the crack. Based on downhole recordings corrected for attenuation, a significant fraction of observed microseismic events are characterized by S/P amplitude ratio < 5. Despite the relatively small aperture of the monitoring arrays, which precludes both full moment-tensor analysis and definitive identification of nodal planes or axes, this ratio provides a strong indication that observed microseismic source mechanisms have a component of tensile failure. In addition, we find some instances of periodic spectral notches that can be explained by an opening/closing failure mechanism, in which fracture propagation outpaces fluid velocity within the crack. Finally, aseismic growth of tensile fractures may be indicative of a scenario in which injected energy is consumed to create new fracture surfaces. Taken together, our observations and modeling provide evidence that failure mechanisms documented by passive monitoring of hydraulic fractures may contain a significant component of tensile failure, including fracture opening and closing, although creation of extensive new fracture surfaces may be a seismically inefficient process that radiates at sub-audio frequencies.

Coal and Open-pit surface mining impacts on American Lands (COAL)

NASA Astrophysics Data System (ADS)

Brown, T. A.; McGibbney, L. J.

2017-12-01

Mining is known to cause environmental degradation, but software tools to identify its impacts are lacking. However, remote sensing, spectral reflectance, and geographic data are readily available, and high-performance cloud computing resources exist for scientific research. Coal and Open-pit surface mining impacts on American Lands (COAL) provides a suite of algorithms and documentation to leverage these data and resources to identify evidence of mining and correlate it with environmental impacts over time.COAL was originally developed as a 2016 - 2017 senior capstone collaboration between scientists at the NASA Jet Propulsion Laboratory (JPL) and computer science students at Oregon State University (OSU). The COAL team implemented a free and open-source software library called "pycoal" in the Python programming language which facilitated a case study of the effects of coal mining on water resources. Evidence of acid mine drainage associated with an open-pit coal mine in New Mexico was derived by correlating imaging spectrometer data from the JPL Airborne Visible/InfraRed Imaging Spectrometer - Next Generation (AVIRIS-NG), spectral reflectance data published by the USGS Spectroscopy Laboratory in the USGS Digital Spectral Library 06, and GIS hydrography data published by the USGS National Geospatial Program in The National Map. This case study indicated that the spectral and geospatial algorithms developed by COAL can be used successfully to analyze the environmental impacts of mining activities.Continued development of COAL has been promoted by a Startup allocation award of high-performance computing resources from the Extreme Science and Engineering Discovery Environment (XSEDE). These resources allow the team to undertake further benchmarking, evaluation, and experimentation using multiple XSEDE resources. The opportunity to use computational infrastructure of this caliber will further enable the development of a science gateway to continue foundational COAL research.This work documents the original design and development of COAL and provides insight into continuing research efforts which have potential applications beyond the project to environmental data science and other fields.

Grid Integrated Distributed PV (GridPV) Version 2.

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

Reno, Matthew J.; Coogan, Kyle

2014-12-01

This manual provides the documentation of the MATLAB toolbox of functions for using OpenDSS to simulate the impact of solar energy on the distribution system. The majority of the functio ns are useful for interfacing OpenDSS and MATLAB, and they are of generic use for commanding OpenDSS from MATLAB and retrieving information from simulations. A set of functions is also included for modeling PV plant output and setting up the PV plant in th e OpenDSS simulation. The toolbox contains functions for modeling the OpenDSS distribution feeder on satellite images with GPS coordinates. Finally, example simulations functions are included tomore » show potential uses of the toolbox functions. Each function i n the toolbox is documented with the function use syntax, full description, function input list, function output list, example use, and example output.« less

SolTrace | Concentrating Solar Power | NREL

Science.gov Websites

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

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

ERIC Educational Resources Information Center

Derringer, Pam

2009-01-01

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

ooi: OpenStack OCCI interface

NASA Astrophysics Data System (ADS)

López García, Álvaro; Fernández del Castillo, Enol; Orviz Fernández, Pablo

In this document we present an implementation of the Open Grid Forum's Open Cloud Computing Interface (OCCI) for OpenStack, namely ooi (Openstack occi interface, 2015) [1]. OCCI is an open standard for management tasks over cloud resources, focused on interoperability, portability and integration. ooi aims to implement this open interface for the OpenStack cloud middleware, promoting interoperability with other OCCI-enabled cloud management frameworks and infrastructures. ooi focuses on being non-invasive with a vanilla OpenStack installation, not tied to a particular OpenStack release version.

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

PubMed Central

Jurica, Peter; van Leeuwen, Cees

2008-01-01

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

Open Source Vision

ERIC Educational Resources Information Center

Villano, Matt

2006-01-01

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

Drove roads: Keystone structures that promote ant diversity in Mediterranean forest landscapes

NASA Astrophysics Data System (ADS)

Azcárate, Francisco M.; Seoane, Javier; Castro, Sara; Peco, Begoña

2013-05-01

Drove roads are the traditional corridors used by pastoralists for seasonal movements of livestock (transhumance). They cover a considerable land area in Mediterranean countries and, although they are an obvious source of landscape diversity, their influence on the diversity and composition of animal assemblages has not been documented. Ant communities were studied on four active drove roads, two in forests (submediterranean and conifer) and two in open environments (croplands and rangelands). They were compared with the respective matrix communities and their contribution to local species richness was evaluated. The effects were heavily dependent on the open or closed nature of the matrix. In forest environments, drove roads increased ant species richness at the local scale, acting as clear keystone structures. Their species richness and functional diversity were highest on the fine scale, species composition was different, and a slight edge effect in the matrix was detected. In contrast, drove roads had little or even a negative effect in open environment locations. We conclude that drove roads have a high conservation value for ants in Mediterranean forest environments, in addition to their importance as reservoirs of plant biodiversity and generators of ecological goods and services.

A-MADMAN: Annotation-based microarray data meta-analysis tool

PubMed Central

Bisognin, Andrea; Coppe, Alessandro; Ferrari, Francesco; Risso, Davide; Romualdi, Chiara; Bicciato, Silvio; Bortoluzzi, Stefania

2009-01-01

Background Publicly available datasets of microarray gene expression signals represent an unprecedented opportunity for extracting genomic relevant information and validating biological hypotheses. However, the exploitation of this exceptionally rich mine of information is still hampered by the lack of appropriate computational tools, able to overcome the critical issues raised by meta-analysis. Results This work presents A-MADMAN, an open source web application which allows the retrieval, annotation, organization and meta-analysis of gene expression datasets obtained from Gene Expression Omnibus. A-MADMAN addresses and resolves several open issues in the meta-analysis of gene expression data. Conclusion A-MADMAN allows i) the batch retrieval from Gene Expression Omnibus and the local organization of raw data files and of any related meta-information, ii) the re-annotation of samples to fix incomplete, or otherwise inadequate, metadata and to create user-defined batches of data, iii) the integrative analysis of data obtained from different Affymetrix platforms through custom chip definition files and meta-normalization. Software and documentation are available on-line at . PMID:19563634

Biological knowledge bases using Wikis: combining the flexibility of Wikis with the structure of databases.

PubMed

Brohée, Sylvain; Barriot, Roland; Moreau, Yves

2010-09-01

In recent years, the number of knowledge bases developed using Wiki technology has exploded. Unfortunately, next to their numerous advantages, classical Wikis present a critical limitation: the invaluable knowledge they gather is represented as free text, which hinders their computational exploitation. This is in sharp contrast with the current practice for biological databases where the data is made available in a structured way. Here, we present WikiOpener an extension for the classical MediaWiki engine that augments Wiki pages by allowing on-the-fly querying and formatting resources external to the Wiki. Those resources may provide data extracted from databases or DAS tracks, or even results returned by local or remote bioinformatics analysis tools. This also implies that structured data can be edited via dedicated forms. Hence, this generic resource combines the structure of biological databases with the flexibility of collaborative Wikis. The source code and its documentation are freely available on the MediaWiki website: http://www.mediawiki.org/wiki/Extension:WikiOpener.

Integrating Socioeconomic and Earth Science Data Using Geobrowsers and Web Services: A Demonstration

NASA Astrophysics Data System (ADS)

Schumacher, J. A.; Yetman, G. G.

2007-12-01

The societal benefit areas identified as the focus for the Global Earth Observing System of Systems (GEOSS) 10- year implementation plan are an indicator of the importance of integrating socioeconomic data with earth science data to support decision makers. To aid this integration, CIESIN is delivering its global and U.S. demographic data to commercial and open source Geobrowsers and providing open standards based services for data access. Currently, data on population distribution, poverty, and detailed census data for the U.S. are available for visualization and access in Google Earth, NASA World Wind, and a browser-based 2-dimensional mapping client. The mapping client allows for the creation of web map documents that pull together layers from distributed servers and can be saved and shared. Visualization tools with Geobrowsers, user-driven map creation and sharing via browser-based clients, and a prototype for characterizing populations at risk to predicted precipitation deficits will be demonstrated.

Standard Test Methods for Textile Composites

NASA Technical Reports Server (NTRS)

Masters, John E.; Portanova, Marc A.

1996-01-01

Standard testing methods for composite laminates reinforced with continuous networks of braided, woven, or stitched fibers have been evaluated. The microstructure of these textile' composite materials differs significantly from that of tape laminates. Consequently, specimen dimensions and loading methods developed for tape type composites may not be applicable to textile composites. To this end, a series of evaluations were made comparing testing practices currently used in the composite industry. Information was gathered from a variety of sources and analyzed to establish a series of recommended test methods for textile composites. The current practices established for laminated composite materials by ASTM and the MIL-HDBK-17 Committee were considered. This document provides recommended test methods for determining both in-plane and out-of-plane properties. Specifically, test methods are suggested for: unnotched tension and compression; open and filled hole tension; open hole compression; bolt bearing; and interlaminar tension. A detailed description of the material architectures evaluated is also provided, as is a recommended instrumentation practice.

Design and implementation of the standards-based personal intelligent self-management system (PICS).

PubMed

von Bargen, Tobias; Gietzelt, Matthias; Britten, Matthias; Song, Bianying; Wolf, Klaus-Hendrik; Kohlmann, Martin; Marschollek, Michael; Haux, Reinhold

2013-01-01

Against the background of demographic change and a diminishing care workforce there is a growing need for personalized decision support. The aim of this paper is to describe the design and implementation of the standards-based personal intelligent care systems (PICS). PICS makes consistent use of internationally accepted standards such as the Health Level 7 (HL7) Arden syntax for the representation of the decision logic, HL7 Clinical Document Architecture for information representation and is based on a open-source service-oriented architecture framework and a business process management system. Its functionality is exemplified for the application scenario of a patient suffering from congestive heart failure. Several vital signs sensors provide data for the decision support system, and a number of flexible communication channels are available for interaction with patient or caregiver. PICS is a standards-based, open and flexible system enabling personalized decision support. Further development will include the implementation of components on small computers and sensor nodes.

Government Documents Departmental Operations Guide.

ERIC Educational Resources Information Center

Wilson, John S.; And Others

This manual for the operation and maintenance of the Government Documents Department at Baylor University's Moody Memorial Library is divided into 13 topical sections. The guide opens with the collection development policy statement, which covers the general collection, the maps division, and weeding government documents. Technical processing…

47 CFR 76.1712 - Open video system (OVS) requests for carriage.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 47 Telecommunication 4 2011-10-01 2011-10-01 false Open video system (OVS) requests for carriage... RADIO SERVICES MULTICHANNEL VIDEO AND CABLE TELEVISION SERVICE Documents to be Maintained for Inspection § 76.1712 Open video system (OVS) requests for carriage. An open video system operator shall maintain a...

47 CFR 76.1712 - Open video system (OVS) requests for carriage.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 47 Telecommunication 4 2010-10-01 2010-10-01 false Open video system (OVS) requests for carriage... RADIO SERVICES MULTICHANNEL VIDEO AND CABLE TELEVISION SERVICE Documents to be Maintained for Inspection § 76.1712 Open video system (OVS) requests for carriage. An open video system operator shall maintain a...

47 CFR 76.1712 - Open video system (OVS) requests for carriage.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 47 Telecommunication 4 2014-10-01 2014-10-01 false Open video system (OVS) requests for carriage... RADIO SERVICES MULTICHANNEL VIDEO AND CABLE TELEVISION SERVICE Documents to be Maintained for Inspection § 76.1712 Open video system (OVS) requests for carriage. An open video system operator shall maintain a...

47 CFR 76.1712 - Open video system (OVS) requests for carriage.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 47 Telecommunication 4 2013-10-01 2013-10-01 false Open video system (OVS) requests for carriage... RADIO SERVICES MULTICHANNEL VIDEO AND CABLE TELEVISION SERVICE Documents to be Maintained for Inspection § 76.1712 Open video system (OVS) requests for carriage. An open video system operator shall maintain a...

47 CFR 76.1712 - Open video system (OVS) requests for carriage.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 47 Telecommunication 4 2012-10-01 2012-10-01 false Open video system (OVS) requests for carriage... RADIO SERVICES MULTICHANNEL VIDEO AND CABLE TELEVISION SERVICE Documents to be Maintained for Inspection § 76.1712 Open video system (OVS) requests for carriage. An open video system operator shall maintain a...

Utility of social media and crowd-intelligence data for pharmacovigilance: a scoping review.

PubMed

Tricco, Andrea C; Zarin, Wasifa; Lillie, Erin; Jeblee, Serena; Warren, Rachel; Khan, Paul A; Robson, Reid; Pham, Ba'; Hirst, Graeme; Straus, Sharon E

2018-06-14

A scoping review to characterize the literature on the use of conversations in social media as a potential source of data for detecting adverse events (AEs) related to health products. Our specific research questions were (1) What social media listening platforms exist to detect adverse events related to health products, and what are their capabilities and characteristics? (2) What is the validity and reliability of data from social media for detecting these adverse events? MEDLINE, EMBASE, Cochrane Library, and relevant websites were searched from inception to May 2016. Any type of document (e.g., manuscripts, reports) that described the use of social media data for detecting health product AEs was included. Two reviewers independently screened citations and full-texts, and one reviewer and one verifier performed data abstraction. Descriptive synthesis was conducted. After screening 3631 citations and 321 full-texts, 70 unique documents with 7 companion reports available from 2001 to 2016 were included. Forty-six documents (66%) described an automated or semi-automated information extraction system to detect health product AEs from social media conversations (in the developmental phase). Seven pre-existing information extraction systems to mine social media data were identified in eight documents. Nineteen documents compared AEs reported in social media data with validated data and found consistent AE discovery in all except two documents. None of the documents reported the validity and reliability of the overall system, but some reported on the performance of individual steps in processing the data. The validity and reliability results were found for the following steps in the data processing pipeline: data de-identification (n = 1), concept identification (n = 3), concept normalization (n = 2), and relation extraction (n = 8). The methods varied widely, and some approaches yielded better results than others. Our results suggest that the use of social media conversations for pharmacovigilance is in its infancy. Although social media data has the potential to supplement data from regulatory agency databases; is able to capture less frequently reported AEs; and can identify AEs earlier than official alerts or regulatory changes, the utility and validity of the data source remains under-studied. Open Science Framework ( https://osf.io/kv9hu/ ).

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

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-14

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

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

PubMed Central

2012-01-01

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

Improving Data Catalogs with Free and Open Source Software

NASA Astrophysics Data System (ADS)

Schweitzer, R.; Hankin, S.; O'Brien, K.

2013-12-01

The Global Earth Observation Integrated Data Environment (GEO-IDE) is NOAA's effort to successfully integrate data and information with partners in the national US-Global Earth Observation System (US-GEO) and the international Global Earth Observation System of Systems (GEOSS). As part of the GEO-IDE, the Unified Access Framework (UAF) is working to build momentum towards the goal of increased data integration and interoperability. The UAF project is moving towards this goal with an approach that includes leveraging well known and widely used standards, as well as free and open source software. The UAF project shares the widely held conviction that the use of data standards is a key ingredient necessary to achieve interoperability. Many community-based consensus standards fail, though, due to poor compliance. Compliance problems emerge for many reasons: because the standards evolve through versions, because documentation is ambiguous or because individual data providers find the standard inadequate as-is to meet their special needs. In addition, minimalist use of standards will lead to a compliant service, but one which is of low quality. In this presentation, we will be discussing the UAF effort to build a catalog cleaning tool which is designed to crawl THREDDS catalogs, analyze the data available, and then build a 'clean' catalog of data which is standards compliant and has a uniform set of data access services available. These data services include, among others, OPeNDAP, Web Coverage Service (WCS) and Web Mapping Service (WMS). We will also discuss how we are utilizing free and open source software and services to both crawl, analyze and build the clean data catalog, as well as our efforts to help data providers improve their data catalogs. We'll discuss the use of open source software such as DataNucleus, Thematic Realtime Environmental Distributed Data Services (THREDDS), ncISO and the netCDF Java Common Data Model (CDM). We'll also demonstrate how we are using free services such as Google Charts to create an easily identifiable visual metaphor which describes the quality of data catalogs. Using this rubric, in conjunction with the ncISO metadata quality rubric, will allow data providers to identify non-compliance issues in their data catalogs, thereby improving data availability to their users and to data discovery systems

SLURM: Simple Linux Utility for Resource Management

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

Jette, M; Dunlap, C; Garlick, J

2002-04-24

Simple Linux Utility for Resource Management (SLURM) is an open source, fault-tolerant, and highly scalable cluster management and job scheduling system for Linux clusters of thousands of nodes. Components include machine status, partition management, job management, and scheduling modules. The design also includes a scalable, general-purpose communication infrastructure. Development will take place in four phases: Phase I results in a solid infrastructure; Phase II produces a functional but limited interactive job initiation capability without use of the interconnect/switch; Phase III provides switch support and documentation; Phase IV provides job status, fault-tolerance, and job queuing and control through Livermore's Distributed Productionmore » Control System (DPCS), a meta-batch and resource management system.« less

NOAO observing proposal processing system

NASA Astrophysics Data System (ADS)

Bell, David J.; Gasson, David; Hartman, Mia

2002-12-01

Since going electronic in 1994, NOAO has continued to refine and enhance its observing proposal handling system. Virtually all related processes are now handled electronically. Members of the astronomical community can submit proposals through email, web form or via Gemini's downloadable Phase-I Tool. NOAO staff can use online interfaces for administrative tasks, technical reviews, telescope scheduling, and compilation of various statistics. In addition, all information relevant to the TAC process is made available online. The system, now known as ANDES, is designed as a thin-client architecture (web pages are now used for almost all database functions) built using open source tools (FreeBSD, Apache, MySQL, Perl, PHP) to process descriptively-marked (LaTeX, XML) proposal documents.

A Toolkit for Forward/Inverse Problems in Electrocardiography within the SCIRun Problem Solving Environment

PubMed Central

Burton, Brett M; Tate, Jess D; Erem, Burak; Swenson, Darrell J; Wang, Dafang F; Steffen, Michael; Brooks, Dana H; van Dam, Peter M; Macleod, Rob S

2012-01-01

Computational modeling in electrocardiography often requires the examination of cardiac forward and inverse problems in order to non-invasively analyze physiological events that are otherwise inaccessible or unethical to explore. The study of these models can be performed in the open-source SCIRun problem solving environment developed at the Center for Integrative Biomedical Computing (CIBC). A new toolkit within SCIRun provides researchers with essential frameworks for constructing and manipulating electrocardiographic forward and inverse models in a highly efficient and interactive way. The toolkit contains sample networks, tutorials and documentation which direct users through SCIRun-specific approaches in the assembly and execution of these specific problems. PMID:22254301

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

PubMed Central

Taylor, Stephen; Noble, Roger

2014-01-01

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

The Palladiolibrary Geo-Models AN Open 3d Archive to Manage and Visualize Information-Communication Resources about Palladio

NASA Astrophysics Data System (ADS)

Apollonio, F. I.; Baldissini, S.; Clini, P.; Gaiani, M.; Palestini, C.; Trevisan, C.

2013-07-01

The paper describes objectives, methods, procedures and outcomes of the development of the digital archive of Palladio works and documentation: the PALLADIOLibrary of Centro Internazionale di Studi di Architettura Andrea Palladio di Vicenza (CISAAP). The core of the application consists of fifty-one reality-based 3D models usable and navigable within a system grounded on GoogleEarth. This information system, a collaboration of four universities bearers of specific skills returns a comprehensive, structured and coherent semantic interpretation of Palladian landscape through shapes realistically reconstructed from historical sources and surveys and treated for GE with Ambient Occlusion techniques, overcoming the traditional display mode.

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

NASA Astrophysics Data System (ADS)

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

2018-01-01

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

Thou Shalt Be Reproducible! A Technology Perspective

PubMed Central

Mair, Patrick

2016-01-01

This article elaborates on reproducibility in psychology from a technological viewpoint. Modern open source computational environments are shown and explained that foster reproducibility throughout the whole research life cycle, and to which emerging psychology researchers should be sensitized, are shown and explained. First, data archiving platforms that make datasets publicly available are presented. Second, R is advocated as the data-analytic lingua franca in psychology for achieving reproducible statistical analysis. Third, dynamic report generation environments for writing reproducible manuscripts that integrate text, data analysis, and statistical outputs such as figures and tables in a single document are described. Supplementary materials are provided in order to get the reader started with these technologies. PMID:27471486

NPTFit: A Code Package for Non-Poissonian Template Fitting

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

Mishra-Sharma, Siddharth; Rodd, Nicholas L.; Safdi, Benjamin R., E-mail: smsharma@princeton.edu, E-mail: nrodd@mit.edu, E-mail: bsafdi@mit.edu

We present NPTFit, an open-source code package, written in Python and Cython, for performing non-Poissonian template fits (NPTFs). The NPTF is a recently developed statistical procedure for characterizing the contribution of unresolved point sources (PSs) to astrophysical data sets. The NPTF was first applied to Fermi gamma-ray data to provide evidence that the excess of ∼GeV gamma-rays observed in the inner regions of the Milky Way likely arises from a population of sub-threshold point sources, and the NPTF has since found additional applications studying sub-threshold extragalactic sources at high Galactic latitudes. The NPTF generalizes traditional astrophysical template fits to allowmore » for the ability to search for populations of unresolved PSs that may follow a given spatial distribution. NPTFit builds upon the framework of the fluctuation analyses developed in X-ray astronomy, thus it likely has applications beyond those demonstrated with gamma-ray data. The NPTFit package utilizes novel computational methods to perform the NPTF efficiently. The code is available at http://github.com/bsafdi/NPTFit and up-to-date and extensive documentation may be found at http://nptfit.readthedocs.io.« less

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.

Putting Home Data Management into Perspective

DTIC Science & Technology

2009-12-01

approaches. However, users of home and personal storage live it. Popular interfaces (e.g., iTunes , iPhoto, and even drop-down lists of recently...users of home and personal storage live it. Popular interfaces (e.g., iTunes , iPhoto, and even drop-down lists of recently-opened Word documents...live it. Popular interfaces (e.g., iTunes , iPhoto, and even drop- down lists of recently-opened Word documents) allow users to navigate file

Birth outcomes among military personnel after exposure to documented open-air burn pits before and during pregnancy.

PubMed

Conlin, Ava Marie S; DeScisciolo, Connie; Sevick, Carter J; Bukowinski, Anna T; Phillips, Christopher J; Smith, Tyler C

2012-06-01

To examine birth outcomes in military women and men with potential exposure to documented open-air burn pits before and during pregnancy. Electronic data from the Department of Defense Birth and Infant Health Registry and the Defense Manpower Data Center were used to examine the prevalence of birth defects and preterm birth among infants of active-duty women and men who were deployed within a 3-mile radius of a documented open-air burn pit before or during pregnancy. In general, burn pit exposure at various times in relation to pregnancy and for differing durations was not consistently associated with an increase in birth defects or preterm birth in infants of active-duty military personnel. These analyses offer reassurance to service members that burn pit exposure is not consistently associated with these select adverse infant health outcomes.

OpenEIS. Users Guide

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

Kim, Woohyun; Lutes, Robert G.; Katipamula, Srinivas

This document is a users guide for OpenEIS, a software code designed to provide standard methods for authoring, sharing, testing, using and improving algorithms for operational building energy efficiency.

Using R to implement spatial analysis in open source environment

NASA Astrophysics Data System (ADS)

Shao, Yixi; Chen, Dong; Zhao, Bo

2007-06-01

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

Microgravity Experiments Safety and Integration Requirements Document Tree

NASA Technical Reports Server (NTRS)

Hogan, Jean M.

1995-01-01

This report is a document tree of the safety and integration documents required to develop a space experiment. Pertinent document information for each of the top level (tier one) safety and integration documents, and their applicable and reference (tier two) documents has been identified. This information includes: document title, revision level, configuration management, electronic availability, listed applicable and reference documents, source for obtaining the document, and document owner. One of the main conclusions of this report is that no single document tree exists for all safety and integration documents, regardless of the Shuttle carrier. This document also identifies the need for a single point of contact for customers wishing to access documents. The data in this report serves as a valuable information source for the NASA Lewis Research Center Project Documentation Center, as well as for all developers of space experiments.

[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.

MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics.

PubMed

Egea, Jose A; Henriques, David; Cokelaer, Thomas; Villaverde, Alejandro F; MacNamara, Aidan; Danciu, Diana-Patricia; Banga, Julio R; Saez-Rodriguez, Julio

2014-05-10

Optimization is the key to solving many problems in computational biology. Global optimization methods, which provide a robust methodology, and metaheuristics in particular have proven to be the most efficient methods for many applications. Despite their utility, there is a limited availability of metaheuristic tools. We present MEIGO, an R and Matlab optimization toolbox (also available in Python via a wrapper of the R version), that implements metaheuristics capable of solving diverse problems arising in systems biology and bioinformatics. The toolbox includes the enhanced scatter search method (eSS) for continuous nonlinear programming (cNLP) and mixed-integer programming (MINLP) problems, and variable neighborhood search (VNS) for Integer Programming (IP) problems. Additionally, the R version includes BayesFit for parameter estimation by Bayesian inference. The eSS and VNS methods can be run on a single-thread or in parallel using a cooperative strategy. The code is supplied under GPLv3 and is available at http://www.iim.csic.es/~gingproc/meigo.html. Documentation and examples are included. The R package has been submitted to BioConductor. We evaluate MEIGO against optimization benchmarks, and illustrate its applicability to a series of case studies in bioinformatics and systems biology where it outperforms other state-of-the-art methods. MEIGO provides a free, open-source platform for optimization that can be applied to multiple domains of systems biology and bioinformatics. It includes efficient state of the art metaheuristics, and its open and modular structure allows the addition of further methods.

MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics

PubMed Central

2014-01-01

Background Optimization is the key to solving many problems in computational biology. Global optimization methods, which provide a robust methodology, and metaheuristics in particular have proven to be the most efficient methods for many applications. Despite their utility, there is a limited availability of metaheuristic tools. Results We present MEIGO, an R and Matlab optimization toolbox (also available in Python via a wrapper of the R version), that implements metaheuristics capable of solving diverse problems arising in systems biology and bioinformatics. The toolbox includes the enhanced scatter search method (eSS) for continuous nonlinear programming (cNLP) and mixed-integer programming (MINLP) problems, and variable neighborhood search (VNS) for Integer Programming (IP) problems. Additionally, the R version includes BayesFit for parameter estimation by Bayesian inference. The eSS and VNS methods can be run on a single-thread or in parallel using a cooperative strategy. The code is supplied under GPLv3 and is available at http://www.iim.csic.es/~gingproc/meigo.html. Documentation and examples are included. The R package has been submitted to BioConductor. We evaluate MEIGO against optimization benchmarks, and illustrate its applicability to a series of case studies in bioinformatics and systems biology where it outperforms other state-of-the-art methods. Conclusions MEIGO provides a free, open-source platform for optimization that can be applied to multiple domains of systems biology and bioinformatics. It includes efficient state of the art metaheuristics, and its open and modular structure allows the addition of further methods. PMID:24885957

CATOS (Computer Aided Training/Observing System): Automating animal observation and training.

PubMed

Oh, Jinook; Fitch, W Tecumseh

2017-02-01

In animal behavioral biology, an automated observing/training system may be useful for several reasons: (a) continuous observation of animals for documentation of specific, irregular events, (b) long-term intensive training of animals in preparation for behavioral experiments, (c) elimination of potential cues and biases induced by humans during training and testing. Here, we describe an open-source-based system named CATOS (Computer Aided Training/Observing System) developed for such situations. There are several notable features in this system. CATOS is flexible and low cost because it is based on free open-source software libraries, common hardware parts, and open-system electronics based on Arduino. Automated video condensation is applied, leading to significantly reduced video data storage compared to the total active hours of the system. A data-viewing utility program helps a user browse recorded data quickly and more efficiently. With these features, CATOS has the potential to be applied to many different animal species in various environments such as laboratories, zoos, or even private homes. Also, an animal's free access to the device without constraint, and a gamified learning process, enhance the animal's welfare and enriches their environment. As a proof of concept, the system was built and tested with two different species. Initially, the system was tested for approximately 10 months with a domesticated cat. The cat was successfully and fully automatically trained to discriminate three different spoken words. Then, in order to test the system's adaptability to other species and hardware components, we used it to train a laboratory rat for 3 weeks.

SU-E-T-103: Development and Implementation of Web Based Quality Control Software

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

Studinski, R; Taylor, R; Angers, C

Purpose: Historically many radiation medicine programs have maintained their Quality Control (QC) test results in paper records or Microsoft Excel worksheets. Both these approaches represent significant logistical challenges, and are not predisposed to data review and approval. It has been our group's aim to develop and implement web based software designed not just to record and store QC data in a centralized database, but to provide scheduling and data review tools to help manage a radiation therapy clinics Equipment Quality control program. Methods: The software was written in the Python programming language using the Django web framework. In order tomore » promote collaboration and validation from other centres the code was made open source and is freely available to the public via an online source code repository. The code was written to provide a common user interface for data entry, formalize the review and approval process, and offer automated data trending and process control analysis of test results. Results: As of February 2014, our installation of QAtrack+ has 180 tests defined in its database and has collected ∼22 000 test results, all of which have been reviewed and approved by a physicist via QATrack+'s review tools. These results include records for quality control of Elekta accelerators, CT simulators, our brachytherapy programme, TomoTherapy and Cyberknife units. Currently at least 5 other centres are known to be running QAtrack+ clinically, forming the start of an international user community. Conclusion: QAtrack+ has proven to be an effective tool for collecting radiation therapy QC data, allowing for rapid review and trending of data for a wide variety of treatment units. As free and open source software, all source code, documentation and a bug tracker are available to the public at https://bitbucket.org/tohccmedphys/qatrackplus/.« less

Naima: a Python package for inference of particle distribution properties from nonthermal spectra

NASA Astrophysics Data System (ADS)

Zabalza, V.

2015-07-01

The ultimate goal of the observation of nonthermal emission from astrophysical sources is to understand the underlying particle acceleration and evolution processes, and few tools are publicly available to infer the particle distribution properties from the observed photon spectra from X-ray to VHE gamma rays. Here I present naima, an open source Python package that provides models for nonthermal radiative emission from homogeneous distribution of relativistic electrons and protons. Contributions from synchrotron, inverse Compton, nonthermal bremsstrahlung, and neutral-pion decay can be computed for a series of functional shapes of the particle energy distributions, with the possibility of using user-defined particle distribution functions. In addition, naima provides a set of functions that allow to use these models to fit observed nonthermal spectra through an MCMC procedure, obtaining probability distribution functions for the particle distribution parameters. Here I present the models and methods available in naima and an example of their application to the understanding of a galactic nonthermal source. naima's documentation, including how to install the package, is available at http://naima.readthedocs.org.

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

PubMed Central

Boulos, Maged N Kamel; Honda, Kiyoshi

2006-01-01

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

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

PubMed

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

2007-11-01

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

Open-Source RTOS Space Qualification: An RTEMS Case Study

NASA Technical Reports Server (NTRS)

Zemerick, Scott

2017-01-01

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

Cyberscience and the Knowledge-Based Economy. Open Access and Trade Publishing: From Contradiction to Compatibility with Non-Exclusive Copyright Licensing

ERIC Educational Resources Information Center

Armbruster, Chris

2008-01-01

Open source, open content and open access are set to fundamentally alter the conditions of knowledge production and distribution. Open source, open content and open access are also the most tangible result of the shift towards e-science and digital networking. Yet, widespread misperceptions exist about the impact of this shift on knowledge…

Learning from hackers: open-source clinical trials.

PubMed

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

2012-05-02

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

Science Directorate Publications and Presentations

NASA Technical Reports Server (NTRS)

Summers, F. G. (Compiler)

2000-01-01

This document lists the significant publications and presentation of the Science Directorate during the period January 1-December 31, 1999. Entries in the main part of the document are categorized according to NASA Reports (arranged by report number). Open Literature, and Presentations (arranged alphabetically by title). Most of the articles listed under Open Literature have appeared in refereed professional journals, books, monographs, or conference proceedings. Although many published abstracts are eventually expanded into full papers for publication in scientific and technical journals, they are often sufficiently comprehensive to include the significant results of the research reported. Therefore, published abstracts are listed separately in a section under Open Literature.

Science Directorate Publications and Presentations

NASA Astrophysics Data System (ADS)

Summers, F. G.

2000-07-01

This document lists the significant publications and presentation of the Science Directorate during the period January 1-December 31, 1999. Entries in the main part of the document are categorized according to NASA Reports (arranged by report number). Open Literature, and Presentations (arranged alphabetically by title). Most of the articles listed under Open Literature have appeared in refereed professional journals, books, monographs, or conference proceedings. Although many published abstracts are eventually expanded into full papers for publication in scientific and technical journals, they are often sufficiently comprehensive to include the significant results of the research reported. Therefore, published abstracts are listed separately in a section under Open Literature.

VarioML framework for comprehensive variation data representation and exchange.

PubMed

Byrne, Myles; Fokkema, Ivo Fac; Lancaster, Owen; Adamusiak, Tomasz; Ahonen-Bishopp, Anni; Atlan, David; Béroud, Christophe; Cornell, Michael; Dalgleish, Raymond; Devereau, Andrew; Patrinos, George P; Swertz, Morris A; Taschner, Peter Em; Thorisson, Gudmundur A; Vihinen, Mauno; Brookes, Anthony J; Muilu, Juha

2012-10-03

Sharing of data about variation and the associated phenotypes is a critical need, yet variant information can be arbitrarily complex, making a single standard vocabulary elusive and re-formatting difficult. Complex standards have proven too time-consuming to implement. The GEN2PHEN project addressed these difficulties by developing a comprehensive data model for capturing biomedical observations, Observ-OM, and building the VarioML format around it. VarioML pairs a simplified open specification for describing variants, with a toolkit for adapting the specification into one's own research workflow. Straightforward variant data can be captured, federated, and exchanged with no overhead; more complex data can be described, without loss of compatibility. The open specification enables push-button submission to gene variant databases (LSDBs) e.g., the Leiden Open Variation Database, using the Cafe Variome data publishing service, while VarioML bidirectionally transforms data between XML and web-application code formats, opening up new possibilities for open source web applications building on shared data. A Java implementation toolkit makes VarioML easily integrated into biomedical applications. VarioML is designed primarily for LSDB data submission and transfer scenarios, but can also be used as a standard variation data format for JSON and XML document databases and user interface components. VarioML is a set of tools and practices improving the availability, quality, and comprehensibility of human variation information. It enables researchers, diagnostic laboratories, and clinics to share that information with ease, clarity, and without ambiguity.

VarioML framework for comprehensive variation data representation and exchange

PubMed Central

2012-01-01

Background Sharing of data about variation and the associated phenotypes is a critical need, yet variant information can be arbitrarily complex, making a single standard vocabulary elusive and re-formatting difficult. Complex standards have proven too time-consuming to implement. Results The GEN2PHEN project addressed these difficulties by developing a comprehensive data model for capturing biomedical observations, Observ-OM, and building the VarioML format around it. VarioML pairs a simplified open specification for describing variants, with a toolkit for adapting the specification into one's own research workflow. Straightforward variant data can be captured, federated, and exchanged with no overhead; more complex data can be described, without loss of compatibility. The open specification enables push-button submission to gene variant databases (LSDBs) e.g., the Leiden Open Variation Database, using the Cafe Variome data publishing service, while VarioML bidirectionally transforms data between XML and web-application code formats, opening up new possibilities for open source web applications building on shared data. A Java implementation toolkit makes VarioML easily integrated into biomedical applications. VarioML is designed primarily for LSDB data submission and transfer scenarios, but can also be used as a standard variation data format for JSON and XML document databases and user interface components. Conclusions VarioML is a set of tools and practices improving the availability, quality, and comprehensibility of human variation information. It enables researchers, diagnostic laboratories, and clinics to share that information with ease, clarity, and without ambiguity. PMID:23031277

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.

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

PubMed

Jurica, Peter; van Leeuwen, Cees

2009-01-01

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

Documents, Dialogue and the Emergence of Tertiary Orality

ERIC Educational Resources Information Center

Turner, Deborah; Allen, Warren

2013-01-01

Introduction: This investigation opens with a description of why studying non-traditional, oral documents can inform efforts to extend traditional library and information science practices, of description, storage, and retrieval, to artefacts made available through emerging media. Method: This study extends the method used to identify a document,…