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GIMIAS

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GIMIAS is a workflow-oriented environment for solving advanced biomedical image computing and individualized simulation problems, which is extensible through the development of problem-specific plug-ins. In addition, GIMIAS provides an open source framework for efficient development of research and clinical software prototypes integrating contributions from the Physiome community while allowing business-friendly technology transfer and commercial product development.

GIMIAS suites are collections of prototypes that build a complete platform for one or more clinical applications.

Homepage: 
http://www.gimias.org/

MassChroQ

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MassChroQ (Mass Chromatogram Quantification) software performs quantification of data obtained from mass-spectrometry techniques. It is particularly well suited for peptide quantification of LC-MS (Liquid Chromatography - Mass Spectrometry) data. It performs chromatographic alignment, XIC extraction, peak detection and quantification on identified peptides, with or without isotopic labeling, on high or low resolution data and it takes into account peptide or protein fractionation.

Homepage: 
http://pappso.inra.fr/bioinfo/masschroq/

cTAKES

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Apache clinical Text Analysis and Knowledge Extraction System (cTAKES) is an open-source natural language processing system for information extraction from electronic medical record clinical free-text. It processes clinical notes, identifying types of clinical named entities from various dictionaries including the Unified Medical Language System (UMLS) - medications, diseases/disorders, signs/symptoms, anatomical sites and procedures.

Homepage: 
https://ctakes.apache.org/

PsychoPy

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PsychoPy is an open-source application to allow the presentation of stimuli and collection of data for a wide range of neuroscience, psychology and psychophysics experiments. It’s a free, powerful alternative to Presentation™ or e-Prime™ . It’s written in Python (a free alternative to Matlab™ ) and combines the graphical strengths of OpenGL with the easy Python syntax to give psychophysics a free and simple stimulus presentation and control package.

Homepage: 
http://www.psychopy.org/

tranSMART

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tranSMART is a knowledge management platform that enables scientists to develop and refine research hypotheses by investigating correlations between genetic and phenotypic data, and assessing their analytical results in the context of published literature and other work.

The integration, normalization, and alignment of data in tranSMART permits users to explore data very efficiently to formulate new research strategies. Some of tranSMART's specific applications include:

Homepage: 
http://www.transmartproject.org/

DeVIDE

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DeVIDE, or the Delft Visualisation and Image processing Development Environment, is a cross-platform software framework for the rapid prototyping, testing and deployment of visualisation and image processing algorithms. The software was developed within the Visualisation group. DeVIDE's primary (and currently only) front-end is a data-flow boxes-and-lines network editor. In this regard, it is very similar to AVS, OpenDX, Khoros or VISSION. DeVIDE integrates functionality from libraries such as VTK, ITK, GDCM, DCMTK, numpy and matplotlib. It is being very actively developed.

Homepage: 
http://www.cg.its.tudelft.nl/Projects/DeVIDE

Bioconductor

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Bioconductor is an open source, open development software project to provide tools for the analysis and comprehension of high-throughput genomic data. It is based primarily on the R programming language.

The Bioconductor release version is updated twice each year, and is appropriate for most users. There is also a development version, to which new features and packages are added prior to incorporation in the release. A large number of meta-data packages provide pathway, organism, microarray and other annotations.

Homepage: 
http://www.bioconductor.org/

Ogles2

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Ogles2 is an interactive slice and volume visualization and analysis tool based on Open Inventor / Coin3D. Ogles2 allows for reproducing the workflow of frame based stereotactic neurosurgery. In the long run it strives for being an open source stereotactic planning and analysis system. Ogles2 is NOT APPROVED FOR CLINICAL USE.

Homepage: 
http://ogles.sourceforge.net/Ogles/ogles2-doc/index.html

ART-DECOR

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ART-DECOR is an open-source tool suite that supports the creation and maintenance of HL7 Templates, Value Sets as well as Data Sets and features cloud-based federated Building Block Repositories (BBR) for Templates and Value Sets. The tool offers a Data Set and a Scenario editor, two Template editors, a Value Set editor and includes browsers for various international terminologies such as LOINC.

Homepage: 
https://art-decor.org/

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