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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/

SCIRun

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SCIRun is a problem solving environment or "computational workbench" in which a user selects software modules that can be connected in a visual programing environment to create a high level workflow for experimentation. Each module exposes all the available parameters necessary for scientists to adjust the outcome of their simulation or visualization. The networks in SCIRun are flexible enough to enable duplication of networks and creation of new modules.

Homepage: 
http://www.sci.utah.edu/cibc-software/scirun.html

MeVisLab

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MeVisLab represents a platform for image processing research and development with a focus on medical imaging. It allows fast integration and testing of new algorithms and the development of application prototypes that can be used in clinical environments.

Homepage: 
http://www.mevislab.de/

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/

ACHILLES

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ACHILLES is a platform which enables the characterization, quality assessment and visualization of observational health databases. ACHILLES provides users with an interactive, exploratory framework to assess patient demographics, the prevalence of conditions, drugs and procedures, and to evaluate the distribution of values for clinical observations.

ACHILLES is intended to be implemented by organizations that have patient-level observational health databases available in their local environment.

Homepage: 
http://www.ohdsi.org/analytic-tools/achilles-for-data-characterization/

Usagi

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Usagi is a software tool created by the Observational Health Data Sciences and Informatics (OHDSI) team and is used to help in the process of mapping codes from a source system into the standard terminologies stored in the Observational Medical Outcomes Partnership (OMOP) Vocabulary (http://www.ohdsi.org/data-standardization/vocabulary-resources/).

Homepage: 
http://www.ohdsi.org/web/wiki/doku.php?id=documentation%3Asoftware%3Ausagi

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

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