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The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to the open mzML/mzXML formats.
mzMatch is a Java collection of small commandline tools specific for metabolomics MS data analysis. The tools are built on top of the PeakML core library, providing mass spectrometry specific functionality and access to the PeakML file format.
A file format for exchanging computational models in systems biology
The Systems Biology Markup Language (SBML) is an XML-based description language for representing computational models in systems biology. Visit the project web site to learn more.
NOTE: Use of this codebase is NOT RECOMMENDED.
This project has been migrated to github at http://jaerproject.net (or https://github.com/SensorsINI/jaer for the Java code).
Commits have been disabled for the subversion sourceforge repository and new development is being done on the github repository.
Java tools for Address-Event Representation (AER) neuromorphic processing. Uses USB hardware.
See wiki at https://sourceforge.net/p/jaer/wiki/
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OpenCV powered image stack analyser for data extraction and preparation.
Can be used in conjunction with nanocalcFX.
You can get sample data at the NISA homepage.
Currently in pre-alpha state.
EMBOSS is a dynamic and comprehensive Open Source package for bioinformatics (DNA and protein sequence analysis, protein structure, phylogenetics, etc.). EMBOSS is written in C, also compatible with C++, and has a separate Java interface (Jemboss)
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