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The Systems Biology Workbench(SBW) is a framework for application intercommunications. It uses a broker-based, distributed, message-passing architecture, supports many languages including Java, C++, Perl & Python, and runs under Linux,OSX & Win32.
It comes with a large number of modules, encompassing the whole modeling cycle: creating computational models, simulating and analyzing them, visualizing the information, in order to improve the models.
An open source framework for LC-MS based proteomics and metabolomics. OpenMS offers data structures and algorithms for the processing of mass spectrometry data. The library is written in C++.
Our source code and wiki lives on GitHub (https://github.com/OpenMS/OpenMS).
Phaistos is a framework for all-atom Monte Carlo simulations of proteins. It incorporates several advanced probabilistic models of protein structure for conformational sampling, efficient move-algorithms and the OPLS and PROFASI forcefields.
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openModeller is a complete C++ framework for species potential distribution modelling. The project also includes a graphical user interface, a web service interface and an API for Python.
Image processing framework to integrate EM software packages.
Scipion is an image processing framework to obtain 3D models of macromolecular complexes using Electron Microscopy (3DEM). It integrates several software packages and presents an unified interface for both biologists and developers. Scipion allows to execute workflows combining different software tools, while taking care of formats and conversions. Additionally, all steps are tracked and can be reproduced later on.
Xmipp is a well-known package in the EM image processing. It is integrated...
A collection of tools for working with the comparative data analysis ontology including import/export facilities for common phylogenetic file formats, and also a triple-store framework.
MIVF - Medical Imaging and Visualization Factory,
is a framework for medical applications. It supplies a platform, in which image processing and 3D visualization algorithms can be employed as reusable components (functional modules or plugins).
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