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A collection of cheminformatics and machine-learning software written in C++ and Python.
NOTE: the RDKit source code and downloads are now in github: https://github.com/rdkit/rdkit
The core algorithms and data structures are written in C++. Wrappers are provided to use the toolkit from either Python or Java.
Additionally, the RDKit distribution includes a PostgreSQL-based cartridge that allows molecules to be stored in relational database and retrieved via substructure and similarity searches.
...Resource of the libSBGN project have been migrated from SourceForge to GitHub.
Latest changes can be found on GitHub now.
The code repository can be found here now
https://github.com/sbgn/libsbgn
The files (releases) can be found here now
https://github.com/sbgn/libsbgn/releases
The bugs and features (issues) can be found here now
https://github.com/sbgn/libsbgn/issues
...A novel particle tracking method with individual particle size measurement and its application to ordering in glassy hard sphere colloids. Soft Matter 9, 1447–1457 (2013). https://dx.doi.org/10.1039/C2SM27107A (http://arxiv.org/pdf/1301.7237.pdf)
A set of tools for working with high-throughput sequencing data
A set of tools (in Java) for working with next generation sequencing data in the SAM/BAM format. Note that development has moved to GitHub at https://github.com/broadinstitute/picard and support is available on the GATK forum at http://gatkforums.broadinstitute.org/categories/ask-the-team
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A pipeline for quantitative proteomics based upon isobaric tags
...This website contains the IQuant software, an example data labeled by iTRAQ-8plex for testing and a user's manual. If you have any question about IQuant, please contact me: wenbo@genomics.cn.
The source code of IQuant can be found here "https://sourceforge.net/p/iquant/code/".
...The installation procedure differs slightly according to your system; but this should remain simple. Have a look at the readme file when you download your new copy from
https://sourceforge.net/projects/rawgeno/files/rawgeno/RawGeno%202.0-1/
Make also sure to have a look at
https://sourceforge.net/projects/rawgeno/files/
where you can find a detailed manual, demo datasets and many demo scripts.
Modern MATLAB-based modelling software for 13C metabolic flux analysis (MFA).
Support available in Google group (https://groups.google.com/d/forum/13cmfa-openflux).
A web based information management system for macromolecular (protein) crystallography X-ray experiments.
This project has moved to https://forge.ill.eu/projects/ispyb
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This Project moved to https://sourceforge.net/projects/synbiowave/ because the name GeneWave is a registered trademark... Please do not use this project anymore.
The JChemPaint Applet and Swing Application are Java programs for drawing 2D chemical structures like those found in most chemistry textbooks. It is based on the Chemistry Development Kit (cdk.sf.net). Downloads, tracker, and source code repository can be found on https://jchempaint.github.io