ChemcialToolBox: A Galaxy of cheminformatic tools in a web browser
I am very happy to finally announce the first release of
ChemicalToolBox!
ChemicalToolBox (CTB) is an open source project that aims for
reproducible, transparent and easy accessible cheminformatic research.
It is based on the Galaxy [1] framework and can be installed on all unix
like platforms. CTB integrates several cheminformatic toolkits and
tools, like Open Babel, RDKit, CDK, chemfp, osra, opsin, silicos-it ...
in one easy to use workbench running in a web browser.
ChemicalToolBox with installation
instructions:https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox
A few highlights of the CTB and its framework:
- every step in your analysis is logged with tool version, input dataset
and used parameters, enabling reproducibility of your analysis at any
time
- building entire cheminformatic protocols/workflows via drag & drop by
chaining small tools together. Abstracting complexness, enabling
creativity, like assembling lego bricks.
- over 40 different tools:
- conversion
- filtering (with predefined filtering rules)
- substructure and similarity search
- > 10 different fingerprints
- structure recognition
- structure depiction
- descriptor calculation
- property prediction
- CTB is accessible via any recent web browser, without any shell
knowledge. You can run a CTB instance for you lab or a whole university,
like we do here at the university of Freiburg
- CTB enables easy access to High-Performance-Computing (HPC). Based on
the Galaxy project, CTB can run on any Cluster/Grid setup, including
Cloud computing, like EC2
- by the means of the Galaxy Tool Shed, CTB comes with installation
routines of all dependencies, like Open Babel, RDKit, osra, opsin ...
once Galaxy is running you can install CTB with a few clicks
- CTB can be accessed via a REST API, for example for massively parallel
execution of workflows
- tools can be easily integrated, independently from its programming
language (it needs to be command line accessible)
- every workflow, dataset, history can be shared with a group of
researchers or can be made public available, enabling transparent and
peer-reviewed research. For example the ChemicalBox,
a merged database of many freely available
compounds:http://galaxy.uni-freiburg.de/u/bgruening/w/preparation-of-a-large-compound-library-by-merging-of-chemical-databases-1
- every tool and every tool-parameter can have (and hopefully has) an
exhaustive description to guide the researcher
- automatic build-in mutiprocessing: most of the CTB tools will split
the input datasets into smaller chunks before execution and merging the
result files after execution
I would like to thank the cheminformatic community, for all the great
tools and libraries, for accepting patches and enlightening discussions!
I hope CTB will be a useful contribution and can open the cheminformatic
universe to many more researchers.
Thanks and happy research!
Björn
[1] http://galaxyproject.org
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