Looks very interesting. I will definitely check it out!
Igor
On Wed, Nov 20, 2013 at 3:49 AM, Greg Landrum <greg.land...@gmail.com>wrote:
> Bjoern,
>
> Congrats on the CTB and thanks for letting us know about it!
>
> -greg
>
>
>
> On Tue, Nov 19, 2013 at 9:30 PM, bjoern.gruen...@googlemail.com <
> bjoern.gruen...@gmail.com> wrote:
>
>> 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
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Shape the Mobile Experience: Free Subscription
>> Software experts and developers: Be at the forefront of tech innovation.
>> Intel(R) Software Adrenaline delivers strategic insight and game-changing
>> conversations that shape the rapidly evolving mobile landscape. Sign up
>> now.
>>
>> http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk
>> _______________________________________________
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>>
>
>
> ------------------------------------------------------------------------------
> Shape the Mobile Experience: Free Subscription
> Software experts and developers: Be at the forefront of tech innovation.
> Intel(R) Software Adrenaline delivers strategic insight and game-changing
> conversations that shape the rapidly evolving mobile landscape. Sign up
> now.
> http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk
> _______________________________________________
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
------------------------------------------------------------------------------
Shape the Mobile Experience: Free Subscription
Software experts and developers: Be at the forefront of tech innovation.
Intel(R) Software Adrenaline delivers strategic insight and game-changing
conversations that shape the rapidly evolving mobile landscape. Sign up now.
http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
