ChemicalToolBoX

What's the ChemicalToolBoX?

The ChemicalToolBoX is a set of tools integrated into the Galaxy-workflow-management system to enable researchers easy-to-use, reproducible, and transparent access to cheminformatics libraries and drug discovery tools. It includes standard applications for similarity and substructure searches, clustering of compounds, prediction of properties and descriptors, filtering, and many other tools that range from drug-likeness classification to fragmentation and fragment-merging. By combinating the various tools many more powerful applications can be designed.

ChemicalToolBox is based on open-source software, web-accessible, freely available, and easily expandable. It can be downloaded and easily deployed locally or on a large scale cluster.

Galaxy

Galaxy is an open, web-based platform for data intensive research. All tools can be combined in workflows without any need of programming skills. Furthermore the platform can be extended with more tools at any time. Each tool has its own information about what it does and how the input is supposed to look like. You can make data available for Galaxy by uploading local files or downloading online content. Inputfiles, workflowsteps and results are stored in a history where you can view them or reaccess them later. It is possible to share workflows and histories with other users or make the public available. Saved workflows can be used with new input files or just to rerun an analyses which ensures repeatability.

Parallelisation

ChemicalToolBoX is capable of accelerating the computation time of resource-intensive processes. Large molecule files are automatically splitted in smaller chunks. Each chunk then is processed on a separate core and merged afterwards. Everything stays the same for the user but computation time decreases.

As the parallelisation is scalable the job will run on a predefined number of cores. The more cores the faster the processing.

Supported Filetypes

InChI

International Chemical Identifier - developed by the IUPAC. Representation of a chemical molecule as a string which can include information about the bond, tautomerism, isotope, charge and stereochemistry. Strings are generated following the InChI-algorithm.
MOL & MOL2

Single chemical molecule. See SDF.
SDF

Structure-data-file consisting of many MOL-files. Molecules are separated by four Dollar signs ($$$$). Allows the storing metainformation like molecular mass or uniqueID. Developed by MDL Information System (Accelrys).
SMILES

A line notation using ASCII strings to represent chemical molecules. Information about the charge, isotope or radical can be included besides the stereo information (CIP convention) and the normal bonds. The Simplified Molecular Input Line Entry Specification was developed by Daylight Chemical Information System Incorporation.

All filetypes are interchangable due to three easy converting options:

the built-in conversion via the pencil icon
the Compound Converter tool described in the Tools section
the import conversion each tool automatically offers

Bug Tracker

Have a bug or a feature request? Please write a new card. Before writing a new card, please search for existing issues.

Contributing

We encourage you to contribute to ChemicalToolBoX! Check out our Trello board or contact us via e-mail.

About Galaxytools

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