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SuBliMinaL Toolbox


The SuBliMinaL Toolbox comprises of a number of independent tools that can be used to automate steps in the development of genome-scale metabolic reconstructions.

A full description of this work can be found in the paper describing this work: The SuBliMinaL Toolbox: automating steps in the reconstruction of metabolic reconstructions.

Installation

The SuBliMinal Toolbox has been tested on Linux, Mac OS X (Snow Leopard onwards) and Windows 7 has a number of dependencies, which are freely available to academic users and are listed below. Please follow the links to install each module if not present on your system.

  1. Java 7
  2. ChemAxon Marvin Beans for Java (requires a licence, which is freely available to academic users.)

In addition, the SuBliMinaL Toolbox requires that users have a BioCyc Data File Licence. This is freely available to academic users at http://biocyc.org/download.shtml.

Finally, download the SuBliMinal Toolbox, and unzip in an appropriate directory.

Usage

To execute the modules of the SuBliMinaL Toolbox, open a Terminal, navigate to the bin/mac directory and type the appropriate command described below. Please refer to the paper describing this work for full descriptions of each module.

  • annotate

    Command: ./annotate

  • kegg-extract

    Command: ./kegg-extract [NCBI TAXONOMY ID | KEGG ORGANISM ID] [OUTPUT DIRECTORY]
    Example: ./kegg-extract 559292 /Users/name/kegg
    Example: ./kegg-extract sce /Users/name/kegg

  • metacyc-extract

    To download the relevant MetaCyc files and generate an SBML representation, run metacyc-extract:

    Command: ./metacyc-extract [METACYC SOURCE] [METACYC USERNAME] [METACYC PASSWORD] [NCBI TAXONOMY ID] [OUTPUT FILE]
    Example: ./metacyc-extract http://bioinformatics.ai.sri.com/ecocyc/dist/flatfiles-xxxxxxxx/ username password 559292 /Users/name/metacyc.xml

    To generate an SBML representation from a local copy of a download of a MetaCyc bundle, run metacyc-extract-no-download:

    Command: ./metacyc-extract-no-download [NCBI TAXONOMY ID] [METACYC DIRECTORY] [OUTPUT FILE]
    Example: ./metacyc-extract-no-download 559292 /Users/name/15.5/ /Users/name/metacyc.xml

  • merge

    To run the merge module in simple mode, such that metabolites are only considered to be the same if they share the same annotation:

    Command: ./merge [INPUT DIRECTORY] [OUTPUT FILE]
    Example: ./merge /Users/name/kegg /Users/name/kegg_merged.xml

    To run the merge module in fuzzy mode, such that metabolites are considered to be the same if they are stereoisomers or conjugate bases/acids of one another:

    Command: ./merge [INPUT DIRECTORY] [OUTPUT FILE] false
    Example: ./merge /Users/name/kegg /Users/name/kegg_merged.xml false

  • protonate

    Command: ./protonate [CHEMAXON DIRECTORY] [INPUT FILE] [OUTPUT FILE] [pH]
    Example: ./protonate /Applications/ChemAxon/ /Users/name/kegg_merged.xml /Users/name/kegg_protonated.xml 7.2

  • balance
    Command: ./balance [INPUT FILE] [OUTPUT FILE]
    Example: ./balance /Users/name/kegg_protonated.xml /Users/name/kegg_balanced.xml

Note that the previous modules uniprot-compartmentalise, psort-compartmentalise, transport-reactions and biomass have been deprecated and are no longer supported.

Additionally, a module exists that generates a workflow from the above modules, as described in the paper describing the path2models project. To execute the full workflow, open a Terminal, navigate to the bin/mac directory and type the command described below:

  • reconstruct

    Command: ./reconstruct [CHEMAXON DIRECTORY] [METACYC SOURCE] [METACYC USERNAME] [METACYC PASSWORD] [OUTPUT DIRECTORY] [NCBI TAXONOMY ID | KEGG ORGANISM ID]
    Example: ./reconstruct /Applications/ChemAxon/ http://bioinformatics.ai.sri.com/ecocyc/dist/flatfiles-xxxxxxxx/ username password /Users/name/reconstruction 559292
    Example: ./reconstruct /Applications/ChemAxon/ http://bioinformatics.ai.sri.com/ecocyc/dist/flatfiles-xxxxxxxx/ username password /Users/name/reconstruction sce

Testing

Test scripts exist for Linux, Mac OS X and Windows. To execute the test suite, open a Terminal, navigate to the test/linux, test/mac or test/win directory, modify the test or test.bat file to specify the metacyc_source, metacyc_username and metacyc_password variables appropriate to your MetaCyc licence, and execute the appropriate shell script / batch file.

Source code

Source code is available at SourceForge.

Feedback

Please direct any questions or comments to Neil Swainston.