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.
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.
- Java 7
- 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.
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.
./kegg-extract [NCBI TAXONOMY ID | KEGG ORGANISM ID] [OUTPUT DIRECTORY]
./kegg-extract 559292 /Users/name/kegg
./kegg-extract sce /Users/name/kegg
To download the relevant MetaCyc files and generate an SBML representation, run metacyc-extract:
./metacyc-extract [METACYC SOURCE] [METACYC USERNAME] [METACYC PASSWORD] [NCBI TAXONOMY ID] [OUTPUT FILE]
./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:
./metacyc-extract-no-download [NCBI TAXONOMY ID] [METACYC DIRECTORY] [OUTPUT FILE]
./metacyc-extract-no-download 559292 /Users/name/15.5/ /Users/name/metacyc.xml
To run the merge module in simple mode, such that metabolites are only considered to be the same if they share the same annotation:
./merge [INPUT DIRECTORY] [OUTPUT FILE]
./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:
./merge [INPUT DIRECTORY] [OUTPUT FILE] false
./merge /Users/name/kegg /Users/name/kegg_merged.xml false
./protonate [CHEMAXON DIRECTORY] [INPUT FILE] [OUTPUT FILE] [pH]
./protonate /Applications/ChemAxon/ /Users/name/kegg_merged.xml /Users/name/kegg_protonated.xml 7.2
./balance [INPUT FILE] [OUTPUT FILE]
./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 [CHEMAXON DIRECTORY] [METACYC SOURCE] [METACYC USERNAME] [METACYC PASSWORD] [OUTPUT DIRECTORY] [NCBI TAXONOMY ID | KEGG ORGANISM ID]
./reconstruct /Applications/ChemAxon/ http://bioinformatics.ai.sri.com/ecocyc/dist/flatfiles-xxxxxxxx/ username password /Users/name/reconstruction 559292
./reconstruct /Applications/ChemAxon/ http://bioinformatics.ai.sri.com/ecocyc/dist/flatfiles-xxxxxxxx/ username password /Users/name/reconstruction sce
Test scripts exist for Linux, Mac OS X and Windows. To execute the test suite, open a Terminal, navigate to the
test/win directory, modify the
test.bat file to specify the
metacyc_password variables appropriate to your MetaCyc licence,
and execute the appropriate shell script / batch file.
Source code is available at SourceForge.
Please direct any questions or comments to Neil Swainston.