MetaboX v1 beta 7/12/2013
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The MetaboX library is a PHP framework to build metabolic networks from KEGG. It provides classes to retrieve information about compounds, enzymes and reaction, cache these to file and build three different networks: reactants, unipartite and bipartite. KEGG (http://www.genome.jp/kegg/) is the default resource provider, but it is possible to implement alternative interfaces to retrieve data from other resource providers. Default cache storage is JSON file, but it is possible to create alternative cache methods (e.g. write data to a database).
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The MetaboX library provides several networks depending on available resources: reactants graph: it is built upon compounds and reactions enzymes graph: it is built upon enzymes (unipartite or bipartite)
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Released under GNU AFFERO GENERAL PUBLIC LICENSE v3
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The MetaboX library requires PHP 5.3+ installed. Just put the library wherever you prefer on your system. You can find some examples in 'examples' folder.
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The examples can be run as follows:
- php path/to/examples/load_resources_from_kegg.php path/to/compounds.csv
- php path/to/examples/build_reactants.php path/to/compounds.csv
- php path/to/examples/destroy_cache.php
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'compounds.csv' file must be a csv (comma separated value) file with a list of KEGG IDs compounds.
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It is possible to use 'config.ini' file to configure some options about resource providers and cache folders.
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Contacts:
- Francesco Maiorano frmaiorano@gmail.com LabGTP, High Performance Computing and Networking Institute, National Research Council of Italy
- Luca Ambrosino luca.bioinfo@gmail.com Dept. of Agricultural Sciences, University of Naples Federico II, Italy
- Mario Guarracino mario.guarracino@gmail.com LabGTP, High Performance Computing and Networking Institute, National Research Council of Italy