biopantograph 0.3.2

Pantograph is a toolbox for the reconstruction, curation and validation of metabolic models.

Author:

Nicolas Loira

Date:

2016-04

Biopantograph is a collection of python modules and programs for the reconstruction, curation and validation of metabolic models. It reads and writes SBML files.

Installation

The recommended installation method is:

pip install biopantograph

Pantograph requires libsbml, but pip will take care of that requirement. If you don’t have permissions to install at the system level, try: pip install biopantograph --user. You can also clone and contribute from the BitBucket repository.

Tools

The basic script you need to know is pantograph, which will help you to reconstruct a metabolic model for your target species. pantograph takes as input an existing SBML model as a template, orthology data between your template and your target genes (from Inparanoid and/or OrthoMCL) and other optional data. Invoke pantograph as follows:

$ pantograph -x scaffold.xml -i inparanoid.data -m orthomcl.data -s org1 -t org2 -o out.xml -l out.log

Where `scaffold.txt` is an existing, well-curated SBML metabolic model, used as a template for the reconstruction; inparanoid.data is the output from Inparanoid, comparing the genes from the template and the reconstructed model; orthomcl.data is the output from OrthoMCL (where org1 is the template model id and org2 is the reconstructed model id); out.xml is the SBML reconstructed model and out.log is the reconstruction log. You can reconstruct a model using any of the two orthology methods (Inparanoid or OrthoMCL), although better results are obtained using both.

The biopantograph package includes many other tools that can be useful for your reconstruction. Try them with the parameter --help to obtain usage information.

Tool	Description
pantograph	Create a new model, from a template model and orthology files
ptg_addbiggreactions	Add reactions from a list of BiGG ids, to a model
ptg_projector	Create a new model, using an existing one as template
ptg_curateSBML	Add new species/reactions to a model, from a CSV
ptg_inparanoid2rel	Parses Inparanoid output for ptg_projector
ptg_omcl2rel	Parses OrthoMCL output for ptg_projector

The modules provided can be used to develop your own applications:

Module	Description
pathtastictools	Algorithms to reconstruct metabolic models from a template
SBMLeditor	High-level modifications to SBML models
BiGG	Module to handle calls to the BiGG Web API
BiGG2SBML	Add elements from BiGG API to a SBML file
SBMLutils	High-level utilities

Biopantograph has been tested under Linux and OS X. For more information, please visit the official Pantograph website: http://pathtastic.gforge.inria.fr. More documentation coming soon!

Reference

If you use Pantograph for your own reconstructions, please cite:

Nicolas Loira, Anna Zhukova and David J Sherman. Pantograph: A template-based method for genome-scale metabolic model reconstruction. J Bioinform Comput Biol, 13(2): 1550006, 2015. DOI: 10.1142/S0219720015500067

For any question, please contact: Nicolas Loira [e-mail]

License

This project is open source and freely available under the GLP v2 license.