- 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 nloira@gmail.com
License
This project is open source and freely available under the GLP v2 license.
1 maintainer
Metadata
1 maintainer
Release files for biopantograph 0.3.2
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