Pantograph

Pantograph is a software toolbox to reconstruct, curate and validate genome-scale metabolic models. It uses existing metabolic models as templates, to start its reconstructions process, to which new, species-specific reactions are added. Pantograph uses an iterative approach to improve reconstructed models, facilitating manual curation and comparisons between reconstructed model's predictions and experimental evidence.

Pantograph uses a consensus procedure to infer relationships between metabolic models, based on several sources of orthology between genomes. This allows for a very detailed rewriting of reaction's gene associations between template models and the model you want to reconstruct.

Pantograph was used to reconstruct the model of the oleaginous yeast Y. lipolytica:

Nicolas Loira, Thierry Dulermo, Jean-Marc Nicaud and David J Sherman. A genome-scale metabolic model of the lipid-accumulating yeast Yarrowia lipolytica. BMC Systems Biology 2012, 6:35. Full text

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.
You can download the postprint PDF (copyright World Scientific Publishing Company)

Pantograph was developed by the MAGNOME team at the Inria Bordeaux research center, and maintained by the Mathomics group (Inria Chile, CMM). Pantograph is open source and is available under the CeCILL license (GPL compatible).

The recommended method to install the current version (0.3) is via pip:

pip install biopantograph

You can check the development of Pantograph visiting the BitBucket repository. To download the old 0.1 version, used to reconstruct iNL895, please click here: pantograph-0.1.1.zip. To try Pantograph online, please visit the experimental Inria Chile Mobyle site: mobyle.inria.cl (beware: this is a development server). From the left column, select: Programs -> Metabolism -> Reconstruction -> pantograph. If you want to add Pantograph to your own mobyle server, please use this service description and example (zip).

For any questions and comments about Pantograph please email nloira@gmail.com.

Pantograph