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Section: New Software and Platforms

Pantograph

Keywords: Systems Biology - Bioinformatics - Genomics - Gene regulatory networks

Scientific Description: Pantograph requires a template model in SMBL format, where every reaction is annotated with a gene association that describes its gene-protein-reaction dependencies as a boolean formula over the genes of the organism.

Pantograph uses a consensus procedure to infer relationships between metabolic models, based on several sources of orthology between genomes. These inter-genome relations are used to rewrite the gene associations. Every successful rewrite is used as evidence that the corresponding reaction should be present in the inferred model.

The resulting models can be validated with respect to phenotypic information obtained from experimental results.

Functional Description: Pantograph is a software toolbox to reconstruct, curate and validate genome-scale metabolic models. It uses existing metabolic models as templates, to start a reconstructions process in 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 genome associations between template models and the model you want to reconstruct.

News Of The Year: Work is in progress to integrate Razanne Issa's Ab-Pantograph modules into Pantograph. Ab-Pantograph uses abductive logic to invert the inference process: a reaction explains the presence of the genes in its gene-protein-reaction formula, rather than the genes justify the reaction. Ab-Pantograph is driven by the goal of explaining all of the genes in the target organism.



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