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corda

by Christian Diener and Osbaldo Resendis-Antonio

Tags: reconstruction


CORDA, short for Cost Optimization Reaction Dependency Assessment is a method for the reconstruction of metabolic networks from a given reference model (a database of all known reactions) and a confidence mapping for reactions developed by A. Schultz and A. Qutub. The package allows you to quickly reconstruct metabolic models for tissues, patients or specific experimental conditions from a set of transcription or proteome measurements and is developed in the Human Systems Biology Group at the INMEGEN, Mexico.

link Webpage code Repository

mackinac

by Mike Mundy

Tags: ModelSEED , models , gapfilling , reconstruction


Reconstructing and analyzing a large number of genome-scale metabolic models is a fundamental part of the integrated study of microbial communities; however, two of the most widely used frameworks for building and analyzing models use different metabolic network representations. Mackinac is a Python package that combines ModelSEED’s ability to automatically reconstruct metabolic models with COBRApy’s advanced analysis capabilities to bridge the differences between the two frameworks and facilitate the study of the metabolic potential of microorganisms.

link Webpage code Repository