CHAP: Modeling Metabolic Pathways as Groups (with Augmentation)
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Updated
Nov 8, 2021 - Python
CHAP: Modeling Metabolic Pathways as Groups (with Augmentation)
Metabolic pathway inference using non-negative matrix factorization with community detection
Tool for the reconstruction of context-specific metabolic models based on omics data from several sources
Software developed and main results obtained in the Master dissertation: A model validation pipeline for healthy tissue genome-scale metabolic models. Dissertation link to be added.
Genome-scale metabolic model of Rhodotorula toruloides
MNXref: Reconciliation of metabolites and biochemical reactions for metabolic networks
A RMosek optimization interface for the Sybil package
Utility to simplify obtaining information from genome-scale models as well as their manipulation. This implementation is available only for working with COBRApy.
Chemical reaction balancing web service
University of Cambridge Part III Systems Biology course, practical exercises for learning flux balance analysis
epigenome scale metabolic modeling for cancer metabolism
Enzymatic Link Prediction
A pathologic file generator (PLFG) is implemented to assist and facilitate the curation progress of every computationally predicted pathway genome database (PGDB).
Diversity-based enumeration of optimal context-specific metabolic networks
Python implementation of mgpipe
Genome-scale model of Yarrowia lipolytica.
An R interface to the omixer-rpm for turning metagenomic functional profiles into pathway/module profiles
Genome-scale metabolic model of Methylococcus capsulatus.
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