Python implementation of mgpipe
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Updated
Oct 9, 2023 - JetBrains MPS
Python implementation of mgpipe
MNXref: Reconciliation of metabolites and biochemical reactions for metabolic networks
A RMosek optimization interface for the Sybil package
University of Cambridge Part III Systems Biology course, practical exercises for learning flux balance analysis
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.
Chemical reaction balancing web service
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).
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
Diversity-based enumeration of optimal context-specific metabolic networks
Utility to simplify obtaining information from genome-scale models as well as their manipulation. This implementation is available only for working with COBRApy.
epigenome scale metabolic modeling for cancer metabolism
Genome-scale metabolic model of Rhodotorula toruloides
Genome-scale metabolic model of Methylococcus capsulatus.
An R interface to the omixer-rpm for turning metagenomic functional profiles into pathway/module profiles
KEGG Module Evaluation Tool
A manually curated database of human gut metabolic modules.
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