Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks
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Updated
May 28, 2024 - R
Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks
The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.
The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:
An integrated visual environment for metabolic modeling with common methods such as FBA, FVA and Elementary Flux Modes, and advanced features such as thermodynamic methods, extended Minimal Cut Sets, OptKnock, RobustKnock, OptCouple and more!
An implementation of genome-scale model reconstruction using Cost Optimization Reaction Dependency Assessment by Schultz et. al
University of Cambridge Part III Systems Biology course, practical exercises for learning flux balance analysis
memote – the genome-scale metabolic model test suite
KEGG Module Evaluation Tool
Python implementation of mgpipe
An R interface to the omixer-rpm for turning metagenomic functional profiles into pathway/module profiles
A pathologic file generator (PLFG) is implemented to assist and facilitate the curation progress of every computationally predicted pathway genome database (PGDB).
epigenome scale metabolic modeling for cancer metabolism
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.
CHAP: Modeling Metabolic Pathways as Groups (with Augmentation)
Metabolic pathway inference using non-negative matrix factorization with community detection
Genome-scale model of Yarrowia lipolytica.
Diversity-based enumeration of optimal context-specific metabolic networks
A RMosek optimization interface for the Sybil package
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