There are 4 repositories under metabolic-reconstruction topic.
The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:
The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.
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!
A Reference Pathways Mapper for turning metagenomic functional profiles into pathway/module profiles.
KEGG Module Evaluation Tool
An implementation of genome-scale model reconstruction using Cost Optimization Reaction Dependency Assessment by Schultz et. al
Genome-scale metabolic model of Methylococcus capsulatus.
An R interface to the omixer-rpm for turning metagenomic functional profiles into pathway/module profiles
Genome-scale model of Yarrowia lipolytica.
Diversity-based enumeration of optimal context-specific metabolic networks
Enzymatic Link Prediction
epigenome scale metabolic modeling for cancer metabolism
University of Cambridge Part III Systems Biology course, practical exercises for learning flux balance analysis
A pathologic file generator (PLFG) is implemented to assist and facilitate the curation progress of every computationally predicted pathway genome database (PGDB).
Chemical reaction balancing web service
Utility to simplify obtaining information from genome-scale models as well as their manipulation. This implementation is available only for working with COBRApy.
A RMosek optimization interface for the Sybil package
Genome-scale metabolic model of Rhodotorula toruloides
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.
Metabolic pathway inference using non-negative matrix factorization with community detection