metabolic-networks

An integrated visual environment for metabolic modeling 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!

Infer metabolic directions from moment differences of mass-weighted intensity distributions

COnstraint-based Reconstruction and Analysis (COBRA) of metabolic networks in R

Drug repositioning of single and drug combinations using Flux Balance Analysis.

A python tool to optimize chemical concentration trajectories in network-based chemical systems

MCMC sampling algorithms for linear inverse models in R

IDARE - Multiomics Visualisation in Cytoscape

Rust reimplementation of gapseq — informed prediction and analysis of bacterial metabolic pathways and genome-scale networks. ~3× faster on pathway detection, in-process LP solver, single static binary.

A robust and scalable framework for resource-constraint models through stochastic tuning of deep learning-predicted kinetic parameters

Reconstruct genome-scale electron transfer networks and calculate electron fluxes from metabolic flux distributions to characterize the cellular electron economy.

A workflow for ranking herbal drugs using metabolic modeling and flux variability anaylsis.

Reproducible topological data analysis and machine-learning study of inferred gut microbial metabolic networks in inflammatory bowel disease.

Glioma metabolic modelling for repurposing of single and combination drugs