Learn metabolic modelling and using ScrumPy for modelling.

A desktop app, web app and CLI to operate and find vulnerabilities in SBML metabolic networks.

An R package to incorporate in a continuous way the gene-expression data as FBA flux boundaries in a metabolic model. Also, functions to calculate and plot the differences between model fluxes in different metabolic scenarios was included. This is an implementation of the algorithm described by Lee et al. (2012) in DOI: 10.1186/1752-0509-6-73.

findCP CLI package - find ChokePoint reactions in genome-scale metabolic models

Python Implementation of PROM

Adjusting for false discoveries in constraint- and sampling-based differential metabolic flux analysis

Pathway-Guided Pruning Reconstruction of Genome-Scale Metabolic Models

A jupyter hub docker app for metabolic modelling using mewpy, troppo, cobra, etfl and cplex.

Python implementation of mgpipe

Cellular economy models based on global optimization using GAMS

MMODES (Metabolic Models based Ordinary Differential Equations Simulation)

Constraint-based metabolic modelling with sparse IPOPT

Create stoichiometric metabolic network models of single-species or multi-species communities

Impose constraints on enzyme abundances ratios in enzyme-constraint metabolic models

Flux response of Pseudomonas putida to increased levels of metabolic burden

Docker image for a full ME model stack.

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.

Contains NAD biosynthesis model and python scripts to simulate the steady-state calculations.

PRESTO: Correction of turnover numbers in enzyme-constraint metabolic models

FBAhv: FBA analysis of host-virus metabolic model (read related publication at: https://www.life-science-alliance.org/content/4/1/e202000869)