COBRApy is a package for constraint-based modeling of metabolic networks.
PEtab - an SBML and TSV based data format for parameter estimation problems in systems biology
The Systems Biology Simulation Core Library (SBSCL) provides an efficient and exhaustive Java implementation of methods to interpret the content of models encoded in the Systems Biology Markup Language (SBML) and its numerical solution.
A Python package for "classic" Constraint-Based Reconstruction and Analysis (COBRA) and the new COBRA with kinetics (COBRA-k). Link to documentation and tutorials:
Spatial bio-chemical reaction model editor and simulator
pymCADRE enables the reconstruction of tissue-specific metabolic models in Python using transcriptomic data and information of the network topology.
sbml2hyb is a tool for SBML compatible hybrid modelling of biological systems
Python package and workflow for EFM calculation via (mp)lrs and efmtool
Interface between the Systems Biology Markup Language and Julia
A tool to for optimizing parameters of ordinary differential equation (ODE) models. SBML2Julia translates a model from SBML/PEtab format into Julia for Mathematical Programming (JuMP), performs the optimization task and returns the results.
Easily use the memote command line interface from a docker container.
An AI agent to build and curate genome scale metabolic network models
This project provides a simulation framework for synthetic biology and metabolic engineering, with a focus on the analysis of metabolic models for the production of novel compounds.
Python package for managing systems and subsystems of SBML models
Physiologically based pharmacokinetic/pharmacodynamic (PBPK/PD) model of canagliflozin
Physiologically based pharmacokinetics/pharmacodynamics (PBPK/PD) model of dulaglutide
Glimepiride Web Application
A graphical editor for systems biology models.
This repository contains all changes made to the strain specific models of Corynebacterium striatum.
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