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Constraint based methods

Flux balance analysis (FBA) is a widely used computational method for characterizing and engineering intrinsic cellular metabolism. The increasing number of its successful applications and growing popularity are possibly attributable to the…
fastcore
Desktop

fastcore

A generic algorithm for reconstructing context-specific metabolic network…

A generic algorithm for reconstructing context-specific metabolic network models from global genome-wide metabolic network models such as Recon X. fastcore takes as input a core set of reactions that…

CORDA
Desktop

CORDA Cost Optimization Reaction Dependency Assessment

Constructs genome scale models in a tissue-specific manner. CODRA based on a…

Constructs genome scale models in a tissue-specific manner. CODRA based on a method that identifies the dependency of desirable reactions on undesirable reactions. It returns a concise, functional…

GEM-PRO
Dataset

GEM-PRO GEnome-scale Models with PROtein structures

Allows users to study two contemporary organisms, T. maritima and E. coli.…

Allows users to study two contemporary organisms, T. maritima and E. coli. GEM-PRO maps genes in a metabolic model to their respective high-quality structural data. The repository connects the…

Coordinate…
Desktop

Coordinate Hit-and-Run with Rounding

Converges to a uniform stationary sampling distribution. CHRR is based on the…

Converges to a uniform stationary sampling distribution. CHRR is based on the provably efficient hit-and-run random walk and crucially uses a preprocessing step to round the anisotropic flux set. It…

DistributedFBA.…
Desktop

DistributedFBA.jl

Solves multiple flux balance analyses on a subset or all the reactions of large…

Solves multiple flux balance analyses on a subset or all the reactions of large and huge-scale networks, on any number of threads or nodes. DistributedFBA.jl is a high-level, high-performance,…

Fast-SL
Desktop

Fast-SL

An efficient algorithm to identify synthetic lethal gene/reaction sets in…

An efficient algorithm to identify synthetic lethal gene/reaction sets in genome-scale metabolic models. Fast-SL enables an efficient enumeration of higher order synthetic lethals in metabolic…

CycleFreeFlux
Desktop

CycleFreeFlux

A simple postprocessing of constraint-based solutions, which removes internal…

A simple postprocessing of constraint-based solutions, which removes internal cycles from any given flux distribution v(0) without disturbing other fluxes not involved in the loops. CycleFreeFlux…

GlobalFit
Desktop

GlobalFit

Finds a globally optimal network, by identifying the minimal set of network…

Finds a globally optimal network, by identifying the minimal set of network changes needed to correctly predict all experimentally observed growth and non-growth cases simultaneously. GlobalFit is an…

RegrEx
Desktop

RegrEx Regularized context-specific model Extraction method

Extracts a context-specific model and provides a flux distribution that…

Extracts a context-specific model and provides a flux distribution that maximizes correlation between data. RegrEx is based on regularized least squares optimization to automatically run without…

iReMet-flux
Desktop

iReMet-flux integration of Relative Metabolite Levels for Flux prediction

Relies on relative metabolomics data alongside the assumptions that reaction…

Relies on relative metabolomics data alongside the assumptions that reaction kinetics follows the ubiquitous mass action law and that organisms tend to minimize change in flux between two scenarios.…

ll-ACHRB
Desktop

ll-ACHRB Artificially Centered Hit-and-Run on a Box

A scalable algorithm for sampling the feasible solution space of metabolic…

A scalable algorithm for sampling the feasible solution space of metabolic networks. ll-ACHRB is inspired by the Hit-and-Run on a Box algorithm for uniform sampling from general regions, but employs…

Fast-SNP
Desktop

Fast-SNP

Reduces the size of the original loopless problem into an easier and equivalent…

Reduces the size of the original loopless problem into an easier and equivalent mixed integer linear programming (MILP) problem. Fast-SNP considerably improves the computational efficiency in several…

FluxModeCalcula…
Desktop

FluxModeCalculator

A tool for performing flux mode analysis in stoichiometric models.…

A tool for performing flux mode analysis in stoichiometric models. FluxModeCalculator enables large-scale elementary flux mode (EFM) computation on ordinary desktop computers. Our implementation uses…

MONGOOSE
Desktop

MONGOOSE MetabOlic Network GrOwth Optimization Solved Exactly

A toolbox for analysing the structure of constraint-based metabolic models in…

A toolbox for analysing the structure of constraint-based metabolic models in exact arithmetic. Unlike other existing software, MONGOOSE uses exact rational arithmetic, which makes its results…

MASS Toolbox
Desktop

MASS Toolbox Mass Action Stoichiometric Simulation Toolbox

Constructs and analyzes kinetic and constraint-based models of biochemical…

Constructs and analyzes kinetic and constraint-based models of biochemical reactions systems. MASS Toolbox is based on an omics and data driven approach. It can reconstruct networks that can be…

integrated…
Desktop

integrated flux-balance analysis

Predicts different and more accurate phenotypes than the ordinary differential…

Predicts different and more accurate phenotypes than the ordinary differential equation (ODE) model for 85 of 334 single gene perturbation simulations, as well for the wild-type simulations. iFBA was…

PyFBA
Desktop

PyFBA

Allows bioinformaticians to build and explore flux-balance analysis (FBA)…

Allows bioinformaticians to build and explore flux-balance analysis (FBA) models using the Python programming language. PyFBA is a python module that also permits to build models from genomes,…

FlexFlux
Desktop

FlexFlux

Allows the analysis of both qualitative regulatory networks and genome-scale…

Allows the analysis of both qualitative regulatory networks and genome-scale metabolic networks. FlexFlux is the first metabolic flux analysis tool that integrates regulatory networks in all of its…

BioOpt
Desktop

BioOpt

Focuses on the flux balance analysis, using linear programming as the…

Focuses on the flux balance analysis, using linear programming as the mathematical support.

VisualCNA
Desktop

VisualCNA

An easy-to-use PyMOL plug-in that allows setup of constraint network analysis…

An easy-to-use PyMOL plug-in that allows setup of constraint network analysis (CNA) runs and analysis of CNA results linking plots with molecular graphics representations. From a practical viewpoint,…

TreeEFM
Desktop

TreeEFM

An algorithm that uses a linear programming-based tree search and efficiently…

An algorithm that uses a linear programming-based tree search and efficiently enumerates a subset of elementary flux modes (EFMs) in genome-scale metabolic networks (GSMNs). The stand-alone software…

CytoSEED
Desktop

CytoSEED

A Cytoscape plugin for viewing, manipulating and analyzing metabolic models…

A Cytoscape plugin for viewing, manipulating and analyzing metabolic models created using the Model SEED.

CellNetAnalyzer
Desktop

CellNetAnalyzer

Allows to perform structural and qualitative analysis of both mass-flow- and…

Allows to perform structural and qualitative analysis of both mass-flow- and signal-flow-based cellular networks. CellNetAnalyzer is a toolbox for analyzing structure and function of biological…

F2C2
Desktop

F2C2 Fast flux coupling calculator

Computes the flux coupling for every pair of reactions in a network. F2C2 is a…

Computes the flux coupling for every pair of reactions in a network. F2C2 is a software which outperforms previous analysis methods by orders of magnitude. It is based on two main principles: (i) it…

FBAME
Desktop

FBAME Flux Balance Analysis Membrane Occupancy

The simultaneous utilization of efficient respiration and inefficient…

The simultaneous utilization of efficient respiration and inefficient fermentation even in the presence of abundant oxygen is a puzzling phenomenon commonly observed in bacteria, yeasts, and cancer…

MultiGEM
Desktop

MultiGEM Multi-tissue GEM framework

A multi-tissue genome-scale metabolic modelling framework for the analysis of…

A multi-tissue genome-scale metabolic modelling framework for the analysis of whole plant systems. Six tissue compartments were created, each with their own distinct set of metabolic capabilities,…

SASITA
Desktop

SASITA

Enables to enumerate all stoichiometrically feasible minimal precursor sets in…

Enables to enumerate all stoichiometrically feasible minimal precursor sets in both models, steady-state and machinery-duplicating. SASITA is a method that can be used in a wide variety of…

ORCA
Desktop

ORCA

A Matlab package extending the scope of established COBRA metabolic modelling.

A Matlab package extending the scope of established COBRA metabolic modelling.

Sybil
Desktop

Sybil

A Systems Biology Library for R, implementing algorithms for constraint based…

A Systems Biology Library for R, implementing algorithms for constraint based analyses of metabolic networks (e.g. flux-balance analysis (FBA), minimization of metabolic adjustment (MOMA), regulatory…

DFBA
Algorithm

DFBA Dynamic Flux Balance Analysis

An algorithm for the quantitative study of the dynamic reprogramming of…

An algorithm for the quantitative study of the dynamic reprogramming of metabolic networks. DFBA was used to simulate the batch growth of E. coli on glucose, and the predictions were found to…

B-DMFA
Desktop

B-DMFA B-spline fitting dynamic metabolic flux analysis

A fast heuristic algorithm developed for knot placement, which is by far the…

A fast heuristic algorithm developed for knot placement, which is by far the most time consuming task when performing DMFA, exploiting the local support property of B-splines. The performance of the…

CycSim
Web

CycSim

A web application dedicated to in silico experiments with genome-scale…

A web application dedicated to in silico experiments with genome-scale metabolic models coupled to the exploration of knowledge from BioCyc and KEGG.

FBA-SimVis
Desktop

FBA-SimVis

A VANTED Plug-in for the constraint-based analysis of metabolic models with…

A VANTED Plug-in for the constraint-based analysis of metabolic models with special focus on the dynamic and visual exploration of metabolic flux data resulting from model analysis.

GEMSiRV
Desktop

GEMSiRV GEnome-scale Metabolic model Simulation, Reconstruction and Visualization

Provides functionalities of easy metabolic network drafting and editing,…

Provides functionalities of easy metabolic network drafting and editing, amenable network visualization for experimental data integration and flux balance analysis tools for simulation studies.

MetaFluxNet
Desktop

MetaFluxNet

A stand-alone program package for the management of metabolic reaction…

A stand-alone program package for the management of metabolic reaction information and quantitative metabolic flux analysis.

SurreyFBA
Desktop

SurreyFBA

Provides constraint-based simulations and network map visualization in a free,…

Provides constraint-based simulations and network map visualization in a free, stand-alone software.

OptFlux…
Desktop

OptFlux visualization plugin

An open-source software that aims to fill the gap between metabolic engineering…

An open-source software that aims to fill the gap between metabolic engineering (ME) and metabolic network visualization is proposed, in the form of a plugin to the OptFlux ME platform. The framework…

DFBAlab
Desktop

DFBAlab Dynamic Flux Balance Analysis laboratory

A MATLAB-based code that performs numerical integration of dynamic flux balance…

A MATLAB-based code that performs numerical integration of dynamic flux balance analysis (dFBA) systems. DFBAlab provides efficient simulation of multi-culture of microbial species based on…

GIMME
Desktop

GIMME Gene Inactivity Moderated by Metabolism and Expression

Uses quantitative gene expression data and one or more presupposed metabolic…

Uses quantitative gene expression data and one or more presupposed metabolic objectives to produce the context-specific reconstruction that is most consistent with the available data. Furthermore,…

DFBSIM
Desktop

DFBSIM

It is numerical integration scheme for large-scale systems of differential…

It is numerical integration scheme for large-scale systems of differential equations encountered in dynamic flux balance analysis (dFBA). DFBSIM provides efficient simulation of multi-culture of…

DyMMM
Desktop

DyMMM Dynamic Multispecies Metabolic Modeling

A mathematical modeling tool that integrates multiple constraint-based…

A mathematical modeling tool that integrates multiple constraint-based metabolic models into a single dynamic community metabolic model. The DyMMM framework was formerly known as the DMMM framework.

fastFVA
Desktop

fastFVA fast Flux Variability Analysis

An efficient Matlab implementation of flux variability analysis (FVA) optimized…

An efficient Matlab implementation of flux variability analysis (FVA) optimized for the GLPK and CPLEX solvers. Compared to a direct implementation of FVA in Matlab, fastFVA results in speedup…

SNA
Desktop

SNA Stoichiometric Network Analysis

A Mathematica toolbox for stoichiometric network analysis.

A Mathematica toolbox for stoichiometric network analysis.

FASIMU
Desktop

FASIMU

A command line oriented software for the computation of flux distributions…

A command line oriented software for the computation of flux distributions using a variety of the most common FBA algorithms.

COBRApy
Desktop

COBRApy COBRA for Python

A Python package that provides support for basic COnstraint-Based…

A Python package that provides support for basic COnstraint-Based Reconstruction and Analysis (COBRA) methods.

FAME
Web

FAME Flux Analysis and Modeling Environment

Web-based modeling tool that combines the tasks of creating, editing, running,…

Web-based modeling tool that combines the tasks of creating, editing, running, and analyzing/visualizing stoichiometric models into a single program.

OptFlux
Desktop

OptFlux

An open-source and modular software aimed at being the reference computational…

An open-source and modular software aimed at being the reference computational application in the field.

SBRT
Desktop

SBRT Systems Biology Research Tool

A free, easy-to-use, open-source, integrated software platform to facilitate…

A free, easy-to-use, open-source, integrated software platform to facilitate the computational aspects of systems biology.

libStruct
Desktop

libStruct Structural Analysis Library

Allows users to analyze the structural properties of stoichiometric networks.

Allows users to analyze the structural properties of stoichiometric networks.

Fluxor
Desktop

Fluxor

Allows users to proceed to flux analysis. Fluxor is a part of the BioSpice…

Allows users to proceed to flux analysis. Fluxor is a part of the BioSpice toolkit.

FBASBW
Desktop

FBASBW FluxBalance Analysis with SBW

Permits users to specify flux constraints based on the utilization of Systems…

Permits users to specify flux constraints based on the utilization of Systems Biology Markup Language (SBML) annotations.

CBMPy
Desktop

CBMPy

Permits constraint based modelling and analysis. CBMPy was developed following…

Permits constraint based modelling and analysis. CBMPy was developed following the same principles as PySCeS. It is based on data structures such as metabolites, reactions, or compartments that are…

MOMA
Desktop

MOMA Minimisation of Metabolic Adjustment

A flux-based analysis technique similar to FBA and based on the same…

A flux-based analysis technique similar to FBA and based on the same stoichiometric constraints, but the optimal growth flux for mutants is relaxed. Instead, MoMA provides an approximate solution for…

ROOM
Algorithm

ROOM Regulatory On/Off Minimization

A constraint-based algorithm for predicting the metabolic steady state after…

A constraint-based algorithm for predicting the metabolic steady state after gene knockouts. ROOM aims to minimize the number of significant flux changes (hence on/off) with respect to the wild type.…

FluxViz
Desktop

FluxViz

An open-source Cytoscape plug-in for the visualization of flux distributions in…

An open-source Cytoscape plug-in for the visualization of flux distributions in networks.

BacArena
Desktop

BacArena

Allows to analyze microbial metabolism where individual-based modeling has been…

Allows to analyze microbial metabolism where individual-based modeling has been employed to examine complex dynamics about interacting organisms. BacArena extends the integration of flux balance…

WEbcoli
Web

WEbcoli

An integrated environment for designing, analyzing and engineering genome-scale…

An integrated environment for designing, analyzing and engineering genome-scale E. coli metabolic model online.

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