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…

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 availability of specific software tools for FBA. Each tool has its unique features and limitations with respect to operational environment, user-interface and supported analysis algorithms.

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…

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…

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…

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…

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,…

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…

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…

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…

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…

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.…

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…

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…

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…

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…

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…

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,…

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…

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,…

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…

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…

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…

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…

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,…

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…

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…

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…

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…

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.

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.

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…

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…

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,…

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…

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.

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…

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…

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…

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.…

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…