Here I have discussed various tools and methods for Flux Balance Analysis (FBA) of metabolic networks.
1. OptFlux: an open-source software platform for in silico metabolic engineering by rocha et. al.
OptFlux is an open-source and modular software aimed at being the reference computational application in the field. It allows the use of stoichiometric metabolic models for (i) phenotype simulation of both wild-type and mutant organisms, using the methods of Flux Balance Analysis, Minimization of Metabolic Adjustment or Regulatory on/off Minimization of Metabolic flux changes, (ii) Metabolic Flux Analysis, computing the admissible flux space given a set of measured fluxes, and (iii) pathway analysis through the calculation of Elementary Flux Modes.
2. MetaFluxNet: the management of metabolic reaction information and quantitative metabolic flux analysis by lee et .al.
MetaFluxNet is a program package for managing information on the metabolic reaction network and for quantitatively analyzing metabolic fluxes in an interactive and customized way. It allows users to interpret and examine metabolic behavior in response to genetic and/or environmental modifications. As a result, quantitative in silico simulations of metabolic pathways can be carried out to understand the metabolic status and to design the metabolic engineering strategies. The main features of the program include a well-developed model construction environment, user-friendly interface for metabolic flux analysis (MFA), comparative MFA of strains having different genotypes under various environmental conditions, and automated pathway layout creation.
3. BioOpt:
BioOpt is a software application running on Windows command prompt. The program focuses on the flux balance analysis, using linear programming as the mathematical support. Given a biological system model, which includes a set of metabolic reactions, the program is able to calculate all internal mass balance fluxes, reduced costs and shadow prices depending on the constraints and objective defined by the user. Running BioOpt with different parameters allows the user to obtain several kinds of outputs that can help in the analysis of the system.
4. SurreyFBA: A command line tool and graphics user interface for constraint based modelling of genome scale metabolic reaction networks.
SurreyFBA, which provides constraint-based simulations and network map visualization in a free, stand-alone software. It is based on a command line interface to the GLPK solver distributed as binary and source code for the three major operating systems. SurreyFBA includes JyMet, a graphics user interface allowing spreadsheet based model presentation, visualization of numerical results on metabolic networks represented in the Petri net convention, as well as in charts and plots.
5. FASIMU: FBA simulation software for metabolomics, fluxomics, and biotechnology
FASIMU, a command line oriented software implementing the most frequently applied FBA algorithms. Moreover, it offers the first freely available implementation of (i) weighted flux minimization, (ii) fitness maximization for partially inhibited enzymes, and (iii) the concentration-based thermodynamic feasibility constraint. It allows heterogenous computation series suited for network pruning, leak analysis, FVA, and systematic probing of metabolic objectives for network curation controlled by an intuitive description file. The metabolic network can be supplied in SBML, CellNetAnalyzer, and plain text format. FASIMU uses the optimization capabilities of free (lp solve and GLPK) and commercial solvers (CPLEX, LINDO). The results can be visualized in Cytoscape or BiNA using newly developed plugins.
Available at: http://www.bioinformatics.org/fasimu/downloads/
6. GEMSiRV: A software platform for GEnome-scale Metabolic model Simulation, Reconstruction and Visualization
GEMSiRV comes with downloadable, ready-to-use public-domain metabolic models, reference metabolite/reaction databases, and metabolic network maps, all of which can be input into GEMSiRV as the starting materials for network construction or simulation analyses. Furthermore, all of the GEMSiRV-generated metabolic models and analysis results, including projects in progress, can be easily exchanged in the research community. GEMSiRV is a powerful integrative resource that may facilitate the development of systems biology studies.
Available at: http://sb.nhri.org.tw/GEMSiRV/en/GEMSiRV
7. CellNetAnalyzer: Structural and Functional Analysis of Cellular Networks
CellNetAnalyzer (CNA) is a MATLAB toolbox providing a graphical user interface and various (partially unique) computational methods and algorithms for exploring structural and functional properties of metabolic, signaling, and regulatory networks.
CellNetAnalyzer (CNA) is a MATLAB toolbox providing a graphical user interface and various (partially unique) computational methods and algorithms for exploring structural and functional properties of metabolic, signaling, and regulatory networks.
Metabolic networks are formalized and analyzed by stoichiometric and constraint-based modeling techniques, including flux balance analysis (FBA), metabolic flux analysis, elementary-modes analysis, minimal cut set analysis, and many more. Several algorithms are provided for computational strain design / metabolic engineering.
Available at: http://www2.mpi-magdeburg.mpg.de/projects/cna/cna.html
8. SNA--a toolbox for the stoichiometric analysis of metabolic networks.
SNA is a Mathematica toolbox for stoichiometric network analysis. Among other things, it supports flux balance analysis and the enumeration of the elementary vectors of the flux and the conversion cone.
Available at: http://www.webcitation.org/mainframe.php
9. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox.
The COBRA Toolbox is a set of MATLAB scripts for constraint-based modeling that are run from within the MATLAB environment. These scripts depend on external libraries for reading and writing SBML-formatted models and for simulations. Additionally, some functions may require additional MATLAB Toolboxes that must be purchased from the MathWorks.
Available at: http://opencobra.sourceforge.net/openCOBRA/Install.html
10. FBA-SimVis: interactive visualization of constraint-based metabolic models.
FBA-SimVis is 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. The program provides a user-friendly environment for model reconstruction, constraint-based model analysis and dynamic visualisation of the simulation results. With the ability to quantitatively analyse metabolic fluxes in an interactive and visual manner, FBA-SimVis supports a comprehensive understanding of constraint-based metabolic flux models in both overview and detail.
Available at: http://fbasimvis.ipk-gatersleben.de/
11. MetaFlux: Construction and completion of flux balance models from pathway databases.
A multiple gap-filling method to accelerate the development of FBA models using a new tool, called MetaFlux, based on mixed integer linear programming (MILP). he method suggests corrections to the sets of reactions, biomass metabolites, nutrients and secretions. The method generates FBA models directly from Pathway/Genome Databases. Thus, FBA models developed in this framework are easily queried and visualized using the Pathway Tools software.
Available at: http://biocyc.org/download.shtml
12. CycSim—an online tool for exploring and experimenting with genome-scale metabolic models
CycSim is a web application dedicated to in silico experiments with genome-scale metabolic models coupled to the exploration of knowledge from BioCyc and KEGG. Specifically, CycSim supports the design of knockout experiments: simulation of growth phenotypes of single or multiple gene deletions mutants on specified media, comparison of these predictions with experimental phenotypes and direct visualization of both on metabolic maps. The web interface is designed for simplicity, putting constraint-based modelling techniques within easier reach of biologists. CycSim also functions as an online repository of genome-scale metabolic models.
Available at: http://www.genoscope.cns.fr/cycsim/org.nemostudio.web.gwt.App/App.html (Standalone version not available)
13. WEbcoli: an interactive and asynchronous web application for in silico design and analysis of genome-scale E.coli model.
WEbcoli is a WEb application for in silico designing, analyzing and engineering Escherichia coli metabolism. It is devised and implemented using advanced web technologies, thereby leading to enhanced usability and dynamic web accessibility. As a main feature, the WEbcoli system provides a user-friendly rich web interface, allowing users to virtually design and synthesize mutant strains derived from the genome-scale wild-type E.coli model and to customize pathways of interest through a graph editor. In addition, constraints-based flux analysis can be conducted for quantifying metabolic fluxes and charactering the physiological and metabolic states under various genetic and/or environmental conditions.
Available at: http://webcoli.org (Standalone version not available)
14. RAST/Model SEED genome-scale metabolic reconstruction pipeline:
RAST and the Model SEED framework were developed as a means of automatically producing annotations and draft genome-scale metabolic models. They break down the model reconstruction process into eight steps: submitting a genome sequence to RAST, annotating the genome, curating the annotation, submitting the annotation to Model SEED, reconstructing the core model, generating the draft biomass reaction, auto-completing the model, and curating the model. Each of these eight steps is documented in detail.
Availbale at: http://seed-viewer.theseed.org/seedviewer.cgi?page=ModelView (Standalone version not available)
15. MicrobesFlux: a web platform for drafting metabolic models from the KEGG database:
MicrobesFlux is an installation-free and open-source platform that enables biologists without prior programming knowledge to develop metabolic models for annotated microorganisms in the KEGG database. Our system facilitates users to reconstruct metabolic networks of organisms based on experimental information. Through human-computer interaction, MicrobesFlux provides users with reasonable predictions of microbial metabolism via flux balance analysis. This prototype platform can be a springboard for advanced and broad-scope modeling of complex biological systems by integrating other “omics” data or 13 C- metabolic flux analysis results.
Available at: http://tanglab.engineering.wustl.edu/static/MicrobesFlux.html (Standalone version not available)
16. FAME the Flux Analysis and Modeling Environment:
The Flux Analysis and Modeling Environment (FAME) is the first web-based modeling tool that combines the tasks of creating, editing, running, and analyzing/visualizing stoichiometric models into a single program. Analysis results can be automatically superimposed on familiar KEGG-like maps.
Available at: http://f-a-m-e.org/ajax/page1.php (Standalone version not available)
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