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FAME specifications


Unique identifier OMICS_05184
Alternative name Flux Analysis and Modeling Environment
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes


  • person_outline Bas Teusink

Publication for Flux Analysis and Modeling Environment

FAME citations


Alignment of microbial fitness with engineered product formation: obligatory coupling between acetate production and photoautotrophic growth

Biotechnol Biofuels
PMCID: 5809919
PMID: 29456625
DOI: 10.1186/s13068-018-1037-8

[…] EX Optimization Studio (IBM) under an academic license. Additional visualization of modeling simulations were carried out using a resource particularly developed for Synechocystis [] available at the FAME online modeling environment []. […]


Biomass composition: the “elephant in the room” of metabolic modelling

PMCID: 4605984
PMID: 26491422
DOI: 10.1007/s11306-015-0819-2

[…] running the COBRA Toolbox (v2.0.3) under MATLAB R2012b (, Mathworks, USA) with SBML Toolbox v4.0.1 and libSBML library v5.0.0b0 using standard linear optimization techniques (GLPK toolbox). FAME was also employed as the flux analysis modelling and visualization environment (Boele et al. ). Mutant flux distributions were also investigated employing the MoMA algorithm as described in (Segr […]


Using Bioconductor Package BiGGR for Metabolic Flux Estimation Based on Gene Expression Changes in Brain

PLoS One
PMCID: 4373785
PMID: 25806817
DOI: 10.1371/journal.pone.0119016

[…] tools are based on MATLAB, such as the COBRA Toolbox 2.0 [], CellNetAnalyzer [], FBA-SimVis [] or the RAVEN toolbox []. Other tools are stand-alone software, for instance SurreyFBA [] or OptFlux []. FAME is the first web-based approach to stoichiometric flux analysis [].BiGGR provides easy access to metabolic flux analysis for the large user base of the R environment. The vast number of open sour […]


Computational Approaches for Microalgal Biofuel Optimization: A Review

Biomed Res Int
PMCID: 4189764
PMID: 25309916
DOI: 10.1155/2014/649453

[…] e tools for automated reconstruction are currently available (some examples are given in ); for instance, AUTOGRAPH [], GEMSiRV [], MicrobesFlux [], MetRxn [], Model SEED [, ], SuBliMinaL Toolbox [], FAME [], and RAVEN Toolbox [] can be named. A systematic comparison between some of these platforms can be found in []. While draft metabolic models can be generated through such software tools, inten […]


Toward a systems level understanding of gene regulatory, protein interaction, and metabolic networks in cyanobacteria

Front Genet
PMCID: 4079066
PMID: 25071821
DOI: 10.3389/fgene.2014.00191

[…] mpt to consolidate these networks, and at the same time to provide a tool for biologists to model their results, a user friendly-interface with a Synechocystis-specific section was added to web-based FAME resource (http://f-a-m-e.org/synechocystis/) (Boele et al., ; Maarleveld et al., ). The model, iTM686, is based on that of Nogales et al. (), but amended to include later findings, such as the co […]


Genome scale metabolic reconstructions of Bifidobacterium adolescentis L2 32 and Faecalibacterium prausnitzii A2 165 and their interaction

BMC Syst Biol
PMCID: 4108055
PMID: 24708835
DOI: 10.1186/1752-0509-8-41

[…] AVEN toolbox has another function to solve this problem by assigning gene to KO using MUSCLE [] and HMMER []. Then it generates the draft model by mapping KO to KEGG reactions. The web-based methods, FAME [] and MicrobesFlux [], are able to produce draft models for ~750 and ~1,200 KEGG genomes, respectively. The disadvantage of both FAME and MicrobesFlux is that they are limited to organisms alrea […]


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FAME institution(s)
Systems Bioinformatics/AIMMS, VU University Amsterdam, Amsterdam, Netherlands

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