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Protocols

SurreyFBA specifications

Information


Unique identifier OMICS_05178
Name SurreyFBA
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.32
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Andrzej Kierzek

Publication for SurreyFBA

SurreyFBA citations

 (6)
library_books

MUFINS: multi formalism interaction network simulator

2016
NPJ Syst Biol Appl
PMCID: 5516860
PMID: 28725480
DOI: 10.1038/npjsba.2016.32

[…] formalism simulations to users who are not familiar with programming, mathematical modeling environments or working in command line. JyMet code is written in Jython (Java/Python), and originates from SurreyFBA. Here, it has been significantly extended through addition of QSSPN simulation and improved visualization of metabolic networks. JyMet integrates all elements of the MUFINS environment (). I […]

library_books

Generation of 2,000 breast cancer metabolic landscapes reveals a poor prognosis group with active serotonin production

2016
Sci Rep
PMCID: 4728432
PMID: 26813959
DOI: 10.1038/srep19771

[…] ensive to generate 2000 metabolic landscapes.Detailed formulation of the Fast iMAT algorithm and comparison with the standard approach is given in the and . The algorithm has been implemented in our SurreyFBA software (v2), which is available at http://sysbio3.fhms.surrey.ac.uk/sfba/index.html. The JyMet interface of SurreyFBA was used for conversion of Recon 2 SBML to SurreyFBA format. GEBRA cal […]

call_split

Flux Balance Analysis with Objective Function Defined by Proteomics Data—Metabolism of Mycobacterium tuberculosis Exposed to Mefloquine

2015
PLoS One
PMCID: 4517854
PMID: 26218987
DOI: 10.1371/journal.pone.0134014
call_split See protocol

[…] guage and are available in the supplementary data file . For solving the flux balance analysis optimization problems we used a freely available wrapper on the GLPK (GNU Linear Programming Kit) called SurreyFBA. The program is freeware and available for download from (http://sysbio3.fhms.surrey.ac.uk/). Its main features have been presented in []. The program can be used as a CLI (command-line inte […]

library_books

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

2015
PLoS One
PMCID: 4373785
PMID: 25806817
DOI: 10.1371/journal.pone.0119016

[…] cope and flavor. Most of the 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. […]

library_books

Somatic transposition in the brain has the potential to influence the biosynthesis of metabolites involved in Parkinson’s disease and schizophrenia

2012
Biol Direct
PMCID: 3534579
PMID: 23176288
DOI: 10.1186/1745-6150-7-41

[…] herefore I assumed that only a single gene is influenced per cell, and the synergistic effects of multiple TE insertions were not investigated.First, flux variability analysis was performed using the SurreyFBA tool [] for each of the 2766 non-boundary metabolites of the human metabolic network, Recon1 [], using an exchange reaction for each metabolite as an objective function. This allowed establi […]

library_books

Construction and completion of flux balance models from pathway databases

2012
Bioinformatics
PMCID: 3268246
PMID: 22262672
DOI: 10.1093/bioinformatics/btr681

[…] Other FBA software packages include the COBRA Toolbox (; ), Acorn (), SimPheny (), SurreyFBA (), FASIMU (), BioMet Toolbox (), CycSim (), WEBcoli () (only for E.coli) and Model SEED (). The capabilities of these systems are as follows. Ability to model essential genes and reactions: […]


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SurreyFBA institution(s)
Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, UK
SurreyFBA funding source(s)
Supported by BBSRC projects (BB/H004262/1 and BB/D011582/1).

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