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OptFlux specifications

Information


Unique identifier OMICS_05174
Name OptFlux
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Windows
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Isabel Rocha

Publication for OptFlux

OptFlux citations

 (22)
library_books

Metabolic flux analysis and the NAD(P)H/NAD(P)+ ratios in chemostat cultures of Azotobacter vinelandii

2018
Microb Cell Fact
PMCID: 5776761
PMID: 29357933
DOI: 10.1186/s12934-018-0860-8

[…] Table , based on the Entner–Doudoroff (ED) pathway, the pentose phosphate (PP) pathway, the TCA cycle, as well as the alginate and P3HB biosynthetic pathways. FBA simulations were performed using the OptFlux 3.3, an open-source and modular software for in silico metabolic engineering []. Maximizing cellular growth rate was used as the objective function for all FBA simulations. […]

library_books

Genome scale modeling of yeast: chronology, applications and critical perspectives

2017
FEMS Yeast Res
PMCID: 5812505
PMID: 28899034
DOI: 10.1093/femsyr/fox050

[…] lished nearly 20 years ago (Edwards and Palsson ), many others have followed. Hitherto, there are GSMMs published and accessible for download in several websites for more than 100 organisms (e.g. www.optflux.org/models and http://systemsbiology.ucsd.edu/InSilicoOrganisms/OtherOrganisms), and the number keeps rising.The yeast Saccharomyces cerevisiae was the first eukaryotic organism to be fully ge […]

library_books

Computational metabolic engineering strategies for growth coupled biofuel production by Synechocystis

2016
Metab Eng Com
PMCID: 5779732
PMID: 29468126
DOI: 10.1016/j.meteno.2016.07.003

[…] Modeling System GAMS 24.4.1 (GAMS Development Corporation, Washington, DC) as described in .OptGene was performed on the iJN678 reaction subset using the “Evolutionary optimization” algorithm in the OptFlux software ().Minimization of metabolic adjustment (MOMA) was used to predict the flux distributions of mutant strains (). The fitness metric was Biomass-Product Coupled Yield (BPCY), the produc […]

library_books

Metabolic Network Modeling of Microbial Interactions in Natural and Engineered Environmental Systems

2016
Front Microbiol
PMCID: 4870247
PMID: 27242701
DOI: 10.3389/fmicb.2016.00673

[…] st of equations is loaded into MATLAB® (The MathWorks, Inc., Natick, Massachusetts, United States.) using the COBRA toolbox. Model loading and simulation can be also done in software packages such as Optflux (Rocha et al., ). In the following step, (ii), Excel and R software are used to record the metabolite concentration curves observed in experimental cultures and then calculate specific rates f […]

library_books

Improving the flux distributions simulated with genome scale metabolic models of Saccharomyces cerevisiae

2016
Metab Eng Com
PMCID: 5779720
PMID: 29468121
DOI: 10.1016/j.meteno.2016.05.002

[…] rovided by the authors in the supplementary material. Yeast 6.06 () was downloaded in SBML format from the project's website: http://sourceforge.net/projects/yeast/files/.Each model was imported into OptFlux 3.07 () and the in silico environmental conditions were set to mimic minimal growth media supplemented with glucose under fully-aerobic conditions (ammonia: unconstrained uptake, phosphate: un […]

library_books

Designing intracellular metabolism for production of target compounds by introducing a heterologous metabolic reaction based on a Synechosystis sp. 6803 genome scale model

2016
Microb Cell Fact
PMCID: 4717628
PMID: 26783098
DOI: 10.1186/s12934-016-0416-8

[…] SyHyMeP is a web-based application implemented in Java and runs on the Apache Tomcat web server (ver. 7.0.64., http://tomcat.apache.org/). FBA was performed with our original command line tool using OptFlux libraries, which use GLPK (GNU Linear Programming Kit) as a linear programming solver []. […]

Citations

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OptFlux institution(s)
IBB-Institute for Biotechnology and Bioengineering/Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal

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