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BioOpt specifications

Information


Unique identifier OMICS_05177
Name BioOpt
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Windows
Computer skills Advanced
Stability No
Maintained No

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Publication for BioOpt

BioOpt in publications

 (5)
PMCID: 5660601
PMID: 28964698
DOI: 10.1016/j.cels.2017.09.002

[…] deposited in the http://www.ebi.ac.uk/arrayexpress/ under accession number e-mtab-4651. an updated l. lactis model, iaop358, is available at https://www.patil.embl.de/media/models/ponomarova/iaop358.bioopt. metabolomics datasets are available at http://dx.doi.org/10.17632/r5bx5cg9y6.1 (fia-tof ms data) and http://dx.doi.org/10.17632/h2fvn2mpp3.1 (lc-ms/ms metabolomics data)., o.p. conceived […]

PMCID: 5111396
PMID: 27868089
DOI: 10.1128/mSystems.00065-16

[…] cytoplasm, and carboxysome) (see in the supplemental material). a summary of ijc568 network properties is given in , and a comparison with the ensemble is given in ., ijc568 model in excel format. bioopt format and raven sbml format are available for download at http://biomet-toolbox.org/. download data set s1, xls file, 0.5 mb., accompanying data sets used and produced in the manuscript. […]

PMCID: 4367363
PMID: 25654717
DOI: 10.3390/s150203362

[…] of waiting time before denoised data are available is an important step towards real-time visualization of processed hyperspectral data. the source code can be found at http://www.github.com/ntnu-bioopt/mnf. this includes an implementation of conventional mnf denoising., push-broom line-scanning hyperspectral cameras can be used for a wide range of applications, e.g., remote sensing, food […]

PMCID: 4192687
PMID: 25141288
DOI: 10.3390/metabo4030680

[…] through biomass synthesis reaction, being the biomass formation rate, is directly related to growth of the modeled organism. simulations were performed using the optgene software [], later termed bioopt [,], more information about the modeling mechanics can be found in montagud et al., 2010 []. readers will find in the model file where all reactions and simulated constraints are depicted […]

PMCID: 1682015
PMID: 17016516
DOI: 10.1038/msb4100085

[…] (mathworks inc.) were utilized for the model preprocessing summarized above and to call the algorithm written in c++ for reporter reaction identification. fba was performed using in-house software bioopt employing lindo api for linear optimization. deconvolution of peaks in gc–ms spectra for the identification of metabolites based on a metabolite library and for the random peak assignment […]


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BioOpt institution(s)
Department of Chemical and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden

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