CBMPy specifications

Information


Unique identifier OMICS_21406
Name CBMPy
Alternative name PySCeS CBMPy
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.7.15
Stability Stable
Requirements
Numpy, libsbml, PyQT4, CPLEX, GLPK
Maintained Yes

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Maintainers


  • person_outline Brett Olivier <>
  • person_outline Brett Olivier <>

Additional information


http://cbmpy.sourceforge.net/reference/cbmpy.html

CBMPy in publications

 (5)
PMCID: 5648915
PMID: 28842544
DOI: 10.1128/AEM.01528-17

[…] differentiating between absolutely required fluxes (auxotrophies) and sets of interchangeable fluxes (see the supplemental material). emaf was implemented in the open-source modeling environment cbmpy ()., we first applied emaf to compute possible sulfur sources. b. pertussis is reported to be auxotrophic for cysteine, i.e., inorganic sulfur sources cannot support growth (). in agreement, […]

PMCID: 5344373
PMID: 28278266
DOI: 10.1371/journal.pone.0173183

[…] of metabolic-exchange fluxes possible from community-level experimental data., all relevant data are within the paper and its supporting information files and on https://sourceforge.net/projects/cbmpy/files/publications/data/2017_hanemaaijer/., microbial communities carry out important processes for the planet’s ecosystem, animal health and industrial purposes. engineering such communities […]

PMCID: 4672519
PMID: 26643044
DOI: 10.1186/s12934-015-0370-x

[…] abolished growth. the media consists of biotine, lactose, milk peptides, nicotinate, pantothenate, phosphate, pyridoxamine, riboflavin, thiamin and water. all simulations have been performed using cbmpy associated to pysces []., the strain lactobacillus rhamnosus yoba 2012 []; strain lmg 27229 was isolated from a powder dairy formula by sybesma et al. []. the streptococcus thermophilus c106 […]

PMCID: 4388735
PMID: 25849486
DOI: 10.1371/journal.pcbi.1004166

[…] and anaerobic (exchange of o2 set to zero) conditions. in all cases, the model required an atp maintenance flux of 8.39 mmol gdw −1 h −1. the model was edited and prepared for enumeration using pysces cbmpy [, ]. all models are provided as supplementary dataset s1. optimization of secondary objectives (minimization of p l, p j, and p c) was also done with pysces cbmpy. we used […]

PMCID: 3669319
PMID: 23741341
DOI: 10.1371/journal.pone.0064567

[…] informative to become a vital component of the workflow of studying communities with modern “omics” approaches., this cfba framework has been coded using python™ programming language and requires cbmpy (http://cbmpy.sourceforge.net/) package and ibm ilog cplex optimizer by ibm. cbmpy has been developed based on the principles of python simulator of cellular systems (pysces) . in supplementary […]


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