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CBMPy specifications


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
Numpy, libsbml, PyQT4, CPLEX, GLPK
Maintained Yes




No version available


  • person_outline Brett Olivier
  • person_outline Brett Olivier

Additional information


CBMPy 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

[…] om/mmp-uva/fruits). All constraint-based analysis techniques used within this pipeline, namely flux balance analysis (FBA) [], flux variability analysis (FVA) [] and OptKnock [], were performed using PySCeS-CBMPy [] (http://cbmpy.sourceforge.net) in combination with ILOG CPLEX Optimization Studio (IBM) under an academic license. Additional visualization of modeling simulations were carried out usi […]


Probing the Genome Scale Metabolic Landscape of Bordetella pertussis, the Causative Agent of Whooping Cough

Appl Environ Microbiol
PMCID: 5648915
PMID: 28842544
DOI: 10.1128/AEM.01528-17

[…] ally 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, EMAF […]


Model based quantification of metabolic interactions from dynamic microbial community data

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

[…] network could fit the experimental data equally well. This analysis indicates a small flexibility, only 41 reactions of the 744 reactions had variable values (5.5%) (https://sourceforge.net/projects/cbmpy/files/publications/data/2017_Hanemaaijer/). Those 41 reactions are involved in either malate cycling, proline and nucleotide biosynthesis, and carry very small fluxes relative to the fluxes in C […]


A novel consortium of Lactobacillus rhamnosus and Streptococcus thermophilus for increased access to functional fermented foods

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

[…] ns 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 []. […]


Interplay between Constraints, Objectives, and Optimality for Genome Scale Stoichiometric Models

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

[…] take) 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 a mixed-intege […]


Community Flux Balance Analysis for Microbial Consortia at Balanced Growth

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

[…] 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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