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DFBAlab specifications


Unique identifier OMICS_06867
Name DFBAlab
Alternative name Dynamic Flux Balance Analysis laboratory
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB
Computer skills Advanced
Stability Stable
Maintained Yes


No version available

Publication for Dynamic Flux Balance Analysis laboratory

DFBAlab citations


Microbiota dysbiosis in inflammatory bowel diseases: in silico investigation of the oxygen hypothesis

BMC Syst Biol
PMCID: 5745886
PMID: 29282051
DOI: 10.1186/s12918-017-0522-1

[…] DFBAlab is freely available for both education and nonprofit research purposes from https://yoric.mit.edu/dfbalab. The MATLAB simulation codes for the multispecies biofilm model are included in this p […]


Parametric studies of metabolic cooperativity in Escherichia coli colonies: Strain and geometric confinement effects

PLoS One
PMCID: 5562313
PMID: 28820904
DOI: 10.1371/journal.pone.0182570

[…] ally-resolved FBA methods have also been developed, and used to study mutualism and competition in two dimensional multispecies communities (COMETS; []) as well as chronic wound biofilm homoeostasis (DFBALab; [, ]).These spatially-resolved methods have the potential to add new relevance to computational biology by bridging temporal and spatial scales that are currently difficult or impossible to s […]


Metabolic modeling of a chronic wound biofilm consortium predicts spatial partitioning of bacterial species

BMC Syst Biol
PMCID: 5015247
PMID: 27604263
DOI: 10.1186/s12918-016-0334-8

[…] ded a set of 8 ODEs at each node point for the local concentrations of P. aeruginosa and S. aureus biomass, glucose, oxygen, acetate, succinate, lactate and pyocyanin.This ODE system was solved using DFBAlab [], a MATLAB tool that explicitly addresses problems associated with LP alternative optima and possible infeasibilities []. DFBAlab employs a lexicographic optimization strategy in which a ser […]


Dynamic flux balance modeling to increase the production of high value compounds in green microalgae

Biotechnol Biofuels
PMCID: 4973557
PMID: 27493687
DOI: 10.1186/s13068-016-0556-4

[…] The numerical solution of the proposed model involves the use of DFBAlab [], a MATLAB code that performs reliable and efficient DFBA simulations. Widespread implementation of DFBA has been hindered by numerical complications resulting from linear programs (LPs) bec […]


Spatiotemporal modeling of microbial metabolism

BMC Syst Biol
PMCID: 4774267
PMID: 26932448
DOI: 10.1186/s12918-016-0259-2

[…] rn the relevant convective and/or diffusional processes in the extracellular environment. The PDE model is spatially discretized and the resulting system of ODEs with embedded LPs is integrated using DFBAlab [], a MATLAB code that performs reliable and efficient dynamic FBA simulations. We demonstrated the capabilities of the method by solving large discretized models for a convection dominated sy […]


Metabolic modeling of synthesis gas fermentation in bubble column reactors

Biotechnol Biofuels
PMCID: 4477499
PMID: 26106448
DOI: 10.1186/s13068-015-0272-5

[…] edure involved spatially discretizing the partial differential equations (PDEs) to generate an ordinary differential equation (ODE) system with embedded linear programs (LPs) that was integrated with DFBAlab [], a MATLAB code that performs reliable and efficient dynamic FBA simulations. We demonstrated the capabilities of our approach by performing dynamic simulations with the syngas bubble column […]


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DFBAlab institution(s)
Process Systems Engineering Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA

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