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DFBAlab specifications

Information


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

Versioning


No version available

Publication for Dynamic Flux Balance Analysis laboratory

DFBAlab citations

 (6)
library_books

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

2017
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 […]

library_books

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

2017
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 […]

library_books

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

2016
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 […]

library_books

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

2016
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 […]

library_books

Spatiotemporal modeling of microbial metabolism

2016
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 […]

library_books

Metabolic modeling of synthesis gas fermentation in bubble column reactors

2015
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 […]

Citations

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

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