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pyTFA specifications

Information


Unique identifier OMICS_30651
Name pyTFA
Alternative names matTFA, TMFA
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages MATLAB, Python, Shell (Bash)
License Apache License version 2.0, GNU General Public License version 3.0
Computer skills Advanced
Version 0.7.1-b2
Stability Stable
Requirements
Git-LFS
Maintained Yes

Download


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Versioning


No version available

Documentation


Maintainer


  • person_outline Vassily Hatzimanikatis

Additional information


The Matlab implementation is available at https://github.com/EPFL-LCSB/matTFA http://pytfa.readthedocs.io/en/latest/index.html

Publications for pyTFA

pyTFA citations

 (11)
library_books

In Silico Knockout Screening of Plasmodium falciparum Reactions and Prediction of Novel Essential Reactions by Analysing the Metabolic Network

2018
Biomed Res Int
PMCID: 5896307
DOI: 10.1155/2018/8985718

[…] ics-based Flux Analysis (TFA) is a variant of metabolic flux analysis presented with the capacity of producing thermodynamically feasible flux and metabolite movement profiles on a genome scale [, ]. TMFA includes the utilization of an arrangement of straight thermodynamic constraints notwithstanding the mass balance limitations ordinarily utilized as a part of MFA [, ]. TMFA produces flux circula […]

library_books

Pathway design using de novo steps through uncharted biochemical spaces

2018
Nat Commun
PMCID: 5766603
PMID: 29330441
DOI: 10.1038/s41467-017-02362-x

[…] wever, after each step, the trade-off between carbon yield, energy (ATP requirements), and thermodynamic feasibility of the main carbon conversion path often remain unexplored. Instead, tools such as TMFA and EFM are used in a posteriori steps to assess energy and carbon efficiency. Computational tools such as optStoic can be used to design mass and energy balanced pathways. However, they are limi […]

library_books

Erroneous energy generating cycles in published genome scale metabolic networks: Identification and removal

2017
PLoS Comput Biol
PMCID: 5413070
PMID: 28419089
DOI: 10.1371/journal.pcbi.1005494

[…] suppress EGCs. In principle, EGCs could be excluded from the solution space by systematically assigning sufficiently detailed thermodynamic constraints. Thermodynamics-Based Metabolic Flux Analysis (TMFA) [], for example, searches for a set of feasible metabolite concentrations such that all reactions proceed in the direction of negative free energy change (ΔG<0) or, equivalently, a ratio of prod […]

library_books

Bioenergetics based modeling of Plasmodium falciparum metabolism reveals its essential genes, nutritional requirements, and thermodynamic bottlenecks

2017
PLoS Comput Biol
PMCID: 5363809
PMID: 28333921
DOI: 10.1371/journal.pcbi.1005397

[…] nts following the systematic approach defined within the framework of Thermodynamics-based Flux Analysis (TFA) [, , ], which has been also referred to as Thermodynamics-based metabolic Flux Analysis (TMFA) [] and Thermodynamics-based Flux Balance Analysis (TFBA) [, ]. Thermodynamic constraints determine the feasible range of ΔrG’ and hence reduce the uncertainty in the reaction directionalities an […]

library_books

Thermodynamics and H2 Transfer in a Methanogenic, Syntrophic Community

2015
PLoS Comput Biol
PMCID: 4509577
PMID: 26147299
DOI: 10.1371/journal.pcbi.1004364

[…] ship between thermodynamics and metabolism, by ensuring that network predictions are consistent with thermodynamic principles [–]. In this study, we used thermodynamics-based metabolic flux analysis (TMFA) to develop a thermodynamic, coculture model of the syntrophic association between the anaerobic bacterium Syntrophobacter fumaroxidans and the methanogenic archaeon Methanospirillum hungatei. In […]

library_books

Mechanistic analysis of multi omics datasets to generate kinetic parameters for constraint based metabolic models

2013
BMC Bioinformatics
PMCID: 3571921
PMID: 23360254
DOI: 10.1186/1471-2105-14-32

[…] mes are known to be unexpressed in certain conditions. Thermodynamic constraints have also been imposed to limit the direction a given reaction can proceed, and thermodynamic metabolic flux analysis (TMFA) uses these constraints to ensure that reactions only proceed in the thermodynamically-favorable direction [-]. TMFA models were some of the first constraint-based models that directly accounted […]

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pyTFA institution(s)
Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland; CentraleSupélec, Université Paris-Saclay, France
pyTFA funding source(s)
Supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 722287, RobustYeast within ERA net project via SystemsX.ch, and the European Union’s Horizon 2020 research and innovation programme under grant agreement No 686070.

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