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Metatool specifications

Information


Unique identifier OMICS_06450
Name Metatool
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

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Publication for Metatool

Metatool in publications

 (40)
PMCID: 5851934
PMID: 29552648
DOI: 10.1016/j.synbio.2017.11.002

[…] graph-based methods can make prediction with similar accuracy as stoichiometry-based methods. moreover, stoichiometry-based pathway search methods can operate on the s matrix alone (such as metatool 5.0 , optstoic , and xtms ) to identify cofactor-balanced pathways. however, the reversibility of a reaction has to be defined as constraints alongside the s matrix while a directed graph […]

PMCID: 5319754
PMID: 28222104
DOI: 10.1371/journal.pone.0171440

[…] irreversible due to biochemical knowledge., let us consider, for example, the system of monosaccharide metabolism (see ) analyzed earlier []. when all reactions are considered reversible, running metatool (or any other appropriate program) shows that 19 pairs of efms are found. in the cited paper, eight reactions such as phosphofructokinase, fructose-biphosphatase and glucose-6-phosphate […]

PMCID: 4993939
PMID: 27595107
DOI: 10.1155/2016/7863706

[…] acid molecules will be converted into membrane phospholipids in order to maintain the fluidity of this biological barrier., the calculation of elementary modes was performed in matlab using the metatool toolbox [] (modo_elementar.m code in the supplemental information). a total of 13 elementary flux modes were found for the fatty acid biosynthesis pathway of e. antarcticum b7 (additional […]

PMCID: 4911368
PMID: 27379244
DOI: 10.3389/fmolb.2016.00022

[…] metabolites”). those flux modes (combinations of enzymes) which cannot be decomposed further without affecting this balance are called elementary modes. we computed these elementary modes using the metatool program (von kamp and schuster, ), which has been integrated within the yana software package (schwarz et al., ). further analysis of the calculated pathways (i.e., all elementary modes) […]

PMCID: 4871961
PMID: 27274618
DOI: 10.1155/2016/1984827

[…] stimulation) using facial descriptors extracted out of existing observational pain assessment scales. this extraction has led to the development of the pain assessment in impaired cognition (paic) metatool [] as part of a european funded cost action (td1005) and we used all facial items of this paic tool (see ). all facial expressions were rated by an independent rater, trained […]


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Metatool institution(s)
Department of Bioinformatics, Friedrich-Schiller-University Jena, Jena, Germany

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