fastcore statistics

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fastcore specifications

Information


Unique identifier OMICS_06009
Name fastcore
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for fastcore

fastcore in publications

 (10)
PMCID: 5813426
PMID: 29444634
DOI: 10.1186/s12859-018-2050-4

[…] combines randomized selection of reactions and a greedy heuristic to prune this selection., ponce de leo et al. use gap filling to unblock the blocked reactions in many metabolic models [] using the fastcore algorithm []., a recent paper by prigent [] is most similar to our work. they also take the approach of randomly degrading an e. coli metabolic model (the ijr904 model []). several […]

PMCID: 5727896
PMID: 29276507
DOI: 10.3389/fmicb.2017.02440

[…] downloaded from the kegg database). in short, fgf constructs a global model by adding a universal set of reactions (in this case all kegg reactions) to the input metabolic model, then runs the fastcore algorithm () which iteratively computes by linear optimization a flux-consistent model comprising of all model reactions and a minimal set of added “universal reactions.” this is a fast […]

PMCID: 5662602
PMID: 29084986
DOI: 10.1038/s41598-017-14067-8

[…] expression data. in essence, these methods aim to select the consistent subset of reactions active for a given cancer sample. a non-exhaustive list of this type of methods includes: gimme, imat, fastcore and others. with these approaches, the construction of different cancer-specific metabolic networks is now possible., however, less work has been directed to contextualize and enrich […]

PMCID: 5570491
PMID: 28806730
DOI: 10.1371/journal.pcbi.1005698

[…] finally, all other net, non-exchange reactions that did not admit a non-zero flux were omitted via the application of a previously reported function (identifyblockedrxns, epsilon = 1e-4) within the fastcore software package for the reconstruction of context-specific metabolic networks []. the number of exchanges added to the model due to minexcard varied between 13 and 28 (). the minexcard […]

PMCID: 5469500
PMID: 28557990
DOI: 10.1371/journal.pcbi.1005568

[…] we take as representative of a network-centered approach. in addition, we show how the optimization program behind corex can be adapted to evaluate not only its alternative optima space, but that of fastcore [] and corda [], two state-of-the-art network-centered approaches., given a gem and (context-specific) gene or protein expression data, the regularized metabolic model extraction (regrex) […]


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fastcore institution(s)
Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Luxembourg City, Luxembourg; Life Sciences Research Unit, University of Luxembourg, Luxembourg City, Luxembourg

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FASTCORE is available here
http://wwwen.uni.lu/recherche/fstc/life_sciences_research_unit/research_areas/systems_biology/software