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mCADRE specifications


Unique identifier OMICS_20376
Alternative name metabolic Context-specificity Assessed by Deterministic Reaction Evaluation
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages MATLAB
License MIT License
Computer skills Advanced
Stability Stable
Maintained Yes



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  • person_outline Nathan Price <>

Publication for metabolic Context-specificity Assessed by Deterministic Reaction Evaluation

mCADRE in publications

PMCID: 5536358
PMID: 28686599
DOI: 10.1371/journal.pcbi.1005618

[…] reactions. the network was curated using more than 1500 primary articles, reviews, and biochemical textbooks. recently, many algorithms, including the model building algorithm (mba) [] and the metabolic context-specificity assessed by deterministic reaction evaluation (mcadre) method [], have been proposed for inferring tissue-specific subnetworks from generic genome-scale human metabolic […]

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

[…] all reactions in the core are able to carry a non-zero flux in at least one steady-state solution. the final context-specific subnetwork is then defined as ra = c∪pa. some approaches, like mba [], mcadre [] and fastcore [], aim at minimizing the size of pa, as to obtain a parsimonious final model. in contrast, corda [] relaxes the parsimony condition as a way to prevent eliminating important […]

PMCID: 5453602
PMID: 28520713
DOI: 10.1371/journal.pcbi.1005489

[…] methods that impose condition-specific flux constraints on metabolic network models based upon gene expression data include gimme [], imat [], e-flux [], made [], gx-fba [], mta [], corereg [], mcadre [] and examo []. however, in many cases, the predictions obtained by fba using a growth maximization objective are as good or better than those obtained using methods that incorporate gene […]

PMCID: 5186797
PMID: 28082911
DOI: 10.3389/fphys.2016.00644

[…] factor is the availability of tissue reconstructions that allow for the required metabolic function (in our case proliferation). unfortunately, many previously published reconstructions obtained by mcadre or tinit tissue reconstructions do not use a growth objective and are therefore not suitable for parsimonious fba with known proliferation rates (wang et al., ; pornputtapong et al., ). […]

PMCID: 4834348
PMID: 27147948
DOI: 10.3389/fnins.2016.00156

[…] group processes the data to create context-specific models from generic metabolic models, such as gimme (becker and palsson, ), imat (shlomi et al., ), init (agren et al., ), adam (töpfer et al., ), mcadre (wang et al., ), and examo (rossell et al., ), which can later be used for flux calculation. it was shown that the two approaches have no clear superiority over each other (machado […]

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mCADRE institution(s)
Institute for Systems Biology, Seattle, WA, USA; Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana, IL, USA; Department of Bioengineering, University of Illinois, Urbana, IL, USA
mCADRE funding source(s)
Supported by a Howard Temin Pathway to I Award in Cancer Research (R00 CA126184), Department of Defense (W81XWH-08-1-0420), a Roy J. Carver Charitable Trust Young Investigator Grant, the Luxembourg-Institute for Systems Biology Consortium, and the Camille Dreyfus Teacher-Scholar Program.

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