CytoSEED specifications

Information


Unique identifier OMICS_05188
Name CytoSEED
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Stability Stable
Requirements
Cytoscape
Maintained Yes

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Publication for CytoSEED

CytoSEED in publications

 (2)
PMCID: 4461095
PMID: 26082651
DOI: 10.2147/AABC.S63534

[…] data. these include, for instance, seed (http://seed-viewer.theseed.org/), and the cobra project. seed has a web-based user interface and allows to read in seed models in cytoscape using the plugin cytoseed. cobra can be used via matlab or python. we predict again a steep learning curve, as the tools are tailored for metabolic modeling applications. depending on the complexity of the research […]

PMCID: 4231531
PMID: 25365062
DOI: 10.1371/journal.pone.0110785

[…] to correct the discrepancy between the model predictions and the in vivo data requirements for tryptophan, some reactions that were initially gap filled by model seed (and identified using cytoseed were removed. the anthranilate synthase (e.c. 4.1.3.21) and tryptophan synthase (e.c. 4.2.1.20) reactions were removed from the 334 and 12a networks, respectively, since […]


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CytoSEED institution(s)
Computer Science Department, Hope College, Holland, MI, USA

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