Model SEED protocols

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Model SEED specifications


Unique identifier OMICS_05183
Name Model SEED
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes



  • person_outline Henry CS <>

Publication for Model SEED

Model SEED in pipeline

PMCID: 3444828
PMID: 22997515
DOI: 10.1155/2012/323472

[…] a minimal set of reactions to add from a universal database so that a specified set of metabolites may be produced. these optimization-based procedures have already been integrated into the model seed metabolic reconstruction pipeline with some success []. reed et al. [] utilize a method that adds a minimum-sized set of reactions from a universal database that allows for a specified […]

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Model SEED in publications

PMCID: 5574706
PMID: 28861526
DOI: 10.1128/mSystems.00091-17

[…] uses components of the rast toolkit for genome annotation (, ). metabolic network reconstructions were obtained using the “build metabolic model” app with default parameters, which relies on the model seed framework () to build a draft metabolic model. to ensure that the reconstructions contained only reactions with genomic evidence, no gap filling was performed. these reconstructions […]

PMCID: 5553986
PMID: 28715411
DOI: 10.1371/journal.pcbi.1005639

[…] in reconstructing full genome metabolic models. while still requiring considerable manual work to refine them, draft models can be produced rapidly and easily from annotated genomes. we used the model seed framework as the starting point for our model. the model seed integrates a range of existing approaches into a coherent pipeline, accessed through a web interface [, ]., our initial model […]

PMCID: 5217662
PMID: 28056772
DOI: 10.1186/s12864-016-3389-4

[…] procedure thus reflect the importance of these two types of key markers for affecting the strain’s potential as cell factories that can be expected to reach a high titer of lipids., since, model seed [] automatically produces annotations and draft genome-scale metabolic models, we used it here to compare its results with the proposed ffasc approach using the ec numbers corresponding […]

PMCID: 5117618
PMID: 27895706
DOI: 10.1186/s13068-016-0665-0

[…] the organism’s genes, and the subsequent assembly of the metabolic reactions that are supported by these enzymes into a network. recently, several automatic reconstruction tools have been proposed. model seed [] is a web based pipeline for creating and analyzing metabolic models using techniques that automate the process. raven [] is a program suite for semi-automated reconstruction […]

PMCID: 4977884
PMID: 27502787
DOI: 10.1186/s12864-016-2887-8

[…] the entire metabolic network or other subsets of metabolism of interest enabling researches to address specific research goals., cmms were built on the previously developed metabolic modeling tool model seed [], where the model construction pipeline begins with gene annotations of microbial genomes provided by rast []. this combined use of rast annotation and model seed reconstruction results […]

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Model SEED institution(s)
Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA

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