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Items tagged with "metabolic network" (9)

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76?size=60x60 Gb Paul Dobson
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Blob ONDEX Graph from the Yeast Jamboree SBML

Created: 2009-02-10 10:51:58 | Last updated: 2009-02-10 12:48:52

Credits: User Paul Dobson

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The oxl file represents in ONDEX the SBML reconstruction of yeast metabolism produced in the "Jamboree", as described in the following paper.   PMID 18846089 A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nature Biotechnology. 2008 Oct;26(10):1155-60. Herrgård MJ, Swainston N, Dobson P, Dunn WB, Arga KY, Arvas M, Blüthgen N, Borger S, Costenoble R, Heinemann M, Hucka M, Le Novère N, Li P, Lieb...

File type: GNU Zip Archive

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Packs (1)
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76?size=60x60 Gb Paul Dobson
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Pack Mapping Metabolites for Metabolic Network Reconstruc...


Created: 2010-06-03 11:43:43 | Last updated: 2010-06-03 11:47:16

The process of metabolic network reconstructions typically begins with the task of collating existing information. For metabolites this poses a relatively straight forward set of cheminformatics problems. These problems include finding identical structures across sources, which is trivial, but also structures that differ due to idiosyncrasies of the sources or annotators. This includes charge differences, varying stereochemistry, tautomers, and so forth. Workflows in this pack allow sets of ...

6 items in this pack

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Workflows (7)
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76?size=60x60 Gb Paul Dobson

Workflow C1 Combined Workflow (1)

The process of metabolic network reconstructions typically begins with the task of collating existing information. For metabolites this poses a relatively straight forward set of cheminformatics problems. This workflow implements matching algorithms M1-M5 in one workflow, yielding a sparse matrix of matches annotated by match types.

Created: 2010-06-03 | Last updated: 2010-06-03

Credits: User Paul Dobson

Pipeline Pilot
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76?size=60x60 Gb Paul Dobson

Workflow M1 Exact Matching (1)

The process of metabolic network reconstructions typically begins with the task of collating existing information. For metabolites this poses a relatively straight forward set of cheminformatics problems. This workflow implements matching algorithm M1 which matches fully specified molecules on the basis of their canonical representations.

Created: 2010-06-03

Credits: User Paul Dobson

Pipeline Pilot
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76?size=60x60 Gb Paul Dobson

Workflow M2 Similarity Matching (1)

The process of metabolic network reconstructions typically begins with the task of collating existing information. For metabolites this poses a relatively straight forward set of cheminformatics problems. This workflow implements matching algorithm M2 which reads molecules from two sources and produces clusters of highly similar molecules.

Created: 2010-06-03

Credits: User Paul Dobson

Pipeline Pilot
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76?size=60x60 Gb Paul Dobson

Workflow M3 Non-stereo Matching (1)

The process of metabolic network reconstructions typically begins with the task of collating existing information. For metabolites this poses a relatively straight forward set of cheminformatics problems. This workflow implements matching algorithm M3 which strips stereochemical information from molecules, performs exact matching, and restores stereochemistry.

Created: 2010-06-03

Credits: User Paul Dobson

Pipeline Pilot
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76?size=60x60 Gb Paul Dobson

Workflow M4 Tautomer Matching (1)

The process of metabolic network reconstructions typically begins with the task of collating existing information. For metabolites this poses a relatively straight forward set of cheminformatics problems. This workflow implements matching algorithm M4 which generates canonical tautomers prior to matching, matches, then restores original structures.

Created: 2010-06-03

Credits: User Paul Dobson

Pipeline Pilot
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76?size=60x60 Gb Paul Dobson

Workflow M5 Charge Matching (1)

The process of metabolic network reconstructions typically begins with the task of collating existing information. For metabolites this poses a relatively straight forward set of cheminformatics problems. This workflow implements matching algorithm M5 which ionises molecules at pH 7 prior to matching, restores original structures.

Created: 2010-06-03

Credits: User Paul Dobson

KNIME
Uploader
Avatar Fr Thomas Duigou

Workflow RetroPath2.0 - a retrosynthesis workflow w... (15)

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The RetroPath2.0 workflow build a reaction network from a set of source compounds to a set of sink compounds.When applied in a retrosynthetic fashion, the source is composed of the target compounds and the sink is composed of the available reactants (for instance in the context of metabolic engineering the sink is the set of native metabolites of a chassis strain). From amongst all the chemical reactions generated using RetroPath2.0 (in the retrosynthetic way), only a subset may effectively l...

Created: 2017-05-24 | Last updated: 2022-02-24

Credits: User Thomas Duigou User Baudoin Delépine Network-member BioRetroSynth

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