About | Give us Feedback | Publications

Home
Tags
metabolic network

Tag Results

Items tagged with "metabolic network" (8)

Note: some items may not be visible to you, due to viewing permissions.

Files (1)

Uploader

Paul Dobson

View

Download

ONDEX Graph from the Yeast Jamboree SBML

Created: 10/02/09 @ 10:51:58 | Last updated: 10/02/09 @ 12:48:52

Credits: 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

Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 387 times | Downloaded: 38 times

Tags:

Packs (1)

Creator

Paul Dobson

View

Download

Mapping Metabolites for Metabolic Network Reconstruc...

Created: 03/06/10 @ 11:43:43 | Last updated: 03/06/10 @ 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

Comments: 0 | Viewed: 50 times | Downloaded: 28 times

Tags:

Workflows (6)

Pipeline Pilot

Original Uploader

Paul Dobson

View

Download (v1)

C1 Combined Workflow (1)

Created: 03/06/10 @ 11:26:48 | Last updated: 03/06/10 @ 11:30:10

Credits: Paul Dobson

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 48 times | Downloaded: 37 times

Tags (6):

Pipeline Pilot

Original Uploader

Paul Dobson

View

Download (v1)

M1 Exact Matching (1)

Created: 03/06/10 @ 11:32:02

Credits: Paul Dobson

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 31 times | Downloaded: 29 times

Tags (7):

Pipeline Pilot

Original Uploader

Paul Dobson

View

Download (v1)

M2 Similarity Matching (1)

Created: 03/06/10 @ 11:33:36

Credits: Paul Dobson

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 34 times | Downloaded: 37 times

Tags (7):

Pipeline Pilot

Original Uploader

Paul Dobson

View

Download (v1)

M3 Non-stereo Matching (1)

Created: 03/06/10 @ 11:35:03

Credits: Paul Dobson

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 23 times | Downloaded: 33 times

Tags (6):

Pipeline Pilot

Original Uploader

Paul Dobson

View

Download (v1)

M4 Tautomer Matching (1)

Created: 03/06/10 @ 11:38:27

Credits: Paul Dobson

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 21 times | Downloaded: 32 times

Tags (7):

Pipeline Pilot

Original Uploader

Paul Dobson

View

Download (v1)

M5 Charge Matching (1)

Created: 03/06/10 @ 11:39:28

Credits: Paul Dobson

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 36 times | Downloaded: 26 times

Tags (7):