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Items tagged with "pipeline pilot" (10)

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Workflows (8)

Makefile Original Uploader Giovanni Dall'Olio	Sample makefile workflow (v1) Created: 30/10/08 @ 09:07:32 \| Last updated: 30/10/08 @ 09:10:56 Credits: Giovanni Dall'Olio License: Creative Commons Attribution-Share Alike 3.0 Unported License A sample makefile workflow. Type 'make help' to print an help message. Nothing else is supported in this version. Interesting links about makefiles in bioinformatics: http://www.nodalpoint.org/2007/03/18/a_pipeline_is_a_makefile http://swc.scipy.org/lec/build.html Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 107 times \| Downloaded: 64 times Tags (5): example \| make \| makefile \| pipeline pilot \| test	View Download (v1)
Pipeline Pilot Original Uploader Paul Dobson	Wash and filter molecules (v1) Created: 20/01/09 @ 10:11:25 Credits: Paul Dobson License: Creative Commons Attribution-Share Alike 3.0 Unported License The Wash and Filter workflow performs some processing on incoming structures to filter out those wildcards or unspecified atom types, standardise stereo and charges, and various other adjustments. This is an advance on the filter used in the paper... Drug Discovery Today Volume 14, Issues 1-2, January 2009, Pages 31-40 ‘Metabolite-likeness’ as a criterion in the design and selection of pharmaceutical drug libraries Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 178 times \| Downloaded: 61 times Tags (2): metabolite-likeness \| pipeline pilot	View Download (v1)
Pipeline Pilot Original Uploader Paul Dobson	C1 Combined Workflow (v1) 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: 36 times \| Downloaded: 31 times Tags (6): cheminformatics \| data integration \| genome scale reconstruction \| metabolic network \| pipeline pilot \| systems biology	View Download (v1)
Pipeline Pilot Original Uploader Paul Dobson	M1 Exact Matching (v1) 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: 21 times \| Downloaded: 23 times Tags (7): cheminformatics \| data integration \| genome scale reconstruction \| metabolic network \| metabolism \| pipeline pilot \| systems biology	View Download (v1)
Pipeline Pilot Original Uploader Paul Dobson	M2 Similarity Matching (v1) 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: 24 times \| Downloaded: 32 times Tags (7): cheminformatics \| data integration \| genome scale reconstruction \| metabolic network \| metabolism \| pipeline pilot \| systems biology	View Download (v1)
Pipeline Pilot Original Uploader Paul Dobson	M3 Non-stereo Matching (v1) 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: 13 times \| Downloaded: 21 times Tags (6): cheminformatics \| data integration \| genome scale reconstruction \| metabolic network \| pipeline pilot \| systems biology	View Download (v1)
Pipeline Pilot Original Uploader Paul Dobson	M4 Tautomer Matching (v1) 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: 11 times \| Downloaded: 16 times Tags (7): cheminformatics \| data integration \| genome scale reconstruction \| metabolic network \| metabolism \| pipeline pilot \| systems biology	View Download (v1)
Pipeline Pilot Original Uploader Paul Dobson	M5 Charge Matching (v1) 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: 21 times \| Downloaded: 21 times Tags (7): cheminformatics \| data integration \| genome scale reconstruction \| metabolic network \| metabolism \| pipeline pilot \| systems biology	View Download (v1)

Packs (1)

Creator:

Paul Dobson

Mapping Metabolites for Metabolic Network Reconstructions

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

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