myExperiment - Tags - systems biology

Workflows (10)

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)
Taverna 1 Original Uploader Duncan Hull	getSynonymsFromSBML (v1) Created: 09/06/09 @ 20:02:05 \| Last updated: 09/06/09 @ 20:08:02 Credits: Duncan Hull License: Creative Commons Attribution-Share Alike 3.0 Unported License This service takes an SBML file (for example from the Biomodels database) and extracts synonyms for each of the SBML species in the file, using ChEBI. Service is written and maintained by Neil Swainston at the MCISB. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 42 times \| Downloaded: 18 times Tags (8): biomodels \| chebi \| mcisb \| miriam \| neil-swainston \| sbml \| synonym \| systems biology	View Download (v1)
Taverna 1 Original Uploader Saeedeh	Escherichia coli : From cDNA Microarray Raw Data to Pathways and Published Abstracts (v1) Created: 08/05/08 @ 15:25:29 \| Last updated: 12/05/08 @ 09:01:37 Credits: Saeedeh Paul Fisher Attributions: HUMAN Microarray CEL file to candidate pathways License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow takes in a CDNA raw file and a normalisation method then returns a series of images/graphs which represent the same output obtained using the R and bioconductor. Also retruned by this workflow are a list of the top differentialy expressed genes (size dependant on the number specified as input - geneNumber), which are then used to find the candidate pathways which may be influencing the observed changes in the microarray data. By identifying the candidate pathways, more detailed... Rating: 5.0 / 5 (1 rating) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 320 times \| Downloaded: 102 times Tags (6): e.coli \| kegg \| Kegg Pathways \| pathways \| pubmed \| systems biology	View Download (v1)
Taverna 1 Original Uploader Peter Li	Identification of differential genes using t-tests by R (v2) Created: 15/04/08 @ 15:37:42 \| Last updated: 01/07/08 @ 17:21:18 Credits: Peter Li License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow starts by retrieving the names of microarray datasets from the Maxd database. The user has to select sets of control and test data for analysis using t-tests by R. A list of significant differentially expressed genes is then analysed using the Go Term Finder tool which generates a list of GO terms associated with the genes. A CSV file containing the list of significant genes is also generated. Rating: 5.0 / 5 (1 rating) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 1 Viewed: 463 times \| Downloaded: 156 times Tags (6): beanshell \| maxd \| microarray \| r \| systems biology \| user_interaction	View Download (v2)
Taverna 1 Original Uploader Michael Gerlich	getInchIfromMassBankPeaklist_ChemSpider_workflow_withImage (v2) Created: 05/06/08 @ 16:00:38 \| Last updated: 16/06/08 @ 11:40:46 Credits: Michael Gerlich License: Creative Commons Attribution-Share Alike 3.0 Unported License uses InChI's retrieved from a MassBank peaklist query to get compound information about those compounds via querying ChemSpider for information and displaying those results with image Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 128 times \| Downloaded: 62 times Tags (8): accurate mass \| bioinformatics \| chemspider \| compound info + image \| mass spectrometry \| massbank \| metabolomics \| systems biology	View Download (v2)

Packs (2)

Creator:

Katy Wolstencroft

useful_for_sysmo

Created: 17/12/08 @ 12:31:48 | Last updated: 10/06/09 @ 09:43:20

These workflows have been collected as potentially useful protocols for the sysmo consortium

21 items in this pack

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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 ...

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Groups (2)

Administrator:

Allyson Lister

SyMBA: Systems and Molecular Biology Data and Metadata Archive

Unique name: symba Created: Wednesday 12 September 2007 @ 11:30:41 (GMT)

SyMBA was originally developed to be a high-throughput data archive for the data created at CISBAN at Newcastle University, but is now a project applicable for many in the biology & bioinformatics community. New developers are always welcome. SyMBA is a data and metadata archive that is based on the Functional Genomics Object Model(FuGE) and which archives, stores, and retrieves raw high-t...

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Administrator:

Katy Wolstencroft

EraSysBio_Tutorial

Created: Wednesday 30 July 2008 @ 12:07:11 (GMT)

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Files (2)

Uploader:

Paul Dobson

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

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