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Items tagged with "systems biology" (16)

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Network-member SyMBA: Systems and Molecular Biology Data ...

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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Network-member EraSysBio_Tutorial


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

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Files (2)
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Blob ONDEX Graph from the Yeast Jamboree SBML

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

Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 132 times | Downloaded: 36 times

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Blob EraSysBio Summer School Taverna Tutorial

Created: 24/07/09 @ 21:54:27

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This tutorial is an introduction to Taverna and myExperiment

File type: application/mspowerpoint

Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 22 times | Downloaded: 34 times

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Workflows (10)
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Workflow C1 Combined Workflow (1)

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

Credits: User 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

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Workflow M1 Exact Matching (1)

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

Credits: User 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: 27 times | Downloaded: 26 times

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Workflow M2 Similarity Matching (1)

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

Credits: User 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.

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Workflow M3 Non-stereo Matching (1)

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

Credits: User 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

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Workflow M4 Tautomer Matching (1)

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

Credits: User 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: 18 times | Downloaded: 21 times

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Workflow M5 Charge Matching (1)

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

Credits: User 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

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Workflow getSynonymsFromSBML (1)

Created: 09/06/09 @ 20:02:05 | Last updated: 09/06/09 @ 20:08:02

Credits: User Duncan Hull

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 49 times | Downloaded: 19 times

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Workflow Escherichia coli : From cDNA Microarray Ra... (1)

Created: 08/05/08 @ 15:25:29 | Last updated: 12/05/08 @ 09:01:37

Credits: User Saeedeh User Paul Fisher

Attributions: Workflow HUMAN Microarray CEL file to candidate pathways

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 336 times | Downloaded: 109 times

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Workflow Identification of differential genes using... (2)

Created: 15/04/08 @ 15:37:42 | Last updated: 01/07/08 @ 17:21:18

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 483 times | Downloaded: 163 times

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Workflow getInchIfromMassBankPeaklist_ChemSpider_wo... (2)

Created: 05/06/08 @ 16:00:38 | Last updated: 16/06/08 @ 11:40:46

Credits: User Michael Gerlich

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 137 times | Downloaded: 80 times

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Packs (2)

Pack 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

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Pack 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 ...

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Comments: 0 | Viewed: 46 times | Downloaded: 24 times

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