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Items tagged with "nbiconworkflows" (7)

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Network-member NBIConWorkflows


Created: Tuesday 22 January 2008 @ 17:46:11 (GMT)

Group for scientists associated with NBIC (Netherlands BioInformatics Centre) to discuss anything about (Taverna) workflows. New members are kindly requested to provide some information about their (future) interest in (Taverna) workflows in their profile description or in a seperate file with a reference in their profile description.

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Files (1)
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Blob From biologist to web service to Taverna to myExperi...

Created: 21/03/08 @ 19:00:12 | Last updated: 23/03/08 @ 10:39:27

Credits: User Marco Roos User Martijn Schuemie Network-member AID Network-member myGrid

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A movie to show the principle of the round trip from a biology question via pieces of code wrapped as web services and combined into a workflow (computational experiment) in Taverna, via uploading to myExperiment and back to the biologist through myExperiment's run facility. NB: at the time of uploading this movie the runner-option was in test-phase. It is important to note that the workflow combines the work of various scientists with different expertise and some at remote locations around ...

File type: AVI video

Rating: 1.0 / 5 (1 rating) | Comments: 1 | Viewed: 291 times | Downloaded: 251 times

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Workflows (5)
Original Uploader

Workflow HUMAN Microarray CEL file to candidate pat... (4)

Created: 03/10/07 @ 18:35:55 | Last updated: 26/11/09 @ 17:34:24

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

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This workflow takes in a CEL file and a normalisation method then returns a series of images/graphs which represent the same output obtained using the MADAT software package (MicroArray Data Analysis Tool) [http://www.bioinf.manchester.ac.uk/MADAT/index.html]. Also returned 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 ...

Rating: 5.0 / 5 (2 ratings) | Versions: 4 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 1463 times | Downloaded: 413 times

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Original Uploader

Workflow Cow-Human Ortholog Pathways and Gene annot... (2)

Created: 03/10/07 @ 18:36:00 | Last updated: 03/12/09 @ 16:16:31

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

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This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in the cow, Bos taurus. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. As the Cow genome is currently unfinished, the workflow subsequently maps the cow ensembl gene ids to human orthologues. Entrez and UniProt identifiers are then identified...

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 1 | Citations: 0

Viewed: 124 times | Downloaded: 55 times

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Original Uploader

Workflow Pathways and Gene annotations for QTL region (7)

Created: 19/11/09 @ 18:18:52 | Last updated: 07/09/12 @ 18:23:36

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in the mouse, Mus musculus. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG path...

Rating: 4.6 / 5 (10 ratings) | Versions: 7 | Reviews: 1 | Comments: 7 | Citations: 1

Viewed: 6121 times | Downloaded: 1014 times

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Original Uploader

Workflow Mouse Microarray Analysis (3)

Created: 03/10/07 @ 18:36:05 | Last updated: 03/12/09 @ 16:20:33

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow takes in probesets from and AffyMetrix micorarray experiment and returns: the genes ; gene start and end positions; chromosome where genes reside; ensembl trasncripts; SwissProt ids; affy probeset identifiers for chips Mouse430_2 and Mouse430a_2. Example ids from the Mouse430_2 affymetrix array are as follows (newline separated): 1447227_at 1440624_at 1436240_at 1454904_at 1435665_at 1418148_at 1429831_at

Rating: 5.0 / 5 (1 rating) | Versions: 3 | Reviews: 0 | Comments: 1 | Citations: 1

Viewed: 561 times | Downloaded: 141 times

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Original Uploader

Workflow BioAID_ProteinDiscovery_filterOnHumanUnipr... (11)

Created: 28/05/09 @ 12:21:05

Credits: User Marco Roos User Martijn Schuemie Network-member AID Network-member AID_myGrid_collaboration

Attributions: Workflow BioAID_DiseaseDiscovery_RatHumanMouseUniprotFilter

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow finds proteins relevant to the query string via the following steps: A user query: a single gene/protein name. E.g.: (EZH2 OR "Enhancer of Zeste"). Retrieve documents: finds 'maximumNumberOfHits' relevant documents (abstract+title) based on query (the AIDA service inside is based on Apache's Lucene) Discover proteins: extract proteins discovered in the set of relevant abstracts with a 'named entity recognizer' trained on genomic terms using a Bayesian approach; the AIDA serv...

Rating: 0.0 / 5 (0 ratings) | Versions: 11 | Reviews: 0 | Comments: 1 | Citations: 0

Viewed: 471 times | Downloaded: 173 times

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