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Taverna 1

Original Uploader

Marco Roos

BioAID_DiseaseDiscovery (v3)

Created: 15/12/08 @ 20:46:09 | Last updated: 15/12/08 @ 20:47:50

Credits: Marco Roos AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow finds disease relevant to the query string via the following steps: 1. A user query: a list of terms or boolean query - look at the Apache Lucene project for all details. E.g.: (EZH2 OR "Enhancer of Zeste" +(mutation chromatin) -clinical); consider adding 'ProteinSynonymsToQuery' in front of the input if your query is a protein. 2. Retrieve documents: finds 'maximumNumberOfHits' relevant documents (abstract+title) based on query (the AIDA service inside is based on Apa...

Rating: 4.0 / 5 (2 ratings) | Versions: 3 | Reviews: 0 | Comments: 2 | Citations: 0

Viewed: 2281 times | Downloaded: 302 times

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Taverna 1

Original Uploader

Paul Fisher

Pathways and Gene annotations for QTL region (v5)

Created: 19/11/09 @ 18:18:52 | Last updated: 20/11/09 @ 10:33:25

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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: 4.5 / 5 (2 ratings) | Versions: 5 | Reviews: 0 | Comments: 2 | Citations: 1

Viewed: 728 times | Downloaded: 169 times

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Taverna 1

Original Uploader

Hamish McWilliam

EBI_InterProScan (v3)

Created: 26/10/08 @ 20:33:34

Credits: Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

Perform an InterProScan analysis of a protein sequence using the EBI’s WSInterProScan service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan). The input sequence to use and the user e-mail address are inputs, the other parameters for the analysis (see Job_params) are allowed to default. InterProScan searches a protein sequence against the protein family and domain signature databases integrated into InterPro (see http://www.ebi.ac.uk/interpro/). A set of matches to the sig...

Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 1 | Citations: 0

Viewed: 340 times | Downloaded: 186 times

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Taverna 1

Original Uploader

Mark Borkum

QR code (matrix code) generator (v4)

Created: 07/10/07 @ 17:17:03 | Last updated: 16/07/08 @ 01:46:13

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The latest (and greatest) version of the QR code generator workflow. This workflow uses the QR code service provided by the ChemTools project.

Rating: 1.0 / 5 (1 rating) | Versions: 4 | Reviews: 0 | Comments: 0 | Citations: 1

Viewed: 278 times | Downloaded: 182 times

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Taverna 1

Original Uploader

Paul Fisher

HUMAN Microarray CEL file to candidate pathways (v4)

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

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 (1 rating) | Versions: 4 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 672 times | Downloaded: 236 times

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Taverna 1

Original Uploader

Alan Williams

BiomartAndEMBOSSAnalysis (v4)

Created: 15/09/09 @ 15:11:11

License: Creative Commons Attribution 3.0 Unported License

Using Biomart and EMBOSS soaplab services, This workflow retrieves a number of sequences from 3 species: mouse, human, rat; align them, and returns a plot of the alignment result. Corresponding sequence ids are also returned.

Rating: 0.0 / 5 (0 ratings) | Versions: 4 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 620 times | Downloaded: 246 times

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Taverna 1

Original Uploader

Paul Fisher

Entrez Gene to KEGG Pathway (v4)

Created: 04/12/09 @ 16:04:38

Credits: Paul Fisher

License: Creative Commons Attribution 3.0 Unported License

This workflow takes in Entrez gene ids then adds the string "ncbi-geneid:" to the start of each gene id. These gene ids are then cross-referenced to KEGG gene ids. Each KEGG gene id is then sent to the KEGG pathway database and its relevant pathways returned.

Rating: 4.8 / 5 (4 ratings) | Versions: 4 | Reviews: 0 | Comments: 2 | Citations: 0

Viewed: 564 times | Downloaded: 285 times

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Taverna 1

Original Uploader

M.B.Mon...

Workflow for Protein Sequence Analysis (v1)

Created: 09/01/08 @ 12:03:03 | Last updated: 09/01/08 @ 12:31:27

Credits: M.B.Monteiro

Attributions: BLAST using DDBJ service Simplify a BLAST text file conditional branch

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow performs a generic protein sequence analysis. In order to do that a novel protein sequence enters into the software along with a list of known protein identifiers chosen by the biologist to perform a homology search, followed by a multiple sequence alignment and finally a phylogenetic analysis.

Rating: 3.0 / 5 (1 rating) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 842 times | Downloaded: 257 times

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Taverna 1

Original Uploader

Andrea Wiggins

Success-Abandonment-Classification (v3)

Created: 06/02/08 @ 14:35:41 | Last updated: 02/07/08 @ 17:15:25

Credits: Andrea Wiggins James Howison

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Retrieves data from FLOSSmole and from the Notre Dame SourceForge repository to compute project statistics based on releases, downloads and project lifespan. Project statistics are then used to classify projects according to the criteria set up in English & Schweik, but comparison criteria are parameterized so that a different set of criterion thresholds can be used to evaluate the project characteristics.

Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 741 times | Downloaded: 6405 times

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