Workflows

View Download (v7)

Pathways and Gene annotations for QTL region (7)

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

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

Viewed: 7095 times | Downloaded: 1255 times

View Download (v4)

BioAID_DiseaseDiscovery_RatHumanMouseUnipr... (4)

Created: 15/12/08 @ 20:46:09 | Last updated: 11/08/11 @ 09:22:23

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: 4 | Reviews: 0 | Comments: 3 | Citations: 0

Viewed: 4509 times | Downloaded: 734 times

View Download (v3)

EBI_InterProScan (3)

Created: 26/10/08 @ 20:33:34 | Last updated: 01/04/11 @ 08:52:28

Credits: Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

Note: the WSInterProScan web service used by this workflow is no longer available haveing been replaced by the EMBL-EBI's InterProScan (REST) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_rest) and InterProScan (SOAP) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_soap) web services. Thus the workflow described here no longer works, see the alternative workflows for the InterProScan (SOAP) service for workflows which use the new services. Perform an InterProScan ...

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

Viewed: 1640 times | Downloaded: 440 times

View Download (v4)

QR code (matrix code) generator (4)

Created: 07/10/07 @ 17:17:03 | Last updated: 15/08/12 @ 10:40:51

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: 1.5 / 5 (2 ratings) | Versions: 4 | Reviews: 0 | Comments: 0 | Citations: 1

Viewed: 1238 times | Downloaded: 430 times

View Download (v4)

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

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: 1657 times | Downloaded: 486 times

View Download (v5)

Entrez Gene to KEGG Pathway (5)

Created: 04/12/09 @ 16:04:38 | Last updated: 30/11/10 @ 12:18:53

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: 5 | Reviews: 0 | Comments: 2 | Citations: 0

Viewed: 1422 times | Downloaded: 571 times

View Download (v4)

BiomartAndEMBOSSAnalysis (4)

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: 1349 times | Downloaded: 468 times

View Download (v1)

Workflow for Protein Sequence Analysis (1)

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: 4.0 / 5 (2 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 1924 times | Downloaded: 513 times

View Download (v1)

Example of a conditional execution workflow (1)

Created: 05/03/08 @ 13:55:45 | Last updated: 23/05/12 @ 11:18:50

Credits: Tomoinn

License: Creative Commons Attribution 3.0 Unported License

If the input is true then the string 'foo' is emited, if false then 'bar'. Just a simple example to show how the monster works, so to speak. Note that this type of workflow is not suitable for Taverna 2. An alternative mechanism is recommended.

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

Viewed: 1831 times | Downloaded: 566 times

View Download (v3)

Success-Abandonment-Classification (3)

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: 5.0 / 5 (2 ratings) | Versions: 3 | Reviews: 0 | Comments: 1 | Citations: 0

Viewed: 2173 times | Downloaded: 6712 times