Workflows

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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 Add Mesh String to Biological Process (2)

Created: 03/10/07 @ 18:36:28 | Last updated: 03/12/09 @ 16:42:48

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

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This workflow is designed to add the following MeSH term to the end of a KEGG pathway name: AND "Metabolic Networks and Pathways" [MeSH Terms]   Example input for this service is as follows:   VEGF signaling pathway Hematopoietic cell lineage GnRH signaling pathway Type II diabetes mellitus  

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

Viewed: 419 times | Downloaded: 90 times

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Original Uploader

Workflow Gene annotation pipeline for the Graves di... (2)

Created: 03/10/07 @ 18:36:09 | Last updated: 22/11/07 @ 16:03:15

Credits: User Katy Wolstencroft User Peter Li

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

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This is a revised workflow for the Graves disease scenario gene annotation pipeline used in the myGrid project. The workflow had to be re-written due to the loss of the services invoked in the original workflow.

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

Viewed: 664 times | Downloaded: 218 times

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Original Uploader

Workflow BLAST using DDBJ service (2)

Created: 03/10/07 @ 18:36:06 | Last updated: 03/12/09 @ 16:31:20

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

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Perform a sequence similarity search using the BLAST algorithm through the DDBJ web service.   Example input for this service are given below. query: >MySequence MATDDSIIVLDDDDEDEAAAQPGPSNLPPNPASTGPGPGLSQQATGLSEPRVDGGSS NSGSRKCYKLDNEKLFEEFLELCKTETSDHPEVVPFLHKLQQRAQSVFLASAEFCNIL SRVLARSRKRPAKIYVYINELCTVLKAHSIKKKLNLAPAASTTSEASGPNPPTEPPSDLT NTENTASEASRTRGSRRQIQRLEQLLALYVAEIRRLQEKELDLSELDDPDSSYLQEAR LKRKLIRLFGRLCELKDCSSLTGRVIEQRIPYRGTRYPEVNRRIERLINKPGLDTFPDY GDVLRAVEKAATRHSLGLP...

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

Viewed: 640 times | Downloaded: 234 times

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Original Uploader

Workflow Genome annotation pipeline demonstrator wo... (2)

Created: 03/10/07 @ 18:35:47

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

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Part of a workflow by Hannah Tipney, adapted by Duncan Hull using GenScan, RepeatMasker and BLAST. http://dx.doi.org/10.1093/nar/gkl320

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

Viewed: 592 times | Downloaded: 178 times

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Original Uploader

Workflow Simplify a BLAST text file (2)

Created: 03/10/07 @ 18:36:06 | Last updated: 28/07/09 @ 13:01:45

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

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This workflow simplifies a BLAST text file into identifiers, descriptions and values (P, E-values). In order to extract the relevant ids etc. you need to pass the relevant string into the corresponding port, e.g. the default port being used is gi. This has been passed "gi". For any other ports simply pass in the string the SAME as the port name, e.g. seq_id, p, per etc.

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

Viewed: 392 times | Downloaded: 151 times

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Original Uploader

Workflow EBI InterProScan (2)

Created: 03/10/07 @ 18:35:46

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

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EBI InterProScan. Stop fannying around with BLAST and use InterProScan instead.

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

Viewed: 523 times | Downloaded: 154 times

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Original Uploader

Workflow KEGG pathways common to both QTL and micro... (3)

Created: 24/11/09 @ 17:14:43 | Last updated: 03/12/09 @ 15:28:49

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

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This workflow takes in two lists of KEGG pathway ids. These are designed to come from pathways found from genes in a QTL (Quantitative Trait Loci) region, and from pathways found from genes differentially expressed in a microarray study. By identifying the intersecting pathways from both studies, a more informative picture is obtained of the candidate processes involved in the expression of a phenotype.   Example input for this workflow is given below (as newline separated values). qt...

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

Viewed: 319 times | Downloaded: 136 times

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Original Uploader

Workflow Translate Nucleotide sequence into Peptide... (2)

Created: 03/10/07 @ 18:36:27

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

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Translate Nucleotide sequence into Peptide sequence using EBI Service. Find nucleotide sequence from EBI wsdbfetch(using ref.seq Id NM_005700) 2. Translation nucleotide sequence(from 1) into peptide sequence using EBI EMBOSS4 transeq.

Rating: 2.0 / 5 (1 rating) | Versions: 2 | Reviews: 0 | Comments: 1 | Citations: 0

Viewed: 242 times | Downloaded: 91 times

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Original Uploader

Workflow Perform a search through NCBI eUtils eSearch (3)

Created: 27/11/09 @ 14:44:11 | Last updated: 03/12/09 @ 16:32:26

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

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This workflow takes in a search term and a database (e.g. snp, gene, protein) in which to perfom the search over. The result is an xml file containing summary information about the search term. Example input for this workflow are given below: database: pubmed terms: cancer AND diabetes

Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 8 | Citations: 0

Viewed: 426 times | Downloaded: 212 times

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