Cd User: Ian Laycock

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Name: Ian Laycock

Joined: Wednesday 10 March 2010 @ 18:53:41 (GMT)

Last seen: Friday 02 July 2010 @ 11:24:18 (GMT)

Email (public): Not specified

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Location: Congo, the Democratic Republic of the

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7 Workflows

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Ian Laycock has been credited 9 times

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Workflow

Taverna 2

Original Uploader

Workflow getGoTermsFromUniprotId (v1)

Created: 09/07/09 @ 07:23:08 | Last updated: 09/07/09 @ 07:24:19

Credits: User Jelena (Obradovic) Dreskai

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

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This service is invoking UniprotAPI to retrive GOTerms associated with the list of UniprotIds provided in the input. It is using Axis2 webservice created using UniprotAPI and published with wsdl. Example uniprotIds for input: "A2ABK7", "A2ABK8", "A2ABK9"

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Workflow

Taverna 1

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Workflow fetchEnsemblSeqsAndBlast (v1)

Created: 18/04/08 @ 11:53:19 | Last updated: 18/04/08 @ 11:58:30

Credits: User Bela

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow allows you to configure a BioMart query to fetch sequences you want from Ensembl. These sequences are retrieved and a blast database of them is created (by default, in the directory you ran taverna from). Warning: This workflow assumes that you have blastall and formatdb installed on the machine, and that by default, these are both found or linked in /usr/local/bin. It also assumes that you have write permission to the directory you have run taverna from. The beanshells "creat...

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Workflow

Taverna 1

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Workflow Simplify a BLAST text file (v2)

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

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Workflow

Taverna 2

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Workflow Get Kegg Pathway information (v1)

Created: 10/03/10 @ 17:15:47 | Last updated: 10/03/10 @ 17:18:47

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow gets a series of information relating to a list of KEGG pathways supplied to it. It also removes any null values from a list of strings. Example input: path:mmu04010 path:mmu05014

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Workflow

Taverna 1

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Workflow Entrez Gene to KEGG Pathway (v5)

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

Credits: User Paul Fisher

License: Creative Commons Attribution 3.0 Unported License

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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

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Workflow

Taverna 1

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Workflow metabolic_pathway.xml (v1)

Created: 12/07/08 @ 10:13:37 | Last updated: 12/07/08 @ 10:13:50

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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A list of Kegg entires are supplied to the Kegg database which then retrieves the associated metabolic pathways for each entry supplied. e.g. Ids takes in a value of 351, whilst abbr takes in a value of hsa. Thus hsa:351 corresponds to neurodegenerative disorders and alzheimers disease pathways. [fisherp@cs.man.ac.uk]

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Workflow

Taverna 1

Original Uploader

Workflow bconv (v1)

Created: 29/09/08 @ 12:13:41 | Last updated: 29/09/08 @ 12:29:01

Credits: User Franck Tanoh

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Converts external IDs to KEGG IDs.External database:  NCBI GI, NCBI GeneID, GenBank , UniGene , OMIM. Database prefix: ncbi-gi:, ncbi-geneid:, genbank: ,unigene: , uniprot: , omim: Example of input parameter: ncbi-gi:10047090 ncbi-geneid:14751

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Workflow

Taverna 1

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Workflow Retrieve Pathways and Compound information from KEGG (v1)

Created: 30/03/09 @ 09:22:36 | Last updated: 30/03/09 @ 09:39:23

Credits: User Michael Gerlich

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Given a KEGG compound identifier (e.g. cpd:C00905), this workflow queries KEGG DB for pathways and compound information for each of these compounds. As the KEGG pathway service tries to find pathways which contain all input compounds, the input list is split up to circumvent this behaviour and to search for only one compound in a pathway at a time. Compounds identified in pathways are marked as red in the resulting pathway image.

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Workflow

Taverna 1

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Workflow color_pathway_by_objects (v1)

Created: 01/10/08 @ 17:03:41 | Last updated: 01/10/08 @ 17:06:10

Credits: User Franck Tanoh

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Color given objects on a pathway map with specified colors and return the URL of the colored image. In the KEGG pathway maps, a gene or enzyme is represented by a rectangle and a compound is shown as a small circle. Example of input: pathway_id: path:eco00260 object_list: (to add as list) eco:b0514 eco:b2913 fg_color: (to add as list) blue orange bg_color: (to add as list) red orange

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Workflow

Taverna 1

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Workflow NCBI Gi to Kegg Pathways (v1)

Created: 08/06/09 @ 18:39:38 | Last updated: 14/12/09 @ 11:51:20

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow converts a list of NCBI gi numbers and  converts them to a list of KEGG genes. Those KEGG gene ids are subsequently turned into KEGG pathway identifiers and descriptions. It also removes any null values from a list of strings. Example input for this workflow is as follows (new line separated): gi:215422388 gi:120407068

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Workflow

Taverna 1

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Workflow Get Kegg Gene information (v2)

Created: 26/01/09 @ 18:06:12 | Last updated: 14/12/09 @ 12:05:21

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow gets a series of information relating to a list of KEGG genes supplied to it. It also removes any null values from a list of strings.   Example input for this workflow is given below (new line separated): mmu:13163 hsa:1616

Rating: 5.0 / 5 (1 rating) | Versions: 2 | Reviews: 0 | Comments: 1 | Citations: 0

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Workflow

Taverna 1

Original Uploader

Workflow keggID to Kegg pathways with BioMoby services (v3)

Created: 03/10/07 @ 18:36:22 | Last updated: 05/03/08 @ 13:59:55

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

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This workflow retrieves KEGG pathway id and image given a KEGG gene id. e.g hsa:6402 or eco:b0002

Rating: 4.0 / 5 (1 rating) | Versions: 3 | Reviews: 0 | Comments: 2 | Citations: 0

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Workflow

Taverna 1

Original Uploader

Workflow Gi_to_pathway.xml (v1)

Created: 12/07/08 @ 09:20:04 | Last updated: 12/07/08 @ 20:07:57

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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

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