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Items tagged with "shim" (13)

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Groups (1)

Network-member myExperimentBeanshellCollection

Unique name: myExperimentBeanshellCollection
Created: Thursday 06 March 2008 @ 11:41:29 (GMT)

Group for development, curation and maintenance of collections of generic Beanshell processors. Join this group if you have some cool Beanshells that you want to share! Please add your Beanshells to the myExperimentBeanshellCollection workflow and don't create new workflows for this purpose. (It's not fun to load dozens of workflows manually to load a fragmented collection of Beanshells.) If t...

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Workflows (12)
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

Tags (12):

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

Tags (22):

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

Tags (18):

Original Uploader

Workflow Entrez Gene to KEGG Pathway (5)

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

Viewed: 1282 times | Downloaded: 504 times

Tags (9):

Original Uploader

Workflow Remove null values (2)

Created: 03/10/07 @ 18:36:05 | Last updated: 13/11/07 @ 16:20:42

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

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This workflow removes any null values from a list of strings

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

Viewed: 80 times | Downloaded: 58 times

Tags (4):

Original Uploader

Workflow Microarray CEL file to candidate pathways (2)

Created: 08/02/08 @ 14:17:23 | Last updated: 13/02/09 @ 11:29:52

Credits: User Paul Fisher User Saeedeh

License: Creative Commons Attribution-Share Alike 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 retruned 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 ch...

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

Viewed: 296 times | Downloaded: 5 times

Tags (17):

Original Uploader

Workflow Human Microarray Analysis (1)

Created: 08/02/08 @ 14:30:17 | Last updated: 03/12/09 @ 16:50:29

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow takes in probesets from and AffyMetrix  Affy HG U133A micorarray experiment and returns: genes ; gene start and end positions; chromosome where genes reside; ensembl trasncripts; SwissProt ids. The final output of the workflow is a list of candidate pathways which are linked to the genes expressed in the microarray data.   Example input for this workflow is: 212283_at 221634_at 220399_at  

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

Viewed: 293 times | Downloaded: 4 times

Tags (17):

Original Uploader

Workflow GBSeq test (2)

Created: 05/03/08 @ 14:15:35 | Last updated: 31/03/08 @ 15:55:09

Credits: User Franck Tanoh

License: Creative Commons Attribution 3.0 Unported License

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This workflow retrieves nucleotide and protein sequences with the literature and references associated to them given a protein and a nucleotide id.

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

Viewed: 249 times | Downloaded: 93 times

Tags (9):

Original Uploader

Workflow myExperimentBeanshellCollection (2)

Created: 06/03/08 @ 11:46:11 | Last updated: 25/03/08 @ 16:23:24

Credits: Network-member myExperimentBeanshellCollection

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Public collection of generic Beanshells curated by the myExperimentBeanshellCollection group on myExperiment. Visit http://www.myexperiment.org for details and updates. To use this collection of beanshells in Taverna: Right click "Available Processors" in the "Design Perspective" Choose "Add new Workflow scavenger..." Provide the URL to this beanshell collection on www.myExperiment.org or if you downloaded this to your hard disk, provide a "file" URL to the absolute path of this file (O...

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

Viewed: 221 times | Downloaded: 108 times

Tags (2):

Original Uploader

Workflow Extract lists from a tab-delimited spreads... (1)

Created: 17/10/08 @ 15:49:50 | Last updated: 18/10/08 @ 21:20:52

Credits: User Andrew Gibson

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow takes a spreadsheet exported as a tab delimited file, such as an Excel spreadsheet. The style is expected as a matrix of data with the first row containing the column names and the first column containing the row names (see below). The top left cell is discarded. The workflow outputs three lists. A list of column names, a list of row names, and a two deep list of data points. The first list is a list of the rows and the sublist is a list of values of the cells from the columns....

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

Viewed: 131 times | Downloaded: 48 times

Tags (3):

Original Uploader

Workflow retry-example (1)

Created: 08/11/10 @ 13:37:33 | Last updated: 08/11/10 @ 13:44:33

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow executes a local beanshell script that has been programmed to fail on some iterations. It demonstrates the advantages of setting retries in your workflows to make them more robust

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

Viewed: 38 times | Downloaded: 20 times

Tags (3):

Original Uploader

Workflow Using a Create_List script with a dot-prod... (1)

Created: 02/02/11 @ 14:39:20 | Last updated: 02/02/11 @ 14:39:22

Credits: User Stian Soiland-Reyes

License: Creative Commons Attribution 3.0 Unported License

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Create_lots_of_strings gives implicit iteration over the service add_a_and_b - assume this is a service that returns two values which you now want to keep in a list [a,b]. The shim Create_list takes two single inputs, and returns a list of [in1, in2]. Configured with the Dot product list strategy it means that it will pipeline out [a1,b1], [a2,b2], [a3,b3] etc.Create_lots_of_strings gives implicit iteration over the service add_a_and_b - assume this is a service that returns two values which...

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

Viewed: 18 times | Downloaded: 11 times

Tags (3):

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Non-Information Resource URI: http://alpha.myexperiment.org/tags/462


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