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Staged iteration strategy (1)

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Consider two lists A and B, of equal size 3. A[1] corresponds to B[1], A[2] to B[2], etc, for instance A are image scans from 2007 and B from 2008, and the index indicates the patient number. A = [a0, a1, a2] B = [b0, b1, b2] There's then two lists of possible parameters P and Q, of different lengths, P has 2 and Q has 4 items. P = [p0, p1] Q = [q0, q1, q2, q3] Each of the A items should be processed in ap using each of the P parameters, and each of the B items ...

Created: 2008-05-07 | Last updated: 2008-05-07

Credits: Stian Soiland-Reyes

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Trivial workflow which will initially fail, retry twice then fall over to the alternative specified for the FailingThing process.

Created: 2007-11-06 | Last updated: 2007-11-20

Credits: Antoon Goderis Carole Goble A. Random Scientist try it out

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Basic eSearch/eFetch cycle (1)

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This is a basic eSearch/eFetch workflow created with taverna and using eUtils from NCBI. It accepts a query term as input (at the moment, for testing purposes, this is a fixed string), interrogate eSearch to retrieve the list of related sequences on the Nucleotide database, and use eFetch to retrieve the corresponding sequences. I wrote this workflow one year ago, when I was trying to understand how taverna and eUtils work; I suspect it broken, and of course it could be enhanced, so I am ...

Created: 2008-12-04 | Last updated: 2008-12-04

Credits: Giovanni Dall'Olio

Execute cmd line app - unix - /bin/ls -R o... (1)

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Note that this workflow only works on Unix systems. The get_temporary_directory beanshell returns the path to the directory in which temporary files are held. This value is passed to the create_and_populate_list beanshell which creates a list of '-R' and the path. The resultant list is passed to the args port of the Execute_cmd_line_app service. The command port of that service has been defaulted to '/bin/ls'. The execute_cmd_line_app service runs the /bin/ls -R command on the temporary ...

Created: 2008-09-27

Credits: Alan Williams

Execute cmd line app - unix - /bin/ls of t... (1)

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Note that this workflow only works on Unix systems. The get_temporary_directory beanshell returns the path to the directory in which temporary files are held. This value is passed to the args port of the execute_cmd_line_app service. The command port of that service has been defaulted to '/bin/ls'. The execute_cmd_line_app service runs the /bin/ls command on the temporary directory. The result is passed to its result port and then to the out port of the workflow.

Created: 2008-09-27

Credits: Alan Williams

querySWS_minimalQuery (2)

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SRS by WS (SWS) is a set of Web Services allowing to retrieve database entries from libraries included in public SRS sites. The querySWS service implement a search on the basis of the database name (lib) and the term to be searched (query). It automatically identifies the best site to query. Additional parameters include in_fields (in which part of the record the terms are searched), out_fields (which information is returned) and site (the SRS site). This workflow is just a demonstration ...

Created: 2007-10-03

Tuiuiu asynchronous workflow (1)

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Tuiuiu removes from a sequence or from a set of sequences areas as large as possible that do not contain researched repeats. Tuiuiu is used as a preliminary step before applying a multiple local aligner tool. Modeling and algorithmic details are provided in the following paper. Please, cite this paper if you use Tuiuiu. P. Peterlongo, G. Sacomoto, A. Pereira do Lago, N. Pisanti, M.-F. Sagot Lossless filter for multiple repeats with bounded edit distance BMC Algorithms for Mole...

Created: 2009-06-29 | Last updated: 2009-06-29

Credits: http://osallou.myopenid.com/ GenOUEST Platform

Kegg_DrugID (1)

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 This workflow accepts looks up drug identifiers from KEGG given a pathway identifier. You can enter a pathway ID in the form path:map07026

Created: 2009-03-18 | Last updated: 2009-03-18

Credits: Rory

Sample grid workflow (1)

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This is a sample workflow submitting jobs to the EGEE grid using the Generic Application Service Wrapper (GASW). The job submission service has to be installed locally.

Created: 2008-10-24 | Last updated: 2008-10-31

Credits: Glatard

Extract elements from a list - single elem... (1)

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The extract_elements_from_a_list is passed the list ['a','b','c','d','e']. The fromIndex is 2 and the toIndex is 3, so the service outputs the single element list ['c'].

Created: 2008-09-29

Credits: Alan Williams