Workflows

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Showing 1566 results. Use the filters on the left and the search box below to refine the results.

Workflow Pipelined list iteration (1)

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Perform multiple iterations of services in order to show pipelining

Created: 2009-12-15

Credits: User Alan Williams

Workflow Retrieve sequence in EMBL format (1)

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This workflow retrieves a sequence associated with its features in embl format

Created: 2009-12-15

Credits: User Alan Williams

Workflow Fetch Dragon images from BioMoby (2)

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Fetch images and annotations of snapdragons

Created: 2009-12-15 | Last updated: 2010-07-14

Credits: User EdwardKawas

Workflow Pattern: Return errors instead of null (1)

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 As Taverna can't (currently) handle null (see http://www.mygrid.org.uk/dev/issues/browse/TAV-653) - in Taverna 2 one can instead return exceptions on individual ports and inside lists. Exceptions are registered as error documents by Taverna, and are passed along. The ErrorBounce layer of processors downstream will prevent execution if they see this 'null'-exception - as showed in this example that the string concatination is just run for the two list elements that are not exceptio...

Created: 2010-01-04 | Last updated: 2010-01-04

Credits: User Stian Soiland-Reyes

Workflow Dummy example of looping (3)

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Example of looping over asynchronous services. The dummy beanshell scripts represents the operations of an asynchronous submit-status-results style service, such as EBI's InterProScan and NCBI Blast. createJob creates a temporary file with the content "0". Filename retuirned as a "job ID". checkStatus reads the job, and return state "RUNNING" as long as the content is less than 10, increasing the number for each call. (As no actual job is being run) getResults reads the file content, with...

Created: 2010-01-27 | Last updated: 2013-10-08

Credits: User Stian Soiland-Reyes

Workflow Rdfise Riken SciNes Database Repository [m... (1)

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This workflow rdfise Riken SciNes Database Repository available at https://database.riken.jp/sw/links/en/crib151s2i/. There is a bug with main page listing databases: version 2p and 3p are similar to 1p.

Created: 2010-02-01 | Last updated: 2010-02-01

Credits: User Francois Belleau

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Workflow SBML to SBML shortand converter (1)

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converts SBML document to SBML shorthand via BASIS web services BASIS: www.basis.ncl.ac.uk:81/Basis SBML shorthand: http://www.staff.ncl.ac.uk/d.j.wilkinson/software/sbml-sh/

Created: 2010-02-03 | Last updated: 2010-02-03

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Workflow SBML shorthand to SBML converter (1)

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converts SBML shorthand to SBML document via BASIS web services BASIS: www.basis.ncl.ac.uk:81/Basis SBML shorthand: http://www.staff.ncl.ac.uk/d.j.wilkinson/software/sbml-sh/

Created: 2010-02-03 | Last updated: 2010-02-03

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Workflow CaliBayes_Client (1)

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A workflow for consuming CaliBayes web services. CaliBayes: www.calibayes.ncl.ac.uk

Created: 2010-02-03 | Last updated: 2010-02-03

Workflow Get Gene Ids for Human (1)

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This workflow gets a list of gene ids (number depending on Ret_Max_value variable) for Homo sapiens. The species may be changed according to that desired, by altering the term_value string constant

Created: 2010-02-04 | Last updated: 2010-02-04

Credits: User Paul Fisher

Workflow PDB2KEGG step 1done during BH2010 (1)

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No description

Created: 2010-02-13

Credits: User Francois Belleau

Workflow LipidMaps Query (1)

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This workflow retrieves database entries from LipidMaps for given exact mass and tolerance inputs.

Created: 2010-02-16

Workflow Clean plain text (ASCII) (1)

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This workflow will remove any XML-invalid and non-ASCII characters (e.g. for sending to the ASCII-only Termine service) from any text supplied to the input port. This is a workflow component, designed to be used as a nested workflow inside a larger text mining or text processing workflow.

Created: 2010-02-18 | Last updated: 2011-12-13

Credits: User James Eales

Workflow Clean plain text (1)

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This workflow will remove any XML-invalid characters (these characters often appear in the output of PDF to text software) from any text supplied to the input port. This is a workflow component, designed to be used as a nested workflow inside a larger text mining or text processing workflow.  

Created: 2010-02-18 | Last updated: 2011-12-13

Credits: User James Eales

Workflow Load plain text from directory (1)

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This workflow will automate the reading of a set of text files stored in a single directory (the path to which should be supplied as a single input value).  It will assume that the text files are saved using the default character encoding for the system that Taverna is running on.  This is a workflow component, designed to be used as a nested workflow inside a larger text mining or text processing workflow.  

Created: 2010-02-18 | Last updated: 2011-12-13

Credits: User James Eales

Workflow Load PDF from directory (1)

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This workflow will automate the reading of a set of PDF files stored in a single directory (the path to which should be supplied as a single input value). This is a workflow component, designed to be used as a nested workflow inside a larger text mining or text processing workflow.  

Created: 2010-02-19 | Last updated: 2011-12-13

Credits: User James Eales

Workflow PDF to plain text (1)

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This workflow will extract the plain text content of PDF files supplied to the input port.  You can connect the Load PDF from directory workflow to this workflows input. We recommend you send the output from this workflow to the Clean plain text workflow, because the PDF to text process can add characters into the text that are XML-invalid and therefore can not be sent to most services as plain text.  Another way round this problem is to encode the text as Base64 using the handy loc...

Created: 2010-02-19 | Last updated: 2011-12-13

Credits: User James Eales

Workflow Sentence splitting (1)

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This workflow will attempt to split up text into sentences, returning a list of sentences to the output port.  The sentence splitting service makes use of the OpenNLP sentence detector and has been trained to work on english text. This workflow can be used to provide input to the Termine with c-value threshold workflow. This is a workflow component, designed to be used as a nested workflow inside a larger text mining or text processing workflow.

Created: 2010-02-19 | Last updated: 2011-12-13

Credits: User James Eales

Workflow Termine with c-value threshold (1)

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This workflow accepts a list of sentences from a single document and returns the terms found by the TerMine web service. It also allows you to set a threshold c-value score so that only terms with a user-controlled probability (of being a real term) are returned as an output.   To get sentences to supply to this workflow you can use the sentence splitting workflow.  The TerMine service (used in this workflow) only accepts text in ASCII encoding, so you should also use the Clean p...

Created: 2010-02-19 | Last updated: 2011-12-13

Credits: User James Eales

Workflow Terms from collection of PDF files (2)

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This workflow will give you a set of candidate terms for each PDF document in a user-specified directory. You can also specify a c-value threshold that will restrict the terms to those with higher scores. This workflow was created using only nested workflows.  These workflow components work on their own and can be linked together to form more complex workflows such as this. You can view the text mining workflow components in this pack. If you receive errors when running this workflow t...

Created: 2010-02-19 | Last updated: 2011-12-13

Credits: User James Eales

Workflow Terms from collection of text files (1)

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This workflow will give you a set of candidate terms for each text file in a user-specified directory. You can also specify a c-value threshold that will restrict the terms to those with higher scores. This workflow was created using only nested workflows.  These workflow components work on their own and can be linked together to form more complex workflows such as this. You can view the text mining workflow components in this pack. If you receive errors when running this workflow then...

Created: 2010-02-22 | Last updated: 2011-12-13

Credits: User James Eales

Uploader

Workflow Tutorial Taverna (1)

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No description

Created: 2010-02-26 | Last updated: 2010-02-26

Credits: User Rodriguez

Uploader

Workflow Taverna Tutorial2 (1)

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No description

Created: 2010-02-26 | Last updated: 2010-02-26

Credits: User Rodriguez

Attributions: Workflow EBI_InterProScan for Taverna 2

Workflow Transciption (DNA into RNA) (1)

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This workflow allows a user to transcibe DNA into RNA.

Created: 2010-03-05 | Last updated: 2010-03-05

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Workflow Get locations from postcode (1)

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 This workflow will return all the areas that correspond to a postcode. Enter the first part of the postcode only, e.g. SW19

Created: 2010-03-08 | Last updated: 2010-03-08

Credits: User Rory

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