Workflows

Using CQL to query protein sequence data (1)

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To query protein sequence infomation out of 3 caGrid data services: caBIO, CPAS and GridPIR Adapted from http://www.myexperiment.org/workflows/600

Created: 2009-05-07

Credits: Stian Soiland-Reyes

Attributions: Using CQL to query protein sequence data

DOI Record Generator (1)

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This workflow generates DOI record files for deposit, using data set metadata for the FLOSSmole project. It reads in an input file generated from a SQL query from an eprints database, and transforms the parts of the source file as necessary to create a comprehensive DOI deposit record. It also generates DOIs for the data sets. These metadata are inserted into an XML record template (based on the std-doi.xsd schema) and the individual resources are aggregated into a single file.

Created: 2009-04-29

Credits: Andrea Wiggins

Attributions: Data Set Metadata Generator

Run XMPP cloud services. (2)

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Basic workflow indicating how a XMPP service can be called with XML input and output. Source code for the activity is available from: github.com/egonw/xws-taverna/tree/master That page explains you how to install the plugin you must install on top of Taverna 2.0. The workflow will not work otherwise.

Created: 2009-04-25 | Last updated: 2010-03-22

Credits: Egon Willighagen

Workflow Pattern - Structured Discriminato... (1)

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This workflow is an alternative GWorkflowDL representation of a structured discriminator (1-out-of-M Join) that invokes C after the first invocation of A or B (M=2). All next (M-1) invocations of A or B are ignored for the same data group. Other tokens on the place "begin" can be processed recurrently if they belong to another data group. Please note that the transitions "C" and "ignore" have different priorities (not shown in the graph) that make the net determ...

Created: 2009-01-20

Credits: Andreas Hoheisel

Workflow Pattern - Structured Loop (C) (2)

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This workflow is a GWorkflowDL representation of a structured loop that counts from 0 to 99.   This workflow is equivalent to the following pseudo code: for ( i:=0; i Please remark that this demonstration workflow does not invoke any external services at all.

Created: 2008-12-09

Credits: Andreas Hoheisel

Attributions: Workflow Pattern - Structured Loop (B)

Download pathways for external references ... (2)

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Takes a list of external references to genes/proteins/metabolites, finds all pathways on WikiPathways that contain one of the given genes/proteins/metabolites and downloads them in a given file format.

Created: 2008-11-14

Credits: Thomaskelder

Attributions: CloneItemsInList

AppendToFile (2)

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Processor to add content to a (existing)  file. The content is added to the end of the file. The inputs: Filename: the file name of a file, if the file does not exists, a new file is added Content: the string to append NewLine [default = true]: if true, a newline is added to the end of the line (useful if you want to add a record each time)   The processor supports Multi-Threading since version 2.

Created: 2008-11-11 | Last updated: 2008-11-11

Credits: Wassinki

Blat against ENSEMBLE Danio_rerio_Genome (1)

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The blat workflow invokes the blat services provided at www.bioinformatics.nl (author Pieter Neerincx). As input, it takes a database name (for example, Danio_rerio_Genome for Zebra Fish) and one or more sequences in Fasta format. The output will be a tab separated output of the blat. An eValue string constant is added to filter on the e-Value. Note, the e-Value is not exactly the same as the blast e-Value. To run this workflow, a certificate to access www.bioinformatics.nl needs to instal...

Created: 2008-10-15 | Last updated: 2008-10-15

Credits: Wassinki

Data Set Metadata Generator (1)

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This workflow generates ePrints XML import files with data set metadata for the FLOSSmole project. It reads in an input file generated from a Notre Dame SourceForge dump SQL query and uses regular expressions to parse the filename for the data set's source repository, download URL, and basic description. It also translates the epoch date into a sql format suitable for import, and the file size from bytes into larger units, e.g. GB, MB, etc. These data are inserted into an XML eprint record te...

Created: 2008-08-19 | Last updated: 2008-08-19

Credits: Andrea Wiggins

Retrieve Protein Sequence (1)

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Retrieves a protein sequence in Fasta format from GenBank, given a GenBank identifier. Example input for this workflow is: EDL10223.1

Created: 2008-07-30 | Last updated: 2009-12-03

Credits: Katy Wolstencroft