Alan Williams' Workflows

Fetch PDB flatfile from RCSB server (1)

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Given an identifier such as '1crn' fetches the PDB format flatfile from the RCSB

Created: 2012-04-05

Credits: Alan Williams

Example workflow for REST and XPath activi... (1)

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This workflow fetches weather forecast for the user-specified location. First of all it uses the provided location name to obtain a WOEID ("Where On Earth ID") of that location, then uses that unique identifier to fetch the weather forecast from Yahoo server. Multiple results may be obtained in case there is no unique translation of the location to a WOEID. REST activity is used to perform HTTP requests and fetch data from remote servers; XPath activity is then used to parse the XML data a...

Created: 2012-04-05 | Last updated: 2012-04-05

Credits: Alan Williams

Example of explicit looping (1)

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This workflow demonstrates how a nested workflow can be called an explicit number of times. Note that the loop iterator does not need to be used in the logic of the loop contents. It can be used as a sentinel (see the conditional workflow)

Created: 2012-04-05

Credits: Alan Williams

Example of conditional invocation (1)

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This workflow demonstrates how nested workflows can be conditionally invoked

Created: 2012-04-05 | Last updated: 2012-04-05

Credits: Alan Williams

Example for external tools with zip and unzip (1)

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This workflow only works on a Unix machine. This workflow takes a fixed URL from which a text file is downloaded (output as Original_file). That file is zipped (output as Zipped_File) and then unzipped again (output as Unzipped_File). The orginal file and the unzipped version are then diff'd/

Created: 2012-04-05 | Last updated: 2012-04-05

Credits: Alan Williams

EBI_InterproScan_NewServices (2)

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This workflow performs an interproscan at the EBI on sequences provided as input. The output is provided as text and xml. This workflow uses the new EBI services, which are asynchronous and require looping over the nested workflow (Status) until the workflow has finished. Many of the EBI services now work in this way, so you can use this workflow as an example of the invocation pattern and looping configuration.

Created: 2012-04-05 | Last updated: 2014-04-09

Credits: Alan Williams

Demonstration of configurable iteration (1)

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This workflow shows the use of the iteration strategy editor to ensure that only relevant combinations of inputs are used during an implicit iteration.

Created: 2012-04-05 | Last updated: 2012-04-05

Credits: Alan Williams

BioMoby tutorial workflow (1)

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A workflow from part of the BioMoby tutorial

Created: 2012-04-05 | Last updated: 2012-04-05

Credits: Alan Williams

BiomartAndEMBOSSMouseRat (1)

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This workflow retrieves all genes on human chromosome 22 that are associated with a disease and aligns the upstream regions of the mouse and rat homologues. The alignments are plotted and corresponding sequence ids are also returned.

Created: 2012-04-05

Credits: Alan Williams

BiomartAndEMBOSSMouseRat (1)

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This workflow retrieves all genes on human chromosome 22 that are associated with a disease and aligns the upstream regions of the mouse and rat homologues. The alignments are plotted and corresponding sequence ids are also returned.

Created: 2012-04-05

Credits: Katy Wolstencroft