Workflows

DemoWorkflow (1)

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 Demo Workflow

Created: 2012-03-22 | Last updated: 2012-03-22

Credits: Jribault

Get Pathway-Genes and gene description by ... (2)

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Given a specific entrez gene id, returns the pathways that this gene participates in and for each of those pathways which genes (including their description) are associated with.

Created: 2012-03-27 | Last updated: 2012-04-03

Credits: Eleni

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

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

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

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

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

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

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 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 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

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

Fetch today's xkcd comic (1)

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Use the local services and some filtering operations to fetch the comic strip image from http://xkcd.com/ Based on the FetchDailyDilbert workflow.

Created: 2012-04-05

Credits: Alan Williams

Fetch Dragon images from BioMoby (1)

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Fetch images and annotations of snapdragons

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

Credits: Alan Williams

GBSeq test (1)

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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.

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

Credits: Alan Williams

Hello Anyone (1)

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An extension to helloworld.t2flow - this workflow takes a workflow input "name" which is combined with the string constant "Hello, " using the local worker "Concatenate two strings", and outputs the produced string to the workflow output "greeting".

Created: 2012-04-05 | Last updated: 2014-03-03

Credits: Alan Williams

Hello World (1)

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One of the simplest workflows possible. No workflow input ports, a single workflow output port "greeting", outputting "Hello, world!" as produced by the String Constant "hello".

Created: 2012-04-05 | Last updated: 2014-03-03

Credits: Alan Williams

Multiple choice quiz (1)

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A fun example workflow showing user-interaction and service looping

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

Credits: Alan Williams

Numerically adding two values. (1)

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This workflow relies on a Unix system. It wraps the "bc" command line calculator. It downloads the calculation script from a URL.

Created: 2012-04-05

Credits: Alan Williams

Pipelined list iteration (1)

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Perform multiple iterations of services in order to show pipelining

Created: 2012-04-05

Credits: Alan Williams

Render gene via BioGPS (3)

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This workflow uses the REST API of BioGPS to list the plugins and then allow the user to select which plugin to use to display the input gene id

Created: 2012-04-05 | Last updated: 2012-05-23

Credits: Alan Williams

Retrieve sequence in EMBL format (1)

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

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

Credits: Alan Williams

Secure REST service call example (2)

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This is an example of a workflow that contains a call to a secure REST service that requires user to authenticate with HTTP Basic Authentication. You can use testuser/testpasswd as username and password for authentication when running the workflow.

Created: 2012-04-05 | Last updated: 2014-01-16

Credits: Alan Williams

Secure Web service call example (2)

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This is an example of a workflow that contains a call to a secure Web service that runs behind HTTPS and requires user to authenticate. The first thing you can expect to see is a pop up dialog asking if you trust the Web service to be invoked over HTTPS. You can use testuser/testpasswd as username and password for authentication when running the workflow. To see where the security is being configured, right-click the service in the diagram and select "Configure security" from the menu. You ...

Created: 2012-04-05 | Last updated: 2013-06-11

Credits: Alan Williams

Simple Python example (1)

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This workflow generates a random number within the range 0 to 100. The generation is done by a python script. The workflow assumes that python is in the path.

Created: 2012-04-05

Credits: Alan Williams