Content from the myGrid group

EBI_InterproScan_NewServices (1)

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This workflow performs an interproscan at the EBI on sequences provided as input. The output is provided as text, xml or png. 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: 2011-07-12 | Last updated: 2011-07-12

Credits: Alan Williams Katy Wolstencroft

Attributions: EBI_InterproScan_NewServices

BiomartAndEMBOSSDisease (2)

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

Created: 2011-07-12 | Last updated: 2012-03-19

Credits: Katy Wolstencroft

Attributions: BiomartAndEMBOSSDisease

Using a Create_List script with a dot-prod... (1)

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Create_lots_of_strings gives implicit iteration over the service add_a_and_b - assume this is a service that returns two values which you now want to keep in a list [a,b]. The shim Create_list takes two single inputs, and returns a list of [in1, in2]. Configured with the Dot product list strategy it means that it will pipeline out [a1,b1], [a2,b2], [a3,b3] etc.Create_lots_of_strings gives implicit iteration over the service add_a_and_b - assume this is a service that returns two values which...

Created: 2011-02-02 | Last updated: 2011-02-02

Credits: Stian Soiland-Reyes

Biomart and Blast (1)

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Perform Rodent BLAST sequence alignments (using DDBJ Blast) on the gene sequences for a (semi-random) selection of genes from Human sapiens chromosome 22. (Using Biomart) Referenced in the Taverna knowledge blog.

Created: 2010-12-13 | Last updated: 2010-12-13

Attributions: BLAST using DDBJ service

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Example R workflows

Created: 2010-12-13 10:44:04 | Last updated: 2010-12-13 16:28:58

10 items in this pack

Comments: 0 | Viewed: 97 times | Downloaded: 40 times

R generic example (1)

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This workflow shows how string vectors can be used to transfer a complex R object (in this case a matrix) between Rshell services

Created: 2010-11-29

Credits: Alan Williams

R Text-file example (1)

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This workflow contains two services. The file_writer uses a File in R to output a string. The file_reader uses a File in R to input a string, the contents of which are output.

Created: 2010-11-29 | Last updated: 2010-11-29

Credits: Alan Williams

R PNG-value example (2)

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This workflow produces a PNG plot on the figure port.

Created: 2010-11-29 | Last updated: 2010-11-29

Credits: Alan Williams

R integer vector example (1)

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This workflow takes a list of integer values and returns a list containing 100 modulus the list's elements, and the sum of the input list's elements.

Created: 2010-11-29 | Last updated: 2010-11-29

Credits: Alan Williams

R integer workflow (1)

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This workflow uses an Rshell service to calculate 100 modulus the integer input

Created: 2010-11-29

Credits: Alan Williams

R string vector example (1)

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The workflow takes a list of strings and outputs a list contains the lower-cased versions of the input elements, and also a concatenation of the input elements

Created: 2010-11-26 | Last updated: 2010-11-26

Credits: Alan Williams

R integer vector example (1)

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This workflow takes a list of integer values and returns a list containing the square of the input list's elements, and the sum of the input list's elements.

Created: 2010-11-26 | Last updated: 2010-11-26

Credits: Alan Williams

R logical vector workflow (1)

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The workflow returns a list containing the logical inversion of the logical vector input

Created: 2010-11-26 | Last updated: 2010-11-26

Credits: Alan Williams

R string workflow (1)

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This workflow determines the lower case version of the input string.

Created: 2010-11-26 | Last updated: 2010-11-26

Credits: Alan Williams

R numeric workflow (1)

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This workflow uses an Rshell service to calculate the square of a numeric inputThis workflow uses an

Created: 2010-11-26

Credits: Alan Williams

R logical workflow (1)

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Checks what the logical_input is in R. For an logical_input of TRUE - is_false should be FALSE and is_true TRUE FALSE - is_false should be TRUE and is_true FALSE For any other input values, is_false and is_true should both be NA

Created: 2010-11-26 | Last updated: 2010-11-26

Credits: Alan Williams

Ask - title and message parameters (1)

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The ask service displays a prompt with 'Some title' and the prompt message 'Some message'. If the user presses cancel, then a service failure is generated. If the user presses OK then their input, even if it is empty, is passed to the answer port of the ask service and so to the output of the workflow.

Created: 2010-10-29

Ask - just title parameter (1)

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The ask service displays a prompt with the title 'Some title' but no prompt message. If the user presses cancel, then a service failure is generated. If the user presses OK then their input, even if it is empty, is passed to the answer port of the ask service and so to the output of the workflow.

Created: 2010-10-29 | Last updated: 2010-10-29

Ask - just message parameter (1)

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The ask service displays a prompt with no title but with the prompt message 'Some message'. If the user presses cancel, then a service failure is generated. If the user presses OK then their input, even if it is empty, is passed to the answer port of the ask service and so to the output of the workflow.

Created: 2010-10-29

Ask - no parameters (1)

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The ask service displays a prompt with no title and no prompt message. If the user presses cancel, then a service failure is generated. If the user presses OK then their input, even if it is empty, is passed to the answer port of the ask service and so to the output of the workflow.

Created: 2010-10-29

String list union - yielding empty list (1)

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The string list union service takes in two empty lists [] and [] and returns an empty list [].

Created: 2010-10-29 | Last updated: 2010-10-29

String list union - yielding non-empty list (1)

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The string list union service takes in ['a','b','c'] and ['a','e','c'] and returns a list equivalent to ['a','b','c','e'].

Created: 2010-10-29

String list intersection - yielding empty ... (1)

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The string list intersection service takes in ['a','b','c'] and ['x','y','z'] and returns the empty list [].

Created: 2010-10-29

String list intersection - yielding non em... (1)

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The string list intersection service takes in ['a','b','c'] and ['a','e','c] and returns the list ['a','c'].

Created: 2010-10-29

String list difference - yielding empty list (1)

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The string list difference service takes in ['a','b','c'] and ['a','c','b'] and returns the empty list [].

Created: 2010-10-29