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Items tagged with "mygrid" (107)

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Network-member myGrid

Unique name: myGrid
Created: Friday 30 November 2007 @ 12:19:26 (GMT)

People working or contributing to the myGrid project, including the Taverna developers. You do not need to join this group to see the shared items. If you are interested in contributing to myGrid or Taverna development or have questions about Taverna, then please email support@mygrid.org.uk

300 shared items   |   0 announcements

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Network-member Taverna 1.7.1 workflow workbench examples

Unique name: tavernaExamples
Created: Wednesday 05 March 2008 @ 13:45:09 (GMT)

The workflows visible from this group correspond to the examples from the Taverna 1.7.1 workflow workbench

17 shared items   |   0 announcements

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Workflows (103)
Original Uploader

Workflow Example of a conditional execution workflow (1)

Created: 05/03/08 @ 13:55:45 | Last updated: 23/05/12 @ 11:18:50

Credits: User Tomoinn

License: Creative Commons Attribution 3.0 Unported License

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If the input is true then the string 'foo' is emited, if false then 'bar'. Just a simple example to show how the monster works, so to speak. Note that this type of workflow is not suitable for Taverna 2. An alternative mechanism is recommended.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 1 | Citations: 0

Viewed: 1708 times | Downloaded: 500 times

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Workflow BiomartAndEMBOSSAnalysis (4)

Created: 15/09/09 @ 15:11:11

License: Creative Commons Attribution 3.0 Unported License

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Using Biomart and EMBOSS soaplab services, This workflow retrieves a number of sequences from 3 species: mouse, human, rat; align them, and returns a plot of the alignment result. Corresponding sequence ids are also returned.

Rating: 0.0 / 5 (0 ratings) | Versions: 4 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 1256 times | Downloaded: 421 times

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Workflow A workflow version of the EMBOSS tutorial (1)

Created: 05/03/08 @ 14:05:20 | Last updated: 25/03/08 @ 14:43:35

Credits: User Tomoinn

License: Creative Commons Attribution 3.0 Unported License

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Designed to show the use of EMBOSS based Soaplab services from Taverna, this workflow has no inputs as all initial values are specified as string constants. A sequence set is fetched using the seqret tool, then simultaneously scanned for predicted transmembrane regions and subjected to a multiple alignment using emma. This alignment is then plotted to a set of PNG images and also used to build a profile using the prophecy and prophet tools.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 419 times | Downloaded: 144 times

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Workflow Fetch today's xkcd comic (1)

Created: 05/03/08 @ 14:08:52 | Last updated: 07/04/08 @ 13:54:04

Credits: User Tomoinn User Stian Soiland-Reyes

Attributions:

License: Creative Commons Attribution 3.0 Unported License

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

Rating: 4.5 / 5 (2 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 514 times | Downloaded: 188 times

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Original Uploader

Workflow Fetch Dragon images from BioMoby (3)

Created: 05/03/08 @ 14:09:35 | Last updated: 14/07/10 @ 16:46:37

Credits: User Tomoinn

License: Creative Commons Attribution 3.0 Unported License

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Fetch images and annotations of snapdragons

Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 326 times | Downloaded: 112 times

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Original Uploader

Workflow Demonstration of configurable iteration (1)

Created: 05/03/08 @ 14:10:51 | Last updated: 25/03/08 @ 14:40:27

Credits: User Tomoinn

License: Creative Commons Attribution 3.0 Unported License

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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.

Rating: 4.0 / 5 (1 rating) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 296 times | Downloaded: 165 times

Tags (5):

Original Uploader

Workflow Retrieve sequence in EMBL format (3)

Created: 17/06/09 @ 16:51:32

Credits: User Franck Tanoh User Tomoinn User Stuart Owen

License: Creative Commons Attribution 3.0 Unported License

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

Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 330 times | Downloaded: 108 times

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Original Uploader

Workflow Fetch PDB flatfile from RCSB server (1)

Created: 05/03/08 @ 14:13:24 | Last updated: 31/03/08 @ 16:01:41

Credits: User Tomoinn

License: Creative Commons Attribution 3.0 Unported License

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Given an identifier such as '1crn' fetches the PDB format flatfile and returns the corresponding 3D image of the protein.

Rating: 3.0 / 5 (1 rating) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 307 times | Downloaded: 121 times

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Original Uploader

Workflow GBSeq test (2)

Created: 05/03/08 @ 14:15:35 | Last updated: 31/03/08 @ 15:55:09

Credits: User Franck Tanoh

License: Creative Commons Attribution 3.0 Unported License

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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.

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 249 times | Downloaded: 93 times

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Original Uploader

Workflow Byte[] to string - empty value (1)

Created: 27/09/08 @ 16:37:04

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The beanshell converts the empty string '' to a byte array which is then converted back to the empty string '' by the Byte[]_to_string service.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 42 times | Downloaded: 28 times

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Original Uploader

Workflow Choose - no title or message parameters (1)

Created: 27/09/08 @ 16:37:50

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The split_string_into_string_list_by_regular_expression parses the string 'a,b,c,d,e' and outputs the list ['a','b','c','d','e']. The choose service displays a dialog with no title or message. The user is able to choose from the values ['a','b','c','d',e']. When the user presses OK the value the user chose is passed to the answer port of the choose service and so to the output of the workflow.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 25 times | Downloaded: 23 times

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Original Uploader

Workflow Choose - title parameter (1)

Created: 27/09/08 @ 16:38:43

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The split_string_into_string_list_by_regular_expression parses the string 'a,b,c,d,e' and outputs the list ['a','b','c','d','e']. The choose service displays a dialog with 'Some title' but no message. The user is able to choose from the values ['a','b','c','d',e']. When the user presses OK the value the user chose is passed to the answer port of the choose service and so to the output of the workflow.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 23 times | Downloaded: 25 times

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Original Uploader

Workflow Choose - title and message parameters (1)

Created: 27/09/08 @ 16:40:10

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The split_string_into_string_list_by_regular_expression parses the string 'a,b,c,d,e' and outputs the list ['a','b','c','d','e']. The choose service displays a dialog with 'Some title' and with 'Some message'. The user is able to choose from the values ['a','b','c','d',e']. When the user presses OK the value the user chose is passed to the answer port of the choose service and so to the output of the workflow.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 32 times | Downloaded: 23 times

Tags (3):

Original Uploader

Workflow Choose - single element list (1)

Created: 27/09/08 @ 16:40:51

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The split_string_into_string_list_by_regular_expression parses the string 'a' and outputs the list ['a']. The choose service displays a dialog with 'Some title' and 'Some message'. The user is only able to choose the value 'a'. When the user presses OK 'a' is passed to the answer port of the choose service and so to the output of the workflow.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 27 times | Downloaded: 27 times

Tags (3):

Original Uploader

Workflow Concatenate files - echo results and multi... (1)

Created: 27/09/08 @ 16:41:51

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The workflow splits the string 'a,b,c,d,e' into its five elements and saves the individual strings to five temporary files. The file paths to those files are then output by the create_and_populate_temporary_file beanshell. The create_temporary_file beanshell creates a file to which the concatentation can be written. The concatenate_files service concatenates the five files and writes the result to the temporary output file. Because the displayresults port has been given a default value of...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 51 times | Downloaded: 27 times

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Workflow Concatenate files - echo results but no files (1)

Created: 27/09/08 @ 16:42:40

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The split_string_into_string_list_by_regular_expresson outputs an empty list since the string to be split is defaulted to ''. As there are no input values, the create_and_populate_temporary_file generates an empty list. The create_temporary_file beanshell creates a file to which the concatentation can be written. The concatenate_files service does not write anything to the temporary output file. Because the displayresults port has been given a default value of 'true', the empty string is ...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 39 times | Downloaded: 30 times

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Original Uploader

Workflow Concatenate files - multiple files (1)

Created: 27/09/08 @ 16:43:43

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The workflow splits the string 'a,b,c,d,e' into its five elements and saves the individual strings to five temporary files. The file paths to those files are then output by the create_and_populate_temporary_file beanshell. The create_temporary_file beanshell creates a file to which the concatentation can be written. The concatenate_files service concatenates the five files and writes the result to the temporary output file. Because the displayresults port has no value, the results are not...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 42 times | Downloaded: 24 times

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Original Uploader

Workflow Concatenate two strings (1)

Created: 27/09/08 @ 16:45:08

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The concatenate two strings service takes the strings 'good' and 'bye' and returns the result 'goodbye'.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 41 times | Downloaded: 30 times

Tags (3):

Original Uploader

Workflow Concatenate two strings - empty strings (1)

Created: 27/09/08 @ 16:45:57

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The concatenate two strings service takes two empty strings and returns an empty string.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 33 times | Downloaded: 27 times

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Original Uploader

Workflow Create lots of strings (1)

Created: 27/09/08 @ 16:46:38 | Last updated: 27/09/08 @ 16:48:00

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The create lots of strings service returns a list containing a large number of strings.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 30 times | Downloaded: 27 times

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Workflow Decode base64 to byte[] (1)

Created: 27/09/08 @ 16:50:22

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The decode base64 to byte[] service decodes the base64 string. The byte array is then converted into the string 'Hello world'.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 39 times | Downloaded: 54 times

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Original Uploader

Workflow Encode byte[] to base64 (1)

Created: 27/09/08 @ 16:51:08

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The encode byte[] to base 64 service encodes the bytes representing (in the local character set) 'hello'.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 54 times | Downloaded: 38 times

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Original Uploader

Workflow Execute cmd line app - unix - /bin/ls of t... (1)

Created: 27/09/08 @ 16:52:16

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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Note that this workflow only works on Unix systems. The get_temporary_directory beanshell returns the path to the directory in which temporary files are held. This value is passed to the args port of the execute_cmd_line_app service. The command port of that service has been defaulted to '/bin/ls'. The execute_cmd_line_app service runs the /bin/ls command on the temporary directory. The result is passed to its result port and then to the out port of the workflow.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 52 times | Downloaded: 50 times

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Workflow Execute cmd line app - unix - /bin/ls -R o... (1)

Created: 27/09/08 @ 16:52:59

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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Note that this workflow only works on Unix systems. The get_temporary_directory beanshell returns the path to the directory in which temporary files are held. This value is passed to the create_and_populate_list beanshell which creates a list of '-R' and the path. The resultant list is passed to the args port of the Execute_cmd_line_app service. The command port of that service has been defaulted to '/bin/ls'. The execute_cmd_line_app service runs the /bin/ls -R command on the temporary ...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 59 times | Downloaded: 32 times

Tags (4):

Original Uploader

Workflow Fail if false - false value (1)

Created: 27/09/08 @ 16:54:07

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The fail if true service throws an exception if given the value 'false'.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 32 times | Downloaded: 29 times

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Original Uploader

Workflow Fail if false - true value (1)

Created: 27/09/08 @ 16:54:53

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The fail if true service executes without an exception if given the value 'true'.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 24 times | Downloaded: 26 times

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Original Uploader

Workflow Fail if false - non false value (1)

Created: 27/09/08 @ 16:55:35

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The fail if true service executes without an exception if given a non-false value such as 'fred'.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 21 times | Downloaded: 24 times

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Original Uploader

Workflow Fail if true - true value (1)

Created: 27/09/08 @ 16:56:32

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The fail if true service throws an exception when passed the value true.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 23 times | Downloaded: 25 times

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Original Uploader

Workflow Fail if true - false value (1)

Created: 27/09/08 @ 16:57:09

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The fail if true service executes without an exception if given the value 'false'.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 22 times | Downloaded: 24 times

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Original Uploader

Workflow Fail if true - non true value (1)

Created: 27/09/08 @ 16:57:48

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The fail if true service executes without an exception if given a value that is not true e.g. 'fred'.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 21 times | Downloaded: 22 times

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Workflow FIlter list of strings by regex with a sui... (1)

Created: 27/09/08 @ 16:58:25

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The workflow filters the five element list split from the first service and returns the three elements that match the regular expression.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 33 times | Downloaded: 33 times

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Original Uploader

Workflow FIlter list of strings by regex with an un... (1)

Created: 27/09/08 @ 16:59:01

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The workflow filters the five element list split from the first service and returns an empty list as no elements match.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 29 times | Downloaded: 23 times

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Original Uploader

Workflow FIlter list of strings by regex extracting... (1)

Created: 27/09/08 @ 16:59:41

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The workflow examines the five element list split from the first service. For each element, if it contains an 'a' followed by two characters, then that triple is included in the output. Thus, for the input ['a','b','abcde','cdef','axy'], only 'abcde' and 'axy' contain a match and so ['abc', 'axy'] is output.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 34 times | Downloaded: 25 times

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Original Uploader

Workflow FIlter list of strings by regex extracting... (1)

Created: 27/09/08 @ 17:00:19

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The workflow examines the five element list split from the first service. For each element, if it contains an 'a' followed by two characters, then the two characters after the 'a' are included in the output. Thus, for the input ['a','b','abcde','cdef','axy'], only 'abcde' and 'axy' contain a match and so ['bc', 'xy'] is output.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 24 times | Downloaded: 28 times

Tags (3):

Original Uploader

Workflow FIlter list of strings by regex extracting... (1)

Created: 27/09/08 @ 17:01:08

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The workflow examines the five element list split from the first service. For each element, if it contains an 'a' followed by two characters, the second character after the 'a' is included in the output. Thus, for the input ['a','b','abcde','cdef','axy'], only 'abcde' and 'axy' contain a match and so ['c', 'y'] is output.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 23 times | Downloaded: 28 times

Tags (3):

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Workflow Get image from URL - only url specified (1)

Created: 27/09/08 @ 17:02:41

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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Retrieve the image at http://www.mygrid.org.uk/files/2008/09/dragon-workflow.png using just the url parameter

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 33 times | Downloaded: 40 times

Tags (3):

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Workflow Get image from URL - url and base specified (1)

Created: 27/09/08 @ 17:03:20

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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Retrieve the image at http://www.mygrid.org.uk/files/2008/09/dragon-workflow.png using both the url and base parameters

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 24 times | Downloaded: 23 times

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Workflow Get image URLs from HTTP document (1)

Created: 27/09/08 @ 17:03:55

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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Retrieve the web page at http://www.mygrid.org.uk/usermanual1.7/user_gettings_started.html and examine it for images. The workflow should return an empty list.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 24 times | Downloaded: 28 times

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Workflow Get image URLs from HTML document and outp... (1)

Created: 27/09/08 @ 17:05:30

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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Retrieve the web page at http://www.mygrid.org.uk, examine it for images and output the images.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 56 times | Downloaded: 35 times

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Workflow Get web page from URL - just url (1)

Created: 27/09/08 @ 17:06:26

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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Fetches a web page from http://www.mygrid.org.uk/tools using just the url parameter of the service. Note that when viewed, the HTML may not be rendered correctly. However, the HTML may be viewed by rendering the result as plain text.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 30 times | Downloaded: 29 times

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Workflow Get web page from URL - url and base (1)

Created: 27/09/08 @ 17:07:08

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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Fetches a web page from http://www.mygrid.org.uk/tools with the base parameter as "http://www.mygrid.org.uk" and the url as "/tools". Note that when viewed, the HTML may not be rendered correctly. However, the HTML may be viewed by rendering the result as plain text.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 34 times | Downloaded: 27 times

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Workflow List files by extension - several answers (1)

Created: 27/09/08 @ 17:07:44

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The create_temporary_directory beanshell creates a temporary directory and outputs the path to that directory. The populate_directory beanshell creates several files within the temporary directory. Once the directory has been populated, it is examined by the List_files_by_extension service and the file paths to the three files ending in ".png" are output.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 36 times | Downloaded: 27 times

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Workflow List files by extension - single answer (1)

Created: 27/09/08 @ 17:08:34

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The create_temporary_directory beanshell creates a temporary directory and outputs the path to that directory. The populate_directory beanshell creates several files within the temporary directory. Once the directory has been populated, it is examined by the List_files_by_extension service and the file path to the one file ending in ".bin" is output.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 25 times | Downloaded: 24 times

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Workflow List files by extension - no answer (1)

Created: 27/09/08 @ 17:09:11

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The create_temporary_directory beanshell creates a temporary directory and outputs the path to that directory. The populate_directory beanshell creates several files within the temporary directory. Once the directory has been populated, it is examined by the List_files_by_extension service. Since no files end in ".fred", an empty list is output.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 23 times | Downloaded: 25 times

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Workflow List files by extension - empty directory (1)

Created: 27/09/08 @ 17:09:50

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The create_temporary_directory beanshell creates a temporary directory and outputs the path to that directory. The empty directory is examined by the List_files_by_extension service. Since no files end in ".png", an empty list is output.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 20 times | Downloaded: 23 times

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Workflow List files by regex - several answers (1)

Created: 27/09/08 @ 17:11:01

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The create_temporary_directory beanshell creates a temporary directory and outputs the path to that directory. The populate_directory beanshell creates several files within the temporary directory. Once the directory has been populated, it is examined by the List_files_by_regex service and the file paths matching the regular expression '.*i.*', i.e. those containing an 'i', are output.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 24 times | Downloaded: 24 times

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Workflow List files by regex - single answer (1)

Created: 27/09/08 @ 17:11:34

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The create_temporary_directory beanshell creates a temporary directory and outputs the path to that directory. The populate_directory beanshell creates several files within the temporary directory. Once the directory has been populated, it is examined by the List_files_by_regex service and the file path to the one file matching 'c.*' i.e. starting with 'c' is output.

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Workflow List files by regex - no answer (1)

Created: 27/09/08 @ 17:12:08

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The create_temporary_directory beanshell creates a temporary directory and outputs the path to that directory. The populate_directory beanshell creates several files within the temporary directory. Once the directory has been populated, it is examined by the List_files_by_regex service. Since no files match the regular expression 'x.*' i.e. no files have a name that starts with 'x', an empty list is output.

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Workflow List files by regex - empty directory (1)

Created: 27/09/08 @ 17:12:38

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The create_temporary_directory beanshell creates a temporary directory and outputs the path to that directory. The empty directory is examined by the List_files_by_regex service. Since there are no files, an empty list is output.

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Workflow Merge string list to string - default sepa... (1)

Created: 27/09/08 @ 17:13:27

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The merge string list to string service takes the list ['a','b','c'] and outputs the string 'a b c'.

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Workflow Merge string list to string - colon separator (1)

Created: 27/09/08 @ 17:13:59

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The merge string list to string service takes the list ['a','b','c'] and using the separator ':' outputs the string 'a:b:c'.

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Workflow Merge string list to string - empty list (1)

Created: 27/09/08 @ 17:14:32

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The merge string list to string service takes an empty list [] and outputs an empty string ''.

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Workflow Pad numeral with leading 0s - default targ... (1)

Created: 27/09/08 @ 17:15:02

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The pad numeral with leading 0s takes the input '12' and pads it to the default target length of 7, yielding the output '0000012'.

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Workflow Pad numeral with leading 0s - specified ta... (1)

Created: 27/09/08 @ 17:15:38

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The pad numeral with leading 0s takes the input '12' and pads it to the specified target length of 4, yielding the output '0012'.

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Workflow Pad numeral with leading 0s - too short ta... (1)

Created: 27/09/08 @ 17:16:08

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The pad numeral with leading 0s takes the input '12' and because the specified target length of 1 is too short, yields the output '12'.

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Workflow Read GenBank file (1)

Created: 27/09/08 @ 17:16:45

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The Get_web_page_from_URL downloads a file from myExperiment that contains GenBank data. That data is then saved to a temporary file generated by the create_and_populate_temporary_file beanshell. The path to the temporary file is then passed to the Read_GenBank_file service. That service reads the file and converts the GenBank data into Agave format. The result is then sent to the workflow's out port.

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Workflow Read SwissProt file (1)

Created: 27/09/08 @ 17:17:24

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The Get_web_page_from_URL downloads a file from myExperiment that contains SwissProt data. That data is then saved to a temporary file generated by the create_and_populate_temporary_file beanshell. The path to the temporary file is then passed to the Read_SwissProt_file service. That service reads the file and converts the SwissProt data into Agave format. The result is then sent to the workflow's out port.

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Workflow Read text file (1)

Created: 27/09/08 @ 17:18:07

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The beanshell write the string 'hello' to a temporary file. The filepath to the temporary file is then passed to the Read_text_file service which reads the file and outputs the string 'hello'.

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Workflow Read text file - several lines (1)

Created: 27/09/08 @ 17:18:46

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The beanshell write the string 'hello' four times separated by a new lineto a temporary file. The filepath to the temporary file is then passed to the Read_text_file service which reads the file and outputs the string 'hello hello hello hello'.

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Workflow Read text file - empty file (1)

Created: 27/09/08 @ 17:19:17

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The beanshell creates an empty temporary file. The filepath to the temporary file is then passed to the Read_text_file service which reads the file and outputs the empty string ''.

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Workflow Remove duplicate strings (1)

Created: 27/09/08 @ 17:19:50

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The remove duplicate strings service takes the list ['a','b','c','b','a','d'], strips out duplicate strings and outputs the result ['a','b','c','d'].

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Workflow Remove duplicate strings - empty list (1)

Created: 27/09/08 @ 17:20:32

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The remove duplicate strings service takes the empty list [] and outputs the result [].

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Workflow Reverse complement DNA (1)

Created: 27/09/08 @ 17:21:03

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The Reverse Complement DNA service takes the DNA sequence, here defaulted to 'gatcctccat' and outputs the corresponding reverse complement sequence, in this example, 'atggaggatc'.

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Workflow Select - no title or message parameters (1)

Created: 27/09/08 @ 17:21:37

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The split_string_into_string_list_by_regular_expression parses the string 'a,b,c,d,e' and outputs the list ['a','b','c','d','e']. The select service displays a dialog with no title or message. The user is able to select from the values ['a','b','c','d',e']. When the user presses OK the value the user selected is passed to the answer port of the select service and so to the output of the workflow. If the user clicks Cancel then a service failure is generated.

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Workflow Select - title parameter (1)

Created: 27/09/08 @ 17:22:04

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The split_string_into_string_list_by_regular_expression parses the string 'a,b,c,d,e' and outputs the list ['a','b','c','d','e']. The select service displays a dialog with 'Some title' but no message. The user is able to select from the values ['a','b','c','d',e']. When the user presses OK the value the user selected is passed to the answer port of the select service and so to the output of the workflow. If the user clicks Cancel then a service failure is generated.

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Workflow Select - message parameter (1)

Created: 27/09/08 @ 17:22:32

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The split_string_into_string_list_by_regular_expression parses the string 'a,b,c,d,e' and outputs the list ['a','b','c','d','e']. The select service displays a dialog with no title but with 'Some message'. The user is able to select from the values ['a','b','c','d',e']. When the user presses OK the value the user selected is passed to the answer port of the select service and so to the output of the workflow. If the user clicks Cancel then a service failure is generated.

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Workflow Select - title and message parameters (1)

Created: 27/09/08 @ 17:23:04

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The split_string_into_string_list_by_regular_expression parses the string 'a,b,c,d,e' and outputs the list ['a','b','c','d','e']. The select service displays a dialog with ''Some title' and 'Some message'. The user is able to select from the values ['a','b','c','d',e']. When the user presses OK the value the user selected is passed to the answer port of the select service and so to the output of the workflow. If the user clicks Cancel then a service failure is generated.

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Workflow Select - single element list (1)

Created: 27/09/08 @ 17:23:38

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The split_string_into_string_list_by_regular_expression parses the string 'a' and outputs the list ['a']. The select service displays a dialog with 'Some title' and 'Some message'. The user is only able to select the value 'a'. When the user presses OK 'a' is passed to the answer port of the select service and so to the output of the workflow. If the user clicks Cancel then a service failure is generated.

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Workflow Split string into string list by regular e... (1)

Created: 27/09/08 @ 17:24:13

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The split string into string list by regular expression takes the string 'a,b,c' and using the default regular expression ',' splits it into the list ['a','b','c']

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Workflow Split string into string list by regular e... (1)

Created: 27/09/08 @ 17:24:44

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The split string into string list by regular expression takes the string 'boo:and:foo' and using the specified regular expression ':' splits it into the list ['boo','and','foo']

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Workflow Split string into string list by regular e... (1)

Created: 27/09/08 @ 17:25:20

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The split string into string list by regular expression takes the string 'boo:and:foo' and using the specified regular expression 'o' splits it into the list ['b','',':and:f']

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Workflow String list difference - yielding non-empt... (1)

Created: 27/09/08 @ 17:25:57

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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

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Workflow String list difference - yielding empty list (1)

Created: 27/09/08 @ 17:26:37

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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

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

Created: 27/09/08 @ 17:27:21

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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

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

Created: 27/09/08 @ 17:28:04

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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

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

Created: 27/09/08 @ 17:28:46

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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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'].

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Workflow String list union - yielding empty list (1)

Created: 27/09/08 @ 17:29:15

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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

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Workflow Tell - no parameters (1)

Created: 27/09/08 @ 17:29:45

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The tell service displays an informative dialog with no title or message. When the user presses OK the string 'answer' is passed to the answer port of the tell service and so to the output of the workflow.

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Workflow Tell - title parameter (1)

Created: 27/09/08 @ 17:30:13

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The tell service displays an informative dialog with 'Some title' but no message. When the user presses OK the string 'answer' is passed to the answer port of the tell service and so to the output of the workflow.

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Workflow Tell - message parameter (1)

Created: 27/09/08 @ 17:30:42

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The tell service displays an informative dialog with no title but with message 'Some message'. When the user presses OK the string 'answer' is passed to the answer port of the tell service and so to the output of the workflow.

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Workflow Tell - title and message parameters (1)

Created: 27/09/08 @ 17:31:37

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The tell service displays an informative dialog with no title but with message 'Some message'. When the user presses OK the string 'answer' is passed to the answer port of the tell service and so to the output of the workflow.

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Workflow Test always fails - no parameters (1)

Created: 27/09/08 @ 17:32:53

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The test always fails service generates a service failure when no parameter values are supplied.

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Workflow Test always fails - one parameter (1)

Created: 27/09/08 @ 17:33:33

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The test always fails service generates a service failure when one parameter value is supplied.

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Workflow Test always fails - two parameters (1)

Created: 27/09/08 @ 17:34:09

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The test always fails service generates a service failure when two parameter values are supplied.

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Workflow Transcribe DNA (1)

Created: 27/09/08 @ 17:34:40

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The Transcribe DNA service takes the DNA sequence, here defaulted to 'gatcctccat' and outputs the corresponding transcribed RNA sequence, in this example, 'gauccuccau'.

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Workflow Transform XML - no output file (1)

Created: 27/09/08 @ 17:35:33

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The get_xml_file_from_web service downloads an example xml from myExperiment. The content of that file is then saved to a temporary file by create_and_populate_xml_file. The path to the temporary file is passed to the inFileURL port of Transform_XML. The get_xslt_file_from_web service downloads an example xslt file from myExperiment. The content of that file is then saved to a temporary file by create_and_populate_xslt_file. The path to the temporary file is passed to the xslFileURL port...

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Workflow Transform XML - explicit output file (1)

Created: 27/09/08 @ 17:36:13

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The get_xml_file_from_web service downloads an example xml from myExperiment. The content of that file is then saved to a temporary file by create_and_populate_xml_file. The path to the temporary file is passed to the inFileURL port of Transform_XML. The get_xslt_file_from_web service downloads an example xslt file from myExperiment. The content of that file is then saved to a temporary file by create_and_populate_xslt_file. The path to the temporary file is passed to the xslFileURL port...

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Workflow Transform XML - output file by extension (1)

Created: 27/09/08 @ 17:36:43

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The get_xml_file_from_web service downloads an example xml from myExperiment. The content of that file is then saved to a temporary file by create_and_populate_xml_file. The path to the temporary file is passed to the inFileURL port of Transform_XML. The get_xslt_file_from_web service downloads an example xslt file from myExperiment. The content of that file is then saved to a temporary file by create_and_populate_xslt_file. The path to the temporary file is passed to the xslFileURL port...

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Workflow Warn - no parameters (1)

Created: 27/09/08 @ 17:37:28

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The warn service displays a prompt with no title or message. When the user presses OK the string 'answer' is passed to the answer port of the warn service and so to the output of the workflow.

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Workflow Warn - title parameter (1)

Created: 27/09/08 @ 17:37:54

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The warn service displays a warning dialog with 'Some title' but no message. When the user presses OK the string 'answer' is passed to the answer port of the warn service and so to the output of the workflow.

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Workflow Warn - message parameter (1)

Created: 27/09/08 @ 17:38:20

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The warn service displays a warning dialog with no title but message 'Some message'. When the user presses OK the string 'answer' is passed to the answer port of the warn service and so to the output of the workflow.

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Workflow Warn - title and message parameters (1)

Created: 27/09/08 @ 17:38:47

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The warn service displays a warning dialog with 'Some title' and message 'Some message'. When the user presses OK the string 'answer' is passed to the answer port of the warn service and so to the output of the workflow.

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Workflow Write text file - specified value (1)

Created: 27/09/08 @ 17:40:07

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The beanshell creates an empty temporary file. The filepath to the temporary file is then passed to the Write_text_file service which writes 'hello' into the file. 'hello' is also output by the service.

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Workflow Write text file - empty string value (1)

Created: 27/09/08 @ 17:40:48

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The beanshell creates an empty temporary file. The filepath to the temporary file is then passed to the Write_text_file service which writes the empty string '' into the file. '' is also output by the service.

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Workflow Write text file - overwriting content (1)

Created: 27/09/08 @ 17:41:23

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The beanshell creates an empty temporary file. The filepath to the temporary file is then passed to the Write_text_file A service which writes the string 'hello' into the file. After service A has run, service B writes 'goodbye' into the file. The file is then read by the Read_Text_File service and its content, 'goodbye', output by the workflow.

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Workflow Echo_with_occasional_failure-1 (1)

Created: 29/09/08 @ 10:52:54

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The echo_with_occasional_failure service mostly echoes the string 'hello' to the out port. Sometimes, it throws a service failure.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 28 times | Downloaded: 22 times

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Workflow Flatten list - two depth (1)

Created: 29/09/08 @ 11:46:16

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The flatten_list service takes the list [[['a']], [['b']], [['c']], [['d']]] and, using the default flatten depth of 2, outputs the list [['a'], ['b'], ['c'], ['d'], ['e']].

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 33 times | Downloaded: 26 times

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Workflow Flatten list - three depth (2)

Created: 29/09/08 @ 11:47:05 | Last updated: 30/09/08 @ 14:38:09

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The flatten_list service takes the list [[['a']], [['b']], [['c']], [['d']],[['e']]] and, using a flatten depth of 3, outputs the list ['a', 'b', 'c', 'd','e'].

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 48 times | Downloaded: 37 times

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Workflow Extract elements from a list - full extrac... (1)

Created: 29/09/08 @ 13:27:21

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The extract_elements_from_a_list is passed the list ['a','b','c','d','e']. The fromIndex is 0 and the toIndex is 5, so the service outputs an identical list.

Rating: 5.0 / 5 (1 rating) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 71 times | Downloaded: 41 times

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Workflow Extract elements from a list - single elem... (1)

Created: 29/09/08 @ 13:27:51

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The extract_elements_from_a_list is passed the list ['a','b','c','d','e']. The fromIndex is 2 and the toIndex is 3, so the service outputs the single element list ['c'].

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 52 times | Downloaded: 35 times

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Workflow Extract elements from a list - extraction ... (1)

Created: 29/09/08 @ 13:28:23

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The extract_elements_from_a_list is passed the list [['a','b','c', 'd'], ['e','f','g','h'],['i','j','k','l'],['m','n','o','p']] with fromIndex of 1 and toIndex of 3 and the default depth of 1, will output the list [['b','c'], ['f','g'],['j','k'],['n','o'']] as it is the list with depth 1 e.g. ['e','f','g','h'] that are considered.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 35 times | Downloaded: 25 times

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Workflow Extract elements from a list - extraction ... (1)

Created: 29/09/08 @ 13:28:49

Credits: User Alan Williams

License: Creative Commons Attribution 3.0 Unported License

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The extract_elements_from_a_list is passed the list [['a','b','c', 'd'], ['e','f','g','h'],['i','j','k','l'],['m','n','o','p']] with fromIndex of 1 and toIndex of 3 and depth 2, will output the list [['e','f','g','h'],['i','j','k','l']] as it is the outermost list i.e. that with depth 2 that is considered.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 55 times | Downloaded: 27 times

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Workflow Fetch Dragon images from BioMoby (1)

Created: 14/07/10 @ 16:20:46 | Last updated: 14/07/10 @ 16:20:48

Credits: User EdwardKawas User Tomoinn

Attributions: Workflow Fetch Dragon images from BioMoby

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Fetch images and annotations of snapdragons

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 24 times | Downloaded: 14 times

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Pack Taverna localworker example pack


Created: 27/09/08 @ 17:57:39 | Last updated: 05/03/12 @ 11:33:29

A pack of examples of the calling of Taverna's localworkers. The example workflows make extensive use of the default value mechanism for associating a value with a port of a service.  An alternative set of workflows that use string constants to make the values more explicit is under development.

0 items in this pack

Comments: 0 | Viewed: 299 times | Downloaded: 59 times

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Pack Carole's Keynotes


Created: 27/09/08 @ 19:52:17 | Last updated: 08/05/10 @ 20:24:47

Carole Goble's 2008 keynote talks that feature myExperiment, in PowerPoint 97-2003 format. All myExperiment presentation can be found on the wiki on http://wiki.myexperiment.org/index.php/Presentations  

5 items in this pack

Comments: 0 | Viewed: 111 times | Downloaded: 29 times

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