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Pack Taverna 1.7 starter pack

Created: 17/07/08 @ 21:06:12 | Last updated: 26/06/09 @ 10:40:01

Everything to get started with Taverna 1.7 - latest version is 1.7.2

16 items in this pack

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Pack Taverna localworker example pack

Created: 27/09/08 @ 17:57:39 | Last updated: 27/09/08 @ 18:23:50

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.

103 items in this pack

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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

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Workflows (146)
Taverna 1

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Workflow 1 (v2)

Created: 06/11/07 @ 16:59:05 | Last updated: 27/11/07 @ 16:18:31

Credits: User Antoon Goderis User Carole Goble User A. Random Scientist Network-member try it out

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License: Creative Commons Attribution-Share Alike 3.0 Unported License

1_25796_2
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Taverna 1

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Workflow polling (v1)

Created: 19/02/08 @ 15:10:38

Credits: User Stuart Owen

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Polling_28290_1
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Taverna 1

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Workflow Extract_GetCompoundDetails_with_xpath (v1)

Created: 28/11/07 @ 15:46:02 | Last updated: 19/02/08 @ 15:35:47

Credits: User Stuart Owen User Egon Willighagen

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Extract_getcompounddetails_with_xpath_10583_1
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Taverna 1

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Workflow Example of a conditional execution workflow (v1)

Created: 05/03/08 @ 13:55:46 | Last updated: 25/03/08 @ 14:46:19

Credits: User Tomoinn

License: Creative Commons Attribution 3.0 Unported License

Example_of_a_conditional_execution_workflow_7882_1
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.

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Taverna 1

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Workflow BiomartAndEMBOSSAnalysis (v4)

Created: 05/03/08 @ 14:01:18 | Last updated: 15/09/09 @ 15:11:11

License: Creative Commons Attribution 3.0 Unported License

Biomartandembossanalysis
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

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Taverna 1

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Workflow A workflow version of the EMBOSS tutorial (v1)

Created: 05/03/08 @ 14:05:21 | Last updated: 25/03/08 @ 14:43:36

Credits: User Tomoinn

License: Creative Commons Attribution 3.0 Unported License

A_workflow_version_of_the_emboss_tutorial_32367_1
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.

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Taverna 1

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Workflow Fetch today's xkcd comic (v1)

Created: 05/03/08 @ 14:08:53 | Last updated: 07/04/08 @ 13:54:04

Credits: User Tomoinn User Stian Soiland-Reyes

Attributions:

License: Creative Commons Attribution 3.0 Unported License

Fetch_today_s_xkcd_comic_5577_1
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

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Taverna 1

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Workflow Fetch Dragon images from BioMoby (v2)

Created: 05/03/08 @ 14:09:37 | Last updated: 25/03/08 @ 14:42:00

Credits: User Tomoinn

License: Creative Commons Attribution 3.0 Unported License

Fetch_dragon_images_from_biomoby_1077_2
Fetch images and annotations of snapdragons

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Taverna 1

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Workflow Demonstration of configurable iteration (v1)

Created: 05/03/08 @ 14:10:52 | Last updated: 25/03/08 @ 14:40:49

Credits: User Tomoinn

License: Creative Commons Attribution 3.0 Unported License

Demonstration_of_configurable_iteration_12320_1
This workflow shows the use of the iteration strategy editor to ensure that only relevant combinations of inputs are used during an implicit iteration.

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Taverna 1

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Workflow Retrieve sequence in EMBL format (v3)

Created: 05/03/08 @ 14:11:19 | Last updated: 17/06/09 @ 16:51:32

Credits: User Franck Tanoh User Tomoinn User Stuart Owen

License: Creative Commons Attribution 3.0 Unported License

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

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Taverna 1

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Workflow Fetch PDB flatfile from RCSB server (v1)

Created: 05/03/08 @ 14:13:25 | Last updated: 31/03/08 @ 16:01:42

Credits: User Tomoinn

License: Creative Commons Attribution 3.0 Unported License

Fetch_pdb_flatfile_from_rcsb_server_27474_1
Given an identifier such as '1crn' fetches the PDB format flatfile and returns the corresponding 3D image of the protein.

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Taverna 1

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Workflow GBSeq test (v2)

Created: 05/03/08 @ 14:15:36 | Last updated: 31/03/08 @ 15:55:10

Credits: User Franck Tanoh

License: Creative Commons Attribution 3.0 Unported License

Gbseq_test_23328_2
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

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Taverna 1

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Workflow Unique tags (v2)

Created: 11/03/08 @ 16:52:42 | Last updated: 11/03/08 @ 16:53:13

Credits: User Don Cruickshank

Attributions: Blob Viking boat

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Unique_tags_18054_2
This workflow takes a comma separated list of tags and removes duplicate entries. Tags may have multiple words in them. An example string is "carrots,handbags,carrots,cheese".

Rating: 3.5 / 5 (2 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

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Taverna 1

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Workflow Staged iteration strategy (v1)

Created: 07/05/08 @ 12:10:27 | Last updated: 07/05/08 @ 12:32:37

Credits: User Stian Soiland-Reyes

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Staged_iteration_strategy_11879_1
Consider two lists A and B, of equal size 3. A[1] corresponds to B[1], A[2] to B[2], etc, for instance A are image scans from 2007 and B from 2008, and the index indicates the patient number. A = [a0, a1, a2] B = [b0, b1, b2] There's then two lists of possible parameters P and Q, of different lengths, P has 2 and Q has 4 items. P = [p0, p1] Q = [q0, q1, q2, q3] Each of the A items should be processed in ap using each of the P parameters, and each of the B items ...

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Taverna 1

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Workflow Ask - no parameters (v1)

Created: 27/09/08 @ 16:33:04

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Ask_-_no_parameters_22018_1
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.

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Taverna 1

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Workflow Ask - just title parameter (v1)

Created: 27/09/08 @ 16:33:49 | Last updated: 27/09/08 @ 16:33:50

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Ask_-_just_title_parameter_8461_1
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.

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Taverna 1

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Workflow Ask - just message parameter (v1)

Created: 27/09/08 @ 16:34:35

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Ask_-_just_message_parameter_11443_1
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.

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

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Taverna 1

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Workflow Ask - title and message parameters (v1)

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

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Ask_-_title_and_message_parameters_22095_1
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.

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

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Taverna 1

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Workflow Byte[] to string - non empty value (v1)

Created: 27/09/08 @ 16:36:09 | Last updated: 27/09/08 @ 16:36:10

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Byte___to_string_-_non_empty_value_7375_1
The beanshell converts the string 'hello' to a byte array which is then converted back to the string 'hello' by the Byte[]_to_string service.

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Taverna 1

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Workflow Byte[] to string - empty value (v1)

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

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Byte___to_string_-_empty_value_4144_1
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.

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Taverna 1

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Workflow Choose - no title or message parameters (v1)

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

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Choose_-_no_title_or_message_parameters_23954_1
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

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Taverna 1

Original Uploader

Workflow Choose - title parameter (v1)

Created: 27/09/08 @ 16:38:43 | Last updated: 27/09/08 @ 16:38:44

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Choose_-_title_parameter_11112_1
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

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Taverna 1

Original Uploader

Workflow Choose - message parameter (v1)

Created: 27/09/08 @ 16:39:24

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Choose_-_message_parameter_9186_1
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 but 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

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Taverna 1

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Workflow Choose - title and message parameters (v1)

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

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Choose_-_title_and_message_parameters_215_1
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

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Taverna 1

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Workflow Choose - single element list (v1)

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

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Choose_-_single_element_list_19555_1
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

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Taverna 1

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Workflow Concatenate files - echo results and multiple files (v1)

Created: 27/09/08 @ 16:41:51 | Last updated: 27/09/08 @ 16:41:52

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Concatenate_files_-_echo_results_and_multiple_files_15778_1
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...

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Taverna 1

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Workflow Concatenate files - echo results but no files (v1)

Created: 27/09/08 @ 16:42:40 | Last updated: 27/09/08 @ 16:42:41

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Concatenate_files_-_echo_results_but_no_files_27595_1
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 ...

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Taverna 1

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Workflow Concatenate files - multiple files (v1)

Created: 27/09/08 @ 16:43:44

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Concatenate_files_-_multiple_files_23166_1
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...

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Taverna 1

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Workflow Concatenate two strings (v1)

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

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Concatenate_two_strings_13288_1
The concatenate two strings service takes the strings 'good' and 'bye' and returns the result 'goodbye'.

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Taverna 1

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Workflow Concatenate two strings - empty strings (v1)

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

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Concatenate_two_strings_-_empty_strings_8309_1
The concatenate two strings service takes two empty strings and returns an empty string.

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Taverna 1

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Workflow Create lots of strings (v1)

Created: 27/09/08 @ 16:46:38 | Last updated: 27/09/08 @ 16:48:01

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Merge_string_list_to_string_-_empty_list_29865_1
The create lots of strings service returns a list containing a large number of strings.

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Taverna 1

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Workflow Decode base64 to byte[] (v1)

Created: 27/09/08 @ 16:50:23

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Decode_base64_to_byte___23848_1
The decode base64 to byte[] service decodes the base64 string. The byte array is then converted into the string 'Hello world'.

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Taverna 1

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Workflow Encode byte[] to base64 (v1)

Created: 27/09/08 @ 16:51:08 | Last updated: 27/09/08 @ 16:51:09

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Encode_byte___to_base64_4336_1
The encode byte[] to base 64 service encodes the bytes representing (in the local character set) 'hello'.

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Taverna 1

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Workflow Execute cmd line app - unix - /bin/ls of temporary directory (v1)

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

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Execute_cmd_line_app_-_unix_-__bin_ls_of_temporary_directory_26172_1
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.

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Taverna 1

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Workflow Execute cmd line app - unix - /bin/ls -R of temporary directory (v1)

Created: 27/09/08 @ 16:53:00

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Execute_cmd_line_app_-_unix_-__bin_ls_-r_of_temporary_directory_32641_1
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 ...

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Taverna 1

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Workflow Fail if false - false value (v1)

Created: 27/09/08 @ 16:54:07 | Last updated: 27/09/08 @ 16:54:08

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Fail_if_false_-_false_value_18959_1
The fail if true service throws an exception if given the value 'false'.

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Taverna 1

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Workflow Fail if false - true value (v1)

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

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Fail_if_false_-_true_value_17269_1
The fail if true service executes without an exception if given the value 'true'.

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Workflow Fail if false - non false value (v1)

Created: 27/09/08 @ 16:55:35 | Last updated: 27/09/08 @ 16:55:36

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Fail_if_false_-_non_false_value_5276_1
The fail if true service executes without an exception if given a non-false value such as 'fred'.

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Workflow Fail if true - true value (v1)

Created: 27/09/08 @ 16:56:32 | Last updated: 27/09/08 @ 16:56:33

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Fail_if_true_-_true_value_24713_1
The fail if true service throws an exception when passed the value true.

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Workflow Fail if true - false value (v1)

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

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Fail_if_true_-_false_value_12560_1
The fail if true service executes without an exception if given the value 'false'.

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Workflow Fail if true - non true value (v1)

Created: 27/09/08 @ 16:57:48 | Last updated: 27/09/08 @ 16:57:49

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Fail_if_true_-_non_true_value_26426_1
The fail if true service executes without an exception if given a value that is not true e.g. 'fred'.

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Workflow FIlter list of strings by regex with a suitable regular expression (v1)

Created: 27/09/08 @ 16:58:25 | Last updated: 27/09/08 @ 16:58:26

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Filter_list_of_strings_by_regex_with_a_suitable_regular_expression_29391_1
The workflow filters the five element list split from the first service and returns the three elements that match the regular expression.

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Workflow FIlter list of strings by regex with an unsuitable regular expression (v1)

Created: 27/09/08 @ 16:59:01 | Last updated: 27/09/08 @ 16:59:02

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Filter_list_of_strings_by_regex_with_an_unsuitable_regular_expression_28005_1
The workflow filters the five element list split from the first service and returns an empty list as no elements match.

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Workflow FIlter list of strings by regex extracting the specified group in the matches (v1)

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

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Filter_list_of_strings_by_regex_extracting_the_specified_group_in_the_matches_31401_1
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.

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Workflow FIlter list of strings by regex extracting the specified group in the matches (v1)

Created: 27/09/08 @ 17:00:20

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Filter_list_of_strings_by_regex_extracting_the_specified_group_in_the_matches_17755_1
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.

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Workflow FIlter list of strings by regex extracting the specified group in the matches (v1)

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

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Filter_list_of_strings_by_regex_extracting_the_specified_group_in_the_matches_2364_1
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.

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Workflow Get image from URL - only url specified (v1)

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

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Get_image_from_url_-_only_url_specified_21901_1
Retrieve the image at http://www.mygrid.org.uk/files/2008/09/dragon-workflow.png using just the url parameter

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Workflow Get image from URL - url and base specified (v1)

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

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Get_image_from_url_-_url_and_base_specified_11209_1
Retrieve the image at http://www.mygrid.org.uk/files/2008/09/dragon-workflow.png using both the url and base parameters

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Workflow Get image URLs from HTTP document (v1)

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

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Get_image_urls_from_http_document_7943_1
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.

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Workflow Get image URLs from HTML document and output the results (v1)

Created: 27/09/08 @ 17:05:31

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Get_image_urls_from_html_document_and_output_the_results_24469_1
Retrieve the web page at http://www.mygrid.org.uk, examine it for images and output the images.

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Workflow Get web page from URL - just url (v1)

Created: 27/09/08 @ 17:06:26 | Last updated: 27/09/08 @ 17:06:27

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Get_web_page_from_url_-_just_url_8269_1
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.

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Workflow Get web page from URL - url and base (v1)

Created: 27/09/08 @ 17:07:08 | Last updated: 27/09/08 @ 17:07:09

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Get_web_page_from_url_-_url_and_base_12994_1
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.

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Workflow List files by extension - several answers (v1)

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

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

List_files_by_extension_-_several_answers_25965_1
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.

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Workflow List files by extension - single answer (v1)

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

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

List_files_by_extension_-_single_answer_31435_1
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.

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Workflow List files by extension - no answer (v1)

Created: 27/09/08 @ 17:09:11 | Last updated: 27/09/08 @ 17:09:12

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

List_files_by_extension_-_no_answer_3943_1
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.

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Workflow List files by extension - empty directory (v1)

Created: 27/09/08 @ 17:09:50 | Last updated: 27/09/08 @ 17:09:51

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

List_files_by_extension_-_empty_directory_10488_1
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.

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Workflow List files by regex - several answers (v1)

Created: 27/09/08 @ 17:11:01 | Last updated: 27/09/08 @ 17:11:02

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

List_files_by_regex_-_several_answers_10756_1
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.

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Workflow List files by regex - single answer (v1)

Created: 27/09/08 @ 17:11:35

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

List_files_by_regex_-_single_answer_4373_1
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 (v1)

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

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

List_files_by_regex_-_no_answer_22819_1
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 (v1)

Created: 27/09/08 @ 17:12:38 | Last updated: 27/09/08 @ 17:12:39

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

List_files_by_regex_-_empty_directory_27381_1
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 separator (v1)

Created: 27/09/08 @ 17:13:27 | Last updated: 27/09/08 @ 17:13:28

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Merge_string_list_to_string_-_default_separator_15363_1
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 (v1)

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

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Merge_string_list_to_string_-_colon_separator_21102_1
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 (v1)

Created: 27/09/08 @ 17:14:33

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Merge_string_list_to_string_-_empty_list_4735_1
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 targetlength (v1)

Created: 27/09/08 @ 17:15:02 | Last updated: 27/09/08 @ 17:15:03

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Pad_numeral_with_leading_0s_-_default_targetlength_10212_1
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 targetlength (v1)

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

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Pad_numeral_with_leading_0s_-_specified_targetlength_258_1
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 targetlength (v1)

Created: 27/09/08 @ 17:16:08 | Last updated: 27/09/08 @ 17:16:09

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Pad_numeral_with_leading_0s_-_too_short_targetlength_1811_1
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 (v1)

Created: 27/09/08 @ 17:16:45 | Last updated: 27/09/08 @ 17:16:46

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Read_genbank_file_22651_1
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 (v1)

Created: 27/09/08 @ 17:17:24 | Last updated: 27/09/08 @ 17:17:25

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Read_swissprot_file_30282_1
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 (v1)

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

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Read_text_file_32416_1
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 (v1)

Created: 27/09/08 @ 17:18:46 | Last updated: 27/09/08 @ 17:18:47

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Read_text_file_-_several_lines_11080_1
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 (v1)

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

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Read_text_file_-_empty_file_8974_1
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 (v1)

Created: 27/09/08 @ 17:19:50 | Last updated: 27/09/08 @ 17:19:51

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Remove_duplicate_strings_5773_1
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 (v1)

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

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Remove_duplicate_strings_-_empty_list_11462_1
The remove duplicate strings service takes the empty list [] and outputs the result [].

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Workflow Reverse complement DNA (v1)

Created: 27/09/08 @ 17:21:04

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Reverse_complement_dna_18129_1
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 (v1)

Created: 27/09/08 @ 17:21:37 | Last updated: 27/09/08 @ 17:21:38

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Select_-_no_title_or_message_parameters_11322_1
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 (v1)

Created: 27/09/08 @ 17:22:04 | Last updated: 27/09/08 @ 17:22:05

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Select_-_title_parameter_9411_1
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 (v1)

Created: 27/09/08 @ 17:22:32 | Last updated: 27/09/08 @ 17:22:33

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Select_-_message_parameter_16053_1
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 (v1)

Created: 27/09/08 @ 17:23:04 | Last updated: 27/09/08 @ 17:23:05

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Select_-_title_and_message_parameters_9756_1
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 (v1)

Created: 27/09/08 @ 17:23:38 | Last updated: 27/09/08 @ 17:23:39

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Select_-_single_element_list_25865_1
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 expression - default regex (v1)

Created: 27/09/08 @ 17:24:13 | Last updated: 27/09/08 @ 17:24:14

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Split_string_into_string_list_by_regular_expression_-_default_regex_2877_1
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 expression - colon regex (v1)

Created: 27/09/08 @ 17:24:45

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Split_string_into_string_list_by_regular_expression_-_colon_regex_18206_1
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 expression - character regex (v1)

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

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Split_string_into_string_list_by_regular_expression_-_character_regex_24213_1
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-empty list (v1)

Created: 27/09/08 @ 17:25:57 | Last updated: 27/09/08 @ 17:25:58

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

String_list_difference_-_yielding_non-empty_list_24798_1
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 (v1)

Created: 27/09/08 @ 17:26:37 | Last updated: 27/09/08 @ 17:26:38

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

String_list_difference_-_yielding_empty_list_12150_1
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 empty list (v1)

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

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

String_list_intersection_-_yielding_non_empty_list_29266_1
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 list (v1)

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

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

String_list_intersection_-_yielding_empty_list_26347_1
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 (v1)

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

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

String_list_union_-_yielding_non-empty_list_17457_1
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 (v1)

Created: 27/09/08 @ 17:29:15 | Last updated: 27/09/08 @ 17:29:16

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

String_list_union_-_yielding_empty_list_24763_1
The string list union service takes in two empty lists [] and [] and returns an empty list [].

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Workflow Tell - no parameters (v1)

Created: 27/09/08 @ 17:29:45 | Last updated: 27/09/08 @ 17:29:46

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Tell_-_no_parameters_21922_1
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 (v1)

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

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Tell_-_title_parameter_16714_1
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 (v1)

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

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Tell_-_message_parameter_28904_1
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 (v1)

Created: 27/09/08 @ 17:31:38

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Tell_-_title_and_message_parameters_17289_1
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 (v1)

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

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Test_always_fails_-_no_parameters_31807_1
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 (v1)

Created: 27/09/08 @ 17:33:34

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Test_always_fails_-_one_parameter_18618_1
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 (v1)

Created: 27/09/08 @ 17:34:09 | Last updated: 27/09/08 @ 17:34:10

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Test_always_fails_-_two_parameters_11784_1
The test always fails service generates a service failure when two parameter values are supplied.

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Workflow Transcribe DNA (v1)

Created: 27/09/08 @ 17:34:41

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Transcribe_dna_21457_1
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 (v1)

Created: 27/09/08 @ 17:35:34

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Transform_xml_-_no_output_file_26571_1
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 (v1)

Created: 27/09/08 @ 17:36:14

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Transform_xml_-_explicit_output_file_25946_1
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 (v1)

Created: 27/09/08 @ 17:36:44

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Transform_xml_-_output_file_by_extension_3395_1
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 (v1)

Created: 27/09/08 @ 17:37:28 | Last updated: 27/09/08 @ 17:37:29

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Warn_-_no_parameters_23598_1
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 (v1)

Created: 27/09/08 @ 17:37:55

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Warn_-_title_parameter_14550_1
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 (v1)

Created: 27/09/08 @ 17:38:20 | Last updated: 27/09/08 @ 17:38:21

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Warn_-_message_parameter_7367_1
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 (v1)

Created: 27/09/08 @ 17:38:47 | Last updated: 27/09/08 @ 17:38:48

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Warn_-_title_and_message_parameters_11808_1
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 (v1)

Created: 27/09/08 @ 17:40:07 | Last updated: 27/09/08 @ 17:40:08

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Write_text_file_-_specified_value_25259_1
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 (v1)

Created: 27/09/08 @ 17:40:48 | Last updated: 27/09/08 @ 17:40:49

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Write_text_file_-_empty_string_value_28401_1
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 (v1)

Created: 27/09/08 @ 17:41:24

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Write_text_file_-_overwriting_content_16384_1
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 (v1)

Created: 29/09/08 @ 10:52:55

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Echo_with_occasional_failure-1_26439_1
The echo_with_occasional_failure service mostly echoes the string 'hello' to the out port. Sometimes, it throws a service failure.

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Workflow Flatten list - two depth (v1)

Created: 29/09/08 @ 11:46:17

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Flatten_list_-_two_depth_18340_1
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']].

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Workflow Flatten list - three depth (v2)

Created: 29/09/08 @ 11:47:06 | Last updated: 30/09/08 @ 14:38:09

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Flatten_list_-_three_depth_13095_2
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'].

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Workflow Extract elements from a list - full extraction (v1)

Created: 29/09/08 @ 13:27:21 | Last updated: 29/09/08 @ 13:27:22

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Extract_elements_from_a_list_-_full_extraction_15242_1
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.

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Workflow Extract elements from a list - single element extraction (v1)

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

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Extract_elements_from_a_list_-_single_element_extraction_22122_1
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'].

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Workflow Extract elements from a list - extraction in nested lists (v1)

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

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Extract_elements_from_a_list_-_extraction_in_nested_lists_28555_1
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.

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Workflow Extract elements from a list - extraction of nested lists (v1)

Created: 29/09/08 @ 13:28:50

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Extract_elements_from_a_list_-_extraction_of_nested_lists_32419_1
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.

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Makefile

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Workflow Sample makefile workflow (v1)

Created: 30/10/08 @ 09:07:32 | Last updated: 30/10/08 @ 09:10:57

Credits: User Giovanni Dall'Olio

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A sample makefile workflow. Type 'make help' to print an help message. Nothing else is supported in this version. Interesting links about makefiles in bioinformatics: http://www.nodalpoint.org/2007/03/18/a_pipeline_is_a_makefile http://swc.scipy.org/lec/build.html

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Taverna 1

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Workflow Sample grid workflow (v1)

Created: 24/10/08 @ 14:30:26 | Last updated: 31/10/08 @ 12:13:24

Credits: User Glatard

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Untitled
This is a sample workflow submitting jobs to the EGEE grid using the Generic Application Service Wrapper (GASW). The job submission service has to be installed locally.

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Taverna 1

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Workflow querySWS_minimalQuery (v2)

Created: 03/10/07 @ 18:36:19

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

Querysws_minimalquery_3139
SRS by WS (SWS) is a set of Web Services allowing to retrieve database entries from libraries included in public SRS sites. The querySWS service implement a search on the basis of the database name (lib) and the term to be searched (query). It automatically identifies the best site to query. Additional parameters include in_fields (in which part of the record the terms are searched), out_fields (which information is returned) and site (the SRS site). This workflow is just a demonstration ...

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Trident (Package)

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Workflow While Sample (v1)

Created: 21/10/08 @ 14:18:08 | Last updated: 21/10/08 @ 14:18:09

Credits: Network-member Trident

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Whilesample
This WF shows how to use while constructs in workflows. The condition block generates a true or false condition. The while loop is executed once, each time the condition is true.

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Trident (Package)

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Workflow If Sample (v1)

Created: 21/10/08 @ 14:10:42 | Last updated: 21/10/08 @ 14:11:03

Credits: Network-member Trident

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Ifsample
This WF is a sample which shows support of common programming constructs within Trident. The If workflow has two parts; the condition block which generates a TRUE or FALSE condition and two parallel branches for ‘If’ and ‘Else’.

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GWorkflowDL

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Workflow GWorkflowDL: Generic execution of programs (v1)

Created: 25/11/08 @ 13:44:02 | Last updated: 25/11/08 @ 13:45:34

Credits: User Andreas Hoheisel

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Gworkflowdl_genericexecution
This workflow is an example of the execution of an arbitrary command line program. This workflow transfers a tar.gz package containing the linux program "date" to a free Grid resource, unpacks, and executes it. After execution the URL to the file with the standard output is available on "stdout", the standard error on "stderr".

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GWorkflowDL

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Workflow Make 28 CPUh load on the Grid (v1)

Created: 25/11/08 @ 14:13:43 | Last updated: 17/12/08 @ 14:26:00

Credits: User Andreas Hoheisel

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Gworkflowdl_makeload28cpuh
This workflow makes 28 CPU hours load on a Grid. Therefore it calls 100 times (represented by 100 input tokens) the program "makeload", which makes 1000 Seconds load each. The processing is done recurrent, so you can use this workflow to benchmark the speedup of your Grid environment, or just to heat up your computer center... This workflow also serves as an example of a typical parameter study modeled with GWorkflowDL. Of cause this workflow can only be invoked with a X509 certif...

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GWorkflowDL

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Workflow Workflow Pattern - Structured Loop (v2)

Created: 28/11/08 @ 16:19:49 | Last updated: 09/12/08 @ 15:58:51

Credits: User Andreas Hoheisel

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Structured-loop
This workflow is a GWorkflowDL representation of a structured loop that updates the variable "x" in each iteration. This workflow is equivalent to the following pseudo code: x:=0; for ( i:=0; i<=99; i++) { x:=x+i; } x_result:=x; Please remark that this demonstration workflow does not invoke any external services at all. The calculation is done only by using the GWorkflowDL's syntax and semantics.

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GWorkflowDL

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Workflow Workflow Pattern - Structured Loop (B) (v2)

Created: 01/12/08 @ 12:51:13 | Last updated: 09/12/08 @ 16:00:39

Credits: User Andreas Hoheisel

Attributions: Workflow Workflow Pattern - Structured Loop

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Structured-loop_b
This workflow is an alternative GWorkflowDL representation of a structured loop that updates the variable "x" in each iteration and which models the control flow separately from the index "i". Here a version of the graph with manual graph layout: This workflow is equivalent to the following pseudo code: x:=0; for ( i:=0; i<=99; i++) { x:=x+i; } x_result:=x; Please remark that this demonstration workflow does not invoke any external services at all. The c...

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GWorkflowDL

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Workflow Workflow Pattern - Structured Loop (C) (v2)

Created: 01/12/08 @ 13:12:30 | Last updated: 09/12/08 @ 16:00:04

Credits: User Andreas Hoheisel

Attributions: Workflow Workflow Pattern - Structured Loop (B)

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Structured-loop_c
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.

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GWorkflowDL

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Workflow Workflow Pattern - Sequence (v1)

Created: 03/12/08 @ 14:17:21 | Last updated: 03/12/08 @ 14:17:23

Credits: User Andreas Hoheisel

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Sequence
This workflow is a GWorkflowDL representation of a sequence that sequentially invokes A and B. This workflow is equivalent to the following pseudo code: end_A = A(); end_B = B(end_A);

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GWorkflowDL

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Workflow Workflow Pattern - Parallel Split (AND-Split) (v1)

Created: 03/12/08 @ 14:25:25 | Last updated: 03/12/08 @ 14:45:16

Credits: User Andreas Hoheisel

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Parallel-split
This workflow is a GWorkflowDL representation of a parallel split that invokes A and B recurrently without synchronization. This workflow is equivalent to the following pseudo code: new Thread( end_A = A() ); new Thread( end_B = B() );

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GWorkflowDL

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Workflow Workflow Pattern - Synchronization (AND-Join) (v2)

Created: 03/12/08 @ 14:32:33 | Last updated: 19/01/09 @ 12:58:18

Credits: User Andreas Hoheisel

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Synchronization
This workflow is a GWorkflowDL representation of a synchronization (AND Join) that waits until A and B finish their execution. This workflow is equivalent to the following pseudo code: threadA = new Thread( end_A = A() ); threadB = new Thread( end_B = B() ); threadA.join(); threadB.join();

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GWorkflowDL

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Workflow Workflow Pattern - Exclusive Choice (XOR-Split) (v2)

Created: 03/12/08 @ 14:42:07 | Last updated: 09/12/08 @ 15:54:59

Credits: User Andreas Hoheisel

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Exclusive-choice
This workflow is a GWorkflowDL representation of an exclusive choice (XOR Split) that invokes either A or B. This workflow is equivalent to the following pseudo code: x = XOR_Split; if (x=="true") { end_A = A(x); } else { end_B = B(x); }

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GWorkflowDL

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Workflow Workflow Pattern - Simple Merge (XOR-Join) (v1)

Created: 03/12/08 @ 14:49:47 | Last updated: 19/01/09 @ 13:56:33

Credits: User Andreas Hoheisel

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Simple-merge
This workflow is a GWorkflowDL representation of a simple merge (XOR Join) that invokes C when either A or B has been invoked. The structure of the GWorkflowDL representation of a simple merge is identical to the multi merge pattern!

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Taverna 1

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Workflow Basic eSearch/eFetch cycle (v1)

Created: 04/12/08 @ 22:47:43 | Last updated: 04/12/08 @ 22:51:43

Credits: User Giovanni Dall'Olio

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Esearch_efetch1
This is a basic eSearch/eFetch workflow created with taverna and using eUtils from NCBI. It accepts a query term as input (at the moment, for testing purposes, this is a fixed string), interrogate eSearch to retrieve the list of related sequences on the Nucleotide database, and use eFetch to retrieve the corresponding sequences. I wrote this workflow one year ago, when I was trying to understand how taverna and eUtils work; I suspect it broken, and of course it could be enhanced, so I am ...

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GWorkflowDL

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Workflow Workflow Pattern - Multi Choice (OR Split) (v2)

Created: 05/12/08 @ 15:48:33 | Last updated: 09/12/08 @ 15:57:14

Credits: User Andreas Hoheisel

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Multi-choice
This workflow is a GWorkflowDL representation of a multi choice (OR Split) that invokes either A or B or A and B.

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GWorkflowDL

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Workflow TextGrid: Test workflow (v2)

Created: 12/12/08 @ 13:36:36 | Last updated: 17/12/08 @ 09:55:00

Credits: User Andreas Hoheisel

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Textgrid-crud-read
This is a first test workflow that demonstrate, how to use the GWES for a document-style Web Service within TextGrid.

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GWorkflowDL

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Workflow TextGrid: Test workflow (on ingrid) (v1)

Created: 17/12/08 @ 09:56:53 | Last updated: 17/12/08 @ 09:56:54

Credits: User Andreas Hoheisel

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Textgrid-crud-read
Test workflow that invokes CRUD read on ingrid.

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Taverna 2

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Workflow What is Paget's disease sparql query example (v3)

Created: 20/01/09 @ 02:36:48 | Last updated: 20/01/09 @ 03:34:08

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

What_is_paget_example
SELECT distinct ?s1 FROM <http://atlas.bio2rdf.org/sparql> WHERE {   ?s1 ?p1 ?o1 .   ?o1 bif:contains "paget" .   FILTER( regex(?s1, "omim")   OR regex(?s1, "geneid") OR regex(?s1, "uniprot")) }   followed by SELECT ?type1, count(*) FROM <http://localhost:8890/sparql> WHERE {   ?s1 ?p1 ?o1 .   ?o1 bif:contains "paget" .   ?s1  

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Taverna 1

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Workflow firstwf (v1)

Created: 13/11/08 @ 20:45:09 | Last updated: 13/11/08 @ 20:45:10

Credits: User Rory

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Firstwf
No description

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Taverna 1

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Workflow Kegg_DrugID (v1)

Created: 18/03/09 @ 14:49:02 | Last updated: 18/03/09 @ 14:51:29

Credits: User Rory

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Kegg_drugid
 This workflow accepts looks up drug identifiers from KEGG given a pathway identifier. You can enter a pathway ID in the form path:map07026

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Taverna 1

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Workflow FirstExampleWorkflow (v1)

Created: 24/06/09 @ 09:30:15

Credits: User Jelena (Obradovic) Dreskai

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Firstexampleworkflow
This is my first test example of Taverna Workflow.

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Taverna 1

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Workflow Tuiuiu synchronous workflow (v1)

Created: 29/06/09 @ 09:42:08 | Last updated: 29/06/09 @ 09:59:58

Credits: User http://osallou.myopenid.com/ Network-member GenOUEST Platform

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Example_workflow_blocking
Tuiuiu removes from a sequence or from a set of sequences areas as large as possible that do not contain researched repeats. Tuiuiu is used as a preliminary step before applying a multiple local aligner tool. Modeling and algorithmic details are provided in the following paper. Please, cite this paper if you use Tuiuiu. P. Peterlongo, G. Sacomoto, A. Pereira do Lago, N. Pisanti, M.-F. Sagot Lossless filter for multiple repeats with bounded edit distance BMC Algorithms for Mole...

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Taverna 1

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Workflow Tuiuiu asynchronous workflow (v1)

Created: 29/06/09 @ 09:53:39 | Last updated: 29/06/09 @ 09:59:24

Credits: User http://osallou.myopenid.com/ Network-member GenOUEST Platform

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Example_workflow_loop
Tuiuiu removes from a sequence or from a set of sequences areas as large as possible that do not contain researched repeats. Tuiuiu is used as a preliminary step before applying a multiple local aligner tool. Modeling and algorithmic details are provided in the following paper. Please, cite this paper if you use Tuiuiu. P. Peterlongo, G. Sacomoto, A. Pereira do Lago, N. Pisanti, M.-F. Sagot Lossless filter for multiple repeats with bounded edit distance BMC Algorithms for Mole...

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Taverna 2

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Workflow Execute GWorkflowDL workflow using Taverna 2 (v1)

Created: 30/06/09 @ 10:01:35 | Last updated: 30/06/09 @ 10:07:26

Credits: User Andreas Hoheisel

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Tavernagoesgwes
This workflow makes use of the "Grid Workflow Execution Service" (GWES) in order to exececute a GWorkflowDL workflow by means of the Taverna Workbench 2. As the GWES is deployed as a regular SOAP service, the WSDL can be imported as a normal service into the Taverna Workbench.

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Taverna 2

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Workflow Execute GWorkflowDL workflow using Taverna 2 (with inputs) (v1)

Created: 30/06/09 @ 14:02:37 | Last updated: 30/06/09 @ 14:02:38

Credits: User Andreas Hoheisel

Attributions: Workflow Execute GWorkflowDL workflow using Taverna 2

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Tavernagoesgwes_withinputs
This workflow makes use of the "Grid Workflow Execution Service" (GWES) in order to exececute a GWorkflowDL workflow by means of the Taverna Workbench 2. As the GWES is deployed as a regular SOAP service, the WSDL can be imported as a normal service into the Taverna Workbench. This workflow contains all the input parameters as string constants, so it can be started right away without user inputs.

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Taverna 2

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Workflow An example workflow with WSRF service (v1)

Created: 28/07/09 @ 17:24:06 | Last updated: 28/07/09 @ 17:24:07

Credits: User Wei Tan User Stian Soiland-Reyes

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Wsrf
An example workflow with WSRF service The service used is http://sidgrid.ci.uchicago.edu:8100/wsrf/services/CounterService The service is included in Globus toolkit installation (ws-core). If the it is down you can host your own and modify the workflow definition file to point to your own. The workflow first creates a counter instance and adds the value 10 for two times to the same counter. Therefore the result should be 20.

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Taverna 2

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Workflow chicken_ensembl_gene_id (v1)

Created: 07/09/09 @ 15:00:01 | Last updated: 09/09/09 @ 14:21:49

Credits: User Rory

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Chicken_ensembl_gene_id
Accepts a chromosome eg. 1 and returns the ensembl gene ids for that chromosome

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Taverna 2

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Workflow CaDSRDataService Sample Workflow (v2)

Created: 02/09/09 @ 16:53:05 | Last updated: 03/09/09 @ 23:11:19

Credits: User Wei Tan

License: Creative Commons Attribution-Share Alike 3.0 Unported License

_untitled_
This workflow is used as an example in this wiki article: https://wiki.cagrid.org/display/knowledgebase/How+to+Create+CaGrid+Workflow+Using+Taverna+2

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Triana

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Workflow EBI_dbfetch_fetchBatch (v1)

Created: 28/08/09 @ 11:55:11 | Last updated: 28/08/09 @ 11:55:12

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

Triana_dbfetch_fetchbatch
Sample workflow illustrating the use of EBI's WSDbfetch service with Triana.

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Taverna 2

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Workflow A workflow version of the EMBOSS tutorial (v1)

Created: 15/12/09 @ 22:10:38 | Last updated: 15/12/09 @ 22:10:39

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A_workflow_version_of_the_emboss_tutorial
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.

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Taverna 2

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Workflow Dummy example of looping (v2)

Created: 27/01/10 @ 14:13:55 | Last updated: 27/01/10 @ 15:56:11

Credits: User Stian Soiland-Reyes

License: Creative Commons Attribution 3.0 Unported License

Dummy_example_of_looping
Example of looping over asynchronous services. The dummy beanshell scripts represents the operations of an asynchronous submit-status-results style service, such as EBI's InterProScan and NCBI Blast.   createJob creates a temporary file with the content "0". Filename retuirned as a "job ID".   checkStatus reads the job, and return state "RUNNING" as long as the content is less than 10, increasing the number for each call. ...

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