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Items tagged with "example" (225)
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Created: 06/11/07 @ 16:59:05 | Last updated: 20/11/07 @ 16:18:31
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Attributions: License: Creative Commons Attribution-Share Alike 3.0 Unported License
Trivial workflow which will initially fail, retry twice then fall over to the alternative specified for the FailingThing process.
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Created: 19/02/08 @ 15:10:38 | Last updated: 22/11/10 @ 17:07:18
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
No description
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Created: 28/11/07 @ 15:46:02 | Last updated: 19/02/08 @ 15:35:47
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
No description
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Created: 05/03/08 @ 13:55:45 | Last updated: 25/03/08 @ 14:46:12
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 15/09/09 @ 15:11:11 License: Creative Commons Attribution 3.0 Unported License
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.
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Created: 05/03/08 @ 14:05:20 | Last updated: 25/03/08 @ 14:43:35
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 05/03/08 @ 14:08:52 | Last updated: 07/04/08 @ 13:54:04
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Attributions: License: Creative Commons Attribution 3.0 Unported License
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: 461 times | Downloaded: 172 times Tags (4): |
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Created: 05/03/08 @ 14:09:35 | Last updated: 14/07/10 @ 16:46:37
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License: Creative Commons Attribution 3.0 Unported License
Fetch images and annotations of snapdragons
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Created: 05/03/08 @ 14:10:51 | Last updated: 25/03/08 @ 14:40:27
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License: Creative Commons Attribution 3.0 Unported License
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: 257 times | Downloaded: 144 times Tags (5): |
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Created: 17/06/09 @ 16:51:32
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License: Creative Commons Attribution 3.0 Unported License
This workflow retrieves a sequence associated with its features in embl format
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Created: 05/03/08 @ 14:13:24 | Last updated: 31/03/08 @ 16:01:41
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License: Creative Commons Attribution 3.0 Unported License
Given an identifier such as '1crn' fetches the PDB format flatfile and returns the corresponding 3D image of the protein.
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Created: 05/03/08 @ 14:15:35 | Last updated: 31/03/08 @ 15:55:09
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License: Creative Commons Attribution 3.0 Unported License
This workflow retrieves nucleotide and protein sequences with the literature and references associated
to them given a protein and a nucleotide id.
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Created: 11/03/08 @ 16:52:42 | Last updated: 11/03/08 @ 16:53:13
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Attributions:
License: Creative Commons Attribution-Share Alike 3.0 Unported License
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 Viewed: 147 times | Downloaded: 58 times Tags (3): |
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Created: 07/05/08 @ 12:10:27 | Last updated: 07/05/08 @ 12:32:36
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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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Created: 27/09/08 @ 16:33:03
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 16:33:49
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 16:34:35
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License: Creative Commons Attribution 3.0 Unported License
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.
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Created: 27/09/08 @ 16:35:15
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License: Creative Commons Attribution 3.0 Unported License
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.
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Created: 27/09/08 @ 16:36:09
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 16:37:04
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 16:37:50
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License: Creative Commons Attribution 3.0 Unported License
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.
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Created: 27/09/08 @ 16:38:43
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License: Creative Commons Attribution 3.0 Unported License
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.
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Created: 27/09/08 @ 16:40:10
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License: Creative Commons Attribution 3.0 Unported License
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.
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Created: 27/09/08 @ 16:40:51
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License: Creative Commons Attribution 3.0 Unported License
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.
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Created: 27/09/08 @ 16:41:51
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 16:42:40
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 16:43:43
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 16:45:08
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License: Creative Commons Attribution 3.0 Unported License
The concatenate two strings service takes the strings 'good' and 'bye' and returns the result 'goodbye'.
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Created: 27/09/08 @ 16:45:57
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License: Creative Commons Attribution 3.0 Unported License
The concatenate two strings service takes two empty strings and returns an empty string.
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Created: 27/09/08 @ 16:46:38 | Last updated: 27/09/08 @ 16:48:00
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License: Creative Commons Attribution 3.0 Unported License
The create lots of strings service returns a list containing a large number of strings.
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Created: 27/09/08 @ 16:50:22
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 16:51:08
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License: Creative Commons Attribution 3.0 Unported License
The encode byte[] to base 64 service encodes the bytes representing (in the local character set) 'hello'.
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Created: 27/09/08 @ 16:52:16
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 16:52:59
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 16:54:07
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License: Creative Commons Attribution 3.0 Unported License
The fail if true service throws an exception if given the value 'false'.
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Created: 27/09/08 @ 16:54:53
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License: Creative Commons Attribution 3.0 Unported License
The fail if true service executes without an exception if given the value 'true'.
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Created: 27/09/08 @ 16:55:35
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License: Creative Commons Attribution 3.0 Unported License
The fail if true service executes without an exception if given a non-false value such as 'fred'.
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Created: 27/09/08 @ 16:56:32
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License: Creative Commons Attribution 3.0 Unported License
The fail if true service throws an exception when passed the value true.
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Created: 27/09/08 @ 16:57:09
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License: Creative Commons Attribution 3.0 Unported License
The fail if true service executes without an exception if given the value 'false'.
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Created: 27/09/08 @ 16:57:48
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License: Creative Commons Attribution 3.0 Unported License
The fail if true service executes without an exception if given a value that is not true e.g. 'fred'.
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Created: 27/09/08 @ 16:58:25
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 16:59:01
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 16:59:41
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:00:19
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:01:08
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:02:41
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License: Creative Commons Attribution 3.0 Unported License
Retrieve the image at http://www.mygrid.org.uk/files/2008/09/dragon-workflow.png using just the url parameter
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Created: 27/09/08 @ 17:03:20
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:03:55
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:05:30
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License: Creative Commons Attribution 3.0 Unported License
Retrieve the web page at http://www.mygrid.org.uk, examine it for images and output the images.
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Created: 27/09/08 @ 17:06:26
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:07:08
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:07:44
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:08:34
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:09:11
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:09:50
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:11:01
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:11:34
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:12:08
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:12:38
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:13:27
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License: Creative Commons Attribution 3.0 Unported License
The merge string list to string service takes the list ['a','b','c'] and outputs the string 'a
b
c'.
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Created: 27/09/08 @ 17:13:59
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:14:32
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License: Creative Commons Attribution 3.0 Unported License
The merge string list to string service takes an empty list [] and outputs an empty string ''.
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Created: 27/09/08 @ 17:15:02
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:15:38
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:16:08
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:16:45
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:17:24
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:18:07
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:18:46
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:19:17
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:19:50
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:20:32
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License: Creative Commons Attribution 3.0 Unported License
The remove duplicate strings service takes the empty list [] and outputs the result [].
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Created: 27/09/08 @ 17:21:03
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:21:37
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:22:04
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:22:32
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:23:04
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:23:38
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:24:13
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:24:44
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:25:20
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:25:57
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License: Creative Commons Attribution 3.0 Unported License
The string list difference service takes in ['a','b','c'] and ['a','e','c'] and returns the list ['b','e'].
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Created: 27/09/08 @ 17:26:37
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License: Creative Commons Attribution 3.0 Unported License
The string list difference service takes in ['a','b','c'] and ['a','c','b'] and returns the empty list [].
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Created: 27/09/08 @ 17:27:21
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License: Creative Commons Attribution 3.0 Unported License
The string list intersection service takes in ['a','b','c'] and ['a','e','c] and returns the list ['a','c'].
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Created: 27/09/08 @ 17:28:04
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License: Creative Commons Attribution 3.0 Unported License
The string list intersection service takes in ['a','b','c'] and ['x','y','z'] and returns the empty list [].
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Created: 27/09/08 @ 17:28:46
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:29:15
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License: Creative Commons Attribution 3.0 Unported License
The string list union service takes in two empty lists [] and [] and returns an empty list [].
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Created: 27/09/08 @ 17:29:45
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:30:13
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:30:42
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:31:37
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:32:53
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License: Creative Commons Attribution 3.0 Unported License
The test always fails service generates a service failure when no parameter values are supplied.
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Created: 27/09/08 @ 17:33:33
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License: Creative Commons Attribution 3.0 Unported License
The test always fails service generates a service failure when one parameter value is supplied.
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Created: 27/09/08 @ 17:34:09
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License: Creative Commons Attribution 3.0 Unported License
The test always fails service generates a service failure when two parameter values are supplied.
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Created: 27/09/08 @ 17:34:40
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:35:33
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:36:13
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:36:43
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:37:28
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:37:54
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:38:20
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:38:47
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:40:07
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:40:48
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/09/08 @ 17:41:23
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 29/09/08 @ 10:52:54
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 29/09/08 @ 11:46:16
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 29/09/08 @ 11:47:05 | Last updated: 30/09/08 @ 14:38:09
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 29/09/08 @ 13:27:21
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 29/09/08 @ 13:27:51
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 29/09/08 @ 13:28:23
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 29/09/08 @ 13:28:49
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 30/10/08 @ 09:07:32 | Last updated: 30/10/08 @ 09:10:56
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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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Created: 24/10/08 @ 14:30:25 | Last updated: 31/10/08 @ 12:13:23
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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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Created: 03/10/07 @ 18:36:19 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License
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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Created: 21/10/08 @ 14:18:07
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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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Created: 21/10/08 @ 14:10:42 | Last updated: 21/10/08 @ 14:11:02
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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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Created: 25/11/08 @ 13:44:02 | Last updated: 25/11/08 @ 13:45:33
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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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Created: 25/11/08 @ 14:13:43 | Last updated: 17/12/08 @ 14:25:59
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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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Created: 09/12/08 @ 15:58:50
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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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Created: 09/12/08 @ 16:00:38
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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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Created: 09/12/08 @ 16:00:03
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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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Created: 03/12/08 @ 14:17:20
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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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Created: 03/12/08 @ 14:25:25 | Last updated: 03/12/08 @ 14:45:16
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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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Created: 19/01/09 @ 12:58:17
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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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Created: 09/12/08 @ 15:54:59
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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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Created: 03/12/08 @ 14:49:47 | Last updated: 19/01/09 @ 13:56:32
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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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Created: 04/12/08 @ 22:47:43 | Last updated: 04/12/08 @ 22:51:42
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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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Created: 09/12/08 @ 15:57:14
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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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Created: 17/12/08 @ 09:54:59
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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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Created: 17/12/08 @ 09:56:52
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Test workflow that invokes CRUD read on ingrid.
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Created: 20/01/09 @ 03:34:08
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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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Created: 13/11/08 @ 20:45:08
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
No description
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Created: 18/03/09 @ 14:49:02 | Last updated: 18/03/09 @ 14:51:28
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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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Created: 24/06/09 @ 09:30:14
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This is my first test example of Taverna Workflow.
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Created: 29/06/09 @ 09:42:08 | Last updated: 29/06/09 @ 09:59:57
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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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Created: 29/06/09 @ 09:53:39 | Last updated: 29/06/09 @ 09:59:23
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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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Created: 30/06/09 @ 10:01:35 | Last updated: 30/06/09 @ 10:07:25
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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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Created: 30/06/09 @ 14:02:36
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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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Created: 28/07/09 @ 17:24:05
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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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Created: 07/09/09 @ 15:00:01 | Last updated: 09/09/09 @ 14:21:48
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Accepts a chromosome eg. 1 and returns the ensembl gene ids for that chromosome
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Created: 25/05/10 @ 19:16:58 | Last updated: 11/06/10 @ 04:50:15
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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
Tested with Taverna 2.1.2 as of 6/10/2010
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Created: 28/08/09 @ 11:55:10
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License: Creative Commons Attribution 3.0 Unported License
Sample workflow illustrating the use of EBI's WSDbfetch service with Triana.
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Created: 15/12/09 @ 22:10:36
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 27/01/10 @ 15:52:50 | Last updated: 27/01/10 @ 15:56:10
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 04/07/10 @ 18:29:33 | Last updated: 04/07/10 @ 18:29:34
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 04/07/10 @ 18:30:58 | Last updated: 04/07/10 @ 18:31:00
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License: Creative Commons Attribution 3.0 Unported License
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.
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Created: 04/07/10 @ 18:31:57 | Last updated: 04/07/10 @ 18:31:59
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License: Creative Commons Attribution 3.0 Unported License
A workflow from part of the BioMoby tutorial
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Created: 04/07/10 @ 18:32:58 | Last updated: 04/07/10 @ 18:33:00
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 04/07/10 @ 18:33:54 | Last updated: 04/07/10 @ 18:33:55
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License: Creative Commons Attribution 3.0 Unported License
Perform an InterProScan analysis of a protein sequence using the EBI’s WSInterProScan service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan). The input sequence to use and the user e-mail address are inputs, the other parameters for the analysis (see Job_params) are allowed to default.
InterProScan searches a protein sequence against the protein family and domain signature databases integrated into InterPro (see http://www.ebi.ac.uk/interpro/). A set of matches to the sig...
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Created: 04/07/10 @ 18:34:57 | Last updated: 04/07/10 @ 18:34:59
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License: Creative Commons Attribution 3.0 Unported License
Given an identifier such as '1crn' fetches the PDB format flatfile from the RCSB
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Created: 04/07/10 @ 18:35:59 | Last updated: 04/07/10 @ 18:36:00
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License: Creative Commons Attribution 3.0 Unported License
Use the local java plugins and some filtering operations to fetch the comic strip image from http://xkcd.com/
Based on the FetchDailyDilbert workflow.
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Created: 04/07/10 @ 18:36:58 | Last updated: 04/07/10 @ 18:37:00
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License: Creative Commons Attribution 3.0 Unported License
This workflow retrieves nucleotide and protein sequences with the literature and references associated
to them given a protein and a nucleotide id.
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Created: 04/07/10 @ 18:37:58 | Last updated: 04/07/10 @ 18:38:00
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License: Creative Commons Attribution 3.0 Unported License
Perform multiple iterations of services in order to show pipelining
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Created: 04/07/10 @ 18:39:07 | Last updated: 04/07/10 @ 18:39:09
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License: Creative Commons Attribution 3.0 Unported License
This workflow retrieves a sequence associated with its features in embl format
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Created: 13/07/10 @ 12:50:54 | Last updated: 13/07/10 @ 12:50:55
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License: Creative Commons Attribution 3.0 Unported License
Example using the SpreadsheetImport service to import data from an Excel spreadsheet.
The workflow imports the file spreadsheet file WaterUse.xlsx and generates a graph from the date.
The source data is from http://data.gov.uk/
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Created: 14/07/10 @ 16:20:46 | Last updated: 14/07/10 @ 16:20:48
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Fetch images and annotations of snapdragons
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Created: 26/07/10 @ 04:12:58 | Last updated: 26/07/10 @ 04:23:35 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License
Hi All,
This workflow connects RapidMiner to Twitter and downloads the timeline. It then creates a wordlist from the tweets and breaks them into key words that are mentioned in the tweets. You can then visualize the key words mentioned in the tweets.
This workflow can be further modified to review various key events that have been talked about in the twitterland.
Do let me know your feedback and feel free to ask me any questions that you may have. Shaily
web: http://advanced-analyti...
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Created: 17/08/10 @ 18:24:05 | Last updated: 17/08/10 @ 19:45:34
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
An example workflow to test the installation of caGrid Workflow Suite and the submission of a workflow to a caGrid workflow service.
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Created: 13/09/10 @ 14:27:25 | Last updated: 13/09/10 @ 14:31:33
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License: Creative Commons Attribution 3.0 Unported License
Note that this workflow depends upon the REST and XPath plugins.
This workflow fetches weather forecast for the user-specified location. First of all it uses the provided location name to obtain a WOEID ("Where On Earth ID") of that location, then uses that unique identifier to fetch the weather forecast from Yahoo server. Multiple results may be obtained in case there is no unique translation of the location to a WOEID. REST activity is used to perform HTTP requests and fetch d...
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Created: 26/10/10 @ 16:10:14 | Last updated: 26/10/10 @ 16:10:15
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Basic example on how to integrate a Web Processing Service (WPS) using PyWPS's WSDL/SOAP
The workflow will accept a GML file with featureCollection where polyon is described using gml:coordinate element structure. This GMl is easely generated with GDAL.
The coodinate structure will be converted to WKT and used to create a polygon using shapely, the output will be a buffer polygon with a defined width.
Output polygon will replace the orginal polygon and the existing XML will be return...
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Created: 04/11/10 @ 16:03:38 | Last updated: 27/04/11 @ 17:24:42
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Example on how to work with an async service, where the statusURL is used to check for Example on how to work with an async service, where the statusURL is used to check for if the process has finished or not
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Created: 08/11/10 @ 13:37:33 | Last updated: 08/11/10 @ 13:44:33
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow executes a local beanshell script that has been programmed to fail on some iterations.
It demonstrates the advantages of setting retries in your workflows to make them more robust
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Created: 26/11/10 @ 15:13:46 | Last updated: 26/11/10 @ 15:13:48
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License: Creative Commons Attribution 3.0 Unported License
This workflow uses an R service running on localhost to calculate sin(0.45)
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Created: 26/11/10 @ 15:44:15 | Last updated: 26/11/10 @ 15:44:18
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License: Creative Commons Attribution 3.0 Unported License
Checks what the logical_input is in R. For an logical_input of
TRUE - is_false should be FALSE and is_true TRUE
FALSE - is_false should be TRUE and is_true FALSE
For any other input values, is_false and is_true should both be NA
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Created: 26/11/10 @ 16:47:02 | Last updated: 26/11/10 @ 16:47:04
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License: Creative Commons Attribution 3.0 Unported License
This workflow determines the lower case version of the input string.
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Created: 26/11/10 @ 17:06:00 | Last updated: 26/11/10 @ 17:06:03
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License: Creative Commons Attribution 3.0 Unported License
The workflow returns a list containing the logical inversion of the logical vector input
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Created: 26/11/10 @ 17:21:45 | Last updated: 26/11/10 @ 17:21:48
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License: Creative Commons Attribution 3.0 Unported License
This workflow takes a list of numbers and outputs a list containing the squares of the numbers and the sum of the numbers in the list
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Created: 26/11/10 @ 17:34:05 | Last updated: 26/11/10 @ 17:34:08
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License: Creative Commons Attribution 3.0 Unported License
This workflow takes a list of integer values and returns a list containing the square of the input list's elements, and the sum of the input list's elements.
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Created: 26/11/10 @ 18:06:35 | Last updated: 26/11/10 @ 18:06:37
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License: Creative Commons Attribution 3.0 Unported License
The workflow takes a list of strings and outputs a list contains the lower-cased versions of the input elements, and also a concatenation of the input elements
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Created: 29/11/10 @ 10:15:37 | Last updated: 29/11/10 @ 10:15:40
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License: Creative Commons Attribution 3.0 Unported License
This workflow takes a list of integer values and returns a list containing 100 modulus the list's elements, and the sum of the input list's elements.
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Created: 29/11/10 @ 12:40:12 | Last updated: 29/11/10 @ 13:13:11
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License: Creative Commons Attribution 3.0 Unported License
This workflow produces a PNG plot on the figure port.
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Created: 13/12/10 @ 16:28:15 | Last updated: 13/12/10 @ 16:28:42
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License: Creative Commons Attribution 3.0 Unported License
This workflow fetches the details of the countries in the world and then uses R to produce a histogram of the log of their population
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Created: 17/01/11 @ 12:51:58 | Last updated: 17/01/11 @ 12:52:03
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow performs an NCBI blast at the EBI. It uses the new EBI services, which are asynchronous and require looping over the nested workflow (Status) until the workflow has finished. Many of the EBI services now work in this way, so you can use this workflow as an example of the invocation pattern and looping configuration.
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Created: 17/01/11 @ 16:08:48 | Last updated: 17/01/11 @ 16:12:40
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow performs an interproscan on provided sequencesThis workflow performs an interproscan at the EBI on sequences provided as input. The output is provided as text, xml or png.
This workflow uses the new EBI services, which are asynchronous and require looping over the nested workflow (Status) until the workflow has finished. Many of the EBI services now work in this way, so you can use this workflow as an example of the invocation pattern and looping configuration.
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Created: 26/01/11 @ 22:10:31 | Last updated: 20/07/11 @ 14:05:59
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This is a Taverna 1 version; if you're using latest Taverna 2 workbench please use: www.myexperiment.org/workflows/2264.html .
Exemplary experiment using Tav4SB (http://bioputer.mimuw.edu.pl/tav4sb/) ODEs simulation and plotting Web service operations.
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Created: 26/01/11 @ 22:14:41 | Last updated: 20/07/11 @ 14:14:30
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This is a Taverna 1 version; if you're using latest Taverna 2 workbench please use: www.myexperiment.org/workflows/2266.html .
Exemplary experiment using Tav4SB (http://bioputer.mimuw.edu.pl/tav4sb/) PRISM model translation and model checking Web service operations.
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Created: 26/01/11 @ 22:17:00 | Last updated: 20/07/11 @ 14:23:03
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This is a Taverna 1 version; if you're using latest Taverna 2 workbench please use: www.myexperiment.org/workflows/2267 .
Exemplary experiment using Tav4SB (http://bioputer.mimuw.edu.pl/tav4sb/) Mathematica plotting Web service operation. This is a second-part for the computationaly exhaustive PMC: compute results workflow (http://www.myexperiment.org/workflows/1790).
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Created: 13/05/11 @ 17:14:06 | Last updated: 13/05/11 @ 19:47:24
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Reference:
Natural Product-likeness Score and Its Application for Prioritization of Compound
Libraries
Peter Ertl,* Silvio Roggo, and Ansgar Schuffenhauer
Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
http://peter-ertl.com/reprints/Ertl-JCIM-48-68-2008.pdf
The natural product likeness scorer implemented by Peter Ertl was originally devised to screen large compound libraries for natural product likeness in drug designing studies. His work is re...
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Created: 13/05/11 @ 17:22:28 | Last updated: 13/05/11 @ 17:26:17
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Prerequisite:
- CDK -Taverna Plugin 0.5.1
http://www.ts-concepts.de/cdk-taverna2/plugin/
- To run this workflow the atom_signatures file of Natural product(NP), Synthetic Molecules(SM) and query structures are needed
- This could be generated from GenerateAtomSignatures.t2flow
http://www.myexperiment.org/workflows/2120/download?version=1
Description of input ports :
NP_file: needs precomputed Atom_signatures of desired Natural product structural data
SM_file:...
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Created: 13/05/11 @ 17:34:58 | Last updated: 13/05/11 @ 17:35:08
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Prerequisite:
CDK -Taverna Plugin 0.5.1
http://www.ts-concepts.de/cdk-taverna2/plugin/
- To run this workflow you need a Score file which is written to text file.
- This could be generated from ScorerActivity.t2flow
http://www.myexperiment.org/workflows/2121/download?version=1
Description of input ports :
score_file: Path to file name that has pre computed scores.
Note:
While passing file as input it could be passed as list of many files or single fi...
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Created: 18/05/11 @ 09:22:50 | Last updated: 18/05/11 @ 09:22:54
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow is self-contained. It has a fixed URL from which a text file is downloaded (output as Original_file). That file is gzipped (output as Compressed_File) and then gunzipped again (output as Decompressed_File).
The workflow wraps external tools from taverna.nordugrid.org and needs a beta version of Taverna 2.3 or later.
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Created: 12/07/11 @ 12:54:05 | Last updated: 12/07/11 @ 12:54:07
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License: Creative Commons Attribution 3.0 Unported License
This workflow retrieves all genes on human chromosome 22 that are associated with a disease and aligns the upstream regions with mouse and rat homologues. The alignments are plotted and corresponding sequence ids are also returned.
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Created: 12/07/11 @ 13:02:49 | Last updated: 12/07/11 @ 13:02:50
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Attributions:
License: Creative Commons Attribution 3.0 Unported License
This workflow performs an interproscan at the EBI on sequences provided as input. The output is provided as text, xml or png.
This workflow uses the new EBI services, which are asynchronous and require looping over the nested workflow (Status) until the workflow has finished. Many of the EBI services now work in this way, so you can use this workflow as an example of the invocation pattern and looping configuration.
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Created: 12/07/11 @ 13:07:58 | Last updated: 12/07/11 @ 13:07:59
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License: Creative Commons Attribution 3.0 Unported License
This workflow fetches weather forecast for the user-specified location.
First of all it uses the provided location name to obtain a WOEID ("Where On Earth ID") of that location, then uses that unique identifier to fetch the weather forecast from Yahoo server.
Multiple results may be obtained in case there is no unique translation of the location to a WOEID.
REST activity is used to perform HTTP requests and fetch data from remote servers; XPath activity is then used to parse the XML data a...
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Created: 12/07/11 @ 13:46:40 | Last updated: 12/07/11 @ 13:46:42
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License: Creative Commons Attribution 3.0 Unported License
A fun example workflow showing user-interaction and service looping
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Created: 12/07/11 @ 13:52:04 | Last updated: 12/07/11 @ 13:52:05
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License: Creative Commons Attribution 3.0 Unported License
Fetch images and annotations of snapdragons
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Created: 12/07/11 @ 13:57:34 | Last updated: 12/07/11 @ 13:57:36
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License: Creative Commons Attribution 3.0 Unported License
Example using the SpreadsheetImport service to import data from an Excel spreadsheet.
The workflow imports the file spreadsheet file WaterUse.xlsx and generates a graph from the date.
The source data is from http://data.gov.uk/
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Created: 12/07/11 @ 14:01:17 | Last updated: 12/07/11 @ 14:01:18
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License: Creative Commons Attribution 3.0 Unported License
This workflow retrieves a sequence associated with its features in embl format
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Created: 12/07/11 @ 14:04:39 | Last updated: 12/07/11 @ 14:04:41
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License: Creative Commons Attribution 3.0 Unported License
Perform multiple iterations of services in order to show pipelining
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Created: 12/07/11 @ 14:08:40 | Last updated: 12/07/11 @ 14:08:41
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License: Creative Commons Attribution 3.0 Unported License
This workflow retrieves nucleotide and protein sequences with the literature and references associated
to them given a protein and a nucleotide id.
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Created: 12/07/11 @ 14:13:35 | Last updated: 12/07/11 @ 14:13:36
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License: Creative Commons Attribution 3.0 Unported License
Use the local services and some filtering operations to fetch the comic strip image from http://xkcd.com/
Based on the FetchDailyDilbert workflow.
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Created: 12/07/11 @ 14:37:08 | Last updated: 12/07/11 @ 14:37:10
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License: Creative Commons Attribution 3.0 Unported License
Given an identifier such as '1crn' fetches the PDB format flatfile from the RCSB
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Created: 12/07/11 @ 14:40:22 | Last updated: 12/07/11 @ 14:40:24
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 12/07/11 @ 15:50:21 | Last updated: 12/07/11 @ 15:50:22
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License: Creative Commons Attribution 3.0 Unported License
A workflow from part of the BioMoby tutorial
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Created: 12/07/11 @ 15:55:06 | Last updated: 12/07/11 @ 15:55:08
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License: Creative Commons Attribution 3.0 Unported License
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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Created: 13/07/11 @ 10:19:35 | Last updated: 13/07/11 @ 10:19:37
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License: Creative Commons Attribution 3.0 Unported License
The tool service outputs a message that greets using the names specified on Greet's input ports.
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Created: 13/07/11 @ 10:21:10 | Last updated: 13/07/11 @ 10:22:52
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License: Creative Commons Attribution 3.0 Unported License
This workflow only works on a Unix machine. This workflow takes a fixed URL from which a text file is downloaded (output as Original_file). That file is zipped (output as Zipped_File) and then unzipped again (output as Unzipped_File). The orginal file and the unzipped version are then diff'd/
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Created: 13/07/11 @ 10:24:40 | Last updated: 13/07/11 @ 10:25:37
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License: Creative Commons Attribution 3.0 Unported License
This workflow relies on a Unix system. It wraps the "bc" command line calculator. It downloads the calculation script from a URL.
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Created: 14/07/11 @ 08:50:26 | Last updated: 21/07/11 @ 10:08:42
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Exemplary multi-parameter sensitivity analysis (MPSA) experiment using Tav4SB (http://bioputer.mimuw.edu.pl/tav4sb/) WS operations. In this version of MPSA, ODEs simulations are basis of analysis of SBML model parameters space.
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Created: 14/07/11 @ 08:59:23 | Last updated: 21/07/11 @ 10:08:07
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Exemplary multi-parameter sensitivity analysis (MPSA) experiment using Tav4SB (http://bioputer.mimuw.edu.pl/tav4sb/) WS operations. In this version of MPSA PRISM probabilistic model checking is basis of analysis of SBML model parameters space.
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Created: 14/07/11 @ 09:03:42 | Last updated: 14/07/11 @ 09:06:16
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Exemplary workflow for plotting error surface using Tav4SB (http://bioputer.mimuw.edu.pl/tav4sb/) mahtPlot WS operation. Data input format is compatibile with Tav4SB MPSA workflows.
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Created: 14/07/11 @ 15:01:03 | Last updated: 14/07/11 @ 15:01:05
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License: Creative Commons Attribution 3.0 Unported License
This is an example of a workflow that contains a call to a secure REST service that requires user to authenticate with HTTP Basic Authentication. You can use testuser/testpasswd as username and password for authentication when running the workflow.
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Created: 14/07/11 @ 15:02:36 | Last updated: 14/07/11 @ 15:02:38
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License: Creative Commons Attribution 3.0 Unported License
This is an example of a workflow that contains a call to a secure Web service that runs behind HTTPS and requires user to authenticate. The first thing you can expect to see is a pop up dialog asking if you trust the Web service to be invoked over HTTPS. You can use testuser/testpasswd as username and password for authentication when running the workflow. To see where the security is being configured, right-click the service in the diagram and select "Configure security" from the menu.
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Created: 20/07/11 @ 13:57:19 | Last updated: 20/07/11 @ 14:02:43
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Exemplary experiment using Tav4SB (http://bioputer.mimuw.edu.pl/tav4sb/) ODEs simulation and plotting Web service operations.
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Created: 20/07/11 @ 14:11:46 | Last updated: 20/07/11 @ 14:12:02
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Exemplary experiment using Tav4SB (http://bioputer.mimuw.edu.pl/tav4sb/) PRISM model translation and model checking Web service operations.
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Created: 20/07/11 @ 14:18:19 | Last updated: 20/07/11 @ 14:21:27
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Exemplary experiment using Tav4SB (http://bioputer.mimuw.edu.pl/tav4sb/) Mathematica plotting Web service operation. This is a second-part for the computationaly exhaustive PMC: compute results workflow (http://www.myexperiment.org/workflows/2266).
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Created: 04/08/11 @ 14:18:09
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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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Created: 16/09/11 @ 17:32:25 | Last updated: 16/09/11 @ 17:32:29
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Example of a WPS service that reprojects a geoTIFF by using a EPSG code. THe example image is in EPSG:32119, lcc projection for north caroline and it comes from GRASS-GIS spearfish dataset. The image is reprojected into EPSG:4326 (lat/long):
Metadata: http://rsg.pml.ac.uk/wps/generic.cgi?request=describeProcess&service=wps&identifier=reprojectImage&version=1.0.0
Library: gdalwarp
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Created: 06/10/11 @ 14:58:34 | Last updated: 06/10/11 @ 14:58:36
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License: Creative Commons Attribution 3.0 Unported License
This workflow generates a random number within the range 0 to 100. The generation is done by a python script.
The workflow assumes that python is in the path.
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Created: 13/10/11 @ 09:46:26
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
r.los generates a raster output map in which the cells that are visible from a user-specified observer position are marked with the vertical angle (in degrees) required to see those cells (viewshed). A value of 0 is directly below the specified viewing position, 90 is due horizontal, and 180 is directly above the observer. The angle to the cell containing the viewing position is undefined and set to 180.
http://grass.fbk.eu/grass62/manuals/html62_user/r.los.html
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Created: 15/11/11 @ 10:20:10 | Last updated: 15/11/11 @ 10:20:11
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow demonstrates how nested workflows can be conditionally invoked
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Created: 15/11/11 @ 10:45:45 | Last updated: 15/11/11 @ 10:45:47
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow demonstrates how a nested workflow can be called an explicit number of times.
Note that the loop iterator does not need to be used in the logic of the loop contents. It can
be used as a sentinel (see the conditional workflow)
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Created: 03/01/12 @ 15:39:47 | Last updated: 03/01/12 @ 15:41:52
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License: Creative Commons Attribution 3.0 Unported License
An extension to helloworld.t2flow - this workflow takes a workflow input "name" which is combined with the string constant "Hello, " using the local worker "Concatenate two strings", and outputs the produced string to the workflow output "greeting".
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Created: 03/01/12 @ 15:38:03 | Last updated: 03/01/12 @ 15:42:35
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License: Creative Commons Attribution 3.0 Unported License
One of the simplest workflows possible. No workflow input ports, a single workflow output port "greeting", outputting "Hello, world!" as produced by the String Constant "hello".
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Created: 17/07/08 @ 21:06:12 | Last updated: 26/06/09 @ 10:55:13
Everything to get started with Taverna 1.7 - latest version is 1.7.2
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Created: 27/09/08 @ 17:57:39 | Last updated: 29/09/08 @ 13:30:24
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.
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Created: 13/05/11 @ 19:35:39 | Last updated: 29/08/11 @ 14:25:47
Reference:
Natural Product-likeness Score and Its Application for Prioritization of Compound
Libraries
Peter Ertl,* Silvio Roggo, and Ansgar Schuffenhauer
Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
http://peter-ertl.com/reprints/Ertl-JCIM-48-68-2008.pdf
The natural product likeness scorer implemented by Peter Ertl was originally devised to screen large compound libraries for natural product likeness in drug designing studies. His work...
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Created: 10/12/09 @ 16:04:54 | Last updated: 18/12/09 @ 11:15:36
The Taverna team are happy to announce that Taverna 2.1 is now
available for download.
It includes many new features and bug fixes based on extensive
usability reviews and hours of testing.
2.1 truly is the next release up from the 1.7.x line.
2.1 features:
* Copy/paste, shortcuts, undo/redo, drag and drop
* An Animated workflow diagram
* Remembers added/removed services
* Secure Web services support
* Up-to-da...
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Created: 13/12/10 @ 10:44:04 | Last updated: 13/12/10 @ 16:28:58
Small workflows illustrating how R can be used within Taverna services
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Created: 12/05/11 @ 16:55:03 | Last updated: 12/05/11 @ 17:26:25
No description
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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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Created: Friday 25 February 2011 @ 14:35:41 (GMT)
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Created: 24/09/11 @ 17:18:56 | Last updated: 24/09/11 @ 17:18:57
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Uploaded as a test for viewing packs.
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Created: 21/11/11 @ 13:44:44 | Last updated: 21/11/11 @ 13:44:45
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
No description
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