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User: Alan Williams
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Name: Alan Williams Joined: Monday 23 July 2007 @ 13:06:43 (GMT) Last seen: Friday 10 February 2012 @ 20:04:51 (GMT) Email (public): alanrw [at] cs.man.ac.uk Website: Not specified Location: Manchester, United Kingdom |
Alan Williams has been credited 201 times Alan Williams has an average rating of: 4.3 / 5 (6 ratings in total) for their items |
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Created: 05/12/11 @ 11:07:46 | Last updated: 05/12/11 @ 11:07:49
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This tutorial gives an introduction to Taverna, myExperiment and BioCatalogue, using a case study from ecological niche modelling.
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Created: 22/11/11 @ 17:59:12
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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Created: 22/11/11 @ 17:58:08
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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Created: 21/11/11 @ 14:50:08
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Created: 21/11/11 @ 13:49:41
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Created: 21/11/11 @ 13:47:13 | Last updated: 21/11/11 @ 13:47:14
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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Created: 21/11/11 @ 13:44:44 | Last updated: 21/11/11 @ 13:44:45
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Created: 13/07/11 @ 10:15:22
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Shell script to be downloaded for tool
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Created: 23/10/08 @ 12:06:50
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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Created: 26/09/08 @ 12:13:31
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
XSLT file to be used for example workflows
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Created: 26/09/08 @ 12:12:41
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
XML file to be used for example workflows
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Created: 25/09/08 @ 15:09:03
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Example SwissProt data to be used for Taverna examples.
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Created: 25/09/08 @ 15:00:28
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Example file containing GenBank data so that it can be used for example Taverna workflows
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Created: 10/02/12 @ 20:06:56 | Last updated: 11/02/12 @ 01:32:07
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow uses the REST API of BioGPS to
list the plugins and then allow the user to select which
plugin to use to display the input gene id
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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: 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: 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: 21/09/11 @ 08:39:27 | Last updated: 21/09/11 @ 08:41:26
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Uses the SpreadsheetImport service to import data from an Excel spreadsheet. The workflow imports two files and generates a single graph comparing the information from the two spreadsheets.
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Created: 14/09/11 @ 04:32:48 | Last updated: 14/09/11 @ 05:01:30
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License: Creative Commons Attribution-Share Alike 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: 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: 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 @ 10:19:35 | 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: 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 @ 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 @ 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 @ 13:07:58 | 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 @ 13:02:49 | Last updated: 12/07/11 @ 13:02:50
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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: 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: 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: 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 @ 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 @ 16:17:23
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License: Creative Commons Attribution 3.0 Unported License
This workflow uses an Rshell service to calculate the square of a numeric inputThis workflow uses an
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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 @ 17:16:08
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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 @ 17:00:19
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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 @ 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 @ 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 @ 17:23:04
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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 @ 17:11:34
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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 @ 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: 15/12/09 @ 22:12:50
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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: 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 @ 17:21:37
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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 @ 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: 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: 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 @ 17:27:21
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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 @ 17:15:38
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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 @ 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: 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: 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 @ 17:22:32
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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 @ 17:09:11
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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 @ 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 @ 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 @ 17:20:32
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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 @ 17:01:08
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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 @ 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: 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: 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 @ 17:25:57
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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 @ 17:12:08
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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: 15/12/09 @ 22:13:44
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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: 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 @ 17:22:04
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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 @ 17:08:34
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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 @ 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 @ 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 @ 17:03:55
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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: 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: 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: 15/12/09 @ 22:14:39
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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: 15/12/09 @ 22:12:00
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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: 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 @ 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 @ 17:35:33
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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 @ 17:19:50
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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 @ 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 @ 16:41:51
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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 @ 16:35:15
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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: 15/12/09 @ 22:17:11
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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: 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: 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 @ 17:03:20
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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 @ 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 @ 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 @ 17:13:27
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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 @ 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 @ 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 @ 16:37:04
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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: 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: 27/09/08 @ 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 @ 17:34:40
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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 @ 17:24:13
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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 @ 17:19:17
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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 @ 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 @ 16:34:35
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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: 15/12/09 @ 22:15:21
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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: 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: 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 @ 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: 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 @ 17:12:38
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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 @ 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 @ 16:43:43
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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: 15/12/09 @ 22:17:56
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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: 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 @ 17:18:46
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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 @ 17:09:50
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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 @ 17:28:46
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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 @ 17:17:24
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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 @ 17:11:01
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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 @ 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 @ 16:42:40
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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: 15/12/09 @ 22:16:23
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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: 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: 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 @ 17:26:37
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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 @ 17:15:02
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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 @ 17:14:32
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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 @ 17:07:44
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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 @ 17:07:08
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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 @ 17:06:26
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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 @ 17:05:30
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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 @ 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 @ 16:56:32
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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 @ 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 @ 17:21:03
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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 @ 17:02:41
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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 @ 17:13:59
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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 @ 17:34:09
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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 @ 17:25:20
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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: 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: 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 @ 17:24:44
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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 @ 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: 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: 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 @ 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 @ 16:52:59
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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 @ 16:52:16
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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: 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 @ 10:03:22
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License: Creative Commons Attribution 3.0 Unported License
This workflow uses an Rshell service to calculate 100 modulus the integer input
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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: 29/11/10 @ 13:18:04 | Last updated: 29/11/10 @ 13:18:05
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License: Creative Commons Attribution 3.0 Unported License
This workflow contains two services. The file_writer uses a File in R to output a string. The file_reader uses a File in R to input a string, the contents of which are output.
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Created: 29/11/10 @ 13:43:11
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License: Creative Commons Attribution 3.0 Unported License
This workflow shows how string vectors can be used to transfer a complex R object (in this case a matrix) between Rshell services
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Created: 26/11/10 @ 15:44:15 | Last updated: 26/11/10 @ 15:44:18
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Checks what the logical_input is in R. For an logical_input of
TRUE - is_false should be FALSE and is_true TRUE
FALSE - is_false should be TRUE and is_true FALSE
For any other input values, is_false and is_true should both be NA
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Created: 26/11/10 @ 15:13:46 | Last updated: 26/11/10 @ 15:13:48
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This workflow uses an R service running on localhost to calculate sin(0.45)
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Created: 08/11/10 @ 13:37:33 | Last updated: 08/11/10 @ 13:44:33
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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: 15/09/09 @ 15:05:11
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This is the Taverna 2 version of the Biomart and Emboss Analysis workflow
http://www.myexperiment.org/workflows/158
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.
Previous versions of this workflow only returned sequences with an ID mapped to a MIM_morbid_accession. This was primarily to reduce the numbe...
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Created: 05/05/08 @ 17:53:21 | Last updated: 05/05/08 @ 17:54:41
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Use the local java plugins and some filtering operations to fetch the comic strip image from http://xkcd.com/ Based on the FetchDailyDilbert workflow.
I just uploaded this example so I can play around with the myexperiment api.
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Created: 05/10/11 @ 15:37:43 | Last updated: 05/10/11 @ 15:37:40
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This workflow uses time series data from Rob Hyndman's Time Series Data Library (TSDL) and graphs it with Google charts. It also provides the citation information with the current date. The outputs are a Google Chart and the corresponding citation information.
The inputs are URL strings for two datasets provided by Rob Hyndman under the subject of Ecology. These datasets include the annual number of lynx pelts and the annual unit price of lynx pelts during the year range 1857 -1911.
This...
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Created: 13/01/10 @ 18:52:45 | Last updated: 17/11/10 @ 14:13:20
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Designed from an example workflow at Traverna, this workflow retrieves a set of sequences from UniProt, then simultaneously scans for transmembrane regions and performs a multiple alignment using EMMA. The alignment is then plotted to a set of PNG images, followed by a profile analysis using prophecy and prophet tools.
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Created: 21/09/11 @ 02:52:40 | Last updated: 21/09/11 @ 03:23:11
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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. Prompts the user to enter a title for the histogram.
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Created: 09/10/11 @ 12:44:10 | Last updated: 09/10/11 @ 12:46:44
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This workflow takes data about agricultural production in New Jersey and New York from 1960 -1965, to compare productivity in broccoli growing.
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Created: 06/10/11 @ 03:53:12 | Last updated: 06/10/11 @ 04:12:18
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow gunzips a *.gbk.gz file, converts it to XML (via agavewriter) and finds the Element ID.
Does not work on *.gz files larger than 10MB.
I upped the JVM settings on Taverna to:
<key>VMOptions</key>
<string>-Xmx4096m -XX:MaxPermSize=1024m</string>
Created my own agave.dtd to get the XPath service to work the XML file generated from the Read_GenBank_File service. You will need to ...
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Created: 27/11/11 @ 12:44:23 | Last updated: 29/11/11 @ 15:34:08
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This workflow uses GBIF to search and report species occurrence data and then displays them on Google Earth. An interactive step then allows you to alter the co-ordinates of data displayed.
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Created: 21/09/11 @ 05:38:20 | Last updated: 21/09/11 @ 05:41:25
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Example using the SpreadsheetImport service to import data from an Excel spreadsheet. The workflow imports the file spreadsheet file FertilizerUse.xlsx and generates a graph from the date. The source data is from http://www.myexperiment.
org/files/568/download/FertilizerUse.xls and ERS, TVA (Tennessee Valley Authority), AAPFCO (Association of American Plant Food Control Officials), TFI (The Fertilizer Institute).
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Created: 21/09/11 @ 18:09:09 | Last updated: 21/09/11 @ 18:09:06
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Based on Spreadsheet Import Example by David WithersSusan
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: 21/09/11 @ 18:13:12 | Last updated: 21/09/11 @ 18:13:09
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Tried to show 2 charts simulatneously.
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Created: 27/01/11 @ 17:03:03 | Last updated: 12/05/11 @ 13:31:41
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This workflow retrieves all genes on human chromosome 22 that are associated with a disease and aligns the upstream regions with mouse and rat homologues. The alignments are plotted and corresponding sequence ids are also returned.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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