myExperiment - Groups

Taverna 2

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Alan Williams

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

Created: 2010-10-28

Taverna 2

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Alan Williams

Reverse complement DNA (1)

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

Created: 2010-10-28

Taverna 2

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Alan Williams

Read SwissProt file (1)

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The Read_SwissProt_file service reads the file at the swiss_prot_file_url and converts the SwissProt data into Agave format. The result is then sent to the workflow's swiss_prot_data port.

Created: 2010-10-28 | Last updated: 2010-10-28

Taverna 2

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Alan Williams

Read GenBank file (1)

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The Read_GenBank_file service reads the file at the genbank_file_url and converts the GenBank data into Agave format. The result is then sent to the workflow's gen_bank_data port.

Created: 2010-10-28 | Last updated: 2010-10-28

Taverna 2

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Alan Williams

Encode byte[] to base64 (1)

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

Created: 2010-10-28

Taverna 2

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Alan Williams

Decode base64 to byte[] (1)

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

Created: 2010-10-28

Taverna 2

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Alan Williams

Example workflow for REST and XPath activi... (1)

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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...

Created: 2010-09-13 | Last updated: 2010-09-13

Credits: Sergejs Aleksejevs

Taverna 2

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Alan Williams

Multiple choice quiz (1)

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A fun example workflow showing user-interaction and service looping

Created: 2010-09-06

Credits: George

Attributions: Multiple Choice Quiz

Taverna 2

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Alan Williams

Spreadsheed Data Import Example (1)

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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/

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: David Withers

Taverna 2

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Alan Williams

Retrieve sequence in EMBL format (1)

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

Created: 2010-07-04 | Last updated: 2010-07-04

Credits: Franck Tanoh

Taverna 2

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Alan Williams

Pipelined list iteration (1)

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Perform multiple iterations of services in order to show pipelining

Created: 2010-07-04 | Last updated: 2010-07-04

Credits: Ian Dunlop Stian Soiland-Reyes

Taverna 2

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Alan Williams

GBSeq test (1)

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This workflow retrieves nucleotide and protein sequences with the literature and references associated to them given a protein and a nucleotide id.

Created: 2010-07-04 | Last updated: 2010-07-04

Credits: Franck Tanoh

Taverna 2

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Alan Williams

Fetch today's xkcd comic (1)

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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.

Created: 2010-07-04 | Last updated: 2010-07-04

Credits: Tomoinn Stian Soiland-Reyes

Taverna 2

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Alan Williams

Fetch PDB flatfile from RCSB server (1)

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Given an identifier such as '1crn' fetches the PDB format flatfile from the RCSB

Created: 2010-07-04 | Last updated: 2010-07-04

Credits: Tomoinn

Taverna 2

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Alan Williams

EBI_InterProScan for Taverna 2 (1)

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Perform an InterProScan analysis of a protein sequence using the EBIâ€™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 s...

Created: 2010-07-04 | Last updated: 2010-07-04

Credits: Alan Williams

Taverna 2

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Alan Williams

Demonstration of configurable iteration (1)

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

Created: 2010-07-04 | Last updated: 2010-07-04

Credits: Tomoinn

Taverna 2

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Alan Williams

BioMoby tutorial workflow (1)

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A workflow from part of the BioMoby tutorial

Created: 2010-07-04 | Last updated: 2010-07-04

Credits: EdwardKawas

Taverna 2

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Alan Williams

BiomartAndEMBOSSAnalysis (1)

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

Created: 2010-07-04 | Last updated: 2010-07-04

Credits: Alan Williams

Taverna 2

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Alan Williams

A workflow version of the EMBOSS tutorial (1)

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

Created: 2010-07-04 | Last updated: 2010-07-04

Credits: Tomoinn

Taverna 1

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Stian Soiland-Reyes

Find/show Taverna's home directory (1)

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Find Taverna's home directory and open that folder using Explorer/Finder/Gnome. This is the folder that is typically something like C:\Users\stain\AppData\Roaming\taverna-2.1.2, C:\Documents and settings\stain\taverna-2.1.2, /home/stain/.taverna-2.1.2 or /Users/stain/Library/Application support/taverna-2.1.2 This workflow should work on both Taverna 1 and Taverna 2. For Taverna 2 the beanshell script uses reflection to try to call ApplicationRuntime.getInstance().getApplicationHome() ...

Created: 2010-04-12 | Last updated: 2010-04-12

Credits: Stian Soiland-Reyes

Taverna 2

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Alan Williams

EBI_InterProScan_T2 (1)

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Perform an InterProScan analysis of a protein sequence using the EBIâ€™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 s...

Created: 2009-12-15

Credits: Alan Williams

Taverna 1

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Alan Williams

Warn - message parameter (1)

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

Created: 2008-09-27

Credits: Alan Williams

Taverna 1

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Alan Williams

Warn - title parameter (1)

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

Created: 2008-09-27

Credits: Alan Williams

Taverna 1

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Alan Williams

Warn - no parameters (1)

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

Created: 2008-09-27

Credits: Alan Williams

Taverna 1

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Alan Williams

Tell - message parameter (1)

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

Created: 2008-09-27

Credits: Alan Williams

Taverna 1

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Alan Williams

Tell - title parameter (1)

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

Created: 2008-09-27

Credits: Alan Williams

Taverna 1

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Alan Williams

Tell - no parameters (1)

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

Created: 2008-09-27

Credits: Alan Williams

Taverna 1

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Alan Williams

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

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

Created: 2008-09-27

Credits: Alan Williams

Taverna 1

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Alan Williams

Select - title and message parameters (1)

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

Created: 2008-09-27

Credits: Alan Williams

Taverna 1

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Alan Williams

Select - message parameter (1)

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

Created: 2008-09-27

Credits: Alan Williams

Taverna 1

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Alan Williams

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

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

Created: 2008-09-27

Credits: Alan Williams

Taverna 1

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Alan Williams

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

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

Created: 2008-09-27

Credits: Alan Williams

Taverna 1

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Alan Williams

List files by regex - single answer (1)

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