Gb User: Alan Williams Admin_badge

1217?size=160x160

Name: Alan Williams

Joined: Monday 23 July 2007 13:06:43 (UTC)

Last seen: Monday 10 May 2021 10:31:05 (UTC)

Email (public): alan.r.williams [at] manchester.ac.uk

Website: http://www.taverna.org.uk

Location: Manchester, United Kingdom

Alan Williams has been credited 237 times

Alan Williams has an average rating of:

4.5 / 5

(8 ratings in total)

for their items

Description/summary not set


Other contact details:

Not specified

Interests:

Workflows, web services, data handling

Field/Industry: Computer science

Occupation/Role(s): Technical manager

Organisation(s):

University of Manchester

 

Note: some items may not be visible to you, due to viewing permissions.


Contents (click to expand/contract)

Workflow Metabolite pathway search (1)

Thumb
The workflow searches for metabolomic pathways that match the entered keywords and returns information about the chosen pathway

Created: 2014-12-18

Credits: User Alan Williams

Workflow Choose_id (1)

Thumb
Make a choice based upon displayed names and return the id corresponding to the choice

Created: 2014-12-18 | Last updated: 2014-12-18

Workflow Extract columns (3)

Thumb
Extracts column data from a newline and tab separated string

Created: 2014-12-18 | Last updated: 2014-12-18

Workflow Increment an integer (1)

Thumb
This workflow uses R to increment the input integer

Created: 2014-10-03

Credits: User Alan Williams

Workflow Species chooser (1)

Thumb
In your browser, choose between marmots and horseshoe crabs

Created: 2014-10-03

Credits: User Alan Williams

Workflow Get weather information (1)

Thumb
Get the weather forcast of the day for you city. Info display: wind, visibility, temperature, sky conditions and pressure.

Created: 2014-10-03

Credits: User Alan Williams User Franck Tanoh

Attributions: Workflow Get weather information

Workflow Species Occurrence (1)

Thumb
Retrieve the first 100 occurrences of a species in Darwin format

Created: 2014-10-03

Credits: User Alan Williams

Workflow Construct viewparams (1)

Thumb
Construct the viewparams parameter to OBIS services

Created: 2014-10-02

Credits: User Alan Williams

Workflow EBI_InterproScan (1)

Thumb
Perform EBI Interproscan

Created: 2014-07-16 | Last updated: 2014-07-16

Workflow Experiments for gene (2)

Thumb
This workflow uses the Allen Brain REST API to fetch the experiements corresponding to a named gene

Created: 2014-07-15 | Last updated: 2014-07-15

Credits: User Alan Williams

Workflow Download images for gene (3)

Thumb
This workflow downloads the first few images corresponding to experiments for the specified gene

Created: 2014-07-13 | Last updated: 2014-07-15

Credits: User Alan Williams

Workflow Demonstration of configurable iteration (1)

Thumb
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: 2014-07-09

Credits: User Alan Williams

Attributions: Workflow Demonstration of configurable iteration

Workflow EBI_InterproScan_broken (1)

Thumb
This workflow performs an interproscan at the EBI on sequences provided as input. The output is provided as text and xml. 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. Note that this workflow is deliberately broken

Created: 2014-07-09

Credits: User Alan Williams User Katy Wolstencroft User Hamish McWilliam

Attributions: Workflow EBI_InterproScan_NewServices

Workflow split_by_newline (1)

Thumb
Splits a string into a list of strings. The initial string must use newline as a separator

Created: 2014-06-24 | Last updated: 2014-10-02

Workflow An iframe test (1)

Thumb
But this works

Created: 2014-03-28

Credits: User Alan Williams

Workflow Hello World (1)

Thumb
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".

Created: 2014-03-06

Workflow Extract_citations (3)

Thumb
Corrected XPath

Created: 2013-12-09 | Last updated: 2013-12-09

Workflow Extract_positions (2)

Thumb
Changed output port name

Created: 2013-12-01 | Last updated: 2013-12-01

Workflow Extract_data_providers (2)

Thumb
Changed output port name

Created: 2013-12-01 | Last updated: 2013-12-01

Workflow nested_echo (2)

Thumb
Just calls the echoer

Created: 2013-10-30 | Last updated: 2013-10-30

Workflow echoer (6)

Thumb
Renamed beanshell

Created: 2013-10-25 | Last updated: 2014-05-07

Workflow String upload (1)

Thumb
The component uploads the string within the InputBody to the File_name within the fixed WebDAV

Created: 2013-09-16 | Last updated: 2014-02-03

Workflow Fundamental matrix (1)

Thumb
This component calculates the fundamental matrix from a stage matrix

Created: 2013-05-28

Workflow ref (2)

Thumb
ref

Created: 2013-05-28 | Last updated: 2013-05-28

Workflow Untitled (1)

Thumb
v2

Created: 2013-03-15

Workflow Untitled (1)

Thumb
2

Created: 2013-03-15

Workflow Untitled (1)

Thumb
Initial version

Created: 2013-03-15

Workflow Untitled (1)

Thumb
Initial version

Created: 2013-03-15

Uploader
Project Biovel

Workflow Data publication example (1)

Thumb
This workflow gives an example of an interaction that makes use of published input data. The data is published on the webdav and the URL passed to the HTML page.

Created: 2012-10-11

Credits: User Alan Williams

Workflow Blah (1)

No description

Created: 2012-09-26 | Last updated: 2012-09-26

Credits: User Alan Williams

Workflow Unix tool service using string replacement (1)

Thumb
The tool service outputs a message that greets using the names specified on Greet's input ports.

Created: 2012-04-05

Credits: User Alan Williams

Workflow Spreadsheet Import Example (1)

Thumb
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: 2012-04-05

Credits: User Alan Williams

Workflow Simple Python example (1)

Thumb
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.

Created: 2012-04-05

Credits: User Alan Williams

Workflow Secure Web service call example (2)

Thumb
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. You ...

Created: 2012-04-05 | Last updated: 2013-06-11

Credits: User Alan Williams

Workflow Secure REST service call example (2)

Thumb
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.

Created: 2012-04-05 | Last updated: 2014-01-16

Credits: User Alan Williams

Workflow Retrieve sequence in EMBL format (1)

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

Created: 2012-04-05 | Last updated: 2012-04-05

Credits: User Alan Williams

Workflow Render gene via BioGPS (3)

Thumb
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

Created: 2012-04-05 | Last updated: 2012-05-23

Credits: User Alan Williams

Workflow Pipelined list iteration (1)

Thumb
Perform multiple iterations of services in order to show pipelining

Created: 2012-04-05

Credits: User Alan Williams

Workflow Numerically adding two values. (1)

Thumb
This workflow relies on a Unix system. It wraps the "bc" command line calculator. It downloads the calculation script from a URL.

Created: 2012-04-05

Credits: User Alan Williams

Workflow Multiple choice quiz (1)

Thumb
A fun example workflow showing user-interaction and service looping

Created: 2012-04-05 | Last updated: 2012-04-05

Credits: User Alan Williams

Workflow Hello World (1)

Thumb
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".

Created: 2012-04-05 | Last updated: 2014-03-03

Credits: User Alan Williams

Workflow Hello Anyone (1)

Thumb
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".

Created: 2012-04-05 | Last updated: 2014-03-03

Credits: User Alan Williams

Workflow GBSeq test (1)

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

Created: 2012-04-05 | Last updated: 2012-04-05

Credits: User Alan Williams

Workflow Fetch Dragon images from BioMoby (1)

Thumb
Fetch images and annotations of snapdragons

Created: 2012-04-05 | Last updated: 2012-04-05

Credits: User Alan Williams

Workflow Fetch today's xkcd comic (1)

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

Created: 2012-04-05

Credits: User Alan Williams

Workflow Fetch PDB flatfile from RCSB server (1)

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

Created: 2012-04-05

Credits: User Alan Williams

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

Thumb
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...

Created: 2012-04-05 | Last updated: 2012-04-05

Credits: User Alan Williams

Workflow Example of explicit looping (1)

Thumb
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)

Created: 2012-04-05

Credits: User Alan Williams

Workflow Example of conditional invocation (1)

Thumb
This workflow demonstrates how nested workflows can be conditionally invoked

Created: 2012-04-05 | Last updated: 2012-04-05

Credits: User Alan Williams

Workflow Example for external tools with zip and unzip (1)

Thumb
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/

Created: 2012-04-05 | Last updated: 2012-04-05

Credits: User Alan Williams

Workflow EBI_InterproScan_NewServices (2)

Thumb
This workflow performs an interproscan at the EBI on sequences provided as input. The output is provided as text and xml. 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.

Created: 2012-04-05 | Last updated: 2014-04-09

Credits: User Alan Williams

Workflow Demonstration of configurable iteration (1)

Thumb
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: 2012-04-05 | Last updated: 2012-04-05

Credits: User Alan Williams

Workflow BioMoby tutorial workflow (1)

Thumb
A workflow from part of the BioMoby tutorial

Created: 2012-04-05 | Last updated: 2012-04-05

Credits: User Alan Williams

Workflow BiomartAndEMBOSSMouseRat (1)

Thumb
This workflow retrieves all genes on human chromosome 22 that are associated with a disease and aligns the upstream regions of the mouse and rat homologues. The alignments are plotted and corresponding sequence ids are also returned.

Created: 2012-04-05

Credits: User Alan Williams

Workflow BiomartAndEMBOSSMouseRat (1)

Thumb
This workflow retrieves all genes on human chromosome 22 that are associated with a disease and aligns the upstream regions of the mouse and rat homologues. The alignments are plotted and corresponding sequence ids are also returned.

Created: 2012-04-05

Credits: User Katy Wolstencroft

Workflow Example of interaction via HTML page (1)

Thumb
No description

Created: 2012-03-05 | Last updated: 2012-03-05

Credits: User Alan Williams

Workflow Render gene via BioGPS (2)

Thumb
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

Created: 2012-02-10 | Last updated: 2012-02-15

Credits: User Alan Williams

Workflow Example of explicit looping (1)

Thumb
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)

Created: 2011-11-15 | Last updated: 2011-11-15

Credits: User Alan Williams

Workflow Example of conditional invocation (1)

Thumb
This workflow demonstrates how nested workflows can be conditionally invoked

Created: 2011-11-15 | Last updated: 2011-11-15

Credits: User Alan Williams

Workflow Simple Python example (1)

Thumb
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.

Created: 2011-10-06 | Last updated: 2011-10-06

Credits: User Alan Williams

Workflow Secure Web service call example (1)

Thumb
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.

Created: 2011-07-14 | Last updated: 2011-07-14

Credits: User Alex Nenadic

Workflow Secure REST service call example (1)

Thumb
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.

Created: 2011-07-14 | Last updated: 2011-07-14

Credits: User Alex Nenadic

Workflow Unix tool for numerically adding two values. (1)

Thumb
This workflow relies on a Unix system. It wraps the "bc" command line calculator. It downloads the calculation script from a URL.

Created: 2011-07-13 | Last updated: 2011-07-13

Credits: User Alan Williams User Steffen Möller

Workflow Unix tools with zip, unzip and diff (1)

Thumb
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/

Created: 2011-07-13 | Last updated: 2011-07-13

Credits: User Alan Williams User Steffen Möller

Attributions: Workflow Example for external tools with gzip and gunzip

Workflow Unix tool service using string replacement (1)

Thumb
The tool service outputs a message that greets using the names specified on Greet's input ports.

Created: 2011-07-13 | Last updated: 2011-07-13

Credits: User Alan Williams

Workflow A workflow version of the EMBOSS tutorial (1)

Thumb
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: 2011-07-12 | Last updated: 2011-07-12

Credits: User Tomoinn

Attributions: Workflow A workflow version of the EMBOSS tutorial

Workflow BioMoby tutorial workflow (1)

Thumb
A workflow from part of the BioMoby tutorial

Created: 2011-07-12 | Last updated: 2011-07-12

Credits: User EdwardKawas

Workflow Demonstration of configurable iteration (1)

Thumb
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: 2011-07-12 | Last updated: 2011-07-12

Credits: User Alan Williams User Tomoinn

Workflow Fetch PDB flatfile from RCSB server (1)

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

Created: 2011-07-12 | Last updated: 2011-07-12

Credits: User Alan Williams User Tomoinn

Workflow Fetch today's xkcd comic (1)

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

Created: 2011-07-12 | Last updated: 2011-07-12

Credits: User Tomoinn User Stian Soiland-Reyes

Attributions: Workflow Fetch today's xkcd comic

Workflow GBSeq test (1)

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

Created: 2011-07-12 | Last updated: 2011-07-12

Credits: User Franck Tanoh

Attributions: Workflow GBSeq test

Workflow Pipelined list iteration (1)

Thumb
Perform multiple iterations of services in order to show pipelining

Created: 2011-07-12 | Last updated: 2011-07-12

Credits: User Ian Dunlop User Stian Soiland-Reyes

Attributions: Workflow Pipelined list iteration

Workflow Retrieve sequence in EMBL format (1)

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

Created: 2011-07-12 | Last updated: 2011-07-12

Credits: User Franck Tanoh

Attributions: Workflow Retrieve sequence in EMBL format

Workflow Spreadsheet Import Example (1)

Thumb
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: 2011-07-12 | Last updated: 2011-07-12

Credits: User David Withers

Attributions: Workflow Spreadsheed Data Import Example

Workflow Fetch Dragon images from BioMoby (1)

Thumb
Fetch images and annotations of snapdragons

Created: 2011-07-12 | Last updated: 2011-07-12

Credits: User Tomoinn

Workflow Multiple choice quiz (1)

Thumb
A fun example workflow showing user-interaction and service looping

Created: 2011-07-12 | Last updated: 2011-07-12

Credits: User Alan Williams User George

Attributions: Workflow Multiple choice quiz

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

Thumb
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...

Created: 2011-07-12 | Last updated: 2011-07-12

Credits: User Alan Williams

Workflow EBI_InterproScan_NewServices (1)

Thumb
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.

Created: 2011-07-12 | Last updated: 2011-07-12

Credits: User Alan Williams User Katy Wolstencroft

Attributions: Workflow EBI_InterproScan_NewServices

Workflow BiomartAndEMBOSSDisease (2)

Thumb
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.

Created: 2011-07-12 | Last updated: 2012-03-19

Credits: User Katy Wolstencroft

Attributions: Workflow BiomartAndEMBOSSDisease

Workflow Dot viewing (1)

Thumb
No description

Created: 2011-05-12

Workflow R generic example (1)

Thumb
This workflow shows how string vectors can be used to transfer a complex R object (in this case a matrix) between Rshell services

Created: 2010-11-29

Credits: User Alan Williams

Workflow R Text-file example (1)

Thumb
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.

Created: 2010-11-29 | Last updated: 2010-11-29

Credits: User Alan Williams

Workflow R PNG-value example (2)

Thumb
This workflow produces a PNG plot on the figure port.

Created: 2010-11-29 | Last updated: 2010-11-29

Credits: User Alan Williams

Workflow R integer vector example (1)

Thumb
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.

Created: 2010-11-29 | Last updated: 2010-11-29

Credits: User Alan Williams

Workflow R integer workflow (1)

Thumb
This workflow uses an Rshell service to calculate 100 modulus the integer input

Created: 2010-11-29

Credits: User Alan Williams

Workflow R string vector example (1)

Thumb
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

Created: 2010-11-26 | Last updated: 2010-11-26

Credits: User Alan Williams

Workflow R integer vector example (1)

Thumb
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.

Created: 2010-11-26 | Last updated: 2010-11-26

Credits: User Alan Williams

Workflow R logical vector workflow (1)

Thumb
The workflow returns a list containing the logical inversion of the logical vector input

Created: 2010-11-26 | Last updated: 2010-11-26

Credits: User Alan Williams

Workflow R string workflow (1)

Thumb
This workflow determines the lower case version of the input string.

Created: 2010-11-26 | Last updated: 2010-11-26

Credits: User Alan Williams

Workflow R numeric workflow (1)

Thumb
This workflow uses an Rshell service to calculate the square of a numeric inputThis workflow uses an

Created: 2010-11-26

Credits: User Alan Williams

Workflow R logical workflow (1)

Thumb
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

Created: 2010-11-26 | Last updated: 2010-11-26

Credits: User Alan Williams

Workflow A Basic example R workflow (3)

Thumb
This workflow uses an R service running on localhost to calculate sin(0.45)

Created: 2010-11-26 | Last updated: 2014-08-20

Credits: User Alan Williams

Workflow Ask - title and message parameters (1)

Thumb
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.

Created: 2010-10-29

Workflow Ask - just title parameter (1)

Thumb
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.

Created: 2010-10-29 | Last updated: 2010-10-29

Workflow Ask - just message parameter (1)

Thumb
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.

Created: 2010-10-29

Workflow Ask - no parameters (1)

Thumb
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.

Created: 2010-10-29

Workflow String list union - yielding empty list (1)

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

Created: 2010-10-29 | Last updated: 2010-10-29

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

Thumb
The string list union service takes in ['a','b','c'] and ['a','e','c'] and returns a list equivalent to ['a','b','c','e'].

Created: 2010-10-29

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

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

Created: 2010-10-29

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

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

Created: 2010-10-29

Workflow String list difference - yielding empty list (1)

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

Created: 2010-10-29

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

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

Created: 2010-10-29

Workflow Split string into string list by regular e... (2)

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

Created: 2010-10-29 | Last updated: 2010-10-29

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

Thumb
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']

Created: 2010-10-29

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

Thumb
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']

Created: 2010-10-29

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

Thumb
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: 2010-10-29

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

Thumb
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: 2010-10-29 | Last updated: 2010-10-29

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

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

Created: 2010-10-29 | Last updated: 2010-10-29

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

Thumb
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.

Created: 2010-10-29

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

Thumb
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.

Created: 2010-10-29

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

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

Created: 2010-10-29

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

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

Created: 2010-10-29

Workflow Concatenate two strings (1)

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

Created: 2010-10-29

Workflow Concatenate two strings - empty strings (1)

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

Created: 2010-10-29 | Last updated: 2010-10-29

Workflow Byte Array to string - non empty value (1)

Thumb
The beanshell converts the string 'hello' to a byte array which is then converted back to the string 'hello' by the Byte_Array_to_string service.

Created: 2010-10-29 | Last updated: 2010-10-29

Workflow Byte Array to string - empty value (1)

Thumb
The beanshell converts the empty string '' to a byte array which is then converted back to the empty string '' by the Byte_Array_To_string service.

Created: 2010-10-29 | Last updated: 2010-10-29

Workflow Echo_with_occasional_failure (1)

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

Created: 2010-10-29 | Last updated: 2010-10-29

Workflow Always fails - two parameters (1)

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

Created: 2010-10-29 | Last updated: 2010-10-29

Workflow Always fails - one parameter (1)

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

Created: 2010-10-29 | Last updated: 2010-10-29

Workflow Always fails - no parameters (1)

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

Created: 2010-10-29 | Last updated: 2010-10-29

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

Thumb
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.

Created: 2010-10-29 | Last updated: 2010-10-29

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

Thumb
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.

Created: 2010-10-29

Workflow Get image URLs from HTTP document and outp... (2)

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

Created: 2010-10-29 | Last updated: 2014-02-12

Workflow Get image URLs from HTTP document - no images (1)

Thumb
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.

Created: 2010-10-29 | Last updated: 2010-10-29

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

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

Created: 2010-10-29 | Last updated: 2010-10-29

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

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

Created: 2010-10-29

Workflow Remove duplicate strings (1)

Thumb
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'].

Created: 2010-10-29

Workflow Remove duplicate strings - empty list (1)

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

Created: 2010-10-29 | Last updated: 2010-10-29

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

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

Created: 2010-10-28

Workflow Merge string list to a string - default se... (1)

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

Created: 2010-10-28

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

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

Created: 2010-10-28

Workflow Flatten list (1)

Thumb
The flatten_list service takes the list [['a'], ['b'], ['c'], ['d']] and outputs the list ['a', 'b', 'c', 'd', 'e'].

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

Workflow Write text file - specified value (1)

Thumb
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.

Created: 2010-10-28

Workflow Write text file - overwriting content (1)

Thumb
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.

Created: 2010-10-28

Workflow Write text file - empty string value (1)

Thumb
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.

Created: 2010-10-28

Workflow Read text file - several lines (1)

Thumb
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'.

Created: 2010-10-28

Workflow Read text file (1)

Thumb
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'.

Created: 2010-10-28

Workflow Read text file - empty file (1)

Thumb
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 ''.

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

Workflow List files by regex - single match (1)

Thumb
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.

Created: 2010-10-28

Workflow List files by regex - several answers (1)

Thumb
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.

Created: 2010-10-28

Workflow List files by regex - no matches (1)

Thumb
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.

Created: 2010-10-28

Workflow List files by regex - empty directory (1)

Thumb
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.

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

Workflow List files by extension - single match (1)

Thumb
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.

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

Workflow List files by extension - several matches (1)

Thumb
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.

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

Workflow List files by extension - no matches (1)

Thumb
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.

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

Workflow List files by extension - empty directory (1)

Thumb
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.

Created: 2010-10-28

Workflow Get Environment Variables as XML (1)

Thumb
The Get_Environment_Variables_as_XML service returns an XML file containing a set of property elements each of which contains the name and value of an environment variable.The Get_Environment_Variables_as_XML service returns an XML file containing

Created: 2010-10-28

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

Thumb
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 output port of the workflow.

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

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

Thumb
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 ...

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

Workflow Concatenate files - multiple files (1)

Thumb
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...

Created: 2010-10-28

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

Thumb
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 ...

Created: 2010-10-28

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

Thumb
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...

Created: 2010-10-28

Workflow Transcribe DNA (1)

Thumb
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

Workflow Reverse complement DNA (1)

Thumb
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

Workflow Read SwissProt file (1)

Thumb
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

Workflow Read GenBank file (1)

Thumb
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

Workflow Encode byte[] to base64 (1)

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

Created: 2010-10-28

Workflow Decode base64 to byte[] (1)

Thumb
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

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

Thumb
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: User Sergejs Aleksejevs

Workflow Multiple choice quiz (1)

Thumb
A fun example workflow showing user-interaction and service looping

Created: 2010-09-06

Credits: User George

Attributions: Workflow Multiple Choice Quiz

Workflow Spreadsheed Data Import Example (1)

Thumb
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: User David Withers

Workflow Retrieve sequence in EMBL format (1)

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

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

Credits: User Franck Tanoh

Workflow Pipelined list iteration (1)

Thumb
Perform multiple iterations of services in order to show pipelining

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

Credits: User Ian Dunlop User Stian Soiland-Reyes

Workflow GBSeq test (1)

Thumb
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: User Franck Tanoh

Workflow Fetch today's xkcd comic (1)

Thumb
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: User Tomoinn User Stian Soiland-Reyes

Workflow Fetch PDB flatfile from RCSB server (1)

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

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

Credits: User Tomoinn

Workflow EBI_InterProScan for Taverna 2 (1)

Thumb
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 s...

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

Credits: User Alan Williams

Workflow Demonstration of configurable iteration (1)

Thumb
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: User Tomoinn

Workflow BioMoby tutorial workflow (1)

Thumb
A workflow from part of the BioMoby tutorial

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

Credits: User EdwardKawas

Workflow BiomartAndEMBOSSAnalysis (1)

Thumb
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: User Alan Williams

Workflow A workflow version of the EMBOSS tutorial (1)

Thumb
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: User Tomoinn

Workflow Fetch Dragon images from BioMoby (2)

Thumb
Fetch images and annotations of snapdragons

Created: 2009-12-15 | Last updated: 2010-07-14

Credits: User EdwardKawas

Workflow Retrieve sequence in EMBL format (1)

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

Created: 2009-12-15

Credits: User Alan Williams

Workflow Pipelined list iteration (1)

Thumb
Perform multiple iterations of services in order to show pipelining

Created: 2009-12-15

Credits: User Alan Williams

Workflow GBSeq test (1)

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

Created: 2009-12-15

Credits: User Alan Williams

Workflow Fetch today's xkcd comic (1)

Thumb
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: 2009-12-15

Credits: User Alan Williams

Workflow Fetch PDB flatfile from RCSB server (1)

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

Created: 2009-12-15

Credits: User Alan Williams

Workflow EBI_InterProScan_T2 (1)

Thumb
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 s...

Created: 2009-12-15

Credits: User Alan Williams

Workflow Demonstration of configurable iteration (1)

Thumb
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: 2009-12-15

Credits: User Alan Williams

Workflow BiomartAndEMBOSSAnalysis (1)

Thumb
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: 2009-12-15

Credits: User Alan Williams

Workflow A workflow version of the EMBOSS tutorial (1)

Thumb
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: 2009-12-15

Credits: User Alan Williams

Workflow BiomartAndEMBOSSAnalysis (4)

Thumb
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: 2009-09-15 | Last updated: 2015-01-26

Workflow Retrieve sequence in EMBL format (3)

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

Created: 2009-06-17

Credits: User Franck Tanoh User Tomoinn User Stuart Owen

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

Thumb
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.

Created: 2008-09-29

Credits: User Alan Williams

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

Thumb
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.

Created: 2008-09-29

Credits: User Alan Williams

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

Thumb
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'].

Created: 2008-09-29

Credits: User Alan Williams

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

Thumb
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.

Created: 2008-09-29

Credits: User Alan Williams

Workflow Flatten list - three depth (2)

Thumb
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'].

Created: 2008-09-29 | Last updated: 2008-09-30

Credits: User Alan Williams

Workflow Flatten list - two depth (1)

Thumb
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']].

Created: 2008-09-29

Credits: User Alan Williams

Workflow Echo_with_occasional_failure-1 (1)

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

Created: 2008-09-29

Credits: User Alan Williams

Workflow Write text file - overwriting content (1)

Thumb
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.

Created: 2008-09-27

Credits: User Alan Williams

Workflow Write text file - empty string value (1)

Thumb
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.

Created: 2008-09-27

Credits: User Alan Williams

Workflow Write text file - specified value (1)

Thumb
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.

Created: 2008-09-27

Credits: User Alan Williams

Workflow Warn - title and message parameters (1)

Thumb
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.

Created: 2008-09-27

Credits: User Alan Williams

Workflow Warn - message parameter (1)

Thumb
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: User Alan Williams

Workflow Warn - title parameter (1)

Thumb
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: User Alan Williams

Workflow Warn - no parameters (1)

Thumb
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: User Alan Williams

Workflow Transform XML - output file by extension (1)

Thumb
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...

Created: 2008-09-27

Credits: User Alan Williams

Workflow Transform XML - explicit output file (1)

Thumb
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...

Created: 2008-09-27

Credits: User Alan Williams

Workflow Transform XML - no output file (1)

Thumb
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...

Created: 2008-09-27

Credits: User Alan Williams

Workflow Transcribe DNA (1)

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

Created: 2008-09-27

Credits: User Alan Williams

Workflow Test always fails - two parameters (1)

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

Created: 2008-09-27

Credits: User Alan Williams

Workflow Test always fails - one parameter (1)

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

Created: 2008-09-27

Credits: User Alan Williams

Workflow Test always fails - no parameters (1)

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

Created: 2008-09-27

Credits: User Alan Williams

Workflow Tell - title and message parameters (1)

Thumb
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: User Alan Williams

Workflow Tell - message parameter (1)

Thumb
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: User Alan Williams

Workflow Tell - title parameter (1)

Thumb
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: User Alan Williams

Workflow Tell - no parameters (1)

Thumb
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: User Alan Williams

Workflow String list union - yielding empty list (1)

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

Created: 2008-09-27

Credits: User Alan Williams

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

Thumb
The string list union service takes in ['a','b','c'] and ['a','e','c'] and returns a list equivalent to ['a','b','c','e'].

Created: 2008-09-27

Credits: User Alan Williams

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

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

Created: 2008-09-27

Credits: User Alan Williams

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

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

Created: 2008-09-27

Credits: User Alan Williams

Workflow String list difference - yielding empty list (1)

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

Created: 2008-09-27

Credits: User Alan Williams

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

Thumb
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: User Alan Williams

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

Thumb
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']

Created: 2008-09-27

Credits: User Alan Williams

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

Thumb
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']

Created: 2008-09-27

Credits: User Alan Williams

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

Thumb
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']

Created: 2008-09-27

Credits: User Alan Williams

Workflow Select - single element list (1)

Thumb
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.

Created: 2008-09-27

Credits: User Alan Williams

Workflow Select - title and message parameters (1)

Thumb
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: User Alan Williams

Workflow Select - message parameter (1)

Thumb
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: User Alan Williams

Workflow Select - title parameter (1)

Thumb
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.

Created: 2008-09-27

Credits: User Alan Williams

Workflow Select - no title or message parameters (1)

Thumb
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.

Created: 2008-09-27

Credits: User Alan Williams

Workflow Reverse complement DNA (1)

Thumb
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: 2008-09-27

Credits: User Alan Williams

Workflow Remove duplicate strings - empty list (1)

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

Created: 2008-09-27

Credits: User Alan Williams

Workflow Remove duplicate strings (1)

Thumb
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'].

Created: 2008-09-27

Credits: User Alan Williams

Workflow Read text file - empty file (1)

Thumb
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 ''.

Created: 2008-09-27

Credits: User Alan Williams

Workflow Read text file - several lines (1)

Thumb
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'.

Created: 2008-09-27

Credits: User Alan Williams

Workflow Read text file (1)

Thumb
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'.

Created: 2008-09-27

Credits: User Alan Williams

Workflow Read SwissProt file (1)

Thumb
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.

Created: 2008-09-27

Credits: User Alan Williams

Workflow Read GenBank file (1)

Thumb
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.

Created: 2008-09-27

Credits: User Alan Williams

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

Thumb
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: User Alan Williams

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

Thumb
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: User Alan Williams

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

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

Created: 2008-09-27

Credits: User Alan Williams

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

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

Created: 2008-09-27

Credits: User Alan Williams

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

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

Created: 2008-09-27

Credits: User Alan Williams

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

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

Created: 2008-09-27

Credits: User Alan Williams

Workflow List files by regex - empty directory (1)

Thumb
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.

Created: 2008-09-27

Credits: User Alan Williams

Workflow List files by regex - no answer (1)

Thumb
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.

Created: 2008-09-27

Credits: User Alan Williams

Workflow List files by regex - single answer (1)

Thumb
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.

Created: 2008-09-27

Credits: User Alan Williams

Workflow List files by regex - several answers (1)

Thumb
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.

Created: 2008-09-27

Credits: User Alan Williams

Workflow List files by extension - empty directory (1)

Thumb
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.

Created: 2008-09-27

Credits: User Alan Williams

Workflow List files by extension - no answer (1)

Thumb
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.

Created: 2008-09-27

Credits: User Alan Williams

Workflow List files by extension - single answer (1)

Thumb
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.

Created: 2008-09-27

Credits: User Alan Williams

Workflow List files by extension - several answers (1)

Thumb
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.

Created: 2008-09-27

Credits: User Alan Williams

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

Thumb
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.

Created: 2008-09-27

Credits: User Alan Williams

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

Thumb
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.

Created: 2008-09-27

Credits: User Alan Williams

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

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

Created: 2008-09-27

Credits: User Alan Williams

Workflow Get image URLs from HTTP document (1)

Thumb
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.

Created: 2008-09-27

Credits: User Alan Williams

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

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

Created: 2008-09-27

Credits: User Alan Williams

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

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

Created: 2008-09-27

Credits: User Alan Williams

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

Thumb
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.

Created: 2008-09-27

Credits: User Alan Williams

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

Thumb
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.

Created: 2008-09-27

Credits: User Alan Williams

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

Thumb
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.

Created: 2008-09-27

Credits: User Alan Williams

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

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

Created: 2008-09-27

Credits: User Alan Williams

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

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

Created: 2008-09-27

Credits: User Alan Williams

Workflow Fail if true - non true value (1)

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

Created: 2008-09-27

Credits: User Alan Williams

Workflow Fail if true - false value (1)

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

Created: 2008-09-27

Credits: User Alan Williams

Workflow Fail if true - true value (1)

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

Created: 2008-09-27

Credits: User Alan Williams

Workflow Fail if false - non false value (1)

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

Created: 2008-09-27

Credits: User Alan Williams

Workflow Fail if false - true value (1)

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

Created: 2008-09-27

Credits: User Alan Williams

Workflow Fail if false - false value (1)

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

Created: 2008-09-27

Credits: User Alan Williams

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

Thumb
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 ...

Created: 2008-09-27

Credits: User Alan Williams

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

Thumb
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.

Created: 2008-09-27

Credits: User Alan Williams

Workflow Encode byte[] to base64 (1)

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

Created: 2008-09-27

Credits: User Alan Williams

Workflow Decode base64 to byte[] (1)

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

Created: 2008-09-27

Credits: User Alan Williams

Workflow Create lots of strings (1)

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

Created: 2008-09-27 | Last updated: 2008-09-27

Credits: User Alan Williams

Workflow Concatenate two strings - empty strings (1)

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

Created: 2008-09-27

Credits: User Alan Williams

Workflow Concatenate two strings (1)

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

Created: 2008-09-27

Credits: User Alan Williams

Workflow Concatenate files - multiple files (1)

Thumb
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...

Created: 2008-09-27

Credits: User Alan Williams

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

Thumb
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 ...

Created: 2008-09-27

Credits: User Alan Williams

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

Thumb
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...

Created: 2008-09-27

Credits: User Alan Williams

Workflow Choose - single element list (1)

Thumb
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.

Created: 2008-09-27

Credits: User Alan Williams

Workflow Choose - title and message parameters (1)

Thumb
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.

Created: 2008-09-27

Credits: User Alan Williams

Workflow Choose - title parameter (1)

Thumb
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.

Created: 2008-09-27

Credits: User Alan Williams

Workflow Choose - no title or message parameters (1)

Thumb
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.

Created: 2008-09-27

Credits: User Alan Williams

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

Thumb
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.

Created: 2008-09-27

Credits: User Alan Williams

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

Thumb
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.

Created: 2008-09-27

Credits: User Alan Williams

Workflow Ask - title and message parameters (1)

Thumb
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.

Created: 2008-09-27

Credits: User Alan Williams

Workflow Ask - just message parameter (1)

Thumb
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.

Created: 2008-09-27

Credits: User Alan Williams

Workflow Ask - just title parameter (1)

Thumb
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.

Created: 2008-09-27

Credits: User Alan Williams

Workflow Ask - no parameters (1)

Thumb
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.

Created: 2008-09-27

Credits: User Alan Williams

Workflow GBSeq test (2)

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

Created: 2008-03-05 | Last updated: 2008-03-31

Credits: User Franck Tanoh

Workflow Fetch PDB flatfile from RCSB server (1)

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

Created: 2008-03-05 | Last updated: 2008-03-31

Credits: User Tomoinn

Workflow Demonstration of configurable iteration (1)

Thumb
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: 2008-03-05 | Last updated: 2008-03-25

Credits: User Tomoinn

Workflow Fetch Dragon images from BioMoby (3)

Thumb
Fetch images and annotations of snapdragons

Created: 2008-03-05 | Last updated: 2010-07-14

Credits: User Tomoinn

Workflow Fetch today's xkcd comic (1)

Thumb
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: 2008-03-05 | Last updated: 2008-04-07

Credits: User Tomoinn User Stian Soiland-Reyes

Attributions:

Workflow A workflow version of the EMBOSS tutorial (1)

Thumb
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: 2008-03-05 | Last updated: 2008-03-25

Credits: User Tomoinn

Workflow Example of a conditional execution workflow (1)

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

Created: 2008-03-05 | Last updated: 2012-05-23

Credits: User Tomoinn

What is this?

Linked Data

Non-Information Resource URI:


Alternative Formats

HTML
RDF
XML