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User: Stian Soiland-Reyes
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Name: Stian Soiland-Reyes Joined: Friday 20 July 2007 @ 16:58:17 (GMT) Last seen: Thursday 10 May 2012 @ 14:39:14 (GMT) Email (public): soilandreyes [at] cs.manchester.ac.uk Website: http://soiland.no/work Location: Manchester, United Kingdom |
Stian Soiland-Reyes has been credited 50 times Stian Soiland-Reyes has an average rating of: 4.5 / 5 (2 ratings in total) for their items |
I am one of the myGrid developers working in University of Manchester, mainly working on Taverna, but also involved in myExperiment development. Most of the workflows I will publish here on myExperiment are either test workflows (that highlight bugs in Taverna!), technique workflows (like how to do iteration or XML parsing) or other people's workflows that again break Taverna in one way or another.
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Not specifiedInterests:
Taverna, Java, Python, REST, open source, web services
Field/Industry: Education
Occupation/Role(s): Software engineer
Organisation(s):
myGrid
OMII-UK
University of Manchester
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Created: 11/03/10 @ 16:39:04
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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Created: 10/05/12 @ 14:40:38 | Last updated: 10/05/12 @ 14:55:37
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License: Creative Commons Attribution 3.0 Unported License
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Created: 08/05/12 @ 11:15:30 | Last updated: 08/05/12 @ 11:19:37
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License: Creative Commons Attribution 3.0 Unported License
Given a t2flow file (Taverna 2 workflow), extract ancestor workflow UUIDs and search myExperiment for matching workflow entries. Note that this will also match the workflow itself and nested workflows, but does not match against other workflows having the same ancestors (but newer UUIDs).
This workflow requires Taverna 2.4 or later and uses myExperiment's SPARQL endpoint, which is refreshed weekly and contains only public workflow entries.
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Created: 08/05/12 @ 10:19:49 | Last updated: 08/05/12 @ 10:19:50
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License: Creative Commons Attribution 3.0 Unported License
Checks if Java Cryptography Extension (JCE) Unlimited Strength Jurisdiction Policy Files is installed, and redirects user to correct download page and relevant lib/security folder if not.
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Created: 20/02/12 @ 23:20:08 | Last updated: 20/02/12 @ 23:23:59
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
The choice of executing choiceA or choiceB is determined by using String_List_Intersection and String_List_Difference. If in="true" then the intersection will yield a non-empty list, triggering execution of choiceA. This list will however not differ from the input, and so choiceB will iterate over an empty list (ie. not execute).
Note how using 'difference' for the else-case here means that if you run the workflow with in="bob", choiceB would still run. Some early if/el...
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Created: 10/01/12 @ 11:01:26 | Last updated: 16/01/12 @ 14:01:32
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Calculation of distances, corrected apparent B magnitude mB-corr and luminosities with values gathered from the HyperLEDA database.
This workflow receives a list of galaxy names (hyperLEDA names. ie: KIG0001) and a file with the morphological types of those galaxies
Using the name of a galaxy, the workflow querys Hyperleda to extract some properties of this galaxy (J2000 Coordinates, velocity, galactic extinction,log of axis ratio, and the Total B-magnitude ). With this properties it calcula...
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Created: 03/01/12 @ 15:38:03 | Last updated: 03/01/12 @ 15:42:35
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License: Creative Commons Attribution 3.0 Unported License
One of the simplest workflows possible. No workflow input ports, a single workflow output port "greeting", outputting "Hello, world!" as produced by the String Constant "hello".
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Created: 03/01/12 @ 15:39:47 | Last updated: 03/01/12 @ 15:41:52
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An extension to helloworld.t2flow - this workflow takes a workflow input "name" which is combined with the string constant "Hello, " using the local worker "Concatenate two strings", and outputs the produced string to the workflow output "greeting".
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Created: 14/09/11 @ 04:32:48 | Last updated: 14/09/11 @ 05:01:30
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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.
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Created: 11/08/11 @ 11:43:55 | Last updated: 11/08/11 @ 11:43:56
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License: Creative Commons Attribution 3.0 Unported License
Using Apache ws-xmlrpc from Beanshell scripts to call time.xmlrpc.com - see http://www.xmlrpc.com/currentTime
To use, download the JARs from http://ws.apache.org/xmlrpc/download.html (ie. http://apache.mirror.anlx.net//ws/xmlrpc/apache-xmlrpc-current-bin.zip ) - unzip and put into Taverna's home directory lib/ folder. Right-click on the Beanshell script and check the "Dependencies" tab to check that all JARs have been ticked off (minimum required: ws-common-util.jar, xmlrpc-client.jar and x...
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Created: 12/07/11 @ 14:13:35 | Last updated: 12/07/11 @ 14:13:36
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Use the local services and some filtering operations to fetch the comic strip image from http://xkcd.com/
Based on the FetchDailyDilbert workflow.
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Created: 12/07/11 @ 14:04:39 | Last updated: 12/07/11 @ 14:04:41
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Perform multiple iterations of services in order to show pipelining
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Created: 02/02/11 @ 14:39:20 | Last updated: 02/02/11 @ 14:39:22
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License: Creative Commons Attribution 3.0 Unported License
Create_lots_of_strings gives implicit iteration over the service add_a_and_b - assume this is a service that returns two values which you now want to keep in a list [a,b].
The shim Create_list takes two single inputs, and returns a list of [in1, in2]. Configured with the Dot product list strategy it means that it will pipeline out [a1,b1], [a2,b2], [a3,b3] etc.Create_lots_of_strings gives implicit iteration over the service add_a_and_b - assume this is a service that returns two values which...
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Created: 17/01/11 @ 16:08:48 | Last updated: 17/01/11 @ 16:12:40
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This workflow performs an interproscan on provided sequencesThis workflow performs an interproscan at the EBI on sequences provided as input. The output is provided as text, xml or png.
This workflow uses the new EBI services, which are asynchronous and require looping over the nested workflow (Status) until the workflow has finished. Many of the EBI services now work in this way, so you can use this workflow as an example of the invocation pattern and looping configuration.
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Created: 02/09/08 @ 20:53:53 | Last updated: 08/09/08 @ 15:35:53
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow takes in a list of KEGG pathway descriptions and searches the PubMed database for corresponding articles. Any matches to the pathways are then retrieved (abstracts only). These abstracts are then returned to the user.
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Created: 04/07/10 @ 18:35:59 | Last updated: 04/07/10 @ 18:36:00
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License: Creative Commons Attribution 3.0 Unported License
Use the local java plugins and some filtering operations to fetch the comic strip image from http://xkcd.com/
Based on the FetchDailyDilbert workflow.
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Created: 04/07/10 @ 18:37:58 | Last updated: 04/07/10 @ 18:38:00
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License: Creative Commons Attribution 3.0 Unported License
Perform multiple iterations of services in order to show pipelining
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Created: 12/04/10 @ 15:11:47 | Last updated: 12/04/10 @ 15:17:57
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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()
...
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Created: 04/01/10 @ 17:42:36 | Last updated: 04/01/10 @ 17:49:58
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
As Taverna can't (currently) handle null (see http://www.mygrid.org.uk/dev/issues/browse/TAV-653) - in Taverna 2 one can instead return exceptions on individual ports and inside lists.
Exceptions are registered as error documents by Taverna, and are passed along. The ErrorBounce layer of processors downstream will prevent execution if they see this 'null'-exception - as showed in this example that the string concatination is just run for the two list elements that are not exceptio...
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Created: 11/09/09 @ 11:49:11
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Perform an InterProScan analysis of a protein sequence using the EBI’s WSInterProScan service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan). The input sequence to use and the user e-mail address are inputs, the other parameters for the analysis (see Job_params) are allowed to default.
InterProScan searches a protein sequence against the protein family and domain signature databases integrated into InterPro (see http://www.ebi.ac.uk/interpro/). A set of matches to the sig...
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Created: 28/07/09 @ 17:24:05
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
An example workflow with WSRF service
The service used is http://sidgrid.ci.uchicago.edu:8100/wsrf/services/CounterService
The service is included in Globus toolkit installation (ws-core). If the it is down you can host your own and modify the workflow definition file to point to your own.
The workflow first creates a counter instance and adds the value 10 for two times to the same counter. Therefore the result should be 20.
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Created: 03/07/09 @ 14:59:53
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Perform multiple iterations of services in order to show pipelining
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Created: 03/07/09 @ 14:50:54 | Last updated: 03/07/09 @ 14:51:15
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Designed to show the use of EMBOSS based Soaplab services from Taverna, this workflow has no inputs as all initial values are specified as string constants. A sequence set is fetched using the seqret tool, then simultaneously scanned for predicted transmembrane regions and subjected to a multiple alignment using emma. This alignment is then plotted to a set of PNG images and also used to build a profile using the prophecy and prophet tools.
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Created: 03/07/09 @ 14:49:48
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow retrieves a sequence associated with its features in embl format
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Created: 03/07/09 @ 14:48:38
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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.
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Created: 03/07/09 @ 14:40:25
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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.
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Created: 03/07/09 @ 14:32:26 | Last updated: 03/07/09 @ 14:33:01
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow shows the use of the iteration strategy editor to ensure that only relevant combinations of inputs are used during an implicit iteration.
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Created: 03/07/09 @ 14:18:28 | Last updated: 03/07/09 @ 14:19:32
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Using Biomart and EMBOSS soaplab services, This workflow retrieves a number of sequences from 3 species: mouse, human, rat; align them, and returns a plot of the alignment result. Corresponding sequence ids are also returned.
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Created: 26/01/10 @ 14:46:07 | Last updated: 26/01/10 @ 14:46:08
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Perform an InterProScan analysis of a protein sequence using the EBI’s WSInterProScan service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan). The input sequence to use and the user e-mail address are inputs, the other parameters for the analysis (see Job_params) are allowed to default.
InterProScan searches a protein sequence against the protein family and domain signature databases integrated into InterPro (see http://www.ebi.ac.uk/interpro/). A set of matches to the sig...
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Created: 30/06/09 @ 11:24:07 | Last updated: 30/06/09 @ 11:25:38
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Attributions: License: Creative Commons Attribution-Share Alike 3.0 Unported License
This T2 version of the Interpro scan workflow is an example of the while loop in action.
This is used to poll the async EBI service for the result (busy waiting)
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Created: 14/10/08 @ 16:17:58 | Last updated: 14/10/08 @ 16:39:03
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License: Creative Commons Attribution 3.0 Unported License
This workflow has a beanshell script for composing the REST URL for the services at xml.nig.ac.jp (WABI) This URL is passed to the local worker Get_web_page_from_URL that fetches the requested data.
Note: This is a proof of concept of accessing REST services through Taverna. All of WABI's services can more easily be browsed and used in Taverna by adding their WSDL, for instance http://xml.nig.ac.jp/wsdl/GetEntry.wsdl
The example invokes the getDDBJEntry(accession) method of the getE...
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Created: 27/08/08 @ 10:40:08
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
No description
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Created: 17/06/08 @ 16:25:49 | Last updated: 20/06/08 @ 14:48:32
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Get the weather forcast of the day for you city. Info display: wind, visibility, temperature, sky conditions and pressure. The default value Stian's home country.
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Created: 07/05/08 @ 12:10:27 | Last updated: 07/05/08 @ 12:32:36
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Consider two lists A and B, of equal size 3.
A[1] corresponds to B[1], A[2] to
B[2], etc, for instance A are image scans from
2007 and B from 2008, and the index indicates the patient
number.
A = [a0, a1, a2]
B = [b0, b1, b2]
There's then two lists of possible parameters P and Q,
of different lengths, P has 2 and Q has 4 items.
P = [p0, p1]
Q = [q0, q1, q2, q3]
Each of the A items should be processed in ap using
each of the P parameters, and each of the B items
...
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Created: 05/03/08 @ 14:08:52 | Last updated: 07/04/08 @ 13:54:04
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Attributions: License: Creative Commons Attribution 3.0 Unported License
Use the local java plugins and some filtering operations to fetch the comic strip image from http://xkcd.com/
Based on the FetchDailyDilbert workflow.
Rating: 4.5 / 5 (2 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0 Viewed: 488 times | Downloaded: 179 times Tags (4): |
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Created: 26/01/10 @ 14:45:46 | Last updated: 24/11/10 @ 10:04:09
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Perform an InterProScan analysis of a protein sequence using the EBI’s WSInterProScan service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan). The input sequence to use and the user e-mail address are inputs, the other parameters for the analysis (see Job_params) are allowed to default.
InterProScan searches a protein sequence against the protein family and domain signature databases integrated into InterPro (see http://www.ebi.ac.uk/interpro/). A set of matches to t...
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Created: 11/05/10 @ 19:04:30 | Last updated: 11/05/10 @ 19:04:32
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Scientific value Using gene-expression patterns associated with DLBCL and FL to predict the lymphoma type of an unknown sample. Using SVM (Support Vector Machine) to classify data, and predicting the tumor types of unknown examples. Steps Querying training data from experiments stored in caArray. Preprocessing, or normalize the microarray data. Adding training and testing data into SVM service to get classification result.
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Created: 07/05/09 @ 14:28:59
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
To query protein sequence infomation out of 3 caGrid data services: caBIO, CPAS and GridPIR
Adapted from http://www.myexperiment.org/workflows/600
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Created: 03/07/09 @ 14:37:14 | Last updated: 03/07/09 @ 14:53:40
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Given an identifier such as '1crn' fetches the PDB format flatfile and returns the corresponding 3D image of the protein.
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Created: 27/01/10 @ 15:52:50 | Last updated: 27/01/10 @ 15:56:10
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License: Creative Commons Attribution 3.0 Unported License
Example of looping over asynchronous services. The dummy beanshell scripts represents the operations of an asynchronous submit-status-results style service, such as EBI's InterProScan and NCBI Blast.
createJob creates a temporary file with the content "0". Filename retuirned as a "job ID".
checkStatus reads the job, and return state "RUNNING" as long as the content is less than 10, increasing the number for each call. ...
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