User: Stian Soiland-Reyes

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

21 Friends

0 Groups (admin)

4 Groups (member)

44 Workflows

8 Packs

3 Favourites

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.

Other contact details:

Not specified

Interests:

Taverna, Java, Python, REST, open source, web services

Field/Industry: Education

Occupation/Role(s): Software engineer

Organisation(s):

myGrid
OMII-UK
University of Manchester

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

Contents (click to expand/contract)

Taverna 2 Original Uploader Stian Soiland-Reyes	Extract DEC and RA from whitespace separated file (v2) Created: 10/05/12 @ 14:40:38 \| Last updated: 10/05/12 @ 14:55:37 Credits: Stian Soiland-Reyes License: Creative Commons Attribution 3.0 Unported License No description Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 6 times \| Downloaded: 7 times Tags (5): astronomy \| dec \| ra \| regex \| regular expression	View Download (v2)
Taverna 2 Original Uploader Stian Soiland-Reyes	Find workflow ancestors (v1) Created: 08/05/12 @ 11:15:30 \| Last updated: 08/05/12 @ 11:19:37 Credits: Stian Soiland-Reyes 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 9 times \| Downloaded: 5 times Tags (9): ancestor \| identifier \| myexperiment \| rest \| sparql \| t2flow \| uuid \| workflow \| xpath	View Download (v1)
Taverna 2 Original Uploader Stian Soiland-Reyes	Check Java Cryptography Unlimited Strength (v1) Created: 08/05/12 @ 10:19:49 \| Last updated: 08/05/12 @ 10:19:50 Credits: Stian Soiland-Reyes Attributions: Find/show Taverna's home directory 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 6 times \| Downloaded: 8 times This Workflow has no tags!	View Download (v1)
Taverna 2 Original Uploader Stian Soiland-Reyes	WCP-04 Exclusive choice - if/else branching (v1) Created: 20/02/12 @ 23:20:08 \| Last updated: 20/02/12 @ 23:23:59 Credits: Stian Soiland-Reyes Attributions: Example of a conditional execution workflow Example of conditional invocation 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... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 0 times \| Downloaded: 1 time Tags (7): branching \| choice \| conditional \| ifelse \| pattern \| wcp \| workflow pattern	View Download (v1)
Taverna 2 Original Uploader Stian Soiland-Reyes	Calculation of distances, magnitutes and luminosities using HyperLEDA (v2) Created: 10/01/12 @ 11:01:26 \| Last updated: 16/01/12 @ 14:01:32 Credits: Stian Soiland-Reyes Attributions: Calculation of distances, magnitutes and luminosities using HyperLEDA Data involved in RO Propagation of quantities Scripts in RO Propagation of quantites License: Creative Commons Attribution-Share Alike 3.0 Unported License 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... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 8 times \| Downloaded: 7 times Tags (5): astronomy \| curation \| database storing \| galaxies \| hyperleda	View Download (v2)
Taverna 2 Original Uploader Stian Soiland-Reyes	Hello Anyone (v1) Created: 03/01/12 @ 15:39:47 \| Last updated: 03/01/12 @ 15:41:52 Credits: Stian Soiland-Reyes Attributions: Hello World License: Creative Commons Attribution 3.0 Unported License An extension to helloworld.t2flow - this workflow takes a workflow input "name" which is combined with the string constant "Hello, " using the local worker "Concatenate two strings", and outputs the produced string to the workflow output "greeting". Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 30 times \| Downloaded: 15 times Tags (5): example \| hello \| helloworld \| input \| world	View Download (v1)
Taverna 2 Original Uploader Stian Soiland-Reyes	Hello World (v1) Created: 03/01/12 @ 15:38:03 \| Last updated: 03/01/12 @ 15:42:35 Credits: Stian Soiland-Reyes 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". Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 36 times \| Downloaded: 20 times Tags (4): example \| hello \| helloworld \| world	View Download (v1)
Taverna 2 Original Uploader Stian Soiland-Reyes	Merge list of errors to string (v2) Created: 13/09/11 @ 14:04:50 \| Last updated: 13/09/11 @ 14:16:05 License: Creative Commons Attribution-Share Alike 3.0 Unported License Based on http://myexperiment.elda.org/workflows/27/ The beanshell scripts collectively builds a temporary file of the merged string (by default using newline as separator). As each item is appended to the file separately by Write_text_append, this means it can handle occassional errors in the list, such as in the output from Sometimes_fails. Such items are not included in the merged string. To use, merge with your workflow and delete "Create_Lots_if_Strings", "Sometimes_Fai... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 2 times \| Downloaded: 4 times Tags (5): beanshell \| error \| file \| handling \| list	View Download (v2)
Taverna 2 Original Uploader Stian Soiland-Reyes	XML-RPC example current time (v1) Created: 11/08/11 @ 11:43:55 \| Last updated: 11/08/11 @ 11:43:56 Credits: Stian Soiland-Reyes 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... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 8 times \| Downloaded: 9 times Tags (2): beanshell \| xmlrpc	View Download (v1)
Taverna 2 Original Uploader Stian Soiland-Reyes	Using a Create_List script with a dot-product to create lists (v1) Created: 02/02/11 @ 14:39:20 \| Last updated: 02/02/11 @ 14:39:22 Credits: Stian Soiland-Reyes 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... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 15 times \| Downloaded: 10 times Tags (3): dot product \| list \| shim	View Download (v1)
Taverna 2 Original Uploader Stian Soiland-Reyes	Biomart and 2x BLAST (v1) Created: 13/12/10 @ 17:11:54 \| Last updated: 13/12/10 @ 17:11:55 License: Creative Commons Attribution 3.0 Unported License Perform Roden and Invertebrates BLAST sequence alignments (using DDBJ Blast) on the gene sequences for a (semi-random) selection of genes from Human sapiens chromosome 22. (Using Biomart). blast_ddbj_invertebrates and blast_ddbj_rodents should execute in parallel as they don't depend on each other. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 14 times \| Downloaded: 10 times This Workflow has no tags!	View Download (v1)
Taverna 2 Original Uploader Stian Soiland-Reyes	Biomart and Blast with concatinated gene id (v1) Created: 13/12/10 @ 14:41:39 \| Last updated: 13/12/10 @ 14:47:55 Attributions: BLAST using DDBJ service Biomart and Blast License: Creative Commons Attribution 3.0 Unported License Perform Rodent BLAST sequence alignments (using DDBJ Blast) on the gene sequences for a (semi-random) selection of genes from Human sapiens chromosome 22. (Using Biomart). Finally (to showcase Taverna pipelining) - the Ensembl gene ID is added as a prefix on the BLAST report. Referenced in the Taverna knowledge blog. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 13 times \| Downloaded: 11 times Tags (9): alignment \| biomart \| BLAST \| ddbj \| emboss \| human \| human sapiens \| rodent \| sequence alignment	View Download (v1)
Taverna 2 Original Uploader Stian Soiland-Reyes	Biomart and Blast (v1) Created: 13/12/10 @ 14:41:12 \| Last updated: 13/12/10 @ 15:15:45 Attributions: BLAST using DDBJ service License: Creative Commons Attribution 3.0 Unported License Perform Rodent BLAST sequence alignments (using DDBJ Blast) on the gene sequences for a (semi-random) selection of genes from Human sapiens chromosome 22. (Using Biomart) Referenced in the Taverna knowledge blog. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 12 times \| Downloaded: 9 times Tags (15): alignment \| biomart \| BLAST \| ddbj \| emboss \| human \| human sapiens \| rodent \| sequence alignment	View Download (v1)
Taverna 1 Original Uploader Stian Soiland-Reyes	Find/show Taverna's home directory (v1) Created: 12/04/10 @ 15:11:47 \| Last updated: 12/04/10 @ 15:17:57 Credits: Stian Soiland-Reyes 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() ... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 18 times \| Downloaded: 12 times Tags (3): commandline \| folder \| taverna	View Download (v1)
Taverna 2 Original Uploader Stian Soiland-Reyes	Dummy example of looping (v2) Created: 27/01/10 @ 15:52:50 \| Last updated: 27/01/10 @ 15:56:10 Credits: Stian Soiland-Reyes 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. ... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 146 times \| Downloaded: 67 times Tags (6): beanshell \| condition \| dummy \| example \| loop \| looping	View Download (v2)
Taverna 2 Original Uploader Stian Soiland-Reyes	EBI_InterProScan for Taverna 2 (v2) Created: 26/01/10 @ 14:46:07 \| Last updated: 26/01/10 @ 14:46:08 Credits: Stian Soiland-Reyes Paolo Katy Wolstencroft Hamish McWilliam Attributions: EBI InterproScan T2 EBI_InterProScan 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... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 175 times \| Downloaded: 122 times Tags (5): interpro \| interproscan \| looping \| sequence \| term	View Download (v2)
Taverna 2 Original Uploader Stian Soiland-Reyes	EBI_InterProScan for Taverna 2 (v2) Created: 26/01/10 @ 14:45:46 \| Last updated: 24/11/10 @ 10:04:09 Credits: Stian Soiland-Reyes Katy Wolstencroft Paolo Hamish McWilliam Attributions: EBI_InterProScan for Taverna 2 EBI InterproScan T2 EBI_InterProScan EBI InterProScan 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... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 394 times \| Downloaded: 197 times Tags (6): interpro \| interproscan \| looping \| sequence \| term	View Download (v2)
Taverna 2 Original Uploader Stian Soiland-Reyes	Pattern: Return errors instead of null (v1) Created: 04/01/10 @ 17:42:36 \| Last updated: 04/01/10 @ 17:49:58 Credits: Stian Soiland-Reyes 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... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 24 times \| Downloaded: 16 times This Workflow has no tags!	View Download (v1)
Taverna 2 Original Uploader Stian Soiland-Reyes	Pipelined list iteration (v1) Created: 03/07/09 @ 14:59:53 Credits: Stian Soiland-Reyes Ian Dunlop License: Creative Commons Attribution-Share Alike 3.0 Unported License Perform multiple iterations of services in order to show pipelining Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 122 times \| Downloaded: 57 times Tags (2): iteration \| list	View Download (v1)
Taverna 2 Original Uploader Stian Soiland-Reyes	A workflow version of the EMBOSS tutorial (v1) Created: 03/07/09 @ 14:50:54 \| Last updated: 03/07/09 @ 14:51:15 Credits: Stian Soiland-Reyes Attributions: A workflow version of the EMBOSS tutorial 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 95 times \| Downloaded: 32 times This Workflow has no tags!	View Download (v1)
Taverna 2 Original Uploader Stian Soiland-Reyes	Retrieve sequence in EMBL format (v1) Created: 03/07/09 @ 14:49:48 Credits: Stian Soiland-Reyes Attributions: Retrieve sequence in EMBL format License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow retrieves a sequence associated with its features in embl format Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 1 \| Citations: 0 Viewed: 48 times \| Downloaded: 28 times This Workflow has no tags!	View Download (v1)
Taverna 2 Original Uploader Stian Soiland-Reyes	GBSeq test (v1) Created: 03/07/09 @ 14:48:38 Credits: Stian Soiland-Reyes Attributions: GBSeq test License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow retrieves nucleotide and protein sequences with the literature and references associated to them given a protein and a nucleotide id. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 36 times \| Downloaded: 20 times This Workflow has no tags!	View Download (v1)
Taverna 2 Original Uploader Stian Soiland-Reyes	Fetch today's xkcd comic (v1) Created: 03/07/09 @ 14:40:25 Credits: Stian Soiland-Reyes Attributions: Fetch today's xkcd comic License: Creative Commons Attribution-Share Alike 3.0 Unported License Use the local java plugins and some filtering operations to fetch the comic strip image from http://xkcd.com/ Based on the FetchDailyDilbert workflow. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 110 times \| Downloaded: 78 times Tags (4): fetch \| http \| image \| xkcd	View Download (v1)
Taverna 2 Original Uploader Stian Soiland-Reyes	Fetch PDB flatfile from RCSB server (v1) Created: 03/07/09 @ 14:37:14 \| Last updated: 03/07/09 @ 14:53:40 Credits: Stian Soiland-Reyes Attributions: Fetch PDB flatfile from RCSB server Fetch PDB flatfile from RCSB server 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 78 times \| Downloaded: 67 times Tags (2): pdb \| protein	View Download (v1)
Taverna 2 Original Uploader Stian Soiland-Reyes	Demonstration of configurable iteration (v1) Created: 03/07/09 @ 14:32:26 \| Last updated: 03/07/09 @ 14:33:01 Credits: Stian Soiland-Reyes Tomoinn Attributions: Demonstration of configurable iteration 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 83 times \| Downloaded: 67 times Tags (2): iteration \| strategy	View Download (v1)
Taverna 2 Original Uploader Stian Soiland-Reyes	Biomart and EMBOSS analysis (v1) Created: 03/07/09 @ 14:18:28 \| Last updated: 03/07/09 @ 14:19:32 Credits: Stian Soiland-Reyes Attributions: BiomartAndEMBOSSAnalysis 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 86 times \| Downloaded: 23 times Tags (6): alignment \| analysis \| sequence \| services \| soaplab \| workflow	View Download (v1)
Taverna 2 Original Uploader Stian Soiland-Reyes	Using CQL to query protein sequence data (v1) Created: 07/05/09 @ 14:28:59 Credits: Stian Soiland-Reyes Attributions: Using CQL to query protein sequence data 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 Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 156 times \| Downloaded: 69 times Tags (10): cabig \| cabio \| cagrid \| cancer research \| cpas \| globus \| grid service \| gridpir \| protein \| sequence	View Download (v1)
Taverna 1 Original Uploader Stian Soiland-Reyes	REST access of xml.nig.ac.jp (WABI) (v1) Created: 14/10/08 @ 16:17:58 \| Last updated: 14/10/08 @ 16:39:03 Credits: Stian Soiland-Reyes 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... Rating: 4.0 / 5 (1 rating) \| Versions: 1 \| Reviews: 1 \| Comments: 2 \| Citations: 0 Viewed: 178 times \| Downloaded: 54 times Tags (4): ddbj \| http \| rest \| wabi	View Download (v1)
Taverna 1 Original Uploader Stian Soiland-Reyes	Pathway to Pubmed (v1) Created: 02/09/08 @ 20:53:53 \| Last updated: 08/09/08 @ 15:35:53 Credits: Stian Soiland-Reyes Paul Fisher Attributions: ProteinSynonymsToQuery 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 25 times \| Downloaded: 13 times This Workflow has no tags!	View Download (v1)
Taverna 1 Original Uploader Stian Soiland-Reyes	missingOutputSplitter (v1) Created: 27/08/08 @ 10:40:08 Credits: Stian Soiland-Reyes License: Creative Commons Attribution-Share Alike 3.0 Unported License No description Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 23 times \| Downloaded: 15 times This Workflow has no tags!	View Download (v1)
Taverna 1 Original Uploader Stian Soiland-Reyes	Staged iteration strategy (v1) Created: 07/05/08 @ 12:10:27 \| Last updated: 07/05/08 @ 12:32:36 Credits: Stian Soiland-Reyes 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 ... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 75 times \| Downloaded: 46 times Tags (7): crossproduct \| dotproduct \| example \| iteration \| staged \| strategy \| taverna	View Download (v1)
Taverna 1 Original Uploader Stian Soiland-Reyes	Pathways and Gene annotations for QTL Phenotype annotated (v1) Created: 30/10/07 @ 13:04:02 \| Last updated: 04/12/07 @ 11:18:33 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License No description Rating: 5.0 / 5 (1 rating) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 40 times \| Downloaded: 24 times This Workflow has no tags!	View Download (v1)