All content

Dummy example of looping (3)

• Download

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. (As no actual job is being run) getResults reads the file content, with...

Created: 2010-01-27 | Last updated: 2013-10-08

Credits: Stian Soiland-Reyes

microRNA to KEGG Pathways and Abstracts (1)

Workflow takes in a text file of microRNAs from microCOSM (at the EBI) and outputs a list of KEGG pathway information, including genes in pathways and pathway abstracts from PubMed. The results can then be used in various text mining applications/workflows to rank the results against a given disease.Workflow takes in a file of microRNAs

Created: 2010-03-17

Credits: Paul Fisher

Attributions: Pathways and Gene annotations for QTL region

Select items from list (1)

• Download

This workflow pops up a window containing an input list of strings. The user is invited to select one or more strings for downstream processing.

Created: 2010-03-30

Credits: Peter Li

Calculating frequencies of gene expression... (1)

This workflow retrieves data from the MaxD microarray database and calculates the frequencies of gene expression levels using an R script

Created: 2010-03-15

Credits: Peter Li

Example of Execute_SQL_Query with parameters (1)

• Download

This workflow connects to a mysql on localhost, queries the "world" database which is one of the test databases on MySQL 5.5, queries it about which countries have Dutch as a language, and emits answers in both Lists and in xml. This workflow is intended as an example to help you see the syntax for the various inputs to this local service beanshell. see: http://www.mygrid.org.uk/dev/wiki/display/taverna/Execute+SQL+Query for instructions on jars, dependencies etc. The jar used he...

Created: 2012-03-16 | Last updated: 2012-03-16

Credits: Helen Hulme

RAWverna image evaluation - Read images (RAW) (1)

• Download

Reads RAW images for evaluation by RAWverna.

Created: 2012-02-21

Credits: Markus Plangg

RAWverna Image evaluation - Read Image (RAW) (1)

• Download

Reads an image from the given path using dcraw for image comparison.

Created: 2012-02-21 | Last updated: 2012-02-21

Credits: Markus Plangg

RAWverna Image evaluation - Read images (R... (1)

• Download

Reads images for evaluation by RAWverna. The read parameters depend on the type of the images.

Created: 2012-02-21 | Last updated: 2012-02-21

Credits: Markus Plangg

getFirstElementDFS (2)

• Download

Returns the first element of a nested list using depth first search. The maximum depth of the input is set to 2. You can savely increase this by increasing the depth of the workflow input port and the beanshell input port. Taverna will wrap the input into a list with correct depth. However this will create a little overhead.

Created: 2012-01-13 | Last updated: 2012-02-13

Merge list of errors to string (2)

• Download

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...

Created: 2011-09-13 | Last updated: 2011-09-13