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Items tagged with "beanshell" (21)

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Groups (1)

Network-member myExperimentBeanshellCollection

Unique name: myExperimentBeanshellCollection
Created: Thursday 06 March 2008 11:41:29 (UTC)

Group for development, curation and maintenance of collections of generic Beanshell processors. Join this group if you have some cool Beanshells that you want to share! Please add your Beanshells to the myExperimentBeanshellCollection workflow and don't create new workflows for this purpose. (It's not fun to load dozens of workflows manually to load a fragmented collection of Beanshells.) If t...

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Packs (1)
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Pack Pathway to Phenotype using Text Mining


Created: 2009-08-10 13:01:47 | Last updated: 2009-08-11 14:51:31

This pack contains a list of workflows and result files obtained from the analysis of candidate pathways believed to play a role in resistance to African Trypanosomiasis in the mouse model organism.

12 items in this pack

Comments: 0 | Viewed: 249 times | Downloaded: 52 times

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Workflows (19)
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Workflow Query Maxd microarray database (1)

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Retrieves data from the maxd database given name of data set

Created: 2007-11-14 | Last updated: 2007-11-22

Credits: User Peter Li

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Workflow Mapping microarray data onto metabolic pat... (1)

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This workflow maps microarray data onto metabolic pathway diagrams represented as SBML models drawn using Cell Designer. To run this workflow requires libsbml to be installed into taverna - see http://www.mcisb.org/software/taverna/libsbml/index.html

Created: 2007-11-14 | Last updated: 2007-11-22

Credits: User Peter Li

Workflow myExperimentBeanshellCollection (2)

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Public collection of generic Beanshells curated by the myExperimentBeanshellCollection group on myExperiment. Visit http://www.myexperiment.org for details and updates. To use this collection of beanshells in Taverna: Right click "Available Processors" in the "Design Perspective" Choose "Add new Workflow scavenger..." Provide the URL to this beanshell collection on www.myExperiment.org or if you downloaded this to your hard disk, provide a "file" URL to the absolute path of this file (O...

Created: 2008-03-06 | Last updated: 2008-03-25

Credits: Network-member myExperimentBeanshellCollection

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Workflow selectworker (1)

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This workflow shows how the selectData beanshell script can be used to select items from a given list for analysis by downstream processors. Use Control and left mouse click to select multiple items.

Created: 2008-03-25 | Last updated: 2008-03-25

Credits: User Peter Li

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Workflow Identification of differential genes using... (2)

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This workflow starts by retrieving the names of microarray datasets from the Maxd database. The user has to select sets of control and test data for analysis using t-tests by R. A list of significant differentially expressed genes is then analysed using the Go Term Finder tool which generates a list of GO terms associated with the genes. A CSV file containing the list of significant genes is also generated.

Created: 2008-04-15 | Last updated: 2008-07-01

Credits: User Peter Li

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Workflow Analysing workflows (3)

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This workflows analyses workflows stored at the myExperiment site. It is used in the paper submitted to the Workshop on Scientific Workflow 2009. The workflow shows the task usage in the Taverna workflows stored at the myExperiment site The amount of services used The amount of local processors used The amount of scripting tasks The amount of sub workflows Furthermore it classifies the local services based on their intended function. The workflow has two inputs: ...

Created: 2009-05-06 | Last updated: 2009-05-06

Credits: User Wassinki User Pieter Neerincx User Katy Wolstencroft User Marco Roos

Workflow fetch_fasta (1)

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This work flow is designed to take an EMBL file containing the genomic data for an identified bacterium. From this information the workflow can determine whether or not that this strain is an MRSA type of bug. This can be determined based on the MecA profile of the given strain. Blast is utilised to find a relationship with given proteins and that of know S. aureus strains. This phylogenic output is generated from a ClustalW algorithm that plots a phylogenic tree. The output is prese...

Created: 2009-03-20 | Last updated: 2009-03-20

Credits: User Jumblejumble

Workflow Dummy example of looping (3)

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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: User Stian Soiland-Reyes

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Workflow Calculating frequencies of gene expression... (1)

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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: User Peter Li

Workflow microRNA to KEGG Pathways and Abstracts (1)

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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: User Paul Fisher

Attributions: Workflow Pathways and Gene annotations for QTL region

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Workflow Select items from list (1)

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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: User Peter Li

Uploader

Workflow Transform XML with parameters (1)

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Similar to Transform_XML local widget but accepts transformation parameters and skips the part with writing to the output file. The essence, i.e. Transform_XML beanshell works with Strings representing file contents, not with file URLs. The XML transfomation parameters are given as a list of strings in the "param_name = param_value" format.

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

Credits: User trybik

Workflow XML-RPC example current time (1)

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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...

Created: 2011-08-11 | Last updated: 2011-08-11

Credits: User Stian Soiland-Reyes

Workflow Merge list of errors to string (2)

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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

Workflow getFirstElementDFS (2)

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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

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

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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: User Markus Plangg

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

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

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

Credits: User Markus Plangg

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

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Reads RAW images for evaluation by RAWverna.

Created: 2012-02-21

Credits: User Markus Plangg

Workflow Example of Execute_SQL_Query with parameters (1)

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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: User Helen Hulme

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Non-Information Resource URI: http://www.myexperiment.org/tags/609


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