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Items tagged with "beanshell" (17)
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Created: 14/11/07 @ 16:01:50 | Last updated: 22/11/07 @ 12:06:32
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Retrieves data from the maxd database given name of data set
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Created: 14/11/07 @ 16:51:26 | Last updated: 22/11/07 @ 10:39:32
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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
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Created: 06/03/08 @ 11:46:11 | Last updated: 25/03/08 @ 16:23:24
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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...
Rating: 5.0 / 5 (1 rating) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0 Viewed: 202 times | Downloaded: 103 times Tags (2): |
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Created: 25/03/08 @ 10:01:38 | Last updated: 25/03/08 @ 10:23:34
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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.
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Created: 15/04/08 @ 15:37:42 | Last updated: 01/07/08 @ 17:21:18
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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.
Rating: 5.0 / 5 (1 rating) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 1 Viewed: 449 times | Downloaded: 153 times Tags (6): |
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Created: 06/05/09 @ 08:49:59 | Last updated: 06/05/09 @ 08:50:29
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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: ...
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Created: 20/03/09 @ 11:22:45 | Last updated: 20/03/09 @ 11:29:16
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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...
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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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Created: 15/03/10 @ 08:43:31
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow retrieves data from the MaxD microarray database and calculates the frequencies of gene expression levels using an R script
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Created: 17/03/10 @ 10:53:02
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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
Rating: 5.0 / 5 (1 rating) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0 Viewed: 129 times | Downloaded: 2 times Tags (21): |
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Created: 30/03/10 @ 14:04:45
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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.
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Created: 29/11/10 @ 11:45:52 | Last updated: 29/11/10 @ 11:53:46
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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.
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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: 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...
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Created: 13/01/12 @ 19:25:22 | Last updated: 16/01/12 @ 00:09:51 License: Creative Commons Attribution-Share Alike 3.0 Unported License
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.
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Created: 10/08/09 @ 13:01:47 | Last updated: 11/08/09 @ 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: 186 times | Downloaded: 34 times Tags: |
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Unique name: myExperimentBeanshellCollection Created: Thursday 06 March 2008 @ 11:41:29 (GMT)
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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