I have received my master's degree in 2005 in computer science. During my masters, I did research on artificial intelligence, multi-agent systems and driving simulation. Currently, I am a Ph.D.student within the Bsik project BioRange at the Human Media Interaction Group at the University of Twente, the Netherlands. My current research is on computer visualisation techniques for life science domain, which is a multidisciplinary domain. My focus is on designing visualisation techniques for life science experiment setups, experiment progress, and task distribution in these experiments, to support these multidisciplinary research teams performing their experiments.

R-Shell plugin for Taverna
We have developed the R-shell plugin for Taverna. This plugin enables the Taverna users to execute R scripts in Taverna using a local or remote installation of the R interpreter. Each R-shell processor (i.e. a node in a Taverna workflow) can have multiple input ports for feeding arguments as well as multiple output ports for collecting the results. To limit data transport between multiple R-shell processors, the R shell plugin supports sessions. In a session, the data is kept at the R interpreter till the last processor in the session is executed.

The life science domain make use of R scripts to perform statistical analyses on their experiment data. Previously, R was only limited supported by Taverna. Therefore, the R-shell plugin for Taverna is a very useful contribution to the life science domain. This plugin is now part of the standard distribution of Taverna.

Other contact details:

Not specified

Interests:

Agent technology, Software Engineering, Workflows, Web service technology, Simulation, Human Computer Interaction

Field/Industry: HCI/Workflow

Occupation/Role(s): PhD student

Organisation(s):

Human Media Interaction Group, University of Twente

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Results of the Mapping oligonucleotides to an assembly

Created: 2008-12-19 09:53:23

Credits: Wassinki

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This zip file contains the results of the complete input set analysed by the "Mapping oligonucleotides to an assembly" workflow.

File type: ZIP archive

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Test Input for Mapping oligonucleotides to an assembly

Created: 2008-12-11 12:06:36 | Last updated: 2008-12-11 12:21:53

Credits: Wassinki

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a small test set to quickly test the workflow. This test set can be run on almost any computer and takes 5 minutes approximately.

File type: XML

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oligonucleotides

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Input for Mapping oligonucleotides to an assembly

Created: 2008-12-11 12:04:22 | Last updated: 2008-12-11 12:21:40

Credits: Wassinki

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The complete input set for "Mapping oligonucleotides to an assembly" When this set is used, the whole workflow run takes about 6 hours on a 3 GHz Linux computer with 24 Gig RAM!

File type: XML

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Installing java certificates for services using SSL

Created: 2008-10-15 09:05:44 | Last updated: 2009-02-16 07:37:39

Credits: Wassinki

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This jar file, designed by sun microsystems, helps you to install certificates for java to access services using a secure socket. The complete documentation of this small java tool, including its source, can be found at: http://blogs.sun.com/andreas/entry/no_more_unable_to_find In this document, I will explain how to create a keystore holding the certificate required to access services provided by www.bioinformatics.nl . To install the certificate for www.bioinformatics.nl, do the follow...

File type: Java archive

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