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.

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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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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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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.

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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!

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Workflow

Taverna 1

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Wassinki

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: Wassinki Pieter Neerincx Katy Wolstencroft Marco Roos

Workflow

Taverna 1

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Mapping OligoNucleotides to an assembly (7)

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Version info The former version of the workflow expected that results from BioMART only report transcripts when the query (the probe in our case) are entirely encapsulated in an exon of that transcript. However, the BioMart service also returns transcripts when the query is not or only partially overlapping with an exon in the stretch on the assembly on which a transcript is defined. This resulted in too many oligos classified as having multiple transcripts or having multiple genes. ...

Created: 2009-02-13 | Last updated: 2009-02-13

Credits: Wassinki Pieter Neerincx

Attributions: Blat against ENSEMBLE Danio_rerio_Genome BlatBlastCombi Blast against ENSEMBLE Danio_rerio_Genome AppendToFile Test Input for Mapping oligonucleotides to an assembly Input for Mapping oligonucleotides to an assembly

Workflow

Taverna 1

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Wassinki

Blat against ENSEMBLE Danio_rerio_Genome (1)

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The blat workflow invokes the blat services provided at www.bioinformatics.nl (author Pieter Neerincx). As input, it takes a database name (for example, Danio_rerio_Genome for Zebra Fish) and one or more sequences in Fasta format. The output will be a tab separated output of the blat. An eValue string constant is added to filter on the e-Value. Note, the e-Value is not exactly the same as the blast e-Value. To run this workflow, a certificate to access www.bioinformatics.nl needs to instal...

Created: 2008-10-15 | Last updated: 2008-10-15

Credits: Wassinki

Workflow

Taverna 1

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BlatBlastCombi (2)

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This workflow combines the blat and blast workflows. It takes as input a database name (Danio_rerio_Genome for Zebra Fish for example) and and a set of Fasta sequences. It first tries to perform a blat (at www.bioinformatics.nl). When this service returns nothing, a blast is done (also at www.bioinformatics.nl). The resulting reports are combined. To run this workflow, a certificate to access www.bioinformatics.nl needs to installed (Some services use an SSL connection). Look at the ...

Created: 2009-02-03 | Last updated: 2009-02-03

Credits: Wassinki

Workflow

Taverna 1

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Blast against ENSEMBLE Danio_rerio_Genome (1)

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This workflow invokes the blast service provided at www.bioinformatics.nl, written by Pieter Neerincx. The workflow takes as input a database name (Danio_rerio_Genome for Zebra Fish for example) and a set of sequences in fasta format. The blast service is invoked (using polling) and the result is a tab separated blast report. To run this workflow, a certificate to access www.bioinformatics.nl needs to installed (Some services use an SSL connection). Look at the link below how to ins...

Created: 2008-10-15 | Last updated: 2008-10-15

Credits: Wassinki

Workflow

Taverna 1

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Wassinki

AppendToFile (2)

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Processor to add content to a (existing) file. The content is added to the end of the file. The inputs: Filename: the file name of a file, if the file does not exists, a new file is added Content: the string to append NewLine [default = true]: if true, a newline is added to the end of the line (useful if you want to add a record each time) The processor supports Multi-Threading since version 2.

Created: 2008-11-11 | Last updated: 2008-11-11

Credits: Wassinki

Workflow

Taverna 1

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Wassinki

Test SoapLab Service Availability (1)

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This workflow tests for all Taverna workflows stored at myExperiment wether theS oapLab services used still exists. For each SOAP/WSDL service it checks wether the SoapLab service can still be accessed. The output is among others a report of accessible SoapLab services inaccessible SoapLab services

Created: 2009-05-29 | Last updated: 2009-05-29

Credits: Wassinki

Workflow

Taverna 1

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Wassinki

Test SOAP/WSDL Service Availability (1)

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This workflow tests for all Taverna workflows stored at myExperiment wether the SOAP/WSDL services used still exists. For each SOAP/WSDL service it checks wether the WSDL file is still accessible and whether the operation is still exists. The output is among others a report of accessible services and operation, operations which WSDL file is not accessible, operations which WSDL file still exists, but the operation is not defined anymore. The last set needs to be checked by hand, because...

Created: 2009-05-29

Credits: Wassinki

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