 |
|
Science summary
I perform 'e-bioscience' research at the Informatics Institute of the University of Amsterdam and the Leiden University Medical Centre in the Netherlands. In Amsterdam, I work for the Adaptive information disclosure (AID) group, headed by prof. dr. Pieter Adriaans. AID is a collaboration between the VU, UvA, and TNO. In Leiden, now my main location, I work for the BioSemantics group within the Human Genetics Department, headed by prof. Dr. GertJan van Ommen. I am a lead investigator there and coordinate the Leiden branch of BioSemantics, which also has a branch at the Medical Informatics Department of the Erasmus University Rotterdam. Dr. Barend Mons is the founder and main scientific adviser of the BioSemantics group.
My original background is biology (molecular cytology), but my speciality is interdisciplinary research. My current research focus is on applicationsofemerging methodologies from e-science, including the technologies developed within AID and BioSemantics. Previously I was involved in setting up integrative bioinformatics research at the Swammerdam Institute for Life Science (until 2006), creating a Human Transcriptome Map (until 2003), and my PhD thesis was on movement of DNA in Escherichia coli (PhD Thesis, 2001).
|
| |
|
|
Title new paragraph
Text of the new paragraph
|
| |
|
|
Biological interests
My main biological interest is the function and structure of DNA in the cell. In the past I have studied this in eukaryotes and bacteria and used several methods to study various aspects: microscopy, image analysis, statistical models, and pattern recognition. Currently, I am involved in the development of e-science technology. With this technology I would like to be able to perform computational experiments where genomic data is coupled to models that can be viewed as the computable counterparts of the 'cartoon models' that we often use in biology. In this way, biological models, embedded in logic, could become a direct point of reference for analysis, thereby allowing experiments to be performed with more computer assistance. Hopefully, it will also allow a more 'biological' approach to integrating biological data. Currently this requires detailed knowledge of the way data is stored, how it was obtained, and how to interpret the data biologically. Poor documentation makes it hard to perform reliable and reproducible computer analysis.
|
| |
|
|
e-Science interests
The main two emerging e-science technologies relevant to my dreamed scenario are 'workflow' (for the steps of elaborate experiments) and 'semantic web' (for the reference models). We are working towards combining these technologies for knowledge-model-based analysis within an international community of e-scientists using tools such as Taverna, which is starting to have substantial impact on bioinformatics. Currently, I am involved in building life science applications of the AIDA (Adaptive Information Disclosure Application) toolbox. This is a suite of web services being developed for knowledge extraction and knowledge management in a Virtual Laboratory for e-Science.
New inspiration comes from my involvement in myExperiment.org. An new initiative for a 'mySpace' for experimental scientists, especially those interested in incorporating computational steps into their research supported by e-Science.
|
| |
|
|
Affiliations
My work is part of the BioRange project that is associated with the Dutch Virtual Laboratory for e-science project. Both are funded by the Dutch ministry of Economics. I am a 'Project or Area Liaison' (PAL) for OMII-UK (especially the myGrid scientists in Manchester), member of the W3C Semantic Web Health Care and Life Science Interest Group (HCLS), member of the UK -e-Science All Hands Meeting Foundation, and member of the steering committee of BioAssist, a national bioinformatics support program lead by the Netherlands BioInformatics Centre (NBIC).
|
| |
|
