dr. M. (Marco) Roos - University of Amsterdam

Science summary

I perform 'e-bioscience' research at the Leiden University Medical Centre in the Netherlands, where I coordinate the BioSemantics group within the Human Genetics Department. Part of my job is to be a liaison between technology and biology, across research projects and between institutes. In this capacity, I am a guest of the Informatics Institute of the University of Amsterdam, where I previously worked for the Adaptive information disclosure (AID) group, headed by prof. dr. Pieter Adriaans. AID is a collaboration between the VU, UvA, and TNO.

My original background is biology (molecular cytology), but my speciality is interdisciplinary research. My current research focus is on elucidating biomolecular mechanisms by applying and co-developing emerging methodologies from the field of e-science. These include semantic technologies developed by the BioSemantics group andAID, and workflow and e-laboratory technology developed by or in association with the myGrid consortium that has its base at the University of Manchester (UK).

I currently supervise two research projects: (i) elucidating the role of epigenetics in Huntington's Disease and (ii) investigation of genotype-phenotype relations in metabolic syndrome. Furthermore, in collaboration with the Netherlands BioInformatics Centre (NBIC) I supervise two software development projects that aim to help bioinformaticians help biologists, and engage in projects to make research across biobanks (collections of biological samples and data) possible.

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).

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 isstored, 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

I am employed at the Leiden University Medical Centre. Previously, I was supported by the BioRange program and the Dutch Virtual Laboratory for e-science project. Both were 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 participate in BioAssist, a national bioinformatics support program lead by the Netherlands BioInformatics Centre (NBIC).

Social networks

I share the ambition to make myExperiment.org a community centre for scientists interested in computational approaches within their discipline (molecular and cellular biology in my case). myExperiment.org has features for scientists such as sharing of research objects like workflows, in addition to professional social features also found on facebook or LinkedIn.

The links below show the social communities and groups I have joined to build my professional network and as an experiment towards myExperiment.org.

LinkedIn

myExperiment group on facebook

Group of scientists at the Institute for Informatics interested in life science (facebook)

Personal (Hyves)

Links