WORK FLOWS IN LIFE SCIENCE INGO WASSINK PhD dissertation committee: Chairman and Secretary: prof.dr.ir. A.J. Mouthaan, Universiteit Twente, NL Promotors: prof.dr.ir. A. Nijholt, University of Twente, NL prof.dr. G.C. van der Veer, Open University, Heerlen, NL Assistant-promotor: dr. P.E.van der Vet, University of Twente, NL Members: prof.dr.ir. W.M.P.van der Aalst, Eindhoven University of Technology, NL dr. T.M. Breit, University of Amsterdam, NL prof.dr. W. Kruijer, University of Twente, NL prof.dr. J.A.M. Leunissen, Wageningen University, NL prof.dr. R.J. Wieringa, University of Twente, NL Paranymphs: bc. M.L. van Schie ir. R.B. Trieschnigg © Copyright 2010 by Ingo Wassink, Groenlo, the Netherlands ISBN: 978-90-365-2932-7 ISSN: 1381-3617 DOI: 10.3990/1.9789036529327 Cover picture: Rehhütte Mühlrad, made by Immanuel Giel Human Media Interaction The research reported in this thesis has been carried out at the Human Media Interaction research group of the University of Twente. CTIT Dissertation Series No. 09-157 Center for Telematics and Information Technology (CTIT) P.O. Box 217 – 7500AE Enschede – the Netherlands ISSN: 1381-3617 NBIC Publication This work is part of the BioRange program carried out by the Netherlands Bioinformatics Centre (NBIC), which is supported by a BSIK grant through the Netherlands Genomics Initiative (NGI). This thesis only re- flects the author’s views and funding agencies are not liable for any use that may be made of the information contained herein. SIKS Dissertation Series No. 2010-02 The research reported in this thesis has been carried out under the auspices of SIKS, the Dutch Research School for Information and Knowledge Systems. WORK FLOWS IN LIFE SCIENCE DISSERTATION to obtain the degree of doctor at the University of Twente, on the authority of the rector magnificus, prof.dr. H. Brinksma, on account of the decision of the graduation committee to be publicly defended on Thursday, January 14th, 2010 at 15:00 by Ingo Wassink born on September 7th, 1981 in Groenlo, the Netherlands This dissertation is approved by the promotor: prof.dr.ir. A. Nijholt, the promotor: prof.dr. G.C. van der Veer, and the assistant-promotor: dr. P.E. van der Vet © Copyright 2010 by Ingo Wassink, Groenlo, the Netherlands ISBN: 978-90-365-2932-7 Acknowledgement This is it; the result of four years hard work, but also a period with a lot of fun and many new experiences. I am happy to present you the results, this thesis. To write this thesis without the help of many people was difficult if not impossible. Therefore I will devote this section to the people that helped me establishing it. I like to thank them by means of a fictitious journey past these people, by starting at my office at the University of Twente to arrive at my home at Groenlo. I will then start the journey at my office, room number 2120, to thank my room mate and project mate Olga Kulyk. We started our PhD projects at the same day. We had a nice time at this office, a lot of talks and laughings. Together with Dolf Trieschnigg, we followed the bioinformatics course at Nijmegen Radboud University. Together with Wim Fikkert, We went to SloßDagstuhl in Germany and to the British HCI 2006 in London, United Kingdom. The room next to ours is Paul van der Vet’s. Paul, I like to thank you for being a great supervisor and assistant-promotor. Our daily walks at 9.30 o’clock were very nice but also very inspiring. The bread sticks we shared during lunch were almost as indispensable as your input was for my PhD project, papers and thesis. I also want to thank you for your ideas and comments about my work and your suggestions how to improve it. Then, I will move to the room at the opposite of the corridor, which is among others, Dolf Trieschnigg’s. Besides being a colleague for the last four years, you are a really good friend for more then twelve years now. In this time, we have had a lot of fun, but also many discussions, work related and non-work related. Sorry for the many times that I used the “Ik zie het probleem niet” argument (I don’t see the problem) ;). A few rooms next to Dolf’s, I want to thank Anton Nijholt for being my promotor, the opportunity he gave to me for being a PhD student, the freedom he gave to me for doing my research and the nice time I had at the HMI group. At the secretaries’ office, I like to viii Acknowledgement j thank Charlotte Bijron and Alice Visser for their maybe invisible but essential support to enable me to do my research. I also want to thank Hendri Hondorp, for facilitating all ICT-related stuff and for his help in case of technical problems. A few rooms further on, there is another project mate I like to thank, Wim Fikkert. You were a nice colleague, with sometimes a completely different, but inspiring view on things. This led, of course, to many interesting discussions. Another colleague in the BioRange project I like to thank is Betsy van Dijk, for her support in the user studies we did. Matthijs Ooms, I want to thank you for your help in designing the e-BioFlow workflow system, the improvements you made to e-BioFlow, the provenance system you have de- signed and the OligoRAP implementation in e-BioFlow. Without you, it was not possible to design, implement and test our workflow system e-BioFlow. I like to thank Lynn Packwood for her help in the design of the NIWS prototype. Fi- nally, I like to thank all other colleagues, for the fun we had during lunches and the nice talks we had near the coffee machine. Then I will leave Enschede and take the train to Amsterdam. First I go to the Free University, to Gerrit van der Veer, my second promotor. I like to thank Gerrit for his inspi- ring talks, his advice and his help in the user study of the NIWS prototype. I also like to thank Elly Lammers. Without her, it was difficult if not impossible to organise meetings with Gerrit because of his full schedule. She was always in for a little talk about project and non-project related matter. Furthermore, I had a nice time with you two, Dhaval and Yujia in Helsinki, Finland during the ECCE 2009 conference. I will continue to the University of Amsterdam. First of all to thank Timo Breit and Han Rauwerda of the MicroArray Department & Integrated Bioinformatics Unit, for their users’ point of view on computer science applications and bioinformatics tools. Additi- onally, I want to thank you both for the papers we wrote together, the experiments we performed and for sharing our frustrations when implementing the workflow for map- ping Vega-designed oligos to the Ensembl assembly ;). At the same university, I like to thank Marco Roos, Informatics Institute, for his help to find participants for the evalu- ation of the NIWS prototype and for inviting Matthijs and me for the Open Provenance Challenge meeting. From Amsterdam Schiphol, I take a flight to Manchester, to thank Katy Wolstencroft, for her comments on the service categorisation. Additionally, I like to thank Alan Williams for rewriting the RShell plugin to be compatible with Taverna 2. Back at Schiphol, I take the train to Nijmegen. But first I take a stop at train station Ede-Wageningen to thank Pieter Neerincx and Jack Leunissen, Laboratory of Bioinforma- tics, Wageningen University and Research, for providing access to their grid web services (in particular the Blat and Bast services) and for providing OligoRAP as a test case for our workflow system. Pieter, I also want to thank you for your comments and suggestions Acknowledgement ix j how to improve interfaces for life science tools, in particular the e-BioFlow user interface. Once arrived in Nijmegen, I want to thank two persons. First of all, I like to thank Gerrit Vriend for allowing us to participate in the bioinformatics course at CMBI, Radboud University, Nijmegen and to perform a user study during this course. Second, I like to thank Martijn van der Bruggen for enabling me to evaluate the NIWS prototype at the Hogeschool Arnhem Nijmegen (HAN) during a Taverna course. Then I finally travel to Groenlo, by taking the train from Nijmegen to Zutphen. As usual, I miss the train connection. Then, after 30 minutes, I can take another train to train station Groenlo-Lichtenvoorde. Once arrived, I have to finish my journey by bike. But first, I have to go to Zieuwent. First, to thank my mother for her love and the nice but late friday evenings we had when watching U2 videos. Second, I like to have a moment of silence for my father. Then, just before leaving Zieuwent, I want to hug Rex for being such a great dog. Then I cycle to Groenlo, to thank my grandmother for being such a young and great grandmother. Of course, I like to thank Jurgen Röring for being family, a friend and es- pecially for the survival trainings we had at difficult moments in my PhD project. I also like to thank Mark van Schie for being a friend for more than 14 years now; for the Cartan, Carcasonne and Stratego matches we played (especially those that I won). Last but not least, I want to thank Ellen Kamp (just Ellen for me) for being such a great girlfriend.