About the author Curriculum Vitae

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1 About the author Curriculum Vitae Morris Swertz was trained as MSc in information engineering and management with propadeuse in Psychology at the University of Groningen. As a young entrepreneur, his first contact with novel biomolecular tools for microbe research was in a software project for the Department of Molecular Genetics at the University of Groningen. This seeded a strong scientific interest in the dynamic field of bioinformatics and the software infrastructures to support it. As a result he started a Ph.D. in 2002 at the Groningen Bioinformatics Center under the supervision of Ritsert Jansen and Bert de Brock. Collaborations with various colleagues served to widen his interest to the information management and analysis of biomolecular experiments on humans, livestock and plants. For two years he studied the integration of biological information resources in the international EU- BioGRID project on protein protein interactions, co-managing a workpackage and resulting in several technical reports. Then he procured funding from the NWO-Biopartner organisation for a one year sabbatical from his PhD project to explore alternative business models for MOLGENIS (and to hire business development, legal and software engineering support). In a multi-disciplinary team he led the development of a business plan, marketing materials, legal support documents, and several pilots of MOLGENIS and supervised software engineers assisting in the professionalization of MOLGENIS. The last two years have been spend on developing informatic concepts for building bioinformatics software, testing them in microarrays and genetical genomics and reporting the results in this thesis. At present, he is developing an independent research line in dynamic software infrastructures for life sciences, improving and applying model-driven/generative strategies to infrastructures for microarrays, sequencing, proteomics, clinical trials, genetical genomics and systems biology. 155

2 Journal publications Swertz MA, Jansen RC (2007) Beyond standardization: dynamic software infrastructures for systems biology. Nature Reviews Genetics 8: Fu J, Swertz MA, Keurentjes JJB and Jansen RC (2007) MetaNetwork: a computational protocol for the genetic study of metabolic networks. Nature Protocols 2: 1-10 Albers R, Fu J, Swertz MA, Lubbers LA, Albers CJ, Jansen RC (2005), Combining microarrays and genetic analysis. Briefings in Bioinformatics 6: Swertz M.A., de Brock EO, Van Hijum SA, de Jong A, Buist G, Baerends RJ, Kok J, Kuipers OP, and Jansen RC (2004), Molecular Genetics Information System (MOLGENIS): alternatives in developing local experimental genomics databases. Bioinformatics 20: Swertz M.A. (2003) Ontwerpcriteria beperken complexiteit EAI (Design criteria reduce complexity enterprise application integration). Invited paper based on NGI master thesis award. Informatie, November 2003: Submitted and draft manuscripts Swertz MA, Tesson BM, Scheltema RA, Vera G, Jansen RC (Submitted) MGG: A customizable software infrastructure for genetical genomics. Submitted to Bioinformatics. Swertz MA, Matthijssen DI, de Brock EO, Jansen RC (Submitted) How to generate dynamic software infrastructures for systems biology: a practical example. Submitted to Bioinformatics. Swertz MA, Oostergo RJ, de Brock EO (Submitted) A system for uniform treatment of clinical data. Submitted to the Journal of the American Medial Informatics Association. Smedley D, Swertz MA, Wolstencroft K, Proctor G (In preparation) Technical issues concerning data compatibility and interoperability: a case example using the mouse community resources. 156

3 Grants and awards NWO BioRANGE Grant (2005) to develop bioinformatic resources (models, methods, algorithms and software) genetical genomics. Jansen RC & Swertz MA. 175keuro/PhD position. NWO Biopartner First Stage Grant (2004) to develop business plan for MOLGENIS. Swertz MA, de Brock EO, Jansen RC. 150keuro/1SE + investigator + consultancy support. 1st prize Informatie/NGI thesis award (2002) for MSc thesis on transactions in federated databases for Ordina finance Utopics, The Netherlands. 5keuro. Best first year report "Training" (1997) Rabeling E, Swertz MA, Reinders JJ, Psychology, University of Groningen; Best first-year report "Informatie Beheer Groep" (1996) Swertz MA & Lubbers LA, Technology management, University of Groningen; Best graduate of class 1995 (1995), VWO, NAC-opleidingen, Groningen. Presentations Swertz MA (2008) Beyond standardization: dynamic software infrastructures for systems biology. Invited presentation at European Bioinformatics Institute and Sanger Institute, January Smedley D, Zouberakis M, Mueller W, Rampp M, Swertz MA (2007) CASIMIR WP5: Technical issues concerning database compatibility and interoperability introduction and summary so far. Co-author on invited presentation at the 1 st Annual (public) meeting for the EU Coordination FP6 action CASIMIR - Coordination and Sustainability of International Mouse Informatics Resources, November 28, Rome, Italy. Swertz MA, Jansen RC (2007) Beyond standardization: dynamic software infrastructures for systems biology. Invited presentation at the 1 st Networking (invited only) meeting for the EU Coordination FP6 action CASIMIR - Coordination and Sustainability of International Mouse Informatics Resources, October 4, Corfu, Greece. Swertz MA, Fu J, Jansen RC (2007) Systems biology through systems genetics. Invited presentation (co-author) at the 6 th Annual meeting of the Complex Trait Consortium, May 26-29, Braunschweig, Germany. Swertz MA, Jansen RC, de Brock EO (2007) Generating Software Infrastructures for High-Throughput Life Science Experiments. Reviewed paper and presentation at the Doctoral Consortium meeting of the 2 nd Dutch/Belgian Conference on Enterprise Information Systems (EIS), June 26, Groningen, The Netherlands. 157

4 Swertz MA (2004) Information infrastructures for the life sciences by example. Selected presentation at the Wageningen Springschool Bioinformatics, March 31- April 2, Wageningen, The Netherlands.. Swertz MA (2002) Ontwerpcriteria beperken complexiteit eai (Design criteria reduce complexity enterprise application integration). Invited prestentation at the Dutch Informatics Soceity (NGI-Noord) meeting, December 9, Groningen, The Netherlands Posters Swertz MA, Tesson BM, Scheltema RA, Vera G, Jansen RC (2007) A Molecular Genetics Information System (MOLGENIS) for Genetical Genomics experiments. Presented at the 15th Annual International Conference on Intelligent Systems for Molecular Biology & 6th European Conference on Computational Biology (ISMB- ECCB), July 2007, Vienna, Austria. Swertz MA, Tesson BM, Scheltema RA, Vera G, de Brock EO, Jansen RC (2006) Beyond standardization: dynamic software infrastructures for Genetical Genomics. Presented at Netherlands Bioinformatics Conference (NBIC-ISNB), April 2007, Amsterdam, The Netherlands. Swertz MA, Scheltema RA, de Brock EO, Jansen RC (2006) Quick development of bioinformatics infrastructures using generative methods. Presented at Netherlands Bioinformatics Conference (NBIC), April 2006, Ede, The Netherlands. Dafas P, Bolser D, de Brock EO, Jansen RC, Kozlenkov A, Papadopoulos GA, Robinson A, Schroeder M, Stavrou A, Swertz MA, Vogiatzis D (2004) The biogrid System: A Trial of GRID Technology for the Biotech Industry. Presented at the Health Grid, January 2004, Clermont Ferrand, France. Reports Swertz MA (2006) MOLGENIS Flexible software life scientists want to have. Contents: Summary of business model, software product, financial scenarios, and legal organization. Business plan, 18 pages, appendixes and software. Swertz MA, de Brock EO (2005) Functional design of the TCC Metabase, a meta database for the controlled distribution of clinical trial databases. Technical report for Trial Coordination Center/UMCG, Groningen, The Netherlands. 25 pages. van Alten SM, Bolser D, de Brock EO, Dafas P, Jansen RC, Kounnapi M, Kozlenkov A, Papadopoulos G, Robinson A, Stavrou A, Swertz MA, Vogiatzis D (2004) Integrated visualization of second functional prototype. Contents: description of prototype, user 158

5 manual and technical documentation of BioGRID demonstrator and underlying meta model. Technical Report EU-BioGRID-D31, 71 pages. Swertz MA, de Brock EO, Robinson A, Dafos P, van der Horst (2003) Metadata model and domain model. Contents: on the generation of processing tools to support research on protein-protein interaction. Technical Report EU-BioGRID-D19, 76 pages. de Brock EO, Jansen RC, Kounnapi M, Papadopoulos G, Stavrou A, Swertz MA, Vogiatzis D (2003) Analysis of existing structured data. Contents: technical description of the components of biogrid, expression data sources, protein and protein-interaction data sources, and literature (classification) data sources. Technical Report EU-BioGRID-D12, 71 pages. de Brock EO, Dafas P, van der Horst E, Jansen RC, Kounnapi M, Kozlenkov A, Papadopoulos G, Schroeder M, Stavrou A, Swertz MA, Vogiatzis D (2003) Integration requirements. Contents: use cases on gene expression, protein expression, protein-protein interaction and knowledge manasgements, required grid components and available technology, and initial design. Technical Report EU-BioGRID-D11, 56 pages. de Brock EO, Dafas P, Jansen RC, Kounnapi M, Papadopoulos G, Stavrou A, Swertz MA, Vogiatzis D (2002) List of available data models. Contents: analysis of available data models and formats for literature, nucleotide, pathways, and microarrays. Technical Report EU-BioGRID-D06, 38 pages. Bolser D, de Brock EO, Dafas P, Jang M, Jansen RC, Kounnapi M, Papadopoulos G, Stavrou A, Swertz MA, Vogiatzis D (2002) List of available data sources. Contents: data sources with literature, ontology, expression, nucleotide, pathways, structure, motif, and mutation information. Technical Report EU-BioGRID-D05, 39 pages. Swertz MA (2001) Transacties binnen federated database systems: criteria voor ontwerp en specificatie van FDBSs in staat tot transactieondersteuning (Transactions in federated database systems: criteria for design and specification of FDBSs capable of transactions). Award-Winning MSc Thesis, University of Groningen. 159

6 Software prototypes Data infrastructures: LIMS-like database for the management of rodent experimental animals in the lab. Van der Velde, J, Boerema AS, Swertz MA (2008) MOLGENIS for Chronobiology. BSc Bioinformatics internship, Dept of Chronobiology/Groningen Bioinformatics Center/Hanze University, Groningen. Online showcase generative methods Generating MOLGENIS software infrastructures online, including a simple catalogue of examples. Swertz MA (2007). Published in NatRevGen. Integration tool for biological databases. Van der Veen, MJ, Scheltema RA, Swertz MA (2006) Using context information to automatically reduce the cardinality in the schema mapping task. MSc Artifical Intelligence project, University of Groningen. Pilot study of LIMS-like database for two-color microarray experiments on plant, human, bacteria and mammals respectively. Swertz MA, Matthijssen DI, Gerbens F, Harders F, Langeveld S (2006) Groningen Bioinformatics Center, UMCG, commercial plant company, semi-governmental animal facility. Publication in progress. Processing infrastructures: Online tool: design an optimal genetical genomics experiment Li Y, Vera G, Swertz MA (2007) Use designgg to design an optimal genetical genomics experiment using genotypes, number of microarrays and number of environmental factors. Groningen Bioinformatics Center. Publication in progress. Online tool to manage and share statistical scripts in the R language. Jacobs S, Vera G, Swertz MA (2007) The R Project Manager (RPM) to manage scripts and data files and to build documentation and downloadable packages therefore. BSc Bioinformatics thesis project, Groningen Bioinformatics Center/Hanze University Groningen. R package for the statistical analysis of the genetics of metabolism. Fu J, Swertz MA (2007) MetaNetwork (mqtl, Correlation, Networks). Groningen Bioinformatics Center. Published in NatProt. Integrative visualization of microarray, protein-interaction and literature data. van Alten SM, Bolser D, de Brock EO, Dafas P, Jansen RC, Kounnapi M, Kozlenkov A, Papadopoulos G, Robinson A, Stavrou A, Swertz MA, Vogiatzis D (2004) BioGRID prototype. EU-BioGRID consortium (D31). 160

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