Proteus Associates
Strategy and System Design Consultancy for the Biomedical Sciences

Recent Engagements


Global Health Network, Oxford, UK

  • Mining of social media to provide early warning of infectious disease outbreaks

Academy of Genomic Medicine (US and UK)

  • Point of care educational and decision support tools for assessing impact of genomic variation on targetted cancer therapy

Balliol Interdisciplinary Institute, University of Oxford, UK

  • Organisation of seminar series and workshop on "Privacy Issues in Genomic Medicine" (forthcoming)

UK Government Agencies

  • Text and social media analytics applied to understanding of roles and behaviours in online forums

University College London (UCL), UK

  • Research in Computational and Systems Medicine. Development of Semantic Web and Linked Data-based infrastructure for management, annotation, integration and query of complex biomedical research information. Requirements analysis and architecture of Petascale research information storage system.

CloudBroker, Zurich, Switzerland

  • Co-founder of a new company to apply cloud computing technologies to large-scale problems in the life sciences and finance/risk management

Oxford Internet Institute, University of Oxford, UK

  • Visiting Research Associate; research on network (technical and social) infrastructures for supporting collaborative research and knowledge management. "Open" (community-driven) models of drug discovery

Swiss National Supercomputing Centre (CSCS), Lugano, Switzerland

  • Project coordinator for SwissBioGRID, a collaboration between the Universities of Basel and Zuerich, the ETH Zuerich, the Swiss Institute of Bioinformatics, CSCS, Novartis and the Friedrich Miescher Institute, to build a GRID-based infrastructure for high-performance computing in the life sciences.

CRS4, Center for Advanced Studies, Research and Development in Sardinia, Cagliari, Sardinia

  • Planning for a new initiative to apply synthetic biology techniques to bioenergy problems. Scientific and business strategy for a new computational systems biology centre providing services for life-science enterprises in Sardinia. Development of relationships with academic and commercial partners. Requirements analysis and specification of a major new high capability computing centre for the life sciences

Department of Physiology, Anatomy and Genetics, University of Oxford, UK

  • Visitor in the lab of Prof. Denis Noble, working on applications of in silico heart modelling to drug discovery and development. Development/coordination of EU/FP7 and other proposals.
  • Co-chair of Scientific Advisory Board for preDiCT, an EU-funded project in computational cardio-toxicology; advisor on Workpackage for development of a Virtual Research Environment for large scale simulations of cardiac function. Development of ontological descriptions of large-scale simulation experiments for use in "provenance management" and data integration

Swiss Institute of Bioinformatics, Lausanne, Switzerland

  • Business/industry-relationship development for the "Vital-IT" initiative on applications of high-performance computing to biology, Teaching of Master's Degree courses in Bioinformatics and Systems Biology

TrueVision Systems, Santa Barbara, CA, USA

  • Member, Scientific Advisory Board, for a start-up company developing real-time 3D imaging systems for microsurgery and image-guided surgery

A US defence systems company

  • Development of techniques for real-time data mining and data fusion on very high volume data

GlaxoSmithKline, plc, Harlow, UK

  • Consultancy on information engineering, with emphasis on drug discovery information integration. Participation in executive task force on innovation, with particular emphasis on more effective information architectures for drug discovery and development

CTI/Mirada Solutions (now Siemens Molecular Imaging), Oxford, UK

  • Consultancy on molecular imaging for drug discovery and development

A US start-up financial systems company

  • Architecture and implementation of a real-time text-mining system for financial and geo-political information, also involving development of descriptive ontologies for a number of financial and geo-political domains

A global computer company

  • Participation in wide-ranging strategy study of opportunities in life science computing, with emphasis on data integration and high-performance computing technologies

BioWisdom, Ltd., Cambridge, UK

  • Co-founder, involved in all aspects of business planning, fund-raising and recruiting. Chair, Scientific Advisory Board. Previously acting Chief Technical Officer: created 8-member start-up technical team and saw first product (an alerting service for drug discovery scientists) to market within 6 months of start.
  • Technical activities in pharma-related ontology development

Probix, Inc., Mountain View, CA, USA

  • Consultancy in planning an Internet-based intellectual property protection system.
  • System architecture planning.
  • Requirements analysis of potential applications in engineering, finance and life sciences

Novartis Pharma AG, Basel, Switzerland

  • Participant in planning workshop for the Novartis "Agora," a physical and virtual space for collaborative work. Member, various external review panels for Research Information Management and for Knowledge Management, reporting to Head of Research and senior IT management.
  • Planning and facilitation of workshop on systems biology.
  • Projects in discovery knowledge management and planning for an initiative in systems biology, working with Head of Molecular and Cellular Biology

Wyeth-Ayerst Research, Princeton, NJ, USA

  • Architecture for chemical/biological data integration.
  • Planning and facilitation of workshops on information management architecture and on systems biology.

Pharmagene, plc., Royston, UK

  • Information management and analysis system for gene expression and pharmacological data

Sanofi/Aventis Pharma (formerly HMR), Frankfurt, Germany, Paris, France and Bridgewater, NJ, USA

  • Leadership of/participation in set of global task forces designing a "next generation" information technology infrastructure for drug discovery, including harmonization of information strategy following merger of research and development organizations; reporting directly to EVP Drug Discovery and Innovation and Global Head R&D IS.
  • Coordination responsibility for an enterprise-wide "Knowledge Management Initiative" aimed at providing a uniform navigational/query interface to a globally-distributed and diverse set of knowledge bases used in drug discovery and development; design and facilitation of workshops on knowledge management for senior research management.
  • Participation in Architecture Group coordinating enterprise-wide use of component-based software design methods; design and facilitation of workshops for scientific and technical management on component-based design.
  • Consultancy in genomics data management and analysis to bioinformatics organization, reporting to Global Head of Bioinformatics

Synomics, Ltd., Cambridge, UK

  • Member, Scientific Advisory Board
  • Consultancy in distributed object computing architectures for drug discovery and pharmaceutical information integration

Teijin America, Inc., San Jose, CA/Tokyo, Japan

  • Strategic/business development consultancy in applications of Internet technology to health-care
  • Comprehensive technical and business survey of 3-dimensional medical visualization algorithms, systems and applications.

Agenda TV, Llanelli, UK and Balliol College, Oxford

  • Pilot project in Internet-based "eLearning" using streaming video technology.
  • Development of Internet-based course on architecture-centric, component-based software engineering.

Hewlett-Packard Co., Palo Alto, CA, USA

  • Business strategy consulting in the life sciences, with emphasis on IT applications in genomics-based drug discovery.

Schroder Ventures, London, UK

  • "Due diligence" consultancy for venture investments in the life sciences..

Paracel Inc., Pasadena, CA (later part of Celera Genomics), USA

  • Founding consultant.
  • Business and technical planning for commercial and scientific applications of a family of ultra-high speed, massively-parallel, pattern-matching engines used for text and genomic pattern matching.
  • Integration with World Wide Web technology for network information discovery and retrieval.
  • Applications to biological sequence similarity matching and motif detection (in collaboration with, among others, Applied Biosystems, Swiss Institute for Cancer Research, European Bioinformatics Institute/EMBL, Chiron Italy).
  • Ontological engineering of a Web-based "current awareness" service (with substantial "data fusion" elements) for the bio-pharmaceutical industry. Design and implementation of graphical workflow editor for genomics applications .

Recent Presentations and Publications

 

"High Performance Computing in Translational Medicine," invited talk, ITAB 2009 Conference, Larnaca, Cyprus.

"Life Science Research and Drug Discovery at the Turn of the 21st Century: The Experience of SwissBioGrid," (with R. Schroeder and M. den Besten), Discovery and Collaboration (in press), 2009.

"Sustaining e-Science in the interplay between infrastructures and scientific fields: the case of Swiss Bio Grid," (with R. Schroeder and M. den Besten), eResearch Conference 2008, Oxford UK.

"Of Molecules and Men: Grid Computing and Molecular Medicine," invited keynote talk, HealthGrid 2007, Geneva, Switzerland.

"Computational Biology: the Next Grand Challenge" invited talk, HP Executive Forum on High Performance Computing, Sophia Antipolis, France, 2007

"Do Grids Matter in Drug Discovery?" invited talk, GridCrunch Day 2007, Bern, Switzerland.

"The SwissBioGrid Project: Objectives, Preliminary Results and Lessons Learned," (with Michael Podvinec et al.), in Proc. eScience 2006: 2nd IEEE Intl. Conf. on e-Science and Grid Computing, Amsterdam, 2006.

"The SwissBioGRID Project," invited talk, SIB/Vital-IT Symposium on High-performance computing in the Life Sciences, Geneva, 2006

Co-chair, Workshop on "Bioinformatics, Chips, Data Mining," BioSquare, Geneva, 2006

"High Performance Computing for the Life Sciences," invited talk, BioData 2006, Geneva.

"From Data to Models: a Biological Theory of Everything?" invited talk, CERN Tutorials on Bioinformatics, 2006.

"Doing eScience with SwissBioGrid," invited talk, SIB/Vital-IT Symposium, Lausanne, 2005.

"Computational Physiology: the next Grand Challenge," invited talk, Swiss Centre for Scientific Supercomputing, Manno, Switzerland, 2005

"Building the Information Architecture," invited talk, Workshop on the Novartis "Agora" project, Basel 2004.

"Information Architectures for Drug Discovery," invited talk, Tripos, Inc. 2004

"The Semantic Web," talk to graduate class in Information Systems, University of San Francisco, CA, USA. 2003

"Drug Discovery: A New Library of Babel?" invited talk and panelist, IIR Conference on Drug Discovery, 2002, San Diego, CA, USA.

"Computational Challenges of Systems Biology." Invited talk, SOS Workshop on High Performance Computing 2002, Leukerbad, Switzerland.

"Information Fusion in Drug Discovery," Invited talk, InfoTech Pharma 2001, London, UK.

"Information Architectures for Drug Discovery," Invited talk, IBC Drug Discovery Technology 2000, Basel, Switzerland.

"Predictive Biology," invited Talk, Amer. Assoc. of Pharmaceutical Scientists 2000, Washington DC, USA.