Michael Travers
  • Email: mt -at- alum.mit.edu
  • Personal site: Hyperphor
Summary of Qualifications
Professional Experience
Quixey (Mountain View, CA)2013-present
Principal Software Engineer Team lead for semantic ingestion pipeline for a large search engine. Developed ontology management tools, Hadoop components for semantic computation, prototypes of of semantic search.
Collaborative Drug Discovery (Burlingame, CA)2012-2013
Principal Software Engineer Led development of API for cloud-based pharmaceutical research application. Developed platform for complex knowledge integration workflows for research grants. Contributed to grant writing and busincess development efforts.
SRI International (Menlo Park, CA)2010-2012
Computer Scientist, Bioinformatics Research Group Contributed to development of Pathway Tools genomic knowledge base, including web-based interface for scientific knowledge management, biochemical pathfinding application for metabolic engineering, graph visualization.
CollabRx/CommerceNet (Palo Alto, CA)2007-2010
Director, Research and Development Lead architect, designer, and product manager for the CollabRx platform, which provides knowledge-based collaborative computing infrastructure for distributed medical research and personalized genomic medicine. Conducted research into knowledge and workflow representation for biomedicine; designed and built prototypes for web-based software platform to support collaboration among scientists working on therapy development.
IO Informatics (Emeryville, CA)2006-2007
Principle Software Engineer, Knowledge Systems Designed and developed tools for integrating and visualizing biological data for metabolomics, proteomics, and related domains, using semantic web technology. Took lead role in architecture, ontology, and product and user interface design. My work continues to be the flagship product of the company four years after I left.
Afferent/MDL/Elsevier (San Francisco CA)1999-2006
Director, User Interface Developed applications for pharmaceutical drug discovery (combinatorial chemistry, LIMS, data integration). Responsible for user interface design, architecture, and implementation, including a sophisticated search tool. Other responsibilities included designing and implementing an object-relational mapping facility, and redesigning architecture for operation in a worldwide enterprise environment. Participated in project planning and management. After successful acquisition of Afferent, continued at MDL and later Elsevier as Principal Software Engineer and Architect. Developed applications for pharmaceutical drug discovery. Lead engineer/architect for the company's client-side platform and data integration strategy. Designed and implemented a visual form design and end-user programming system deployed to consultants and customers. Developed ontology and protocols to unify cheminformatics data across applications.
IBM Research (Hawthorne, NY)1997-1999
Research Scientist Worked with the Java Tools research group designing advanced interactive programming and visualization tools; explored agent-based component architectures. Worked on XML-related application tools and contributed to schema and query standards efforts. Developed web-based knowledge management tools for corporate intranet.
Centre Mondial Informatique et Resources Humaine (Paris, France)1985-86
Senior Research Engineer Designed and implemented a knowledge base and graphic editor for a medical diagnostic expert system for use on portable computers in third-world countries.
Consulting1988-present
Consulting services in knowledge representation, end-user programming, and human-computer interaction for a variety of clients, including MCC, Apple, Science Commons, Nixle, and IS Robotics.
Publications
Groups: Knowledge Spreadsheets for Symbolic Biocomputing, Database 2013 (w. Suzanne Paley et al)
A systematic comparison of the MetaCyc and KEGG pathway databases, BMC Bioinformatics 2013 (w. Tomer Altman et al)
EcoCyc: fusing model organism databases with systems biology, Nucleic Acids Research 2013 (w. Ingrid Keseler et al)
Accurate Atom-Mapping Computation for Biochemical Reactions, Journal of Chemical Information and Modeling 2012 (w. Mario Latendresse et al)
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases, Nucleic Acids Research 2012 (w. Ron Caspi, Tomer Altman, et al)
Politics and Pragmatism in Scientific Ontology Construction, Proceedings of Inconsistency Robustness 2011
Cancer Commons: Biomedicine in the Internet Age, in Collaborative Computational Technologies for Biomedical Research, ed Ekins, Hupcey, and Williams, 2011. (with Jeff Shrager and Jay M. Tenenbaum)
A Melanoma Molecular Disease Model, PLoS ONE, 2011 (with S. J. Vidwans, K. T. Flaherty, D. E. Fisher, J. M. Tenenbaum, and J. Shrager)
BioBIKE: A Web-based, programmable, integrated biological knowledge base . Nucleic Acids Research, 2009 (with J. Elhai, A. Taton, J.P. Massar, J.K. Myers, J. Casey, M. Slupesky, and J. Shrager).
The (Re)Birth of the Knowledge Operating System. International Lisp Conference 2005 (with J. Shrager and J.P. Massar).
BioLingua: A programmable knowledge environment for biologists. BioInformatics 2005 (with J.P. Massar, J. Elhai, and J. Shrager)
A Brief Overview of the Narrative Intelligence Reading Group. In Narrative Intelligence, eds. Michael Mateas and Phoebe Sengers, 2003. (with Marc Davis)
Dynamic Interaction in Java (retitled What is Interactive Scripting?), Dr. Dobb's Journal , January 2000.
Recursive Interfaces for Reactive Objects, Proceedings of CHI '94, in Boston, 1994.
Emotion and the Dynamics of Representation Use, MIT Media Laboratory Music and Cognition Group Technical Report #3, 1992.
Programming with Characters, International Workshop on Intelligent User Interfaces, 1993 (with Marc Davis)
Informal Interaction in Virtual Spaces, 2nd International Confereence on Cyberspace, 1991.
Two Approaches to Informal Interaction Over Computer and Video Networks. In Proceedings of CHI 1991 (with Alan Borning)
A Visual Representation for Knowledge Structures. In Proceedings of Hypertext '89, 1989.
Animal Construction Kits. In Artificial Life: SFI Series in the Sciences of Complexity, ed. C. Langton. Addison-Wesley, 1988.
Education
MIT Media Laboratory, Ph.D. in Media Arts and Sciences
Research in programming environments, languages, and agent-based systems. Co-founded Narrative Intelligence Group. Dissertation title: Programming with Agents: New metaphors for thinking about computation. Nominated for ACM Doctoral Dissertation Award. (1996)
MIT Media Laboratory, S.M. in Visual Studies
Research in programming environments, behavior simulation, and artificial life. Thesis title: Agar: An Animal Construction Kit, 1988
Massachusetts Institute of Technology, S.B. in Mathematics, 1986
Miscellaneous
Ribbonfarm, blogger-in-residence, 2012-2013
BACE Timebank, technical advisor, 2010-present.
Behave!, visual programming system for the Virtual Fishtank exhibit, The Computer Museum, Boston, 1998.
The Electric Anthill, SIGGRAPH Art Show, 1989
Technical
Experienced in design and implementation at all levels from operating system internals to user interfaces. Languages: Clojure, Java, C#, .Net, Common Lisp, Ruby/Rails, JavaScript, Python, C. Internet standards: TCP, HTML, HTTP, CSS, XML, SVG, WSDL, REST, RDF, OWL. Databases: MySQL, Oracle, MySQL, Postgres, Hibernate, Virtuoso, AllegroGraph. Tools: Eclipse, Visual Studio, CVS, SVN, Mercurial, Git, Selenium, Hudson/Jenkins. Deployment/Cloud: EC2, Heroku. Visualization: d3.js, prefuse