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 and Spark components for named entity extraction, entity normalization, and computation of search ranking parameters. Designer and owner of the knowledge base, developed an internal knowledge management website and API for surfacing knowledge to other components of the architecture and company. Designed and prototyped a variety of research systems to illustrate semantic search concepts. Contributed to the development of query understanding and ranking algorithms.
Collaborative Drug Discovery (Burlingame, CA)2012-2013
Principal Software Engineer Worked on small team developing a complex Rails application to support cloud-based pharmaceutical drug development research. Led development of the API, also created client software for integrating the CDD product into scientific workflows. Worked closely with product management to design new features such as a notification feed. Contributed to grant writing and business development efforts. Prototyped new exploratory knowledge management tools.
SRI International (Menlo Park, CA)2010-2012
Computer Scientist, Bioinformatics Research Group Research and developer for the BioCyc genomic database. Developed graph algorithms and an exploratory user interface for synthetic biology reaction pathfinding. Led the design and development of SmartTables, a web-based semantic spreadsheet for bioinformatics. Rebuilt the web platform underlying BioCyc to meet modern security standards and enable more dynamic user interfaces. Did outreach with the user community to define and refine new features.
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. Designed and developed a tool to support doctor-patient communication.
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 of companies flagship product.
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.
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.
Experienced in design and implementation at all levels from operating system internals to user interfaces. Languages: Java, C#, Ruby/Rails, Common Lisp, Clojure, JavaScript, Python. Internet standards: TCP, HTML, HTTP, CSS, XML, JSON, SVG, WSDL, REST, RDF, OWL. Databases: MySQL, Oracle, MySQL, Postgres, Virtuoso, Elastic Search, Cassandra. Tools: CVS, SVN, Mercurial, Git, Selenium, Hudson/Jenkins. Deployment/Cloud: EC2, Heroku, Docker. Visualization: d3.js, prefuse. Big Data: Hadoop, Pig, Spark.
Selected Publications
Groups: Knowledge Spreadsheets for Symbolic Biocomputing, Database 2013 (w. Suzanne Paley et al)
Accurate Atom-Mapping Computation for Biochemical Reactions, Journal of Chemical Information and Modeling 2012 (w. Mario Latendresse et al)
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).
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.
Programming with Characters, International Workshop on Intelligent User Interfaces, 1993 (with Marc Davis)
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.
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
BACE Timebank, technical advisor, 2010-2013
Behave!, visual programming system for the Virtual Fishtank exhibit, The Computer Museum, Boston, 1998.
The Electric Anthill, SIGGRAPH Art Show, 1989