Curriculum Vitae

Employment

  • Broad Institute of MIT and Harvard, Cambridge, MA
    Senior Software Engineer, July 2014 – Present

    • Lead architect and developer on the GenePattern Notebook project, an initiative to merge the functionality of the GenePattern reproducible research and analytic pipeline engine with Jupyter Notebook and associated Python-based analytic tools.
    • Collaborated with Jupyter core development team in Berkley, CA and with academic collaborators at University of California, San Diego.

  • Broad Institute of MIT and Harvard, Cambridge, MA
    Software Engineer, December 2010 – July 2014

    • Developed software as part of the Mesirov Lab, primarily focusing on GenePattern, a platform for functional genomics and reproducible research.
    • Contributing developer on the GenomeSpace initiative, a cloud-based interoperability framework for bioinformatic tools, including Galaxy, IGV, Cytoscape, Genomica and GenePattern.

  • Lime Brokerage LLC, Waltham, MA
    Software Engineer, May 2007 – October 2010

    • Experience developing complex real-time web applications, including both front end and back end systems.
    • Responsibilities included development in the Java enterprise environment, including familiarity with JBoss and Tomcat application servers.
    • Further experience with front end web application development using JavaScript, and both JSON and XML for asynchronous client-server transport.

Education

  • Massachusetts Institute of Technology, Cambridge, MA
    Affiliate Education

    • Attended biology classes as a part of the Broad Institute's affiliate education program.

  • Brandeis University, Waltham, MA
    Master's Degree, Computer Science, May 2006 — May 2007

    • GPA: 4.0

  • Brandeis University, Waltham, MA
    Bachelor's Degree, Computer Science, August 2002 — May 2006

    • Concentrations in information theory and internet studies.

Entrepreneurship

  • Tab Creations LLC
    Founder and Board Member, July 2013 – Present

    • Publisher and developer of hobby games, including card games and tabletop roleplaying games.
    • Oversaw three successful crowdfunding efforts.
    • Chairman, July 2013 – July 2015
    • Treasurer, March 2015 – July 2016
    • Webmaster, July 2013 – Present

  • Tab Creations LLC
    Founder and Board Member, June 2002 – August 2003

    • Developer of the browser-based online multiplayer game, Dark Ages: Trystell.
    • Over 1000 active players at its height.

Peer-Reviewed Articles

  • The GenePattern Notebook Environment: Bringing interactive notebooks to nonprogramming researchers
    Michael Reich, Thorin Tabor, Ted Liefeld, Helga Thorvaldsdottir, Barbara Hill, Pablo Tamayo and Jill P. Mesirov
    • Publication currently pending

Talks and Posters

  • GenePattern Notebooks: An integrative analytical environment for genomic research
    Michael Reich, Thorin Tabor, Peter Carr, David Eby, Helga Thorvaldsdottir, Barbara Hill, Ted Liefeld, Pablo Tamayo, Jill Mesirov

    • Poster presented at the International Conference on Intelligent Systems for Molecular Biology (ISMB) 2016, Bioinformatics Open Source Conference (BOSC 2016), July 2016, Orlando, FL

  • GenePattern Notebooks: An integrative analytical environment for cancer research
    Michael M. Reich, Thorin Tabor, John T. Liefeld, Peter Carr, Barbara Hill, Marc-Danie Nazaire, David Eby, Helga Thorvaldsdottir, Pablo Tamayo and Jill P. Mesirov

    • Poster presented at the Annual Meeting of the American Association for Cancer Research (AACR) 2016, April 2016, New Orleans, LA
    • Also presented at the National Cancer Institute's Informatics Technology for Cancer Research Annual Meeting 2016, May 2016, Cambridge, MA

  • GenePattern Notebooks: Jupyter for Bioinformatic Research
    Thorin Tabor, Ted Liefeld, Michael Reich, Helga Thorvaldsdottir, Barbara Hill, Pablo Tamayo and Jill P. Mesirov

    • Talk presented at JupyterDays Boston 2016, March 2016, Cambridge, MA

  • GenomeSpace: an environment for frictionless bioinformatics
    Michael Reich, Ted Liefeld, Marco Ocana, Dongkeun Jang, Jon Bistline, James Robinson, Peter Carr, Barbara Hill, Judith McLaughlin, Nathalie Pochet, Diego Borges-Rivera, Thorin Tabor, Helga Thorvaldsdóttir, Aviv Regev, Jill P. Mesirov

    • Poster presented at the Joint 21st Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and 12th European Conference on Computational Biology (ECCB) 2013, July 2013, Berlin, Germany
    • Also presented at the 10th Annual Network Biology Symposium & Cytoscape Workshop, October 2013, Paris, France
    • Also presented at the 2014 Galaxy Community Conference, June 2014, Baltimore, MD

  • GenePattern: A software environment for integrative computational and biological science
    Marc-Danie Nazaire, Peter Carr, Thorin Tabor, Michael Reich, Ted Liefeld, David Eby, Chet Birger, Barbara Hill, Catherine Stein Judith McLaughlin, Jon Bistline, Chris Williams, Helga Thorvaldsdóttir, Pablo Tamayo, Jill P. Mesirov

    • Poster presented at the Broad Institute Eighth Annual Retreat, November 2012, Boston, MA

Publishing & Crowdfunding

  • Dime Adventures: Pulp Alternate History Roleplaying
    Writing, Design, Crowdfunding, Layout and Team Coordination, January 2017

    • A pulp roleplaying game set in an alternate history of the year 1904. This game has been written and developed, but is currently waiting for its crowdfunding and subsequent publication. This is scheduled for January 2017.

  • Tab Creations Roleplaying Game Adventure Patreon
    Writing, Design, Crowdfunding, Layout and Team Coordination, March 2016

    • An ongoing project to crowdfund the development of roleplaying game adventures and supplements for Shadows Over Sol, Against the Dark Yogi and other associated games.

  • Shadows Over Sol: Science Fiction Horror Roleplaying
    Writing, Design, Crowdfunding, Layout and Team Coordination, September 2015

    • A science fiction horror roleplaying game set in our own solar system, some 200 years in the future. Humanity has spread throughout the inner planets and is making headway into the outer solar system, but humankind has brought its own dark workings into space.

  • We're All Going to Die Here: A Tongue-in-Cheek Horror Card Game
    Writing, Design, Crowdfunding, Layout and Team Coordination, October 2014

    • A tongue-in-cheek card game based on the tropes of the horror genre. In it a group of teenagers explore a haunted mansion, only to be picked off one by one in overly cliche ways. Those players whose characters are eliminated then "join the haunt," working to make the game harder for the remaining players.

  • Against the Dark Yogi: Mythic India Roleplaying
    Writing, Design, Crowdfunding, Layout and Team Coordination, February 2014

    • A tabletop roleplaying game set in a fantasy world based on mythological India. It's a game of high action and cosmically-chosen heroes with fantastic abilities, working to thwart the coming of the final age.

  • Ganjifa: Traditional Indian Playing Cards
    Crowdfunding and Team Coordination, May 2013

    • Crowdfunded the first general printing of Ganjifa cards in the United States since the 1950s. Ganjifa cards are traditional round playing cards from India and Persia.

  • Saga Machine: A Roleplaying Game of Actions and Consequences
    Writing, Design and Layout, December 2008

    • A tabletop roleplaying game designed to run any number of genres or settings. It is meant to be quick and easy, while supporting a variety of styles of play. This system was later revised, improved and used in both Against the Dark Yogi and Shadows Over Sol.

  • Dark Ages: Trystell
    Writing, Design and System Administration, July 2002

    • A browser-based strategy game, where players would take on the role of empires in a fantasy world. The game was competitive and would pit players against each other for domination over the continent. At its height it had over 1000 active players.

Software

  • GenePattern Notebook
    http://genepattern-notebook.org

    • An extension for Jupyter Notebook which bridges the functionality of Jupyter and GenePattern. It provides access to hundreds of bioinformatic tools within Jupyter Notebook, all within a friendly user interface.

  • Notebook Repository
    https://github.com/genepattern/notebook-repository

    • A web service intended to run alongside a JupyterHub instance. It integrates with the JupyterHub authenticator API, providing notebook publication and sharing functionality within the proxied Jupyter Notebook instances.

  • GenePattern Server
    http://genepattern.org

    • A platform for bioinformatic research that wraps hundreds of analytic tools for the analysis of gene expression (RNA-seq and microarray), sequence variation and copy number, proteomic, flow cytometry and network analysis. It also provides a REST API and queueing system integrations.

  • GenePattern Python Library
    https://github.com/genepattern/genepattern-python

    • A Python wrapper for the GenePattern API. It provides programmatic access for searching and selecting analysess, uploading files, submitting jobs, retrieving the analysis results and sending those results to a downstream step in an analysis pipeline.

  • Jupyter WYSIWYG Editor
    https://github.com/genepattern/jupyter-wysiwyg

    • A extension for Jupyter Notebook that adds WYSIWYG editing functionality to markdown/HTML cells. It does this by integrating the popular CKEditor.

  • GenomeSpace
    http://genomespace.org

    • A cloud-based interoperability framework, bridging the gaps between a diverse set of popular bioinformatic tools. This makes it possible to frictionlessly use the available analyses and visualizations in each tool with others in the GenomeSpace ecosystem.

  • IGV.js Jupyter
    https://github.com/igvteam/igv.js-jupyter

    • A Python wrapper and nbextension for the JavaScript version of Integrative Genomics Viewer (IGV.js), allowing the popular genomic visualization tool to be easily configured and embedded inside the Jupyter Notebook environment.

  • Django Simple Ticket
    https://github.com/tmtabor/django-simpleticket

    • A simple ticket-tracking app that can easily be dropped into a new or existing Django site. It aims for bare bones simplicity rather than elaborate features, minimizing dependencies and allowing the app to be set up in as little time as possible.

Competencies & Interests

  • Computer Languages

    • Strong Familiarity: Python, Java, JavaScript, SQL, CSS, JSON, HTML 5, XML
    • Basic Familiarity: R, PHP, Perl, Flex, Scala, Ruby

  • Platforms & Technologies

    • Jupyter, IPython, Docker, Amazon EC2, REST, GIT, Django, jQuery, Tomcat, JSF

  • Biological Interests

    • CRISPR-Cas9 systems and applications, RNA-Seq analysis, Oncogenetics

  • Operating Systems

    • Macintosh OSX, Linux, Windows