Summary

Designer and implementer of web-based database applications. Specializing in Java, backed up by JSP, HTML, JavaScript and Perl. Creative problem solver, with strong programming, database, and user interface design skills.

Skills

Languages: Java, JSP, Perl, HTML, JavaScript/ECMAScript, SQL, R, WML, VBScript/VBA, Visual Basic.

Databases: JDBC, Oracle, MySQL, MongoDB, SQL Server, Sybase, MS Access, Hypersonic SQL , Solid.

Web technologies: jQuery, Java Server Pages, AJAX, server-side applications, SMTP, POP3, NNTP, SNMP, SNTP, IIS, ASP.

OSes: Linux, MacOS X, Windows, Solaris, Unix SVR4, BSD Unix.

Electronic Design Concierge

Newton, MA

3/2012-present

Concordant

Chelmsford, MA

1/2010-2/2010

CTO.  Conceived of, designed and developed software to allow highly context-sensitive searches of an electronic components database using a block diagram design tool as a front end.  When designs are completed, they are referred to chip vendors, who are then able to send in their highly trained, scarce field application engineers to help the designers optimize the design and consider alternative choices.  Project uses jQuery, JSP, Lucene/Solr, MongoDB, Nutch.

Consultant. User experience design for Concordant's self-service version of their high-touch consulting methodology for physician groups converting from paper to electronic health records. Worked with Concordant project managers and outsourced software development firm to design the portal embodying Concordant's time-proven methodology in a web-based format.

stealth-mode startups

2008-2009

Consultant (2008-2009). Assisted several stealth-mode startups in planning and architecting their software solutions. These included:

• a web portal for solar- and wind-farm developers, a place where contractors, banks, lawyers, landowners, regulators and utilities could come together to plan new clean generation projects. Software would assist with optimizing siting (wind strength, solar insolation, grid interconnect distance and requirements, zoning), help identify partners and financing opportunities, and create a marketplace for equipment and services.
• developing consumer-level power monitoring and control systems to enable homeowners to get a detailed profile of how they used power at each appliance and over time. With this information, they could then plan how to conserve power more rationally.
• helping connect audiences with local performances (music, theatre) that they might not otherwise know about. Based on zip codes, expressed preferences, and their own music collection, the software would track local venue schedules and notify registered members.
• Bloobike, has been involved in developing bike sharing in the Boston area. They needed help with development of software and system criteria for selecting kiosk and rack vendors and integrating with other systems. I assisted by identifying numerous companies (mostly in Europe) who are doing this for various municipalities and beginning conversations with them about requirements, costs, integration capabilities, etc.

Broad Institute of MIT & Harvard

[formerly Whitehead Institute,

Center for Genomics Research]

Cambridge, MA

10/2002-5/2007

Consultant (9/2002-5/2007). Key architect and developer of GenePattern, a gene expression analysis framework for statistically directed analysis of cancer microarray data. System provides web services access to tens of modules for data acquisition, filtering, clustering, and visualization. It allows wiring of a pipeline from data import to data reduction, prediction, and visualization in a batch or interactive fashion. High level wrappers in R, Java or Perl allow publication of reproducible research and simplify usage for non-programming biologists. Project used Java, SOAP, XML, "R" (a statistical language), SQL, Tomcat, HTML, and Javascript. www.genepattern.org

Developed ELI, Enhanced LIMS Information, a system for annotating samples in a LIMS pipeline with metadata about the sample and processing it has undergone. In addition to capturing key lab notebook data online, it also assisted in creating good 96- and 384-well plate layouts, enabled ad-hoc queries based on metadata, assisted in lab workflow tracking, and made sharing of data, metadata and results simple. Lab users could continue using their favorite database, Excel, while downstream users had access to all of the raw and processed data. Project used Java, Oracle, Tomcat, HTML, Excel and Javascript.

Developed an Illumina software pipeline, taking Illumina raw bead data, scrubbing, reducing, normalizing and concatenating into manageable flat files that feed into a GenePattern analysis pipeline. Initial deployment was for a prostate cancer study in conjunction with Dana-Farber Cancer Institute and the Karolinska Institutet (Stockholm). The same system was later modified to support a ChemBank high-throughput gene expression screening project. Project used Java, GenePattern and Excel. See "Gene Expression in Fixed Tissues and Outcome in Hepatocellular Carcinoma" in publications for more details.

Enhanced GeneCruiser, a publicly-accessible gene and microarray probe annotation system that allows gene accessions to be mapped between various manufacturers' chip types and to capture additional useful information about each accession. Project used Java, Oracle, Perl, and Apache. www.genecruiser.org

Developed Connectivity Map portal, a database and public website that allows investigation of linkages between drugs, diseases, and differential gene expression. Project used Java, Oracle, Tomcat and Apache, HTML, Javascript, and Perl. www.connectivitymap.org

Developed web front end, back-end tools, and scrubbers for data embedded within the Molecular Signatures Database. This publicly-accessible tool allows users to select gene sets and collections of gene sets from among the numerous ones that are part of the Gene Set Enrichment Analysis package (also from Broad). Gene sets each have documentation describing them and expression signatures can be created from a compendium of expression profiles. Users can examine overlaps between gene sets and view categorized gene families and learn more about them through annotations. www.broad.mit.edu/gsea/msigdb

Millennium 

Pharmaceuticals, Inc

Cambridge, MA

4/2002-10/2002

1/2001-9/2001

Consultant to the Animal Resource Group (5/2002-6/2002). Defined requirements for a custom animal ordering, order tracking, monitoring, and protocol management system to replace an existing commercial system. Interfaces with Ariba for approvals and order placement, and with Palm Pilot-based censusing software. Complies with Federal animal recordkeeping regulations. Also developing a process model for the Mouse Model department ranging from protocol acceptance, through creation of the transgenic strain, breeding, genotyping, and reporting.

Consultant to the Scientific Development Group (4/2002-10/2002). Created an agreement management system for tracking intellectual property, scientific, financial, publications, and contact information. Entirely metadata-driven, generating forms and reports that can be modified by non-programmers. Reports are displayed in either browser or Excel. Daily alerts delivered via email for critical milestone dates. Command center created daily to-do list and allowed quick checkoff of completed items. Project used Oracle, Tomcat, JSP, Java, tag libraries and Excel, running on Unix server and Windows desktops.

Consultant to the Protein Production Group (1/2001-9/2001). Created a tracking system (database, forms, reports) for protein constructs and clones, tracking where the original gene sequence came from, hybridoma formulation, mono- and poly-clonal antibody production, virus and cell line propogation, batch quality and usage results, and amount and location of current inventory. System is used by protein production group (scientists and technicians), enabling faster location of existing products, warning when inventory is about to be used up, quality tracking, and creating equipment and personnel scheduling efficiencies. Project used Access.

Zipcar, Inc.

Cambridge, MA

1/2000-12/2000

Consultant. Architected, designed, and implemented entire member and administrator portions of website for Zipcar's car sharing reservation and monitoring system. Capabilities include online new user application workflow, car reservations, electronic credit card billing, reporting of delayed returns and all other operational reporting and monitoring requirements, replication to backup server, WAP-enabled cell phone access. System placed 34th in InfoWorld 2001 top 100 innovators list. Project used Java Server Pages, Java, Solid database, Linux, Apache, Tomcat, and WML. zipcar.com

Woods Hole

Oceanographic Institute

Woods Hole, MA

9/1999-12/1999

Consultant/Guest Investigator. Developed web-based 3-D data visualization software for large decentralized distributed biological and chemical datasets collected by independent investigators, enabling ad hoc cross-project global data mining.  Project used C (for CGI application), IBM Visual Age for Java, Solaris.

Digital Gizmo, Inc.

Cambridge, MA

1/1999-1/2000

Consultant. Provided technical advice on database selection, configuration and integration for web site supporting a series of oceanography books produced by Turnstone Publishing for Woods Hole Oceanographic Institute. Developed servlets for discussion forums and content editing. Designed database schema. Project used Microsoft J++, IBM Visual Age for Java, New Atlanta Servlet Exec, Gefion InstantOnline, JSP, Allaire JRun, Apache, MySQL. digitalgizmo.com/projects/proj_tpg.php

Factpoint, Inc.

Burlington, MA

1/1999-6/1999

Consultant. Developed adapters for client-side cut/copy/paste, redlining, deleting, and document and folder management in new Novation document management and workflow automation product. Created protocol handlers for standard and proprietary data access. Developed platform-independent factory classes to support Windows, Solaris and other CDE platforms. Wrote JNI wrappers to invoke native application APIs. Project used IBM Visual Age for Java, Windows NT, and Solaris 2.6.

Roving Software, Inc.

Needham, MA

9/1997-12/1998

Consultant. Developed server-side Java-based web agent software for e-commerce system to allow turnkey personalization of web sites. Designed and implemented COM integration with MS Exchange and MS Scripting Host, created scripting capability by integrating JavaScript engine, rewrote HTML parser, developed numerous agents for clients, developed meta-agent system, analyzed and implemented critical performance improvements, created servlet interface to agent engine. Roving Software is now Constant Contact. Project used Visual J++, ASP, JavaScript, ServletExec, PSE Pro, MS FrontPage, JDBC, SQL Server, Oracle, Sybase, VBScript, and HTML.

Lakes Region

Conservation Trust

Meredith, NH

5/1997-8/1997

6/1998-8/1998

6/1999-8/1999

Consultant (volunteer). Analyzed information requirements of LRCT staff, recommended converting their information systems from documents to intranet- and internet-based databases of shared data. Designed and implemented web site to track land acquisitions, manage holdings through site monitoring and scouting reports, communicate with volunteers and members, increase productivity of staff in report preparation, and educate the public about needs and methods of land conservation. Project used FrontPage.

Lucent Corp.

[formerly Prominet Corp.]

Concord, MA

10/1996-4/1997

Consultant. Designed, prototyped, and developed Java user interface for browser-based administration of gigabit-per-second network switches offering high degree of customizability to support unique hardware capabilities. Developed interfaces for both bundled product and unbundled add-on (allowing network-wide configuration and reporting) using FrontPage and Visual Café. Designed and implemented network performance load/graphical benchmark program to demonstrate benefits of switch using Visual Café and Visual J++.

Lightbridge, Inc.

Burlington, MA

12/1996-2/1997

Consultant. Designed and implemented new Java-based extranet front-end to existing cellular phone credit check and activation back-end. Design allows non-programmers to create customer-specific screens easily by automatically gluing together components that have a user interface, validation logic, and back-end connection information into a flexible transaction processing engine. Project used Visual Café.

Vectis Corp.

Waltham, MA

5/1994-8/1996

Director of Product Development. Architected, designed, implemented, and managed development of pen computer-based point-of-care system for outpatient physicians to record patient charts into a replicated database environment. Brought prototype software to commercial readiness, significantly enhanced core product, devised mechanisms to integrate outside information feeds (insurance eligibility, drug history, lab results, etc.) to bring it to the examining room using WAN and wireless LAN. Responsible for overall architecture, look and feel, user interface style guidelines, navigation and database interfaces, design and development of many original screens, report engine architecture, performance tools, software build tools (VB, Access, C). Using Lotus Notes, designed and managed databases for bug tracking, software release management, project planning, and customer enhancement tracking.

Sun Microsystems, Inc.

Chelmsford, MA

4/1987-5/1994

Manager of Nomadic Computing (11/1992-5/1994). Devised new product to exploit portable computing devices, with software links to networked desktop systems. Responsible for conception, design, identifying and negotiating with key vendors, hiring, managing engineers, growing team, coordinating work with partners. Developed overall metaphor and prototyped user interface (VB and C).

Manager of PC Emulation. (4/1987-10/1992). Chief PC expert within Sun. Responsible for all aspects of development of new PC emulation software and hardware, including bi-coastal and cross-Atlantic joint development. As product team manager, directed work of 50 people in software, hardware, release engineering, quality assurance, documentation, customer support, and manufacturing. Provided DOS/Windows expertise to key ISVs and customers.

Rock Software

Newton, MA

1/1990-1/1995

Entrepreneur. Developed two products for off-line manipulation of Unix email on non-networked PCs. Portable Mail for DOS and Portable Mail for Windows were published by Qualix Group (6/1991 and 1/1994). Created software, worked with beta test sites, located and signed with publisher, and continued to enhance and maintain.

Kurzweil Applied

Intelligence, Inc.

Waltham, MA

6/1983-4/1987

Manager of KVS Software Development. Led team of 5 senior engineers in creation and enhancement of Kurzweil Voice System (world's first 1000 word speech recognizer). Key contributor in architecture, design, implementation, testing, internal documentation for KVS. Prioritized product enhancements, coordinated new software releases with manufacturing, selected and supported beta test sites, visited customer sites, and developed OEM programs. Daily working contact with customers, support, marketing, sales, vendors, and distributors

Paramin, Inc.

Wellesley, MA

10/1981-6/1983

Consultant. Proposed, scheduled, designed, and implemented office and factory automation systems. Projects included: 3274/3278-protocol emulation, semiconductor plant automation, wire bonder NC program generation, optimal layout for NC tooling. Responsible for writing and negotiating proposals, creating fixed-price bid schedules, working to schedule, and creating user-level documentation. High client satisfaction resulted in substantial contract additions and follow-on projects.

Raytheon Co.

Sudbury, MA

7/1978-10/1981

Software engineer. Designed, coded, tested air traffic control system for German government. Managed group of 6 engineers in development and enhancement of oil well logging recorder, including scheduling, budgeting, feature enhancement, customer support, customer training, and handoff of final product to customer.

Education

B.S. Computer Science/Biology from Union College, 1978. Graduated with honors in both Computer Science and Biology. Elected to Sigma Xi membership. Founder and president (two years) of ACM chapter.

Publications

• "Gene Expression in Fixed Tissues and Outcome in Hepatocellular Carcinoma"; New England Journal of Medicine, 10.1056, October 15, 2008
• "The Connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes, and Disease"; Science, September 29, 2006
• "GenePattern 2.0"; Nature Genetics, May 2006 (v38n5)
• "Coping with DOS"; Sun Expert Magazine, January 1990 (v1n3)
• "DOS on the Sun386i"; SunTechnology, Summer 1988 (v1n3)

Patents

• ‘Voice controlled system and method for generating text from a voice controlled input’, US 5231670.
• ‘Memory-mapped bus mouse’, US 5261054.
• ‘Historical database storing relationships of successively spoken words’, US 5970448.

Languages

English (native), French (good), German (good)