SUMMARY:

Oct 2006  – Present, Intellicare, Inc., South Portland, ME

Director, Software Systems Architecture

Summary: Tasked with bringing in open source solutions and introducing a new team programming paradigm involving Subversion and Maven. Introduced Hibernate as an alternative to hand coded JDBC. Performed due diligence on a AJAX web browser framework. Designed and coded core business application.

·       Conduct training sessions, writing team shared utilities and frameworks with the goal of bringing the following modern software technologies to this development team: Unit Testing, Test-Driven Design, n-Tier software design with clear seperaton of concerns; Effective use of Subversion and Maven to ensure software integrity of the release codebase.

·       Created 'ground-up' solution for designing and deploying highly branched patient disease management assessments and educational interactions. This project involved creating the database design, ORM modelling, AJAX GUI design and reporting functionalities. Assessments are represented as mathematical directed graphs, node transitions can be based on simple 'Yes' or 'No' responses or on a set of rules, based on any number of previous patient responses. The Inquiry Designer module is featured prominently in partnership demonstrations.

·       Integrated JBoss Rules Engine (DROOLS) on a small scale within a patient survey to perform branching decisions and on a large scale to determine the path of workflow processes

Mar 2004  – Oct 2006, Informagen, Inc., Newington, NH

Bioinformatics Consultant

Summary: Serving as a consultant to Human Genome Sciences following company restructuring and departure of CIO.

 

·       Maintain software which I previously designed for HGS

·       Update and expand “Resource Informagen” an online collection of information about companies in the biotechnology arena

·       Design wrote a desktop application "Sequence Analysis" and made it available as freeware.  "Sequence Analysis" is written in Java and runs on Macintosh, Windows and Linux. 'Sequence Analysis' download page

·       Contributor to Java based Open Source projects: Karora.org, DynaDTO

·       Took over the lead position on the ANT task "JarBundler" at sourceforge.net. Refactored to moved task attributes into sub-tasks vastly improving it's usefulness.  This ANT task creates a Mac OS X application bundle form a set of JAR files. 'JarBundler' download page

 

 

Jan 2002 – Apr 2004, Human Genome Sciences, Rockville, MD

 Principal Bioinformatics Scientist (as HGS Employee)

Summary: Software development support for project completed while working as a consultant. Technical lead for and member of the software architecture group. Both routine computational biology support and computational algorithm development.

 

·       Continue to develop and enhance the custom HGS LIMS system “CoGenesys” (see below)

·       Using the “CoGenesys” system described below developed a content management system (CMS) as a Java client side application as the front end and a Sybase database as the back end.   Data within the CMS is stored as small atoms of information instead of documents. Using this atomic approach, desired data is selected at a small level of granularity then merged into an larger XML document. This XML data structure is then transformed into a read-only PDF for end user consumption. 

 

 

 

1993  – Dec 2001, Informagen, Inc., Newington, NH

Bioinformatics Consultant

Summary: Informagen, Inc. is an S-Chapter corporation in the State of New Hampshire. Served as a consultant to emerging biotechnology startups in the Boston, Massachusetts and Rockville, Maryland area most notably, Human Genome Sciences and Millennium Pharmaceuticals.  Other consulting clients included Genetics Institute (MA), Proteome (MA), Life Technologies (MD), Genome Therapeutics (MA), and Apple Computer (CA). Apple Feature, CNN Interview

 

 

1993 – Dec 2001, Human Genome Sciences, Rockville, MD

Bioinformatics Consultant via Informagen, Inc.

Summary: Worked directly with the CIO providing both biological insights and programming

 

·       Deployed desktop BLAST client; Sequence analysis applets; Laboratory prep applets

·       Rework NCBI BLAST server code in order to integrate results into high throughput sequencing pipeline

·       Inherited LIMS system, “IRIS”, for maintenance and development. IRIS was based on a proprietary server and user interface components.  HGS quickly outgrew this LIMS.

·       Developed a new, custom LIMS system as a client-side, cross-platform Java application which interacted with an RDBMS system to download functionality (plug-in modules) in real time.  These plug-in modules could be written by staff with a wide range of programming skills, from novice to expert, thus allowing all members of the staff to make immediate contributions.  Modules would be checked into the RDBMS by programmers, end-users would access these updated modules during the next invocation from the client-side application.  This paradigm allowed us to deploy zero install time bug fixes and upgrades with a very rapid turn around time.  We could also deploy new functionality without individual client installation. This application was called “CoGenesys”, not be confused with the HGS spinout company by the same name.

 

 

1994 – 1997, Millennium Pharmaceuticals, Cambridge, MA                                                

Bioinformatics Consultant via Informagen, Inc.

Summary: Worked with the genotyping group both as an interface to the information technology group and as a contract programmer developing front end GUI application for their in house databases.

 

·       Write C++ GUI applications to serve as front end to the Sybase database. This software required using the Sybase CT-Lib

·       Developed applications based around the needs of the bench scientists.  These applications effectively replaced the genotyping software from ABI

·       Assist design of RDBMS schema for large scale genotyping projects by interpreting the needs of the scientists for the programmers

 

 

1987 — 1993, Whitehead Institute. Cambridge, MA                                                              

 Director of Computing

·       Created computer facility modeled after the success at the Whitaker College

·       Introduced desktop workstations

·       Directed a staff of six, the group was responsible for scientific applications as well as purchasing, payroll and office support 

·       Project lead for wiring the entire building with thin wire Ethernet drops; connecting to the MIT network

 

 

1984 — 1987, Whitaker College, MIT. Cambridge, MA                                                          

Director of Computing

·       System manager for VAX/VMS 11/780 for College of Health Sciences and Technology, managed 2 staff members; grew facility into a fiscally self sustaining business unit

·       Brought in Genetics Computer Group (GCG) software. Created an MIT wide computing resource

·       Contributed software to the GCG package. Worked with John Devereux, president of the GCG to redesign GCG’s sequence database structure

·       Designed and developed MSE – Multiple Sequence Editor; this software was later incorporated into the GCG package as “GelAssemble”

 

 

1979-1982, Department of Chemistry, MIT. Cambridge, MA                                                 

 Postdoctoral Research Fellow

·       System manager for PDP 11 Model 60 used in crystallographic analysis

·       Low temperature X-Ray crystallography of the enzyme Ribonuclease. The goal of this project was to capture structures of the enzyme active site during various moments of catalysis.  Protein crystals were cooled to a temperature of –20C in an alcohol solvent.  Reaction substrate and product would be flowed over the crystal, binding to the active site, resulting in active site conformational shifts. The low temperature slowed catalysis to the order of days instead of milliseconds allowing data set to be collected.

·       Developed system for mounting a protein crystal in a capillary flow cell

·       Installed and maintained the FRODO crystallographic software package

·       Maintained Vector General three dimensional graphic system

 

1979-1983: Post Doc – Gregory Petsko, Department of Chemistry, MIT, Cambridge, MA

 

1978: Ph.D. Dept. of Biochemistry & Molecular Biology, University of Florida, Gainesville, FL

 

1974: B.S. Dept. of Microbiology, University of Florida, Gainesville, FL

 

German, Level A2, Goethe Institute, Boston, Ma. 2004-2005.  German Level B1, Goethe Institute, Schwäbisch Hall, Germany, Sep 2005

 

2003-2005: Build a high school league sized baseball field on my property. Currently, this facility is used by high school aged players in the Seacoast New Hampshire area. In the Fall, we sponsor the Seacoast Fall Baseball League.

 

German Language: Have studied German at the Goethe Institute in Boston and Germany. Am an active self-learner and have e-mail pals in Zürich and Hannover. Have exchanged visits with both families.

 

Maintain a 'herd' of two Pinzgauer cattle. Not used for eating but for keeping our fields, wetlands and woods clear.