Software High School

Donald Jeff Milton

Address: *** ******** ***, ** *****, CA 92037

Email: abnkfz@r.postjobfree.com

Tel: 858-***-****

Experience

Tissue Match LLC. La Jolla, CA

March 2009 – Present

Managing partner and Technical Lead

Lead developer and architect of TMArrayBase, an enterprise virtual biobank annotation tool and

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biological specimen tracker.

Built TMArrayBase from the bottom up. UML/Use-cases,

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Java/Tomcat/Hibernate/Spring/GWT/MySQL (Includes integration with multiple biological

databases and ontologies)

http://www.tissuematch.com/TM/

Linux and Windows systems administration and development: I managed Linux server tools for

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CentOS, (e.g. Security, IPTables, Mail, database and development tools)

Managed the design and development of the primary specimen search engine hosted at

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http://www.tissuematch.com

Torrey Path Inc., La Jolla, CA

October 2007 - June 2009

Director of Product Development

Responsible for overseeing the development of all Torrey Path software products: Enterprise

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software tools for management of large volumes of biological data, specifically large gene

expression databases

UML/Use-cases, Java, Hibernate, MySQL, R-Project, Tomcat, JSP, GWT-Ext,

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XML/XSLT, CVS, ANT, Linux Administration, Windows Administration

Developed in Eclipse 3.x on Windows, Mac OSX v10.5, CentOS v5.x

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Hired and managed a team of software developers, biostatisticians and research scientists

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Negotiated corporate partnership with Accelrys to become an independent software provider for

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Pipeline Pilot

Successfully delivered installations to two top-ten pharmaceutical companies in the United States

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Presented tutorials and demonstrations to research scientists at site installations

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Bioinformatics and Software Instructor/Lecturer, La Jolla, CA

June 2005 – present

Biology/Bioinformatics Instructor

Upcoming presentations:

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o “Accessible Scientific Programming: Course Curriculum Design for

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Introductory Computer Science”, November 7, 2009; San Diego Supercomputer Center

o “Scripps Research Institute/ UCSD Supercomputer Center SMART Team workshop”,

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SDSC auditorium, UCSD, Oct 10 2009

Past presentations include numerous workshops on software tools and data in life sciences to

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various programs at several local institutions, including UCSD, SDSU, Miramar College, San

Diego City College and California State University, East Bay

Most recent presentations include:

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CONTIG Conference July 29, 2009; a two hour workshop on using Protein Structure

(RCSB PDB) at the San Diego Supercomputer Center (Rated best lecturer of the series)

San Diego Science Festival 2009, Small Wonders CAVE presentation, "Visualizing Nano-

Scale Science in Virtual Environments"

Designed and instructed a two courses for bioinformatics as part of the Howard Hughes Scholars

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program at UCSD

W rote a SNP (Single Nucleotide Polymorphism) visualization tool for protein structure using the

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Molecular Biology Toolkit (MBT:http://mbt.sdsc.edu; Java/JOGL) and Protein Workshop (RCSB);

the tool is used for in-class demonstrations of nonsynonymous mutations for Howard Hughes

Scholars at UCSD.

Protein Data Bank, San Diego Supercomputer Center, UCSD

June 2005 - October 2007

Software developer and Outreach Coordinator

• Responsible for introductory bioinformatics classes and seminars on software techniques to

access and analyze genomic and proteomic data, specifically protein structure

Creator of ImmersivePDB a 3D virtual reality molecular viewer for 3D protein structures. This is

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currently available for viewing at the Calit2 visualization laboratory. (full demonstration are

available by sending email to abnkfz@r.postjobfree.com)

Designed and built exhibits in science museums and libraries around San Diego, some of which

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are still on display today. This includes a kiosk display at the Biomedical Library at UCSD.

Installations were written in Java/Swing/JOGL/WebStart

W rote several technical tutorials and publications to support the Protein Data Bank

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(www.pdb.org), including much of the Help documentation found on the website today.

Organized and Presented at conferences, including International Society for Molecular Biology

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(ISMB 2006), Metagenomics, and the NSTA National Meeting

Reissung Enterprises, San Diego, Ca

January 2003 - June 2005

General Manager, Modeling and Informatics

Contributed to the design of a diesel cycle airplane engine: This involved close interaction with a

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small team of engineers and investors

W orked in Solid Works to develop a 3D model of engine components for mechanical and stress

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testing analysis

Finite element modeling in Matlab and Solid Works for various components for heat transfer

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Attended SAE Diesel Engine Training

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Obtained single engine pilot certificate with an instrument rating

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W rote a Java Swing/C++ application wrapping numerous algorithms for plotting highly

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specialized and very large data sets

Carnegie Mellon University, Pittsburgh, Pa

September 2000 - January 2003

Sr. Software Engineer and Project Technical Lead

Project lead for a research grant to developer software tools and infrastructure to the National

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Science Digital Library (http://www.nsdl.org). The project is now called the ChemCollective.org

Developed and published technology for rapid application development relying extensively on the

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Java Swing and reflection for an extremely loose-coupled software framework

Published the software framework called "Linked-Active Content"; a code-free way of building

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Java Swing user interfaces.

Co-founded and wrote many of the software tools at ChemCollective.org, an education site for

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delivering online chemistry tools. Many of these tools are used extensively in postsecondary

classrooms

Presented and published at conferences including American Chemical Society annual meeting,

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IEEE and ACM (Association of Computing Machinery)

Molecular Simulations/Accelrys, San Diego, Ca

October 1997 - August 2000

Software Engineer

Developed enterprise bioinformatics software applications (Gene Explorer, Medchem Explorer)

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Managed customer support for first-generation enterprise software solutions for genomic and

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biological macromolecular analysis

W rote distributed software services that included CORBA, Java, Perl and SQL

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Education

New Mexico Military Institute (High School), Roswell, NM

Carnegie Mellon University, Pittsburgh, PA

B.A., Chemistry

W ork-study program with The Society for Protective Coatings (http://www.sspc.org/)

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CMU Swim team

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Private Pilot with Instrument Rating (Experienced in DA-40, DA-20, C-172)

Software Languages, Applications and API's

OO Design/UML: I have a strong background in design patterns for large team-oriented

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application development.

Java/J2EE (Experience in many graphics, network and database libraries including Swing,

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Java2D, Java3D, Java Advanced Imaging, Java Media Framework, JNI, JDBC, "New I/O"), Perl,

SQL, C++, XML/XSLT, HTML,CSS

Extensive experience in Google Web Toolkit (including EXT and SMART GWT libraries),

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Hibernate, MySQL, Perl, SOAP (using Axis), Apache Tomcat, Apache Lucene, Apache Solr,

SOAP, XML/XSL

Developed applications on Windows, Mac and Linux using Eclipse/ MyEclipse with Apache ANT

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(Maven)

Most recent work is developing an enterprise application for biological specimen demand

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management called Tissue Match (TM). The technology includes the Java/J2EE, Spring-

Hibernate, MySQL, Apache Solr, GWT/SmartGWT/EXT, Google App Engine and Apache Tomcat

Basic Linux server administration including firewall (Iptables), database, email and server

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management

Appointments

Vice President, Board of Trustees to Arroyo Paseo High School City Heights, San Diego, CA; a

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high tech high school for underrepresented kids (Elected into second term).

o http://www.arroyopaseohigh.org/about/governance.html

Served on advisory boards to the UCSD Extension bioinformatics program, 2005

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Advisory Board to Sweetspot.dm Inc., a diabetes management company

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Press, Publications and Patents

"Web-integrated biospecimen demand management system and related methods"; a process and

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pathology informatics tool for biospecimen disbursement, Patent #61/ 185,567, June 2009.

Featured in "High School Students Get The Big Picture on Nanotechnology at UC San Diego",

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April 6, 2009, By Andrea Siedsma http://ucsdnews.ucsd.edu/newsrel/science/03-

09Nanotechnology.asp

StarCAVE: A Virtual Environment, short documentary and interview with Jurgen Schultze Ph.D.

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Produced by April Baily, interview by Jeff Milton, Calit2/Jacobs School of Engineering, UCSD

Nov. 9, 2007. http://www.scivee.tv/node/3648

Protein Data Bank Kiosk Viewer:

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http://www.pdb.org/pdb/static.do?p=education_discussion/educational_resources/index.html

PDB structures on exhibit at the Birch Aquarium, “Protein of the Sea”, PDB news, No32, Winter

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2007, by Jeff Milton

Proteins, Amino Acids and the Bioinformatics of Insulin, by Jeff Milton, Protein Data Bank,

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University of California, San Diego, 2006

Software featured in Science Magazine: "Chemistry Class Gets Real", Net Watch, Science Mag.,

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Vol 304, p183, April 9, 2004

David Yaron, D. Jeff Milton, Rebecca Freeland: Linked Active Content for Digital Libraries for

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Education. J. Digit. Inf. 2(4): (2002)

David Yaron, D. Jeff Milton, Rebecca Freeland: Linked active content: a service for digital

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libraries for education. JCDL 2001: 25-32 "Mixed Reception" Virtual Chemistry Laboratory Game,

Dave Yaron, Jeff Milton, Carnegie Mellon Univeristy, Chemcollective.org

(http://www.chemcollective.org/mr/index.php)

1997 Two Java programs featured in "The Official Gamelan Java Directory" by Nova Spivak, Jack

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D. Hidary, Murray Hidary, Alexander Day Chaffee, Rebecca Tapley, Ziff Davis Pr September 1,

1996

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