Software Engineer Developer

J. Christopher Bare

**** *** ****** *. *******, WA 98109

***************@*****.***

206-***-****

Seattle, WA USA

www.cbare.org

Summary

Experienced software engineer knowledgeable in bioinformatics, data manipulation, and

building software tools for data analysis and visualization. Interested in machine

learning and programming languages. Enthusiastic learner.

Skills in Java, R, Python, Ruby, JavaScript, REST/HTTP, HTML, CSS, bioinformatics,

messaging, SQL, database design, object-oriented design, functional programming, revision

control, unit testing, Scheme, 6502 assembler.Professional Experience

Jun. 2006 - PresentInstitute for Systems Biology, Seattle, WA

Software Engineer

Developed Network Portal, a database of gene regulatory networks. Python, Django,

PostgreSQL, Solr, jQuery, R.

Created the Gaggle Genome Browser, an interactive visualization of high-throughput data

plotted against the genome featuring integration with the R statistical computing

environment and a highly flexible data model. Java, Swing, SQLite, R.

Implemented Firegoose, an extension for the Firefox browser enabling data exchange

between desktop applications and web resources. Javascript, Java, Web services,

Microformats.

Maintained and extended Gaggle, an interoperability framework for bioinformatics

applications based on messaging. Java, RMI, R.

Maintained community resources (web site, mailing lists, wiki, screencasts) and organized

developer conferences.

Wrote manuscripts, documentation, and grant proposals.

Designed tiling array probe sets and curated scientific data.

Assisted in management of outsourced development project.

Aug. 2002 - Mar. 2006Software Developer, contract and freelance

Expedia, developed business-to-business integration (EAI) using Java, web services, XML,

and XSLT.

Tenzing/OnAir, reviewed codebase prior to merger. Java/J2EE.

Amgen, developed a rich client application enabling researchers to define experimental

protocols using a controlled vocabulary. Java/J2EE.

Wrote documentation, unit tests, and build scripts.

Sept. 2000 - Aug. 2002PeopleLink, Santa Monica, CA

Senior Software Developer

Designed and coded online community (social media) applications. Java, JSPs, JDBC, SQL,

and XML.

Served as Technical Lead, mentored junior developers, and assisted Project Managers with

requirements, specifications, and scheduling.

Refactored existing software to Model-View-Controller architecture increasing

maintainability and cleanly separating domain logic and display concerns.

Co-wrote a data abstraction layer to support multiple database engines (Oracle and DB2).

Wrote documentation, unit tests, load tests, and build scripts and managed source code

repository.

Oct. 1992 - Jun. 2000

Prior experience developing software for applications in genomics, e-commerce,

pharmaceuticals, and research. [+]

Jan. 2000 - Jun. 2000Ingenuity Systems, Mountain View, CA

Software Developer

Contributed to team developing web applications in Java featuring a functional genomics

knowledge base.

Developed cross-browser UI elements using HTML, JavaScript, Java Applets, and CSS.

Implemented unit tests in Java.

Jun. 1999 - Dec. 1999Business Data Services / Tallan, Costa Mesa, CA

Senior Consultant

Developed e-commerce web applications using ASP, SQL Server, Java, and Javascript.

Jun. 1998 - Mar. 1999

Around-the-world travel

Traveled to Spain, France, Italy, Greece, Turkey, Egypt, Thailand, Malaysia, Singapore,

Australia, Fiji, Hawaii, and California.

Aug. 1995 - Jun. 1998Merck & Company, West Point, PA

Computer Programmer

Wrote multimedia, client-server, and database applications using Visual Basic, C, and

C++, deployed in Merck's sales force, at trade shows, and internally.

Wrote a multimedia testing engine for sales training with web application for reporting

test results and statistics.

Sept. 1994 - May 1995Pennsylvania State University, University Park, PA

Computer Programmer / Research Assistant

Wrote neural network simulation in C++.

Prepared graphs and data analysis using Mathematica.

Performed biological sequence analysis using BLAST and ClustalV.

Wrote programs for data smoothing, curve fitting, and translating gene sequence file

formats.

Oct. 1992 - Jun. 1994Hahnemann University Hospital, Philadelphia, PA

Computer Programmer / Assistant System Administrator

Assisted in maintenance and programming of a medical research database using Ingres 4GL.

Education

Jun. 2004 - Jun. 2007

University of Washington, Seattle, WA

M.S., Computer Science & Engineering

Coursework in Mathematics, AI, Transaction processing, Algorithms, Compilers, Programming

Languages, Cryptography, Computational Biology, and Data mining.

Jun. 1989 - Aug. 1992

Pennsylvania State University, University Park, PA

B.S., Mathematical Science, Minor Computer Science

Additional coursework in Biology and Economics.

Publications

miRvestigator: web application to identify miRNAs responsible for co-regulated gene

expression patterns discovered through transcriptome profiling

Plaisier CL, Bare JC, Baliga NS.

BMC Bioinformatics. 2011 May 20;39 (suppl 2): W125-W131.

Plaisier et al., Nucleic acids research, May 2011

Integration and visualization of systems biology data in context of the genome.

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