Lead developer on “Foundation Core” database, which aggregates all variant data from samples sequenced to provide insights into frequency of variants associated with different types of cancer and enable further research.

Developer on in-house LIMS platform supporting CLIA lab operations. REST API drove lab processes across the company, feeding resulting information to genetic counselors and patient facing systems. Implemented changes to allow accepting and handling Genomic DNA and Saliva in addition to Blood, wrote workflows to bring confirmation of positive copy-number variant results in-house by implementing support for new protocols, and implemented changes that shortened turn-around-time for priority samples.

Continued as core developer for Torrent Suite.Lead team working on Torrent Suite Plugin Framework and an internal run tracking system (LIMS for R&D scientists).Working with IGV Team at the Broad Institute, managed internal grant funded project to improve BED file handing, and implement BED and VCF support in IGV.js, a web based genome browser.Python, Django, jQuery, Kendo, PostgreSQL, MySQL, CMake, SGE, Ruby, Git[ 2004 - 2015 ] Note: Positions listed below through 2004 are all continuous with same organization. Left after >10 years in 2015.

Core Developer for Torrent Suite, which is installed alongside every Ion Torrent sequencing instrument. https://github.com/iontorrent/TS/Crafted large portions of UI and REST API code, both driven by Django, for interaction with analysis pipeline and viewing completed reports. Developed analytical tools to support analysis of barcoded and targeted resequencing runs during research and development phase.[ 2004 - 2015 ] Life Technologies acquired by Thermo Fisher Scientific

Developed tertiary analysis tools for PCR Duplicate detection and calculation of Targeted Resequencing metrics (in C++ and Java) for AB SOLiD sequencing data and the LifeScope platform. Lead for Scrum meetings with globally distributed team.Manager and mentor for summer interns working on data warehousing and analysis.Java, C++, Perl[ 2004 - 2015 ] Applied Biosystems merged with Invitrogen to become Life Technologies

Within spinoff startup group, reworked primary analysis pipelines to quickly and reliably produce DNA sequences at scale from the SOLiD platform using cluster computing. Supported research scientists by developing variations of the analysis pipeline customized to test rapidly evolving experimental protocols.[ 2004 - 2015 ] Agencourt Personal Genomics was spun off and acquired by Applied Biosystems

Software developer for the Agencourt Personal Genomics R&D group. Developed initial proof of concept code and data analysis pipelines for what would become the SOLiD sequencing instrument. Reverse engineered Linux drivers for hardware devices for control of prototype autofocus stage, with Java UI for image acquisition. Introduced version control to production instrument control and analysis scripts, created internal wiki for use by research scientists. Built initial compute cluster using Gentoo, NFS, and Torque.Java/JNI, Perl, Matlab, USB/Serial interfaces, Image / Signal Processing, Subversion[ 2004 - 2015 ] Agencourt Bioscience acquired by Beckman Coulter

Responsible for developing tools to support a group of computer finishers who work to close gaps in sequenced genomes. (Including original Human Genome Project and Mouse Genome Project.) Generate reports for management to help identify potential problems and improve throughput. Worked on lab status tool to predict arrival of incoming data for finishing projects, allowing each finisher to handle a larger workload. Developed new strategies for finishing genomes more efficiently by automatically targeting problem regions.Perl, BioPerl, TCL, GAP4, Consed, PCR primer3, BLAST, Java, LSF

Worked independently to develop web site and online product database for Discovery Labware division. (BD Falcon brand tubes and plates). Changed web site that originally consisted of small excerpts from brochures for new products, into a complete listing of all products by category, and later fed data into an interactive online catalog integrated across the other business units within BD.

Managed receipt of manuscripts and distributed for peer review. Relayed responses to authors, and passed favorably reviewed manuscripts to editor for approval for publication. Assisted in enhancement to several large MS Access databases tracking authors and manuscripts for paper and abstract submissions. Converted collection of static web pages for article abstracts to dynamically generated, database driven website. http://cancerprev.org/Registered speakers, setup venue, and staffed international symposium in Nice, France.PHP, Perl, HTML, CSS, Microsoft Access, Peer Review