Personal Summary: I enjoy solving complex informatics problems and simplifying difficult procedures through the development of automated systems. Go ahead and throw me in the deep end—I’ll swim.
Computational Biologist 2 – Genomic Services Laboratory at HudsonAlpha Institute for Biotechnology
January 2014 – present
In my current position I write web and desktop applications to automate and simplify complicated laboratory processes, provide insights into various data and efficiency metrics, and improve existing procedures. I also handle a wide variety of data analysis challenges based on customer and lab inquiries.
- Designed and developed a Lab Information Management System (LIMS) and successfully transitioned to it from an older system while porting all of the old data. This new system saves tens of hours of lab staff time per week.
- Designed and developed a metrics pipeline to automatically compute and store a wide variety of quality metrics for sequencing data products. The metrics are stored in a NoSQL database (RethinkDB). Users can view the metrics in tables or as visualizations using a web application I wrote in Backbone with an Express.js back end.
- Designed and developed informatics pipeline software in NodeJS to maximize the utilization of a specialized hardware system (Dragen by Edico, Inc) for rapid analysis and turnaround of clinical sample data.
- Designed and developed a user-friendly web application to simplify and electronically document a highly-sophisticated and critical lab procedure for High-Throughput Sequencing sample preparation and pooling. The application saved hundreds of hours of labor through identifying possible problems and errors, generating visual representations of lab procedures and plate layouts, and providing a convenient reporting interface for investigating previous operations.
- Wrote an application in C#/WPF to validate incoming lab inventory and help users immediately catch mistakes when performing highly time sensitive data entry.
- Wrote an application in C#/WPF to help users through the complex process of hybridizing high-throughput sequencing samples.
- I improved and fixed issues with the existing lab information management system web application.
- I wrote a suite of applications and APIs to simplify and automate data processing and delivery.
Consultant – Eurofins Genomics
May 2013 – June 2015
I provide custom software solutions in C#/.NET for automation needs and advise the executive team on business model strategies for high-throughput sequencing.
- Wrote software to interface with a liquid handler in a production environment and rapidly provide detailed, thorough validation of labware barcodes and positions.
- Wrote applications to automate complex production lab processes such as oligo pooling for gene synthesis. These applications eliminated burdensome error-checking, preparation, and record-keeping components of the production process and increased product turnaround time, which was a crucial competitive focal point.
- Wrote software to communicate with an automated sample packaging robot. The software uses information from the production database to make real-time decisions on how the robot should handle samples and negotiate difficulties.
- Conceived and wrote a web application for worldwide high-throughput sequencing sample coordination and instrument usage allocation.
- Wrote a systems specification detailing a strategy to handle data output from worldwide sequencing sites for subsequent computation and delivery.
Owner – Dorset Automation
January 2013 – present
I write web applications (including stores) and custom software for a wide variety of clients. Current and past clients include Diagnovus, Leovard, Fire and Iron Cosmetics, Southern Sports Leagues, and Speedway Tile.
Manager of Scientific Information – Vanderbilt University Medical Center
November 2011-January 2014
I oversaw the informatics aspects of the Vanderbilt Technologies for Advanced Genomics (VANTAGE) core facility. I handled a variety of logistical and data management challenges arising from the merger of four previously-independent core facilities.
- Designed and deployed the departmental website (http://vantage.vanderbilt.edu) on a local server virtual machine using an open-source content-management system.
- Deployed and wrote extensions for an open-source genomics analysis web application, Galaxy, on a cluster-computing gateway server running Red Hat Enterprise Linux. Galaxy is used by the Vanderbilt community to simplify the running of complex genomics data analysis tools in a high-performance computing environment. I also handle end-user technical support.
- Wrote an automated data pipeline for parallel processing and characterizing Next-Generation Sequencing data for customer delivery. This reduced our delivery time by three days and reduced the number of errors arising from performing the analysis manually.
- Wrote a set of programs to automatically organize hundreds of gigabytes per week of Next-Generation Sequencing data. These programs saved approximately 35 hours of work per week and reduced our data storage footprint by approximately 40%.
- Developed a series of workflows for automating and simplifying lab bench work processes, which entailed writing programs and scripts to retrieve information from databases and format it into tables, protocols, and reports.
- Wrote a suite of web applications to provide customer-friendly, Ajax-enabled interfaces to lab information management systems and created companion screencasts to support these. I also wrote a library of scripts to curate, process and streamline server-side application data.
- Wrote Windows desktop applications in C#/.NET based on lab staff requirements to automate the processing of Excel files to instrument input files and HTML reports. These applications save approximately 70 hours of work per week, facility-wide.
- Administered a collection of ten RedHat Enterprise Linux and CentOS servers which process and store over 100 TB of in-house-sequenced genomic data.
Lab Automation Engineer – Vanderbilt University Medical Center
July 2007-November 2011
I was responsible for the smooth functioning of a high-throughput screening facility. This entailed maintaining, upgrading, and servicing a wide variety of laboratory and robotic equipment. I also worked with the facility’s customers to help them prosecute large-scale drug-discovery screening projects.
- Wrote hundreds of lab automation routines which utilized various combinations of articulated robot arms and laboratory instrumentation.
- Designed custom machined and 3D-printed components for lab equipment using CAD.
- Oversaw eleven projects from conception through the full screening process, resulting in eighteen peer-reviewed publications.
- Managed the automation and informatics aspects of a screening library consisting of hundreds of thousands of unique chemical compounds.
- Created and curated a Sharepoint knowledge base to catalogue instrument maintenance history, repair and maintenance procedures, and tutorials.
- Conducted thorough, hands-on training sessions for lab instrument use for over two hundred individual users.
- MS Systems Engineering – Penn State University – August 2013 (3.92 GPA)
- MS Biomedical Engineering – Vanderbilt University – August 2006 (3.71 GPA)
- BS Biotechnology – Middle Tennessee State University – August 2004 (3.89 GPA)
Engineering: Development of automated systems, advanced troubleshooting, repair, installation, and improvement of laboratory hardware and software systems, programming and troubleshooting of articulated robotic arms, CAD.
Administrative: Linux server administration, recordkeeping, data management, end-user training, communicating technological problems and needs to third parties and management, technical writing and screencasts, designing and delivering dynamic, efficient, engaging, and informative presentations.