• Developed a sequencing dataset uploader which runs on Illumina instruments (MiSeq, MiniSeq, NextSeq 2000) and sends results directly to AWS S3. Uploader was written in Java and uses the AWS SDK for Java.• Automated a production sequence analysis pipeline using an AWS S3 trigger (when sequencing data arrives), AWS Lambda, and AWS Batch (Docker). • Created production order fulfillment tools in Python for the NEB NextDirect Target Enrichment Custom Ready product line.• Architected and built an AWS Ubuntu Linux custom AMI multi-server compute environment which auto-scales instances based on usage to minimize EC2 costs.• Created resource tagging and reporting tools to allow tracking of AWS costs by project customer.• Developed RNA-Seq and ATAC-Seq pipelines and summary reports in Scala.• Generated tools for bioinformatics visualizations in R. These include TPM transcript expression correlation plots, Venn diagrams, and GC-content and transcript length histograms.• Ran bioinformatics pipelines and interpreted results.• Evaluated RNA-Seq samples for various sources of contamination (TSO, adapters, mitochondrial reads, foreign reads).• Supported lab personnel on systems and tools as needed.• Software tools include Scala, Python, R, Node.js, JSON, macOS, Linux, bash scripting, Git, CircleCI, Agile, AWS (Batch, Lambda, EC2, S3, S3 Glacier, EFS, CloudWatch, ECR, SNS, SQS), Docker• Bioinformatics tools include Picard Tools, STAR aligner, Salmon, Samtools, Bedtools, Macs2 callpeak, bedGraphToBigWig, Homer annotatePeaks.pl, FastQC, IGV, BLAST+, Trimmomatic

• Architected and developed a massively-parallel, cloud-based, object-oriented WGS DNA assembly & annotation pipeline, which interfaces to MySQL and Spotfire for real-time viewing of quality metrics and clickable access to results on S3.• Developed an RNA-Seq transcriptomics data analysis pipeline for evaluating the effects of our endophytes on plants.• Configured and supported our LIMS system, which houses metadata on all our plant microbiome strains and is the world's largest plant microbiome database. Developed custom data import capabilities in C# and ASP.NET MVC, including a front-end web interface.• Designed and developed a pathogen database solution in Python with both curation and query capabilities. • Developed a freedom-to-operate (FTO) application using AWS Batch and Docker.• Software tools include Python, R, macOS, Linux, C#, .NET, Windows, MySQL, MySQL Workbench, ETL, Visual Studio Code, Git, AWS (Batch, EC2, S3, EFS), Docker, Ansible, Spotfire, TDD, Agile, Jira, Kanban, Confluence, REST, JSON, HTTP• Bioinformatics tools include DESeq2, FastQC, Trimmomatic, STAR aligner, Samtools, RSeQC, htseq-count, Salmon, Quast, Bowtie, BUSCO, Augustus, Prokka, SPAdes, Velvet, ABySS, IGV

• Key contributor for commercialization of the PathoGenetix Genome Sequence Scanning (GSS)technology in the Resolution instrument for bacterial identification in complex samples.• Designed and developed a real-time application for visualization of fluorescently tagged DNA molecule signals that are acquired as the DNA flows through a microfluidic chip.• Programmed much of the fluidics, robotics, and optics functionality of the Resolution instrument.• Designed and wrote the logic to lock onto the fluorescent (DNA) signal in the fluidic stream and adjust instrument pressures as necessary to capture an optimal signal with unattended operation.• Enhanced a software tool that calculates correlations between signals to handle two fluorescent tags.• Regularly worked in a networked environment as the Resolution instrument contained 9 hardware boards, each with a TI Stellaris ARM processor and configured at a unique IP address.• Responsible for software releases, installations, firmware flashing, and SQL Server configurations• Tools included C#, .NET, WPF, WCF, .NET Remoting, SQL Server, WireShark, C++/CLI, Mathematica

• Project involved next-gen sequencing of the black widow spider venom and silk transcriptome• Verified that the de novo transcriptome assembly was reliable• Performed direct Entrez queries (via Biopython) to NCBI for annotation purposes• Inspected results for possible chimeric and highly conserved sequences as well as novel proteins• Tools included Python, Biopython, Linux, BLAST+, CAP3, Kalign, Jalview

• Wrote program modules in R and Python for an Arabidopsis gene mapping project.• Created a simulation program to exercise the mapping optimization algorithm.

• Maintained the software interface between the IntelliVue patient monitoring system and the individual networked patient monitoring devices. • This included work on a kernel mode Windows NT driver as well as user mode C++ code.• Performed diagnostic testing and debugging of systems sent from clinical sites.• Responsibilities strictly followed ISO 9001 SQA standards and FDA guidelines.

• Responsible for a frame grabber/video board SDK. Written in C for Windows 95/NT.• Designed a fully object-oriented (C++) SDK architecture to allow for different board types.• Developed VxDs and an NT kernel-mode driver for frame grabbers. These drivers included ISRs, scatter-gather DMA, event signaling, multiple threads, timers, and DPCs.• Modified Tseng Labs ET4000/ET6000 display drivers to support an 8-bit RAMDAC.

Developed AVP’s line of client/server-based medical imaging and PACS systems. • Enhanced image processing and display products for multiple hi-res display boards in an MS-DOS / Novell NetWare / Btrieve configuration.• Debugged image acquisition applications running over TCP/IP, working at packet level using FTP’s PC/TCP developer’s kit.(AVP was sold to E3 Systems and relocated to Texas)

• Responsible for development of the video imaging module of the $paceMAX line of retail shelf space management products. This was a CAD-like graphical application for designing retail shelving sections and store layouts and analyzing them to maximize use of space.• Further enhanced this graphical application by adding raster graphics capabilities to allow viewing on either a TARGA+ or VGA video board and printing on hi-res printers.• Developed a draw/paint module which allowed the user to generate either vector shapes or raster images.• Responsible for the management and direction of three software engineers who maintained and enhanced both the graphical product and a relational database product.• Developed a firmware data-collection application implemented in TCAL (similar to COBOL) for a Telxon PTC-701 handheld. Added the ability to communicate with a PC via RS-232c or modem.Additional responsibilities at MarketMAX included sales presentations, trade shows, and customer training and support.