I spent the majority of my time at Counsyl maintaining the laboratory information management system (LIMS), an internal website written with Django/Python and javascript. I also worked on the sequencing pipeline, robotics, and health insurance EOB processing.

A few notable projects I worked on:

• I implemented the pipeline for fragile X syndrome testing, the most common inherited cause of intellectual disability. This included implementing the algorithm for processing the raw data, uploading and presenting the data to the laboratory reviewers in our LIMS (including visualizations made with d3.js and Protovis, the predecessor to d3.js), and generating the PDF results to be viewed by the patient and their doctor.

• I created the first version of our pre-amplification robotics pipeline, which included a Django app for controlling the liquid handling robots that are used for diluting the lab samples to a specific concentration.

• I designed the oligonucleotide probes for capturing and amplifying specific regions of the genome for sequencing. This involved modifying an existing Python program that we had used in the past to design similar probes, and verifying that the probes met certain standards, such as not overlapping with multiple sections of the genome, and having a specific ratio of GC nucleotides required for our lab process.