You will be part of a team of molecular biologists, medical geneticists, and bioinformaticians working together to analyze new and archival clinical cases using high throughput sequencing. As one of a newer team of software engineers, you will have the unique opportunity to design new in-house infrastructure for the UCLA Molecular Diagnostics Laboratories at the Department of Pathology and Lab Medicine.
If interested, submit application here.
A successful applicant will operate in these major areas:
Bioinformatics Pipelines. Sequencing data alignment, variant calling, and clinical reporting.
- Current tools for workflow development include Docker, Nextflow, and Python.
- Current compute platforms include Azure CycleCloud, DNAnexus, and Illumina Dragen.
- Current storage platforms include SMB shares, Azure Blob Storage, and Amazon Glacier.
- Strong focus on code reusability and scientific reproducibility of all work, manual or automated.
Lab Automation. Help colleagues automate manual or tedious steps in their daily workflows.
- Write scripts to parse, update, or even obsolete spreadsheets used by the lab to track work.
- Build APIs and tools that talk to our EPIC Beaker Lab Information System to track samples.
- Build databases and UIs to track samples and their associated metadata.
- Build web-based or Win32 graphical user-interfaces to structure and simplify data entry.
Translational Research. Feature extraction, clinical correlation, and data visualization.
- Extract clinical covariates and molecular data from health records and pathology reports.
- Structure data using natural language processing, neural networks, and regular expressions.
- Speak with pathologists, clinicians, and molecular biologists to understand the data.
- Perform ad-hoc analyses in Jupyter Notebooks, R Markdown, or well documented scripts.
Qualifications
- BS or MS in Computer Science, Molecular Biology, or a related discipline.
- 3+ years’ experience or strong aptitude for software design and engineering.
- Expertise with command-line tools on Linux batch systems and cloud compute.
- Advanced skills in Python or R with attention to documentation and style.
- Familiarity with version control using git and continuous integration platforms.
- Familiarity with workflow specification (CWL/Nextflow) and executors (Toil/Snakemake).
- Excellent written and verbal communication skills with both biologists and coders.
- Enjoys working in a team but can solve problems independently.
- Self-motivated with a strong desire to learn and troubleshoot.
- Strong organizational skills and ability to manage ambiguity.
