A new computational biology research group in the Center for Public Heath Genomics at the University of Virginia led by Nathan Sheffield is recruiting a programmer with skills in Python and/or R.

About the lab

The group (http://www.databio.org) occupies wet and dry lab space in the Center for Public Health Genomics. We are also affiliated with the Department of Biomedical Engineering, in the School of Engineering, and Departments of Biochemistry and Molecular Genetics and Public Health Sciences in the School of Medicine. I am also affiliated with the Data Science Institute and the Child Health Research Center.

These affiliations across grounds demonstrate the interdisciplinarity and collaboration priority of the group. We make use of UVA’s high-performance cluster (named Rivanna) for computational analysis. Our research is at the interface of computation and biology, drawing on techniques in computer science, data science, bioinformatics, and statistics, and applying them to biological questions in cancer, epigenetics, single-cell analysis, development, and genomics.

Teamwork is the foundation of my research. I’m trying to build a team of intelligent, creative people who are interested in working together to accomplish great things. I use GitHub to build a shared code base so others can benefit from my work, and I hope to build a team that will contribute to this goal. Writing readable, reusable code pays off as we accumulate useful code and re-apply it to new biological systems. I want to challenge the norm in academic computational research of individual scientists writing isolated code, and instead push open, multi-author code development.

If these topics excite you, please read more about our research interests and open source philosophy.

About the university

The University of Virginia, founded by Thomas Jefferson in 1819, is a UNESCO World Heritage site located near the foothills of the Appalachian Mountains in Charlottesville, Virginia. UVA routinely competes for the #1 rank among public universities in the United States, with a co-located School of Medicine and a top-tier environment for research. Charlottesville is also a great place to live. If you’re unfamiliar with area, please read the many reasons you should consider coming to UVA.

Job description

The scientific programmer will have two primary responsibilities:

  1. Contributing to high quality bioinformatics software. The programmer will be responsible for improving methods developed within our group, such as generalizing them to build robust software that is useful beyond the initial project. This will include code review and will potentially include building web-accessible user interfaces to increase outside access.

  2. Processing large biological data sets through computational pipelines. This will require curating raw input data, documenting data in biological projects, configuring software, and using local supercomputing resources (SLURM) to process the data. This will include monitoring and improving pipeline performance and developing reports to describe data quality and summarize results. The programmer will curate hundreds of terabytes of raw and processed disk space and work with professional systems administrators.

Interested in joining?

I’m recruiting a team-oriented scientific programmer with coding experience. Applicants should be familiar with or interested in some of the skills listed on my page of skills and training materials. For this position, you should have some interest in either building bioinformatics applications or analyzing large biomedical datasets.

Qualifications:

  • Computational experience with scripting in R or Python is required.
  • Skill with C++, object-oriented programming, and git is preferred but not required.
  • Knowledge of biology would be a plus, but not required – however, you must be willing to work with biological data and communicate with biologists.
  • Most important is a willingness to contribute to team projects (such as building communal software) and demonstrated commitment to sharing software and data with the community.
  • Candidates at all levels are acceptable; your experience level (undergraduate, bachelors degree, or masters degree) is less important than your coding skills, work ethic, and interest in working with a team.

Include with your application:

  • Your education and publication history, if any
  • Your career goals, and what you think you would gain from experience in our group
  • Why you think you would fit well, and what you would contribute
  • Your biggest ideas for what projects or types of projects you find exciting
  • A link to GitHub or other public repository with code you showcase, if any

The University of Virginia is an equal opportunity and affirmative action employer. Applications will be reviewed on a rolling basis and the position will remain open until filled.

This position is posted at http://databio.org/scientific_programmer.html and is active as of October 2016.

Informal inquiries and application materials can be directed to the attention of Dr. Nathan Sheffield at . But ultimately, official applications must be submitted at the official UVA application system (posting number 0619750).