The Department of Public Health Sciences at the University of Virginia seeks scientific programmers for two openings in a computational biology research group led by Nathan Sheffield.
The Scientific Programmers will help support a tech stack that includes Python, R, C++, PostgreSQL, Docker, AWS, Azure, React, Bioconductor, FastAPI, and NodeJS. They are expected to both build new software and use it to process biological data.
The scientific programmers have two primary responsibilities:
About the Lab:
Contributing to high-quality bioinformatics software. The programmer is responsible for improving methods developed within our group, such as generalizing them to build robust software that is useful beyond the initial project. This includes code review and potentially includes building web-accessible user interfaces to increase outside access.
Processing large biological data sets through computational pipelines. This requires curating raw input data, documenting data in biological projects, configuring software, and using local supercomputing resources (SLURM) to process the data. This includes monitoring and improving pipeline performance and developing reports to describe data quality and summarize results. The programmers curate hundreds of terabytes of raw and processed disk space and work with professional systems administrators.
The Databio group (http://www.databio.org
) is an interdisciplinary and collaborative computational biology research group located in the Center for Public Health Genomics
. We are also affiliated with the Department of Biomedical Engineerin
g, Department of Biochemistry and Molecular Genetics
, Department of Public Health Sciences
, the School of Data Science
, the Cancer Center
, and the Child Health Research Center
Our research is at the interface of computation and biology, drawing on techniques in computer science, data science, bioinformatics, and machine learning, and applying them to biological questions in cancer, epigenetics, single-cell analysis, development, and genomics. We collect both novel data and public data and make use of UVA's high-performance cluster
for computational approaches to biological questions.
Our biological questions are focused on understanding gene regulation and epigenetics in development and disease, such as cancer, atherosclerosis, and kidney disease. How does DNA encode regulatory networks that enable cellular differentiation? We rely on experimental data from sequencing-based epigenome experiments, like ATAC-seq, bisulfite-seq, and ChIP-seq, and we use the data to study fundamental principles of regulatory DNA in human health.
We are building a team of intelligent, creative people who are interested in working together to accomplish great things. We collaborate extensively. We emphasize social coding, using GitHub
to share code both within the group and so others can benefit from our work. We seek to write readable, reusable code and apply it to new biological questions. We 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, recent publications, and philosophy of open data.
For this position, you should have some interest in either building bioinformatics applications or analyzing large biomedical datasets.
Bachelor's degree in computer science, MIS, computer engineering, or a related discipline and at least 1 year of related experience, orR an equivalent combination of experience, education, and certifications.
Computational experience with scripting in R or Python.
A willingness to contribute to team projects (such as building communal software) and demonstrated commitment to sharing software and data with the community.
Anticipated Hiring Range:
Experience with git and GitHub
Skill with C++ and object-oriented programming
Knowledge of biology
$60,000 - $77,000
The selected candidate will be required to complete a background check and health assessment per University policy.
COVID Vaccination Requirement and Guidelines
Please visit the UVA COVID-19 Job Requirements and Guidelines webpage prior to applying for current information regarding vaccination requirements and guidelines for employment at UVA.