Mary Gates Endowment For Students

Software Engineering Intern at BioDepot LLC

Faculty PI Name:

Ka Yee Yeung, Professor

Wes Lloyd, Assistant Professor

Project or Start-Up Company Name:

BioDepot LLC is an early startup company spinoff from the bioinformatics research group at University of Washington Tacoma.

Lab/Project Website:

http://faculty.washington.edu/kayee/

Work Location:

Combination of remote and UW Tacoma campus (in-person interactions if circumstances allow)

Work Hours (include times of recurring group meetings, special events, etc.):

  • This intern will join a bioinformatics research group consisting of graduate and undergraduate students. We have a weekly group meeting in which students will give an update on progress. Working hours are flexible, and one-on-one meetings are scheduled if needed.
  • We also have a group slack channel to facilitate interactions.
  • We will provide an interdisciplinary project experience, spanning computer science, data science, statistics and biomedical research.
    In addition, we will offer enrichment activities including webinars, seminars, workshops, training, graduate school preparation, and team building activities (e.g. lunch, museum visits if circumstances allow).

Overall Program Goal:

Our team is federally funded to develop cost-effective cloud-based solutions for biomedical data analysis.  We have developed the Biodepot-workflow-builder (Bwb, https://github.com/BioDepot/BioDepot-workflow-builder) to support the creation and reproducible execution of modular, accessible, and cloud-enabled bioinformatics workflows.  The next step is to expand the utilities and applications of our platform.

Intern Project Description and Responsibilities:

This position will develop, test, and benchmark software tools to allow biomedical researchers to easily analyze big data from federally funded databases.  Specifically, this intern will add tools to leverage new data types in Bwb.

Pre-requisites:

This position is open to students in any majors who have satisfactorily completed coursework in one or more of the following: computer programming, data science, and bioinformatics.

Required skills: Proficient programming skills in Python.

Preferred (but not required) skills: Familiarity with bash, Git, Amazon Web Services, Linux, Docker.

Level of Independence:

This is a well-structured position: we will provide specific case studies and tools to be added to the Bwb.  Dr. Yeung will provide mentoring in bioinformatics and data science. Dr. Lloyd will provide mentoring in cloud computing.  Dr. Hung is the chief architect of the Bwb. He will provide hands-on training in how to add new tools to Bwb.

Learning Opportunities:

Upon completion of this internship, this student intern will be able to:

  • Gain hands-on experience in software development, software testing, code management, and version control
  • Acquire hands-on experience using cloud-based tools such as Amazon Web Services (AWS)
  • Gain knowledge of data science workflows in cancer research