Similar to other software programming-based fields, there is a severe lack of diversity among biomedical data scientists and tool contributors. In particular, the field of precision medicine is facing enormous challenges and needs diverse perspectives to advance the field and ensure that precision medicine benefits everyone, no matter their background. The future of precision medicine will depend on who we foster as the next generation of genomic data scientists and tool contributors.

Our mentored internship program is for underrepresented UCSC students to apprentice with UCSC Xena. Participating in the Xena project will enable students to gain experience in open source development with an emphasis on genomic and biomedical applications. Students will learn essential skills, including manipulating and analyzing ‘big data’ genomics datasets, using cloud-computing resources, developing automated tests, code documentation, and bioinformatics knowledge. Students will also learn how to participate in open source software development through participation in a real-world genomics project, as well as receive exposure to the many genomics projects based at the UC Santa Cruz Genomics Institute.

Student must meet at least one of the criteria here: https://www.nsf.gov/statistics/2017/nsf17310/digest/introduction/.

Please apply through UCSC Genomics Institute Computational Genomics Lab & Platform (CGL/P) Undergraduate Research Assistant program http:https://bit.ly/38Y0cbd

UCSC Xena helps biologists, both with and without computation skills, to visualize and analyze cancer genomics datasets. Our web-based data browser enables cancer researchers around the world to discover trends and test their hypotheses. Unique in the medical genomics research field, we allow users to easily view both large public resources generated by consortium around the world AND their own data or data from a publication. We accomplish this using a decoupled server-client architecture, where data is distributed across both public and private servers while being securely combined and visualized in one web-based browser.

Read more about UCSC Xena

We are a team of 4 people:

• Jing Zhu - Principle Investigator, software programmer, data wrangler
• Mary Goldman - UX design, outreach, writing
• Brian Craft - lead software architect
• Cally Lin - bioinformatics programmer

• Interns must commit to 15 hours per week for an academic quarter and 20 hours per week for a summer quarter. Note that you can take the internship as a 5-credit course. The schedule will be determined in consultation with the Xena mentor team.
• We will provide a laptop for working on the project, as well as any cloud compute credits needed.
• We will provide a quarterly stipend for participating student ($3,500 for an academic quarter and $4,500 for a summer quarter)
• It will be completely virtual with no in-person meetings, except for picking up the laptop, if needed
• Jing Zhu will be the lead mentor, with co-mentors Mary Goldman, Cally Lin, and Zia Isola, Director of the UCSC Genomics Institute Office of Diversity Programs.

• Students are expected to be able to work and learn independently with some guidance from mentors.

• Students are expected to have some programming experience, either from a class or self-taught.

• Students are not expected to know how to do all aspects of a project but they are expected to attempt to research answer questions on their own and to frequently ask questions.

• Students are expected to meet weekly with our team to present weekly work progress using a mix of slide presentation and screenshots of the results, as well as to follow up (e.g. problems fixed) on feedbacks given from the previous meeting(s) or through slack.

• Students are expected to check in at least twice a week on Slack.

• Students are expected to have a single google doc serving as their lab notebook, this is for students themselves to record what has been done, the results, the commands that used, screenshots of outputs etc.

• Proposal and report: At the beginning of a project, students are expected to write a proposal of the project after discussing with mentor, proposal (introduction section for why do you do this project, timeline section for plan of work), final draft need to be approved by mentor. At the end of a project, students are expected to add a result section to complete a report, which also need to be approved by the mentor. A discussion section can also be added if there are additional thoughts, alternative method etc.

• Two evaluations are required for both student and mentor each quarter: one at the mid-point and another at the end of the quarter.

• If a student is in the RMI program, students are expected to attend 3 events a quarter. If not, attending RMI events are recommended.

Each student enter the mentorship initially for one academic quarter. If the first quarter works out for both the student and mentor, student will be offered to continue to stay on, with a strong possibility to last till graduation. Continuation is conditioned upon mutually satisfactory quarterly evaluation.