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RSEM - OSPO Spring Internship Program

Apply now(opens in a new window) Job No: 509731
Division/Organization: Office of the Vice Chancellor for Research
Department: Data Science Institute
Job Type: UW Student Jobs
Remote Eligbility: Partially Remote
Location: MCARDLE BUILDING
Salary/Wage Range or Lump Sum: $15.00-17.00
Job Categories: Interpersonal Communication, Critical Thinking/Problem Solving, Digital Technology, Teamwork/Collaboration, Professionalism/Work Ethic, Information Technology and Computers, STEM, Data Analysis

Department Overview:

 The Open Source Program Office (OSPO) is looking to connect interns with meaningful open-source projects as part of a new cohort of the internship program in collaboration with Madison College. During the internship, students will join a mentored open source project, participate in an initial training session, and weekly check-ins with the Open Source Program Office, and learn crucial skills related to managing open source software projects and growing software user communities.

Anticipated Start Date:

 2/2/2026

Anticipated End Date (If Applicable):

 5/1/2026

Remote Work Eligibility Detail:

Partially Remote

 

Anticipated Hours Per Week:

 Minimum: 10 Maximum: 15

Schedule:

 Internship work schedules will be established in collaboration with the project mentors, with a general expected commitment of 10-15 hours/week. In addition to the work schedule established with the project lead, interns will participate in a weekly group session with the OSPO for check-ins, trainings, and guest speakers.

Salary/Wage Range/Lump Sum:

 Minimum: $15.00 Maximum: $17.00

Number of Positions:

 1

Qualifications:

 UW-Madison and Madison College undergraduate and graduate students with applicable backgrounds in any field are eligible to apply. Students must be enrolled in a degree program during the calendar year with at least one semester remaining after the internship’s conclusion.

Application materials should include:
- A one-page cover letter that highlights your qualifications based on skills identified in the project listing and your interest in open source broadly.
- A resume that includes your name, school email address, phone number, field(s) of study (major, minor, degree, certificate), relevant coursework, extracurricular activities, expected graduation date, relevant sample work (ex: GitHub link, personal website, etc.) and any relevant work or research experience.
-The names and contact information of three references.

Submit a resume, cover letter, and three references as part of your application.

Knowledge, Skills & Abilities:

For coding tasks, it would be helpful for contributors to have programming skills in C/C++ and Python, as well as some familiarity with Perl. It would be helpful for contributors to have some experience in bioinformatics and with high-throughput sequencing data in particular.

Position Summary/Job Duties:

Estimating gene expression levels from RNA sequencing (RNA-seq) data is one of the most widely used applications of high throughput sequencing technology. Our group developed RSEM (RNA-Seq by Expectation Maximization), methodology and associated software that is considered by many as the gold standard for expression level estimation from RNA-seq data. RSEM has been highly impactful: it has been cited over 23,000 times (Google Scholar), been used in several big consortia projects such as ENCODE, TCGA, GTEx and TOPMed, and influenced other popular quantification tools such as Kallisto and Salmon.

Although still widely used, the RSEM software, originally written 15 years ago, is in need of maintenance to keep it compatible with current libraries and compilable across platforms. The software project would also benefit from updates to use current best practices in open source software development, including automated testing. Once the software has been properly modernized, there are a number of new features that we would like to add and that will benefit its large user base.

Software Repository: https://github.com/deweylab/RSEM

Interns could contribute to the project in several ways, including:
1. Updating the code to support proper compilation across all platforms and current versions of its dependencies
2. Creating automated test suites and adoption of continuous integration
3. Porting the current Perl front-end scripts to Python
4. Debugging subsets of known issues

Physical Demands:

Interns are expected to be able to sit for extended periods. Specific physical demands will be discussed with mentors during the interview process.

Institutional Statements:

Equal Employment Opportunity Statement:

UW-Madison is an Equal Employment, Equal Access Employer committed to increasing the diversity of our workforce.

Institutional Statement on Diversity:

Diversity is a source of strength, creativity, and innovation for UW-Madison. We value the contributions of each person and respect the profound ways their identity, culture, background, experience, status, abilities, and opinion enrich the university community. We commit ourselves to the pursuit of excellence in teaching, research, outreach, and diversity as inextricably linked goals.

The University of Wisconsin-Madison fulfills its public mission by creating a welcoming and inclusive community for people from every background-people who as students, faculty, and staff serve Wisconsin and the world.

For more information on diversity and inclusion on campus, please visit: diversity.wisc.edu

Accommodation Statement:

If you need to request an accommodation because of a disability, you can find information about how to make a request at the following website:https://employeedisabilities.wisc.edu/disability-accommodation-information-for-applicants/
 
 

Advertised: Central Standard Time
Applications close: Central Standard Time

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