Open Source Program Office

RSEM

Project description:

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: 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

Intern needs:

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.

Application Requirements:

1. Review the available projects by visiting the various project pages.
2. Interns should apply through the UW Student Jobs portal. Applicants who are not currently admitted or enrolled as a UW-Madison Student or without a UW NetID can login as well as create an account. Please note, you must apply to each project individually that you want to be considered for.
3. Application materials submitted through the UW Student Jobs portal 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.
4. Submit a resume, cover letter, and three references as part of your application.
5. Interviews will be arranged for selected candidates on a rolling basis after applications close.