Temporary Bioinformatics Pipeline Assistant

UofL; United States; On-site; USD 34,000 - 55,000; Part time

Job summary

University of Louisville is seeking a part‑time temporary worker for the Brown Cancer Center Bioinformatics Core to automate and streamline computational biology pipelines. The role is approximately 10 hours per week for about six months and focuses on improving reproducibility, reducing manual steps, and deploying workflows on HPC resources.

The ideal candidate will refactor scripts into modular pipelines, apply best practices in software engineering, and collaborate with core members and the

Qualifications

• Four (4) or more years of related experience or equivalent combination of education and experience.
• Experience in automating pipelines and HPC workflows.

Responsibilities

• Refactor and automate existing bioinformatics pipelines (RNA-Seq, DNA-Seq, ChIP-Seq, scRNA, long-read) for reproducibility.
• Convert ad hoc scripts into modular, parameterized workflows.
• Set up automated execution on HPC clusters, including job scheduling and dependencies.
• Add error handling, logging, and basic testing to pipelines.
• Use GitHub to manage code and version control.
• Communicate progress and troubleshoot with Core members and PI.

Skills

Python

R

Bash

Unix/Linux

Version control

Documentation

Testing

Education

Degree in Computer Science and Engineering

Tools

Docker

Singularity

GitHub

Job description

Minimum Requirements

Four (4) or more years of related experience or equivalent combination of education and experience.

Position Description

The Brown Cancer Center Bioinformatics Core is seeking a part‑time (10 hours per week) temporary worker to help automate existing computational biology pipelines. The position will last for approximately 6-months.

Essential Duties

• Refactor and automate existing bioinformatics pipelines (e.g., RNA-Seq, DNA-Seq, ChIP-Seq, single-cell, and long-read sequencing workflows) to improve reproducibility and reduce manual steps.
• Convert ad hoc analysis scripts into modular, parameterized, and well-documented workflows.
• Set up and maintain automated execution on high-performance computing (HPC) clusters, including job scheduling and dependency management.
• Add error handling, logging, and basic validation/testing to existing pipelines.
• Use version control (e.g., GitHub) to manage code.
• Communicate progress regularly and troubleshoot issues in coordination with Core members and the Principal Investigator.

Preferred Qualifications

• Degree in Computer Science and Engineering.
• Proficiency in at least one scripting/programming language commonly used in data pipelines (Python, R, and/or Bash).
• Familiarity with Unix/Linux command-line environments.
• Understanding of software engineering best practices: version control, modular design, documentation, and testing.
• Experience with containerization (Docker/Singularity) and/or HPC/cluster computing.
• Prior exposure to bioinformatics, computational biology, or handling large scientific datasets.

Competencies

• Strong problem-solving skills, attention to detail, and the ability to work both independently and collaboratively.
• Good written and verbal communication skills.

Compensation will be commensurate to candidate experience.

Equal Employment Opportunity

The University of Louisville is an Equal Employment Opportunity employer. The University strives to provide equal employment opportunity on the basis of merit and without unlawful discrimination on the basis of race, sex, age, color, national origin, ethnicity, creed, religion, disability, genetic information, sexual orientation, gender, gender identity or expression, veteran status, marital status, or pregnancy. In accordance with the Rehabilitation Act of 1973 and the Vietnam Era Veteran Readjustment Act of 1974, the University prohibits job discrimination of individuals with disabilities, Vietnam era veterans, qualified special disabled veterans, recently separated veterans, and other protected veterans. The University acknowledges its obligations to ensure affirmative steps are taken to ensure equal employment opportunities for all employees and applicants for employment. It is the policy of the University that no employee or applicant for employment be subject to unlawful discrimination in terms of recruitment, hiring, promotion, contract, contract renewal, tenure, compensation, benefits, and/or working conditions. No employee or applicant for employment is required to endorse or condemn a specific ideology, political viewpoint, or social viewpoint to be eligible for hiring, contract renewal, tenure, or promotion. Consistent with applicable law, demographic information is collected for aggregate reporting requirements. Demographic information provided through this application is not available to hiring managers/committees and is not considered in hiring or employment decisions.

Assistance and Accommodations

Computers are available for application submission at the Human Resources Department located at 2315 South First Street Walk, Room 02C - Louisville, Kentucky 40292.

If you require assistance or accommodation with our online application process, please contact us by email at [e-mail] or by phone [phone].