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The Center for Applied Bioinformatics (CAB) at the St. Jude Children’s Research Hospital (SJCRH) is seeking a creative Software Engineer with a strong background in bioinformatics to join our development team to create and maintain our vital analytical infrastructure. The new hire will work closely with a team of computer scientists, bioinformatics scientists, and clinical research staff to develop genomics workflows/pipelines and high-quality user interfaces. Success in this position requires a firm grounding in software engineering, the ability to work seamlessly in a team, and the ability to provide fast turnaround to ensure the timely delivery of defined functionality. The new hire will also gain the experiences and skills to handle big data and develop expertise in data-centric workflow development and management.
is an institutional shared resource, with the mission to provide state-of-the-art bioinformatics services to SJCRH investigators. We maintain the highest level of scientific rigor by carefully vetting and documenting all bioinformatics methods and pipelines. All methods are shared with the international biomedical research community. At the CAB, we believe that “Discovery Leads to Cure”, which is what we are striving for.
Responsibilities
- Use Nextflow to build bioinformatics pipelines that take FASTQ or BAM files as input and process them using bioinformatic tools.
- Write Python/R scripts to process, summarize, and visualize outputs created by other tools.
- Ensure that the pipeline is modular and flexible, with the ability to add or remove tools as needed.
- Implement a reporting system to generate a clinic-ready report that summarizes the findings and provides actionable recommendations.
- Ensure that the pipeline is reproducible, with the ability to generate the same results from the same input data.
- Provide clear and concise documentation on how to use and manage the pipeline, including instructions on how to install and configure the necessary software and tools.
- Create R Shiny Apps and other web-based user interfaces for new and existing pipelines.
- Provide regular updates on progress and any issues or challenges encountered.
Minimum Education
- Bachelor’s degree in engineering, computer science, physical science, or related field required
- Master’s degree or PHD is preferred
Minimum Experience
- Eight (8) years of experience in software development is required
- Four (4) years of experience may be acceptable with a Master’s degree
- Zero years of experience may be acceptable with a PhD
- Experience with Linux is required
- Experience working with large data sets or bioinformatics data is required
- Experience working with HPC schedulers (LSF, Slurm, Torque, Moab, SGE, etc.) is required
- Experience working distributed storage (blob storage, GPFS / Spectrum Scale, Lustre, Hadoop, Spark, etc.) is required
- Experience with one or more interpreted languages (Python, Bash, R, etc.) is required
- Experience with one or more compiled languages (C/C++, Rust, Go, etc.) is required
- Experience with one or more workflow languages (CWL, WDL, Nextflow) is required
- Experience with database development and SQL is required
- Experience working with cloud environments (AWS, Azure, GCP) and containerization (Docker, Singularity, Kubernetes) is preferred
- Advanced degree in bioinformatics, genomics, computer science, or a related field, or equivalent experience preferred
Other Information
No Search Firms
St. Jude Children’s Research Hospital does not accept unsolicited assistance from search firms for employment opportunities. Please do not call or email. All resumes submitted by search firms to any employee or other representative at St. Jude via email, the internet or in any form and/or method without a valid written search agreement in place and approved by HR will result in no fee being paid in the event the candidate is hired by St. Jude.
St. Jude Children’s Research Hospital is an Equal Opportunity Employer. St. Jude does not discriminate on the basis of race, national origin, sex, genetic information, sexual orientation, gender identity, transgender status, age, religion, disability, veteran’s status or disabled veteran’s status with respect to employment opportunities. All qualified applicants will be considered for employment. St. Jude engages in affirmative action to increase employment opportunities for minorities, women, veterans and individuals with disabilities.