Bioinformatics Analyst II (HPI) - Laboratory of Dr. Todd Michael

Job location is at 10010 N Torrey Pines Rd, La Jolla, CA 92037

The Harnessing Plants Initiative at the Salk Institute for Biological Studies is seeking a Bioinformatics Analyst II to be a member of participating labs (Pereira, Busch, Michael) focused on cutting-edge research in plant biology through the development and implementation of software for large-scale genetic and phenotypic data management using web technologies.

The candidate will have the unique opportunity to work at the intersection of plant biology, climate change and artificial intelligence, applying the latest technologies to extract quantitative measures of crop plant phenotypes, gene expression and other multi-omics modalities. They will assist with implementation of software used to analyze multi-terabyte-scale datasets at unprecedented resolution. Working closely with software engineers and research scientists, they will assist in the development of Bloom, our in-house cloud-based data repository, to enable integration of multi-omics data as part of an effort to build generative models for biology.

For this specific role, candidates will be developing cloud-based modules for Bloom and thus will be expected to have substantial experience with Python and web development languages and frameworks. This will involve primarily backend, but also some frontend work.

This is a primarily software engineering role. We STRONGLY recommend that applicants provide a link to their GitHub profile with examples of their previous programming experience to receive full consideration (including previous research code or class projects).

Who We Are

The Salk Institute is an internationally renowned research institution that values diversity, equity, and inclusion. We seek bold and interactive leaders passionate about exploring new frontiers in science. Our collaborative community embraces diverse perspectives and unique life experiences, fostering innovation, and a sense of belonging. Together, we strive to improve the wellbeing of humanity through groundbreaking research.

Founded by Jonas Salk, developer of the first safe and effective polio vaccine, the Institute is an independent, nonprofit research organization and architectural landmark: small by choice, intimate by nature, and fearless in the face of any challenge. Salk's vibrant community comprises a diverse and talented group of individuals, each playing a crucial role in driving our mission forward. From visionary leaders to dedicated administrators and brilliant faculty members, the Institute is united by a shared passion for scientific exploration and innovation.

What Your Key Responsibilities Will Be

• Carries out tasks pertaining to development and implementation of computational pipelines in Python and web technologies.
• Carries out tasks pertaining to software development.
• Participate in team meetings to discuss project progress.
• May coordinate with other Salk labs.
• May assist with the supervision of undergraduate students and other lab members.
• Perform additional duties as assigned.

Supervisory Responsibilities:

• This job has no supervisory responsibilities.

What we Require 

• Bachelor’s degree in bioinformatics, computational biology, computer science, bioengineering, data science, plant biology, neuroscience, physics, computer science, or related fields.
• Preferred – Master’s degree or post-baccalaureate certification.
• Intermediate to advanced programming experience in Python.
• Advanced programming experience in JavaScript/TypeScript and other web development languages and frameworks.
• Proficiency with version control systems (Git) and standard DevOps (CI/CD).
• Proficiency with containerization (e.g., Docker, Kubernetes).
• Proficiency with deploying applications on major cloud providers (e.g., AWS, GCP).
• Strong presentation and communication skills.

Preferred: 

• Proficiency with modern web technologies (e.g., WebAssembly, WebRTC, WebGPU).
• Proficiency with frontend frameworks (e.g., Svelte, React, Angular, Vue).
• Proficiency with database design and data flows for cloud backends.
• Proficiency with data science and deep learning frameworks (e.g., TensorFlow, PyTorch, or Jax).
• Proficiency with modern bioinformatics pipeline and workflow libraries (e.g., Galaxy, Parabricks, GATK, RAPIDS).
• Experience with analyzing plant field, lab and genome data.
• Familiarity with next-generation sequencing technologies and assays

What We Can Offer

The expected pay range for this position is $67,500 to $88,750 per annum. Salk Institute provides pay ranges representing its good faith estimate of what the institute reasonably expects to pay for a position. The pay offered to a selected candidate will be determined based on factors such as (but not limited to) the scope and responsibilities of the position, the qualifications of the selected candidate, departmental budget availability, internal equity, geographic location, and external market pay for comparable jobs.

Benefits

Salk Institute offers competitive benefits, including medical, dental, vision, retirement, paid time off, tuition reimbursement, patient advocacy services, and transit/parking program.

Salk Values

The Salk Community, both scientists and administrators, worked together to define values that we believe support Salk’s pursuit of excellence. To be truly the best scientific institution requires not only incredible discoveries, but a common understanding of how we should work together to enable those discoveries.

The acronym “I CARE” provides a simple way to remember each of the values and reminds each of us of the importance of what we do each day.

Equal Employment Opportunity Statement

The Salk Institute for Biological Studies is an Equal Opportunity Employer and is committed to providing equal access to opportunities for students, employees, applicants for employment and other visitors. Salk has also adopted and maintains a policy to encourage professional and respectful workplace behavior and prevent discriminatory and harassing conduct in our workplace.

Accordingly, the Institute prohibits harassment and discrimination in employment on the basis of, and considers all qualified applicants for employment without regard to, actual or perceived race, color, religion, religious creed (including religious dress and grooming practices), national origin, ancestry, citizenship, physical or mental disability, medical condition (including cancer and genetic characteristics), genetic information, marital status, age, sex (including pregnancy, childbirth, breastfeeding, or related medical conditions), gender, gender identity, gender expression, sexual orientation, veteran and/or military status (disabled veteran, veteran of the Vietnam era, other covered veteran status), political affiliation, and any other status protected by state or federal law.