Open Source Research Software Engineer — BioJupyter & AI for Science

University of California

Berkeley (CA)

On-site

USD 102,000 - 190,000

Full time

14 days+

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Job summary

Berkeley Institute for Data Science (BIDS) at UC Berkeley is hiring an Open Source Research Software Engineer to advance BioJupyter and open science. The role involves building open source infrastructure for data-intensive AI biomedical research, collaborating with scientists and developers across Jupyter projects and the UC Berkeley Open Source Program Office.

You will work on distributed data analysis, HPC workflows, and access control, contributing to cutting-edge tools in a multidisciplinary

Qualifications

Advanced programming skills including Python expertise.
Experience with high-performance computing and scientific workflow systems such as job schedulers (eg: SLURM), containerization (eg: Docker, Apptainer / Singularity, Kubernetes), and workflow tools (eg: Snakemake, CWL, Dask, Nextflow).
Demonstrated software development and maintenance skills: version control with git, testing, continuous integration and/or continuous deployment with GitHub Actions or similar. Advanced knowledge of secure software development.
Experience participating in multi-stakeholder open source communities: distributed decision making, navigating uncertainty, building consensus, coordinating paid and volunteer contributors, mentoring new members.
Experience reviewing code through open discussion and iterations on GitHub. Demonstrated track record using issues and pull requests (or similar) for transparent and distributed project management.
Experience structuring and analyzing complex and multi-modal datasets, ideally following and contributing back to open standards.
A curious mindset and appetite for navigating complexity and uncertainty. A track record of scoping and delivering on requirements from interdisciplinary teams of domain experts and trainees with varied technical expertise.

Responsibilities

40% Applies advanced software concepts to plan, design, develop, modify, debug, deploy, and evaluate highly complex interface, software, and/or infrastructure solutions in interdisciplinary research collaborations.
20% Contributes to and supports the maintenance and sustainability of 1-4 projects within the scientific open source ecosystem. Maintenance can include issue triage, code and documentation review, contributing new features, mentoring new contributors, continuous integration testing, and release management.
10% Develops project plans as part of an interdisciplinary team, delivers allocated tasks, and communicates progress regularly.
5% Analyzes existing highly complex open source software or works to formulate logic and devise algorithms for new modular and composable software systems. Understands and applies industry practices, open source community standards, and department policies and procedures in depth.
5% Enables collaborators to design, implement, reproduce, and extend highly complex data analyses to address real-world research problems, including accessing data from varied multi-modal processing pipelines, working directly with domain scientists and open source communities as appropriate.
5% Stays up to date on applicable research and software engineering standards, including applications of agentic AI for science (new models and tools, agentic architectures, and evaluation methods), and security and accessibility practices. Implements cutting-edge practices into software and protocol standards, meeting UCBerkeley-specific policy requirements and national and international standards as applicable.
5% Prepares and approves or obtains approval for user and developer documentation. Initiates and oversees changes in development, maintenance and system standards. Sets the technical requirements for software specifications, engaging across open source communities as appropriate. Communicates technical requirements to interdisciplinary experts and trainees with varied technical expertise.
5% Serves as technical lead for one or two software development projects of moderate to broad scope. Meets with interdisciplinary project teams and provides regular updates on progress.
5% Advances the work of the UC Berkeley Open Source Program Office (OSPO) by demonstrating the value and impact of open source practices. Delivers trainings and provides technical and community mentorship to members of the UC-wide OSPO network. Participates actively in monthly meetings and workshops.