About
Build with biology, in three days.
A hands-on hackathon where computational biologists, bioinformaticians, software engineers, and lab scientists team up to ship working tools — from generative protein design and single-cell embeddings to interactive viewers and pipelines for shared infrastructure.
Who can participate
- Researchers (faculty, postdocs, students) at Scripps Research and partner institutes.
- Software engineers, ML practitioners, and data scientists with an interest in biology.
- External collaborators by invitation.
Participants do not need to be experts in everything — projects are scoped so that wet-lab biologists, computational researchers, and engineers can contribute meaningfully on the same team.
Format
Three days of focused work:
- Day 1 — kickoff, project pitches, team formation, first work session.
- Day 2 — full-day work sessions with checkpoints; an evening social.
- Day 3 — final sprint, project presentations, wrap-up.
See the schedule for timings.
What you’ll get out of it
- A small, focused team built around a real problem you want to solve.
- Time, space, and snacks to actually make progress.
- Feedback from organizers and peers throughout the event.
- A finished project page on this site, archiving what your team built.
Topics
Themes & project areas
Project proposals can fall into any of the following broad themes — but we encourage cross-cutting work.
- Protein structure & design — folding, docking, generative design, binders, antibody engineering.
- Single-cell & spatial omics — atlas integration, foundation-model embeddings, lineage tracing, perturbation analysis.
- Machine learning & deep learning for biology — pretrained models, benchmarking, interpretability, active learning.
- Genomics & population genetics — variant interpretation, GWAS, ancestry, simulation.
- Imaging — segmentation, registration, hyperspectral analysis, interactive viewers.
- Tooling & infrastructure — pipelines, WebAssembly, GPU acceleration, reproducible environments, web portals for shared tools.
- Open data & FAIR practices — metadata, schema design, ontology alignment, archival.
Submit a project proposal
If you want to lead a project, submit a proposal by the deadline. Proposals should describe:
- The problem you want to tackle and why it matters.
- The data, tools, or models the project will build on.
- What a successful three-day output looks like.
- The skills or roles you’re hoping to recruit on your team.
Schedule
Agenda
Day 1 — Friday, May 29
Hazen Seminar Room
| Time | Session |
|---|---|
| 9:05 am | Welcome |
| 9:20 am | Keynote — Jamie Williamson |
| 9:30 am | Project pitches |
| 9:40 am | Team formation |
| 10:00 am | Project outlining |
| 10:15 am | Agentic AI bootcamp (Andrew Su) — Claude Code setup, example use-cases, limitations, Scripps HPC skill |
| 11:00 am | AWS 101 (Omar Tabbakha) — working within AWS, Amazon Open Data, Amazon Bio Discovery |
| 12:15 pm | Lunch (hackathon & training-session participants) |
| 12:45 pm | Time for hacking |
| 4:45 pm | End-of-day announcements |
| 5:00 pm | Dinner (hackathon participants only) |
Day 2 — Monday, June 1
Hazen Dining Room
| Time | Session |
|---|---|
| 11:00 am | Welcome |
| 11:10 am | Project presentations (5–10 min/project) |
| 12:00 pm | Lunch / judge deliberations |
| 12:30 pm | Prize announcements |
| 12:35 pm | Wrap-up and acknowledgements |
This year
Projects
Each team’s project — click through for goals, methods, and outcomes.
Benchmarking LLMs for automated scRNA-seq analysis
Test which LLM produces the fastest, most accurate cell-type annotation pipeline using expert-curated public scRNA-seq datasets as ground truth.
View project Structural biology & visualizationCaspar–Klug T-Number Explorer
An interactive tool for exploring the geometry of viral icosahedral capsids — T-number, triangular subdivisions, pentamers and hexamers, and how simple rules generate complex viral shells.
Lead: ,
View project Neuroscience, machine learning, computational modelingInferring brain organoid structure from electrode recordings
Reverse-infer the structure of a brain organoid from multi-electrode recordings using computational models and machine learning.
View project Visualization & AI agentsNatural-Language Control for Molstar
Drive the Molstar molecular viewer with chat — generate MolViewSpec scenes (and, as a stretch, MolViewStories) from plain-English requests.
Lead: ,
View project Structural biology & outreachPDB to 3D Print
One-click conversion from any PDB ID or uploaded structure file to a printable, mesh-repaired 3D file — with a short scientific 'structure card' to go with it.
Lead: ,
View project ImmunologyPeptide–MHC binding affinity vs. viral evolution in COVID-19
Test whether peptide–MHC binding affinity correlates with viral mutation rates in SARS-CoV-2 across the pandemic.
View project Protein engineering, machine learningProtein language model embeddings for property prediction
Extract embeddings from protein language models, train prediction heads on a chosen property, and benchmark across PLMs and head architectures.
View project Research tooling & AI agentsProtocol-to-Agent Builder
Turn any protocol — wet-lab SOP, microscopy workflow, computational pipeline — into a grounded, queryable assistant that can answer practical execution questions and produce checklists.
Lead: ,
View project Behavioral analysis, machine learningTooling for C. elegans behavior analysis
Apply or build behavioral analysis tools to study how specific motor neurons shape C. elegans behavior, using a perturbation video dataset.
View project Single-cell, transcriptomics, machine learningTraining a 'virtual cell' model for gene expression inference
Train a virtual-cell model from public scRNA-seq perturbation data and benchmark it against entries from the November 2025 Virtual Cell Challenge.
View project AI agents, scientific toolingTrying and developing agentic AI for science
Stand up agentic AI scaffolds (Biomni, Claude Scientific Skills, Claude for Life Sciences) and either evaluate them or extend them on a real Scripps research workflow.
View project Mixed reality & conversational AIVirtual Professor Art
Talk to a virtual scientific mentor in mixed reality — real-time conversation, synthesized voice, and an animated avatar that can react to what the headset sees.
Lead: ,
View projectOrganizers
Organizing committee
The team running the hackathon. Reach the committee at hackathon@example.org.
Chair
TBD Organizer One
Scripps Research
Co-chair
TBD Organizer Two
Scripps Research
Programs
TBD Organizer Three
Scripps Research
Partners
Partners & sponsors
We’re grateful for the support of the following institutes and organizations.
Interested in sponsoring or partnering on the next hackathon? Get in touch at hackathon@example.org.
FAQ
Frequently asked questions
Who can participate?
The hackathon is open to Scripps Research faculty, postdocs, students, and staff, plus invited collaborators. Software engineers, ML practitioners, and lab scientists are equally welcome — projects are scoped so that wet-lab and computational backgrounds can both contribute.
Do I need to come with a team?
No. Day 1 starts with project pitches followed by team formation — pitch your own idea or join one that’s already on the board.
Is there a registration fee?
No. Registration is free for eligible participants.
What should I bring?
A laptop, your charger, and any specialty adapters you need. Power strips will be available at every team table.
Will food be provided?
Yes. Lunch is provided on both days, and dinner is provided on Day 1 for hackathon participants. Let us know any dietary needs on the registration form.
Can I attend remotely?
The hackathon is in-person at Scripps Research, La Jolla. Project teams can include remote collaborators, but at least one team member should be on site.
Will there be GPUs and compute available?
Yes. Amazon Web Services is providing cloud compute, including GPU instances — the AWS 101 session on Day 1 walks through getting set up. The Scripps HPC environment is also available; both are covered in the Day 1 morning sessions.
Will I have access to Claude during the event?
Yes. Claude (including Claude Code) access will be provided. The Day 1 Agentic AI bootcamp walks through Claude Code setup, example use cases, limitations, and how to plug into the Scripps HPC skill.
Who owns the code we write?
Teams retain ownership of what they build. We encourage open-source releases under permissive licenses, but the choice is up to each team.
Will there be prizes?
Yes — final project presentations on Day 2 are followed by judge deliberations and prize announcements at lunchtime.
What happens after the hackathon?
Each team’s project gets a permanent page on this site documenting goals, methods, and outcomes. Teams are encouraged to keep going beyond the event.
What's the code of conduct?
Be respectful, be inclusive, and contribute to a space where everyone can do their best work. Issues can be reported to any organizer or by email to hackathon@example.org.
Contact
Get in touch
For questions of any kind, email hackathon@example.org. We typically respond within a few working days.
What to include
- Project proposals — a short description, target outcome, and the skills or roles you’re looking to recruit.
- Sponsorship enquiries — your organization, sponsorship level, and what you’re hoping to get out of the partnership.
- Press / coverage — your outlet, deadline, and the angle you’re working on.
- General questions — eligibility, format, accommodation, anything else.