Product · Private beta
Helix.AI — your co-pilot for biotechnology tools & workflows
Helix.AI is an autonomous bioinformatics agent. It takes a natural-language request, proposes a plan, and — once you approve — generates code, chooses infrastructure, runs it, and returns real, reproducible results. It instantly translates exploratory analysis into scalable, production-ready pipelines.
Open source · MIT
Helix.AI is open source at its core — read the code, run it yourself, and build on it. Customizations we build for a collaborator are that collaborator's intellectual property.
How you use it
Three steps, no terminal
1. Upload data (optional)
Bring your files — sequencing reads, tables, and more. Helix.AI profiles them on upload.
2. Ask or command
Describe the analysis you need in plain language. Helix.AI proposes a plan and waits for your approval.
3. View results
Get plots, tables, and a reproducible bundle — plus the standalone script that produced them.
Capabilities
Universal biological data
Upload CSV, Excel, FASTQ, FASTA, BAM/SAM, VCF, H5AD and more — profiled at upload time.
Code interpreter
Generates and executes sandboxed Python scripts for tabular and custom analyses.
Infrastructure routing
Per-run decision: local sandbox, cloud VM, or cluster, based on data size and cost.
20+ built-in tools
Bulk and single-cell RNA-seq, QC, alignment, phylogenetics, sequence databases, enrichment, variant calling, and more.
Tool generation
No matching tool? The agent writes a new one on demand.
Iterative refinement
“Change the threshold to 0.01” patches the script and re-runs — not a fresh prompt.
Reproducibility bundle
Every run produces a standalone analysis script plus a bundle with plots, tables, and full history.
Behind the scenes
A multi-agent system
Helix.AI coordinates specialized agents, each an expert in its domain — so you get scientific rigor, clean code, and the right infrastructure, automatically.
Bioinformatics expert
Understands your biological needs and data, and selects the right scientific approach.
Coding expert
Writes the analysis with software-engineering best practices — readable, correct, reproducible.
DevOps expert
Provisions and sizes the computational infrastructure each run needs, then tears it down.
How Helix.AI differs from general AI coding assistants
General assistants help you write code. Helix.AI runs it — safely, reproducibly, in the right place.
| General AI coding assistants | Helix.AI | |
|---|---|---|
| Execution | Generates code; you run it | Generates and runs code in a sandbox |
| Infrastructure | Your local machine only | Chooses the right environment per run |
| Approval loop | Applies changes immediately | Proposes a plan; nothing runs until you confirm |
| Domain knowledge | General-purpose | Bioinformatics-first, with biological file-format awareness |
| Reproducibility | You manage the outputs | Every run yields a script plus a full provenance bundle |
| Iteration | Regenerate from scratch | Patches the actual script and re-runs |
See it on your data.
We're onboarding a small group of biotech and biopharma teams to private beta.
Request beta access