AI agents for bioinformatics
Describe your goal. Pipette brings together the tools, compute, and workflows to run your analysis.
Product overviewTrusted by researchers at
The workflows and tools your research needs
Backed by managed compute and established bioinformatics workflows.
From raw data to analysis
- Genomics
- Transcriptomics
- Single-cell
- ChIP-seq
- Molecular docking
- Metagenomics
- 105+ agent skills
150+ bioinformatics tools, managed together
Examples include:
Outputs ready for your review
- Figures for review and refinement
- Downloadable result tables
- Written analysis reports
- Software versions and parameters
- Analysis code and execution records
See Pipette run real biological analyses
Explore real sessions where raw data becomes figures, tables, methods, and downloadable results.
RNA-seq differential expression
Rice salt-alkali stress: DEG discovery, volcano plots, and enrichment from raw sequencing data.
Single-cell clustering & markers
Human pancreatic islets: cell-type clustering, UMAP embeddings, and marker-gene identification.
Variant interpretation
KRAS variants in pancreatic cancer, linked to survival outcomes across a patient cohort.
Comparative genomics
FOXP2 "language gene": protein comparison across mammals and birds with phylogenetics.
Drug design & docking
Imatinib against ABL1 crystal structure 2HYY: receptor preparation, docking, and residue-contact analysis.
How agentic bioinformatics works in Pipette
01 / Data & context
Start with your data and a goal
Add your files and explain the experiment. Pipette uses that context to plan the analysis.
Compare treated and control samples. Show me which genes and pathways change.
02 / Plan & approval
Know what will run, and why
Review the proposed methods, comparison, and assumptions. Clarify the design before approving execution.
- Check the count matrix, sample groups, and replicates.
- Compare treated and control samples for differential expression.
- Explore enriched pathways and prepare figures and a report.
03 / Managed execution
The plan becomes a working analysis
Pipette runs the tools on managed compute and records the methods, parameters, and outputs.
- Validate inputsCounts, sample labels, and experimental designComplete
- Run differential expressionApply the approved comparisonComplete
- Explore pathways & build outputsFigures, tables, code, and reportComplete
Illustrated sequence. Actual steps and runtime depend on your analysis.
04 / Results & follow-up
Results you can inspect and build on
Review the findings alongside the underlying outputs. Ask a follow-up question or extend the analysis.
- PNGFigures
- CSVResult tables
- CODEAnalysis code
- PDFAnalysis report
Which pathways should I investigate further?
Your research should compound
When a colleague picks up a project, they need more than a folder of results. Pipette gives your team a shared place to find prior analyses, revisit decisions, and continue the work.
- Shared workspaces keep active projects and results accessible to the team.
- Institutional knowledge retention preserves why methods and parameters were chosen—not only the final scripts.
- Organization-owned workflows can be added, reused, and standardized across projects.
- Operational capacity supports 100–250 GB inputs per session and 250 GB–1 TB active workspaces, depending on plan.
Your data stays yours
Research data is encrypted in transit and at rest, processed in managed analysis environments, and not used to train Pipette or third-party AI models. Review the full data lifecycle on our Security page.
Encrypted by default
Research data is encrypted in transit and at rest on managed cloud infrastructure.
Never used for training
Your data, prompts, and results are never used to train AI models — ever.
Private, isolated compute
Every analysis runs in an isolated environment. Your data is never shared with other users.
You stay in control
Export or delete your data anytime, with full provenance over every result.
Published science, open to inspection
Pipette's SkillGraph connects 105+ curated bioinformatics skills with evidence from more than 20,000 papers. Explore it online or connect the public MCP server to an AI client.
Start with credits, scale with your team
Start on the Free tier with 20 credits per month. Buy more when needed, or move your team onto shared infrastructure.
Self-serve credits
For individual researchers and small projects. Packs include 50 GB input per session and a 100 GB active workspace; purchased credits never expire.
Lab & team plans
For groups that need seats, shared billing, and higher usage across the team.
Trusted by genomics and computational biology researchers
"I've been testing the Pipette.bio agent over the past few days, running both RNA-seq and PTCH2 analyses to evaluate reproducibility and interpretability. My experience was really good."
"I used Pipette for single cell analysis of my fish samples. Uploading the data and getting started was easy. The pipeline did most of what I expected. I would recommend Pipette to other users."
"Pipette is a great tool for lab biologists. It takes minutes to perform data analysis tasks that otherwise took days to complete."
"Tried Pipette.bio for my prokaryotic pipeline and it was genuinely solid. The AI actually understands bioinformatics workflows."
"I must say this a great platform, like one I always had in mind to develop."
Frequently asked
Yes. Pipette is a general-purpose bioinformatics AI agent for analyses across genomics, proteomics, drug design, plant breeding, and more. It uses established tools on managed compute. You can review the plan, inspect figures and code, and ask follow-up questions about the results.
Look for reviewable analysis plans, established tools, inspectable code, and clear limitations. Our practical guide to AI agents in biology and comparison of AI agents with workflow managers explain what to check before trusting a result.
Pipette is for researchers analyzing biological data and for labs, bioinformatics teams, and core facilities that want to share analyses and workflows across projects.
You can download code, parameters, software versions, and outputs to inspect and rerun the work. You will also need the input data, reference resources, and a compatible computing environment.
No. Pipette runs entirely in your browser. Log in, upload your data, and start analyzing.
150+ open-source tools across RNA-seq, single-cell, ChIP/ATAC-seq, variant calling, metagenomics, and more — including STAR, Salmon, DESeq2, Seurat, GATK, MACS2, and bcftools. See real analyses →
Bring your data to Pipette
Start an analysis yourself, or bring Pipette into your lab or R&D team.
Start an Analysis