About ginkgo-cloud-lab
Ginkgo Cloud Lab gives researchers remote access to automated lab protocols for protein, RNA, and assay work. It offers a protocol catalog and EstiMate, an AI agent that assesses feasibility and pricing for custom workflows.
Key features
- 01Catalog of automated lab protocols
- 02Protein expression and purification workflows
- 03Characterization and assay protocols
- 04EstiMate feasibility and pricing assessment
- 05Online protocol ordering workflow
Use cases
- 01Screen sequences for expression
- 02Produce and purify proteins
- 03Assess protein stability or enzyme products
- 04Request feasibility and pricing for a custom protocol
Install
Copy the command and run it in a terminal.
npx skills add https:/After installing, type/ginkgo-cloud-labin Claude Code to confirm it loaded.
Bundled files
References and scripts installed along with SKILL.md.
references/cell-free-protein-expression-hibit.mdcell-free-protein-expression-optimization.mdcell-free-protein-expression-validation.mdcfps-expression-purification-quantification.mdcfps-strep-purification-thermal-shift.mdcfps-strep-tag-purification-a280.mdecho-ms-cfps-detection.mdecho-ms-method-onboarding.mdecoli-expression-purification-quantification.mdecoli-minibinder-expression-histag-a280.mdecoli-protein-expression-hibit.mdecoli-protein-expression-histag-a280.mdfluorescent-pixel-art-generation.mdivt-rna-synthesis-qpcr.mdminibinder-strep-tag-a280.mdpichia-protein-expression-labchip.mdspr-target-onboarding.mdDetails
From the project READMEGinkgo Cloud Lab
Overview
Ginkgo Cloud Lab (https://cloud.ginkgo.bio) provides remote access to Ginkgo Bioworks' autonomous lab infrastructure. Protocols are executed on Reconfigurable Automation Carts (RACs) -- modular units with robotic arms, maglev sample transport, and industrial-grade software spanning 70+ instruments.
The platform also includes EstiMate, an AI agent that accepts human-language protocol descriptions and returns feasibility assessments and pricing for custom workflows beyond the listed protocols.
The catalog is organized into Expression & Purification (in vitro / cell-free / E. coli / Pichia), Characterization & Assay, Method & Target Onboarding, and Specialty. Pick a protocol below, then read its reference file for inputs, outputs, the automated workflow, and ordering details.
Available Protocols
Expression & Purification - In vitro
| Protocol | Readout | Price | Turnaround | Status |
|---|---|---|---|---|
| IVT mRNA/circRNA Synthesis | qPCR (mRNA or circRNA, 384-well) | $99/sample | up to 12 business days | Certified |
Expression & Purification - Cell-free (E. coli CFPS)
| Protocol | Readout | Price | Turnaround | Status |
|---|---|---|---|---|
| Validate sequence expression | Go/no-go titer + purity (up to 1800 bp) | $39/sample | up to 10 days | Certified |
| Optimize expression conditions | DoE across 24 conditions | $199/sample | up to 11 days | Certified |
| Express + quantify (HiBiT) | Luminescence, no purification | $39/sample | up to 11 days | Certified |
| Express + purify (A280) | Strep-tag, A280 yield | $149/sample | up to 11 days | Certified |
| Express + purify minibinder | Strep-tag, A280, LabChip | $149/sample | up to 11 days | Certified |
| Express + purify (A280 + LabChip) | Strep-tag, A280 + purity/size | $159/sample | up to 12 days | Certified |
Expression & Purification - E. coli
| Protocol | Readout | Price | Turnaround | Status |
|---|---|---|---|---|
| Express + quantify (HiBiT) | Luminescence (up to 384 constructs) | $79/sample | up to 3 weeks | Certified |
| Express + purify (A280) | His-tag, A280 yield | $199/sample | up to 3 weeks | Certified |
| Express + purify minibinder | His-tag, A280 yield | $199/sample | up to 3 weeks | Certified |
| Express + purify (A280 + LabChip) | His-tag, A280 + purity/size | $209/sample | up to 3 weeks | Certified |
Expression & Purification - Pichia
| Protocol | Readout | Price | Turnaround | Status |
|---|---|---|---|---|
| Express + quantify (LabChip) | Secreted protein, size/purity (up to 96) | $89/sample | up to 4 weeks | Certified (New) |
Characterization & Assay
| Protocol | Readout | Price | Turnaround | Status |
|---|---|---|---|---|
| Express + thermal shift | SYPRO Orange Tm (Tonset, TM1-3) | $159/sample | up to 12 days | Certified |
| Detect enzymatic products (Echo-MS) | Substrate/product by Echo-MS | $44/sample | up to 13 days | Beta |
Method & Target Onboarding
| Protocol | Readout | Price | Turnaround | Status |
|---|---|---|---|---|
| Onboard Echo-MS method | Calibration curve, LOD/LOQ | $799/molecule | up to 3 weeks | Certified |
| Onboard SPR target | Validated SPR capture method | $1,399/target | up to 4 weeks | Beta |
Specialty
| Protocol | Readout | Price | Turnaround | Status |
|---|---|---|---|---|
| Generate fluorescent pixel art | UV photo, 7-color E. coli palette | $25/plate | up to 7 days | Beta |
Coming soon: Protein Expression and Binding Affinity Characterization (express + purify, then screen binding affinity against a target).
Choosing a Protocol
- Quick expressibility screen? Cell-free HiBiT ($39) or Validate sequence expression ($39).
- Need purified protein + yield? A280 tiers (cell-free or E. coli); add LabChip for purity/size.
- Difficult / membrane / disulfide / cofactor targets? Cell-free Optimize (24-condition DoE).
- Secreted or eukaryotic targets? Pichia expression.
- Screening de novo binders/minibinders? Cell-free or E. coli minibinder tiers, then SPR onboarding for kinetics.
- Enzyme activity / biocatalysis? Echo-MS enzymatic detection (onboard the analyte method first).
- Stability / developability ranking? Thermal shift assay.
- RNA (mRNA/circRNA)? IVT synthesis + qPCR.
General Ordering Workflow
- Select a protocol at https://cloud.ginkgo.bio/protocols
- Configure parameters (number of proteins/samples/molecules/targets, replicates, plates)
- Download the protocol's input template and upload inputs (FASTA/CSV/XLSX for sequence protocols; Design Tool for pixel art; vendor catalog numbers for onboarding)
- Add any special requirements in the Additional Details field
- Provide an email, agree to the protocol terms, and add to cart / submit to receive a feasibility report and price quote
For protocols not listed above, use the EstiMate chat (https://cloud.ginkgo.bio/estimate) to describe a custom protocol in plain language and receive a compatibility assessment and pricing.
Authentication
Access Ginkgo Cloud Lab at https://cloud.ginkgo.bio. Account creation or institutional access may be required. Contact Ginkgo at [email protected] for access questions.
Key Infrastructure
- RACs (Reconfigurable Automation Carts): Modular robotic units with high-precision arms and maglev transport
- Catalyst Software: Protocol orchestration, scheduling, parameterization, and real-time monitoring
- 70+ integrated instruments: Agilent Bravo liquid handlers, Beckman/Labcyte Echo acoustic dispensers, BMG PHERAstar / Tecan Spark readers, Revvity LabChip, Bio-Rad CFX Opus, Nicoya Alto SPR, SciEx Echo-MS, Inheco/Cytomat incubators, and more
- Nebula: Ginkgo's autonomous lab facility in Boston, MA
Agent operating procedure
- Check the environment. Confirm the instrument or platform model, API version, credentials and whether a simulator is available.
- Pin down the inputs. Confirm formats, identifiers and parameters from the data or the user. Ask rather than guess any value that changes the result.
- Run a small version first. Simulate the protocol or run it with water or dummy labware before using real samples.
- Execute the full task using the instructions and references above.
- Validate the result. Verify volumes, deck layout and labware definitions; have a human approve the protocol before execution.
- Report. State what was run (versions, commands, parameters), what was checked, and what is still uncertain.
| If this happens | Do this |
|---|---|
| The protocol fails in simulation | Fix it in simulation; never run an unvalidated protocol on hardware. |
| A function, flag or endpoint in these instructions is missing in the installed version | Check the installed version's own documentation (help(), --help, official docs), adapt, and tell the user. Never invent an API. |
| A required input, identifier or parameter is ambiguous | Ask the user, or state the assumption explicitly before running. |
Integrity rules
- Never fabricate results, parameters, identifiers, citations or statistics. If something cannot be run or verified, say so plainly.
- Never trigger physical actions, orders or charges without explicit user confirmation.
- Treat version-specific details here as possibly outdated: confirm them against the official documentation for the installed version.
- Ask before actions that cost money, consume shared GPUs or cloud quota, touch personal or patient data, or cannot be undone.
Related skills
adaptyv: How to use the Adaptyv Bio Foundry API and Python SDK for protein experiment design, submission, and results retrieval.