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Ginkgo Cloud Lab

k-dense-ai/ginkgo-cloud-lab

Submit and manage protocols on Ginkgo Bioworks Cloud Lab (cloud.ginkgo.bio), a web-based interface for autonomous lab execution on Reconfigurable Automation Carts (RACs). Use when the user wants to run protein expression and purification (cell-free, E. coli, or Pichia), HiBiT or A280 or LabChip quantification, IVT mRNA/circRNA synthesis, thermal shift / developability assays, Echo-MS enzyme or analyte methods, SPR target onboarding, fluorescent pixel art, or otherwise interact with Ginkgo Cloud Lab services. Covers protocol selection, input preparation, pricing, and ordering workflows.

This is a copy. The original lives at lingxling/ginkgo-cloud-lab.

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Install

one command, takes just this skill from the repository 
npx skills add https://github.com/K-Dense-AI/scientific-agent-skills --skill ginkgo-cloud-lab

The instruction itself

14 sections, as written by the author

Ginkgo 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

How to use it

Copy the folder

Take k-dense-ai/ginkgo-cloud-lab from the repository into ~/.claude/skills for personal use, or into .claude/skills inside a project.

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