Agent-Skills.md

Agent Skills: 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.

UncategorizedID: K-Dense-AI/claude-scientific-skills/ginkgo-cloud-lab

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K-Dense-AI/claude-scientific-skills
K-Dense-AILicense: MIT
30,2803,052

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skills/ginkgo-cloud-lab/SKILL.md

Skill Metadata

Name
ginkgo-cloud-lab
Description
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.

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

  1. Select a protocol at https://cloud.ginkgo.bio/protocols
  2. Configure parameters (number of proteins/samples/molecules/targets, replicates, plates)
  3. 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)
  4. Add any special requirements in the Additional Details field
  5. 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 cloud@ginkgo.bio 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