/ginkgo-cloud-lab

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.
license: MIT license
allowed-tools: Read
metadata:
  version: "2.1"
  skill-author: K-Dense Inc.

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](references/ivt-rna-synthesis-qpcr.md) | 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](references/cell-free-protein-expression-validation.md) | Go/no-go titer + purity (up to 1800 bp) | $39/sample | up to 10 days | Certified | | [Optimize expression conditions](references/cell-free-protein-expression-optimization.md) | DoE across 24 conditions | $199/sample | up to 11 days | Certified | | [Express + quantify (HiBiT)](references/cell-free-protein-expression-hibit.md) | Luminescence, no purification | $39/sample | up to 11 days | Certified | | [Express + purify (A280)](references/cfps-strep-tag-purification-a280.md) | Strep-tag, A280 yield | $149/sample | up to 11 days | Certified | | [Express + purify minibinder](references/minibinder-strep-tag-a280.md) | Strep-tag, A280, LabChip | $149/sample | up to 11 days | Certified | | [Express + purify (A280 + LabChip)](references/cfps-expression-purification-quantification.md) | Strep-tag, A280 + purity/size | $159/sample | up to 12 days | Certified |

Expression & Purification - E. coli

| Protocol | Readout | Price | Turnaround | Status | |---|---|---|---|---| | [Express + quantify (HiBiT)](references/ecoli-protein-expression-hibit.md) | Luminescence (up to 384 constructs) | $79/sample | up to 3 weeks | Certified | | [Express + purify (A280)](references/ecoli-protein-expression-histag-a280.md) | His-tag, A280 yield | $199/sample | up to 3 weeks | Certified | | [Express + purify minibinder](references/ecoli-minibinder-expression-histag-a280.md) | His-tag, A280 yield | $199/sample | up to 3 weeks | Certified | | [Express + purify (A280 + LabChip)](references/ecoli-expression-purification-quantification.md) | His-tag, A280 + purity/size | $209/sample | up to 3 weeks | Certified |

Expression & Purification - Pichia

| Protocol | Readout | Price | Turnaround | Status | |---|---|---|---|---| | [Express + quantify (LabChip)](references/pichia-protein-expression-labchip.md) | 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](references/cfps-strep-purification-thermal-shift.md) | SYPRO Orange Tm (Tonset, TM1-3) | $159/sample | up to 12 days | Certified | | [Detect enzymatic products (Echo-MS)](references/echo-ms-cfps-detection.md) | Substrate/product by Echo-MS | $44/sample | up to 13 days | Beta |

Method & Target Onboarding

| Protocol | Readout | Price | Turnaround | Status | |---|---|---|---|---| | [Onboard Echo-MS method](references/echo-ms-method-onboarding.md) | Calibration curve, LOD/LOQ | $799/molecule | up to 3 weeks | Certified | | [Onboard SPR target](references/spr-target-onboarding.md) | Validated SPR capture method | $1,399/target | up to 4 weeks | Beta |

Specialty

| Protocol | Readout | Price | Turnaround | Status | |---|---|---|---|---| | [Generate fluorescent pixel art](references/fluorescent-pixel-art-generation.md) | 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