alterlab-ginkgo-cloud

$npx mdskill add AlterLab-IEU/AlterLab-Academic-Skills/alterlab-ginkgo-cloud

Submit and manage protocols on Ginkgo Bioworks Cloud Lab for autonomous lab execution.

  • Enables remote execution of cell-free protein expression and fluorescent pixel art protocols.
  • Depends on Ginkgo Cloud Lab account and Reconfigurable Automation Carts (RACs).
  • Uses EstiMate AI agent for feasibility and pricing of custom protocols.
  • Returns protocol submission status, pricing, and ordering workflow results.

SKILL.md

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---
name: alterlab-ginkgo-cloud
description: Submits and manages protocols on Ginkgo Bioworks Cloud Lab (cloud.ginkgo.bio), a web-based interface for autonomous lab execution on Reconfigurable Automation Carts (RACs), covering protocol selection, input preparation, pricing, and ordering workflows. Use when running cell-free protein expression (validation or optimization), generating fluorescent pixel art, or interacting with Ginkgo Cloud Lab services. Part of the AlterLab Academic Skills suite.
license: MIT
allowed-tools: Read Write Edit Bash(curl:*) Bash(python:*)
compatibility: Requires a Ginkgo Cloud Lab account (cloud.ginkgo.bio); account creation or institutional access may be needed to submit and order protocols
metadata:
    skill-author: AlterLab
    version: "1.0.0"
---

# 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.

## Available Protocols

### 1. Cell Free Protein Expression Validation

Rapid go/no-go expression screening using reconstituted E. coli CFPS. Submit a FASTA sequence (up to 1800 bp) and receive expression confirmation, baseline titer (mg/L), and initial purity with virtual gel images.

- **Price:** $39/sample | **Turnaround:** 5-10 days | **Status:** Certified
- **Details:** See [references/cell-free-protein-expression-validation.md](references/cell-free-protein-expression-validation.md)

### 2. Cell Free Protein Expression Optimization

DoE-based optimization across up to 24 conditions per protein (lysates, temperatures, chaperones, disulfide enhancers, cofactors). Designed for difficult-to-express and membrane proteins.

- **Price:** $199/sample | **Turnaround:** 6-11 days | **Status:** Certified
- **Details:** See [references/cell-free-protein-expression-optimization.md](references/cell-free-protein-expression-optimization.md)

### 3. Fluorescent Pixel Art Generation

Transform a pixel art image (48x48 to 96x96 px, PNG/SVG) into fluorescent bacterial artwork using up to 11 E. coli strains via acoustic dispensing. Delivered as high-res UV photographs.

- **Price:** $25/plate | **Turnaround:** 5-7 days | **Status:** Beta
- **Details:** See [references/fluorescent-pixel-art-generation.md](references/fluorescent-pixel-art-generation.md)

## General Ordering Workflow

1. Select a protocol at https://cloud.ginkgo.bio/protocols
2. Configure parameters (number of samples/proteins, replicates, plates)
3. Upload input files (FASTA for protein protocols, PNG/SVG for pixel art)
4. Add any special requirements in the Additional Details field
5. Submit and receive a feasibility report and price quote

For protocols not listed above, use the **EstiMate** chat to describe a custom protocol in plain language and receive 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:** Sample prep, liquid handling, analytical readouts, storage, incubation
- **Nebula:** Ginkgo's autonomous lab facility in Boston, MA

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