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Support for Ginkgo Cloud Lab
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Timothy Kassis
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scientific-skills/ginkgo-cloud-lab/SKILL.md
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scientific-skills/ginkgo-cloud-lab/SKILL.md
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name: ginkgo-cloud-lab
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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 cell-free protein expression (validation or optimization), generate fluorescent pixel art, or interact with Ginkgo Cloud Lab services. Covers protocol selection, input preparation, pricing, and ordering workflows.
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---
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# Ginkgo Cloud Lab
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## Overview
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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.
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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.
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## Available Protocols
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### 1. Cell Free Protein Expression Validation
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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.
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- **Price:** $39/sample | **Turnaround:** 5-10 days | **Status:** Certified
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- **Details:** See [references/cell-free-protein-expression-validation.md](references/cell-free-protein-expression-validation.md)
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### 2. Cell Free Protein Expression Optimization
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DoE-based optimization across up to 24 conditions per protein (lysates, temperatures, chaperones, disulfide enhancers, cofactors). Designed for difficult-to-express and membrane proteins.
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- **Price:** $199/sample | **Turnaround:** 6-11 days | **Status:** Certified
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- **Details:** See [references/cell-free-protein-expression-optimization.md](references/cell-free-protein-expression-optimization.md)
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### 3. Fluorescent Pixel Art Generation
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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.
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- **Price:** $25/plate | **Turnaround:** 5-7 days | **Status:** Beta
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- **Details:** See [references/fluorescent-pixel-art-generation.md](references/fluorescent-pixel-art-generation.md)
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## General Ordering Workflow
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1. Select a protocol at https://cloud.ginkgo.bio/protocols
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2. Configure parameters (number of samples/proteins, replicates, plates)
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3. Upload input files (FASTA for protein protocols, PNG/SVG for pixel art)
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4. Add any special requirements in the Additional Details field
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5. Submit and receive a feasibility report and price quote
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For protocols not listed above, use the **EstiMate** chat to describe a custom protocol in plain language and receive compatibility assessment and pricing.
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## Authentication
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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.
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## Key Infrastructure
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- **RACs (Reconfigurable Automation Carts):** Modular robotic units with high-precision arms and maglev transport
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- **Catalyst Software:** Protocol orchestration, scheduling, parameterization, and real-time monitoring
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- **70+ integrated instruments:** Sample prep, liquid handling, analytical readouts, storage, incubation
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- **Nebula:** Ginkgo's autonomous lab facility in Boston, MA
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# Cell Free Protein Expression Optimization
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**URL:** https://cloud.ginkgo.bio/protocols/cell-free-protein-expression-optimization
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**Status:** Ginkgo Certified
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**Price:** $199/sample (default: $597 for 1 protein x 3 replicates = 3 samples)
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**Turnaround:** 6-11 days
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## Overview
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Design of Experiment (DoE) approach to expressing protein targets in a proprietary reconstituted E. coli transcription-translation system. Each construct is evaluated in up to 24 reaction conditions per protein, including target-specific additives such as chaperones, disulfide-bond enhancers, and cofactors. Designed for difficult-to-express proteins including membrane proteins and targets with disulfide or cofactor requirements.
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## Input
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- **DNA sequence** in `.fasta` format
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## Output
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- **Comparative Yield:** Titer data mapped across all tested variables (lysates, temps, additives)
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- **Purity Profiling:** Target protein vs. background impurities to find highest quality yield
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- **Optimal Conditions:** Overlaid electropherograms pinpointing the exact formulation for a given sequence
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## Automated Workflow
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### Phase 1 - Reagent Prep
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1. Retrieve plates from 4 deg C
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2. Thaw at room temperature
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3. PBS backfill
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### Phase 2 - CFPS Reaction Setup & Incubation
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1. Retrieve plates from 4 deg C
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2. Dispense lysate
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3. QC plate read
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4. Incubate (shaking or static, condition-dependent)
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### Phase 3 - Quantification Prep & Read
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1. Dispense PBS
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2. Unseal plate
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3. LabChip quantification
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4. Seal plate
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5. Store at 4 deg C
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## Protocol Parameters
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- Payloads & Reagents
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- Bravo Stamp
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- HiG Centrifuge
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- Incubation & Storage
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## Optimization Variables
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The DoE matrix can span up to 24 conditions per protein, varying:
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- **Lysate composition** (different E. coli extract formulations)
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- **Temperature** (incubation temperature profiles)
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- **Additives:**
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- Chaperones (for folding-challenged targets)
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- Disulfide-bond enhancers (for targets requiring disulfide bridges)
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- Cofactors (metal ions, coenzymes, prosthetic groups)
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- Other target-specific supplements
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## Ordering
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- **Number of Proteins:** configurable
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- **Number of Replicates:** configurable
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- **File Upload:** CSV, Excel, FASTA, TXT, PDF, ZIP
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- **Additional Details:** free-text field for special requirements
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## Certification Milestones
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- Dry Run Complete
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- Wet Run Complete
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- Biovalidation Complete
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- App Note Complete
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## Use Cases
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- Optimizing expression of difficult-to-express proteins
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- Membrane protein expression screening
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- Identifying optimal conditions for disulfide-bonded proteins
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- Cofactor-dependent protein expression
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- Systematic exploration of expression parameter space
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- Finding the best formulation before scaling up production
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# Cell Free Protein Expression Validation
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**URL:** https://cloud.ginkgo.bio/protocols/cell-free-protein-expression-validation
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**Status:** Ginkgo Certified
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**Price:** $39/sample (default: $936 for 8 proteins x 3 replicates = 24 samples)
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**Turnaround:** 5-10 days
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## Overview
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Fastest path from a protein sequence to a quantitative go/no-go readout on expression. Uses a proprietary reconstituted E. coli transcription-translation (cell-free protein synthesis, CFPS) system. Reactions complete in 4-16 hours. Designed for early-stage screening, novel construct evaluation, and rapid triage of candidate sequences before committing resources to downstream optimization or purification.
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## Input
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- **DNA sequence** in `.fasta` format
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- Sequences up to 1800 bp supported
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## Output
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- **Expression Confirmation:** Verification of target protein at expected molecular weight
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- **Baseline Titer:** Initial quantitative yield measurement (mg/L)
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- **Initial Purity:** Percentage of target protein vs. impurities, delivered with virtual gel images
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## Automated Workflow
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### Phase 1 - CFPS Reaction Setup & Incubation
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1. Retrieve plates
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2. Stamp DNA templates
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3. Seal plate
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4. Incubate shaking at 30 deg C
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### Phase 2 - Quantification Prep
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1. Dispense PBS diluent
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2. Seal plate
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3. Store at 4 deg C
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### Phase 3 - LabChip Quantification
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1. Unseal plate
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2. LabChip quantification
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3. Seal plate
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4. Store at 4 deg C
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## Protocol Parameters
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- Payloads & Reagents
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- Bravo Stamp
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- HiG Centrifuge
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- Incubation & Storage
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## Ordering
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- **Number of Proteins:** configurable
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- **Number of Replicates:** configurable
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- **File Upload:** CSV, Excel, FASTA, TXT, PDF, ZIP
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- **Additional Details:** free-text field for special requirements
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## Certification Milestones
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- Dry Run Complete
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- Wet Run Complete
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- Biovalidation Complete
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- App Note Complete
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## Use Cases
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- Screening candidate protein sequences for expressibility
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- Go/no-go decisions before investing in optimization
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- Evaluating novel constructs in a cell-free system
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- Comparing expression levels across sequence variants
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# Fluorescent Pixel Art Generation
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**URL:** https://cloud.ginkgo.bio/protocols/fluorescent-pixel-art-generation
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**Status:** Beta
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**Price:** $25/plate
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**Turnaround:** 5-7 days
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## Overview
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Transforms a digital image into a living, fluorescent bacterial artwork printed on an agar omni-tray. Customers submit a pixel art design and colors are mapped to distinct fluorescent E. coli strains. Overnight cultures are prepared from frozen glycerol stocks, diluted, and dispensed onto selective LB-chloramphenicol agar plates via Echo acoustic liquid handling at 50 nL per spot. Plates are incubated at 30 deg C for 16 hours, followed by 4 deg C for 12 hours to stabilize colony morphology and fluorescence. High-resolution photographs are captured under UV illumination and delivered digitally.
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## Input
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- **Image file:** `.png` or `.svg` format
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- **Resolution:** 48x48 to 96x96 pixels
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- **Color mapping:** Match image colors to the fluorescent strain palette
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- **Orientation:** Confirm plate orientation and multi-plate designs (identical vs. distinct)
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## Available Fluorescent E. coli Strains (11 colors)
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| Strain/Protein | Color |
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| sfGFP | Green |
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| mRFP | Red |
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| mKO2 | Orange |
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| Venus | Yellow |
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| Azurite | Blue |
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| mClover3 | Bright Green |
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| mJuniper | Dark Green |
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| mTurquoise2 | Cyan |
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| Electra2 | Electric Blue |
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| mWasabi | Light Green |
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| mScarlet-I | Scarlet |
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## Output
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- **Digital delivery:** High-resolution UV images in TIFF/JPEG format
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- **Optional add-ons:** Framed archival prints
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## Automated Workflow
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### Phase 1 - Source Plate Preparation
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1. Shake source plate
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2. Centrifuge source plate
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3. Peel source plate seal
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### Phase 2 - Acoustic Dispensing (per destination plate)
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1. Peel destination seal
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2. Echo hit-pick dispensing (50 nL per spot)
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3. Seal destination plate
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4. Shake destination plate
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5. Centrifuge destination
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6. Store destination at 30 deg C (16 hr incubation)
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### Phase 3 - Source Storage
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1. Seal source plate
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2. Store source plate
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### Post-Processing
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1. Transfer to 4 deg C for 12 hours (fluorescence stabilization)
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2. UV illumination photography
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3. Image processing and delivery
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## Ordering
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- **Number of Plates:** configurable
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- **File Upload:** CSV, Excel, FASTA, TXT, PDF, ZIP, PNG, JPG, GIF, SVG, WEBP
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- **Additional Details:** free-text field for special requirements
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## Certification Milestones
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- Dry Run Complete
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- Wet Run Complete
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- Biovalidation Complete
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- App Note Complete
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## Use Cases
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- Educational outreach and demonstrations
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- Unique scientific art and gifts
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- Conference displays and promotional materials
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- Lab team celebrations
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- Visualizing biological art concepts
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