Support for Ginkgo Cloud Lab

.claude-plugin/marketplace.json

@@ -6,7 +6,7 @@
   },
   "metadata": {
     "description": "Claude scientific skills from K-Dense Inc",
-    "version": "2.24.0"
+    "version": "2.25.0"
   },
   "plugins": [
     {
@@ -39,6 +39,7 @@
         "./scientific-skills/geniml",
         "./scientific-skills/geopandas",
         "./scientific-skills/gget",
+        "./scientific-skills/ginkgo-cloud-lab",
         "./scientific-skills/gtars",
         "./scientific-skills/histolab",
         "./scientific-skills/imaging-data-commons",

README.md

@@ -462,8 +462,9 @@ This repository contains **148 scientific and research skills** organized across
 - Exploratory data analysis: EDA workflows
 - Statistical analysis: Statistical Analysis workflows
 
-#### 🧪 **Laboratory Automation** (3 skills)
+#### 🧪 **Laboratory Automation** (4 skills)
 - Liquid handling: PyLabRobot
+- Cloud lab: Ginkgo Cloud Lab (cell-free protein expression, fluorescent pixel art via autonomous RAC infrastructure)
 - Protocol management: Protocols.io
 - LIMS integration: Benchling, LabArchives
 

docs/scientific-skills.md

@@ -44,6 +44,7 @@
 
 ### Laboratory Automation
 - **Opentrons Integration** - Toolkit for creating, editing, and debugging Opentrons Python Protocol API v2 protocols for laboratory automation using Flex and OT-2 robots. Enables automated liquid handling, pipetting workflows, hardware module control (thermocycler, temperature, magnetic, heater-shaker, absorbance plate reader), labware management, and complex protocol development for biological and chemical experiments
+- **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). Supports three protocols: Cell Free Protein Expression Validation ($39/sample, 5-10 day turnaround), Cell Free Protein Expression Optimization ($199/sample, DoE across 24 conditions, 6-11 days), and Fluorescent Pixel Art Generation ($25/plate, bacterial artwork with 11 fluorescent E. coli strains, 5-7 days). Includes EstiMate AI agent for custom protocol feasibility and pricing
 
 ### Electronic Lab Notebooks (ELN)
 - **LabArchives Integration** - Toolkit for interacting with LabArchives Electronic Lab Notebook (ELN) REST API. Provides programmatic access to notebooks (backup, retrieval, management), entries (creation, comments, attachments), user authentication, site reports and analytics, and third-party integrations (Protocols.io, GraphPad Prism, SnapGene, Geneious, Jupyter, REDCap). Includes Python scripts for configuration setup, notebook operations, and entry management. Supports multi-regional API endpoints (US, UK, Australia) and OAuth authentication

scientific-skills/ginkgo-cloud-lab/SKILL.md

@@ -0,0 +1,56 @@
+---
+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 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.
+---
+
+# 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 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:** Sample prep, liquid handling, analytical readouts, storage, incubation
+- **Nebula:** Ginkgo's autonomous lab facility in Boston, MA

scientific-skills/ginkgo-cloud-lab/references/cell-free-protein-expression-optimization.md

@@ -0,0 +1,85 @@
+# Cell Free Protein Expression Optimization
+
+**URL:** https://cloud.ginkgo.bio/protocols/cell-free-protein-expression-optimization
+**Status:** Ginkgo Certified
+**Price:** $199/sample (default: $597 for 1 protein x 3 replicates = 3 samples)
+**Turnaround:** 6-11 days
+
+## Overview
+
+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.
+
+## Input
+
+- **DNA sequence** in `.fasta` format
+
+## Output
+
+- **Comparative Yield:** Titer data mapped across all tested variables (lysates, temps, additives)
+- **Purity Profiling:** Target protein vs. background impurities to find highest quality yield
+- **Optimal Conditions:** Overlaid electropherograms pinpointing the exact formulation for a given sequence
+
+## Automated Workflow
+
+### Phase 1 - Reagent Prep
+
+1. Retrieve plates from 4 deg C
+2. Thaw at room temperature
+3. PBS backfill
+
+### Phase 2 - CFPS Reaction Setup & Incubation
+
+1. Retrieve plates from 4 deg C
+2. Dispense lysate
+3. QC plate read
+4. Incubate (shaking or static, condition-dependent)
+
+### Phase 3 - Quantification Prep & Read
+
+1. Dispense PBS
+2. Unseal plate
+3. LabChip quantification
+4. Seal plate
+5. Store at 4 deg C
+
+## Protocol Parameters
+
+- Payloads & Reagents
+- Bravo Stamp
+- HiG Centrifuge
+- Incubation & Storage
+
+## Optimization Variables
+
+The DoE matrix can span up to 24 conditions per protein, varying:
+
+- **Lysate composition** (different E. coli extract formulations)
+- **Temperature** (incubation temperature profiles)
+- **Additives:**
+  - Chaperones (for folding-challenged targets)
+  - Disulfide-bond enhancers (for targets requiring disulfide bridges)
+  - Cofactors (metal ions, coenzymes, prosthetic groups)
+  - Other target-specific supplements
+
+## Ordering
+
+- **Number of Proteins:** configurable
+- **Number of Replicates:** configurable
+- **File Upload:** CSV, Excel, FASTA, TXT, PDF, ZIP
+- **Additional Details:** free-text field for special requirements
+
+## Certification Milestones
+
+- Dry Run Complete
+- Wet Run Complete
+- Biovalidation Complete
+- App Note Complete
+
+## Use Cases
+
+- Optimizing expression of difficult-to-express proteins
+- Membrane protein expression screening
+- Identifying optimal conditions for disulfide-bonded proteins
+- Cofactor-dependent protein expression
+- Systematic exploration of expression parameter space
+- Finding the best formulation before scaling up production

scientific-skills/ginkgo-cloud-lab/references/cell-free-protein-expression-validation.md

@@ -0,0 +1,71 @@
+# Cell Free Protein Expression Validation
+
+**URL:** https://cloud.ginkgo.bio/protocols/cell-free-protein-expression-validation
+**Status:** Ginkgo Certified
+**Price:** $39/sample (default: $936 for 8 proteins x 3 replicates = 24 samples)
+**Turnaround:** 5-10 days
+
+## Overview
+
+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.
+
+## Input
+
+- **DNA sequence** in `.fasta` format
+- Sequences up to 1800 bp supported
+
+## Output
+
+- **Expression Confirmation:** Verification of target protein at expected molecular weight
+- **Baseline Titer:** Initial quantitative yield measurement (mg/L)
+- **Initial Purity:** Percentage of target protein vs. impurities, delivered with virtual gel images
+
+## Automated Workflow
+
+### Phase 1 - CFPS Reaction Setup & Incubation
+
+1. Retrieve plates
+2. Stamp DNA templates
+3. Seal plate
+4. Incubate shaking at 30 deg C
+
+### Phase 2 - Quantification Prep
+
+1. Dispense PBS diluent
+2. Seal plate
+3. Store at 4 deg C
+
+### Phase 3 - LabChip Quantification
+
+1. Unseal plate
+2. LabChip quantification
+3. Seal plate
+4. Store at 4 deg C
+
+## Protocol Parameters
+
+- Payloads & Reagents
+- Bravo Stamp
+- HiG Centrifuge
+- Incubation & Storage
+
+## Ordering
+
+- **Number of Proteins:** configurable
+- **Number of Replicates:** configurable
+- **File Upload:** CSV, Excel, FASTA, TXT, PDF, ZIP
+- **Additional Details:** free-text field for special requirements
+
+## Certification Milestones
+
+- Dry Run Complete
+- Wet Run Complete
+- Biovalidation Complete
+- App Note Complete
+
+## Use Cases
+
+- Screening candidate protein sequences for expressibility
+- Go/no-go decisions before investing in optimization
+- Evaluating novel constructs in a cell-free system
+- Comparing expression levels across sequence variants

scientific-skills/ginkgo-cloud-lab/references/fluorescent-pixel-art-generation.md

@@ -0,0 +1,87 @@
+# Fluorescent Pixel Art Generation
+
+**URL:** https://cloud.ginkgo.bio/protocols/fluorescent-pixel-art-generation
+**Status:** Beta
+**Price:** $25/plate
+**Turnaround:** 5-7 days
+
+## Overview
+
+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.
+
+## Input
+
+- **Image file:** `.png` or `.svg` format
+- **Resolution:** 48x48 to 96x96 pixels
+- **Color mapping:** Match image colors to the fluorescent strain palette
+- **Orientation:** Confirm plate orientation and multi-plate designs (identical vs. distinct)
+
+## Available Fluorescent E. coli Strains (11 colors)
+
+| Strain/Protein | Color |
+|---|---|
+| sfGFP | Green |
+| mRFP | Red |
+| mKO2 | Orange |
+| Venus | Yellow |
+| Azurite | Blue |
+| mClover3 | Bright Green |
+| mJuniper | Dark Green |
+| mTurquoise2 | Cyan |
+| Electra2 | Electric Blue |
+| mWasabi | Light Green |
+| mScarlet-I | Scarlet |
+
+## Output
+
+- **Digital delivery:** High-resolution UV images in TIFF/JPEG format
+- **Optional add-ons:** Framed archival prints
+
+## Automated Workflow
+
+### Phase 1 - Source Plate Preparation
+
+1. Shake source plate
+2. Centrifuge source plate
+3. Peel source plate seal
+
+### Phase 2 - Acoustic Dispensing (per destination plate)
+
+1. Peel destination seal
+2. Echo hit-pick dispensing (50 nL per spot)
+3. Seal destination plate
+4. Shake destination plate
+5. Centrifuge destination
+6. Store destination at 30 deg C (16 hr incubation)
+
+### Phase 3 - Source Storage
+
+1. Seal source plate
+2. Store source plate
+
+### Post-Processing
+
+1. Transfer to 4 deg C for 12 hours (fluorescence stabilization)
+2. UV illumination photography
+3. Image processing and delivery
+
+## Ordering
+
+- **Number of Plates:** configurable
+- **File Upload:** CSV, Excel, FASTA, TXT, PDF, ZIP, PNG, JPG, GIF, SVG, WEBP
+- **Additional Details:** free-text field for special requirements
+
+## Certification Milestones
+
+- Dry Run Complete
+- Wet Run Complete
+- Biovalidation Complete
+- App Note Complete
+
+## Use Cases
+
+- Educational outreach and demonstrations
+- Unique scientific art and gifts
+- Conference displays and promotional materials
+- Lab team celebrations
+- Visualizing biological art concepts