[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"skill:01M6QERGSFTSDXXB05YN50RY52":3,"skill-same:01M6QERGSFTSDXXB05YN50RY52":153},{"skillNo":4,"name":5,"nameZh":6,"description":7,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":16,"categories":17,"keywords":28,"publishedAt":49,"linkOnly":50,"markdownContent":51,"markdownBody":52,"frontMatter":53,"refName":60,"commitSha":61,"skillDirectory":62,"forksCount":14,"repositoryHtmlUrl":63,"repositoryHomepageUrl":64,"ownerHtmlUrl":65,"ownerBlogUrl":66,"ownerDescription":67,"updatedAt":68,"install":69,"resources":82},"01M6QERGSFTSDXXB05YN50RY52","ginkgo-cloud-lab",null,"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\u002FcircRNA synthesis, thermal shift \u002F 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.","Tashima-Tarsh\u002FDisha6.6","Tashima-Tarsh","https:\u002F\u002Favatars.githubusercontent.com\u002Fu\u002F269906498?v=4","01M6PBH98X03XERH0HFT4PFB1P","NITISH KUMAR","01M6PBH9DA0M6KM3Z12P848F0K",0,"MIT","https:\u002F\u002Fgithub.com\u002FTashima-Tarsh\u002FDisha6.6\u002Fblob\u002Fmain\u002F.agents\u002Fskills\u002Fkal-ginkgo-cloud-lab\u002FSKILL.md",[18,23],{"categoryNo":19,"categoryName":20,"taxonomyType":21,"taxonomyTypeDesc":22},"01JBSEEDCAT000000000000023","Skill与智能体开发","SCENARIO","使用场景",{"categoryNo":24,"categoryName":25,"taxonomyType":26,"taxonomyTypeDesc":27},"01JBSEEDCAT000000000000038","人力资源","PROFESSION","适用职业",[29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48],"ginkgo cloud lab","lab","cloud","free","run","interface","biology","quantification","expression","submit","input","synthetic","workflows","pixel","selection","Echo","Art","ms","autonomous","read","2026-11-10 10:12:30",false,"---\nname: ginkgo-cloud-lab\ndescription: 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\u002FcircRNA synthesis, thermal shift \u002F 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.\nlicense: MIT\nallowed-tools: Read\nmetadata:\n  version: '2.1'\n  category: lab-automation\n  maintainer: Kalaris Labs\n  tags: cloud lab, lab automation, protein expression, synthetic biology\n---\n\n# Ginkgo Cloud Lab\n\n## Overview\n\nGinkgo Cloud Lab (https:\u002F\u002Fcloud.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.\n\nThe 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.\n\nThe catalog is organized into **Expression & Purification** (in vitro \u002F cell-free \u002F E. coli \u002F 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.\n\n## Available Protocols\n\n### Expression & Purification - In vitro\n\n| Protocol | Readout | Price | Turnaround | Status |\n|---|---|---|---|---|\n| [IVT mRNA\u002FcircRNA Synthesis](references\u002Fivt-rna-synthesis-qpcr.md) | qPCR (mRNA or circRNA, 384-well) | $99\u002Fsample | up to 12 business days | Certified |\n\n### Expression & Purification - Cell-free (E. coli CFPS)\n\n| Protocol | Readout | Price | Turnaround | Status |\n|---|---|---|---|---|\n| [Validate sequence expression](references\u002Fcell-free-protein-expression-validation.md) | Go\u002Fno-go titer + purity (up to 1800 bp) | $39\u002Fsample | up to 10 days | Certified |\n| [Optimize expression conditions](references\u002Fcell-free-protein-expression-optimization.md) | DoE across 24 conditions | $199\u002Fsample | up to 11 days | Certified |\n| [Express + quantify (HiBiT)](references\u002Fcell-free-protein-expression-hibit.md) | Luminescence, no purification | $39\u002Fsample | up to 11 days | Certified |\n| [Express + purify (A280)](references\u002Fcfps-strep-tag-purification-a280.md) | Strep-tag, A280 yield | $149\u002Fsample | up to 11 days | Certified |\n| [Express + purify minibinder](references\u002Fminibinder-strep-tag-a280.md) | Strep-tag, A280, LabChip | $149\u002Fsample | up to 11 days | Certified |\n| [Express + purify (A280 + LabChip)](references\u002Fcfps-expression-purification-quantification.md) | Strep-tag, A280 + purity\u002Fsize | $159\u002Fsample | up to 12 days | Certified |\n\n### Expression & Purification - E. coli\n\n| Protocol | Readout | Price | Turnaround | Status |\n|---|---|---|---|---|\n| [Express + quantify (HiBiT)](references\u002Fecoli-protein-expression-hibit.md) | Luminescence (up to 384 constructs) | $79\u002Fsample | up to 3 weeks | Certified |\n| [Express + purify (A280)](references\u002Fecoli-protein-expression-histag-a280.md) | His-tag, A280 yield | $199\u002Fsample | up to 3 weeks | Certified |\n| [Express + purify minibinder](references\u002Fecoli-minibinder-expression-histag-a280.md) | His-tag, A280 yield | $199\u002Fsample | up to 3 weeks | Certified |\n| [Express + purify (A280 + LabChip)](references\u002Fecoli-expression-purification-quantification.md) | His-tag, A280 + purity\u002Fsize | $209\u002Fsample | up to 3 weeks | Certified |\n\n### Expression & Purification - Pichia\n\n| Protocol | Readout | Price | Turnaround | Status |\n|---|---|---|---|---|\n| [Express + quantify (LabChip)](references\u002Fpichia-protein-expression-labchip.md) | Secreted protein, size\u002Fpurity (up to 96) | $89\u002Fsample | up to 4 weeks | Certified (New) |\n\n### Characterization & Assay\n\n| Protocol | Readout | Price | Turnaround | Status |\n|---|---|---|---|---|\n| [Express + thermal shift](references\u002Fcfps-strep-purification-thermal-shift.md) | SYPRO Orange Tm (Tonset, TM1-3) | $159\u002Fsample | up to 12 days | Certified |\n| [Detect enzymatic products (Echo-MS)](references\u002Fecho-ms-cfps-detection.md) | Substrate\u002Fproduct by Echo-MS | $44\u002Fsample | up to 13 days | Beta |\n\n### Method & Target Onboarding\n\n| Protocol | Readout | Price | Turnaround | Status |\n|---|---|---|---|---|\n| [Onboard Echo-MS method](references\u002Fecho-ms-method-onboarding.md) | Calibration curve, LOD\u002FLOQ | $799\u002Fmolecule | up to 3 weeks | Certified |\n| [Onboard SPR target](references\u002Fspr-target-onboarding.md) | Validated SPR capture method | $1,399\u002Ftarget | up to 4 weeks | Beta |\n\n### Specialty\n\n| Protocol | Readout | Price | Turnaround | Status |\n|---|---|---|---|---|\n| [Generate fluorescent pixel art](references\u002Ffluorescent-pixel-art-generation.md) | UV photo, 7-color E. coli palette | $25\u002Fplate | up to 7 days | Beta |\n\n**Coming soon:** Protein Expression and Binding Affinity Characterization (express + purify, then screen binding affinity against a target).\n\n## Choosing a Protocol\n\n- **Quick expressibility screen?** Cell-free HiBiT ($39) or Validate sequence expression ($39).\n- **Need purified protein + yield?** A280 tiers (cell-free or E. coli); add LabChip for purity\u002Fsize.\n- **Difficult \u002F membrane \u002F disulfide \u002F cofactor targets?** Cell-free Optimize (24-condition DoE).\n- **Secreted or eukaryotic targets?** Pichia expression.\n- **Screening de novo binders\u002Fminibinders?** Cell-free or E. coli minibinder tiers, then SPR onboarding for kinetics.\n- **Enzyme activity \u002F biocatalysis?** Echo-MS enzymatic detection (onboard the analyte method first).\n- **Stability \u002F developability ranking?** Thermal shift assay.\n- **RNA (mRNA\u002FcircRNA)?** IVT synthesis + qPCR.\n\n## General Ordering Workflow\n\n1. Select a protocol at https:\u002F\u002Fcloud.ginkgo.bio\u002Fprotocols\n2. Configure parameters (number of proteins\u002Fsamples\u002Fmolecules\u002Ftargets, replicates, plates)\n3. Download the protocol's input template and upload inputs (FASTA\u002FCSV\u002FXLSX for sequence protocols; Design Tool for pixel art; vendor catalog numbers for onboarding)\n4. Add any special requirements in the Additional Details field\n5. Provide an email, agree to the protocol terms, and add to cart \u002F submit to receive a feasibility report and price quote\n\nFor protocols not listed above, use the **EstiMate** chat (https:\u002F\u002Fcloud.ginkgo.bio\u002Festimate) to describe a custom protocol in plain language and receive a compatibility assessment and pricing.\n\n## Authentication\n\nAccess Ginkgo Cloud Lab at https:\u002F\u002Fcloud.ginkgo.bio. Account creation or institutional access may be required. Contact Ginkgo at cloud@ginkgo.bio for access questions.\n\n## Key Infrastructure\n\n- **RACs (Reconfigurable Automation Carts):** Modular robotic units with high-precision arms and maglev transport\n- **Catalyst Software:** Protocol orchestration, scheduling, parameterization, and real-time monitoring\n- **70+ integrated instruments:** Agilent Bravo liquid handlers, Beckman\u002FLabcyte Echo acoustic dispensers, BMG PHERAstar \u002F Tecan Spark readers, Revvity LabChip, Bio-Rad CFX Opus, Nicoya Alto SPR, SciEx Echo-MS, Inheco\u002FCytomat incubators, and more\n- **Nebula:** Ginkgo's autonomous lab facility in Boston, MA\n\n## Agent operating procedure\n\n1. **Check the environment.** Confirm the instrument or platform model, API version, credentials and whether a simulator is available.\n2. **Pin down the inputs.** Confirm formats, identifiers and parameters from the data or the user. Ask rather than guess any value that changes the result.\n3. **Run a small version first.** Simulate the protocol or run it with water or dummy labware before using real samples.\n4. **Execute the full task** using the instructions and references above.\n5. **Validate the result.** Verify volumes, deck layout and labware definitions; have a human approve the protocol before execution.\n6. **Report.** State what was run (versions, commands, parameters), what was checked, and what is still uncertain.\n\n| If this happens | Do this |\n|---|---|\n| The protocol fails in simulation | Fix it in simulation; never run an unvalidated protocol on hardware. |\n| A function, flag or endpoint in these instructions is missing in the installed version | Check the installed version's own documentation (`help()`, `--help`, official docs), adapt, and tell the user. Never invent an API. |\n| A required input, identifier or parameter is ambiguous | Ask the user, or state the assumption explicitly before running. |\n\n**Integrity rules**\n\n- Never fabricate results, parameters, identifiers, citations or statistics. If something cannot be run or verified, say so plainly.\n- Never trigger physical actions, orders or charges without explicit user confirmation.\n- Treat version-specific details here as possibly outdated: confirm them against the official documentation for the installed version.\n- Ask before actions that cost money, consume shared GPUs or cloud quota, touch personal or patient data, or cannot be undone.\n\n## Related skills\n\n- `adaptyv`: How to use the Adaptyv Bio Foundry API and Python SDK for protein experiment design, submission, and results retrieval.\n","# Ginkgo Cloud Lab\n\n## Overview\n\nGinkgo Cloud Lab (https:\u002F\u002Fcloud.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.\n\nThe 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.\n\nThe catalog is organized into **Expression & Purification** (in vitro \u002F cell-free \u002F E. coli \u002F 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.\n\n## Available Protocols\n\n### Expression & Purification - In vitro\n\n| Protocol | Readout | Price | Turnaround | Status |\n|---|---|---|---|---|\n| [IVT mRNA\u002FcircRNA Synthesis](references\u002Fivt-rna-synthesis-qpcr.md) | qPCR (mRNA or circRNA, 384-well) | $99\u002Fsample | up to 12 business days | Certified |\n\n### Expression & Purification - Cell-free (E. coli CFPS)\n\n| Protocol | Readout | Price | Turnaround | Status |\n|---|---|---|---|---|\n| [Validate sequence expression](references\u002Fcell-free-protein-expression-validation.md) | Go\u002Fno-go titer + purity (up to 1800 bp) | $39\u002Fsample | up to 10 days | Certified |\n| [Optimize expression conditions](references\u002Fcell-free-protein-expression-optimization.md) | DoE across 24 conditions | $199\u002Fsample | up to 11 days | Certified |\n| [Express + quantify (HiBiT)](references\u002Fcell-free-protein-expression-hibit.md) | Luminescence, no purification | $39\u002Fsample | up to 11 days | Certified |\n| [Express + purify (A280)](references\u002Fcfps-strep-tag-purification-a280.md) | Strep-tag, A280 yield | $149\u002Fsample | up to 11 days | Certified |\n| [Express + purify minibinder](references\u002Fminibinder-strep-tag-a280.md) | Strep-tag, A280, LabChip | $149\u002Fsample | up to 11 days | Certified |\n| [Express + purify (A280 + LabChip)](references\u002Fcfps-expression-purification-quantification.md) | Strep-tag, A280 + purity\u002Fsize | $159\u002Fsample | up to 12 days | Certified |\n\n### Expression & Purification - E. coli\n\n| Protocol | Readout | Price | Turnaround | Status |\n|---|---|---|---|---|\n| [Express + quantify (HiBiT)](references\u002Fecoli-protein-expression-hibit.md) | Luminescence (up to 384 constructs) | $79\u002Fsample | up to 3 weeks | Certified |\n| [Express + purify (A280)](references\u002Fecoli-protein-expression-histag-a280.md) | His-tag, A280 yield | $199\u002Fsample | up to 3 weeks | Certified |\n| [Express + purify minibinder](references\u002Fecoli-minibinder-expression-histag-a280.md) | His-tag, A280 yield | $199\u002Fsample | up to 3 weeks | Certified |\n| [Express + purify (A280 + LabChip)](references\u002Fecoli-expression-purification-quantification.md) | His-tag, A280 + purity\u002Fsize | $209\u002Fsample | up to 3 weeks | Certified |\n\n### Expression & Purification - Pichia\n\n| Protocol | Readout | Price | Turnaround | Status |\n|---|---|---|---|---|\n| [Express + quantify (LabChip)](references\u002Fpichia-protein-expression-labchip.md) | Secreted protein, size\u002Fpurity (up to 96) | $89\u002Fsample | up to 4 weeks | Certified (New) |\n\n### Characterization & Assay\n\n| Protocol | Readout | Price | Turnaround | Status |\n|---|---|---|---|---|\n| [Express + thermal shift](references\u002Fcfps-strep-purification-thermal-shift.md) | SYPRO Orange Tm (Tonset, TM1-3) | $159\u002Fsample | up to 12 days | Certified |\n| [Detect enzymatic products (Echo-MS)](references\u002Fecho-ms-cfps-detection.md) | Substrate\u002Fproduct by Echo-MS | $44\u002Fsample | up to 13 days | Beta |\n\n### Method & Target Onboarding\n\n| Protocol | Readout | Price | Turnaround | Status |\n|---|---|---|---|---|\n| [Onboard Echo-MS method](references\u002Fecho-ms-method-onboarding.md) | Calibration curve, LOD\u002FLOQ | $799\u002Fmolecule | up to 3 weeks | Certified |\n| [Onboard SPR target](references\u002Fspr-target-onboarding.md) | Validated SPR capture method | $1,399\u002Ftarget | up to 4 weeks | Beta |\n\n### Specialty\n\n| Protocol | Readout | Price | Turnaround | Status |\n|---|---|---|---|---|\n| [Generate fluorescent pixel art](references\u002Ffluorescent-pixel-art-generation.md) | UV photo, 7-color E. coli palette | $25\u002Fplate | up to 7 days | Beta |\n\n**Coming soon:** Protein Expression and Binding Affinity Characterization (express + purify, then screen binding affinity against a target).\n\n## Choosing a Protocol\n\n- **Quick expressibility screen?** Cell-free HiBiT ($39) or Validate sequence expression ($39).\n- **Need purified protein + yield?** A280 tiers (cell-free or E. coli); add LabChip for purity\u002Fsize.\n- **Difficult \u002F membrane \u002F disulfide \u002F cofactor targets?** Cell-free Optimize (24-condition DoE).\n- **Secreted or eukaryotic targets?** Pichia expression.\n- **Screening de novo binders\u002Fminibinders?** Cell-free or E. coli minibinder tiers, then SPR onboarding for kinetics.\n- **Enzyme activity \u002F biocatalysis?** Echo-MS enzymatic detection (onboard the analyte method first).\n- **Stability \u002F developability ranking?** Thermal shift assay.\n- **RNA (mRNA\u002FcircRNA)?** IVT synthesis + qPCR.\n\n## General Ordering Workflow\n\n1. Select a protocol at https:\u002F\u002Fcloud.ginkgo.bio\u002Fprotocols\n2. Configure parameters (number of proteins\u002Fsamples\u002Fmolecules\u002Ftargets, replicates, plates)\n3. Download the protocol's input template and upload inputs (FASTA\u002FCSV\u002FXLSX for sequence protocols; Design Tool for pixel art; vendor catalog numbers for onboarding)\n4. Add any special requirements in the Additional Details field\n5. Provide an email, agree to the protocol terms, and add to cart \u002F submit to receive a feasibility report and price quote\n\nFor protocols not listed above, use the **EstiMate** chat (https:\u002F\u002Fcloud.ginkgo.bio\u002Festimate) to describe a custom protocol in plain language and receive a compatibility assessment and pricing.\n\n## Authentication\n\nAccess Ginkgo Cloud Lab at https:\u002F\u002Fcloud.ginkgo.bio. Account creation or institutional access may be required. Contact Ginkgo at cloud@ginkgo.bio for access questions.\n\n## Key Infrastructure\n\n- **RACs (Reconfigurable Automation Carts):** Modular robotic units with high-precision arms and maglev transport\n- **Catalyst Software:** Protocol orchestration, scheduling, parameterization, and real-time monitoring\n- **70+ integrated instruments:** Agilent Bravo liquid handlers, Beckman\u002FLabcyte Echo acoustic dispensers, BMG PHERAstar \u002F Tecan Spark readers, Revvity LabChip, Bio-Rad CFX Opus, Nicoya Alto SPR, SciEx Echo-MS, Inheco\u002FCytomat incubators, and more\n- **Nebula:** Ginkgo's autonomous lab facility in Boston, MA\n\n## Agent operating procedure\n\n1. **Check the environment.** Confirm the instrument or platform model, API version, credentials and whether a simulator is available.\n2. **Pin down the inputs.** Confirm formats, identifiers and parameters from the data or the user. Ask rather than guess any value that changes the result.\n3. **Run a small version first.** Simulate the protocol or run it with water or dummy labware before using real samples.\n4. **Execute the full task** using the instructions and references above.\n5. **Validate the result.** Verify volumes, deck layout and labware definitions; have a human approve the protocol before execution.\n6. **Report.** State what was run (versions, commands, parameters), what was checked, and what is still uncertain.\n\n| If this happens | Do this |\n|---|---|\n| The protocol fails in simulation | Fix it in simulation; never run an unvalidated protocol on hardware. |\n| A function, flag or endpoint in these instructions is missing in the installed version | Check the installed version's own documentation (`help()`, `--help`, official docs), adapt, and tell the user. Never invent an API. |\n| A required input, identifier or parameter is ambiguous | Ask the user, or state the assumption explicitly before running. |\n\n**Integrity rules**\n\n- Never fabricate results, parameters, identifiers, citations or statistics. If something cannot be run or verified, say so plainly.\n- Never trigger physical actions, orders or charges without explicit user confirmation.\n- Treat version-specific details here as possibly outdated: confirm them against the official documentation for the installed version.\n- Ask before actions that cost money, consume shared GPUs or cloud quota, touch personal or patient data, or cannot be undone.\n\n## Related skills\n\n- `adaptyv`: How to use the Adaptyv Bio Foundry API and Python SDK for protein experiment design, submission, and results retrieval.\n",{"name":5,"license":15,"metadata":54,"description":7,"allowed-tools":59},{"tags":55,"version":56,"category":57,"maintainer":58},"cloud lab, lab automation, protein expression, synthetic biology","2.1","lab-automation","Kalaris 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Companion to run-without-you; the last stop before phase=done.","https:\u002F\u002Fgithub.com\u002FTashima-Tarsh\u002FDisha6.6\u002Fblob\u002Fmain\u002F.agents\u002Fskills\u002Fwrap-up\u002FSKILL.md",[],[241,242,243,244,245,33,246,247,248,204,249,175,250,251,252,253,254,255,256,257],"wrap up","up","wrap","gemini","deployment","file","hardening","closeout","stop","upgrade","founder","close","companion","you","tables","directions","phase",{"skillNo":259,"name":260,"nameZh":6,"description":261,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":262,"categories":263,"keywords":265,"publishedAt":49},"01M6QRA5AYC1RBFZ39GTWGS3N8","workflow-builder","Design and write deterministic multi-agent workflow scripts (.js files in .claude\u002Fworkflows\u002F) for Claude Code's Workflow tool. 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Walks David Allen's three-phase loop — GET CLEAR, GET CURRENT, GET CREATIVE — with deterministic scripts that inventory open loops, gate the checklist with named gaps, and score commitment health 0-100.","https:\u002F\u002Fgithub.com\u002FTashima-Tarsh\u002FDisha6.6\u002Fblob\u002Fmain\u002F.agents\u002Fskills\u002Fweekly-review\u002FSKILL.md",[],[288,289,290,291,292,293,294,295,296,273,297,298,299,300,301,302,176,303,304,257],"review","weekly review","weekly","deterministic scripts","reflect","feeds","inventory","open","team","projects","project-management","scanner","conversation","back","project","sprint","cadence"]