{ "@context": "https://schema.org", "@graph": [ { "@type": "SoftwareSourceCode", "@id": "https://github.com/modarresi1913/OrganoidOS#software", "name": "OrganoidOS", "description": "Open operating-system specification and Python reference emulator for biological neural networks — cortical organoids on multi-electrode arrays, plus in-silico emulators using Izhikevich and Hodgkin-Huxley neuron models with spike-timing-dependent plasticity (STDP).", "codeRepository": "https://github.com/modarresi1913/OrganoidOS", "programmingLanguage": "Python", "runtimePlatform": "Python 3.9+", "author": { "@type": "Organization", "name": "OrganoidOS Contributors", "url": "https://github.com/modarresi1913/OrganoidOS" }, "license": "https://opensource.org/licenses/MIT", "copyrightHolder": { "@type": "Organization", "name": "OrganoidOS Contributors" }, "datePublished": "2026-08-24", "dateModified": "2026-08-24", "version": "0.1.0", "releaseNotes": "Initial v0.1 stable release: 4 spec documents + L0 reference emulator with Izhikevich, Hodgkin-Huxley, STDP, scheduler, migration, health monitoring, mini kernel, mock CL1-style API, CLI, examples, benchmarks, and 15 passing tests.", "keywords": [ "organoid", "biological neural network", "MEA", "multi-electrode array", "operating system", "spiking neural network", "STDP", "spike-timing-dependent plasticity", "Izhikevich", "Hodgkin-Huxley", "bio-computing", "neuromorphic", "Cortical Labs", "CL1", "DishBrain", "FinalSpark", "open source", "MIT license", "Python", "neuroscience" ], "applicationCategory": "Science/Research", "applicationSubCategory": "Bioinformatics", "operatingSystem": "Cross-platform (Python)", "softwareRequirements": "numpy>=1.20", "softwareHelp": "https://github.com/modarresi1913/OrganoidOS/blob/main/docs/INDEX.md", "readme": "https://github.com/modarresi1913/OrganoidOS/blob/main/README.md", "installUrl": "https://github.com/modarresi1913/OrganoidOS", "discussionUrl": "https://github.com/modarresi1913/OrganoidOS/discussions", "isAccessibleForFree": true, "isPartOf": { "@type": "SoftwareApplication", "name": "OrganoidOS Project" } }, { "@type": "FAQPage", "@id": "https://github.com/modarresi1913/OrganoidOS#faq", "mainEntity": [ { "@type": "Question", "name": "What is OrganoidOS?", "acceptedAnswer": { "@type": "Answer", "text": "OrganoidOS is an MIT-licensed open-source specification and Python reference emulator for biological neural network operating systems. It abstracts the differences between cultured cortical organoids on multi-electrode arrays and in-silico models, exposing a stable behavioral API for stimulation, recording, training, snapshotting, restoring, and health monitoring. The repository ships with a working L0 emulator using Izhikevich and Hodgkin-Huxley neuron models with spike-timing-dependent plasticity (STDP)." } }, { "@type": "Question", "name": "Is OrganoidOS the same as Cortical Labs CL1 or DishBrain?", "acceptedAnswer": { "@type": "Answer", "text": "No. CL1 and DishBrain are commercial products of Cortical Labs. OrganoidOS is an open specification unaffiliated with Cortical Labs. It uses the names CL1 and DishBrain only for interoperability documentation under nominative fair use, and contains no Cortical Labs source code." } }, { "@type": "Question", "name": "Can I run OrganoidOS on my laptop without wetware?", "acceptedAnswer": { "@type": "Answer", "text": "Yes. The L0 reference emulator runs on any Python 3.9+ installation with numpy. No biological tissue, no multi-electrode array, no vendor SDK is required. The full smoke-test-to-trained-model workflow takes 30 to 60 seconds on a modern laptop." } }, { "@type": "Question", "name": "What neuron models does OrganoidOS implement?", "acceptedAnswer": { "@type": "Answer", "text": "The OrganoidOS L0 reference emulator implements two biophysical neuron models: Izhikevich (2003) — a fast 2-variable spiking-neuron model with 5 presets (regular spiking, fast spiking, intrinsically bursting, chattering, low-threshold spiking); and Hodgkin-Huxley (1952) — a 4-variable conductance-based model about 10x slower but biophysically detailed. Both models share the same Python interface." } }, { "@type": "Question", "name": "What plasticity rule does OrganoidOS use?", "acceptedAnswer": { "@type": "Answer", "text": "The default plasticity rule is pair-based spike-timing-dependent plasticity (STDP) as formulated by Bi and Poo (1998) and Song, Miller and Abbott (2000), augmented with multiplicative homeostatic normalization (Turrigiano 2008). All plasticity is computed locally at the synapse; the OS never back-propagates a global gradient into the culture." } }, { "@type": "Question", "name": "How do I migrate learned state between organoids?", "acceptedAnswer": { "@type": "Answer", "text": "Migration is not a copy — biological cultures cannot be copied bit-for-bit. Migration is a directed re-training of a target organoid toward a learned behavioral state using a MigrationSnapshot (JSON document plus binary weight matrix). The kernel computes a convergence_score in [0, 1]; migration is declared successful when the score exceeds 0.75 sustained for 1 hour." } }, { "@type": "Question", "name": "How does OrganoidOS detect a dying culture?", "acceptedAnswer": { "@type": "Answer", "text": "A HealthReport carries mean firing rate, burst rate, synchrony index, active electrodes, and a degradation boolean. A culture is degraded if any of these hold sustained for 30 minutes: firing rate below 0.05 Hz, fewer than 50 percent of electrodes active, synchrony below 0.10, or bursting disappeared with tonic firing persisting. Critical cases recommend physical replacement." } }, { "@type": "Question", "name": "Is OrganoidOS patented or proprietary?", "acceptedAnswer": { "@type": "Answer", "text": "No. OrganoidOS is released under the MIT license, the most permissive open-source license. Anyone may implement, extend, fork, or commercialize the spec without royalty or attribution beyond the license terms." } } ] }, { "@type": "TechArticle", "@id": "https://github.com/modarresi1913/OrganoidOS#spec", "headline": "OrganoidOS Specification v0.1", "description": "Open operating-system specification for biological neural networks.", "author": { "@type": "Organization", "name": "OrganoidOS Contributors" }, "datePublished": "2026-08-24", "about": [ {"@type": "Thing", "name": "biological neural networks"}, {"@type": "Thing", "name": "cortical organoids"}, {"@type": "Thing", "name": "multi-electrode arrays"}, {"@type": "Thing", "name": "spike-timing-dependent plasticity"}, {"@type": "Thing", "name": "Izhikevich model"}, {"@type": "Thing", "name": "Hodgkin-Huxley model"} ], "isPartOf": { "@id": "https://github.com/modarresi1913/OrganoidOS#software" } }, { "@type": "BreadcrumbList", "itemListElement": [ { "@type": "ListItem", "position": 1, "name": "GitHub", "item": "https://github.com" }, { "@type": "ListItem", "position": 2, "name": "modarresi1913", "item": "https://github.com/modarresi1913" }, { "@type": "ListItem", "position": 3, "name": "organoid-os-spec", "item": "https://github.com/modarresi1913/OrganoidOS" } ] } ] }