Public code for four products, two free open-source tools, and the companions that ship with Ferrum. Conformance tooling, reproducible demos, and a clear licence story — not one suite product.
For decision makers
Why this page matters if you are not deep in the stack
Short plain-language context. GA4GH in one sentence. How inclusion fits us. The rest of this page keeps the full technical depth.
Our public repositories and the white paper are how we show serious engineering before a long customer reference list exists: reproducible demos, conformance tooling, and clear licensing.
What is GA4GH?
The Global Alliance for Genomics and Health (GA4GH) is an international initiative that defines shared technical interfaces for genomic data and analyses. Partners connect under clear contracts instead of rebuilding bespoke integrations for every link.
Synaptic Four combines rigorous engineering with an explicit, lived commitment to neurodiversity and autism inclusion. That is part of who we are—not an add-on to the tech story. More: About Alex Autism
We distinguish between licenses that match the common Open Source Definition (OSI) and models where code is public but use is restricted.
Licences such as Apache-2.0 or MIT are what many people mean by true open source: public source, reuse and modification within the licence terms, and alignment with the OSI definition. HelixTest, ga4gh-infra, Ferrum GA4GH Demo, GA4GH Community Stack, and HELIOS use Apache-2.0 or MIT.
The Business Source License is not “open source” in the OSI sense: code is visible and often free for defined uses (e.g. non-commercial research), while commercial use is restricted or only unlocked after a set period. We publish Ferrum, Ferrum Lab Kit, Solum, and BioResearch Assistant under BUSL-1.1 – transparent and inspectable, but strategically different from Apache-2.0.
Commercial products (e.g. Ferrum, Solum, BioResearch Assistant) may use BUSL or other models; the LICENSE file in each repository and the product page are authoritative.
Ferrum (data/compute, BUSL), GA4GH Infra (identity, Apache-2.0 — software free; commercial motion is support), Solum (clinical overlay, BUSL), BioResearch Assistant (workbench, BUSL). Glue is GA4GH, plus Solum when clinic meets genomics. HelixTest and HELIOS are free open-source tools. Lab Kit and ferrum-meta ship with Ferrum. Demos prove a tagged release locally — they are not a product. The GA4GH Community Stack (MIT) is a transparent upstream alternative for teaching and pilots.
Standalone Rust conformance and integration suite for GA4GH-style platforms: API contracts (WES, TES, DRS, TRS, Beacon v2, htsget), workflow execution, cross-service E2E (TRS → DRS → WES → TES → Beacon), Passports, and Crypt4GH-oriented checks. Usable by any compatible stack—not only Ferrum. Results are a technical signal, not official GA4GH certification.
GitHub →Self-hostable Rust identity plane for GA4GH: OIDC brokering, Passport/Visa issuance, access decisions (ADS), DUO matching, and Service Registry. Co-deploys with Ferrum; native ARM/Pi builds for edge settings.
GitHub →Reproducible demonstration and benchmark: one command runs Ferrum TRS · DRS · WES · TES on a small GIAB-style subset, then hap.py vs truth. Structured JSON evidence (benchmark, metrics, DRS micro: plain vs Crypt4GH-at-rest). Optional co-deploy with ga4gh-infra. HELIOS / Solum / evidence packs are Showcase stages — not this Demo. Apache-2.0; Ferrum upstream remains BUSL-1.1.
GitHub →Integrated on-premise-first GA4GH runtime in Rust (DRS, WES/TES, TRS, Beacon, htsget, Passports, Crypt4GH, MII Connect pathways). Source-available under BUSL-1.1; HelixTest and demos provide technical signals, not official GA4GH certification.
GitHub →On-ramp to Ferrum: selective GA4GH surfaces (monolith gateway + ENABLE flags) against your storage, scheduler, and identity stack. Profiles named full-elixir-node and gdi-national-node are onboarding stubs, not a live ELIXIR or GDI node. Optional ga4gh-infra co-deploy and Solum consent companion; Raspberry Pi kit generator (`lab-kit generate raspberry-pi`). Complements the main Ferrum repo; JSON conformance reports are open, licensed PDF output see repository.
GitHub →Archive-agnostic genomics metadata schema for Ferrum nodes (LinkML core + archive profiles). Early access, schema only. validate checks YAML against the schema. export copies a committed fixture (shutil.copyfile) — it does not talk to Ferrum, list DRS objects, or upload to EGA/GHGA.
GitHub →Clinical EHDS compliance layer (Stage 1): enforce, translate, evidence—standalone or optional Ferrum companion. Source-available under BUSL-1.1; early development, not a legal compliance certificate.
GitHub →Curated open-source GA4GH deployment kit from upstream implementations (Beacon, WES, TES, DRS) with an honest comparison to Ferrum Lab Kit. For teaching, pilots, and teams that want maximum upstream transparency.
GitHub →Genomics pipeline audit and validation: signed run records, compliance-oriented checks, JSON/PDF/RO-Crate exports. Core OSS under Apache-2.0 (alpha). PyPI publishes helios-audit 0.1.1; GitHub main may be ahead. HELIOS reads export JSON — it does not orchestrate Ferrum or Solum. Synaptic Four sells support and optional dashboard hosting separately. Not a certification.
GitHub →Public evidence pack and pin checkout for the Ferrum / GA4GH repositories. Reference / demo — not a product. The default golden path is a subset (Ferrum-GA4GH-Demo + HELIOS). A green fixture job is not live proof of product main.
GitHub →Open research prototype: adaptive, non-diagnostic questionnaire with ten continuous routing dimensions (F–V), consent-first flows, multi-locale copy, optional Supabase logging for studies, and optional research-oriented exports (e.g. session bundles, paper/CSV replay, offline-friendly static bank). The repository also ships larger optional item banks (~200 prompts) with regional stem bundles where configured; operators set an explicit adaptive policy, and a documented research mode steers studies toward full-session artefacts rather than compressed URL shares. Public instance: map.synapticfour.com. Personal project—not a Synaptic Four commercial product; see the research note under Publications.
GitHub →On-premise research platform: literature mining, pseudonymisation, MII/FHIR export, GA4GH-oriented interfaces, optional Locus RAG module, BLAST, ELN, and FAIR export. Public GitHub repository (BUSL-1.1); commercial production use requires a licence per LICENSE.
GitHub →LAN and nearby-device mesh messaging — no phone number, offline WiFi/BLE. Technical beta; not a replacement for emergency services. Android app and relay; AGPL-3.0 — repository access on request.
Request repository access →Apache-2.0 proof-of-concept for secure collaboration patterns. Explicitly not production-ready for patient data; explore the repository, do not treat it as a clinical product.
GitHub →Software that implements the Cognitive Landscape Research Programme (CLRP). Technical documentation lives in each repository; CLRP defines programme principles and validation standards.
Adaptive web research instrument
Computational model library
Programme constitution and validation reports: Research programme hub .
Additional repositories on GitHub include NeuroAttune (Dart tests; hosts not shipped; access on request), Mycelium (AGPL-3.0 mesh; access on request), and SynaptiSec (source by arrangement; living app in Synaptic Products with a public sandbox demo plus allowlisted Google Vollzugang). SitePulse AI and AZAV-Akte are commercial apps on the Synaptic Products hub, not separate GitHub products. SecureCollab appears above as a labelled PoC card.
gatk-rs — early public Apache-2.0 Rust work on GATK-class germline calling; independent and alpha. Proof of approach, not a product.
Ferrum: building GA4GH-oriented infrastructure as a first-principles practice—motivation, architecture, HelixTest conformance checks, GA4GH demo benchmarks, and how we work (incl. transparent AI-assisted engineering).
All publications →