brinter-am-technologies-oy/3mf-bio

Purpose and Entry Points

This repository defines the pre-1.0 3MF Bio Extension: an XML schema and reference toolchain for recording biofabrication geometry, biological materials, process, evidence, calibration, maturation, and results inside a 3MF package. Primary user entry points are package validation (verify.py, spec/validate_bio.py), package generation from mesh plus questionnaire answers (tools/integrate.py), and local package inspection (tools/viewer.html).

Canonical Format Layer

The normative format is the Bio XML Schema and Schematron rules, extending a 3MF model’s <resources> section under the Bio namespace. It defines typed resources for evidence, substances, cell populations, bioinks, process, printheads, calibration, regulatory determination, open items, maturation, characterization, protocols, results, and volumetric field bindings.

• spec/bio.xsd

• spec/bio.sch

• spec/3MF Bio Extension.md

The key semantic boundary is that schema validity establishes structural and declared-rule conformance, not truth of scientific or regulatory claims.

Validation Pipeline

Validation is intentionally split by capability. XSD validation checks document structure; Schematron checks portable intra-document constraints; Python performs package-aware checks that need ZIP/OPC relationships, external-part existence, bibliography keys, full index bounds, strict/release policy, and cross-part logic.

• spec/validate_schema.py

• spec/validate_bio.py

• spec/bio.libxml.xsd

validate_bio.py accepts either an unpacked package directory or .3mf ZIP. --strict escalates warnings; --release rejects any estimated value. bio.libxml.xsd is a generated compatibility variant for libxml2/lxml.

Provenance, Unknowns, and Release Semantics

The central data-policy model requires numeric values to declare provenance. Estimated values are allowed but must be represented honestly and tied to tracked open items describing ownership and closure actions. This allows the integrator to emit incomplete packages rather than force fabricated inputs; release validation becomes the enforcement boundary.

• spec/bio.xsd

• spec/validate_bio.py

• dossier/Parameter-Dossier.md

Derived process claims additionally require their declared inputs, particularly for extrusion/shear relationships. Acceptance criteria are recorded per laboratory rather than prescribed by the format.

Package Authoring and Consumption

The authoring flow is: select a machine profile, generate/fill a questionnaire response, combine it with STL/OBJ geometry, then emit a validating 3MF package. The browser-only viewer reads a local package and prioritizes an operational run sheet, constraints, open items, dossiers, maturation, and geometry; it has no server or upload dependency.

• tools/questionnaire.py

• tools/integrate.py

• tools/viewer.html

Machine-specific capability input is currently represented as JSON profiles, beginning with Brinter.

• tools/machine_profiles/brinter.json

Reference Packages and Conformance

Two package directories are executable reference data: a volumetric tomographic build and a multi-head extrusion/deposition build with toolpath, biological records, protocols, certificates, and results. They exercise the 3MF OPC structure as well as Bio resources.

• examples/

• examples-extrusion/

• examples-extrusion/bio/toolpath/extrusion.gcode

Conformance testing injects faults through both rule engines; additional round-trip, corpus-generation, red-team, and tool integration checks protect format behavior.

• spec/conformance_tests.py

• spec/roundtrip_test.py

• verify.py

Evidence, Review, and Publication Infrastructure

Dossiers hold parameter sources, calibration references, regulatory mapping, bibliography, and fact-check outcomes that support schema vocabulary rather than runtime execution. External review is explicitly scoped to factual/regulatory assessment and collecting a real dataset.

• dossier/

• review/REGULATORY-REVIEW.md

• review/DATASET-SHEET.md

A static documentation/namespace site is generated from repository Markdown and deployed via GitHub Pages. CI validates the repository and publishes the site.

• site/build_site.py

• .github/workflows/validate.yml

• .github/workflows/pages.yml