Examples · end-to-end walkthroughs

The framework, in motion.

Each example takes a real scientific or engineering scenario, models it as a series of typed chain commits, and shows the audit closure the conclusion carries. Read these to see Eigenius doing work. If you want the conceptual ideas first, head to Concepts instead.

Available walkthroughs

Two complete chains.

Drug screening Domain-bridge pattern

From IC₅₀ readings to a strong-inhibitor designation.

A medicinal chemist has six IC₅₀ readings of compound EIG_0291 and wants the chain to attest "EIG_0291 is a strong CDK2 inhibitor" — only by mechanical derivation, not by author assertion. The statistics institution emits a strictly statistical conclusion; a chain-resident domain bridge translates it to the medicinal-chemistry vocabulary; a literature rule specialises at the compound; the kernel type-checks the composition. The final conclusion carries an audit trail that walks back to the raw plate readings.

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Kinase potency mapping Comorphism pattern

Five Julia institutions in composition.

A biophysicist runs a kinase potency mapping campaign in which the same data must flow through symbolic math (Symbolics.jl), an ODE integrator (OrdinaryDiffEq.jl), non-linear regression (NonlinearSolve.jl), JuMP+HiGHS optimisation, and a ranking routine. Each institution speaks its own vocabulary; declared comorphisms mediate the translation. Showcases the runtime-seam analogue of the domain-bridge pattern: typed translation between institution boundaries instead of between user-defined vocabularies.

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Coming soon

The Lean-verified primary endpoint.

A regulatory-submission example is in preparation. It will show how a Lean-verified result enters the chain as a Verified artifact and composes with Observed and Derived evidence in a downstream sentence — the case where the framework earns its keep against ALCOA+ and FAIR alignment.

Run them yourself

Every walkthrough has a runnable artifact.

Each example corresponds to either a Jupyter-style notebook under notebooks/examples/ or an integration-test fixture under crates/eigenius-*/tests/fixtures/. The last section of each walkthrough links to the canonical artifact and gives reproduction instructions.

The fastest path from zero to a running chain is the notebook flow on the Get started page — clone the repo, bring up docker compose, and open the drug-screening notebook.

Set it up locally Or read the reference