Skip to content
Eigenius

Julia institution tutorials

Slow-walk worked examples of substrate-hosted Julia institutions. Each one exercises the install flow described in platform §11 — Runtime substrate against a real Julia library, wires up the institution’s chain shapes, and runs at least one verdict end-to-end.

Two sets of declarations exist; only one is live. The live declarations these tutorials describe are under julia/institutions/<name>/declarations/, with IRIs shaped urn:eigenius:catalyst:ReactionNetwork. A second, superseded set survives under ontologies/julia/ with the prefix urn:eigenius:julia:catalyst:…. It is loaded by no Rust source, no shell script and no test, it mentions FormulaTerm nowhere in its sixteen files, and it is referenced only by one paragraph of D27. A reader grepping the ontologies/ tree for ReactionNetwork or OptimisationProblem will find the wrong one. Check the IRI prefix.

Read in order if this is your first substrate institution. The intervals tutorial covers the substrate plumbing (mirror generator, env image, worker container, AutoOnLoad gate) at a slow pace; the others assume that plumbing knowledge and focus on what’s domain-specific to each institution.

TutorialWrapsWhat’s distinctive
IntervalsIntervalArithmetic.jlThe simplest possible external-runtime institution — one class, one AutoOnLoad gate, one handler. The recommended first read.
SymbolicsSymbolics.jlThree dispatch roles in one institution (AutoOnLoad / OnDemand / Decidable); the FormulaTerm-as-EigenTT-fragment story end-to-end.
CatalystCatalyst.jlChemical reaction networks; companion to the DiffEq tutorial via the Catalyst → DiffEq comorphism. The one institution that declares no FormulaTerm-typed property — it reaches the shared payload through handler code instead.
DiffEqOrdinaryDiffEq.jlODE integration; the gate re-integrates the FormulaTerm RHS to verify a claimed solution.
JuMP-HiGHSJuMP + HiGHSLP/QP optimisation; the smart-pow walker rule that keeps quadratic objectives in QuadExpr rather than NonlinearExpr.

All three shipped comorphisms declare an identity middle, but at three different types — formulas:FormulaTerm for Symbolics → IntervalArithmetic, diffeq:OdeProblem for Catalyst → DiffEq, jump:OptimisationProblem for Symbolics → JuMP. In the latter two the translation lives in the source institution’s ExportFormat procedure, not in the middle. See composition §2.4.

The end-to-end “everything together” demo notebook that exercises all five institutions plus three cross-institution comorphisms lives at notebooks/examples/kinase-institutions.json (setup script: notebooks/examples/kinase-institutions-setup.sh). See platform §8.4 for the demo overview.

Cross-references