Execution contract

Execute the competitive blueprint as governed research objects.

This contract converts competitor lessons into concrete dataset-import, Cell Browser, ModelRun, perturbation-network, prospective-benchmark and outcome-chain gates. It makes the next work executable without pretending that pathway deltas are already predicted.

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Execution, not overclaimSix execution units are now frozen as acceptance gates. DMD pathway delta, cell-state delta and functional prediction outputs remain locked.

Implemented work

The project now has execution gates, not only competitor lessons.

Execution units6

Network nodes15

Network edges18

DMD delta predictions0

Perturbation network contract

A real virtual-cell path is now represented as a locked, auditable network.

Runnable gates

Each unit has a current state, next action and acceptance gate.

Unit	Axis	State	Next action	Acceptance gate
`V95-DATASET-IMPORT`	Dataset import	EXECUTABLE_SPEC_READY	Register candidate DMD single-cell, single-nucleus and spatial datasets with donor, disease, state, perturbation and checksum fields before browsing.	At least two disease-relevant datasets have stable accessions, donor-level metadata, raw/processed SHA-256, license and prohibited-use fields.
`V95-CELL-BROWSER`	Real Cell Browser	PLANNED_REQUIRES_DATA_IMPORT	Replace concept-only context cards with donor-filtered cell-state panels, expression lookup, pseudobulk differential tables and exportable selections.	Browser selections resolve to Dataset object IDs and never summarize disease effect without donor-aware aggregation.
`V95-MODELRUN`	ModelRun adapter	LEDGER_RELEASED_NO_DMD_RUN	Use the frozen ModelRun ledger as the single execution-history source and require every future baseline or advanced model to append the same envelope.	Completed negative runs remain visible; model id, revision, container status, data release, split, seed, metrics, gate and missing provenance are explicit.
`V95-PERTURBATION-NETWORK`	Perturbation delta network	CONTRACT_READY_DELTA_LOCKED	Bind candidate perturbations to pathway modules, cell-state transitions, functional readouts and the missing evidence edge that would unlock each delta.	Every edge declares observed, inferred, planned or locked state; layout seed is fixed and node position is not interpreted as biology.
`V95-PROSPECTIVE-BENCHMARK`	Prospective benchmark	SPEC_READY_NO_HIDDEN_OUTCOMES	Freeze Study Card, Prediction Card and Outcome slots before laboratory outcomes are visible.	Timestamped prediction objects exist before outcome access, with null, toxic, failed-QC and abstained outcomes preserved.
`V95-OUTCOME-CHAIN`	Outcome return path	OBJECT_SCHEMA_READY_NO_MEASURED_OUTCOME	Append measured outcomes to the same object chain that generated the study and prediction records.	Study -> Prediction -> Experiment -> Outcome IDs remain linked without regenerating downstream IDs from URL parameters.

V95-* prefixes are immutable research-object identifiers retained for citation; they are not the current interface build.

Edge audit

Every edge says whether it supports a delta prediction.

Edge	Relation	Evidence state	Supports delta prediction
`QUESTION` -> `GENE_ZNF133`	candidate_input	USER_SELECTABLE	No
`QUESTION` -> `GENE_MON1A`	candidate_input	USER_SELECTABLE	No
`QUESTION` -> `GENE_GFOD2`	audit_input	USER_SELECTABLE	No
`GENE_ZNF133` -> `DATASET_IMPORT`	requires_matched_context	PLANNED	No
`GENE_MON1A` -> `DATASET_IMPORT`	requires_matched_context	PLANNED	No
`GENE_GFOD2` -> `DATASET_IMPORT`	requires_external_audit	LOCKED_PENDING_IMPORT	No
`DATASET_IMPORT` -> `CELL_BROWSER`	populates_browser	PLANNED	No
`CELL_BROWSER` -> `PATHWAY_MYOGENESIS`	annotates_module	CONTEXT_ONLY	No
`CELL_BROWSER` -> `PATHWAY_FIBROSIS`	annotates_module	CONTEXT_ONLY	No
`CELL_BROWSER` -> `PATHWAY_MITO`	annotates_module	CONTEXT_ONLY	No
`PATHWAY_MYOGENESIS` -> `CELL_STATE`	would_emit_cell_state_delta	LOCKED_NO_MATCHED_TRUTH	No
`PATHWAY_FIBROSIS` -> `CELL_STATE`	would_emit_cell_state_delta	LOCKED_NO_MATCHED_TRUTH	No
`PATHWAY_MITO` -> `FUNCTION`	would_emit_function_delta	LOCKED_NO_FUNCTIONAL_OUTCOME	No
`CELL_STATE` -> `MODELRUN`	candidate_training_target	REQUIRES_OUTCOME	No
`FUNCTION` -> `MODELRUN`	candidate_training_target	REQUIRES_OUTCOME	No
`MODELRUN` -> `PREDICTION_CARD`	writes_prediction_object	SPEC_READY_EMPTY	No
`PREDICTION_CARD` -> `OUTCOME`	prospective_comparison	LOCKED_NO_OUTCOME	No
`OUTCOME` -> `CLAIM_BOUNDARY`	could_update_claim_boundary_after_validation	FUTURE_ONLY	No

Boundary. This contract executes the object layer and network rules. It does not emit a DMD pathway delta, cell-state delta, functional effect, calibrated response probability, clinical recommendation or therapeutic target ranking. v1.0 is a database and evidence-governance release; it is not a validated disease-prediction or clinical decision-support release.