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Contributions (work in progress)

Work in progress

Contributions are a design under active development. This page describes the intended model; the tooling is not yet implemented.

A contribution is a unit of contribution that an individual or a group offers to everyone else. It is the building block of a compositional choreography (see Choreographies): a lab or centre poses a question, and each contributor offers a contribution that tackles it from their own angle.

A contribution is deliberately general. Contributors' approaches span the whole spectrum from classic low-throughput human biology to a fully AI-driven algorithm, and no single contribution need answer the whole question; each may add insight.

Steps and transitions

A contribution is built from two kinds of component, which are themselves offerable and reusable across groups:

  • A step applies an analysis to data, transforming an input X' into a new output X'' (a docking calculation, a binding assay, a generative model run).
  • A transition inspects a step's output and makes a decision: rank, filter, or select (given a set of generated analogues, keep the plausible binders and rank the top 100).

Steps and transitions chain into a small graph. A contribution eventually produces an output that is expressed for people to read (a figure, a spreadsheet, an HTML report), by the Artist.

What a contribution declares: the output contract

For contributions to be combined, each contribution declares a typed output contract describing the shape and meaning of what it produces:

  • a candidate-identity key: the shared identifier that lets two contributions refer to the same thing (for a small-molecule problem, an InChIKey or SMILES);
  • the metric it reports, its units, and its direction (is higher better?);
  • an uncertainty estimate.

The contract is recorded as Tier-2 memory, a schema-validated entry carrying frontmatter the same way Oracle entries do, so it is durable and human-readable. The contribution's output is served at runtime through an MCP server, and any bulk data it references lives in Tier-3 append_only/ storage. The candidate-identity key is the join column that makes "where do these contributions agree or disagree?" a well-defined question.

Offering a contribution: methods and services

A contribution is offered to everyone. There are two cases, with different governance:

  • A method contribution is a shared recipe that anyone can run on their own data. Offering it requires nothing beyond publishing it to the contribution catalog.
  • A service contribution requires the offering party to act on their own resource (run their instrument, use their private data). Using a service contribution across a group boundary keeps a governance gate: the offering group's PI approves the request, and a data-access grant scopes what the requester may see. This is the cross-group governance that the earlier "SEA" concept carried; SEA is retired, and the gate is re-homed onto service-contribution use.

Example

A lab decides that optimizing a Pin1 inhibitor (say, sulfopin) matters. Three members offer contributions from different points on the spectrum:

  • a wet-lab biochemist offers a contribution whose step is a binding assay and whose transition ranks measured affinities;
  • a computational chemist offers a contribution that docks candidate analogues and filters by predicted binding energy;
  • an ML researcher offers a contribution whose step generates analogues with a model and whose transition scores and shortlists them.

Each contribution declares the same candidate-identity key (the molecule), so their outputs can be aligned even though their metrics differ (a measured K_D in nM, a docking score in kcal/mol, a model score). How these contributions combine into one answer is the job of the choreography's judge; see Choreographies.

In the dashboard

A member authors contributions privately in their vault (<vault>/contributions/, via murmurent contribution spec new). The dashboard's My contributions panel lists them, each showing the question it answers, its output contract as a compact signature (candidate_key → metric (units) direction), and its step/transition counts.

To make a contribution known to the group as an offered method or service, the member states it: the panel's state to group action publishes the contribution — its spec and its contract — into the group's governance repo under contributions/ (a sibling of choreographies/). Two things then work that could not before: other members see the offered contribution, and a choreography (which lives in the same repo) can resolve it to check joinability. Authoring stays private; stating is the deliberate step that shares. A choreography assembles stated contributions — see Choreographies.