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CoSci

Worked example

CoSci ships with a complete, reproducible worked example: the DNA replication–transcription conflict case, run end to end with real tools. It’s the fastest way to see the whole lifecycle actually work.

Run it

Terminal window
cd backend
RC_OFFLINE=0 RC_USE_TOOLS=1 RC_DATA_DIR=$PWD/data_walkthrough \
    uv run python walkthrough_conflict.py
# → test-results/conflict-walkthrough/REPORT.md  (+ 10 step JSONs)

What it does

In one run, CoSci:

  1. Incubates the idea and sweeps the literature for it.
  2. Resolves 4 E. coli proteins — RpoB, DnaB, Mfd, Rep — to real UniProt accessions, with InterPro domains and PDB structure counts.
  3. Designs a killer experiment that passes the kill-criteria gate.
  4. Writes a proposal, then citation-checks the claims against real 2024–26 papers.

What you get

A readable REPORT.md plus a JSON artifact for each of the ~10 steps, so you can inspect exactly what happened at every stage — the questions, the resolved entities, the experiment and its kill-criteria, and the citation audit.

Because it runs with real tools, this is also a good smoke test that your providers and ToolUniverse are wired up correctly.