2.0.0

First public release of the code behind the preprint "LLM-based agents can autonomously generate, execute, and refine in silico models" (Chandratre et al., 2026).

The release contains the benchmark runner, the Morpheus skill and MCP server, the biological scoring criteria with the automated scorer (latest versions), and the analysis and figure scripts. The subject-facing files are those of benchmark version 3, which produced the preprint's main results. The README section "Reproducing the preprint" lists the software versions, the run commands and a demo that regenerates the comparison statistics from the deposited runs in about 10 s.

The paper PDFs are not included; benchmark_papers/papers.csv gives their DOIs. The benchmark runs and manual scores are archived in a separate Zenodo dataset.