A tool-first, calibrated multi-agent system for RNA bioinformatics design and analysis. The language model orchestrates, reviews and reports — every designed molecule traces to a deterministic generator call, and every prediction claim is checked against the measured capability of the tool that produced it.
The system packages 41 scientific tools (20 vendored external repositories) behind local microservices and exposes them through 11 domain workflows: mRNA design (CDS and full-length), siRNA and ASO design, sgRNA design, RNA structure prediction and inverse folding (secondary and tertiary), aptamer design, RNA–ligand and RNA–protein interaction scoring, and IRES prediction.
git clone --recurse-submodules https://github.com/xlab-BioAI/RNADesignAgent.git
cd RNADesignAgent/rna_agent_system
pip install -r requirements.txt
PYTHONPATH="$(pwd):$PYTHONPATH" python cli/form_chat.pyThe CLI walks you through a resource check, workflow selection, automatic microservice startup and a structured per-workflow form. Three submodules are pinned to patched forks and several services need manually placed model weights — see the deployment guide before your first run.
All documentation lives under rna_agent_system/docs/:
| Document | Purpose |
|---|---|
docs/README.md |
Project overview and quick start |
docs/DEPLOYMENT.md |
Full environment setup, weights, compilation, curl examples |
docs/WORKFLOWS.md |
The 11 domain workflows in depth |
docs/TOOLS.md |
All 41 tools, port registry, microservice notes |
docs/ARCHITECTURE.md |
Seven-layer architecture and core module APIs |
The benchmark datasets used in the paper are included under
rna_agent_system/data/benchmarks/
(210-task platform benchmark, 31-session process-aware benchmark, and the
mRNA/aptamer target sets). The frozen final-form datasets, the external
anchor sets, the packaged capability map and the model-usage register are
deposited at Zenodo under DOI 10.5281/zenodo.22736194.
See docs/README.md §8 for how to
reproduce a benchmark task through the CLI.
Released under the license in LICENSE.