GenoMAS
VerifiedMulti-agent framework for automated gene expression analysis and discovery.
What is GenoMAS?
GenoMAS combines a general multi-agent framework with a specialized genomics implementation. Agents communicate via typed messages, follow notebook-style steps for planning and debugging, and support custom roles for domain tasks.
The genomics component pulls data from GEO and TCGA, identifies relevant genes, and produces findings backed by literature checks. It balances structured workflows with agent flexibility for reliable results.
This tool targets researchers in computational biology and AI-driven science who need reproducible automation for large-scale expression studies.
What you can build with GenoMAS
Transcriptomic dataset analysis
Load GEO or TCGA data and run multi-step code workflows to detect trait-related genes while controlling for confounders.
Benchmark evaluation
Execute experiments on GenoTEX to measure performance against other agents and validate output quality.
Literature-supported discovery
Generate gene associations, cross-check high-confidence results with existing papers, and flag novel candidates for follow-up.
Install GenoMAS
conda create -n genomas python=3.10 && pip install -r requirements.txtconda create -n genomas python=3.10
conda activate genomas
pip install -r requirements.txt- 1Download the GenoTEX input data (~42 GB) from the provided Google Drive folder and place it in the parent directory.
- 2Run the validator script to confirm data integrity before proceeding.
- 3Create a conda environment with Python 3.10 and install packages from requirements.txt.
- 4Copy env.example to .env and add at least one LLM provider API key.
- 5Launch experiments using the command-line interface with model, version, and API index arguments.
GenoMAS: pros & cons
Pros
- +Strong benchmark results on gene expression tasks compared to generic agents.
- +Notebook-style execution supports planning, debugging, and backtracking.
- +Customizable agent roles and communication protocol for different domains.
- +Open-source code with clear setup for reproducible experiments.
Cons
- –Requires downloading a large 42 GB dataset before use.
- –Depends on external LLM API keys and associated costs.
- –Primarily focused on genomics, limiting immediate use in other fields.
Frequently asked questions
It analyzes publicly available transcriptomic datasets from GEO and TCGA.
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