GSurgeon is an AI tool to dissect biology of model organisms through genomic information. It leverages LLM capabilities to send dynamic requests in natural language to genomic databases and extract any biological information.
GSurgeon has been tested on questions related to model organisms involving markers, genes and traits.
As such it has good performance on queries such as:
- Which genes on chromosome 1 of the mouse genome are related to inflammation and diabetes at the same time?
- List traits measured in GeneNetwork that are related to diabetes.
Other queries in the realm of biology and genomics are also possible.
You can clone this repository.
git clone https://github.com/johanmed/gsurgeon.gitGSurgeon expects a number of parameters to be defined for the surgery:
- N_ITERATIONS: number of operations
- MODEL_NAME: DSPy model identifier
- API_KEY: provider key
- EMAIL: email address for NCBI authentication
We recommend creating them in an environment file. For more details, see file env_example.
export PATH="$PATH:/path/to/project"Replace the path above by yours. You can also add it to your file ~/.bashrc.
gsurgeon --env-file env_example "Which genes on chromosome 1 of the mouse genome are related to inflammation and diabetes at the same time?"Replace the query above by yours.
Accessing genomic information is a pain. It requires knowledge of right databases to query but also skills to dig deep and find relevant information. GSurgeon makes the process easier for the community by providing a simpler, yet powerful interface to interact in real time with biological databases.
In the research ecosystem, this can be used for a variety of applications:
- literature review
- cross-checking of research findings against current knowledge
- hypothesis exploration
- biological link discovery
- advanced bioinformatic analyses
Despite advances in language AI, hallucination remains a serious concern in biological research. GSurgeon offers a scalable solution by grounding generation in true information from biological databases. Current databases supported include:
- GeneNetwork: database service to explore biology of model organisms with bioinformatic tools
- NCBI: database service for access and analysis of biological information
GSurgeon exploits reasoning capabilities of LLM to orchestrate the search of biological information. Using its knowledge of biological databases, it finds dynamically the best approach of answering or completing the task you have in mind.
The execution logic is abstracted to give full control to the agents. No need for extra coding!
The tool footprint is lightweight. Most of the computational resources required to run the system are handled by the provider. No need to have monstruous specs to get started!
GSurgeon can be executed on the command-line on any model, provided sufficient training.