gsurgeon 1.0.0

A tool to dissect biology of model organisms using genomic information

GSurgeon: the genomic surgeon

What is GSurgeon?

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.

What questions can you ask GSurgeon?

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.

How to install and run GSurgeon?

1. Get the source code

You can clone this repository.

git clone https://github.com/johanmed/gsurgeon.git

2. Set tool parameters

GSurgeon 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.

3. Add gsurgeon path to your search path

export PATH="$PATH:/path/to/project"

Replace the path above by yours. You can also add it to your file ~/.bashrc.

4. Run your query

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.

Why use GSurgeon?

1. Access to up-to-date biological information

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

2. Prevent hallucination, trust a bit more language models used in biology

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

3. Empower your LLM to handle with surgical precision the hard work for you with no limits

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.