BioInformatics Agent (BIA): Unleashing the Power of Large Language Models to Reshape Bioinformatics Workflow

Installation

pip install -e .

Examples

Set up your API key first

# for dashscope
export DASHSCOPE_API_KEY="<your_api_key>"
# for openai
export OPENAI_API_KEY="<your_api_key>"
export OPENAI_API_BASE="<your_api_base>"

Search for samples

biagent geo_search "breast cancer"

Metadata extraction

Extract metadata from a chosen GEO sample, e.g.,

biagent --model qwen-max metadata --gsm_id GSM3676057

The tool also supports processing multiple GEO samples provided in a line separated text file, e.g.,

head -n 1 gse_soft_files.txt
# /path/to/GSE132nnn/GSE132396/soft/GSE132396_family.soft.gz
biagent --model qwen-max metadata --soft_file_list gse_soft_files.txt --parallel 2 --output metadata.csv --cache_dir $PWD/cache

Count matrix reading

Read the count matrix from a chosen GEO sample, e.g.,

biagent --model qwen-max count_matrix --gsm_id GSM3676057 --output count_matrix.h5ad

Pipeline extraction

Extract the pipeline from a given paper in markdown, e.g.,

biagent --model gpt-4o pipeline_extractor --parsed_paper <path_to_paper_markdown> --output pipeline.html

Roadmap

• [ ] Add frontend and backend support for biagent