Borzoi Human Model Predictor (Linder et al. 2025) using the Genomic API for Model Evaluation (GAME) Framework

This record provides a Predictor container for the Borzoi human model (Linder et al. 2025, Nature Genetics). Borzoi is a deep learning model that predicts cell-type and tissue-specific RNA-seq coverage directly from DNA sequence, enabling interpretation of genetic variants across multiple layers of gene regulation, including transcription, splicing, and polyadenylation. It is trained on human RNA-seq data from ENCODE (with 866 datasets across diverse biosamples, including cell lines and adult tissues) and Genotype-Tissue Expression (GTEx) data (with 2-3 replicates for each tissue, processed by the recount3 project). The training dataset also includes epigenomic datasets from the Enformer model, such as CAGE, DNase-seq, ATAC-seq, and ChIP-seq tracks. The Predictor container (borzoi_human_predictor.sif) includes: Predictor script for sequence processing and error handling. Integrated Borzoi model with its dependencies and borzoi-gpu conda environment created using borzoi_gpu_environment.yml. Baskerville and Borzoi packages, installed from local source copies of repositories (as of March 2025), which also contain helper scripts and 4 replicate model weights. Support scripts like: api_preprocessing_utils.py, error_message_functions_updated.py, predictor_help_message.json. NOTE: This container requires a GPU for execution because the Borzoi model relies on TensorFlow's GPU-accelerated operations. Running the container: Ensure Apptainer is intalled in the system the container is intended to run. Always run the Predictor first, so it can listen for incoming connections from Evaluators: apptainer run --containall --nv borzoi_human_predictor.sif HOST_IP HOST_PORT MATCHER_IP MATCHER_PORT Additional information about the GAME framework can be found on GitHub: Genomic API for Model Evaluation Borzoi Human Predictor-specific information, along with a sample Evaluator, can be found within the same repository: Borzoi Predictor Code repository for Borzoi models: Borzoi GitHub Paper can be found here: Linder, J., Srivastava, D., Yuan, H. et al. Predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation. Nat Genet 57, 949–961 (2025). https://doi.org/10.1038/s41588-024-02053-6

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