README.md

# Containers for Genomic API for Model Evaluation (GAME) using DREAM-RNN Model

Authors Nikita Penzin, Ivan V Kulakovskiy, Ilya Vorontsov, Dmitry Penzar

## The Predictor container (`predictor.sif`) includes:

- Predictor script for sequence processing and error handling.
- Integrated MPRALegNet model with its dependencies and LegNet conda environment created using legnet_environment.yml.
- Pre-trained model weights (k562_best_model_test1_val2.ckpt, hepg2_best_model_test1_val2.ckpt, wtc11_best_model_test1_val2.ckpt) for predictions downloaded from https://zenodo.org/records/10558183.
- Support scripts like:
  - api_preprocessing_utils.py
  - error_checking_functions.py
  - predictor_help_message.json.
- Dependencies required by the Predictor.

## The Evaluator container (`evaluator.sif`) includes:

- Evaluator API script for genomic sequence evaluation.
- Dependencies required by the Evaluator.

## Evaluator data directory (`evaluator_data.zip`)
This ZIP file contains sample JSON data for testing the Evaluator container. 

Contents:
  - evaluator_message_gosai_5seqs.json (Default input)
  - evaluator_message_more_complex.json
  - evaluator_message_simple_test.json
  - evaluator_input_sample_test.json

## Important Notes:
1. Input JSON file restriction:
    1. Currently, the script in this container can only process `evaluator_message_simple_test.json` as input. 
    2. If a different JSON needs to be tested, please rename the JSON file to 'evaluator_message_simple_test' to allow for the script to be able to find the mounted path in `evaluator_data/`
2. Predictions directory must be created:
    1. Before running the Evaluator container, please also create and mount predictions/ directory.
Additional information can be found on GitHub: [Genomic Model Evaluation API](https://github.com/de-Boer-Lab/Genomic-Model-Evaluation-API)
MPRALegNet Model-specific information can be found within the same repository: MPRALegNet(will be availabe later)