• 🧬 GWAS → fine-map🔻🧣→ TREDNet 🤖💎 →[..tba..]→ assays 👩‍🔬🧫 → translation 💊

TREDNet is a genomics tool developed at NIH for functional studies with translational potential. It is particularly powerful for diseases where noncoding enhancer variants drive pathology, like type 2 diabetes (T2D). This repo contains BioDataSci's port of the original TREDNet to Google Colab's NVIDIA-GPU environment.

TREDNet_v1.1-colab Setup Instructions

Launch TREDNet.ipynb notebook by clicking . It builds and runs a TREDNet deep learning pipeline on your own Colab managed GPU instance.

The Colab jupyter notebook:

• installs from github TREDNet python code, this file, and large model files
• builds the required TREDNet Conda/Tensorflow environment on a target GPU host
• pulls hg38 (human genome) reference data from a remote server into the GPU instance
• runs the deep learning pipeline on genomic input data and outputs classification results
• shows summary of the TREDNet classification performance results

BioDataSci.com - AI/ML/Ops support

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