RiboGL

Repository of "Towards improving full-length ribosome density prediction by bridging sequence and graph-based representations". The dataset files can be found here: https://zenodo.org/records/12180308

RiboGL Model

Plotly Server

Setup

Inside the interpret subfolder one can find the code to run the Plotly server to intepret the RiboGL predictions.

In order to run the server:

1. Install the dependecies in a conda envirorment ribogl (arbitrary name):

   conda env create -n ribogl -f interpret/requirements.yaml

2. Download the data from https://zenodo.org/records/12180308 into the data subfolder.
3. Extract RiboGL_Attributions.h5.gz into RiboGL_Attributions.h5 using gzip -d RiboGL_Attributions.h5.gz. The uncompressed size will be around 43 GB.
4. Run the server:

   conda activate ribogl
   python interpret/app.py --port 8050

   The server will be available at http://localhost:8050/. The port can be changed with the port argument.