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GeMI Tool

Welcome to the Genomic Metadata Integration tool! with this web-tool is possible to extract structured tables from the metadata of all the experiments contained in the Gene Expression Omnibus.

KDD promo video

Installation

  • Install the last version of Docker
  • Download the containers with the commands:
    docker pull 2603931630/gemi:frontend
    docker pull 2603931630/gemi:backend
  • Download the repository:
    git clone https://github.com/armando2603/gemi
  • Install the nodes.js dependencies:
    docker run --rm -it -v "/$(pwd)/gemi/frontend/:/usr/src/app/" -p 51111:8080 2603931630/gemi:frontend npm install
  • Download the pretrained model at this link drive
  • Copy the downloaded file in the background/Models/ folder

Usage

  • Run the containers:
    docker run -d --rm -it -v "/$(pwd)/gemi/frontend/:/usr/src/app/" -p 51111:8080 2603931630/gemi:frontend quasar dev && docker run -d -v "/$(pwd)/gemi/backend/:/workspace/" -p 51113:5003 -it --rm --gpus all 2603931630/gemi:backend flask run -p 5003 -h 0.0.0.0
  • In the browser go to the page http://localhost:51111/#/

Remember that you need a gpu NVIDIA in your machine

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