README.md

ProteInfer

ProteInfer is an approach for predicting the functional properties of protein sequences using deep neural networks.

📝 Read about the method in our interactive paper (or in the static version, published in eLife).

Usage instructions

Go to https://google-research.github.io/proteinfer/ to use an interactive demo in your browser, and read the related paper.

Or if you're interested in the command line interface instead, see below.

Install gcloud on your local machine if you don't have it installed

sudo apt install -y google-cloud-sdk
gcloud auth login

Create GCP instance with a GPU

gcloud compute instances create proteinfer-gpu --machine-type n1-standard-8 --zone us-west1-b --accelerator type=nvidia-tesla-v100,count=1  --image-family ubuntu-2004-lts --image-project ubuntu-os-cloud --maintenance-policy TERMINATE --boot-disk-size 250

ssh into the machine

# You may need to wait ~30 seconds for the machine to boot up first.
gcloud compute ssh proteinfer-gpu

Install cuda dependencies for GPU support

sudo apt update
sudo add-apt-repository ppa:graphics-drivers -y

wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/cuda-keyring_1.0-1_all.deb -O /tmp/cuda-keyring_1.0-1_all.deb
sudo dpkg -i /tmp/cuda-keyring_1.0-1_all.deb

sudo bash -c 'echo "deb http://developer.download.nvidia.com/compute/machine-learning/repos/ubuntu1804/x86_64 /" > /etc/apt/sources.list.d/cuda_learn.list'
sudo apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/machine-learning/repos/ubuntu1804/x86_64/7fa2af80.pub

sudo apt update
sudo apt install -y cuda-10-0 libcudnn7

Install local python virtual environment

sudo apt update
sudo add-apt-repository ppa:deadsnakes/ppa -y
sudo apt install -y python3-venv python3.7 python3-pip python3.7-venv 
mkdir ~/python_venv
cd ~/python_venv
python3.7 -m venv proteinfer
source ~/python_venv/proteinfer/bin/activate
cd ~

Get our code from github and install python dependencies (e.g. numpy)

git clone https://github.com/google-research/proteinfer
cd ~/proteinfer
pip3 install -r requirements.txt

Run our code on test sequences

cd ~/proteinfer
python3 install_models.py
python3 proteinfer.py -i testdata/test_hemoglobin.fasta -o ~/hemoglobin_predictions.tsv

# View your predictions.
cat ~/hemoglobin_predictions.tsv

Copy your sequences as a fasta file to the GCP instance

# exit the ssh session by typing ctrl D
gcloud compute scp <YOUR_FASTA_FILE_HERE> proteinfer-gpu:~/
# Then ssh back in again
gcloud compute ssh proteinfer-gpu
# Then run your inference
python3 proteinfer.py -i ~/<YOUR_FASTA_FILE_HERE> -o ~/predictions.tsv

Delete the instance when you're done to save money

gcloud compute instances delete 'proteinfer-gpu'

Running unit tests

bash -c 'for f in *_test.py; do python3 $f || exit 1; done'