FORECasT

Favoured Outcomes of Repair Events at Cas9 Targets

FORECasT is a web application that gives access to a predictor of Cas9 editing outcome resulting from Cas9-induced double strand breaks. The paper is available on BioRxiv, and the application itself at https://partslab.sanger.ac.uk.

The application consists of two components: a React front end (this repository) and a predictor. Having it as two separate servers allows to decouple the model from the interface and develop both components independently.

Running

Locally

1. Start predictor server (see README). According to instructions, it will run on port 5001

2. Install packages and run the FORECasT server, it will be opened in a browser automatically

   npm install
   REACT_APP_MODEL_HOST=http://127.0.0.1:5001 npm run start

With Docker

docker pull quay.io/cellgeni/mprofile-web
docker pull quay.io/felicityallen/selftarget
docker network create forecast-net
docker run -d --name selftarget --net forecast-net quay.io/felicityallen/selftarget
docker run -d --name forecast -p 80:80 --net forecast-net -e "REACT_APP_MODEL_HOST=http://selftarget:8006" quay.io/cellgeni/mprofile-web

Open http://127.0.0.1 in browser

Cleaning up

docker rm -f selftarget forecast
docker network rm forecast-net

With Kubernetes

1. Check FORECasT and SelfTarget Docker images for the latest tags and update corresponding tags in k8s/forecast.deployment.yaml and k8s/predictor.deployment.yaml in "spec > template > spec > containers > image"
2. Deploy each component:

   kubectl apply -f k8s/forecast.deployment.yaml
   kubectl apply -f k8s/forecast.service.yaml
   kubectl apply -f k8s/predictor.deployment.yaml
   kubectl apply -f k8s/predictor.service.yaml
   

3. An external IP for the forecast service will be requested and assigned from the infrastructure provider. It can take a couple minutes.

   $ kubectl get services
   NAME              TYPE           CLUSTER-IP      EXTERNAL-IP     PORT(S)          AGE
   predictor         NodePort       10.233.48.4     <none>          80:31935/TCP     16d
   forecast          LoadBalancer   10.233.47.253   172.27.18.205   8000:32146/TCP   16d

   If EXTERNAL-IP is stuck in pending state, check the reason with kubectl describe service forecast.