edinburgh-genome-foundry / dab

:point_right: EGF Design and Build, the Foundry's DNA design ordering portal

EGF Design And Build

This repository contains the source code of dab.genomefoundry.org, a DNA construct design website of the Edinburgh Genome Foundry.

How is it built ?

This project is based on the CAB boilerplate, making it easy to create new apps with a form in the frontend and custom computations in the backend. It features job queues (with progress feedback for the user), form widgets like file uploaders, help buttons, and many more.

This comes with the following advantages:

• Creating a new app is super simple: just add one file in the front end (for the input form) and one file in the back-end (the code for computations).
• Full live-reload ! The changes you make to your backend or frontend code take effect immediately. No need to refresh a page or restart a server by hand.
• Plenty of easy-to-use library of components to build your user interface without headache, using Element.
• Works on any nachine: one-line install, one-line deploy. No clash with the rest of your system since everything runs inside containers.

User Guide

DAB app requires a good familiarity with Python, Vue, and base knowlege of Docker and Git.

Getting started

The next steps will download, install, and launch DAB on your computer.

1. Install docker and docker-compose on your machine. This step depends on your machine (Windows, Linux, MacOS) so you'll need to google it.

2. Download DAB from Github:

git clone git+github.com/Edinburgh-Genome-Foundry/DAB.git

3. Go to the root DAB/ directory (the one containing this README and the docker-compose.yml) and launch your application in development mode. The first time you try this, Docker will download and build a lot of things, which may take several minutes. It will only take a few seconds the next times you run this command.

docker-compose up

4. Go to your browser and type localhost or 127.0.0.1 in the address bar. You should see the website appear. the console in which you launched docker-compose will keep printing logs of the different components (django, vue) so you can keep track and debug.

How standards are stored / adding a new standard

Deploying the website on the web

The next steps will put your website on the web. Note that many other deployment workflows are possible.

1. Get a hosting server (for instance from Amazon Web Services or Digital Ocean). Get the IP address of this server (we'll assume it is 123.12.123.123).

2. Log in this server (ssh [email protected]) and install Docker and Docker-Compose (some Digital Ocean servers come with these already installed).

3. From your computer, in the DAB root directory, run the following command to create a code repository on the distant server, and register that distant repository under the name prodserver

./init_remote_git.sh [email protected] DAB prodserver

4. On the remote server, in the folder DAB.git, start the website in production mode:

docker-compose -f docker-compose.yml -f docker-compose.prod.yml up -d

5. Wait some time and go in your browser at the address 123.12.123.123, your website should be live !

Every time you want to update the website, from your computer in the DAB root directory run git push prodserver master. You will need to rebuild the containers on the server if you have modified the frontend or added dependencies to the backend (we may simplify this later).

Licence

DAB is an open source software originally written by Zulko, Isaac Luo and Aitor Bleda at the Edinburgh Genome Foundry and released on Github under the MIT licence (¢ Edinburgh Genome Foundry). Everyone is welcome to contribute !

More biology software

EGF Codon is powered by the EGF Codons <https://edinburgh-genome-foundry.github.io/>_ synthetic biology software suite for DNA design, manufacturing and validation.