Graphical User Interface for DNA Editing Screens (GUIDES)
Description: Genome-scale CRISPR-Cas9 knockout libraries have emerged as popular tools for unbiased, phenotypic screening but easy-to-use software for designing customized guide RNA libraries has lagged behind. GUIDES is a web application for automated, tissue-specific library design. It integrates on-target scores, expression data, and protein structure into an easily accessible web interface.
- Technology stack: Python/Flask backend with Angular.js front-end.
- Status: Release (1.0)
- Links to production or demo instances: Hosted on the Sanjana Lab's website.
- Recently, library design tools such as CRISPR Library Designer have used on-target efficiency scoring to help automate guide design. In addition to on-target scores, our tool integrates expression data and protein structure, while also providing a more easily accessible web interface.
Most of the front-end code is written in Coffeescript. Angular.js is used as a front-end framework.
Redis is used for local storage. Celery is used for background processing.
Static data files which are too large for hosting on GitHub must also be added. Installation is described below.
After pulling this repository, change the current directory to the GUIDES root folder.
First, setup a Python virtual environment by executing
virtualenv venv from the root directory of the repository. Activate the virtual enviornment by executing
Then, install the required Python modules by running
pip install -r requirements.txt. At this point, the virtual environment can be deactivated by executing
Next, install node modules by executing
npm install from the GUIDES root folder.
Next, substitute the folder
static/data with the
data folder from the Zhang Lab Dropbox.
Alternatively, run ./install.sh from the GUIDES root folder.
Next, open 3 terminal windows. Run the following commands in each window:
source venv/bin/activate export DEV=false export PORT=YOUR_PORT export SMTPenabled=false
To enable emailed summaries of library generation, instead run the following commands in each window:
source venv/bin/activate export DEV=false export PORT=YOUR_PORT export SMTPenabled=true export SMTPserver=YOUR_SMTP_SERVER export SMTPsender=donotreply@YOUR_DOMAIN export SMTPpassword=YOUR_SMTP_PASSWORD
Then, run the following 3 commands, in this order (one in each window):
celery worker -A app.celery
How to test the software
Code for running the tests in our manuscript is located in
static/data/functional_tests. Some data analysis is required to produce the plots included in our paper.
Feel free to reach out to the GUIDES team at firstname.lastname@example.org.
Please get in touch if you are interested in contributing, so we can coordinate our efforts. In particular, we are interested in expanding our tool to include more species.
Open source licensing info
Copyright (c) 2015-2017 Joshua Meier, Feng Zhang and Neville Sanjana. Released under BSD 3. See LICENSE file for details.
If you're interested in getting access to this system under a different license, please contact us.