Single Cell Explorer

Thank you for visiting wiki of Single Cell Explorer. Singel Cell Explorer is available open-source under the GNU LGPLv3 license. This web application only run on Linux.

Authors: Di Feng, Dechao Shan

Contact: di_feng@yahoo.com

Site URL:

http://singlecellexplorer.org

http://54.159.6.229:8000/

Source code, database files, python scripts for Jupyter notebook

http://54.159.6.229/download.html

Jupyter Notebook walkthrough

http://54.159.6.229/analysis.html

Installation guide

http://54.159.6.229/install.html

Installation of Single Cell Explorer from Source

quickest way: run setup shell scripts from http://54.159.6.229/downloads/setupSCexplorer.sh

From console (step by step)

Update (based on ubuntu 18.04 or 16.04)

sudo apt-get update

sudo apt-get install -y build-essential

sudo apt-get install -y ssh libssl-dev libffi-dev libxml2-dev libxslt1-dev zlib1g-dev zip unzip libfftw3-dev libcurl3 openssl

Install python3

sudo apt-get install -y python3 python3-pip python3-dev

Install MongoDB, create database paths, and start MongoDB server

cd ~

mkdir -p mongodb

cd mongodb

wget https://fastdl.mongodb.org/linux/mongodb-linux-x86_64-ubuntu1604-4.0.10.tgz

tar -zxvf mongodb-linux-x86_64-ubuntu1604-4.0.10.tgz

mkdir scdb

mkdir log

sudo ./mongodb-linux-x86_64-ubuntu1604-4.0.10/bin/mongod --dbpath "./scdb" --port 27017 --wiredTigerCacheSizeGB 1 --fork --logpath "./log/scdb.log"

Load database schema & sample data into MongoDB

cd ~/mongodb/

wget http://54.159.6.229/downloads/scDB.zip

unzip scDB.zip

mkdir dumpfiles

mv scDB dumpfiles

mongodb-linux-x86_64-ubuntu1604-4.0.10/bin/mongorestore dumpfiles

Launch Single Cell Explorer web application

sudo pip3 install --upgrade pip

sudo pip3 install numpy gunicorn pymongo sklearn pandas django==2.2 torchvision

cd ~

mkdir singleCell

cd singleCell

wget http://54.159.6.229/downloads/singleCellExplorer.zip

unzip singleCellExplorer.zip

cd singleCellExplorer

python3 manage.py runserver 0.0.0.0:8000