BioHub is a software tool for synthetic biologists developed by USTC-Software. It aims at helping synthetic biologists to deal with data from different types such as regulatory proteins, regulatory elements in gene expression.
BioHub is done using an extensive plug-in system with some handy utility such as pathway-finding, one key blast and quick query. Users can have their own personalized Biohub according to their need.
If you just want to try it, please visit our example website biohub.tech.
We strongly recommend you to use Chrome web browser, since other browsers are not fully supported.
We suggest users use Docker to deploy BioHub. It just needs two steps:
docker run -d --name biohubdb -e MYSQL_ROOT_PASSWORD=password mysql
docker run -d --name biohub --link biohubdb:db -p 80:5000 biohubtech/biohub
You can also use -e BIOHUB_DB_HOST=<host> and/or -e BIOHUB_DB_USER=<user> -e BIOHUB_DB_PASSWORD=<password> to connect to other databases.
Also, you can clone the repo and run it manually. We've tested this on Debian 8:
sudo apt update
sudo apt install git python3 python3-pip python3-biopython python3-flask python3-sqlalchemy python3-scipy libmysqlclient-dev mysql-server mysql-client wget
git clone https://github.com/igemsoftware2016/USTC-Software-2016.git
cd USTC-Software-2016
sudo pip3 install flask_login mysqlclient pymysql
echo CREATE DATABASE biohub | mysql -u<user> -p # please fill in the blanks
wget http://parts.igem.org/partsdb/download.cgi?type=parts_sql -O biobricks.sql.gz
gunzip biobricks.sql.gz
mysql -u<user> -p biohub < biobricks.sql # please fill in the blanks
mysql -u<user> -p biohub < ncbi_562.sql
echo "DATABASE_URI = 'mysql://<username>:<password>@localhost/biohub'" >config.py # please fill in the blanks
echo "SECRET_KEY = '<a random string>'" >>config.py # please fill in the blanks
./run.py
# then the server will start on port 5000
After the installation, only one of the species databases is imported for demo. You can download databases from NCBI and import them manually by our script.
Copy and run the code below to install ABACUS:
We assume that USTC-Software-2016 is the path to our git repo.
wget http://download.biohub.tech/ABACUS.tar.gz
wget http://download.biohub.tech/ABACUS.db.tar.gz
tar -xvzf ABACUS.tar.gz
tar -xvzf ABACUS.db.tar.gz
mv ABACUS $BioHubPath/USTC-Software-2016/plugins/ABACUS/
# $BioHubPath is the path you install BioHub
cd $BioHubPath/USTC-Software-2016/plugins/ABACUS/ABACUS/
sh setup.sh
# You will get a message like set ABACUSPATH=$BioHubPath/USTC-Software-2016/plugins/ABACUS/ABACUS
export ABACUSPATH=$BioHubPath/USTC-Software-2016/plugins/ABACUS/ABACUS/
# Don’t forget the last slash
cd bin
mkdir pdbs
# If you are on Intel platform, please do the following steps
rm psdSTRIDE
wget http://download.biohub.tech/psdSTRIDE
# All done!
Goto root direction, open ncbiuploader.py. Change filepath to the path you store NCBI data file, and change column_num to the number of columns in data file.
It’s recommended to download file from following url:
ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/GENE_INFO/All_Data.gene_info.gz, column_num=15.
ftp://ftp.ncbi.nlm.nih.gov/pub/biosystems/biosystems.20161008/biosystems_gene_all.gz, column_num=3
Add index for tables:
alter table biosystems add index all_index (gene_id, bsid);
alter table allgeneinfo_all add index all_index (gene_id, tax_id, Symbol);
alter table allgeneinfo_all add fulltext('Symbol');
To create database for pathfinder, execute the following SQL statement:
create table biosys_562 (
id int primary key AUTO_INCREMENT,
gene_id char(10),
tax_id char(10),
bsid int,
Symbol char(64));
alter table biosys_562 add index all_index(gene_id, bsid);
insert into biosys_562 (gene_id, tax_id, bsid, Symbol)
select a.gene_id, a.tax_id, b.bsid, a.Symbol
from allgeneinfo_all a, biosystems b
where a.gene_id = b.gene_id and a.tax_id='%tax_id%';