/histonedb

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View CURATED SET at http://intbio.org/histonedb/CURATED_SET

HistoneDB 3.0

A database for all histone proteins in NR organized by their known non-allelic protein isoforms, called variants. This resource can be used to understand how changes in histone variants affect structure, complex formation, and nucleosome function. For more information, please read our paper (citation below).

The database can be accessed at https://histonedb.bioeng.ru

To test HistoneDB you can use instructions how to run via virtual machine or follow the instructions below.

Requirements

  • Python 3.6.9

  • Required python packages are specified in requirements.txt (use "pip install -r requirements.txt"). They include: --biopython==1.74 --colour==0.1.5 --Django==1.8.19, django-extensions, django-filter --gunicorn>=19.5.0 --mysqlclient --networkx==1.10 --PyMySQL --pyparsing==2.4.6 --numpy, pandas, scikit-learn, scipy, sklearn --matplotlib==1.4.3, seaborn==0.6.0

  • HMMER 3.1b2

  • BLAST+ v 2.2.26

  • EMBOSS v6.5.7

  • MUSCLE v3.8.31

  • ClustalW2 v2.1 All executables must be present in the bin dir of virual environment.

System setup

If you want to test the server on your own machine, you must make sure you have all of the dependencies listed above, or if you have Ubuntu 18.04 you can follow the instructions below:

  1. Change file system_setup/db_setup_query.sql by replacing db_name, db_user and pwd
CREATE DATABASE IF NOT EXISTS db_name;
CREATE USER 'db_user'@'localhost' IDENTIFIED BY 'db_password';
GRANT ALL PRIVILEGES ON db . * TO 'db_user'@'localhost';
ALTER DATABASE db CHARACTER SET utf8 COLLATE utf8_general_ci;
  1. Store the login information in the file HistoneDB/databse_info.txt, which is formatted in the following way (key = value):
name = DB_NAME
user = DB_USER
password = DB_PASS
host = DB_HOST
port = DB_PORT
SECRET_KEY = DJANGO_SECRET_KEY

#Reference another file with same paramters, useful if it needs be hidden
file = /path/to/other/file.txt

#Root of site when accessed from a browser
STATIC_URL = /static/
  1. If running on the mweb, these values will already be set. Finally, make sure the database has the correct charset:
ALTER DATABASE DB_NAME CHARACTER SET utf8 COLLATE utf8_general_ci

  1. To start project run sh run.sh

  2. For reinitialization of DB you can run sh reinit_histdb_local.sh

For more information about server setup and database intitializaition including how to update, rebuild and add new variants you can read HistoneDB setup instructions.

Cite

Coming soon.

Acknowledgements

  • Eli Draizen
  • Alexey K. Shaytan
  • Anna Panchenko
  • Leonardo Marino-Ramirez
  • David Landsman
  • Paul Talbert