3DBIONOTES-WS v3.10.2

Integrating molecular biology

3DBIONOTES-WS is a web application designed to automatically annotate biochemical and biomedical information onto structural models. Current sources of information include:

• post-translational modifications
• genomic variations associated to diseases
• short linear motifs,
• immune epitopes sites,
• disordered regions and
• domain families.

Setup

Setup Development

Use rvm or rbenv to select the Ruby version specified in Gemfile and then run:

$ git submodule update --recursive --init
$ rvm install ruby-2.4.1
$ gem install bundler:2.2.15
$ sudo apt install libgsl-dev libmysqlclient-dev # Debian/Ubuntu
$ bundle install
$ cp config/database.example.yml config/database.yml
$ cp config/secrets.example.yml config/secrets.yml
$ bundle exec rake db:migrate RAILS_ENV=development
$ bundle exec rails server

Setup Developent on macOS

Before you start your setup, make sure you have homebrew, ruby, rvm and python2 installed. Use rvm or rbenv to select the Ruby version specified in Gemfile and then run:

$ git submodule update --recursive --init
$ rvm install ruby-2.4.1
$ gem install bundler:2.2.15
$ brew install gsl mysql
$ gem install bundler:2.0.0.pre.3

In the Gemfile, remove Gem specs for mini_racer and libv8 and the dependency for mini_racer

$ bundle _2.0.0.pre.3_ install
$ cp config/database.example.yml config/database.yml
$ cp config/secrets.example.yml config/secrets.yml
$ bundle exec rake db:migrate RAILS_ENV=development
$ bundle exec rails server

Setup Viewer

If you want to set up the React protein viewer as well, open up a separate terminal tab (while the Ruby app is running!) and run:

$ cd app/assets/javascripts/3dbio_viewer/
$ yarn install
$ yarn start

Then go to localhost:3001 and you'll see the viewer!

Setup Production

Add Passenger setup to /etc/apache2/apache2.conf:

LoadModule passenger_module /services/bionotes/.rvm/gems/ruby-2.4.1@bionotes/gems/passenger-5.1.12/buildout/apache2/mod_passenger.so
   <IfModule mod_passenger.c>
     PassengerRoot /services/bionotes/.rvm/gems/ruby-2.4.1@bionotes/gems/passenger-5.1.12
     PassengerDefaultRuby /services/bionotes/.rvm/gems/ruby-2.4.1@bionotes/wrappers/ruby
     PassengerMaxPoolSize 64
     PassengerMinInstances 32
     PassengerPoolIdleTime 60
   </IfModule>

The site configuration file (/etc/apache2/sites-enabled/bionotes) for Apache should like this:

<VirtualHost *:80>
   ServerName XXX.cnb.csic.es
   PassengerRoot /services/bionotes/.rvm/gems/ruby-2.4.1@bionotes/gems/passenger-5.1.12
   PassengerRuby /services/bionotes/.rvm/gems/ruby-2.4.1@bionotes/wrappers/ruby
   DocumentRoot /services/bionotes/apps/bionotes/public
   RailsEnv production
   <Directory /services/bionotes/apps/bionotes/public>
      # This relaxes Apache security settings.
      AllowOverride all
      # MultiViews must be turned off.
      Options -MultiViews
      # Uncomment this if you're on Apache >= 2.4:
      #Require all granted
   </Directory>
</VirtualHost>

And finally, run:

$ rvm install ruby-2.4.1
$ passenger-install-apache2-module --auto
$ sudo a2ensite bionotes
$ sudo ln -s /services/bionotes/apps/node/bin/node /usr/local/bin/node
$ RAILS_ENV=production bundle exec rake assets:precompile
$ sudo /etc/init.d/apache2 restart

To perform an app restart after a change, just run:

$ touch tmp/restart.txt

Delayed Jobs

The network sections run a set of jobs in the background on the server. To work properly, a delayed job daemon needs to be running on the server:

$ RAILS_ENV=production bin/delayed_job -n 6 restart

Sub-modules

The application contains two git sub-modules:

• myProtVista

  • Repository: https://github.com/3dbionotes-community/myProtVista
  • Path: app/assets/javascripts/annotations_viewer/myProtVista
  • Installation dependencies: node version 8
  • How to install:

    $ npm install
    $ npm run build
    

• extendProtVista

  • Repository: https://github.com/3dbionotes-community/extendProtVista
  • Path: app/assets/javascripts/annotations_viewer/extendProtVista
  • Installation dependencies: node version 8
  • How to install:

    $ npm install
    $ npm run build
    

Some extra modules are also part of the application:

• featureAnalysis

  • Path: app/assets/javascripts/annotations_viewer/featureAnalysis
  • Installation dependencies: node version 8
  • How to install:

    $ npm install
    $ npm run build
    

• structure_viewer

  • Path: app/assets/javascripts/structure_viewer
  • Installation dependencies: node version 8
  • How to install:

    $ npm install
    $ npm run build
    

• interface_viewer

  • Path: app/assets/javascripts/interface_viewer
  • Installation dependencies: node version 8
  • How to install:

    $ npm install
    $ npm run build
    

Other dependencies

• ngl

  • Repository: https://github.com/arose/ngl

• jsmol

  • Path: app/assets/javascripts/jsmol

Copyright (c) 2020, Biocomputing Unit, CNB-CSIC