1. Requirements

• Python 2.7+ with modules:

  • biopython
  • matplotlib
  • mysqldb
  • networkx
  • openpyxl 1.9+
  • webcolors

• MySQL 5.5+

• optional: libSBML 5.10+ built with python API (requirements: swig, libxml2)

  Suggested command(s) for installation on Ubuntu 14.04

$ sudo apt-get install build-essential mysql-server python-biopython \
python-webcolors python-networkx python-mysqldb python-matplotlib \
libxml2 libxml2-dev python-dev python-pip zlib1g zlib1g-dev bzip2 libbz2-dev
$ sudo pip install python-libsbml
$ sudo pip install openpyxl

1. Suggestions

• phpmyadmin (to more easily inspect database)

• optional: Grant FILE permissions to database user
  Note: Mysql clients connecting to the database server need to enable infile_local to make use of the above!

  Suggested command(s) for installation on Ubuntu 14.04

$ sudo apt-get install phpmyadmin
$ mysql -u root -p
> GRANT FILE ON *.* TO <user>@'%';
> quit

Call ./miRwb.py -h to get an overview of the possible options.

At the moment, it is possible to

• run a database update (-u, (re)parses files in the (data/db_files)[data/db_files], but does not download new ones),
• reconstruct interaction networks from scratch (option -b/-B),
• convert CellDesigner files to GML (option -p),
• expand existing networks (more involved commands).

Before you start, you have to acquire the desired database files from their respective origin and set up the database in MySQL. There is a file called database_schema.sql in the repository's root directory which you can use to get the database skeleton like this:

$ mysql -u <user> -p BioNetworks < database_schema.sql