SIMBA BASIC REQUIREMENTS

The basic requirements for SIMBA installation are: 
(i) Linux Operational System 64 bit (we recommend Ubuntu 14.04 or CentOS 6.4); 
(ii) Apache Server; 
(iii) PHP 5.3 or superior with libraries Mcrypt, Imagick and PHP-SQLite; 
(iv) Python with library Biopython; and 
(v) NCBI-BLAST+.



Installing basic requirements in O. S. Ubuntu 14.04
Apache server  Web server required to manage SIMBA pages which will be accessed by a browser. In the Linux terminal type the following command line: 
•	sudo apt-get install apache2 

SIMBA also requires Apache mod_rewrite capability. It can be enabled by editing the Apache list of mods-enabled.
•	sudo gedit /etc/apache2/sites-available/default

Edit the file based on the information provided in Table 1.
Table 1. Configuration to enable mod-rewrite in Apache Server.

Where you see:
	


Options Indexes FollowSymLinks MultiViews
AllowOverride None
Order allow,deny
Allow from all
	



Change to:


Options Indexes FollowSymLinks MultiViews
AllowOverride All
Order allow,deny
Allow from all


Now, run the command below and restart the Apache server.
•	sudo a2enmod rewrite
•	sudo service apache2 restart

PHP5 and libraries  These are required to interpret the source code of SIMBA back-end. Mcrypt is a security library used to encrypt data, and SQLite is the database management system (DBMS) used by SIMBA.
•	sudo apt-get install php5 php5-mcrypt php5-sqlite php5-imagick


Python and Biopython library  These are required to run sequence analysis by SIMBA. Python is installed by default in Linux. To install the Biopython library it is necessary to download the installation package at http://biopython.org/wiki/Download. Uncompressing the Biopython package, open the folder with Biopython in the Linux terminal and type the following on the command line to build and install: 

•	python setup.py build
•	python setup.py test
•	sudo python setup.py install



NCBI-BLAST+  This is required to run local alignments between sequences using BLAST. In the Linux terminal, type the following command: 
•	sudo apt-get install ncbi-blast+ 
3	INSTALLING SIMBA

To install SIMBA, first download the source code at http://ufmg-simba.sourceforge.net. Extract the file downloaded in the directory /var/www. Give permission to apache user through the command lines:
•	chown –R www-data:www-data /var/www/simba
•	chmod –R 755 /var/www/simba

Configuring SIMBA
SIMBA requires two simple configurations: (i) the URL of your application; and (ii) a security random key of 32 bit. Open the file /var/www/samba/app/config/app.php with a text editor. Edit the lines 29 (if you don’t have a personal URL use http://localhost/simba/public for only local access) and 68 (type 32 random characters).

Accessing SIMBA by a browser
Now, SIMBA can be accessed by a browser, as Google Chrome, Firefox, Opera or Safari, using the address configured in the “app.php” file. We point out that SIMBA can run on Internet Explorer, however some pages can present layout problems. We recommend the Google Chrome browser.

SIMBA VM requirements:

To run SIMBA VM is necessary a virtualization software, e.g.:

WINDOWS: 
VirtualBox 
VMware Player 
VMware vCenter Converter 
VMware Workstation 

MAC OS:
VM VirtualBox 
VMware OVF Tool 

LINUX:
VMware OVF Tool 
VMware Workstation