SBSI Files

README
---------

Welcome to the SBSIVisual 1.5.0 release notes. This document describes some installation notes for the supported
platforms of Windows, Linux and MacOSX (10.5 or greater).

Version 1.5.0 is an update from 1.4.5 that adds:
  - support for the new RandomLinear and RandomLog setup features in SBSI Numerics
  - changed to overcome bugs of hardwired server addresses

Linux users please note: There are 2 versions of SBSIVisual;  32 bit and 64 bit. Please 
make sure you download the correct version for your operating system.
 
Windows users please note: You will need to install a small Microsoft library in order to use the Copasi library for simulations - please see Windows launching instructions below.

There is a new SBSI Web Service address: http://turip.bio.ed.ac.uk/sbsiservices

This address must be used instead of the old mook or sbsisdev1 addresses.

To use the COPASI version of SBSI Numerics use the web service addresss:
http://turip.bio.ed.ac.uk/sbsiservices_copasi


Launching
---------
---------
For Mac and Linux users, a Java JRE needs to be already installed, version 1.5 or newer.
Windows users already have a Java installation bundled with the application.
To see if you have Java installed, open a terminal window and type 

java -version

1. Windows launching notes
--------------------------

This is straightforward  - just double-click on the launch icon.

Important notice for Windows Users: 
Whether you're updating from an earlier version of SBSIVisual,
or installing for the first time, there is an important installation to add if you want to use the 
Copasi library simulators for running simulations. Release 4.7 of the Copasi API libraries requires 
some Microsoft libraries to be installed first: 

Go to the link:

http://www.microsoft.com/download/en/details.aspx?id=5555

and click the 'Download' button for 'vcredist_x86.exe'. This will install automatically.
After launching SBSIVisual, it should be possible to run simulations using 'Copasi LSODA' options.
If not, please get in touch with us.



2. MacOSX 10.5-10.7
----------------------
 
      1. Open a Terminal window
      2. cd to the installation directory ( the directory containing this README file).
      3. Enter the command :
           ./Launch_mac.commmand 
      
       
    You may need to set the executable permission for the launch script, you can do this by executing:
    
     chmod 755 ./Launch_mac.commmand 
     
3. Linux 32 bit GTK:
--------------------

	  1. Open a Terminal window
      2. cd to the installation directory ( the directory containing this README file).
      3. Enter the command :
      
         ./Launch_linux_x86.command
      
       
    You may need to set the executable permission for the script, you can do this by executing:
    
     chmod 755 ./Launch_linux_x86.command 
     
     In the event that you are unable to connect to the remote server, you will have to install the certificate yourself.
     In order to do so , please follow the instruction in this website:
      http://blogs.sun.com/gc/entry/unable_to_find_valid_certification 
      using the website sbsidev1.inf.ed.ac.uk:8083
     
4.  Linux 64 bit GTK:
--------------------

	  1. Open a Terminal window
      2. cd to the installation directory ( the directory containing this README file).
      3. Enter the command :
         ./Launch_linux_x86_64.command
      
       
    You may need to set the executable permission for the script, you can do this by executing:
    
     chmod 755 ./Launch_linux_x86_64.command 
    
     
Acknowledgments
----------------

Many thanks to the following for enabling software:

- Ralph Gauges and the Copasi team for the Java library version of Copasi
- The libSBML development team for great SBML support. 
- Florian Erhard for usage of the Fern stochastic simulation library.



Please get in touch if you have any queries about SBSI.


Ally Hume
May, 2015