• Virtual-Box

CaliBayes Virtual Box

We understand that setting up the environment for using CaliBayes APIs and consuming CaliBayes web services can be indeed very difficult for many users, and we have tried our best to improve the usability of our systems. However, given the great complexity of the system and the limitations of the dependent software tools, it is almost impossible for us to make things any easier after all the efforts we have made so far.

In order to encourage the users to start using CaliBayes, and immediately benefit from the powerful tool, we have developed a CaliBayes Virtual Box to make all the functionalities of CaliBayes readily available in a compact VirtualBox virtual image.

Installed packages

• Ubuntu 9.10 - server (Karmic)

• CaliBaeys web services (Note: because of some temporary technical difficulties, autostart is for Fern simulation only, using Copasi simulation mode requires a manual restart of the web application server)

  • WSDL: http://192.168.56.3:8080/CaliBayesService_v2.wsdl

• CaliBayes simulation web services (autostart)

  • Supported simulation modes:
    • fern-stochastic
    • copasi-stochastic
    • copasi-deterministic
    • copasi-hybrid_rk
    • copasi-hybrid_lsoda

  • WSDL: http://192.168.56.3:8080/Simulator_v2/SimulatorWSService?WSDL

• R-2.9.2 (with all dependent packages required for consuming the built-in and NCL CaliBayes web services)

  • SSOAP, etc

  • SBMLModels (v0.1-1)

  • basisR (v0.1-4)

  • calibayesR (v0.1-6)

• libsbml-v4.0.1 (with Java and Python binding)
• Java-1.6
• Python-2.6.4
• SSH service
• DHCP client (auto IP address)

• X11 desktop (manually start with "startxfce4", will consume more memory)

• Firefox
• Admin user account:
  • username: "calibayes"
  • password: "calibayes"
• non-addmin user account:
  • username: "user"
  • password: "user"

How to use

• Download CaliBayes Virtual-Box (require 3Gb disk space)

• Install the latest VirtualBox Open Source Edition or Commercial Edition

  • Ubuntu:

    • > sudo apt-get install linux-headers-'uname -r'

    • > sudo apt-get install virtualbox-ose

  • Other OSs: http://www.virtualbox.org/

• Load and run the CaliBayes Virtual-Box virtual image in VirtualBox (see Installation and Settings)

• The built-in CaliBayes web services automatically start up and can be accessed from:

  • WSDL: http://192.168.56.3:8080/CaliBayesService_v2.wsdl

  • or http://localhost:8080/CaliBayesService_v2.wsdl with the built-in R.

CaliBayes Virtual Box installation and settings

Installation

• 1. create a new virtual machine
• 2. name the virtual machine with whatever you like (e.g. CaliBayesVBox)
• 3. select OS type:
  • Operation System: Linux
  • Version: Ubuntu
• 4. set base memory size: 512M (recommend : 1Gb)
• 5. tick "Boot Hard Disk" option and choose "Use existing hard disk, follow the wizard and add "CaliBayesVBox.vdi"
• 6. Finish

VirualBox Settings

• 1. select "File > Preferences"

• 2. select "Network"
• 3. add a Host-only network: (e.g. vboxnet0 network)
• 4. make sure DHCP Server is enabled
  • a. Lower Address Bound: 192.168.56.3 (default value: 192.168.56.3 or 192.168.56.101)
  • b. Upper Address Bound: 192.168.56.3 or e.g. 192.168.56.6 (optional)

Virual Machine Settings

• 1. select "Machine > Settigns"

• 2. select "System": the settings here can dramatically improve the performance of the virtual machine
  • Motherboard: enable ACPI (recommended)
  • Processor:
    • select the number of Processors (depends on your computer specs, please make sure leave at lease one core for the host OS!)
    • Enable PAE/NX (optional)
  • Acceleration: please make sure hardware virtualization is enabled in the bios of your computer
    • Enable VT-x/AMD-V (strongly recommended)
    • Enable Nested Paging (recommended for AMD CPUs)
• 3. select "Network"
  • Enable Internet access in the Virtual Machine (optional):
    • Enable Network Adapter: attache to NAT, or
    • Bridged Adapter (an global IP address will be assigned to the guest OS, more details please consult your computer administrators)
  • Enable Network Adapter: this setting enables communation between the host and the guest machines
    • attached to Host-only Adapter

    • Name: vboxnet0 (see VirtualBox settings)

Start the CaliBayes Virtual Box

• Start the virtual machine (e.g. CaliBayesVBox)
  • GUI: Click "Run", the guest OS operating screen will show.
  • Command line: VBoxManage startvm CaliBayesVBox --type headless
  • To shut down the guest OS from the host: VBoxManage controlvm CaliBayesVBox poweroff

• The built-in CaliBayes web services and the Simulation engines will automatically start up

• Guest OS GUI:
  • login

  • to activate Copasi simulation modes: ' sudo /etc/init.d/glassfish restart '

  • to start xfce X11 Desktop: ' startxfce4 '

  • in terminal: ' R '

• SSH access: (recommended)
  • the virtual box can be accessed via SSH:

    • from the host OS (with X11 tunneling): ' ssh -Y user@192.168.56.3 '

    • from a remote computer (with bridged networking and an allocated global IP address), please consult your computer administrators

    • to active Copasi simulation modes:' sudo /etc/init.d/glassfish restart '

    • in terminal: ' R '

  • ping 192.168.56.3 to check if the box is already up with the expected IP address.