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Biskit Virtual Machine

VMBiskit is a VMware snapshot of a Ubuntu server with the complete Biskit package and most helper applications pre-installed. -- Work in progress --


  1. Download and install the free VMWare Server or Player for your platform from:

  2. Download the vmbiskit snapshot -- pending --

  3. Unpack the snapshot

    • On Unix:

      tar jvfx vmbiskit_ubuntuserver.tar.bz2
    • On Windows: Find an archiving tool -- tell me which one supports bzip2!

  4. Open the virtual machine in VMWare

    • File / Open / Browse -> vmbiskit_ubuntuserver/
    • Start
    • login with user name biskit and password biskit
  5. Connect to the virtual machine

    The vmbiskit snapshot is a text-only installation but it can 'forward' graphical x11 windows to your host computer. The system is configured to fetch a dynamic IP address from DHCP (modify these settings in /etc/network/interfaces). To access it from outside, you need to know which IP address was assigned to it.

    • on vmbiskit: read the IP address with ifconfig:

      vmbiskit|~> ifconfig
      eth0      Link encap:Ethernet  HWaddr 00:0C:29:4F:52:46
                inet addr:  Bcast:  Mask:
                inet6 addr: fe80::20c:29ff:fe4f:5246/64 Scope:Link
    • Note the address given after 'inet addr:'

    • Now connect to the vmbiskit machine from your host:

      ssh biskit@

      Replace '' with the address noted above.

      And check that you can open graphical windows:

      vmbiskit~> pymol

      If pymol doesn't open, try to re-connect with 'ssh -X biskit@'

Working with the VMBiskit machine

The Biskit project is installed locally in ~/biskit. The Biskit scripts are in the search PATH.

Updating the VMBiskit machine

  1. Update the Operating system:

    sudo aptitude upgrade
  2. Update the biskit installation:

    cd ~/py/biskit
    svn update
  3. Install databases:

    VMBiskit comes without the PFam and Blast databases to keep its size manageable. Before using Conservation profile method (PDBDope.addConservation) you need to download and install the Pfam database:

    Before using the homology modeling pipeline you need to download and install the blast database:

    • follow the instructions in setup Blast (skip point 1, the NCBI toolkit is already installed)

A better option would be if you would mount an existing folder with these databases into the virtual machine. For that you have to edit /etc/fstab. [Put in detailed instructions]

Good luck!