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We provide the VMware snapshot of a Ubuntu server with the complete Biskit package and many helper applications pre-installed. This allows you to evaluate the package without going through all the installation steps. -- work in progress --

The following packages are pre-installed on the virtual machine:

Library purpose
numpy fast numeric calculations in Python
Numeric predecessor of numpy
gnuplot basic plotting
biggles advanced plotting in Python
Scientific Scientific Python
Biopython sequence-related tools
pypvm PVM-interface for Python
Biskit ...
Program purpose
Python version 2.5.2
SurfaceRacer surfaces and curvatures [see SurfaceRacer license]
MSMS surfaces [see MSMS license]
DSSP secondary structure analysis [see DSSP license]
pymol visualisation
PVM Parallelization
NCBI toolkit blast, blast_clust, (blast databases are not pre-installed)
HMMER conservation profiles (the Pfam database is not pre-installed)
T-Coffee sequence alignments
ICM-browser use CAD rather than RMS
Hex Protein-Protein docking [see Hex license]

Note, that some of the above programs are distributed under non-free licenses that restrict their use to academic, non-commercial purposes. Study their license and use them at your own responsibility.

Other useful programs could not be bundled into vmbiskit because you need to explicitly register before using them. Apart from Amber (400 USD for an academic license), these are still "free for academic use" but cannot be freely distributed or adapted.

So, not yet installed are:

Program purpose
xplor-nih refinement, sampling, ..., see setup xplor
amber structure sampling, entropy calculations, see Amber
modeller homology modeling, see Modeller & setup Modeller
prosa2003 complex scoring, see Prosa2003 & setup Prosa
foldX scoring, see Fold-X and setup Fold-X

Xplor-NIH, in particular, is used a lot throughout Biskit and completes the docking pipeline implemented in Biskit.Dock. Amber also comes in handy for the docking protocol and is prereqiuisite for the conformational entropy calculations.

For space reasons, we also did not bundle any databases into the virtual machine. Before using the Hmmer-interface of Biskit (to map conservation profiles into a structure), you would need to install a local Pfam database (three easy steps). And before using the homology modeling pipeline, you also need to install local blast databases and the Modeller program (which again is excluded for license reasons).

Sorry about the inconvenience! This is a perfect demonstration how any license other than genuine Open Source restricts our freedom of research. Special thanks, nevertheless, to Charles Schwieter from the XPlor-NIH team and Yann Dublanche from the CRG. Charles tried hard to find a solution for bundling XPlor despite their license requirements; and Yann has experimented with a server for authenticated download.

Download VMBiskit

(from the Serrano group server at the CRG)