Algorithms in Structural Bio-informatics :

Winter School

2-7 december 2012, Inria Sophia Antipolis, France

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Practicals

Each participant is expected to bring his/her laptop, running under Linux or MacOSX.

For each class, the practical will consist of running binary programs and/or scripting in python and/or using web servers.

Apart from web servers, two setups will be used:

• Virtual servers running under fedora (server name: algosb-f1.inria.fr) and ubuntu (server name: algosb-u1.inria.fr). Each participant is provided with an account on this servers.

  A page listing the (login, passwd) for these servers has been printed, and is available in the bag given to the participants.

  Note that to copy files back and forth between a server and one's machines, one needs to use scp.

  Practicals concerned: C. Robert, F. Cazals, J. Cortés.

• A virtual box to be installed on one's computer.

  Practical concerned: C. Prévost and M. Zacharias.

In the following, basic information is provided. The instructions for the practicals themselves will be provided by the faculties.

General pre-requisites

The following software should be installed on one's machine (the client machine):
• VMD and pymol, since the visualization will be carried out on one's machine.
• an SSH client: openssh on Linux and MacOs, Putty for example on Windows.
• a VNC client, for example TigerVnc RealVnc or UltraVnc.

Connecting to the wifi and to the internet

Each participant has been sent the information directly.

Connecting to the virtual servers

The connexion will use VNC, as explained in the following file , which is the /data/etc/motd file available upon login.

Then, upon login, the following information is provided:

The practicals are located in: /usr/local/algoSB/practicals

More detailed description in: /data/etc/motd

Pre-requisites and information for the practical by F. Cazals

• The visualization of the constructions done with the software intervor will require the following fast_load plugin for VMD. Make sure to install it, as indicated in the header of the file fast_load.tcl.

Pre-requisites and information for the practical by J. Cortés

• The MoMA-LigPath web server to investigate ligand motions.

Pre-requisites and information for the practical by M. Zacharias and C. Prévost

• The students should have installed the virtual box software already : oracle web-site.