Practicals
Lecture notes and practicals can be found here!
The afternoon sessions will be devoted to practicals consisting of running software tools implementing concepts and algorithms studied during the lectures.
A virtual machine (VM) running Ubuntu will be provided for the practicals. The VM is launched on the participant's laptop (host machine) using VirtualBox (see required software below).
Required software
- VirtualBox (Oracle, free download).
- VMD (Univ Illinois site)
- NAMD (same site as VMD, even easier to install)
- PyMol is already installed on the virtual machine but you may wish to install it on your laptop as well.
- Familiarity with a scripting language such a Python is expected.
Before starting the Virtual Machine the first time
You will receive the VM as a compressed file, which you should first expand in the "VirtualBox VMs" directory that was created on your laptop by VirtualBox.
A directory called "shared" is defined in your home directory on the VM that is shared between the host (your laptop's OS) and guest (the Ubuntu VM). Before launching the VM with VirtualBox, you must first create a folder called "shared" on your laptop, then select the VM in the VirtualBox panel and navigate to the "Settings: Shared Folders" menu.
Other setting you can change are the number of processors (depending on the number of cores you have on your laptop), the RAM allotted to the VM (not all your RAM; 1 GB should do unless one of the professors says otherwise). Other settings to change may be 3D acceleration for better graphics performance if your laptop supports it.
Launching the Virtual Machine
The VM will open a small window as it boots. Some errors may appear, but it's OK. The login prompt will appear. The login is "algo" and the password also. Note: the keyboard is initially set up as a US keyboard, so if your laptop has a French keyboard you will need to type "qlgo" "qlgo". See below to change the keyboard layout.
Once logged in, type "startx" (ou "stqrtx" pour les francais) to get a (bigger) X11 window. In the Ubuntu Applications:Settings:Keyboard:Layout preferences panel you may now change the keyboard to French (or French Macintosh if you have a Mac)
Data and Binaries for specific tutorials
Binaries and data for certain practicals will be pre-installed on the VM, others can be obtained from the links below:
- Monday: Okamoto - VM
- Tuesday: Chipot - See choice of tutorials at this link
- Wednesday: Wales - VM, files download link to be provided at school
- Thursday: Cortes - VM, files download link to be provided at school
- Friday: Cazals and Robert - VM, files download link to be provided at school