Master AIV

UE: Computational Biology II

This course takes place on Friday, room 20.N (Montparnasse Tower), between 2PM and 6PM.


The use of the machines that are available in room 20.N is highly recommended for practical works. We will support for the installation and the use of the necessary software on these machines. We will not support the installation and use of software on personal machines. For the practical works, the following software are required (and will be provided for the machines in room 20.N): The binaries provided in the following tarballs should be enough:

Neither Graphviz, nor Omnigraffle is provided in the tarballs.
Windows tarball contains KaSim only.
Neither Graphviz, nor Omnigraffle is available on the machine of Room 2.05.

Typical installation in room 20.N

  1. Download the following tarball: Mac OS installation
  2. Double click on the tarball in the Download folder.
  3. Drag and drop the newly created repository on your Desktop.
  4. Open a terminal
  5. Prompt:
  6. mkdir TP_kappa
    cd TP_kappa
    cp -r ~/Desktop/TP_kappa_mac/bin/* .
    chmod +x plot
    chmod +x Ka*

KaSim/KaSa handbook

The KaSim and KaSa handbook is available on line.


Lesson 1: November 18th 2016, by Jean Krivine

Topic: Introduction to Kappa

Lesson 2: November 25th 2016, by Jean Krivine

Topic: Stochastic simulation, causality

Lesson 3: December 2nd 2016, by Jérôme Feret

Topic: Reachability analysis

Lesson 4: December 8th 2015, by Jérôme Feret

Topic: Model reduction

Lesson 5: December 9th 2016, by Jean Krivine

Topic: Model on DNA repair

Lesson 6: December 16th 2016, TBA