Master AIV

UE: Computational Biology II

Software

The use of the machines that are available in room 2.05 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 personnal machines. For the practical works, the following software are required (and will be provided for the machines in room 2.05):

KaSim
a plotting engine such as gnuplot, plot2, or PhiBPlot.

example1.data

example1.pdf

a graph vizualization software such as graphviz or omnigraffle.

example2.dot

example2.pdf

The binaries provided in the following tarballs should be enough:

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

Lessons

Lesson 1: November 21st 2014, by Vincent Danos

Topic: Introduction to Kappa

Slides.
Materials: to come;
Suggested references:

Vincent Danos, Jérôme Feret, Walter Fontana, Russell Harmer,& Jean Krivine.
Rule-based modelling of cellular signalling.
Invited in International Conference on Concurrency Theory(CONCUR 2007),
number 4703 in Lecture Notes in Computer Science. 2007, © Springer.

Lesson 2: November 28th 2014, by Jean Krivine

Topic: Stochastic simulation and DNA model

Materials: ptb.ka, DNA.ka.
Suggested references:

Vincent Danos, Jérôme Feret, Walter Fontana,& Jean Krivine.
Scalable modelling of biological pathways.
Invited in Asian Symposium on Programming Systems(APLAS 2007),
number 4807 in Lecture Notes in Computer Science. 2007, © Springer.

Lesson 3: December 5th 2014, by Vincent Danos

Topic: Coupling of Two Motor Proteins

Slides;
Suggested references:

Evgeny Stukalin, Hubert Phillips,& Anatoly Kolomeisky.
Coupling of Two Motor Proteins: A New Motor Can Move Faster.
In Phys. Rev. Lett. 94, 238101 - 13 June 2005.

Lesson 4: December 12th 2014, by Jérôme Feret

Topic: Reachability analysis

Slides;
Materials: egfr.ka, fgf.ka, sfb.ka, bugged_egfr.ka;
Suggested references:

Jérôme Feret.
Reachability analysis of biological signalling pathways by abstract interpretation.
In International Conference of Computational Methods in Sciences and Engineering(ICCMSE'07),
numero 963(2) in American Institute of Physics conference proceedings. 2007, © American Institute of Physics.
Vincent Danos, Jérôme Feret, Walter Fontana,& Jean Krivine.
Abstract interpretation of cellular signalling networks.
In Verification, Model Checking, and Abstract Interpretation(VMCAI 2008),
number 4905 in Lecture Notes in Computer Sciences. 2008, © Springer.