Master AIV

UE: Computational Biology II

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

Software

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):

• KaSim An online interface can be used for simulation. More complex usage will require the use of the provided distribution.
• a plotting engine such as gnuplot, plot2, or PhiBPlot.
For instance, one should be able to convert the file example1.data into the file example1.pdf
• a graph visualisation software such as graphviz, omnigraffle, or an online interface.
For instance, one should be able to convert the file example2.dot into the file example2.pdf.
Please note that the javascript interface does not support comments, thus, please remove them before copying/pasting the graph in the window.

The binaries provided in the following tarballs should be enough:

• Linux installation
• Linux installation (without TK dependencies)
• Mac OS installation
• Mac OS installation (without TK dependencies)
• Windows installation

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:
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.

Lessons

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

• Slides: introduction, reachability analysis
• Materials:
• Binaries for complx specialized for view analyses
  • Complx_views for MacOS with tk binding
  • Complx_views for MacOS without tk binding
  • Complx_views for Linux with tk binding
  • Complx_views for Linux with tk binding
• Case studies:
• model of the early events of the epidermic growth factor
• model of the fibroblast growth factor
• a more complete model of the epidermic growth factor
• a model with a global invariant
• 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.

Lesson 4: December 8th 2015, by Jérôme Feret

Topic: Model reduction

• Slides:
• Materials:
• Binaries for complx specialized for ODEs
• MacOS with tk binding
• ode generator (ground systems)
• rule simplifier
• model reduction tool
• MacOS without tk binding
• ode generator (ground systems)
• rule simplifier
• model reduction tool
• Linux with tk binding
• ode generator (ground systems)
• rule simplifier
• model reduction tool
• Linux without tk binding
• ode generator (ground systems)
• rule simplifier
• model reduction tool
• Case study
• model of the early events of the epidermic growth factor
• Suggested references:
• Jérôme Feret, Vincent Danos, Jean Krivine, Russell Harmer,& Walter Fontana.
  Internal coarse-graining of molecular systems.
  Proceedings of National Academy of Sciences of the United States of America(PNAS), volume 106.(16), 6 pages. © 2009 National Academy of Sciences.

Lesson 5: December 9th 2016, by Jean Krivine

Topic: Model on DNA repair

• Suggested references
• Agned Köhler, Jean Krivine,& Jakob Vidmar.
  A Rule-Based Model of Base Excision Repair.
  Published in Computation methods in Systems Biology(CMSB 2014),
  number 8859 in LNCS/LNBI 2014, © Springer.

Lesson 6: December 16th 2016, TBA

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Jérôme Feret, Last modified: 13 Feb 2025, 04:42:35 CET