Master AIV

UE: Computational Biology II

This course takes place on Friday, room 2.05 (Charles V), between 2PM and 6PM.

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 personal 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.
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 2.05

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

KaSim/KaSa handbook

The KaSim and KaSa handbook is available on line.

Lessons

Lesson 1: October 30th 2015, by Jean Krivine

Topic: Introduction to Kappa

• Slides: Part 1 - Part 2
• Materials: abc.ka;
• Homework 1 (due to Friday Nov 6, 2PM)
Within a group of 2/3 persons, read and discuss the following article in Science:

https://www.sciencemag.org/content/347/6221/465.summary

and post an essay on the moddle (with your names) about it.
• Suggested references:
• Vincent Danos, Jérôme Feret, Walter Fontana, Russell Harmer,& Jean Krivine.
  Rule-based modelling of cellular signalling.
  Invited in Concurrency Theory(CONCUR 2007),
  number 4703 in Lecture Notes in Computer Science. 2007, © Springer.

Lesson 2: November 6th 2015, by Jean Krivine

Topic: Stochastic simulation, causality
Case study: DNA model

• Slides: Part 3
• Materials: to come;
• 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.

• 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 3: November 20th 2015, 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: November 27th 2015, by Vincent Danos

Topic: Coupling of Two Motor Proteins

• The material is available on the moodle (only for students).

Lesson 5: December 4th 2015, by Vincent Danos

Topic: Geometric constraints, thermodynamical constraints

• The material is available on the moodle (only for students).

Lesson 6: December 11th 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.

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Jérôme Feret, Last modified: 21 Nov 2022, 16:56:07 CET