Topic outline

  • General

    Qualitative modelling of dynamical systems

    Lausanne, 15-16 April 2014


    The aim of this workshop will be to describe the qualitative modelling techniques. Description of the basic underlying methodologies and worked example will be taken.


    Gain the necessary know-how in modelling.


    - Biologists with a keen interest in modelling, no special background necessary.
    - A MAC or PC laptop with VirtualBox installed and wi-fi. You will be given a virtual machine image with all software and packages needed for this course


    Application is now closed.

    The registration fees for swiss academics are 50 CHF. The fees include course content material and coffee breaks.

    For european academics, fees are funded by AgedBrainSysBio.

    Deadline for registration and free-of-charge cancellation is set to April 7, 2014


    Genopode Building

    Additional information

    It is a joint workshop with CoLoMoTo meeting, which will take place at the same location on April 17-18. Please note that participation to CoLoMoTo meeting is independent from the application to Qualitative modelling of dynamical systems workshop.

    Potential participants can subscribe to our course announcement mailing-list and will be kept updated with news about other courses organized by the SIB.

    For more information, please contact

  • Tuesday 15 April 2014


    General introduction (Ioannis Xenarios)

    Introduction to logical models - Some tools to handle complex models (Aurélien Naldi)

    Cell Collective: A collaborative approach to logical models (Tomáš Helikar)

    Afternoon (hands-on)

    The Cell Collective (Tomáš Helikar): EGFR network - Erk pathway

    GINsim tutorial  (Aurélien Naldi)

  • Wednesday 16 April 2014


    Modeling with SQUAD (Luis Mendoza)

    X-­PRED:optmize a network using expression data (Isaac Crespo)

    CellNOpt: a brief overview (Thomas Cokelaer)

    Afternoon (hands-on)

    SQUAD tutorial - presentation (Luis Mendoza/Ioannis Xenarios)

    SQUAD tutorial -  SQUAD software (Luis Mendoza/Ioannis Xenarios)

    CellNOpt tutorial (Thomas Cokelaer)