AIMMS post-graduate course: Analysis tools to understand metabolic networks

02/08/2018

09.30 - 16.00h

Vrije Universiteit Amsterdam

AIMMS post-graduate course: Analysis tools to understand metabolic networks

Amsterdam Institute for Molecules, Medicines and Systems

Sciences

Course / training

On Thursday February 8, there will be a very interesting one-day postgraduate course entitled  'Analysis tools to understand metabolic networks'.

The course will be given by Prof. Jannie Hofmeyr from the Centre for Complex Systems in Transition and Dept. of Biochemistry, Stellenbosch University, Stellenbosch, South Africa.

Background

For the aim of understanding the often complex regulation of cellular metabolism, computational systems biology develops mathematical models that simulate metabolic processes. A good metabolic model is extremely valuable for gaining a deep understanding of the behaviour of metabolic processes, for studying aspects of metabolic control and regulation, for finding potential drug targets and testing prospective drugs, for designing biotechnological interventions, and for answering general what-if questions. However, as anyone who has attempted such model-building knows, the development and validation of an accurate kinetic metabolic model is a huge task, especially if the kinetic data for the enzymes involved have to be determined experimentally. Because of this, just developing and publishing the model is where it often ends, and very little is actually done with the model afterwards. A major reason is that the deep analysis of a kinetic model, whether your own or someone else’s, needs theoretical and computational tools. This 1-day course will introduce you to the theory and ways of thinking about metabolic networks, and to a suite of corresponding tools and their use.

Theory in the morning

  • Metabolic control analysis: a powerful framework for understanding the control properties of a metabolic pathway.
    - Good for finding potential drug targets.
  • Supply-demand analysis: using rate characteristics to visualise the regulatory properties of metabolic pathways.
    - Good for knowing when to pull and when to push.
  • Kinetic and thermodynamic contributions to metabolic regulation: the thermokinetics of reaction rate and elasticity.
    - Good for differentiating between mass-action, binding, cooperativity and allosteric regulation
  • Symbolic control analysis: dissecting the effects of perturbations into control patterns.
    - Good for following the chains of effects that percolate through a pathway after a perturbation.
        

Practice in the afternoon

PySCeS (Python Simulator for Cellular Systems) was developed in Stellenbosch by Brett Olivier, Jannie Hofmeyr and Johann Rohwer. Recently Carl Christensen developed a suite of tools called PySCeSToolboxfor analysing aspects of metabolic models built in PySCeS. These tools --- RateChar, SymCA, and ThermoKin --- are quite unique in the field of computational systems biology. In the afternoon session their use will be demonstrated, and, if you have set up your laptop with the necessary software, we will do a few exercises together. The documentation for PySCeS and PySCeSToolbox is available and contains the setup instructions.

Target audience:

PhD students and postdocs. AIMMS members will get priority.

Date:

Thursday February 8, 2018

Time:

9:30-16:00

Location:

Vrije Universiteit Amsterdam

Costs:

Free of charge

Credits:

VU and AIMMS PhD students can get 1 EC for this course. You will receive a certificate of attendance.

Registration

Send an email to info@aimms.vu.nl with your name, email, whether you are a PhD student or a postdoc, whether you are part of AIMMS and the name of your supervisor.

Note that the number of available places is 40.

Deadline for registration is Jan 29, 2018.