Course: Programming in Matlab (2nd edition)

Date

Next edition 2018 – you can pre-register here

Last edition: 13 March 2017

Location

Wageningen, Forum Building C0529 & PC0771 for practicals
Address: Droevendaalsesteeg 2, Wageningen (route)

Course coordinators

Hans Stigter (WUR), Celia van Gelder (BioSB, celia.van.gelder@biosb.nl)

Goal

The main goal of this course is to get acquainted with Matlab software for use within Systems Biology. After this introductory course you will have gained the basic knowledge to pursue further use via self-study of Matlab in order to apply more advanced programming techniques within Matlab in your own research. In summary, the sub-goals are:

  1. To learn the philosophy behind Matlab and its syntax
  2. To program simple Systems Biology models in Matlab (in ordinary differential equation format) and to solve these differential equations with Matlab

Course description

This is a one-day introduction to the possibilities of Matlab as a programming environment for simulation and analysis of biological models. We will start with a simple introduction of the basics of Matlab (matrices, vectors, manipulation of matrices and presentation of data). Having obtained some basic programming knowledge (writing of simple scripts and functions in Matlab), we will move on to more advanced topics. These include programming and solving ordinary differential equation models (ODEs) and the concept of “vectorized thinking” while writing Matlab-code. Finally, calibration of parameters in ODE type of models using measured data will be discussed and examples will be given. The course also includes the basics of presenting your results (graphing) in various types of plots that can easily be drawn in Matlab. Participants will, of course, get hands-on experience with Matlab and write code themselves in a practical.

Target audience

Primarily researchers from academia, but participants from the private sector are also welcome. The course focusses on the use of Matlab for building dynamic Systems Biology Models in terms of ordinary differential equations.

Programme

09:45 Coffee/Tea
10:00 Welcome
10:05 Introduction Matlab Basics (functions, variables, matrices, etc)
10:45 Advanced Programming (vectorised thinking, solving dynamic ordinary differential equation models in Matlab, parameter estimation for ODE-models)
12:00 Afternoon: Solving basic and advanced problems in Matlab – hands-on experience on a PC. Exercises will be provided, but you can also bring your own problems that you have encountered in your own research.
12:30 Lunch
15:00 Coffee/tea
16:30 End

Registration

Registration for the course is closed. You can pre-register for the next edition via the pre-registration form.

Previous editions