Optimisation Techniques in Bioinformatics and Systems Biology

17 may - 21 may 2010

Detailed Course Programme

Monday, May 17th  

INTRODUCTION AND FOUNDATIONS  

10:00 – 13:00 Foundations of optimisation: Matrix algebra and other mathematical topics (AvK)  

13:00 – 14:00 Lunch  

14:00 – 15:00 Paper reading in groups  

15:00 – 16:00 Paper presentations and opposition  

16:00 – 17:30  Introduction univariate optimisation (AvK)      

Tuesday, May 18th  

LOCAL OPTIMISATION  

10:00 – 13:00 Local optimisation techniques: Simplex method, Steepest Descent, Conjugate gradient (AvK)  

13:00 – 14:00 Lunch  

14:00 – 15:00 Paper reading in groups  

15:00 – 16:00 Paper presentations and opposition  

16:00 – 17:30  Computer practical: Simplex (Nelder-Mead) and related techniques (TB)    

Wednesday, May 19th  

STOCHASTIC OPTIMISATION  

10:00 – 13:00 Stochastic optimisation techniques: Monte Carlo, Simulated Annealing, Particle Swarm Optimisation (JK)  

13:00 – 14:00 Lunch  

14:00 – 15:00 Paper reading in groups  

15:00 – 16:00 Paper presentations and opposition  

16:00 – 17:30  Computer practical: Simulated annealing and Particle Swarm Optimisation (TB)    

Thursday, May 20th  

GLOBAL OPTIMISATION  

10:00 – 13:00 Global optimisation techniques: Genetic Algorithm, Dynamic programming, Expectation Maximisation (JK and JH)  

13:00 – 14:00 Lunch  

14:00 – 15:00 Paper reading in groups  

15:00 – 16:00 Paper presentations and opposition  

16:00 – 17:30  Computer practical: Genetic Algorithm, Dynamic programming (TB and JH)    

Friday, May 21th  

APPLYING MULTI-OBJECTIVE OPTIMISATION  

10:00 – 13:00 Mixed and hybrid techniques: Application to Genetic networks  (JK)   13:00 – 14:00 Lunch  

14:00 – 15:00 Paper reading in groups  

15:00 – 16:00 Paper presentations and opposition  

16:00 – 17:30  Social optimisation: Drinks and bites