*BioSB Course Discovering Systems Biology Principles, 23-27 November 2015, Amsterdam* *Website:* http://biosb.nl/education/course-portfolio-2/course-discovering-systems-biol... *Coordinators:* Frank Bruggeman (VU), Celia van Gelder (BioSB, celia.van.gelder@biosb.nl) *Registration: * http://biosb.nl/education/course-portfolio-2/course-discovering-systems-biol... . *Please note that this course is free of charge for PhDs who are or will become a member of the BioSB research school, and with a reduced fee for other researchers who are or will become a member of BioSB. *More information about the BioSB membership can be found here: http://biosb.nl/about/members/biosb-membership-information/ . *Course description* A large part of systems biology is concerned with studying how the molecular networks inside living cells function. What they do. How their molecular interactions, including feedback circuitry, give rise to cellular properties, such as sensing, adaptation, division and death, that transcend those of single molecules. This includes figuring out how gene mutations, causing changes in proteins, cause networks, and their cellular hosts, to malfunction. In order to do this, systems biology focusses on the dynamics of molecular networks, using quantitative experiments and mathematical modeling. Mathematical models help systems biologists to figure out: i. how molecular properties relate to the functional, systemic properties of molecular networks, and ii. how molecular networks assist in the survival and functioning of cells. This 1-week course serves as an introduction to mathematical modeling as it is used in systems biology. *Target audience* This course does not require any introductory reading or courses, it should be accessible to students with diverse backgrounds. *Course programme* We start from physical and chemical principles of molecules, cells and reactions. Next, you will learn how you can relate the changes in the concentrations of molecules over time to the activity of reactions and the underlying molecular properties. You will be introduced to enzyme kinetics and the dynamics of small enzyme systems, in metabolism and signal transduction. We also briefly deal with models of genetic circuits. We will illustrate a number of unexpected, functional properties of molecular networks that can be studied with simple mathematical models. You will make and analyse models yourself, on paper and with software. We will close the week with a short overview of some more advanced topics, to introduce you to approaches and concepts that you will often hear about in systems biology. The course material concerns a syllabus (with exercises and answers), handouts, and computer exercises. At the end of this 1-week course, you will have a good understanding how mathematical models are made, what biology they require and how you can use them in systems-biology research. *Course schedule* *Monday, Nov 23* 09:30-10:30 Diffusion 11:00-12:30 Diffusion 13:30-15:00 Mass balances and kinetics 15:30-17:00 Mass balances and kinetics *Tuesday, Nov 24* 09:30-10:30 Mathematica or JWS online, basics 11:00-12:30 Mathematica or JWS online, basics 13:30-15:00 Simulating differential equation models 15:30-17:00 Simulating differential equation models *Wednesday, Nov 25* 09:30-10:30 Enzyme kinetics 11:00-12:30 Enzyme kinetics 13:30-15:00 Rate characteristics 15:30-17:00 Supply demand theory and ultrasensitivity *Thursday, Nov 26* 09:30-12:30 Cool systems: kinetic proofreading, TF-DNA search, robustness, fold-change detection, optimal gene expression 13:30-17:00 Making models in JWS online or Mathematica *Friday, Nov 27* 09:30-10:30 Stoichiometric analysis, N, K, L 11:00-12:30 Flux balance analysis 13:30-15:00 Stability analysis, phase-plane analysis 15:30-17:00 Bistability and oscillations with JWS Online or Mathematica *BioSB Education Programme* This course is part of the Education Programme of BioSB, the Netherlands Bioinformatics and Systems Biology Research School, which offers training and education in bioinformatics and systems biology. More information about BioSB can be found at www.biosb.nl or via education@biosb.nl.