Today’s high-impact biological journals require scientific results that tightly combine experimental data with theoretical predictions or verifications. However, there is still a large gap between the experimental and the theoretical / computational communities in terms of common language as well as capabilities and limitations of modelling tools. The current course bridges this gap by presenting an overview of systems biology with emphasis on the necessity, uses and pitfalls of dynamical modelling in biology. It introduces the required language and philosophy for a smooth and fruitful collaboration between life scientists and theoreticians (i.e. mathematicians, physicists, computer scientists). The main goal of this course is not a detailed description of the modelling tools in systems biology, but a thorough overview of the terminology and applicability range of these methodologies. The time dedication throughout this course will be one third for theoretical introduction, and two thirds for modelling applications for very diverse biological systems. The modelling applications will employ NetLogo*, the free open-source modelling environment.
The participants will get acquainted with the fundamentals of algebra and differential equations; with the history, concepts and tools of theoretical biology with emphasis on dynamic systems; and with the modelling of noise and spatial features in biological systems. As a result, they will acquire the necessary skills to understand and interpret models and modelling results from scientific articles, and will take the first steps into building their own mathematical models.
* Wilensky, U. 1999. NetLogo. http://ccl.northwestern.edu/netlogo/. Center for Connected Learning and Computer-Based Modelling, Northwestern University. Evanston, IL.
Dr. Andreea Munteanu
(Centre for Genomic Regulation, Spain).
Dr. Carlos Rodríguez-Caso
(Universitat Pompeu Fabra, Spain).
Dr. Soledad De Esteban-Trivigno
(Transmitting Science, Spain).
The participants should hold a degree in biological or (bio)medical disciplines, and be interested or involved in interdisciplinary research. All participants must bring their own personal laptop (Windows, Macintosh, Linux). Recent version (5.0.2 or later) of the free software NetLogo, a multi-agent programmable modelling environment, has to be installed on the participant’s laptop (http://ccl.northwestern.edu/netlogo/). This free software will be used for the practical sessions.
Premises of Sabadell of the Institut Català de Paleontologia Miquel Crusafont (ICP), C/ de l’Escola Industrial, 23, 08201 Sabadell, Barcelona (Spain). How to arrive.
|Monday 19th January 2015. Concepts: Which tools do we need?
The first day will introduce the main tools and concepts employed throughout the course, both for the theoretical and the practical sessions. From the theoretical perspective, we shall introduce the meaning of equations, variables and parameters, vectors, integration methods as well as the interpretation of probability measures. From the practical perspective, we shall present the NetLogo environment and its main commands.
Tuesday 20th January 2015. Dynamic systems: What is a dynamical model?
The second day will present the theoretical-biology history with emphasis on dynamic systems modelling. Using ordinary differential equations, we shall define the main concepts and tools of dynamic systems, and subsequently apply them to well-established biological cases mainly from population dynamics.
|Wednesday 21st January 2015. Genetic networks: How do we model genetic interactions?
The third day will address gene-regulation models. We shall construct the mathematical models, assess assumptions, obtain results, review caveats and limitations. Among classical examples, we shall address the lambda phage, genetic competence, toggle switch and synthetic oscillators.
Thursday 22nd January 2015. Stochasticity and spatial systems: When and why should we model noise and space?
The fourth day will address two concepts: Noise and spatial systems. Firstly, we shall expand on the role of noise observed the previous day, and the most common modelling methods for studying stochastic systems. Secondly, we shall model spatial systems where noise, diffusion and compartmentalization are important, such as habitat fragmentation, animal coats and morphogenesis.
Brief overview of the course and other modelling tools.
- Bialek W, Botstein D (2004) Introductory science and mathematics education for 21st-century biologists. Science, 303 (5659): 788-790.
- Enver T, Pera M, Peterson C, Andrews PW (2009) Stem cell states, fates, and the rules of attraction. Cell Stem Cell, 4 (5): 387-397.
- Roth S (2011) Mathematics and biology: A Kantian view on the history of pattern formation theory. Dev Genes Evol, 221 (5-6): 255-279.
- Fawcett TW, Higginson AD (2012) Communicating theory effectively requires more explanation, not fewer equations. Proc. Natl. Acad. Sci. USA, 109 (45): E3058-E3059.
- Jaeger J, Irons D, Monk N (2012) The inheritance of process: A dynamical systems approach. J Exp Zool B Mol Dev Evol, 318 (8): 591-612.
- Mogilner A, Allard J, Wollman R (2012) Cell polarity: Quantitative modeling as a tool in cell biology. Science, 336 (6078): 175-179.
- Hefferon J (2011) Linear algebra, http://joshua.smcvt.edu/linearalgebra/.
- Ingalls B (2012) Mathematical modeling in systems biology: An introduction, http://www.math.uwaterloo.ca/~bingalls/MMSB/.
28 hours on-site.
Monday 19th to Thursday 22nd January 2015:
9:30 to 13:30 Lessons.
13:30 to 15:00 Lunch.
15:00 to 18:00 Lessons.
- There will be a coffee break each day, halfway through each morning lesson session.
Places are limited to 16 participants and will be occupied by strict registration order.
This course can be validated by 1 ECTS (European Credit Transfer System) by the Life Science Zurich Graduate School, Zurich, Switzerland.
Reduced registration fee until October 31, 2014: 420 €. Full registration fee after October 31, 2014: 590 €. Participation fees include course material, coffee breaks and lunches.
Former participants will have a 5 % discount** on the current course fee.
We offer the possibility of paying in two instalments (contact us at firstname.lastname@example.org).
Please complete and submit your Registration Form (see below); we will confirm your acceptance by e-mail. This course will be held if at least 50 % of the places are filled.
If you wish to cancel your participation in this course, cancellations up to 20 days before the course start date will incur a 30 % cancellation fee. For later cancellations, or non-attendance, the full course fee will be charged.
If Transmitting Science must cancel this course due to unforeseen circumstances beyond the control of Transmitting Science, you will either be entitled to a full refund of the course fee, or your fee can be credited toward a future course / workshop. Transmitting Science is not responsible for travel fees, or any expenses incurred by you as a result of such cancellation. Every effort will be made to avoid the cancellation of any planned course / workshop.
The course will take place in the city of Sabadell, Barcelona (Spain).
You can stay in Barcelona city or Sabadell. Information about Hotels and Hostel in Sabadell here.
How to arrive to Sabadell from Barcelona city.
Unfortunately there are no internal grants available for this course. However some discounts are offered to people belonging to some of the Associations, Institutions or Universities listed here. If you want to apply to this discount please state the name of your Association, Institution or University in the “Comments” field of the Registration Form (proof will be asked later). For information on External Financial Support, please check the link.
Spanish unemployed scientists, as well as Spanish PhD students without any grant to develop their PhD, could benefit from a 40 % discount** on the course fee. If you want to ask for this discount, please contact us at email@example.com. That would apply for a maximum of 2 places and they will be covered by strict inscription order.
For further information contact: firstname.lastname@example.org.
** Discounts are not cumulative.