Médiateur :
Minus van Baalen (Laboratoire d'Ecologie - UMR 7625, ENS, Université Pierre et Marie Curie)
Pour Darwin, l'évolution était fermement liée à l'écologie qui l'incorporait. En effet, même s'il n'était pas le 1er biologiste de l'évolution, avec un peu de justification, on pourrait revendiquer qu'il était le 1er écologiste. Malgré cela, l'Evolution et l'Ecologie sont devenues dans le temps des domaines scientifiques complémentaires pratiquement sans interactions.
Les écologistes ont considéré que l'évolution était trop lente pour pouvoir la prendre en compte, tandis que les biologistes considéraient que l'écologie était si rapide qu'ils pourraient sans risque supposer qu'elle était dans un équilibre stable (et l'ignorer). Cependant, dans les années 1950 et 60, la discipline de l'écologie évolutive est née du fait que l'on ne peut pas toujours démêler ces deux processus.
Cette discipline maintenant couvre de nombreux sous domaines : théorie de l'exploitation optimale des ressources, théorie évolutive des traits d'histoire de vie, théorie des jeux, pour n'en citer que certains. Dans les années 90, la théorie de la dynamique adaptative a été développée, pour créer une base théorique solide.
Dans ce cours, Minus van Baalen traitera les aspects de base de la dynamique adaptative (6 heures), et présentera en détail 2 exemples qui montrent comment elle peut être appliquée (Evolution de la Virulence, 6 heures) et ce qui restera un problème ouvert et passionnant (Structure de la population et Evolution de la Communication, 6 heures).
Durée : 18 heures
Dates : 6 demi-journées le lundi de 9h30 à 12h30, à partir du lundi 25 janvier 2010
Mediator : JC Thalabard, MD, PhD (University Paris Descartes & APHP)
Summary
In the land of the monolingual : "Translating a basic finding into a new therapy requires us to speak many languages - scientific, clinical, legal and financial. Yet most of us are hopelessly monolingual, a limitation that substantially slows translational research. Steps have been taken to address this problem, but a lot remains to be done." Nature Medicine 15, 975 (2009) To achieve this goal, in addition to original articles, the major medical journals bring regularly to their readers updates on various aspects of basic research which could potentially be translated to humans. This excursion mainly into major medical journals will help the students; i)to discover their contents, their target readership and how they are structured; ii) to summarize and present the results of both original and review articles.
Program
The following journals will be regularly browsed to form the reading list: Lancet, New England Journal of Medicine, JAMA, Nature Medicine, PLoS Medicine An initial list of articles will be posted in the corresponding section for the course in the M1 moodle web- area. It presently includes the following topics
- Genetic and Molecular Epidemiology
- Infectious diseases
- HIV
- Modelisation of the spread of infectious disease and their prevention
- Systematic Review and Meta-analysis
- Causality
- General Hypotheses
For each session, 1- 2 papers will be selected and read by all the students, who are individualy expected to prepare a written short critical review. A
A group of 2-3 students will be in charge of presenting the selected paper,with an open discussion based on the questions and comments raised by the audience.
Sessions will be held in 2009-2010 on mondays
Mediators : Gregory Batt (INRIA Rocquencourt), Vincent Danos (U. Edinburgh), Vincent Schachter
8 sessions
Basics of numerical simulation and limitations: 1 course-- (Gregory Batt)
Computational aspects of numerical simulation for ODEs, conversion from stochastic to differential rates (including transport), stochastics DEs, Gillespie algorithm. Numerical errors, computational cost of numerical simulation, stiffness, dimensionality, parameter uncertainties and the question of biological significance. Spatially heterogeneous systems, crowding, diffusion limited kinetics.
Boolean and qualitative models: 2 courses, 3TDs (Gregory Batt)
1st TD: (yes, we start with a TD!) modeling and basic analysis of a simple gene network
1st course: Boolean and qualitative models and their dynamics. Thomas' rules.
example "yeast robust cell cycle "http://www.pnas.org/content/101/14/4781.abstract
2nd TD: detailed analysis of a complex gene network (nutritional stress response in E. coli) using GNA
2nd course: computational aspects: search for steady states, formal verification, network inference
3rd TD: connection with experimental data: Saint-Savage et al.
Model building and analysis: 2 courses, 2TDs-- (Gregory Batt)
1st course: notions of sensitivity: local, solution-based and global, sensitivities computation; notions of robustness and computational aspects
1st TD: optimizing genetic circuits by global sensitivity analysis, X.-J. Feng, S. Hooshangi, D. Chen, G. Li, R. Weiss, and H. Rabitz, Biophys. J., 87(2):2195-2202, 2004. Kitano's paper on a theory of biological robustness. A general computational method for robustness analysis with applications to synthetic gene networks, http://bioinformatics.oxfordjournals.org/cgi/content/full/25/12/i169 Bioinformatics paper
classical papers such as von Dassow et al and Ingolia et al.
2nd course: parameter estimation: identifiability, various optimization-based search methods
2nd TD: benchmarks for identification of ordinary differential equations from time series data, Gennemark and Wedelin, Bioinformatics, 2009; or actual parameter search on a simple but difficult example
Metabolic networks: 3 courses and TDs (Vincent Schachter )
Steady state assumption, admissible flows, decomposition into extreme modes, biomass production rate predictions, analysis, reconstruction
Mediators : Vincent Danos (U. Edinburgh), Gregory Batt (INRIA Rocquencourt), Vincent Schachter
8 sessions
Rules and reactions: 6 courses, 3 TD
1st course: soft introduction to the kappa basics, relation to ordinary reaction networks, refinement of rule sets (qualitative), stochastic vs. deterministic dynamics, reminder on stochastic and deterministic rate constants (units, typical magnitudes, conversion), basics of simulations, refinement of rule sets (quantitative),
TD: trivial circuits to illustrate the basic definitions, small circuits, kinase cascades
2nd course: large scale ppi network dynamics (and percolation), compositional drift
TD: simple allosteric systems, large networks, percolation experiments
3rd course: causality and stories (formal notion of pathway), model reduction
TD: dna processing models (VD + JK,3) 4th course: thermodynamic model of complex assembly, energy functions, positional entropy model, Wegsheider conditions for reactions and rules;
Advanced allosteric models, kinetic traps.
5th course: rule-based molecular dynamics (a la Peter Dittrich, le Novere)
6th course: pde and patterns a la Meinhardt, Kholodenko, Stelling (VD)
Membrane interactions/bigraphs (JK)
Motivations, from rules to bigraphs [1] and bigraphical molecular systems [2,3]representing transport, dynamic compartmentalisation
[1] The Space and Motion of Communicating Agents, Cambridge University Press 2009
[2] Stochastic Bigraphs. Jean Krivine, Robin Milner and Angelo Troina.Proceedings of MFPS XXIV. Vol 218, p73-96, ENTCS 2008.
[3] A Language for the Cell. Troels C. Damgaard, Jean Krivine andVincent Danos. RR-116 ITU Copenhagen. 2009.
MGS and morphogenesis (Antoine Spicher ou Olivier Michel)