Systems Biology includes the study of interaction networks and, in particular, their dynamic and spatiotemporal aspects. It typically requires the import of concepts from across the disciplines and crosstalk between theory, benchwork, modelling and simulation. The quintessence of Systems Biology is the discovery of the design principles of Life. The logical next step is to apply these principles to synthesize biological systems. This engineering of biology is the ultimate goal of Synthetic Biology: the rational conception and construction of complex systems based on, or inspired by, biology, and endowed with functions that may be absent in Nature.
The second round of applications for the Master 2 Systems Biology and Synthetic - MSSB - is open until 9 June 2014 on the site www.mssb.fr.
The M2 is offered by the University of Evry -Val d'Essonne , in partnership with AgroParis Tech, Ecole Centrale Paris , Telecom SudParis and Sup'Biotech , it offers an original scientific training in a privileged environment including the proximity of Genopole ®.
The MSSB is designed for students wishing to acquire a trans-disciplinary high-level training , regardless of their initial course ( Biology, Computer Science , Applied Mathematics, Physics, Chemistry, Engineering Sciences ) . That is why we are asking for the widest possible dissemination to teachers , managers , and especially students from all scientific and engineering disciplines.
This course of 25 lectures, filmed at Cornell University in Spring 2014, is intended for newcomers to nonlinear dynamics and chaos. It closely follows Prof. Strogatz's book, "Nonlinear Dynamics and Chaos: With Applications to Physics, Biology, Chemistry, and Engineering." The mathematical treatment is friendly and informal, but still careful. Analytical methods, concrete examples, and geometric intuition are stressed. The theory is developed systematically, starting with first-order differential equations and their bifurcations, followed by phase plane analysis, limit cycles and their bifurcations, and culminating with the Lorenz equations, chaos, iterated maps, period doubling, renormalization, fractals, and strange attractors. A unique feature of the course is its emphasis on applications. These include airplane wing vibrations, biological rhythms, insect outbreaks, chemical oscillators, chaotic waterwheels, and even a technique for using chaos to send secret messages. In each case, the scientific background is explained at an elementary level and closely integrated with the mathematical theory. The theoretical work is enlivened by frequent use of computer graphics, simulations, and videotaped demonstrations of nonlinear phenomena. The essential prerequisite is single-variable calculus, including curve sketching, Taylor series, and separable differential equations. In a few places, multivariable calculus (partial derivatives, Jacobian matrix, divergence theorem) and linear algebra (eigenvalues and eigenvectors) are used. Fourier analysis is not assumed, and is developed where needed. Introductory physics is used throughout. Other scientific prerequisites would depend on the applications considered, but in all cases, a first course should be adequate preparation
Nonlinear Dynamics and Chaos - Steven Strogatz, Cornell University
The topic “GitHub for Science” has been explored quite a few times before and with good reason: it is quite exciting to envision what breakthroughs in scientific collaboration could come from GitHub backed explorations, with substantial capital to invest and a formidable team to execute.
With GitHub’s founder saying that: "In science, I think there’s huge changes that can be made there as well. — Tom Preston-Werner" (...) - by Jure Triglav, 11 January 2014
As the Thematic School is about to begin on the coming Monday (24th of March). I will be scooping here some pertinent introductory resources on Systems and Synthetic Biology that are available online. Starting with a comprehensive set of directives, ideas and strategies as they have been laid down by NCBI in 2011.
Complex adaptive systems (cas), including ecosystems, governments, biological cells, and markets, are characterized by intricate hierarchical arrangements of boundaries and signals. In ecosystems, for example, niches act as semi-permeable boundaries, and smells and visual patterns serve as signals; governments have departmental hierarchies with memoranda acting as signals; and so it is with other cas. Despite a wealth of data and descriptions concerning different cas, there remain many unanswered questions about "steering" these systems. In Signals and Boundaries, John Holland argues that understanding the origin of the intricate signal/border hierarchies of these systems is the key to answering such questions. He develops an overarching framework for comparing and steering cas through the mechanisms that generate their signal/boundary hierarchies.
Holland lays out a path for developing the framework that emphasizes agents, niches, theory, and mathematical models. He discusses, among other topics, theory construction; signal-processing agents; networks as representations of signal/boundary interaction; adaptation; recombination and reproduction; the use of tagged urn models (adapted from elementary probability theory) to represent boundary hierarchies; finitely generated systems as a way to tie the models examined into a single framework; the framework itself, illustrated by a simple finitely generated version of the development of a multi-celled organism; and Markov processes.
It is our pleasure to announce the Evry'14 Thematic Research School on "advances in Systems and Synthetic Biology - Modelling complex biological systems in the context of genomics". The upcoming session will take place in Evry on March 24-28, 2014. The program includes conferences (listed below), hands-on tutorials, selected talks by students and post-docs, posters sessions, and meetings between biologists and modellers. This cross-disciplinary Thematic School on Systems and Synthetic Biology is the thirteenth edition of a series started in 2002. A dedicated website is open at http://epigenomique.free.fr/en/index.php
Best wishes, The Evry'14 Scientific Board,
EVRY'14 TOPICS AND SPEAKERS:
Systems Biology of drug discovery Nicolas Froloff (Dassault Systems, Velizy, FR) and Cécile Bonnard (Sobios, Boulogne, FR) Antoine Bril (Centre de Recherches Servier, Suresnes, FR)
A BRIEF GUIDE TO THE IDEAS AND ARTEFACTS OF COMPUTATIONAL ARTIFICIAL LIFE Alan Dorin, Animaland, 2014 This guide provides broad coverage of computational Artificial Life, a field encompassing the theories and discoveries underpinning the invention and study of technology-based living systems. It is targetted at students of all ages who are new to Artificial Life or are hoping to gain a broad understanding of its themes. The book focusses specifically on Artificial Life realised in computer software. Topics include: • pre-history of Artificial Life • artificial chemistry • artificial cells • organism development • locomotion • group behaviour • evolution • ecosystem simulation
Biological Bits includes animations and interactive software for experimentation with key processes. Simulations are included to allow exploration of cellular automata, developmental models, group behaviour and ecosystem simulation to aid in illustrating the text. The book can be read cover-to-cover as a general introduction to Artificial Life, or it can serve as a textbook for university or advanced high-school courses.
This lecture treats some enduring misconceptions about modeling. One of these is that the goal is always prediction. The lecture distinguishes between explanation and prediction as modeling goals, and offers sixteen reasons other than prediction to build a model. It also challenges the common assumption that scientific theories arise from and 'summarize' data, when often, theories precede and guide data collection; without theory, in other words, it is not clear what data to collect. Among other things, it also argues that the modeling enterprise enforces habits of mind essential to freedom. It is based on the author's 2008 Bastille Day keynote address to the Second World Congress on Social Simulation, George Mason University, and earlier addresses at the Institute of Medicine, the University of Michigan, and the Santa Fe Institute.
Power grids, road maps, and river streams are examples of infrastructural networks which are highly vulnerable to external perturbations. An abrupt local change of load (voltage, traffic density, or water level) might propagate in a cascading way and affect a significant fraction of the network. Almost discontinuous perturbations can be modeled by shock waves which can eventually interfere constructively and endanger the normal functionality of the infrastructure. We study their dynamics by solving the Burgers equation under random perturbations on several real and artificial directed graphs. Even for graphs with a narrow distribution of node properties (e.g., degree or betweenness), a steady state is reached exhibiting a heterogeneous load distribution, having a difference of one order of magnitude between the highest and average loads. Unexpectedly we find for the European power grid and for finite Watts-Strogatz networks a broad pronounced bimodal distribution for the loads. To identify the most vulnerable nodes, we introduce the concept of node-basin size, a purely topological property which we show to be strongly correlated to the average load of a node.
Understanding how the genetic material is organized in space in eukaryotes and bacteria is one of the big challenges of current molecular biology.
It is now clear that the complexity of the cellular machinery is so profound that its full comprehension can be pursued only through the joint efforts of scientists coming from cross-related disciplines like molecular biology, systems biology, bioinformatics and physics.
The Workshop aims at bringing scientists from these different disciplines in a real interdisciplinary context. The state-of-the-art of experimental, modeling and physical aspects in chromosome organization will be discussed, with particular emphasis on future important challenges.
- High-throughput and imaging methods for chromosome structure and dynamics;
- Gene regulatory networks in eukaryotes and bacteria: experiments and modeling;
- Large-scale physical modeling and simulation of chromosome structure;
- System biology of gene expression and regulation.
A poster session is previewed.
The best 4-5 posters will be selected for short (~15 minutes) oral presentations.
Dear all, It is our pleasure to announce the Nice'13 Thematic Research School on "Advances in Systems and Synthetic Biology - Modelling complex biological systems in the context of genomics". The upcoming session will take place in La Colle sur Loup (Nice), in the south of France, on March 25-29, 2013. The program includes conferences, hands-on tutorials, selected talks by students and post-docs, and posters sessions. This Thematic School on Systems and Synthetic Biology is the twelfth edition of a series started in 2002. A dedicated website is open at http://epigenomique.free.fr/en/index.php
We look forward to seeing you at Nice in March, best wishes! The Nice'13 Scientific Board, Nice'13 TOPICS AND SPEAKERS:
Richard Kitney (Dept of BioEngineering, Imperial College London, UK)
Birgit Wiltschi (Austrian Center of Industrial Biotechnology, Graz, AT)
Mark Bedau (Reed College, Portland, OR, US)
Ricard Solé (U. Pompeu Fabra, Barcelona, SP)
EVOLUTION OF NETWORKS
Orkun S. Soyer (U. Exeter, UK)
Dominique Schneider (U. Joseph Fourier, Grenoble, FR)
TISSUE MORPHOLOGY AND THE HUMAN TOPONOME PROJECT
Andreas Dress (MPG-CAS, Shangai, China & MPI Leipzig, DE)
Walter Schubert (MPG-CAS, Shangai, China & U. Magdeburg, DE)
Rachel Giles (Univ Medical Center, Utrecht, NL)
Helen Byrne (OCCAM, U Oxford, UK)
NICE'13 SCIENTIFIC BOARD:
Patrick Amar (U. Orsay, FR)
Gilles Bernot (U. Nice-Sophia, FR)
Marie Beurton-Aimar (U. Bordeaux, FR)
Attila Csikasz-Nagy (U. Trento, IT)
Jürgen Jost (MPI-MIS Leipzig, DE)
Ivan Junier (CRG, Barcelona, ES)
Marcelline Kaufman (U. Libre de Bruxelles, BE)
François Képès (CNRS Evry, FR), Chair
Pascale Le Gall (Ecole Centrale Paris, FR)
Reinhard Lipowsky (MPI-KG Potsdam, DE)
Jean-Pierre Mazat (U. Bordeaux, DE)
Victor Norris (U. Rouen, FR)
William Saurin (Sobios, Sophia-Antipolis, FR)
El Houssine Snoussi (U. Mohammed 5-Souissi, Rabat, MA).