Introduction. Dagmar Iber Jörg Stelling. CSB Deterministic, SS 2015, 1.
|
|
- Amice Dean
- 5 years ago
- Views:
Transcription
1 Introduction Dagmar Iber Jörg Stelling CSB Deterministic, SS 2015, 1
2 Origins of Systems Biology On this assumption of the passage of blood, made as a basis for argument, and from the estimation of the pulse rate, it is apparent that the entire quantity of blood passes from the veins to the arteries through the heart, and likewise through the lungs. Systems approach by William Harvey,
3 Computational Approaches to Biology Bioinformatics / Computational Biology CSB CCGACCATGCTGGCTTC CGGGCGCCCCCTGGTGC E A CAGGCATAAATTCAGTG AGAGCCGGAACTAGTCC B D GTGAGGCGCGCGTTGCC H. Lodish et al., Molecular Cell Biology, 5 th ed., C Linearly Structure and Interacting encoded function of components: genetic components networks and information (proteins,...) their behavior 3
4 Cellular Networks: Challenges High numbers of Protein interactions in Drosophila: Giot et al. (2003) Science 302: 1727 components Dynamic, non-linear interactions Self-modifying system Low molecular copy numbers: 'noise' Spatial organization 4
5 Cellular Networks: Challenges Complexity: Protein interactions in Drosophila: J. Giot et al. (2003) Science 302: 1727 Many components Dynamic interactions Self-modifying system Spatial organization Uncertainty: Incomplete inventory Few quantitative data Conflicting hypotheses Molecular 'noise' 5
6 Systems Biology & Complexity 6
7 Systems Biology & Uncertainty Unknown function Figure from: H. Lodish et al., Molecular Cell Biology, 5 th ed., ~ 50% of gene functions unknown in all (model) organisms. 7
8 Systems Biology & Uncertainty Figure from: C. von Mering et al. (2002) Nature 417: 399. Example: Protein-protein interactions, different studies. General phenomenon: Trade-offs coverage - accuracy. 8
9 Systems Biology & Uncertainty Experiment Model Emphasis on massive data generation as a prerequisite. Representation of biology in a 'true' mathematical model. Efficient way for making statements about biology? 9
10 Systems Biology & Uncertainty Main limitations for the development of mechanistic mathematical models for biological systems: Unknown parameter values and model structures for (nearly all) biological systems of interest. Stochastic effects as a consequence of low molecular copy numbers and environmental fluctuations. Effects of heterogeneous spatial distribution of cellular components / complicated cellular geometries. 10
11 Example: 'Probabilistic Dynamics' Experimental Simulation M. Kaltenbach, S. Dimopoulos & J. Stelling. FEBS Letters 583: (2009). 11
12 Example: Stochastic Noise M.J. Dunlop, R.S. Cox, J.H. Levine, R.M. Murray & M.B. Elowitz. Nat. Genetics 40: 1493 (2008). 12
13 Example: Spatial Effects B: w/o localization B: with localization B. di Ventura, C. Lemerle, K. Michalodimitrakis & L. Serrano. Nature 443: 527 (2006). Positive feedback circuit with high initial B, low A: Effect of kinase / phosphatase localization to opposite cell poles. 13
14 Science 284: 87 (1999). Every good model starts from a question. The modeler should always choose the correct level of detail to answer the question. Use the right level of description to catch the phenomena of interest. Don t model bulldozers with quarks. 14
15 Reverse Engineering / Systems Identification Reverse engineering / systems identification: Given a set of experimental data / prior knowledge, reconstruct and understand the network structure and function. Inference from system behavior in contrast to measurements of all individual interactions and subsequent assembly of facts. D.W. Selinger et al. (2003). On the complete determination of biological systems. Trends Biotechnol. 21,
16 Possible Aim: Whole-Cell Models
17 Computational Systems Biology Part of computational science: Development of methods and tools that help solving problems in (natural) science. Most problems in systems biology are mathematically and computationally hard (and cannot be solved in general). Domain knowledge (biological reality) as well as methods knowledge are needed to understand the problems and to develop real-world solutions. 17
18 Cohen JE, PLoS Biol 2(12): e439 (2004). 18
19 Aims of the Course Provide advanced mathematical and computational methods for the analysis of biological systems in real world settings State of the art, open problems. Focus on the interplay of theoretical and experimental approaches to typical questions in systems biology. Focused on examples from cell to organismal biology. 19
20 Course Structure Introduction / review ODEs (1) Structural network analysis (2) Network structures and data (2) Identification and experimental design (4) for dynamic (ODE) models Uncertainty quantification and network (2) inference Spatial effects and PDEs (3) 20
21 Modus Operandi Credits for this course: 6 ECTS. Session examination: Oral exam of 20 mins. Exercises: Will help a lot in learning the material, but not mandatory (no testate). Combination of analytic and computer (Matlab) exercises. Start next week. Materials via: 21
22 ODE-based Models: A Brief Review 22
23 ODE-based Model Development: Approach Pictogram Reaction list Approximations Figure from: Aldridge et al. (2006) Nature Cell Biology 8: Pathway diagram Differential equations 23
24 Reaction Kinetics: Dynamic Systems Reaction network System of elementary reactions: 1, j X 1 n, j X n k j 1, j X 1 n, j X n Law of mass action System of differential equations: dc i t dt q = j=1 k j i, j i, j l c l t l, j Equivalence to: d c t dt = N r t 24
25 Reaction Kinetics: Dynamic Models d c t dt = N r c t,u t, p Reactand concentrations c(t) To be determined. Stoichiometric matrix N Systems invariant. Reaction rates r Time- and state-dependent: Kinetic rate law r( ) From reaction structure. Parameters (kinetic constants) p Identification. Inputs u(t) Additional (time-varying) influences. 25
26 ODE Models: General Form d x t dt = f x t,u t, p System of ordinary, first-order, linear or nonlinear differential equations (ODEs) characterized by: Right hand sides f(x(t),u(t),p) = function in. System states x(t) = n x x 1 state vector. Parameters p = n p x 1 parameter set. Inputs u(t) = n u x 1 input vector. R n x 26
27 ODE Models: Solution d x t dt = f x t, p, x t 0 =x 0 Existence and uniqueness of solution to the initial value problem (IVP) of finding x(t) with given x 0 guaranteed. Three possible ''solution'' methods: Analytical Only applicable for simple systems. Numerical Always possible for well-posed IVPs. Graphical Qualitative analysis methods. 27
28 ODE Models: Analytical Solution d x t dt = f x t, p, x t 0 =x 0 Determine a closed-form formula g(x 0,p) that can be evaluated at any (time) point t to determine x(t). Example: Linear homogeneous system of ODEs: d x dt = A x, x 0 = i=1 n x n x i v i x t = i v i e t i i=1 Solutions for all linear systems in terms of exponential functions exp(λ i t) and harmonic functions sin(ω i t+φ i ). 28
29 ODE Models: Numerical Solution d x t dt = f x t, p, x t 0 =x 0 Replace differential equation with algebraic equation whose solution approximates that of the ODE. Example: Explicit finite-difference approximation x i t t x i t f i x t, p t Many different numerical algorithms for integration (e.g. Euler, Adams-Gear, Runge-Kutta,...). 29
30 ODE Models: Graphical ''Solution'' x 2 x(t) d x t dt = f x t, p x 0 x x t 0 =x 0 x 1 Derivatives dx(t)/dt define vector field in state space Solution x(t) obtained by following the field from x 0. Qualitative analysis in two-dimensional systems Determine characteristic features of the vector field. 30
31 Simple Dynamic Systems: Kinetics (Bio)chemical reaction networks ODE models Simplifications / assumptions (separation of time- and concentration-scales) Derivation of rate laws. Example: Gene G bound by transcription factor T: Without repression: Competitive repressor R: Cooperative binding: [G T ] = [G ]T [T ] [T ] K [G T ] = [G T ] [G ] T [T ] [T ] K 1 [ R]/ K I = [G]T [T ] n [T ] n K n 31
32 Feedback Systems Signal +/- Subsystem Output Circular patterns of interactions can establish feedback loops with positive or negative net effect. Intertwined feedback loops Complex dynamics. 32
33 Feedback Systems Negative Feedback u Positive Feedback u X X Y P E Y Y E Y P Single steady state. Multiple steady states. Homeostasis, rejection of perturbations. Bistability, hysteresis Switches, decisions. 33
34 Negative Feedback: Example System u X Y P E Y Protein X: Phosphatase that dephosphorylates Y P. Protein Y: Dephosphorylated form activates degradation of X Negative feedback. Input signal u: Control of production rate for X. 34
35 Negative Feedback: Example System u R 1 X R 2 Y P R 3 E R 4 Y Two-state (ODE) model: Michaelis-Menten kinetics d [ X ] = k dt 1 u k 2 [Y ] [ X ] d [Y ] dt = k 3 [ X ] [Y ] T [Y ] K M3 [Y ] T [Y ] k 4 [ E ][Y ] K M4 [Y ] Re-scaling: Sigmoidal Goldbeter-Koshland function. 35
36 Negative Feedback: Phase Plane Analysis Example trajectory Y-Nullcline Steady state X-Nullcline 36
37 Positive Feedback: Example System u X Y E Y P Protein X: Phosphatase that dephosphorylates Y P. Protein Y: Dephosphorylated form activates production of X Positive feedback. Input signal u: Control of production rate for X. 37
38 Positive Feedback: Example System u R 1 X R 3 R 2 Y R 4 E R 5 Y P Two-state (ODE) model: Michaelis-Menten kinetics d [ X ] dt d [Y ] dt = k 1 u k 2 [Y ] k 3 [ X ] = k 4 [ X ] [Y ] T [Y ] K M4 [Y ] T [Y ] k 5[ E ] [Y ] K M5 [Y ] 38
39 Positive Feedback: Phase Plane Analysis Example trajectory Y-Nullcline Stable steady state Stable steady state X-Nullcline Unstable steady state 39
40 Relations Between Spaces Parameter space Flux space State space 40
41 Positive Feedback: Stability Classification of steady states (nodes) according to directions of the vector field: unstable node stable node saddle point (unstable) Stability: Global vs. local (w.r.t. 'small' perturbations). 41
42 Positive Feedback: Bifurcation Diagram [X] ss u crit1 u u crit2 History dependence of the system's state (here with respect to changes in the input): Hysteresis. Used, for example, to establish (computer) memory. 42
43 Combined Feedback: Activator-Inhibitor Protein X: Phosphatase u that dephosphorylates Y P. Protein Y: Y form activates X production of X Positive feedback (on X). Y E Z Y P Protein Z: Production mediated by Y, activates degradation of X Negative feedback (on X). Input signal u: Control of X. 43
44 Activator-Inhibitor: Simplification Three state variables X, Y u Y R 4 X E R 5 Z Y P and Z No simple geometric interpretation of the system behavior. Simplification: Quasi steady-state assumption for species of protein Y. Module already contained in simple feedback system. 44
45 Activator-Inhibitor: Phase Plane Analysis Example trajectory Unstable steady state Stable limit cycle X-Nullcline Z-Nullcline 45
46 Activator-Inhibitor: Bifurcation Diagram stable unstable [X] ss stable u crit1 u u crit2 Bifurcations between single stable steady state and stable oscillations (dotted lines amplitude of oscillations). 46
47 Stability Analysis: Systematic Approach Convert nonlinear ODE system to linear ODE system Linearization around operating point (steady state). d x t dt = f x t, p, t d x dt A x Characterize solution for linear homogeneous system Analysis of local stability properties. Systematic evaluation of system behavior Existence & stability of steady states as a function of parameters Bifurcation analysis. 47
48 Stability Analysis: Linearization d x t dt = f x t, p,t, x t 0 =x 0 Determine a closed-form formula g(x,p,t) that can be evaluated at any (time) point t to determine x(t). Solution for linear homogeneous system of ODEs: d x dt = A x, x 0 = i=1 n x n x i v i x t = i v i e t i i=1 Solutions for all linear systems in terms of exponential functions exp(λ i t) and harmonic functions sin(ω i t+φ i ). 48
49 Stability Analysis: Linear ODE Systems Matrix notation (two dimensions) with system matrix A: d x ' dt = A x ' y, x ' = x 1', y= y 1 2, x 2 ' y A= a 11 a 12 a 21 a 22 Local stability of steady states x ss of interest: d x ss dt = A x ss y = 0 y = A x ss With deviation from steady state solution x = x' - x ss Canonical form of linear ODEs for stability analysis. d x dt = A x 49
50 Stability Analysis: Linear ODE Systems Canonical solution for homogeneous linear ODEs: d x dt = A x n x x t = i=1 i v i e i t Eigenvectors v i Direction of system movement. Eigenvalues λ i Exponential part (time-dependent). Constants α i Adjusted to meet initial conditions. Dynamics from eigenvalue decomposition of A: A v = v A = v v 1 50
51 Stability Analysis: Linear ODE Systems Canonical solution for homogeneous linear ODEs: d x dt = A x n x x t = i=1 i v i e i t Local system stability means x(t) 0 for t : Real parts of all eigenvalues have to be negative (otherwise some solutions do not converge locally). Complex eigenvalues associated with oscillations: exp i =exp exp i =exp cos i sin 51
52 Systems Identification Most important aspects of the system? Complete knowledge on components / interactions? Exact mechanisms of interactions? Level of detail for the mathematical descriptions? Modeling approach (qualitative / mechanistic /...)? Experimental data for identification & validation? 52
53 Identification for ODE Models d x t dt = f x t,u t, p, t System of ordinary, first-order, linear or nonlinear differential equations (ODEs) characterized by: f(x(t),u(t),p) Mechanistic uncertainties. System states x(t) (Experimentally observable). Parameters p Parameter estimation. Inputs u(t) Control for experimental design. 53
54 Parameter Identification: Estimation N p = i=1 [e i T Q i e i ] min e i = e i x, p, t i = x p,t i x M t i General formulation as an optimization problem: Minimization of deviation between model and experiment: Φ( p ) : Identification functional for parameter set p. e i (x, p, t i ) : Error vector for time point t i (i = 1... N). x( p, t i ) : Model prediction (state vector) at time t i. x M ( t i ) : Experimental data (measurement) at time t i. 54
55 Optimization: Local vs. Global Optima Φ( p ) N p = i=1 Gobal optimization: p* that minimizes Φ( p ) over all p [e i T Q i e i ] min possible values of p No efficient algorithms known. Local optimization: Φ( p* ) Φ( p ) for all p close to p*. 55
56 Introduction: Summary Uncertainty in biology as a major factor that limits systems biology modeling (and poses interesting mathematical challenges). Systems identification beyond traditional parameter estimation Structural model uncertainties, experimental design, spatial effects... Challenges: Modeling approaches as well as advanced identification / experimental design methods. Review of ODE systems: Fundamental kinetics, feedback systems, linear systems and stability, parameter estimation approaches Foundation for everything that follows... 56
57 "All models are wrong but some models are useful." George Box (1979) Robustness in the strategy of scientific model building. 57
COURSE NUMBER: EH 590R SECTION: 1 SEMESTER: Fall COURSE TITLE: Computational Systems Biology: Modeling Biological Responses
DEPARTMENT: Environmental Health COURSE NUMBER: EH 590R SECTION: 1 SEMESTER: Fall 2017 CREDIT HOURS: 2 COURSE TITLE: Computational Systems Biology: Modeling Biological Responses COURSE LOCATION: TBD PREREQUISITE:
More informationNetworks in systems biology
Networks in systems biology Matthew Macauley Department of Mathematical Sciences Clemson University http://www.math.clemson.edu/~macaule/ Math 4500, Spring 2017 M. Macauley (Clemson) Networks in systems
More informationFUNDAMENTALS of SYSTEMS BIOLOGY From Synthetic Circuits to Whole-cell Models
FUNDAMENTALS of SYSTEMS BIOLOGY From Synthetic Circuits to Whole-cell Models Markus W. Covert Stanford University 0 CRC Press Taylor & Francis Group Boca Raton London New York Contents /... Preface, xi
More informationLecture 7: Simple genetic circuits I
Lecture 7: Simple genetic circuits I Paul C Bressloff (Fall 2018) 7.1 Transcription and translation In Fig. 20 we show the two main stages in the expression of a single gene according to the central dogma.
More informationPrinciples of Synthetic Biology: Midterm Exam
Principles of Synthetic Biology: Midterm Exam October 28, 2010 1 Conceptual Simple Circuits 1.1 Consider the plots in figure 1. Identify all critical points with an x. Put a circle around the x for each
More informationBE 150 Problem Set #2 Issued: 16 Jan 2013 Due: 23 Jan 2013
M. Elowitz and R. M. Murray Winter 2013 CALIFORNIA INSTITUTE OF TECHNOLOGY Biology and Biological Engineering (BBE) BE 150 Problem Set #2 Issued: 16 Jan 2013 Due: 23 Jan 2013 1. (Shaping pulses; based
More informationWhy This Class? James K. Peterson. August 22, Department of Biological Sciences and Department of Mathematical Sciences Clemson University
Why This Class? James K. Peterson Department of Biological Sciences and Department of Mathematical Sciences Clemson University August 22, 2013 Outline 1 Our Point of View Mathematics, Science and Computer
More informationBasic modeling approaches for biological systems. Mahesh Bule
Basic modeling approaches for biological systems Mahesh Bule The hierarchy of life from atoms to living organisms Modeling biological processes often requires accounting for action and feedback involving
More informationMath 331 Homework Assignment Chapter 7 Page 1 of 9
Math Homework Assignment Chapter 7 Page of 9 Instructions: Please make sure to demonstrate every step in your calculations. Return your answers including this homework sheet back to the instructor as a
More informationCourse plan Academic Year Qualification MSc on Bioinformatics for Health Sciences. Subject name: Computational Systems Biology Code: 30180
Course plan 201-201 Academic Year Qualification MSc on Bioinformatics for Health Sciences 1. Description of the subject Subject name: Code: 30180 Total credits: 5 Workload: 125 hours Year: 1st Term: 3
More informationIntroduction to Model Order Reduction
Introduction to Model Order Reduction Lecture 1: Introduction and overview Henrik Sandberg Kin Cheong Sou Automatic Control Lab, KTH ACCESS Specialized Course Graduate level Ht 2010, period 1 1 Overview
More informationCS-E5880 Modeling biological networks Gene regulatory networks
CS-E5880 Modeling biological networks Gene regulatory networks Jukka Intosalmi (based on slides by Harri Lähdesmäki) Department of Computer Science Aalto University January 12, 2018 Outline Modeling gene
More informationStochastic simulations
Stochastic simulations Application to molecular networks Literature overview Noise in genetic networks Origins How to measure and distinguish between the two types of noise (intrinsic vs extrinsic)? What
More informationAnalysis and Simulation of Biological Systems
Analysis and Simulation of Biological Systems Dr. Carlo Cosentino School of Computer and Biomedical Engineering Department of Experimental and Clinical Medicine Università degli Studi Magna Graecia Catanzaro,
More informationSupporting Information. Methods. Equations for four regimes
Supporting Information A Methods All analytical expressions were obtained starting from quation 3, the tqssa approximation of the cycle, the derivation of which is discussed in Appendix C. The full mass
More informationBioinformatics 3. V18 Kinetic Motifs. Fri, Jan 8, 2016
Bioinformatics 3 V18 Kinetic Motifs Fri, Jan 8, 2016 Modelling of Signalling Pathways Curr. Op. Cell Biol. 15 (2003) 221 1) How do the magnitudes of signal output and signal duration depend on the kinetic
More informationBioinformatics 3! V20 Kinetic Motifs" Mon, Jan 13, 2014"
Bioinformatics 3! V20 Kinetic Motifs" Mon, Jan 13, 2014" Modelling of Signalling Pathways" Curr. Op. Cell Biol. 15 (2003) 221" 1) How do the magnitudes of signal output and signal duration depend on the
More informationIs chaos possible in 1d? - yes - no - I don t know. What is the long term behavior for the following system if x(0) = π/2?
Is chaos possible in 1d? - yes - no - I don t know What is the long term behavior for the following system if x(0) = π/2? In the insect outbreak problem, what kind of bifurcation occurs at fixed value
More informationExam 2 Study Guide: MATH 2080: Summer I 2016
Exam Study Guide: MATH 080: Summer I 016 Dr. Peterson June 7 016 First Order Problems Solve the following IVP s by inspection (i.e. guessing). Sketch a careful graph of each solution. (a) u u; u(0) 0.
More informationLIMIT CYCLE OSCILLATORS
MCB 137 EXCITABLE & OSCILLATORY SYSTEMS WINTER 2008 LIMIT CYCLE OSCILLATORS The Fitzhugh-Nagumo Equations The best example of an excitable phenomenon is the firing of a nerve: according to the Hodgkin
More informationLecture 2: Analysis of Biomolecular Circuits
Lecture 2: Analysis of Biomolecular Circuits Richard M. Murray Caltech CDS/BE Goals: Give a short overview of the control techniques applied to biology - uncertainty management - system identification
More informationBasic Synthetic Biology circuits
Basic Synthetic Biology circuits Note: these practices were obtained from the Computer Modelling Practicals lecture by Vincent Rouilly and Geoff Baldwin at Imperial College s course of Introduction to
More informationIntroduction to Bioinformatics
Systems biology Introduction to Bioinformatics Systems biology: modeling biological p Study of whole biological systems p Wholeness : Organization of dynamic interactions Different behaviour of the individual
More informationModeling and Analysis of Dynamic Systems
Modeling and Analysis of Dynamic Systems by Dr. Guillaume Ducard Fall 2016 Institute for Dynamic Systems and Control ETH Zurich, Switzerland based on script from: Prof. Dr. Lino Guzzella 1/33 Outline 1
More informationFrom cell biology to Petri nets. Rainer Breitling, Groningen, NL David Gilbert, London, UK Monika Heiner, Cottbus, DE
From cell biology to Petri nets Rainer Breitling, Groningen, NL David Gilbert, London, UK Monika Heiner, Cottbus, DE Biology = Concentrations Breitling / 2 The simplest chemical reaction A B irreversible,
More informationMathematical Biology - Lecture 1 - general formulation
Mathematical Biology - Lecture 1 - general formulation course description Learning Outcomes This course is aimed to be accessible both to masters students of biology who have a good understanding of the
More informationProgram for the rest of the course
Program for the rest of the course 16.4 Enzyme kinetics 17.4 Metabolic Control Analysis 19.4. Exercise session 5 23.4. Metabolic Control Analysis, cont. 24.4 Recap 27.4 Exercise session 6 etabolic Modelling
More informationANALYSIS OF BIOLOGICAL NETWORKS USING HYBRID SYSTEMS THEORY. Nael H. El-Farra, Adiwinata Gani & Panagiotis D. Christofides
ANALYSIS OF BIOLOGICAL NETWORKS USING HYBRID SYSTEMS THEORY Nael H El-Farra, Adiwinata Gani & Panagiotis D Christofides Department of Chemical Engineering University of California, Los Angeles 2003 AIChE
More informationComputational Systems Biology Exam
Computational Systems Biology Exam Dr. Jürgen Pahle Aleksandr Andreychenko, M.Sc. 31 July, 2012 Name Matriculation Number Do not open this exam booklet before we ask you to. Do read this page carefully.
More informationCONTROL OF STOCHASTIC GENE EXPRESSION BY A NONLINEAR BIOLOGICAL OSCILLATOR
PHYSCON 27, Florence, Italy, 7 9 July, 27 CONTROL OF STOCHASTIC GENE EXPRESSION BY A NONLINEAR BIOLOGICAL OSCILLATOR Federica Colombo Division of Genetics and Cell Biology San Raffaele Scientific Institute
More information7.32/7.81J/8.591J: Systems Biology. Fall Exam #1
7.32/7.81J/8.591J: Systems Biology Fall 2013 Exam #1 Instructions 1) Please do not open exam until instructed to do so. 2) This exam is closed- book and closed- notes. 3) Please do all problems. 4) Use
More informationA review of stability and dynamical behaviors of differential equations:
A review of stability and dynamical behaviors of differential equations: scalar ODE: u t = f(u), system of ODEs: u t = f(u, v), v t = g(u, v), reaction-diffusion equation: u t = D u + f(u), x Ω, with boundary
More informationBiophysical Journal Volume 92 May
Biophysical Journal Volume 92 May 2007 3407 3424 3407 Dynamics of a Minimal Model of Interlocked Positive and Negative Feedback Loops of Transcriptional Regulation by camp-response Element Binding Proteins
More informationMath 215/255 Final Exam (Dec 2005)
Exam (Dec 2005) Last Student #: First name: Signature: Circle your section #: Burggraf=0, Peterson=02, Khadra=03, Burghelea=04, Li=05 I have read and understood the instructions below: Please sign: Instructions:.
More informationProblem Set 2. 1 Competitive and uncompetitive inhibition (12 points) Systems Biology (7.32/7.81J/8.591J)
Problem Set 2 1 Competitive and uncompetitive inhibition (12 points) a. Reversible enzyme inhibitors can bind enzymes reversibly, and slowing down or halting enzymatic reactions. If an inhibitor occupies
More informationIntroduction to Mathematical Modeling
Introduction to Mathematical Modeling - Systems Theory in the Toolbox for Systems Biology The 5 th International Course in Yeast Systems Biology 2011 June 6, 2011, PhD, Assoc Prof Head of Department Systems
More informationBiological Pathways Representation by Petri Nets and extension
Biological Pathways Representation by and extensions December 6, 2006 Biological Pathways Representation by and extension 1 The cell Pathways 2 Definitions 3 4 Biological Pathways Representation by and
More informationModelling chemical kinetics
Modelling chemical kinetics Nicolas Le Novère, Institute, EMBL-EBI n.lenovere@gmail.com Systems Biology models ODE models Reconstruction of state variable evolution from process descriptions: Processes
More informationControl Theory: Design and Analysis of Feedback Systems
Control Theory: Design and Analysis of Feedback Systems Richard M. Murray 21 April 2008 Goals: Provide an introduction to key concepts and tools from control theory Illustrate the use of feedback for design
More informationMOL 410/510: Introduction to Biological Dynamics Fall 2012 Problem Set #4, Nonlinear Dynamical Systems (due 10/19/2012) 6 MUST DO Questions, 1
MOL 410/510: Introduction to Biological Dynamics Fall 2012 Problem Set #4, Nonlinear Dynamical Systems (due 10/19/2012) 6 MUST DO Questions, 1 OPTIONAL question 1. Below, several phase portraits are shown.
More informationBiomolecular Feedback Systems
Biomolecular Feedback Systems Domitilla Del Vecchio MIT Richard M. Murray Caltech Version 1.0b, September 14, 2014 c 2014 by Princeton University Press All rights reserved. This is the electronic edition
More informationComputer Simulation and Data Analysis in Molecular Biology and Biophysics
Victor Bloomfield Computer Simulation and Data Analysis in Molecular Biology and Biophysics An Introduction Using R Springer Contents Part I The Basics of R 1 Calculating with R 3 1.1 Installing R 3 1.1.1
More informationIntroduction. ECE/CS/BioEn 6760 Modeling and Analysis of Biological Networks. Adventures in Synthetic Biology. Synthetic Biology.
Introduction ECE/CS/BioEn 6760 Modeling and Analysis of Biological Networks Chris J. Myers Lecture 17: Genetic Circuit Design Electrical engineering principles can be applied to understand the behavior
More informationUnderstand the existence and uniqueness theorems and what they tell you about solutions to initial value problems.
Review Outline To review for the final, look over the following outline and look at problems from the book and on the old exam s and exam reviews to find problems about each of the following topics.. Basics
More informationModeling Cellular Networks
06_4774 12/7/06 3:02 PM Page 151 CHAPTER 6 Modeling Cellular Networks Tae Jun Lee, Dennis Tu, Chee Meng Tan, and Lingchong You 6.1 Introduction Systems-level understanding of cellular dynamics is important
More informationStem Cell Reprogramming
Stem Cell Reprogramming Colin McDonnell 1 Introduction Since the demonstration of adult cell reprogramming by Yamanaka in 2006, there has been immense research interest in modelling and understanding the
More informationRui Dilão NonLinear Dynamics Group, IST
1st Conference on Computational Interdisciplinary Sciences (CCIS 2010) 23-27 August 2010, INPE, São José dos Campos, Brasil Modeling, Simulating and Calibrating Genetic Regulatory Networks: An Application
More informationQualitative Analysis of Tumor-Immune ODE System
of Tumor-Immune ODE System L.G. de Pillis and A.E. Radunskaya August 15, 2002 This work was supported in part by a grant from the W.M. Keck Foundation 0-0 QUALITATIVE ANALYSIS Overview 1. Simplified System
More informationAnalog Electronics Mimic Genetic Biochemical Reactions in Living Cells
Analog Electronics Mimic Genetic Biochemical Reactions in Living Cells Dr. Ramez Daniel Laboratory of Synthetic Biology & Bioelectronics (LSB 2 ) Biomedical Engineering, Technion May 9, 2016 Cytomorphic
More informationLecture 4: Importance of Noise and Fluctuations
Lecture 4: Importance of Noise and Fluctuations Jordi Soriano Fradera Dept. Física de la Matèria Condensada, Universitat de Barcelona UB Institute of Complex Systems September 2016 1. Noise in biological
More informationLecture 5: Travelling Waves
Computational Biology Group (CoBI), D-BSSE, ETHZ Lecture 5: Travelling Waves Prof Dagmar Iber, PhD DPhil MSc Computational Biology 2015 26. Oktober 2016 2 / 68 Contents 1 Introduction to Travelling Waves
More informationBioControl - Week 2, Lecture 1
BioControl - Week 2, Lecture Goals of this lecture: CDS tools for bio-molecular systems Study of equilibria Dynamic performance Periodic behaviors Main eample: Negative autoregulation Suggested readings
More informationGenetic transcription and regulation
Genetic transcription and regulation Central dogma of biology DNA codes for DNA DNA codes for RNA RNA codes for proteins not surprisingly, many points for regulation of the process https://www.youtube.com/
More informationMathematical Models of Biological Systems
Mathematical Models of Biological Systems CH924 November 25, 2012 Course outline Syllabus: Week 6: Stability of first-order autonomous differential equation, genetic switch/clock, introduction to enzyme
More informationRegulation of metabolism
Regulation of metabolism So far in this course we have assumed that the metabolic system is in steady state For the rest of the course, we will abandon this assumption, and look at techniques for analyzing
More informationCHAPTER 1 Introduction to Differential Equations 1 CHAPTER 2 First-Order Equations 29
Contents PREFACE xiii CHAPTER 1 Introduction to Differential Equations 1 1.1 Introduction to Differential Equations: Vocabulary... 2 Exercises 1.1 10 1.2 A Graphical Approach to Solutions: Slope Fields
More informationCalculus and Differential Equations II
MATH 250 B Second order autonomous linear systems We are mostly interested with 2 2 first order autonomous systems of the form { x = a x + b y y = c x + d y where x and y are functions of t and a, b, c,
More informationLecture 1 Modeling in Biology: an introduction
Lecture 1 in Biology: an introduction Luca Bortolussi 1 Alberto Policriti 2 1 Dipartimento di Matematica ed Informatica Università degli studi di Trieste Via Valerio 12/a, 34100 Trieste. luca@dmi.units.it
More informationAnalysis of Mode Transitions in Biological Networks
Analysis of Mode Transitions in Biological Networks Nael H. El-Farra, Adiwinata Gani, and Panagiotis D. Christofides Dept. of Chemical Engineering, University of California, Los Angeles, CA 90095 DOI 10.1002/aic.10499
More informationChapter 2 Optimal Control Problem
Chapter 2 Optimal Control Problem Optimal control of any process can be achieved either in open or closed loop. In the following two chapters we concentrate mainly on the first class. The first chapter
More informationURL: <
Citation: ngelova, Maia and en Halim, sma () Dynamic model of gene regulation for the lac operon. Journal of Physics: Conference Series, 86 (). ISSN 7-696 Published by: IOP Publishing URL: http://dx.doi.org/.88/7-696/86//7
More informationA systems approach to biology
A systems approach to biology SB200 Lecture 5 30 September 2008 Jeremy Gunawardena jeremy@hms.harvard.edu Recap of Lecture 4 matrix exponential exp(a) = 1 + A + A2/2 +... + Ak/k! +... dx/dt = Ax matrices
More informationModelling in Biology
Modelling in Biology Dr Guy-Bart Stan Department of Bioengineering 17th October 2017 Dr Guy-Bart Stan (Dept. of Bioeng.) Modelling in Biology 17th October 2017 1 / 77 1 Introduction 2 Linear models of
More informationPHYSFLU - Physics of Fluids
Coordinating unit: 230 - ETSETB - Barcelona School of Telecommunications Engineering Teaching unit: 748 - FIS - Department of Physics Academic year: Degree: 2018 BACHELOR'S DEGREE IN ENGINEERING PHYSICS
More informationNonlinear dynamics & chaos BECS
Nonlinear dynamics & chaos BECS-114.7151 Phase portraits Focus: nonlinear systems in two dimensions General form of a vector field on the phase plane: Vector notation: Phase portraits Solution x(t) describes
More informationI/O monotone dynamical systems. Germán A. Enciso University of California, Irvine Eduardo Sontag, Rutgers University May 25 rd, 2011
I/O monotone dynamical systems Germán A. Enciso University of California, Irvine Eduardo Sontag, Rutgers University May 25 rd, 2011 BEFORE: Santa Barbara, January 2003 Having handed to me a photocopied
More informationA Simple Protein Synthesis Model
A Simple Protein Synthesis Model James K. Peterson Department of Biological Sciences and Department of Mathematical Sciences Clemson University September 3, 213 Outline A Simple Protein Synthesis Model
More informationAPPPHYS 217 Tuesday 6 April 2010
APPPHYS 7 Tuesday 6 April Stability and input-output performance: second-order systems Here we present a detailed example to draw connections between today s topics and our prior review of linear algebra
More informationMultistability in the lactose utilization network of Escherichia coli
Multistability in the lactose utilization network of Escherichia coli Lauren Nakonechny, Katherine Smith, Michael Volk, Robert Wallace Mentor: J. Ruby Abrams Agenda Motivation Intro to multistability Purpose
More informationSolutions to Math 53 Math 53 Practice Final
Solutions to Math 5 Math 5 Practice Final 20 points Consider the initial value problem y t 4yt = te t with y 0 = and y0 = 0 a 8 points Find the Laplace transform of the solution of this IVP b 8 points
More informationLesson 4: Non-fading Memory Nonlinearities
Lesson 4: Non-fading Memory Nonlinearities Nonlinear Signal Processing SS 2017 Christian Knoll Signal Processing and Speech Communication Laboratory Graz University of Technology June 22, 2017 NLSP SS
More informationBioinformatics: Network Analysis
Bioinformatics: Network Analysis Kinetics of Gene Regulation COMP 572 (BIOS 572 / BIOE 564) - Fall 2013 Luay Nakhleh, Rice University 1 The simplest model of gene expression involves only two steps: the
More informationGene Expression as a Stochastic Process: From Gene Number Distributions to Protein Statistics and Back
Gene Expression as a Stochastic Process: From Gene Number Distributions to Protein Statistics and Back June 19, 2007 Motivation & Basics A Stochastic Approach to Gene Expression Application to Experimental
More information7 Hyperbolic Differential Equations
Numerical Analysis of Differential Equations 243 7 Hyperbolic Differential Equations While parabolic equations model diffusion processes, hyperbolic equations model wave propagation and transport phenomena.
More informationModelling biological oscillations
Modelling biological oscillations Shan He School for Computational Science University of Birmingham Module 06-23836: Computational Modelling with MATLAB Outline Outline of Topics Van der Pol equation Van
More informationSPATIO-TEMPORAL MODELLING IN BIOLOGY
SPATIO-TEMPORAL MODELLING IN BIOLOGY Prof Dagmar Iber, PhD DPhil ((Vorname Nachname)) 04/10/16 1 Challenge: Integration across scales Butcher et al (2004) Nat Biotech, 22, 1253-1259 INTERDISCIPLINARY WORK
More informationLinear Systems of ODE: Nullclines, Eigenvector lines and trajectories
Linear Systems of ODE: Nullclines, Eigenvector lines and trajectories James K. Peterson Department of Biological Sciences and Department of Mathematical Sciences Clemson University October 6, 203 Outline
More informationBrief contents. Chapter 1 Virus Dynamics 33. Chapter 2 Physics and Biology 52. Randomness in Biology. Chapter 3 Discrete Randomness 59
Brief contents I First Steps Chapter 1 Virus Dynamics 33 Chapter 2 Physics and Biology 52 II Randomness in Biology Chapter 3 Discrete Randomness 59 Chapter 4 Some Useful Discrete Distributions 96 Chapter
More informationA(γ A D A + γ R D R + γ C R + δ A )
Title: Mechanisms of noise-resistance in genetic oscillators Authors: José M. G. Vilar 1,2, Hao Yuan Kueh 1, Naama Barkai 3, and Stanislas Leibler 1,2 1 Howard Hughes Medical Institute, Departments of
More information1 Periodic stimulations of the Incoherent Feedforward Loop network
1 Periodic stimulations of the Incoherent Feedforward Loop network In this Additional file, we give more details about the mathematical analysis of the periodic activation of the IFFL network by a train
More informationWritten Exam 15 December Course name: Introduction to Systems Biology Course no
Technical University of Denmark Written Exam 15 December 2008 Course name: Introduction to Systems Biology Course no. 27041 Aids allowed: Open book exam Provide your answers and calculations on separate
More informationBioControl - Week 6, Lecture 1
BioControl - Week 6, Lecture 1 Goals of this lecture Large metabolic networks organization Design principles for small genetic modules - Rules based on gene demand - Rules based on error minimization Suggested
More informationA Model of Evolutionary Dynamics with Quasiperiodic Forcing
paper presented at Society for Experimental Mechanics (SEM) IMAC XXXIII Conference on Structural Dynamics February 2-5, 205, Orlando FL A Model of Evolutionary Dynamics with Quasiperiodic Forcing Elizabeth
More informationChapter One. Introduction
Chapter One Introduction A system is a combination of components or parts that is perceived as a single entity. The parts making up the system may be clearly or vaguely defined. These parts are related
More informationACM/CMS 107 Linear Analysis & Applications Fall 2016 Assignment 4: Linear ODEs and Control Theory Due: 5th December 2016
ACM/CMS 17 Linear Analysis & Applications Fall 216 Assignment 4: Linear ODEs and Control Theory Due: 5th December 216 Introduction Systems of ordinary differential equations (ODEs) can be used to describe
More informationLinear Systems of ODE: Nullclines, Eigenvector lines and trajectories
Linear Systems of ODE: Nullclines, Eigenvector lines and trajectories James K. Peterson Department of Biological Sciences and Department of Mathematical Sciences Clemson University October 6, 2013 Outline
More informationComplex Dynamic Systems: Qualitative vs Quantitative analysis
Complex Dynamic Systems: Qualitative vs Quantitative analysis Complex Dynamic Systems Chiara Mocenni Department of Information Engineering and Mathematics University of Siena (mocenni@diism.unisi.it) Dynamic
More informationSimon Fraser University School of Engineering Science ENSC Linear Systems Spring Instructor Jim Cavers ASB
Simon Fraser University School of Engineering Science ENSC 380-3 Linear Systems Spring 2000 This course covers the modeling and analysis of continuous and discrete signals and systems using linear techniques.
More informationSystems biology and complexity research
Systems biology and complexity research Peter Schuster Institut für Theoretische Chemie, Universität Wien, Austria and The Santa Fe Institute, Santa Fe, New Mexico, USA Interdisciplinary Challenges for
More informationNetwork Dynamics and Cell Physiology. John J. Tyson Department of Biological Sciences & Virginia Bioinformatics Institute
Network Dynamics and Cell Physiology John J. Tyson Department of Biological Sciences & Virginia Bioinformatics Institute Signal Transduction Network Hanahan & Weinberg (2000) Gene Expression Signal-Response
More informationDynamic modeling and analysis of cancer cellular network motifs
SUPPLEMENTARY MATERIAL 1: Dynamic modeling and analysis of cancer cellular network motifs Mathieu Cloutier 1 and Edwin Wang 1,2* 1. Computational Chemistry and Bioinformatics Group, Biotechnology Research
More informationDifferential Equations with Boundary Value Problems
Differential Equations with Boundary Value Problems John Polking Rice University Albert Boggess Texas A&M University David Arnold College of the Redwoods Pearson Education, Inc. Upper Saddle River, New
More informationCellular Automata Approaches to Enzymatic Reaction Networks
Cellular Automata Approaches to Enzymatic Reaction Networks Jörg R. Weimar Institute of Scientific Computing, Technical University Braunschweig, D-38092 Braunschweig, Germany J.Weimar@tu-bs.de, http://www.jweimar.de
More informationAC&ST AUTOMATIC CONTROL AND SYSTEM THEORY SYSTEMS AND MODELS. Claudio Melchiorri
C. Melchiorri (DEI) Automatic Control & System Theory 1 AUTOMATIC CONTROL AND SYSTEM THEORY SYSTEMS AND MODELS Claudio Melchiorri Dipartimento di Ingegneria dell Energia Elettrica e dell Informazione (DEI)
More informationModelling Biochemical Pathways with Stochastic Process Algebra
Modelling Biochemical Pathways with Stochastic Process Algebra Jane Hillston. LFCS, University of Edinburgh 13th April 2007 The PEPA project The PEPA project started in Edinburgh in 1991. The PEPA project
More informationIntroduction to Model Order Reduction
KTH ROYAL INSTITUTE OF TECHNOLOGY Introduction to Model Order Reduction Lecture 1: Introduction and overview Henrik Sandberg, Bart Besselink, Madhu N. Belur Overview of Today s Lecture What is model (order)
More informationControl Systems I. Lecture 2: Modeling. Suggested Readings: Åström & Murray Ch. 2-3, Guzzella Ch Emilio Frazzoli
Control Systems I Lecture 2: Modeling Suggested Readings: Åström & Murray Ch. 2-3, Guzzella Ch. 2-3 Emilio Frazzoli Institute for Dynamic Systems and Control D-MAVT ETH Zürich September 29, 2017 E. Frazzoli
More informationInverse Problems in Systems Biology
Inverse Problems in Systems Biology Heinz W. Engl Johann Radon Institute for Computational and Applied Mathematics, Austrian Academy of Sciences, Altenbergerstraße 69, 4040 Linz, Austria E-mail: heinz.engl@oeaw.ac.at
More informationMath 345 Intro to Math Biology Lecture 19: Models of Molecular Events and Biochemistry
Math 345 Intro to Math Biology Lecture 19: Models of Molecular Events and Biochemistry Junping Shi College of William and Mary, USA Molecular biology and Biochemical kinetics Molecular biology is one of
More informationProcess Modelling, Identification, and Control
Jan Mikles Miroslav Fikar Process Modelling, Identification, and Control With 187 Figures and 13 Tables 4u Springer Contents 1 Introduction 1 1.1 Topics in Process Control 1 1.2 An Example of Process Control
More information