In silico feedback for in vivo regulation of a gene expression circuit Shared by lxshen.

Slides:



Advertisements
Similar presentations
FUNCTION FITTING Student’s name: Ruba Eyal Salman Supervisor:
Advertisements

Michael R. Smith, Mark Clement, Tony Martinez, and Quinn Snell
Enhanced Single-Loop Control Strategies
A SYNTHETIC GENE- METABOLIC OSCILLATOR Reviewed by Fei Chen.
An Intro To Systems Biology: Design Principles of Biological Circuits Uri Alon Presented by: Sharon Harel.
Model Checking Genetic Regulatory Networks with Parameter Uncertainty Grégory Batt, Calin Belta, Ron Weiss HSCC 2007 Presented by Spring Berman ESE :
Robustness analysis and tuning of synthetic gene networks February 15, 2008 Eyad Lababidi Based on the paper “Robustness analysis and tuning of synthetic.
The Hole Filler Helper By Russell Palmiter. Holes Where do they come from? –Geometry acquisition and simplification Why fill them? –Many graphics algorithms.
Robust control Saba Rezvanian Fall-Winter 88.
Introduction to Signals and Systems David W. Graham EE 327.
Signal Processing in Single Cells Tony 03/30/2005.
NUU meiling CHENModern control systems1 Lecture 01 --Introduction 1.1 Brief History 1.2 Steps to study a control system 1.3 System classification 1.4 System.
280 SYSTEM IDENTIFICATION The System Identification Problem is to estimate a model of a system based on input-output data. Basic Configuration continuous.
SYNTHETIC BIOLOGY Guillermo RODRIGO Alfonso JARAMILLO.
Enhanced Single-Loop Control Strategies
Goals of Adaptive Signal Processing Design algorithms that learn from training data Algorithms must have good properties: attain good solutions, simple.
Communications & Multimedia Signal Processing Formant Track Restoration in Train Noisy Speech Qin Yan Communication & Multimedia Signal Processing Group.
Comparative survey on non linear filtering methods : the quantization and the particle filtering approaches Afef SELLAMI Chang Young Kim.
Assigning Numbers to the Arrows Parameterizing a Gene Regulation Network by using Accurate Expression Kinetics.
An E.coli Cell-Free Expression Toolbox: Application to Synthetic Gene Circuits and Artificial Cells Jonghyeon Shin and Vincent Noireaux ACS Synthetic Biology,
Asymptotic Techniques
Introduction to estimation theory Seoul Nat’l Univ.
Brief history of automatic control (I) 1868 first article of control ‘on governor’s’ –by Maxwell 1877 Routh stability criterien 1892 Liapunov stability.
First Institute of Higher Education in Modern China Since 1895 A World-class, Progressive, and Multidisciplinary Research University.
1 SWE 513: Software Engineering Usability II. 2 Usability and Cost Good usability may be expensive in hardware or special software development User interface.
Synthetic biology: New engineering rules for emerging discipline Andrianantoandro E; Basu S; Karig D K; Weiss R. Molecular Systems Biology 2006.
Using Kalman filter to voltage harmonic identification in single-phase systems Raúl Alcaraz, Emilio J. Bueno, Santiago Cóbreces, Francisco J. Rodríguez,
CSCE555 Bioinformatics Lecture 16 Identifying Differentially Expressed Genes from microarray data Meeting: MW 4:00PM-5:15PM SWGN2A21 Instructor: Dr. Jianjun.
Linac Marx Modulator Update Trevor Butler 5/20/2015.
MAE 555 Non-equilibrium Gas Dynamics Guest lecturer Harvey S. H. Lam November 16, 2010 On Computational Singular Perturbation.
The Programming of a Cell By L Varin and N Kharma Biology and Computer Engineering Departments Concordia University.
es/by-sa/2.0/. Design Principles in Systems Molecular Biology Prof:Rui Alves Dept Ciencies.
Chapter 8 Model Based Control Using Wireless Transmitter.
Gene repression and activation
Session III. Information Systems A system, whether automated or manual, that comprises people, machines, and/or methods organized to collect, process,
Examples Lecture Three Plan Pros and cons of logistic model Checking the solution The method of integrating factors Differentiation from first principles.
Why synthetic Biology? Reverse Engineering vs. Forward engineering: »Synthetic replicas of natural genetic circuits.
SYNBIOLOGY - An Analysis of Synthetic Biology Research in Europe and North America 4,5/4,5 CM SYNBIOLOGY: An Analysis of Synthetic Biology Research in.
Model Predictive Impedance Control MPIC
IMPROVED RECONSTRUCTION OF IN SILICO GENE REGULATORY NETWORKS BY INTEGRATING KNOCKOUT AND PERTURBATION DATA Yip, K. Y., Alexander, R. P., Yan, K. K., &
Melbourne Uni What is iGEM? International Genetically Engineered Machine competition Started in 2003 within MIT.
Lecture 25: Implementation Complicating factors Control design without a model Implementation of control algorithms ME 431, Lecture 25.
In silico gene targeting approach integrating signaling, metabolic, and regulatory networks Bin Song Jan 29, 2009.
Numerical Analysis – Differential Equation
Chapter 5 Dynamics and Regulation of Low-order Systems
A Yeast Synthetic Network for In Vivo Assessment of Reverse-Engineering and Modeling Approaches Cantone, I., Marucci, L., Iorio, F., Ricci, M., Belcastro,
Differential Equations Linear Equations with Variable Coefficients.
Andreas Milias-Argeitis, Sean Summers, Jacob Stewart-Ornstein, Ignacio Zuleta, David Pincus, Hana El-Samad, Mustafa Khammash, and John Lygeros Nature Biotechnology.
… Work in progress at CTF3 … Davide Gamba 01 July 2013 Study and Implementation of L INEAR F EEDBACK T OOLS for machine study and operation.
1 Use of Multiple Integration and Laguerre Models for System Identification: Methods Concerning Practical Operating Conditions Yu-Chang Huang ( 黃宇璋 ) Department.
Welcome to MT140 Introduction to Management Unit 9 Seminar Communication.
Chapter 6 Discrete-Time System. 2/90  Operation of discrete time system 1. Discrete time system where and are multiplier D is delay element Fig. 6-1.
Network applications Sushmita Roy BMI/CS 576 Dec 9 th, 2014.
BASIC CONCEPTS OF CONTROL SYSTEM SEM :- V CONTROL ENGINEERING ENROLLMENT NO: GUIDED BY PROF. S.P.PATEL.
Introduction to Differential Equations
Supplementary figure 5.
The synthetic microbial consortium oscillator
Noise Propagation in Gene Networks
Using MathCAD, Matlab and PSpice for electronics simulations
Lesson 3 – 1.6/1.7 – Linear Equations & Inequalities
Linear Control Systems
Synthetic Gene Circuits Learn to Classify
Modeling Biological Systems
Digital Control Systems Waseem Gulsher
The Frequency Dependence of Osmo-Adaptation in Saccharomyces cerevisae
Comparison of N. gonorrhoeae gene expression during infection in men and women in vivo. Comparison of N. gonorrhoeae gene expression during infection in.
I Like, Like Like Terms, Like Really.
Solving a System of Linear Equations
Research in mathematical biology
Recapitulation of Lecture 12
Presentation transcript:

In silico feedback for in vivo regulation of a gene expression circuit Shared by lxshen

Biological feedback Signals Biological control circuits Implement of control

Comparison of control circuits Synthetic biological circuits Nature circuits robust Difficulty in artificial circuits Not easy to control slow Electronic circuits Prosperous Easy to control More functions Fast

Interface

model Fourth-order linear ordinary differential equation Identification experiment to determine five parameters fluorescence delay (fluorescence ≠ gene expression)

Applying model Ⅰ Task: increasing fluorescence 4 or 7 times over a 7-h period Open-loop(OL)control Fail to regulate fluorescence to desired levels due to inaccuracies of the model and something unpredictable

Applying model Ⅱ Closed-loop(CL) feedback control Kalman filter

Significance More predictable and accurate Avoid the disadvantage of bio-circuits Facilitate synthetic systems

Q ﹠ A