Copasi exercise Consider the following model Exercise:

Slides:

Advertisements

Similar presentations

Enzymes - Attempt 3 (your target + 1 up and down) E: Which monomer are enzymes made from? D: What is activation energy? C: Describe the effect of enzymes.

Advertisements

Aim: Creating the model of thermal decomposition of energetic material (tetryl). Data:4 results (data sets) of DSC experiment carried out in linear heating.

Numerical Analysis. TOPIC Interpolation TOPIC Interpolation.

Theory. Modeling of Biochemical Reaction Systems 2 Assumptions: The reaction systems are spatially homogeneous at every moment of time evolution. The.

Reinforcement Learning (II.) Exercise Solutions Ata Kaban School of Computer Science University of Birmingham 2003.

Åbo Akademi University & TUCS, Turku, Finland Ion PETRE Andrzej MIZERA COPASI Complex Pathway Simulator.

Simulation of Biological Systems using Dynetica. Dynetica is a simulation tool It can be downloaded for free from the web (

Exercise Exercise3.1 8 Exercise3.1 9 Exercise

Exercise Exercise Exercise Exercise

Exercise Exercise Exercise Exercise

Exercise Exercise6.1 7 Exercise6.1 8 Exercise6.1 9.

David Nickerson 1 (with help from Dagmar Waltemath 2 & Frank Bergmann 3 ) 1 Auckland Bioengineering Institute, University of Auckland 2 University of Rostock.

Reinforcement Learning (II.) Exercise Solutions Ata Kaban School of Computer Science University of Birmingham.

Polypeptide Chain Synthesis: A Paper Simulation Actitivy

COPYRIGHT © All rights reserved by Sound acoustics Germany The averaged quality measures over all test cases indicate the real influence of a test object.

Study of Pentacene clustering MAE 715 Project Report By: Krishna Iyengar.

Marc Fink & Yan Liu & Shangying Wang Student Project Proposal

There are two main kinds of polymers. Type 1: Addition Polymers Each small molecule adds to the end of a growing chain. Polyethylene is an example Type.

The Polytomous Unidimensional Rasch Model: Understanding its Response Structure and Process ACSPRI Social Science Methodology Conference, Sydney, December.

Reverse engineering of regulatory networks Dirk Husmeier & Adriano Werhli.

Thinking Mathematically Algebra: Equations and Inequalities 6.4 Linear Inequalities in One Variable.

Modeling and Simulation of Signal Transduction Pathways Mark Moeller & Björn Oleson Supervisors: Klaus Prank Ralf Hofestädt.

How to solve.  This method requires that a reaction be run several times.  The initial concentrations of the reactants are varied.  The reaction rate.

Q is the reaction quotient Gives the condition of the reaction at any point during the reaction. [X] o indicates the initial concentration of a species.

Chapter 3: Molecules of Life

Marc Fink & Yan Liu & Shangying Wang Student Project Proposal

Evaluating the Thermodynamics of Self and Cross-Clustering on Strongly Associating Systems Donald P. Visco, Jr., Department of Chemical Engineering, Tennessee.

Curve fitting methods for complex and rank deficient chemical data

4. organization of pigments

Pathway Modeling and Problem Solving Environments

Jingkui Wang, Marc Lefranc, Quentin Thommen Biophysical Journal

MBA 5008 Enthusiastic Study/snaptutorial.com

Volume 84, Issue 6, Pages (June 2003)

الاحتراق.

- PARTING KNOWLEDGE ABOUT FRACTIONAL NUMBERS

FPLC gel‐filtration analysis of RepA–WT and ΔN37.

Analysis of mutational effects of parameters on the phenotype (i. e

A Computational Study of the Solvation Chemistry of Zr4+ Cation

Numerical Study of the Entropy Loss of Dimerization and the Folding Thermodynamics of the GCN4 Leucine Zipper Jorge Viñals, Andrzej Kolinski, Jeffrey.

الفعل ورد الفعل ♠ ♠ ♠ مجلس أبوظبي للتعليم منطقة العين التعليمية

Today’s Objective BIO.3b-c

Reaction time زمن الرجع.

Enzymes - Attempt 3 (your target + 1 up and down)

Volume 13, Issue 12, Pages (December 2005)

Runs, Parameter Sets, Outputs and Projects

مديريت موثر جلسات Running a Meeting that Works

Volume 84, Issue 2, Pages (February 2003)

Jae Kyoung Kim, Krešimir Josić, Matthew R. Bennett Biophysical Journal

Volume 54, Issue 5, Pages (June 2014)

Chapter 7: Introduction to Sampling Distributions

Andreas Hilfinger, Thomas M. Norman, Johan Paulsson Cell Systems

Volume 85, Issue 4, Pages (October 2003)

Task 1: All-Optical Wavelength Converter (AOWC)

Three examples of mechanistic abstractions using macros.

Volume 8, Issue 5, Pages (November 2001)

Paolo Mereghetti, Razif R. Gabdoulline, Rebecca C. Wade

Quantifying the Interaction between EGFR Dimers and Grb2 in Live Cells

Daniel K. Schwartz, Department of Chemical & Biological Engineering

Volume 110, Issue 12, Pages (June 2016)

Oriol Canela-Xandri, Francesc Sagués, Javier Buceta

Scarlet S. Shell, Christopher D. Putnam, Richard D. Kolodner

Volume 8, Issue 5, Pages (November 2001)

Exercise Write 100 as a standard numeral. 1.

Jennifer D. Stone, Jennifer R. Cochran, Lawrence J. Stern

*Organic compounds= contain carbon

Volume 109, Issue 10, Pages (November 2015)

dsRBDs 3 and 4 of hStau1 dimerize on the RNA.

Self-Consistent Proteomic Field Theory of Stochastic Gene Switches

Paolo Mereghetti, Razif R. Gabdoulline, Rebecca C. Wade

Gennady V. Miloshevsky, Peter C. Jordan Biophysical Journal

Presentation transcript:

Copasi exercise Consider the following model Exercise: A protein can be in any of the following forms: monomer, dimer, trimer Two monomers form a dimer (reversible reaction) A monomer and a dimer form a trimer (reversible reaction) Exercise: Write the corresponding Copasi model Indicate reversible reactions wit h = rather than -> Run a deterministic numerical simulation Do parameter estimation to find the parameter values and the initial values Experimental data for the model: Time is in seconds Data is in micromoles Copasi exercise November 5, 2008 Jelgava, Latvia