My Masters Thesis Open Notebook
This is the open notebook of my thesis project. I will collect here all the ideas and notes I will come across in this period; I hope you will find them useful (however, don't take them too seriously!) for your research too!
Modelling Life: a Systems Biology Approach
Brief Introduction to Molecular Cell Biology
DNA, Genes and RNA
Proteins as Sensors and Actuators
Measurement Approaches
Model Organisms
Cells from a Control System-Theoretic Perspective
Dimerizations
Bifurcations
Activation and Inhibition as Control Mechanisms
Species Interaction and Modelling Formalisms
Phase Space and Step Response
Systems Properties and Modelling Formalisms
Biological Systems Properties
Challenges to Control Systems Theory in Molecular Biology
Realization and Identification Issues
Consistent Graphs and Monotone Systems
Manipulating Life: Engineering Cellular Logic Gates
Biochemical Reaction Systems and Models
Kinetic Models
Detailed Kinetic Models
Simplified Kinetic Models
Example: Modelling a Signal Trasduction System
Ordinary Differential Equation based Representation
[math]\displaystyle{ \pi }[/math]-calculus and Stochastic [math]\displaystyle{ \pi }[/math]-calculus
Stochastic Differential Equation Representation
Hybrid Networks
Representations
Deterministic and Probabilistic Boolean Networks
Petri Networks
Bayesian Networks
The EGFR model
Kholodeko's Model
Oda's Model
Systems Structural and Dynamic Properties Investigation in Systems Biology
Connectivity
Cohesive Subgroups
N-Clicque
K-Plex
K-Core
λ-sets
Radius of a Graph
Jacobian
Elasticity and Plasticity
Sensitivity
Eigenvalues
Stability
Oscillations
Systems Identification Theory in Systems Biology
General Framework for System Identification Experiments
Transfer Function Identification
Spectral Identification
State Space Models Identification
Box-Jenkins and Derived Models
AR/ARX Models
ARMA/ARMAX Models
I/O Error
ARAR/ARXAR
NARMA
Model Sets, Model Structures and Identifiability
Asymptotic Distribution of Parameter Estimates in Fitness Function Design
Prediction Error
Final Prediction Error
Akaike Information Criterion
Minimum Description Length
Asymptotic Variance
Frequency Domani Expression of the Asymptotic Variance
Algorithms for System Identification
Prediction Error Minimization
Linear Regressions, Least Squares Method and Maximum Likelihood Method
Heuristic Approaches in System Identification
Genetic Algorithms
Pattern Search Methods
Hybrid Algorithms
Characterizing Spectral Properties for Optimal Experimental Design in Systems Biology
Fisher Information Matrix
Cramer-Rao Inequality and Cramer-Rao Bound
A, D, E, L Optimality Methods
Specific pathway properties elicitation via time varying driving inputs
Informative Dataset
Convergence and Consistency
Covariance Matrix and Identifiability
Persistence of excitation
Experimental Design
Open loop identification
Closed loop identification
Algorithms for System Identification
Developing and Constraining Input Signals
Micropumps and Micropumping Systems
Technological Constraints to Systems Perturbations in Bioreactors
Microfluidics Systems for Cell Stimulation
Model Simulations in Integrated Environments
Systems Biology Toolbox (MATLAB)
SimBio Toolbox (MATLAB)
Potterswheel Toolbox (MATLAB)
Systems Biology Workbench
Jarnac
Jacobian Viewer
Structural Analysis GUI
Bifurcation Discovery
Oscill8
Microfluidics and Optoelectronics for System Identification in Systems Biology
Theoretical Introduction to Microfluidics and Optoelectronics
Fluids and Mechanical Equilibrium
Hydraulic Resistance
Diffusion
Micropumps and Micro-pumping Systems
Opto-spectroscopy
Developing Application Specific Microfluidics Chips: Modules and Systems
Modulating Signals in Microfluidics Channels
Droplet based Approaches
Controllig Diffusion Phenomena
T-Shape Micromixer
Magnetically Driven Micro-Mixing
Ferrofluid Based Mixing
Physical Phenomena based Signal Modulation: Controlling Flow and Instability
Proportional Flow Controller
Rayleigh-Taylor Instability
Kelvin-Helmholtz Instability
von Karman Vortex Streets
Evaluating Bio-Compatibility of Optofluidic Devices
Integrating Microfluidics and Optoelectronics towards Optofluidics: Labrys
Labrys web page on OWW
Design Principles
Fluid Dynamics Simulations
Implementation Details and PDMS Technology
Numerical Simulations
Model Discrimination via Constrained/Time-Varying Input Stimuli: a Conceptual Framework with Applications
Conclusions