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Foundations of Algorithms and Computational Techniques in Systems Biology >> Content Detail



Lecture Notes



Lecture Notes

This section contains documents created from scanned original files, which are inaccessible to screen reader software. A "#" symbol is used to denote such documents.

Notes from lectures 3 through 25 are courtesy of Laura Proctor. Used with permission.


LEC #TOPICS
Protein Modeling
1Introduction and Protein Modeling Questions (PDF)
2Models of Proteins (PDF)
3Discrete Conformational Search (PDF)#
4Binding and Docking (PDF)#
5Molecular Dynamics Simulation (PDF)#
6Molecular Dynamics and Electrostatics (PDF)#
7Continuum Electrostatic Modeling I (PDF)#
8Continuum Electrostatic Modeling II (PDF)#
9Electrostatic Optimization and Design (PDF)#
10Electrostatics Modeling (PDF 1)# (PDF 2)#
11Statistical Mechanics (PDF)#
Network Modeling
12Statistical Mechanics (cont.) (PDF)#
13Formulating and Simulating Network Models in Biology (PDF)#
14Formulating Models (PDF)#
15Nonlinear Dynamics and Stability (PDF)#
16Steady-State Problems (PDF)#
17Parameter Fitting and Estimation (PDF)#
18Parameter Estimation; Robustness, Fragility, Control (PDF)#
Image Modeling
192-D and 3-D Light Microscopy; Image Reconstruction (PDF)#
20Deconvolution (PDF)#
21Deconvolution II (PDF)#
22Blind Deconvolution (PDF)#
23Optical Flow (PDF)#
24High-Throughput Data and its Analysis (PDF)#
25Inference and Statistics (PDF)#
26Roundup



Supplemental Notes


Adjoint Sensitivity Analysis for Optimization (PDF) (Courtesy of Joshua Apgar and Jared Toettcher. Used with permission.)


 








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