rnwatanabe / BMC

Notes on Scientific Computing for Biomechanics and Motor Control

BMC - Notes on Scientific Computing for Biomechanics and Motor Control

Marcos Duarte and Renato Watanabe

This repository is a collection of lecture notes and code on scientific computing and data analysis for Biomechanics and Motor Control.
These notes (notebooks) are written using Jupyter Notebook, part of the Python ecosystem for scientific computing.

Introduction

• Biomechanics
• The Biomechanics and Motor Control Laboratory @ UFABC

Scientific programming

• Python for scientific computing
• How to install Python
• Python tutorial
• Version control with Git and GitHub
• Code structure for data analysis

Numerical data analysis

• Scalar and vector
• Basic trigonometry
• Matrix
• Descriptive statistics
• Confidence and prediction intervals
  • One-dimensional intervals
  • Prediction ellipse (2D) and prediction ellipsoid (3D)
• Curve fitting
  • Fundamentals of curve fitting
  • Polynomial fitting
• Propagation of uncertainty
• Frequency analysis
  • Basic properties of signals
  • Fourier series
  • Fourier transform
• Signal processing
  • Data filtering
  • Residual analysis for the optimal cutoff frequency
• Ordinary Differential Equation
• Optimization
• Change detection
  • Detection of peaks
  • Detection of onset
  • Detection of changes using the Cumulative Sum (CUSUM)
  • Detection of sequential data
• Time normalization of data
• Ensemble average
• C3D files
  • C3D format
  • Read C3D files using the EZC3D library

Mechanics

Kinematics

• Frame of reference
• Time-varying frame of reference
• Polar and cylindrical frame of reference
• Kinematics of particle
  • One-dimensional motion
  • Projectile motion
  • Spatial and temporal characteristics
  • Minimum jerk hypothesis
• Kinematics of Rigid Body
  • Angular kinematics (2D)
  • Kinematic chain
  • Velocity and Acceleration of a point of a rigid body
  • Rigid-body transformations (2D)
  • Rigid-body transformations (3D)
  • Angular velocity in of a rigid body in three dimensions
  • Determining rigid body transformation using the SVD algorithm

Kinetics

• Fundamental concepts
• Center of Mass and Moment of Inertia
• Newton Laws for particles
• Newton-Euler Laws
• Free body diagram
  • Free body diagram for particles
  • Free body diagram for rigid bodies
• 3D Rigid body kinetics
• Matrix formalism of the Newton-Euler equations
• Lagrangian Mechanics

Modeling and simulation of human motion

• Body segment parameters
• Muscle modeling
• Muscle simulation
• Musculoskeletal modeling and simulation
• Multibody dynamics of simple biomechanical models

Human motion data analysis

• The inverted pendulum model of the human standing posture
• Measurements in stabilography
• Rambling and Trembling decomposition of the COP
• Biomechanical analysis of vertical jumps
• Gait analysis (2D)
• Force plates
  • Kistler force plate calculation
  • Zebris pressure platform

Electromyography

• Introduction to data analysis in electromyography

How to cite this work

Here is a suggestion to cite this GitHub repository:

Duarte, M., Watanabe, R.N. (2018) Notes on Scientific Computing for Biomechanics and Motor Control. GitHub repository, https://github.com/BMClab/BMC.

And a possible BibTeX entry:

@misc{Duarte2018,  
    author = {Duarte, M. and Watanabe, R.N.},
    title = {Notes on Scientific Computing for Biomechanics and Motor Control},  
    year = {2018},  
    publisher = {GitHub},  
    journal = {GitHub repository},  
    howpublished = {\url{https://github.com/BMClab/BMC}}  
}

License

The non-software content of this project is licensed under a Creative Commons Attribution 4.0 International License, and the software code is licensed under the MIT license.