README.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# BMC - Notes on Scientific Computing for Biomechanics and Motor Control\n",
    "\n",
    "Marcos Duarte and Renato Watanabe\n",
    "\n",
    "This repository is a collection of lecture notes and code on scientific computing and data analysis for Biomechanics and Motor Control.  \n",
    "These notes (notebooks) are written using [Jupyter Notebook](http://jupyter.org/), part of the [Python ecosystem for scientific computing]( http://scipy.org/).\n",
    "\n",
    "## Introduction\n",
    "\n",
    "* [Biomechanics](./notebooks/Biomechanics.ipynb)  \n",
    "* [The Biomechanics and Motor Control Laboratory @ UFABC](./notebooks/BMClab.ipynb)  \n",
    "\n",
    "## Scientific programming\n",
    "\n",
    "* [Python for scientific computing](./notebooks/PythonForScientificComputing.ipynb)  \n",
    "* [Python tutorial](./notebooks/PythonTutorial.ipynb)\n",
    "* [Version control with Git and GitHub](./notebooks/VersionControlGitGitHub.ipynb)  \n",
    "* [Code structure for data analysis](./notebooks/CodeStructure.ipynb)  \n",
    "\n",
    "## Numerical data analysis\n",
    "\n",
    "* [Scalar and vector](./notebooks/ScalarVector.ipynb)  \n",
    "* [Basic trigonometry](./notebooks/TrigonometryBasics.ipynb)  \n",
    "* [Matrix](./notebooks/Matrix.ipynb)  \n",
    "* [Descriptive statistics](./notebooks/Statistics-Descriptive.ipynb)  \n",
    "* [Bayesian Statistics](./notebooks/statistics_bayesian.ipynb)  \n",
    "* [Confidence and prediction intervals](./notebooks/ConfidencePredictionIntervals.ipynb)  \n",
    "  * [Prediction ellipse and prediction ellipsoid](./notebooks/PredictionEllipseEllipsoid.ipynb)  \n",
    "* [Curve fitting](./notebooks/CurveFitting.ipynb)  \n",
    "  * [Polynomial fitting](./notebooks/PolynomialFitting.ipynb)  \n",
    "* [Propagation of uncertainty](./notebooks/PropagationUncertainty.ipynb)  \n",
    "* Frequency analysis  \n",
    "  * [Basic properties of signals](./notebooks/SignalBasicProperties.ipynb)  \n",
    "  * [Fourier series](./notebooks/FourierSeries.ipynb)\n",
    "  * [Fourier transform](./notebooks/FourierTransform.ipynb)\n",
    "* [Data filtering in signal processing](./notebooks/DataFiltering.ipynb)  \n",
    "  * [Residual analysis for the optimal cutoff frequency](./notebooks/ResidualAnalysis.ipynb)  \n",
    "* [Ordinary Differential Equation](./notebooks/OrdinaryDifferentialEquation.ipynb)  \n",
    "* [Optimization](./notebooks/Optimization.ipynb)  \n",
    "* Change detection  \n",
    "  * [Detection of peaks](./notebooks/DetectPeaks.ipynb)  \n",
    "  * [Detection of onset](./notebooks/DetectOnset.ipynb)  \n",
    "  * [Detection of changes using the Cumulative Sum (CUSUM)](./notebooks/DetectCUSUM.ipynb)  \n",
    "  * [Detection of sequential data](./notebooks/detect_seq.ipynb)  \n",
    "* [Time normalization of data](./notebooks/TimeNormalization.ipynb)  \n",
    "* [Ensemble average](./notebooks/EnsembleAverage.ipynb)  \n",
    "* [Select data vectors by similarity using a metric score](./notebooks/Similarity.ipynb)  \n",
    "* [Open files in C3D format](./notebooks/OpenC3Dfile.ipynb)  \n",
    "\n",
    "## Mechanics\n",
    "\n",
    "### Kinematics\n",
    "\n",
    "* [Frame of reference](./notebooks/ReferenceFrame.ipynb)  \n",
    "* [Time-varying frame of reference](./notebooks/PathFrame.ipynb)\n",
    "* [Polar and cylindrical frame of reference](./notebooks/PolarBasis.ipynb)\n",
    "* [Kinematics of particle](./notebooks/KinematicsParticle.ipynb)  \n",
    "  * [Projectile motion](./notebooks/ProjectileMotion.ipynb)  \n",
    "  * [Spatial and temporal characteristics](./notebooks/SpatialTemporalCharacteristcs.ipynb)  \n",
    "  * [Minimum jerk hypothesis](./notebooks/MinimumJerkHypothesis.ipynb)  \n",
    "* [Kinematics of Rigid Body](./notebooks/KinematicsOfRigidBody.ipynb)  \n",
    "  * [Angular kinematics (2D)](./notebooks/KinematicsAngular2D.ipynb)  \n",
    "  * [Kinematic chain](./notebooks/KinematicChain.ipynb)  \n",
    "  * [Rigid-body transformations (2D)](./notebooks/Transformation2D.ipynb)  \n",
    "  * [Rigid-body transformations (3D)](./notebooks/Transformation3D.ipynb)  \n",
    "  * [Determining rigid body transformation using the SVD algorithm](./notebooks/SVDalgorithm.ipynb)  \n",
    "\n",
    "### Kinetics\n",
    "\n",
    "* [Fundamental concepts](./notebooks/KineticsFundamentalConcepts.ipynb)  \n",
    "* [Center of Mass and Moment of Inertia](./notebooks/CenterOfMassAndMomentOfInertia.ipynb)  \n",
    "* [Newton Laws for particles](./notebooks/newtonLawForParticles.ipynb)\n",
    "* [Newton-Euler Laws](./notebooks/newton_euler_equations.ipynb)\n",
    "* [Free body diagram](./notebooks/FreeBodyDiagram.ipynb)\n",
    "  * [Free body diagram for particles](./notebooks/FBDParticles.ipynb)\n",
    "  * [Free body diagram for rigid bodies](./notebooks/FreeBodyDiagramForRigidBodies.ipynb)\n",
    "* [3D Rigid body kinetics](./notebooks/Kinetics3dRigidBody.ipynb)\n",
    "* [Matrix formalism of the Newton-Euler equations](./notebooks/MatrixFormalism.ipynb)  \n",
    "* [Lagrangian Mechanics](./notebooks/lagrangian_mechanics.ipynb)  \n",
    "\n",
    "## Modeling and simulation of human movement\n",
    "\n",
    "* [Body segment parameters](./notebooks/BodySegmentParameters.ipynb)\n",
    "* [Muscle modeling](./notebooks/MuscleModeling.ipynb)  \n",
    "* [Muscle simulation](./notebooks/MuscleSimulation.ipynb)  \n",
    "* [Musculoskeletal modeling and simulation](./notebooks/MusculoskeletaModelingSimulation.ipynb)  \n",
    "* [Multibody dynamics of simple biomechanical models](./notebooks/MultibodyDynamics.ipynb)  \n",
    "\n",
    "## Biomechanical tasks Analysis\n",
    "\n",
    "* [The inverted pendulum model of the human standing posture](./notebooks/IP_Model.ipynb)\n",
    "* [Measurements in stabilography](./notebooks/Stabilography.ipynb)  \n",
    "* [Rambling and Trembling decomposition of the COP](./notebooks/IEP.ipynb)  \n",
    "* [Biomechanical analysis of vertical jumps](./notebooks/VerticalJump.ipynb)  \n",
    "* [Gait analysis (2D)](./notebooks/GaitAnalysis2D.ipynb)  \n",
    "* Force plates  \n",
    "  * [Kistler force plate calculation](./notebooks/KistlerForcePlateCalculation.ipynb)  \n",
    "  * [Zebris pressure platform](./notebooks/ReadZebrisPressurePlatformASCIIfiles.ipynb)  \n",
    "\n",
    "## Electromyography\n",
    "\n",
    "* [Introduction to data analysis in electromyography](./notebooks/Electromyography.ipynb)  \n",
    "\n",
    "## How to cite this work\n",
    "\n",
    "Here is a suggestion to cite this GitHub repository:\n",
    "\n",
    "> Duarte, M., Watanabe, R.N. (2018) Notes on Scientific Computing for Biomechanics and Motor Control. GitHub repository, <https://github.com/BMClab/BMC>.\n",
    "\n",
    "And a possible BibTeX entry:\n",
    "\n",
    "```tex\n",
    "@misc{Duarte2018,  \n",
    "    author = {Duarte, M. and Watanabe, R.N.},\n",
    "    title = {Notes on Scientific Computing for Biomechanics and Motor Control},  \n",
    "    year = {2018},  \n",
    "    publisher = {GitHub},  \n",
    "    journal = {GitHub repository},  \n",
    "    howpublished = {\\url{https://github.com/BMClab/BMC}}  \n",
    "}\n",
    "```\n",
    "\n",
    "## License\n",
    "\n",
    "The non-software content of this project is licensed under a [Creative Commons Attribution 4.0 International License](http://creativecommons.org/licenses/by/4.0/), and the software code is licensed under the [MIT license](https://opensource.org/licenses/mit-license.php).\n"
   ]
  }
 ],
 "metadata": {
  "hide_input": false,
  "kernelspec": {
   "display_name": "Python 3",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.7.6"
  },
  "toc": {
   "base_numbering": 1,
   "nav_menu": {},
   "number_sections": true,
   "sideBar": true,
   "skip_h1_title": true,
   "title_cell": "Contents",
   "title_sidebar": "Contents",
   "toc_cell": true,
   "toc_position": {},
   "toc_section_display": true,
   "toc_window_display": false
  },
  "varInspector": {
   "cols": {
    "lenName": 16,
    "lenType": 16,
    "lenVar": 40
   },
   "kernels_config": {
    "python": {
     "delete_cmd_postfix": "",
     "delete_cmd_prefix": "del ",
     "library": "var_list.py",
     "varRefreshCmd": "print(var_dic_list())"
    },
    "r": {
     "delete_cmd_postfix": ") ",
     "delete_cmd_prefix": "rm(",
     "library": "var_list.r",
     "varRefreshCmd": "cat(var_dic_list()) "
    }
   },
   "types_to_exclude": [
    "module",
    "function",
    "builtin_function_or_method",
    "instance",
    "_Feature"
   ],
   "window_display": false
  },
  "widgets": {
   "application/vnd.jupyter.widget-state+json": {
    "state": {},
    "version_major": 2,
    "version_minor": 0
   }
  }
 },
 "nbformat": 4,
 "nbformat_minor": 4
}