Lectures on animal locomotion
by Manny Azizi and Matt McHenry, UC Irvine (2020).
by Manny Azizi and Matt McHenry, UC Irvine (2020).
Awesome Biomechanics
A curated, public list of resources for biomechanics and human motion analysis: datasets, processing tools, software for simulation, educational videos, lectures, etc.
This page lists names, links and short descriptions. The original list on GitHub is the source and belongs to its authors.
Learning >Online Courses
Lectures on multibody dynamics
by Jason Moore at UC Davis (2017).
KNES 789W - Advanced Projects in Kinesiology; Modeling & Simulation of Human Movement
by Ross Miller, University of Maryland (2020).
Mathematical Tools for Neuroscience (Neurobio 212 at Harvard)
by Ella Batty et al. (2021).
Mechanical Systems Design
by Steve Collins (Biomechatronics Lab, Stanford University). A Junior-level course that develops experience and confidence with: 1. An approach to mechanical systems design that incorporates ideation, back-of-the-envelope analysis, computational analysis, and prototyping, iteratively and with an…
Neuromechanics course material
by Joshua Cashaback (University of Delaware).
Graduate Level Statistics Course with Biomedical Engineering Examples
by Joshua Cashaback (University of Delaware).
Neuromatch Academy
the Neuromatch Academy aims to introduce traditional and emerging tools of computational neuroscience to trainees.
Robotics 101: Computational Linear Algebra
by University of Michigan Robotics Institute (Fall 2020). The course includes lecture videos and GitHub resources, including the lecture notes.
Quantitative methods in biomedical sciences
16 week class taught by Ken Campbell at the University of Kentucky. A graduate-level class designed for PhD students and others who wish to develop skills relating to data analysis and interpretation, including data handling, plotting, statistics, and image analysis. The course uses MATLAB and…
Sport Biomechanics Lecture Series
curated by Stuart McErlain-Naylor. Includes introductory topics like presentations of motion capture techniques by Vicon (lecture 1 and lecture 2) and an introduction of electromyography (EMG) by Delsys.
BPK 409: Wearable Technology and Human Physiology
by Max Donelan (Simon Fraser University). The course teaches to use state-of-the-art wearable technology to measure, analyze, and understand human physiological systems including muscular, nervous, and cardiovascular systems. 📄 description of labs | 💾 code
Introduction to Reinforcement Learning with David Silver
by David Silver, DeepMind (2015).
Statistical shape modelling
by the Graphics and Vision research group of the University of Basel. This is an introductory course in statistical shape modelling (partially hosted on Futurelearn). Its focus lies on the concept of Gaussian processes, and how these can be used to model shape variability. It also discusses simple…
Learning >YouTube Channels
Biomch-V
includes videos from the 2015 Congress of the International Society of Biomechanics.
BOOM: Biomechanics On Our Minds
videos of the postcad hosted by Melissa Boswell and Hannah O'Day (Stanford University). They talk to researchers around the world about the exciting field of biomechanics. They also cover overcoming failures, collaborations, open science, leadership, and more.
International Society of Biomechanics in Sports (ISBS)
videos from ISBS2020 virtual conference.
Neuromech TV
by the Research Group on Applied Neuromechanics from the Federal University of Pampa, Brazil. It aims to help students and scientists interested in the study of the human movement, and its related topics.
UCalgary Human Performance Lab
lots of very interesting videos from the ISB/ASB2019 (joint congresses of the International Society of Biomechanics and American Society Biomechanics) and Dynamic Walking 2019 conferences.
BassettBiomechanics
includes a Biomechanics of the Musculoskeletal System course and Visual3D tutorials.
Sport Biomechanics Lecture Series
curated by Stuart McErlain-Naylor. Includes introductory topics like presentations of motion capture techniques by Vicon (lecture 1 and lecture 2) and an introduction of electromyography (EMG) by Delsys.
Learning >Videos
A critique of Induced Acceleration Analysis
by Andy Ruina (WCB2014).
Analysis of upright posture by force platform (in Portuguese with English subtitles)
videos produced by Felipe Fava de Lima about the use of force plataforms.
Biomechanics playlist
by Kath Boyer. Playlist of Youtube videos of biomechanical interest.
CNB-ASB Muscle Workshop
presentations on the topic Integrative Muscle Modelling for Neuromechanics.
F8 2019 - VR Full Body Tracking & Avatars
and blog post
Running with bone pins
video of data collection in subject running with bone pins shared by Ton Van den Bogert.
Introduction to Trajectory Optimization
by Matthew Kelly. Very clear introduction to the topic with MATLAB resources linked in the video description.
A free/opensource workflow from CT scan to FEA
by Peter L. Falkingham: workflow for carrying out finite element analysis (FEA) using free and open-source software (Dragonfly for segmentation, Blender for mesh refinement and FEBio for finite element analysis. Quick overview of the main steps.
Learning >Learning to Code
Python official website
is by far the most popular language in science, due in no small part to the ease at which it can be used and the vibrant ecosystem of user-generated packages. To install packages, there are two main methods: Pip (invoked as pip install), the package manager that comes bundled with Python, and…
In 8 listsDetails
Scipy Lecture Notes
a set of tutorials on the scientific Python ecosystem: a quick introduction to central tools, modules and techniques.
Scientific Python Lectures
Lectures on scientific computing with python, as IPython notebooks by Robert Johansson.
In 3 lists
The Hitchhiker’s Guide to Python
by Real Python. A very comprehensive guide about various aspects of scripting in Python and structuring Python projects.
In 2 lists
Python for Everybody
a freely available book to learn how to use Python. A pdf is available here.
Python Programming And Numerical Methods: A Guide For Engineers And Scientists
by the University of California, Berkeley. Materials used in the class E7: Introduction to computer programming for scientists and engineers.
Google Python Style Guide
is a style guide of dos and don’ts used in Google Python programs. Useful to set some guidelines on how you write code.
In 5 listsDetails
Python testing style guide
few suggestions on how to write tests for your python code.
Matplotlib cheatsheet
Official cheatsheets for the Matplotlib plotting library in Python.
In 3 lists
Notes on Scientific Computing for Biomechanics and Motor Control
by Marcos Duarte and Renato Watanabe. A beautiful collection of lecture notes and code on scientific computing and data analysis for Biomechanics and Motor Control in the form of Jupyter notebooks (python).
Biomechanical Analysis using Python and Kinetics Toolkit
by Félix Chénier. A free electronic book that guides new programmers from the basics to advanced, generic 3D biomechanical analysis. It is a precious resource because it includes practical tips to start programming, including Python and IDE setup.
Julia Language website
High-level, general-purpose dynamic programming language suited for numerical analysis and computational science; :heavy_plus_sign: VimBindings.jl - A Julia package which emulates Vim directly in the Julia REPL
In 5 listsDetails
Julia Academy
a collection of free learning resources for Julia, ranging from the basics to advanced topics.
Version Control for Researchers
by Ryan Alcantara. Tutorial for ASB2020 introducing GitHub and version control for biomechanists. Accompanying tutorial material located at the ASB_Tutorial repository.
Software Carpentries (ENG + ESP)
an amazing set of lectures on version control with Git, but also on how to use the Unix shell and Python.
In 2 lists
Atlassian Git tutorial
the most approachable and complete tutorials for git I have found online.
In 2 lists
Learning >Teaching Resources
Anatomy Standard
by Jānis Šavlovskis and Kristaps Raits (2020). Project aiming at creating an evidence-based 3D model of the human body, create high-quality, interactive illustrations of the model, and share them here to provide a resource for teaching and explaining anatomy. Images are licensed under the Creative…
Anybodyrun
by AnyBody Technology. This is a website where you can generate videos of full-body models of running based on principal components analysis. The approach behind the application is described on John Rasmussen's blog.
Bayesian Data Analysis course
by AKi Vehtari at Aalto University (2020). 💾 code | 📄 book
Biomch-L discussions
classic discussions from the archives of the LISTSERV Biomch-L database:
Joint Attitude Debate Summary
by H. J. Woltring (1990).
3D Joint Power Debate Summaary
by J. Rubenson (2004).
Engineers Code
collection of Python :snake: resources developed by Lorena Barba et al. for teaching engineering computation.
Graphical User Interfaces (GUI) for Research
course by Imperial College London on principles to build research GUI. GitHub resources available at this link. Recording of the lessons are available on Youtube.
How to get meaningful and correct results from your finite element model
by Martin Baeker (2018). This document gives guidelines to set up, run, and postprocess correct simulations with the finite element method. It is not an introduction to the method itself, but rather a list of things to check and possible mistakes to watch out for when doing a finite element…
Julia notebooks on dynamic systems
by Adam MacLean (2021).
Muscle Atlas
by the Dept of Radiology of the University of Washington. The medical illustrations contained in this online atlas are copyrighted © 1997 by the University of Washington but receiving a license to use these images is generally quite easy, particularly for academic and scholarly purposes. For more…
ASB Teaching Repository
by the American Society of Biomechanics. Does not require membership to access.
Biomechanics Toolbar
by Jos Vanrenterghem (2016). The Biomechanics Toolbar is freeware designed to make data processing more accessible for undergraduate teaching. It works as a traditional toolbar in Microsoft Excel.
Biomechanics of Movement Classroom
by Tom Uchida et al. (2021). Free resources associated with the book Biomechanics of Movement: The Science of Sports, Robotics, and Rehabilitation.
Biomechanics of Movement
video lectures by Scott Delp. Lectures for the accompanying book by Uchida and Delp.
Scientific Animation of Muscle Contraction
by Brule Design Studio. Press Demo to try it.
Scientific Animation of Human Locomotion
by Brule Design Studio. Press Demo to try it.
Kwon3d website
website with theory about most basic topics in biomechanics.
GitHub resources for teaching
GitHub offers support for automating certain aspects of teaching.
How to review a paper
from Science Magazine.
How to write a systematic review for Health
by the University of Tasmania.
A roadmap for searching literature in PubMed
by Vrije Universiteit Amsterdam.
Interactive Simulations for Science and Math
by the University of Colorado Boulder. Very intuitive and interactive simulations of phenomena and notions from Physics, Chemistry, Math, Earth Science and Biology.
In 2 lists
Kuo's course homeworks
interesting homework materials used in Art Kuo's courses (public on GitHub).
Manim: Mathematical Animation Engine
by Grant Sanderson. Manim is an engine for precise programatic animations, designed for creating explanatory math videos similar to those presented in the contents of 3Blue1Brown.
In 2 lists
MoLib (Motion Library)
from The Biomechanist: sample experimental data collected on one participant intended as tutorial for OpenSim processing. See related post by Markus Kurz.
Trajectory Optimization Toolbox
by Matthew Kelly, including some excellent examples and some course materials.
In 2 lists
Notes on Scientific Computing for Biomechanics and Motor Control
by Marcos Duarte and Renato Watanabe. A beautiful collection of lecture notes and code on scientific computing and data analysis for Biomechanics and Motor Control in the form of Jupyter notebooks (python).
Optimal Control Workshop
by BJ Fregly. Files distributed at the NSF-funded Optimal Control Workshop held on July 9, 2015 at the University of Edinburgh as part of the XV International Symposium on Computer Simulation in Biomechanics.
OpenSim teaching Hub
by the OpenSim Team. Includes materials from the Neuromuscular Biomechanics Lab in the Department of Bioengineering at Stanford University. Does not require membership to access.
ODE Integration Best Practices With Octave/Matlab
by by Jason Moore from his EME 171: Analysis, Simulation and Design of Mechatronic Systems course at UC Davis.
Seeing theory
a visual introduction to probability and statistics by Daniel Kunin (Brown University).
In 3 lists
Teaching and Learning with Jupyter
by Lorena Barba et al. (2019). This is a collaboratively written book including explanations and examples on many key topics of interest for those interested in using Jupyter in the classroom.
Tips for setting up remote lessons
by Grant Sanderson, from the 3blue1brown Youtube Channel.
Tutorial: 3D Kinematics and Inverse Dynamics MATLAB scripts
by Raphael Dumas, including some examples.
Tutorial: Musculoskeletal Model for Simulation of Walking
by Van den Bogert's tutorial (Dynamic Walking, 2011), including a section on computational muscle modelling and one on walking simulation using a 2D musculoskeletal model.
Tutorial: Kane’s Method for an inverted pendulum
by Ross Miller. A tutorial on Kane's Method for deriving equations of motion, demonstrated on an inverted pendulum.
VIRTUAL LAB: Australopithecus afarensis KNEE JOINT
by John Hawks Laboratory (University of Wisconsin-Madison).
VIRTUAL LABS IN BIOLOGICAL ANTHROPOLOGY
by John Hawks Laboratory (University of Wisconsin-Madison).
Understanding p-values Through Simulations: An Interactive Visualization
by Kristoffer Magnusson (2021). The goal of the page is to explain p-values through an interactive simulations.
Python Tutor - Visualize code execution
this website helps understanding what happens as the computer runs each line of code. It can be used to run for running Python, Java, C, C++, JavaScript, and Ruby code in a web browser and see its execution visualized step by step.
In 3 lists
NonlinearContinuumMechanics
by Kevin Moerman, A Jupyter notebook featuring a detailed treatment of Ogden hyperelastic formulations and their implementation for uniaxial loading based model response analysis. Both theory and numerical implementation of the constrained, uncoupled, and coupled (unconstrained) formulations is…
Learning >Books
Biomechanics and Motor Control of Human Movement (4th Edition)
by David A. Winter.
Calculus made Easy
by Silvanus P. Thompson.
In 2 lists
Computer-Aided Analysis of Mechanical Systems
by P.E. Nikravesh (1998).
Computer Aided Kinematics And Dynamics Of Mechanical Systems
by Edward J. Haug (1989).
Convex Optimization
by Steven Boyd and Lieven Vandenberghe (2004).
In 2 lists
Dynamics: Theory and Applications
by Kane and Levinson (1985).
Dynamics of Human Gait (2nd Edition)
by Christopher Vaughan, Brian Davis and Jeremy O'Connor (1999).
Experimental Methods in Biomechanics (link)
by John Challis (2021).
Handbook of Human Motion (First Edition)
Editors-in-Chief Bertram Müller and Sebastian I. Wolf (2018). This book is a large cross-disciplinary reference work which covers the many interlinked facets of the science and technology of human motion and its measurement.
Power Analysis with Superpower
by Caldwell et al. (2021). The book displays a variety of ways the R Superpower package can be used for power analysis and sample size planning for factorial experimental designs.
Reinforcement Learning: An Introduction
by Richard S. Sutton and Andrew G. Barto (2018).
In 2 lists
Research Methods in Biomechanics (Second Edition)
by Gordon Robertson, Graham Caldwell, Joseph Hamill, Gary Kamen, and Saunders Whittlesey (2014). This book demonstrates the range of available research techniques and how to best apply this knowledge to ensure valid data collection.
The ABC of EMG
by Peter Konrad (2005).
The Feynman Lectures on Physics
by Richard Feynman (1961-1963). Includes audio recordings.
In 2 lists
Gait Analysis and Motion Capture >Gait Analysis Markersets
LAMB
by Marco Rabuffetti et al. (2019).
Gait Analysis and Motion Capture >Motion Capture Data Import and Processing
c3dserver
C++/MATLAB)
ezc3d: An easy C3D file I/O cross-platform solution for C++, Python and MATLAB
(C++/MATLAB/Python) by Benjamin Michaud et al. (2021). Ezc3d is a light and comprehensive library that allows to easily read and write c3d files. The C++ core includes an API for fast file I/O library, and convenient MATLAB and Python3 interfaces for researchers. It supports c3d files from the…
MOKKA
GUI built on BTK functionalities. Allows visualisation of c3d contents and basic processing, such as filtering and event detection. Great open source alternative to Vicon Nexus for these functionalities. 💻 (unofficial) tutorial by biomechanist.net
Subject-Specific Modelling >Segmentation of Medical Images
3DSlicer
3D Slicer is an open source software platform for medical image informatics, image processing, and three-dimensional visualization. 📄 paper (Slicer v4) | 💻 website | 📄 Documentation | 🎥 Youtube tutorials; Extensions of 3DSlicer:; SlicerMorph by Sara Rolfe et al. (2020). SliceMorph is a toolkit…
Dragonfly
by Object Research Systems. Dragonfly is a software platform for the intuitive inspection and processing of multi-scale multi-modality image data. Includes a Deep Learning tool for training deep models for image segmentation and regression tasks. It also offers rendering capabilities and…
ITK-Snap
📄 paper | 🎥 Video tutorials
InVesalius
📄 paper list | 🎥 Youtube tutorials
Materialise Mimics
(commercial)
MITK
📄 paper | 📄 tutorials
MITK-GEM
is based on MITK but includes also mesh processing functionalities. Aimed to generation of finite element models. 📄 paper | 💻 website | resources
Rhino3Dmedical
commercial. 🎥 webinar
SASHIMI Segmentation
sushi: by Bart Bolsterlee. SASHIMI Segmentation is a MATLAB App for segmentation of multi-slice images.
Simpleware ScanIP
(commercial).
Subject-Specific Modelling >Manipulation, Processing and Comparison of Surface Meshes
Autodesk Netfabb
is a software that offers a complete toolset for design and implementation for additive manufacturing. It streamlines workflows and automates processes around 3D print preparation. The software also includes access to Fusion 360, Fusion 360 Team, and additional capabilities through Fusion 360…
In 2 lists
Blender Remeshing Guide
by Eva Herbst.
Gmsh
Three-dimensional finite element mesh generator with pre- and post-processing facilities. (C++, GPL, GitLab)
In 2 lists
CloudCompare
allows quantitative comparison of surface meshes.
Subject-Specific Modelling >Volumetric Meshers of Surface Models
NetGen
source
Hypermesh
(commercial): HyperMesh is a multi-disciplinary finite element pre-processor which manages the generation of large, complex models, starting with the import of a CAD geometry.
CUBIT (The CUBIT™ Geometry and Mesh Generation Toolkit)
two- and three-dimensional finite element mesh generation toolkit for solid models.
Finite Element Analysis >Finite Element Analysis Software
Finite Element Analysis >Finite Element Libraries
FreeFEM
by Frédéric Hecht Laboratoire Jacques-Louis Lions, Sorbonne University, Paris. FreeFEM is a partial differential equation solver for non-linear multi-physics systems in 1D, 2D, 3D and 3D border domains (surface and curve).
Firedrake
by the departments of Mathematics, Computing, and Earth Science and Engineering at Imperial College London, the Department of Computer Science at Durham University, the Department of Mathematics at Baylor University, the Applied Physics Laboratory at the University of Washington and the broad…
In 2 lists
FEniCS Project
by the FEniCS Community. FEniCS is a popular open-source (LGPLv3) computing platform for solving partial differential equations (PDEs). FEniCS enables users to quickly translate scientific models into efficient finite element code using high-level Python and C++ interfaces.
In 2 lists
deal.II
is C++ software library supporting the creation of finite element codes and an open community of users and developers.
In 2 lists
MFEM
is a free, lightweight, scalable C++ library for finite element methods.
In 2 lists
GLVis
is a lightweight tool for accurate and flexible finite element visualization, based on the MFEM library.
Statistical Analysis
spm1d
by Todd Pataky. This is a package for one-dimensional statistical Parametric Mapping. spm1d uses Random Field Theory expectations regarding the behavior of smooth, one-dimensional Gaussian fields to make statistical inferences regarding a set of one-dimensional continua. 📄spm1d paper | 📚spm1d…
power1D
by Todd Pataky. This package is a Python toolbox for numerical power estimates in experiments involving one-dimensional continua. 📄paper | 💾code | 💻website
SPSS Statistics
(commercial)
JASP
(@JASPStats): An open-source low-cost alternative to commercial statistical software.
jamovi
(@jamovistats): An open-source statistical software platform based on R, making it accessible to users who are not familiar with R.
In 2 lists
R
(@_R_Foundation): A free software environment for statistical computing and graphics.
In 2 lists
Scientific Data Visualization
Paraview
ParaView is an open-source, multi-platform data analysis and visualization application based on Visualization Toolkit (VTK) (Source Code) BSD-3.
In 4 lists
Mayavi
Python tool :snake:
In 3 lists
MicroDicom
MicroDicom is application for primary processing and preservation of medical images in DICOM format. It is equipped with most common tools for manipulation of DICOM images and it has an intuitive user interface. Free for use and accessible to everyone for non-commercial use.
Reproducibility
Docker
is an open platform for developing, shipping, and running applications. Docker enables you to separate your applications from your infrastructure so you can deliver software quickly working in collaboration with cloud, Linux, and Windows vendors, including Microsoft.
In 18 listsDetails
Binder
Open notebooks in an executable environment, making your code immediately reproducible by anyone, anywhere.
In 4 lists
Colab
free jupyter notebook online. Google Colab also comes with free GPU hours.; Free and powerful.; Share and collaborate on the same notebook.; Can be saved in GitHub or Google Drive.
In 6 listsDetails
Choose a license
by GitHub Inc. This is a website with can help you choosing the license for your shared data based the intended use that you want to allow.
CreativeCommons
by Creative Commons. This website can guide you in the process of choosing a Creative Commons license based on your preferences.
Societies and Initiatives
Miscellaneous Online Resources
Richard Baker's blog
(unmaintained).
Stuart McErlain-Naylor's personal website
includes a list of resources for PhD students.
https://distill.pub/
Blog. Machine Learning Videos Data Science Notebooks Recommender Systems (Microsoft) Datascience Cheatsheets
In 4 listsDetails
https://paperswithcode.com/
Definitive database linking papers to open code and datasets.
In 3 lists
Miscellaneous Online Resources >Blogging platforms
Jekyll
Jekyll is a simple, blog-aware, static site generator perfect for personal, project, or organization sites.
In 5 listsDetails
Pelican
Static site generator that requires no database or server-side logic.
In 2 lists
In 2 lists
WiX
the easiest and fullest-featured website builder, that allows you to create your own highly customized site.
In 3 lists
More Datasets and repositories
Biomechanical Datasets
by Moon Ki Jung (Imperial College London).
Datasets of complex physiological signals
from Physionet.
Sandbox
GeoGram is a programming library of geometric algorithms.
https://homepages.loria.fr/BLevy/GEOGRAM/ http://alice.loria.fr/software/geogram/doc/html/index.html https://gforge.inria.fr/frs/?group_id=5833
pyomo Python-based, open-source optimization modeling language with a diverse set of optimization capabilities.
https://github.com/Pyomo/PyomoGallery
Hypothesis testing demonstration by Michael Pyrcz youtube:
github: https://github.com/GeostatsGuy/PythonNumericalDemos/blob/master/Interactive_Hypothesis_Testing.ipynb
reproducibility initiatives [reprohack]:
[reproducibilitea]: https://reproducibilitea.org/ [turing-way]: https://www.turing.ac.uk/research/research-projects/turing-way-handbook-reproducible-data-science [software carpentry]: https://swcarpentry.github.io/r-novice-gapminder/
In 2 lists
VIRTUAL LABS IN BIOLOGICAL ANTHROPOLOGY
by John Hawks Laboratory (University of Wisconsin-Madison).
VIRTUAL LAB: Australopithecus afarensis KNEE JOINT
by John Hawks Laboratory (University of Wisconsin-Madison).
JointTrack
https://ufdcimages.uflib.ufl.edu/UF/E0/02/17/84/00001/mu_s.pdf
DTI and fibre tractography
Related lists in Miscellaneous
See category94
Awesome OpenClaw Skills
VoltAgent/awesome-openclaw-skills
The awesome collection of OpenClaw skills. 5,400+ skills filtered and categorized from the official OpenClaw Skills Registry.🦞
92
Awesome DeepSeek Harness (DSH) Plugin
awesome-dsh-plugin/awesome-dsh-plugin
A curated list of plugins for DeepSeek Harness (dsh) · DeepSeek Harness 插件精选列表
91
Awesome Guidelines
Kristories/awesome-guidelines
Programming style, best practices, and coding conventions.
90
Awesome
sindresorhus/awesome
😎 Awesome lists about all kinds of interesting topics [NOTE: Pull requests are temporarily disabled until I have a chance to catch up with the existing ones]
90
Awesome Prompts
ai-boost/awesome-prompts
Curated list of chatgpt prompts from the top-rated GPTs in the GPTs Store. Prompt Engineering, prompt attack & prompt protect. Advanced Prompt Engineering papers.
90
Awesome README
matiassingers/awesome-readme
A curated list of awesome READMEs