Project Tree
Now limiting view to projects in the following categories:
All Topics :: Primary Content :: Educational and Training Material [Remove This Filter]
All Topics > Biocomputational Focus > Physics-Based Simulation |
Browse By: |
25 projects in result set. Displaying 20 per page. Projects sorted by alphabetical order.
<1> <2>
OpenSim
- OpenSim is a freely available, user extensible software system that lets users develop models of musculoskeletal structures and create dynamic simulations of movement.
Find out how to join the community and see the work being performed using OpenSim at <a href="http://opensim.stanford.edu">opensim.stanford.edu</a>.
Access all of our OpenSim resources at the new <br /><a href="http://opensim.stanford.edu/support/index.html"><b style="color:#900; font-size:16px;">Support Site</b></a>.
Watch our <a href="http://www.youtube.com/watch?v=ME0VHfCtIM0">Introductory Video</a> get an overview of the OpenSim project and see how modeling can be used to help plan surgery for children with cerebral palsy.
<iframe width="560" height="315" src="https://www.youtube.com/embed/ME0VHfCtIM0" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe> | |
|
Registered: 2006-03-23 18:48 |
Open Knee(s): Virtual Biomechanical Representations of the Knee Joint
- Open Knee(s) was aimed to provide free access to three-dimensional finite element representations of the knee joint (<A HREF="https://doi.org/10.1007/s10439-022-03074-0">https://doi.org/10.1007/s10439-022-03074-0</A>). The development platform remains open to enable any interested party to use, test, and edit the model; in a nut shell get involved with the project.
This study was primarily funded by the National Institute of General Medical Sciences, National Institutes of Health (R01GM104139) and in part by National Institute of Biomedical Imaging and Bioengineering (R01EB024573 and R01EB025212). Previous activities leading towards this project had been partially funded by the National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health (R01EB009643).
Open Knee(s) by Open Knee(s) Development Team is licensed under a <A HREF="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</A>.
| |
|
Registered: 2010-02-18 20:41 |
SCONE: Open Source Software for Predictive Simulation
- If SCONE is helpful for your research, please cite the following paper:
Geijtenbeek, T (2019). SCONE: Open Source Software for Predictive Simulation of Biological Motion. Journal of Open Source Software, 4(38), 1421, https://doi.org/10.21105/joss.01421 | |
|
Registered: 2016-10-27 13:07 |
Computational Methods in Cardiovascular
Bioengineering Course (BioE484)
- This research PhD-level class was taught during Spring 2007 by Alberto Figueroa, from the Taylor lab. For their final project, students were organized into five teams and each team worked on a different cardiovascular research project.
The basic research tool the students used is the software SimVascular, which is a Cardiovascular Modeling and Simulation
application currently in the process of being open-sourced through http://Simbios.stanford.edu. This project presents a summary of the final projects. All presentations were taped and made available from the download section on the left menu. | |
|
Registered: 2007-06-15 17:20 |
CoBi Core Models, Data, Training Materials
- This project contains a variety of materials from Computational Biomodeling (CoBi) Core of the Cleveland Clinic, relevant to physics-based simulation of the biomechanical system. These may include various published/unpublished models, data, and training material generated through various small projects. | |
|
Registered: 2010-10-07 13:09 |
Tim's OpenSim Utilities
- This project site is concerned with extending the functionality of OpenSim through the use of scripting tools and plugins.
Click on the downloads link to browse the set of freely available OpenSim tools for download.
*******************************************************
Previously delivered interactive webinars demonstrating
the use of the Pseudo-Inverse Induced Acceleration
plugin for OpenSim (IndAccPI).
http://www.stanford.edu/group/opensim/support/webinars.html
******************************************************* | |
|
Registered: 2009-09-01 00:52 |
Easy-to-use interactive musculoskeletal simulations and curriculum (OpenSim).
- This project brings "life" to the physical sciences. Its curriculum and simulations are correlated with National and State Standards for Physics and the Physical Sciences and helps high-school, college, and professionals combine biology with physics. | |
|
Activity Percentile: 60.23 Registered: 2010-08-28 02:06 |
Neuromusculoskeletal Modeling (NMSM) Pipeline
- <div style="display:inline-block"><a href="https://nmsm.rice.edu"><img src="https://nmsm.rice.edu/img/nmsm-pipeline-social-card.jpg" style="float:left;max-width:calc(100% - 40px);"></a></div>
Full project information is available at: https://nmsm.rice.edu. Please direct any inquiries about the NMSM Pipeline to us by posting your questions on this SimTK project forum or emailing nmsm@rice.edu.
Neuromusculoskeletal Modeling (NMSM) Pipeline is a set of tools for personalizing models and designing treatments for movement impairments and other pathologies.
The NMSM Pipeline consists of two toolsets:
Model Personalization - Personalize joint, muscle-tendon, neural control, and ground contact model properties.
Treatment Optimization - Design treatments using personalized models and an optimal control methodology.
At this time, Treatment Optimization requires the use of <a href="https://www.gpops2.com/">GPOPS-II optimal control solver</a>.
The NMSM Pipeline is written in MATLAB to lower the barrier for entry and to facilitate accessibility to the core codebase. We encourage users to modify the code to meet their needs.
The core codebase and examples are available to download for use in research. At this time, we ask that you wait to publish any work that uses the NMSM Pipeline until the journal article reference for the software is available. Please get in touch with us if you have any questions.
If you need help or want to start a discussion, please use the SimTK forum for this project.
Note: This project is a living entity. Updates will be made available as the Pipeline, examples, and tutorials are developed further and improved. | |
|
Registered: 2022-07-07 14:55 |
Framework for Predictive Simulation of Treadmill Gait
- This project was divided into two tasks:
(1) We created a simple model of a block on a treadmill to understand how to develop a framework to track and predict motion between a moving platform and a body moving relative to it. We simulated the block falling, rotating, and translating to mimic heel strike, heel rocker, and translation of the foot posteriorly with respect to the treadmill.
(2) Modified the example2DWalking musculoskeletal model and MATLAB code to track and predict treadmill gait at slow, comfortable, and fast belt speeds.
What is included in the download:
(1) Block Model
- Model files (.osim) - note model file is the same for the translation & falling simulations,
but slightly different for rotation, so there are 2 different model files
- Manually generated reference coordinates data (.sto) for each tracking problem
- MATLAB scripts (.m) written to track & predict each block motion
(2) Treadmill Gait Model
- Model files (.osim) - note the treadmill speed is defined in the model so the model files
are different for each speed condition, so there are 3 different model files
- Reference coordinates data for tracking problems (.sto)
- One MATLAB script to track & predict treadmill gait (.m)- note: this script asks the user to
select their model file from the current folder, so just be sure to select the desired speed
condition
- Solutions generated from tracking & predictive problems for all three speeds
Note: To perform comparison with the overground gait simulation described in the manuscript run the example2DWalking code in the OpenSim Moco download.
| |
|
Registered: 2022-03-08 12:50 |
Fiber Tractography for Finite-Element Modeling of Transversely Isotropic Tissues
- This project demonstrates the process for fiber tractography of complex biological tissues with transverse isotropy, such as tendon and muscle. This is important for finite element studies of these tissues, as the fiber direction must be specified in the constitutive model. This project contains code, models, and data that can be used to reproduce the results of our publication on this technique. The supplied instructional videos will enable researchers to easily and efficiently apply this method to a variety of other tissues. The software used in the fiber tractography process and demonstrated in this project is Matlab, Autodesk Inventor (free for educators), and Autodesk Simulation CFD (free for educators). Full demonstrations and process instructions can be found in the 7 videos posted at https://vimeo.com/album/3414604:
Contents:
Chapter 1: Introduction (2:35)
This video introduces the CFD fiber tractography software pipeline
<!-- This version of the embed code is no longer supported. Learn more: https://vimeo.com/s/tnm --> <object width="500" height="281"><param name="allowfullscreen" value="true" /><param name="allowscriptaccess" value="always" /><param name="movie" value="https://vimeo.com/moogaloop.swf?clip_id=129107314&force_embed=vimeo.com&fullscreen=1" /><embed src="https://vimeo.com/moogaloop.swf?clip_id=129107314&force_embed=vimeo.com&fullscreen=1" type="application/x-shockwave-flash" allowfullscreen="true" allowscriptaccess="always" width="500" height="281"></embed></object>
Chapter 2: Supplementary materials code, models and data (20:21)
This video shows the shared models, code, and data posted online at simtk.org/m3lab_cfd4fea.
Chapter 3: Finite element simulations (5:38)
This video shows finite element simulations using the fiber mapping process.
Chapter 4: Iliacus example walkthrough (21:38)
This video shows the step-by-step process for fiber mapping the iliacus muscle (a hip flexor).
Chapter 5: Bflh example walkthrough (12:09)
This video shows the step-by-step process for fiber mapping the biceps femoris longhead muscle (a hamstring).
Chapter 6: Autodesk Inventor segmentation (9:09)
This video shows how to do segmentation of medical images in Autodesk Inventor in order to simplify the solid model for the CFD and FEA software.
Chapter 7: Curved inlet surfaces (6:28)
This video shows how to create curved inlet surfaces for use in Autodesk Simulation CFD. | |
|
Activity Percentile: 35.23 Registered: 2015-05-28 18:52 |
Extendable OpenSim-Matlab Infrastructure Using Class Oriented C++ Mex Interface
- The objective of this project is to provide an alternative interface between OpenSim and Matlab®, based on an extended C++ mex interface. Despite the fact that there is a user friendly OpenSim interface for Matlab, it lacks the ability to extend new functionalities based on the Java API (e.g. custom controller). Inspired by the relative project “Dynamic Simulation of Movement Based on OpenSim and MATLAB®/Simulink®”, where the user can easily interface OpenSim with Simulink, the proposed framework moves one step further by providing new capabilities to link custom written C++ OpenSim extensions to Matlab and to harvest both the powerful OpenSim C++ API and Matlab functionalities. The implementation is based on Matlab mex interface, which is further extended to support more complex functionalities based on the project mexplus. The latter is a C++ Matlab mex development kit that contains a couple of C++ classes and macros to make mex development easy in Matlab.
An example project is provided in the download section with instructions on how-to use. | |
|
Activity Percentile: 22.73 Registered: 2015-09-28 14:09 |
CCIvsJointStiffness
- Muscle co-contraction generates joint stiffness to improve stability and accuracy during limb movement but at the expense of higher energetic cost. However, quantification of joint stiffness is difficult using either experimental or computational means. In contrast, quantification of muscle co-contraction using an EMG-based Co-Contraction Index (CCI) is easier and may offer an alternative for estimating joint stiffness. This study investigated the feasibility of using two common CCI’s to approximate lower limb joint stiffness trends during gait.
Please cite the following paper:
G. Li, M.S. Shourijeh, D. Ao, C. Patten, B.J. Fregly, How Well Do Commonly Used Co-Contraction Indices Approximate Lower Limb Joint Stiffness Trends during Gait?, Frontiers in Bioengineering and Biotechnology, 2020, DOI: 10.3389/fbioe.2020.588908 | |
|
Registered: 2020-10-31 05:04 |
BioGears: An open source mathematical model of the human physiology.
- BioGears is an open source, comprehensive, extensible human physiology engine that will drive medical education, research, and training technologies. BioGears enables accurate and consistent physiology simulation across the medical community. The engine can be used as a standalone application or integrated with simulators, sensor interfaces, and models of all fidelities. | |
|
Activity Percentile: 0.00 Registered: 2014-10-09 18:12 |
Synergy Optimization: A plug-in to couple muscle activity in OpenSim
- The Synergy Optimization plug-in was developed to enable synergy-based control in OpenSim. It extends Static Optimization to let users specify a matrix of synergies to constrain and couple muscle activations. Beyond synergies, this plug-in can also be used to (1) provide varying weights to different actuators in static optimization or (2) require specific actuators to be activated together. | |
|
Activity Percentile: 0.00 Registered: 2016-01-11 16:36 |
Biosimulation Education and Training
- Biosimulation education and training resources for Neuromuscular Biomechanics, RNA folding, Cardiovascular Dynamics, and Myosin Dynamics.
Course material can be found by clicking the documents link on the left menu. | |
|
Activity Percentile: 0.00 Registered: 2006-08-02 20:35 |
Biomechanics Education Modules
- This project contains biomechanics modules on “Understanding Forces on the Body” and “Imaging, Materials, and Failure”. The modules include powerpoint slides and exercises to support the lessons. Exercises illustrate moment arms via a knee experiment and strength of materials via an imaging-based ACL tear example.
This project was supported by the National Science Foundation through:
Population-based evaluation of knee mechanics considering inter-subject and surgical alignment variability
Investigators: P. Laz, P. Rullkoetter, D. Dennis, R. Kim
General and Age Related Disabilities Engineering, CBET-1034251.
MRI: Acquisition of a biplane fluoroscopy system for dynamic imaging of in-vivo human motion.
Investigators: P. Rullkoetter, B. Davidson, C. Fitzpatrick, P. Laz, K. Shelburne
Division of Computer and Network Systems CNS-1229148.
For more information on the related statistical shape modeling work, please visit https://simtk.org/home/ssm_knee/ | |
|
Activity Percentile: 0.00 Registered: 2014-09-12 19:28 |
C++ and Python code, distributed computing and OpenMM interfaces for simulations
- please cite: "Interplay of Protein and DNA Structure Revealed in Simulations of the lac Operon" (PLOS One 2013)
for any code related to protein-DNA modeling and
"Free Energy Monte Carlo Simulations on a Distributed Network" (Lecture Notes in Computer Science Journal for PARA 2010)
http://link.springer.com/chapter/10.1007%2F978-3-642-28145-7_1
for parallel client-server code, users of additional code should cite this web site. Code is provided as-is with no warranty and examples are provided to illustrate the usage of these modeling techniques with some sample systems. Code is the intellectual property of Luke Czapla, developer and biophysicist. Examples are provided in C/C++ and Python. | |
|
Activity Percentile: 0.00 Registered: 2014-02-01 22:32 |
Muscle function of overground running across a range of speeds
- This project is a repository of overground running data (3.5m/s 5.2m/s, 7.0m/s and 9.0m/s) along with a working musculoskeletal model to perform simulations and derive the function of individual muscles. | |
|
Registered: 2011-08-07 14:01 |
Optimal Control Workshop
- This project provides 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. The workshop material was organized into three sections: 1) Motivational material, 2) Technical material, and 3) Tutorial material. Slides from each section, along with all tutorial material (requires a license of GPOPS-II optimal control software), are included. | |
|
Activity Percentile: 0.00 Registered: 2015-08-01 16:35 |
HTMD - High Throughput Molecular Dynamics
- In a single script, it is possible to plan an entire computational experiment, from manipulating PDBs, building, executing and analyzing simulations, computing Markov state models, kinetic rates, affinities and pathways.
See more information on <a href="https://www.htmd.org/">https://www.htmd.org</a>.
HTMD Forum: <a href="https://forum.htmd.org/">https://forum.htmd.org</a>
We are also on Github: <a href="https://github.com/Acellera/htmd">https://github.com/Acellera/htmd</a>
Report issues on: <a href="https://github.com/Acellera/htmd/issues">https://github.com/Acellera/htmd/issues</a> | |
|
Registered: 2016-05-13 07:45 |
25 projects in result set. Displaying 20 per page. Projects sorted by alphabetical order.
<1> <2>