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51 projects in result set. Displaying 20 per page. Projects sorted by alphabetical order.
<1> <2> <3>
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> | |
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Registered: 2006-03-23 18:48 |
OpenMM
- OpenMM is a toolkit for molecular simulation. It can be used either as a stand-alone application for running simulations, or as a library you call from your own code. It
provides a combination of extreme flexibility (through custom forces and integrators), openness, and high performance (especially on recent GPUs) that make it truly unique among simulation codes.
<b>NEED HELP?</b> Check out the discussion forums under <a href="https://simtk.org/forums/viewforum.php?f=161">Public Forums</a> and the material from our workshops under <a href="https://simtk.org/project/xml/downloads.xml?group_id=161">Downloads</a>.
<b>GET STARTED QUICKLY:</b> Tutorials and sample scripts to run OpenMM are available in the <a href="http://wiki.simtk.org/openmm/VirtualRepository">OpenMM Code Repository</a>.
<b>SOURCE CODE:</b> The source code for OpenMM is available under <a href="https://simtk.org/project/xml/downloads.xml?group_id=161">Downloads</a> and also from the <a href="http://www.github.com/SimTk/openmm">Github Source Code Repository</a>.
<b>BENCHMARKS:</b> A collection of <a href="http://wiki.simtk.org/openmm/Benchmarks">benchmarks</a> is available to show the performance of OpenMM simulating a variety of molecular systems.
<b>CITING OPENMM:</b> Any work that uses OpenMM should cite the papers listed on the <a href="https://simtk.org/project/xml/publications.xml/?group_id=161">Publications</a> page. | |
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Registered: 2006-11-16 18:27 |
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>.
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Registered: 2010-02-18 20:41 |
Statistical analysis of conformational ensembles
- This project provides computational tools and methods to analyze conformational ensembles of biomolecules, as well as their assemblies, such as those obtained from molecular simulations.
(A) PROTEINS: The molecular understanding of the functional regulation of proteins requires assessment of various states, including active and inactive states, as well as their interdependencies. For several proteins, their various states can be distinguished from each other on the basis of their minimum energy 3D structures. For many other proteins, like GPCRs, PDZ domains, nuclear transcription factors, heat shock proteins, T-cell receptors and viral attachment proteins, their states can be distinguished categorically from each other only when their finite-temperature conformational ensembles are considered alongside their minimum-energy structures. We are developing tools/methods for:
(A1) Direct comparison of conformational ensembles - The traditional approach to compare two or more conformational ensembles is to compare their respective summary statistics. This approach is, however, prone to artifactual bias, as data is compared after dimensionality reduction. The proper way to compare ensembles is to compare them directly with each other and prior to any dimensionality reduction. g_ensemble_comp is a tool we have developed that does just that and reports the difference between ensembles in terms of a true metric defined by the zeroth law of thermodynamics.
(A2) Prediction of allosteric signaling networks - method under development.
(B) LIPID MEMBRANES: The surface area of a lipid bilayer is related fundamentally to many other observables, such as thermal phase transitions and domain formation in mixed lipid bilayers. We have developed g_tessellate_area to compute the 3D surface area of a bilayer using Delunay tessellation. | |
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Activity Percentile: 95.08 Registered: 2015-09-15 17:52 |
Are subject-specific musculoskeletal models robust to parameter identification?
- This study analyzed the sensitivity of the predictions of an MRI-based musculoskeletal model (i.e., joint angles, joint moments, muscle and joint contact forces) during walking to the unavoidable uncertainties in parameter identification, i.e., body landmark positions, maximum muscle tension and musculotendon geometry. To this aim, we created an MRI-based musculoskeletal model of the lower limbs, defined as a 7-segment, 10-degree-of-freedom articulated linkage, actuated by 84 musculotendon units. We then performed a Monte-Carlo probabilistic analysis perturbing model parameters according to their uncertainty, and solving a typical inverse dynamics and static optimization problem using 500 models that included the different sets of perturbed variable values. Model creation and gait simulations were performed by using freely available software that we developed to standardize the process of model creation, integrate with OpenSim and create probabilistic simulations of movement. | |
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Activity Percentile: 92.80 Registered: 2014-11-10 15:19 |
Model of the Scapulothoracic Joint
- In this study, we developed a rigid-body model of a scapulothoracic joint to describe the kinematics of the scapula relative to the thorax. This model describes scapula kinematics with four degrees of freedom: 1) elevation and 2) abduction of the scapula on an ellipsoidal thoracic surface, 3) upward rotation of the scapula normal to the thoracic surface, and 4) internal rotation of the scapula to lift the medial border of the scapula off the surface of the thorax. The surface dimensions and joint axes can be customized to match an individual’s anthropometry. We compared the model to “gold standard” bone-pin kinematics collected during three shoulder tasks and found modeled scapula kinematics to be accurate to within 2 mm root-mean-squared error for individual bone-pin markers across all markers and movement tasks. As an additional test, we added random and systematic noise to the bone-pin marker data and found that the model reduced kinematic variability due to noise by 65% compared to Euler angles computed without the model. Our scapulothoracic joint model can be used for inverse and forward dynamics analyses and to compute joint reaction loads. The computational performance of the scapulothoracic joint model is well suited for real-time applications, is freely available as an OpenSim 3.2 plugin, and is customizable and usable with other OpenSim models. | |
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Activity Percentile: 88.64 Registered: 2015-01-14 23:10 |
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 | |
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Registered: 2016-10-27 13:07 |
Reference Models for Multi-Layer Tissue Structures
- This project aims to establish the founding knowledge, data and models for the mechanics of multi-layer tissue structures of the limbs, particularly of the lower and upper legs and arms. The activity is targeted to promote scientific research in layered tissue structures and allow reliable virtual surgery simulations for clinical training and certification.
This research and development project titled “Reference Models for Multi-Layer Tissue Structures" was conducted by the Cleveland Clinic Foundation and was made possible by a contract vehicle which was awarded and administered by the U.S. Army Medical Research & Materiel Command under award number: W81XWH-15-1-0232. The views, opinions and/or findings contained in this website are those of the authors and do not necessarily reflect the views of the Department of Defense and should not be construed as an official DoD/Army position, policy or decision unless so designated by other documentation. No official endorsement should be made. | |
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Registered: 2015-08-24 12:54 |
Cal Poly Human Motion Biomechanics Lab Knee Joint Finite Element Model
- This project offers a subject-specific, total knee joint finite element model. In the MS thesis associated with this project, the model is used to predict articular cartilage stress and strain during the stance phase of gait. The model was partially validated with in vivo and other finite element analyses, but requires further validation and development to accurately predict articular cartilage contact parameters. Specific limitations include material properties, as well as potentially loading boundary conditions. Special attention should be paid to the "Future Work" section of the referenced thesis document in order to further develop the model for use in other studies. | |
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Activity Percentile: 73.86 Registered: 2014-07-23 03:48 |
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. | |
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Registered: 2010-10-07 13:09 |
Simulated Assistive Devices for Loaded Walking
- This project contains experimental data and muscle-actuated tracking simulations of male subjects walking while carrying heavy load, and OpenSim simulations of these subjects wearing hypothetical ideal assistive devices. We collected motion capture data of 7 subjects walking in 4 different conditions: walking (a) without load at a freely selected speed, (b) without load at 80% of the freely selected speed, (c) while carrying 38 kg on the torso at a new freely selected speed, and (d) while carrying 38 kg at the same speed as in (a).
Based on the simulations of loaded walking (condition (c) above), we created new simulations to predict the effect of ideal assistive devices on the metabolic cost of walking. We examined 7 massless devices that each provided unrestricted torque at one degree of freedom and in one direction: hip abduction, hip flexion, hip extension, knee flexion, knee extension, ankle plantarflexion, and ankle dorsiflexion. We estimated the optimal device torques, and the devices' effect on metabolic cost and muscle activity.
Dembia CL, Silder A, Uchida TK, Hicks JL, Delp SL (2017) Simulating ideal assistive devices to reduce the metabolic cost of walking with heavy loads. PLoS ONE 12(7): e0180320. https://doi.org/10.1371/journal.pone.0180320 | |
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Registered: 2016-05-07 02:08 |
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
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Registered: 2009-09-01 00:52 |
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. | |
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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.
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Registered: 2022-03-08 12:50 |
Simulating Ideal Assistive Devices to Reduce the Metabolic Cost of Running
- We used simulation to predict and gain insight into the biomechanical and energetic effects of assisted running, and to demonstrate the potential for simulation to complement experimental approaches to device design. We performed muscle-driven simulations of running at 2 and 5 m/s, then added ideal, massless assistive devices and examined the predicted changes in muscle recruitment patterns and metabolic power consumption. We predicted the optimal assistive device torque profiles and sought explanations for the observed changes in muscle activity. By ignoring device mass and other practical factors, we avoided confounding the beneficial effects of adding assistance with the detrimental side effects often encountered experimentally. | |
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Activity Percentile: 47.73 Registered: 2016-02-24 01:34 |
OpenSim plugin to extract the muscle lines of action
- The OpenSim plugin made available with this project extends the functionality of OpenSim and allows the user to extract the directionality of the muscle lines of action for a given kinematics. Also the muscle attachments can be exported if required by the user.
With this information it is generally possible to define loads representative of the muscle forces in finite element models of bone structures.
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Registered: 2012-04-22 20:49 |
Evertor and invertor muscle co-activation prevents ankle inversion injury
- The study described in this publication used musculoskeletal simulations to compare the capacity of planned invertor/evertor co-activation versus stretch reflexes with physiologic delay to prevent ankle inversion injuries. To achieve this, developed a novel model, muscle stretch controllers, and muscle reflex controllers for simulating landing in OpenSim. By freely providing the models, software plugins defining the controllers, and the resulting simulations, we hope to enable others to answer questions about landing control and injuries using simulations.
All models, data, and simulation results are provided in the downloads area of this project.
For software and sourcecode defining the novel stretch feedback controller and stretch reflex controller, see the related repository on GitHub.
https://github.com/msdemers/opensim-reflex-controllers
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Activity Percentile: 40.91 Registered: 2015-07-20 20:18 |
OpenSim Utilities
- <i>This collection is no longer being maintained through this project. To find OpenSim utilities, you now have two options:
1) Visit the summary table on the OpenSim documentation pages (http://simtk-confluence.stanford.edu:8080/display/OpenSim/Tools+for+Preparing+Motion+Data)
2) Conduct a search on SimTK. Click here (https://simtk.org/search/search.php?srch=opensim&type_of_search=soft) and then narrow your search to "Scripts, Plug-Ins, and Other Utilities" by checking the box on the left.</i>
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A repository of tools written by members of the OpenSim community to support their usage of the software.
<hr> </hr><b>Please respect your fellow OpenSim Users.</b>
In using these utilities we ask that you respect the hard work of your fellow researchers by citing their work appropriately. When you go to the Download section you will be directed to individual project pages for each model which contain all of the files and documentation. Please carefully review the publications and cite the references in your future papers, presentations, grant applications, etc.
<hr> </hr><b>Have a utility to contribute?</b>
Do you have a utility which you would like to make available through this library? Providing others with access to your tools and utiities can stimulate future studies, provide a foundation for young researchers, and maximize the impact of your work. It’s easy to set up a project page to post your work. This will allow you to track who is using your utilities and be in contact with them. Please consider contributing! If you would like to have your project included on this site, please contact Jennifer Hicks, listed as one of the Project Leads.
<hr> </hr>
No guarantees about quality, correctness or support are provided by the SimTK team or OpenSim team. Use at your own risk.
<hr> </hr>
To find out more about the OpenSim project, please visit <a href="http://opensim.stanford.edu">http://opensim.stanford.edu</a> | |
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Registered: 2007-09-17 21:53 |
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
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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. | |
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Activity Percentile: 35.23 Registered: 2015-05-28 18:52 |
How Tendon Compliance Affects the Metabolic Cost of Running
- We investigated the effect of tendon compliance on the metabolic cost of running using a full-body musculoskeletal model with a detailed model of muscle energetics. We performed muscle-driven simulations of running at several speeds and tendon compliances, and computed the average metabolic power consumed by each muscle. We used modeling and simulation to gain insight into the energy consumed by individual muscles throughout the gait cycle. We compared trends observed in muscle activations, metabolic power, and fiber mechanical power over a broad range of tendon compliances and at four running speeds. | |
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Activity Percentile: 31.44 Registered: 2016-01-06 21:36 |
51 projects in result set. Displaying 20 per page. Projects sorted by alphabetical order.
<1> <2> <3>