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23 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> | |
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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 |
MITK-GEM: Software pipeline to GEnerate Models from images
- An attempt to provide a software pipeline to interactively create finite element models from medical images. Primarily intended to model bone fracture risk.
An application with graphical user interface and image processing plugins is provided. The application is build using the MITK Workbench software framework. The following plugins are available: fast image segmentation using graph cut, volume meshing using tetgen and density to modulus conversion for bone material property assignment.
Documentation and tutorials are available on our <a href="http://araex.github.io/mitk-gem-site/">tutorial website</a>.
Along with pre-compiled executables available here, the source code is available on our <a href="https://github.com/araex/mitk-gem">github page</a>.
The graph cut segmentation plugin and the material mapping plugin were developed as part of research studies.
If you use the software or source code in your research, please cite the corresponding journal <a href="https://simtk.org/project/xml/publications.xml/?group_id=1063">publications</a>. | |
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Registered: 2015-12-23 02:46 |
Matlab-Opensim Interfaces
- Matlab is a common analysis tool used for data manipulation, signal processing and function integration. These features can be used in conjunction with simulation tools provided by the Opensim interface.
This project provides tools for using different aspects of Opensim within the Matlab environment. This includes 1) using the command line tools by generating XML setup files etc (Scaling, Inverse Kinematics, Inverse Dynamics, Forward Dynamics) 2) using the Java classes that the Opensim GUI is built on to access aspects of the Opensim API.
Provided in this project are -
1) Tools for taking motion capture data from C3D files and generating the required input files (marker files {*.trc} motion files {*.mot}, GRF xml files {*.xml}) as well as setup files for each of the different tools that can be called from the command line. Example data from different models and data sets are provided including example pipelines to analyse data using Opensim. Some of this implementation has taken inspiration from Tim Dorn's excellent GaitExtract toolbox. A new page with more up-to-date tools can be found here - http://simtk-confluence.stanford.edu:8080/display/OpenSim/Tools+for+Preparing+Motion+Data
2)Matlab functions and example scripts for accessing the Opensim API through Matlab. This utilises the Java wrapping classes that the Opensim GUI is built on. Examples are shown to open and edit models as well as perform a 'Muscle Analysis'. Please now use the inbuilt support from Opensim rather than this toolbox! (http://simtk-confluence.stanford.edu:8080/display/OpenSim/Scripting+with+Matlab) | |
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Activity Percentile: 79.39 Registered: 2011-08-06 20:22 |
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 |
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 |
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 |
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: 24.05 Registered: 2015-05-28 18:52 |
ForceBalance : Systematic Force Field Optimization
- ForceBalance is free software for force field optimization.
It facilitates the development of more accurate force fields using a systematic and reproducible procedure.
ForceBalance is highly versatile and can optimize nearly any set of parameters using experimental measurements and/or ab initio calculations as reference data.
<b>SOURCE CODE:</b> For the newest features, visit the GitHub source code repository at https://github.com/leeping/forcebalance.
The SVN repository on the left frame is an outdated archive.
<b>RELEASES:</b> Stable versions of the code updated once every few months. Click "Releases" on the left frame for the most recent release and notes.
<b>CONTACT:</b> Please contact me (Lee-Ping, right frame) if you have questions or comments! | |
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Registered: 2011-12-20 17:04 |
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. | |
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Activity Percentile: 6.11 Registered: 2015-09-28 14:09 |
Stiffness Modulation of Redundant Musculoskeletal Systems
- This work presents a framework for computing the limbs' stiffness using inverse methods that account for the musculoskeletal redundancy effects. The musculoskeletal task, joint and muscle stiffness are regulated by the central nervous system towards improving stability and interaction with the environment during movement. Many pathological conditions, such as Parkinson's disease, result in increased rigidity due to elevated muscle tone in antagonist muscle pairs, therefore the stiffness is an important quantity that can provide valuable information during the analysis phase. Musculoskeletal redundancy poses significant challenges in obtaining accurate stiffness results without introducing critical modeling assumptions. Currently, model-based estimation of stiffness relies on some objective criterion to deal with muscle redundancy, which, however, cannot be assumed to hold in every context. To alleviate this source of error, our approach explores the entire space of possible solutions that satisfy the action and the physiological muscle constraints. Using the notion of null space, the proposed framework rigorously accounts for the effect of muscle redundancy in the computation of the feasible stiffness characteristics. To confirm this, comprehensive case studies on hand movement and gait are provided, where the feasible endpoint and joint stiffness is evaluated. Notably, this process enables the estimation of stiffness distribution over the range of motion and aids in further investigation of factors affecting the capacity of the system to modulate its stiffness. Such knowledge can significantly improve modeling by providing a holistic overview of dynamic quantities related to the human musculoskeletal system, despite its inherent redundancy.
https://github.com/mitkof6/musculoskeletal-stiffness | |
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Registered: 2018-11-12 13:00 |
Modeling kinematic and dynamic redundancy
- The coordination of the human musculoskeletal system is deeply influenced by its redundant structure, in both kinematic and dynamic terms. Noticing a lack of a relevant, thorough treatment in the literature, we formally address the issue in order to understand and quantify factors affecting the motor coordination. We employed well-established techniques from linear algebra and projection operators to extend the underlying kinematic and dynamic relations by modeling the redundancy effects in null space. We distinguish three types of operational spaces, namely task, joint and muscle space, which are directly associated with the physiological factors of the system. A method for consistently quantifying the redundancy on multiple levels in the entire space of feasible solutions is also presented. We evaluate the proposed muscle space projection on segmental level reflexes and the computation of the feasible muscle forces for arbitrary movements. The former proves to be a convenient representation for interfacing with segmental level models or implementing controllers for tendon driven robots, while the latter enables the identification of force variability and correlations between muscle groups, attributed to the system’s redundancy. Furthermore, the usefulness of the proposed framework is demonstrated in the context of estimating the bounds of the joint reaction loads, where we show that misinterpretation of the results is possible if the null space forces are ignored. This work presents a theoretical analysis of the redundancy problem, facilitating application in a broad range of fields related to motor coordination, as it provides the groundwork for null space characterization. The proposed framework rigorously accounts for the effects of kinematic and dynamic redundancy, incorporating it directly into the underlying equations using the notion of null space projection, leading to a complete description of the system.
https://github.com/mitkof6/musculoskeletal-redundancy
https://github.com/mitkof6/feasible_muscle_force_analysis | |
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Registered: 2018-05-17 10:19 |
WraptMor
- WraptMor is a model that can be used to estimate ligament fiber insertion-to-insertion length with wrapping around osseous surfaces. The code for the WraptMor model and examples that demonstrate the model's usage can be found in SourceCode. See the Wiki page for information on the required packages needed to run the WraptMor code, and an example demonstrating the code's usage.
Citing - Please cite this article if you use the WraptMor code or approach:
Zaylor, William, and Halloran, Jason P. (May 6, 2021). "WraptMor: Confirmation of an Approach to Estimate Ligament Fiber Length and Reactions With Knee-Specific Morphology." ASME. J Biomech Eng. August 2021; 143(8): 081012. https://doi.org/10.1115/1.4050810 | |
Registered: 2020-07-31 17:04 |
Forces Plugin: A library defining additional passive forces in OpenSim
- This project hosts source code and prebuilt libraries defining custom forces in the OpenSim plugin API. The plugin library adds several passive forces to OpenSim, including:
- FunctionBasedBushgingForce
- PointToPointDashpot | |
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Activity Percentile: 0.00 Registered: 2012-08-27 20:36 |
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. | |
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Activity Percentile: 0.00 Registered: 2014-02-01 22:32 |
Application for the simulation of the prosthetic gait
- This application has a dataset belonging to macha prosthetic patterns , in which the angle of the socket and prosthetic foot is changed.
It focuses on patients with transtibial amputation and uses opensim in MATLAB libraries to link and generate a model for opensim , based on data captured from a measuring TECHNAID brand. | |
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Registered: 2016-08-24 14:21 |
C3D Extraction Toolbox
- This toolbox is of benefit to musculoskeletal modellers in the field of biomechanics / bioengineering to assist extracting kinematic, kinetic, and EMG information directly from a C3D file for Matlab manipulation or for input to OpenSim biosimulation software. The scripts can be configured for any laboratory configuration. This software is free without warranty but I do ask for acknowledgement if used in publications. Free download is available with documentation and two examples included.
Main features of this script include:
Custom markerset extraction
Foot-plate detection algorithm
Kinetic extraction (ground reaction forces / moments)
Center of pressure calculation
Transformation to customizable model coordinate system
Custom EMG acquisition & processing tools
XML file production (for OpenSim)
Lab customizable
The scripts require Motion Labs C3D Server software (freeware) and XML Toolbox (Marc Molinari)(freeware) which is included with the script download. Also requires Matlab 2008 or greater (32 bit only) with the Signal Processing Toolbox.
Additional C3D software may be useful and these are available at http://www.c3d.org/c3dapps.html. Review the included manual for version updates and additions. Please inform me of bugs / suggestions to improve as this will be an ongoing project. | |
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Registered: 2008-10-03 01:17 |
Supplemental data and scripts for Nicholas Tatonetti's PhD Dissertation
- The data files and scripts used for the analysis presented in the dissertation. | |
Activity Percentile: 0.00 Registered: 2012-05-21 16:51 |
3D Numerical Investigation of Endothelial Shear Stress in Arteries
- 3D numerical investigation of endothelial shear stress in coronary arteries. | |
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Activity Percentile: 0.00 Registered: 2015-11-30 13:34 |
23 projects in result set. Displaying 20 per page. Projects sorted by alphabetical order.
<1> <2>