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44 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 |
Whole-Cell Computational Model of Mycoplasma genitalium
- The goal of this project was to develop the first detailed, "whole-cell" computational model of the entire life cycle of living organism, <i>Mycoplasma genitalium</i>. The model describes the dynamics of every molecule over the entire life cycle and accounts for the specific function of every annotated gene product.
We anticipate that whole-cell models will be critical for synthetic biology and personalized medicine. Please see the project website <a href="http://wholecell.org">wholecell.org</a> and the Downloads page to explore the whole-cell knowledge base and simulations and obtain the model code. | |
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Registered: 2012-01-24 03:21 |
Simulation of Constrained Musculoskeletal Systems in Task Space
- Objective: This work proposes an operational task space formalization of constrained musculoskeletal systems, motivated by its promising results in the field of robotics.
Methods: The change of representation requires different algorithms for solving the inverse and forward dynamics simulation in the task space domain. We propose an extension to the Direct Marker Control and an adaptation of the Computed Muscle Control algorithms for solving the inverse kinematics and muscle redundancy problems respectively.
Results: Experimental evaluation demonstrates that this framework is not only successful in dealing with the inverse dynamics problem, but also provides an intuitive way of studying and designing simulations, facilitating assessment prior to any experimental data collection.
Significance: The incorporation of constraints in the derivation unveils an important extension of this framework towards addressing systems that use absolute coordinates and topologies that contain closed kinematic chains. Task space projection reveals a more intuitive encoding of the motion planning problem, allows for better correspondence between observed and estimated variables, provides the means to effectively study the role of kinematic redundancy and, most importantly, offers an abstract point of view and control, which can be advantageous towards further integration with high level models of the precommand level.
Conclusion: Task-based approaches could be adopted in the design of simulation related to the study of constrained musculoskeletal systems.
The source code of the project can be found at: https://github.com/mitkof6/opensim-task-space.git
The new API of task space and constraint projection for OpenSim V4.0 is available at: https://github.com/mitkof6/task-space
<iframe width="560" height="315" src="https://www.youtube.com/embed/jfE14iWRZDs" frameborder="0" allow="autoplay; encrypted-media" allowfullscreen></iframe> | |
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Registered: 2017-08-28 12:06 |
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. | |
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Registered: 2022-07-07 14:55 |
Examining Muscle Forces during Sit to Stand Transfer with Full Body Model 2016
- Our STS transfer analysis required a three-dimensional musculoskeletal model that had lower extremities, flexibility in the lumbar vertebrae, and arms. Capturing the dynamics of the lower back and arms was critical for 1) ensuring more dynamically accurate calculations of muscle forces and induced accelerations and 2) developing benchmark simulations for young healthy adults using a model that could be applied in future studies to capture possible compensatory strategies (e.g., the use of arms or torso) in various populations completing the STS transfer. Because no previously developed model met these criteria, we created a three-dimensional musculoskeletal model, the Full Body Model 2016, by combining these models: Lower Limb Model 2010, Musculoskeletal Model of the Lumbar Spine, MoBL-ARMS Upper Limb Model, and Head and Neck Musculoskeletal Biomechanics Model. It has 46 degrees of freedom with 194 Hill-type muscle-tendon actuators. A description of how the model was assembled and evaluated is in Appendix 1 of our manuscript, Muscle Forces and Their Contributions to Vertical and Horizontal Acceleration of the Center of Mass during Sit-to-Stand Transfer in Young, Healthy Adults (see publications).
Watch this video to get a sneak peek of STS transfer simulation with the Full Body Model 2016. <object width="475" height="381"><param value="http://www.youtube.com/v/j-o94qfJKvM&showsearch=0&rel=0&fs=1&autoplay=0&ap=%2526fmt%3D18" name="movie" /><param value="window" name="wmode" /><param value="true" name="allowFullScreen" /><embed width="475" height="381" wmode="window" allowfullscreen="true" type="application/x-shockwave-flash" src="http://www.youtube.com/v/j-o94qfJKvM&showsearch=0&fs=1&rel=0&autoplay=0&ap=%2526fmt%3D18"></embed></object><br /><a href="http://www.youtube.com/watch?v=j-o94qfJKvM" target="_blank">View on YouTube</a> | |
Activity Percentile: 55.73 Registered: 2014-07-23 19:00 |
Predictive Simulation of Standing Long Jumps
- This project is aimed at creating a predictive simulation framework for standing long jumps and studying how using a how such a framework can be used to study performance differences due to various perturbations.
In particular, we have used this framework to study how simulation can be used to aid in device design. In our publication, we first show that the framework could generate a simulation that captured salient features of a standing long jump, including kinematics and kinetics. We then used the framework to design active and passive devices to increase simulated jump performance. | |
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Registered: 2014-01-30 23:21 |
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. | |
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Activity Percentile: 24.05 Registered: 2015-05-28 18:52 |
Modeling the Intervertebral Discs as a Stiffness Matrix: a SpineBushing element
- This project features a "SpineBushing" element that can be used to model the intervertebral disc as a 6x6 stiffness matrix. This permits the study of the disc's force-motion relationship for the case where the coordinates are coupled to each other.
The guiding equation is,
F_2 = -K * Delta_Q
where F_2 is the generalized 6x1 force vector acting on the upper vertebra, K is a stiffness matrix, and Delta_Q is the generalized 6x1 displacement vector specifying the change in position from neutral between the points of attachment of the stiffness element.
By Newton's 3rd law,
F_1 = - F_2.
The SpineBushing features two *key* differences from the existing bushing element:
(1) we incorporated a full 6x6 stiffness matrix instead of the current three translational and three rotational stiffnesses.
(2) the **change** in relative motion is used and not the relative motion itself. In 1-D, you can think of this as having a spring with a resting length equal to the distance between the specified attachment points on the two bodies in the neutral posture. (The typical bushing element, on the other hand would be analogous to a spring with zero resting length.)
Further details are provided in the accompanying documents. | |
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Activity Percentile: 15.65 Registered: 2011-10-12 05:41 |
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 |
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 | |
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Registered: 2020-10-31 05:04 |
Open MM and Zephyr applications to XBOX360 platform.
- This project is intended to use the OpenMM and Zephyr source code for compilation upon the XBOX 360 platforms. An executable with the functionality of Zephyr is desired. | |
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Activity Percentile: 0.00 Registered: 2009-12-25 17:02 |
Stretch Reflexes in OpenSim
- This project involves developing and evaluating new model components in OpenSim that represent stretch reflexes. Our planned design is intended to be sufficiently general-purpose that it can used to simulate normal, healthy stretch reflex responses as well as pathological conditions, such as spasticity. Our design separates the sensory components from the response components to provide greater flexibility for researchers to implement specific types of muscle spindle models and neural response mechanisms. | |
Activity Percentile: 0.00 Registered: 2014-04-08 15:22 |
Relational database for data analysis and integrated OpenSim simulations.
- OpenSim relies on morphometric measures, motion capture signals, and clinical data to simulate and analyze muscle dynamics. While this biomechanical tool is sufficiently robust to analyze single trials and to batch-process selected multiple trials, the subject-specific model scaling and the relevant data has to be manually picked and analyzed. The relational database that combines meta- and signal- information can automate both the model scaling and the automation of data analysis. The goal of this project is to integrate SciBox relational database toolbox with OpenSim environment. BOXsci is a lightweight relational database with transparent scripting library and graphical user interface implemented fully in Matlab, the data analysis package of choice in academia and private industry. BOXsci consists of a single library for data storage, access, and analysis that is freely available for academic, research and non-profit organizations. We will create pipeline interactions between recorded biomechanical signals, task and subject specific information (e.g. model composition and morphometric measurements) and the environment of OpenSim to perform inverse and forward dynamic simulations, and to store results within the relational database of SciBox. | |
Activity Percentile: 0.00 Registered: 2011-08-26 00:19 |
2007BioE15 Bruns
- Project for class. Hey! Guess what! It is required to put a longer \"detailed\" description into this area by the set up form! The retarded error message just says \"longer\", so who knows how long I have to keep spitting up this junk to keep the darn thing happy? | |
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Activity Percentile: 0.00 Registered: 2007-04-11 01:29 |
2007BioE215 Eser
- BioE215 Coursework Spring 2007 | |
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Activity Percentile: 0.00 Registered: 2007-04-07 02:13 |
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 |
Induced Accelerations-based controller for balance
- We attempt to use an Induced Accelerations Analysis of a biomechanical model to control position and maintain balance. | |
Activity Percentile: 0.00 Registered: 2013-06-07 06:31 |
LoopTK: Protein Loop Kinematic Toolkit
- Analyzing the motion of flexible protein loops is becoming increasingly important in understanding the various roles that proteins play in human body. LoopTK is a C++ based object-oriented toolkit which models the kinematics of a protein chain and provides methods to explore its motion space. In LoopTK, a protein chain is modeled as a robot manipulator with bonds acting as arms and the dihedral degree of freedoms acting as joints.
LoopTK is designed specifically to model the kinematics of protein loops, but it can be used to analyze the motion of any part of the protein chain. LoopTK provides methods for sampling the conformation space of protein loops as well as the self motion space of a loop. Example applications for LoopTK include x-ray crystallography, homology modeling, and drug design.
LoopTK was developed in close collaboration with the Joint Center for Structural Genomics (JCSG) at the Stanford Linear Accelerator Center. Now a part of the JCSG's protein structure determination process, loopTK models missing protein fragments into experimental data (http://smb.slac.stanford.edu/XpleoServer/Xpleo.jsp).
This material is based upon work supported by the National Science Foundation under Grant No. 0443939. Any opinions, findings, and conclusions or recommendations expressed in the above material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. | |
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Activity Percentile: 0.00 Registered: 2007-05-13 22:32 |
Platform for Dynamic Simulation and Control of Movement based on OpenSim&MATLAB
- Numerical simulations are playing an increasingly important role in solving complex engineering problems, and have the potential to revolutionize medical decision making and treatment design. Musculoskeletal diseases cost the United States economy an estimated $849 billion a year (equal to 7.7% of the gross domestic product) and place great demands on the healthcare system. This research area could greatly benefit from computational tools that offer greater understanding of neuromuscular biomechanics, and predictive capabilities for optimal surgical and rehabilitation treatment planning.
The MATLAB®/Simulink® package is the world’s leading mathematical computing software for engineers and scientists in industry, government, and education. Although Simulink® extends MATLAB® with a graphical environment for rapid design, control, and simulation of complex dynamic systems, this powerful package has limited resources for simulations of neuromusculoskeletal systems. On the contrary, OpenSim is a popular open-source platform for modeling, simulating, and analyzing neuromusculoskeletal systems, but it is lacks the robust design and control tools of Simulink®.
This project is an interface between OpenSim and MATLAB®/Simulink® that combines relevant strengths (e.g., neuromusculoskeletal dynamics, rapid model-based design, control systems, and numerical simulation) of each individual software package. The foundation of this interface is a MATLAB® S-function (system-function) based on an OpenSim model as a Simulink® block written in C++ and compiled as a MEX-file using the MATLAB® mex utility. | |
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Activity Percentile: 0.00 Registered: 2012-07-26 21:40 |
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 |
44 projects in result set. Displaying 20 per page. Projects sorted by alphabetical order.
<1> <2> <3>