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28 projects in result set. Displaying 20 per page. Projects sorted by alphabetical order.
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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 |
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 |
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 |
Muscle-actuated Simulation of Human Running
- The purpose of this study was to determine how muscles contribute to propulsion (i.e., the fore-aft acceleration) and support (i.e., the vertical acceleration) of the body mass center during running at 3.96 m/s (6:46 min/mile), including the effects of the torso and arms. To achieve this, we developed a three-dimensional muscle-actuated simulation of running that included 92 musculotendon actuators representing 76 muscles of the lower extremities and torso. By using a three-dimensional model with lower extremity muscles, a torso, and arms, we were able to quantify the contribution of muscles and arm dynamics to mass center accelerations in three dimensions, which provided insights into the actions of muscles during running. The simulation is freely available (simtk.org) allowing other researchers to reproduce our results and perform additional analyses. | |
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Registered: 2010-06-04 01:25 |
Dynamic Arm Simulator
- This project aims to develop a musculoskeletal model for the real-time, dynamic simulation of arm movement. It features a large-scale model of the shoulder and elbow, including the joints of the shoulder girdle and scapulo-thoracic contact. The simulation is implemented using a Matlab MEX function and uses OpenSim for pre-processing and visualisation. | |
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Registered: 2008-07-24 18:10 |
Specimen-Specific Models of the Healthy Knee
- As part of research funded by the National Institutes of Health, National Institute of Biomedical Imaging and Bioengineering (NIBIB), investigators at the University of Denver Center for Orthopaedic Biomechanics have made available a repository of experimental, image, and computational modeling data from mechanical testing of natural human knee biomechanics. It is uncommon for such a comprehensive dataset to be obtained. Therefore, we have made this repository available to assist the greater research community interested in the complexities and pathologies of knee health and mechanical function. Data are provided for 7 human knees (5 cadaveric subjects) and fall under two categories:
Image Data and Experimental & Computational Modeling Data.
Additional details about the data can be found at:
http://ritchieschool.du.edu/research/centers-institutes/orthopaedic-biomechanics/downloads/natural-knee-data/
This repository of natural knee data has been made available thanks to funding from the National Institutes of Health through National Institute of Biomedical Imaging and Bioengineering R01-EB015497. | |
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Registered: 2008-06-12 23:15 |
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 |
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 |
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: 51.91 Registered: 2015-07-20 20:18 |
The Musculoskeletal Modeler's Kitchen
- Making musculoskeletal models and simulations is a lot like cooking. Anything complicated is going to take a while to get just right and there will probably be a few failed attempts along the way. Unfortunately, in research we only see the tasty, beautifully presented, dish served at the fancy party (the paper in a journal) and not the burnt, over-salted, misshapen disasters that preceded it (all those failed simulations and ideas that didn't pan out). But there's a lot of great stuff in those failed attempts and we should document it somewhere.
Did you spend 2 weeks debugging something that was fixed with one line of code? Share it!
Do you have a simulation that you need help with? Ask for help here!
Did someone give you a great time saving tip? Pass it on!
Did you make something cool but unpublishable? Brag about it!
Have strong opinions about modeling and simulation? Climb on that soapbox!
Fail proudly. | |
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Registered: 2010-10-08 00:42 |
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 |
2007BioE215 Eser
- BioE215 Coursework Spring 2007 | |
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Activity Percentile: 0.00 Registered: 2007-04-07 02:13 |
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. | |
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Activity Percentile: 0.00 Registered: 2014-10-09 18:12 |
Shoulder mechanics: Undergrad research in muscle mechanics of the shoulder
- This project is a combination of experimental and computational approaches to understanding shoulder mechanics. We are investigating the role of muscle architecture in joint mechanics. | |
Registered: 2010-03-26 19:28 |
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 |
OpenSim for the Warrior Web
- Online support and resource portal for teams developing Warrior Web Technologies.
Access all of our OpenSim resources at the <br /><a href="http://www.stanford.edu/group/opensim/support/index.html"><b style="color:#900; font-size:16px;">Support Site</b></a>.
Also see the <br /><a href="http://simtk-confluence.stanford.edu:8080/display/OpenSim/Warrior+Web+Wiki"><b style="color:#900; font-size:16px;">Warrior Web Wiki</b></a>.
This project includes the following (see links at left):
1) A Team page, where you can see our team members and get in touch for support and questions.
2) A Downloads page, where you can find models, plug-ins, data, and other code and software for Warrior Web teams. Additional downloads are available on the main OpenSim Simtk project page.
3) A Documents page, where you can find handouts, slides, and links to relevant OpenSim resources and downloads.
4) A Public Forums page, a discussion forum for Warrior Web teams using OpenSim
5) Under the Advanced tab, you will find:
- A repository for uploading and sharing models and code
- A mailing list to receive OpenSim Warrior Web news and events | |
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Registered: 2012-05-31 00:39 |
Creating a Tensegrity Robot
- This project is to study the applicability of utilizing this program to create a tensegrity robot and a virtual environment for the tensegrity robot. | |
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Activity Percentile: 0.00 Registered: 2010-08-11 01:17 |
Dynamic Simulation of Joints Using Multi-Scale Modeling
- This research is funded by the National Science Foundation, Grant Number 506297, under the IMAG program for Multiscale Modeling. It is a collaborative effort that capitalizes on a diversity of expertise in areas such as clinical, experimental and computational biomechanics, nano-micro scale material modeling, finite element modeling, and neural networks.
Grant Numer: 506297
Principle Investigator: Trent Guess
Co-Investigators: Ganesh Thiagarajan, Amil Misra, Reza Derakhshani (University of Missouri - Kanas City), Lorin Maletsky (University of Kansas), Terence McIff (University of Kansas Medical Center)
Abstract from grant proposal
Dynamic loading of the knee is believed to play a significant role in the development and progression of tissue wear disease and injury. Macro level rigid body joint models provide insight into joint loading, motion, and motor control. The computational efficiency of these models facilitates dynamic simulation of neuromusculoskeletal systems, but a major limitation is their simplistic (or non-existent) representation of the non-linear, rate dependent behavior of soft tissue structures. This limitation prevents holistic computational approaches to investigating the complex interactions of knee structures and tissues, a limitation that hinders our understanding of the underlying mechanisms of knee injury and disease.
The objective of this project is to develop validated neural network models that reproduce the dynamic behavior of menisci-tibio-femoral articulations and to demonstrate the utility of these models in a musculoskeletal model of the leg. The specific aims of this study are:
Aim 1: Develop finite element (FE) models from micro-structure based constitutive methods that bridge the nano-micro scale behavior at the tissue level
Aim 2: Develop neural network (NN) based models that learn from FE simulation of dynamic behavior of menisci-tibio-femoral articulations
Aim 3: Validate the NN models within a rigid body dynamic model of a natural knee placed within a dynamic knee simulator
Aim 4: Demonstrate the utility of the NN models by placing them within a dynamic musculoskeletal model of the leg to study the interdependencies of the menisci and other knee tissues
Aim 5: Distribute the validated NN models of menisci-tibio-femoral dynamic response and contact pressure for use in any rigid body model of the knee or leg
The final product will be Neural Network (NN) models that conform to a modular application programming interface (API) that can be exported to any commercial integrated development environment (IDE) or in-house multi-body model. The NN models will be built upon a multi-scale approach and describe the non linear, rate dependent, non-homogenous dynamic response of menisci-tibio-femoral articulations in a computationally efficient modular package. The multi-scale modeling approach will be validated using a dynamic knee loading machine and the utility of the approach demonstrated by studying the interdependencies of menisci properties, tibio-femoral contact, and anterior cruciate ligament strain during a dual limb squat. A synergistic interdisciplinary team has been assembled to address the objective and aims of the proposed project comprising experts in rigid body dynamics and knee modeling, FE modeling, nano-micro scale material modeling, neural networks, and clinical and experimental biomechanics.
The proposed research will benefit society at large as the results of this work have potential applications to orthopedics, tissue engineering, and biomaterials. The work will also be a valuable asset to the musculoskeletal research community providing computational tools that may aid research in broad areas such as human movement, prosthetics, tissue engineering, sport injury, and disease. | |
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Registered: 2006-10-18 19:49 |
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 |
The Reference Model for Disease Progression
- The Reference Model is now:
• <a href="http://dx.doi.org/10.7759/cureus.9455" target="_blank"> COVID-19 model for US states and territories </a>
• <a href="https://jacob-barhak.github.io/InteractivePoster_MSM_IMAG_2019.html" target="_blank"> The Most Validated Cardiovascular (CVD) Diabetes Model known </a>
• <a href="https://patents.google.com/patent/US20140297241A1/en" target="_blank"> United States Patent 9,858,390</a>
• <a href="https://patents.google.com/patent/US20170286627A1/en" target="_blank"> United States Patent Number 10,923,234</a>
The Reference Model can now:
• Attempt to explain COVID-19 for US states
• Determine CVD models that significantly behave better on several diabetic populations
• Deduce that CVD probability halves every 5 years due to medicine improving - according to information from the last 3 decades
• Calculate life tables for diabetics
• Interface with ClinicalTrials.Gov
• Include human interpretation in the model
• Create an interactive map of our <a href="https://jacob-barhak.github.io/InteractivePoster_MSM_IMAG_2019.html" target="_blank"> <b> cumulative computational knowledge gap</b>
<a href="http://dx.doi.org/10.7759/cureus.9455" target="_blank"> <b> COVID-19 MODEL</b> </a>
The interactive plot below shows our cumulative knowledge gap by showing the error in the vertical axis for US states and territories listed on the horizontal axis. Circles at the bottom have a better fit between observed COVID-19 results and model results. Results are for normalized population of size 10,000 individuals. Hover over the circles to see additional details about each state. The slider determines the model optimization iteration. User can explore the map by changing size and color attributes.
<iframe width="1000" height="400" src="https://jacob-barhak.netlify.app/thereferencemodel/results_covid19_2020_06_27/populationplot" frameborder="0" > </iframe>
<a href="https://simtk.org/projects/mist" target="_blank"> <b> TECHNOLOGY </b> </a>
The Reference Model is a good way to cross reference information to find out pieces of information and assumptions that fit together, and allow competition against accumulated known data to guide our perception. High Performance Computing is a key to those capabilities and it provided using capabilities of the <a href="https://simtk.org/projects/mist" target="_blank"> MIcro Simulation Tool (MIST) </a> .
MIST also provides advance population generation techniques using Evolutionary computation. The Reference Model uses publicly available data such as clinical trial publications. This allows it to access more information since it allows accessing data that otherwise will be restricted from sharing. The Reference Model has an interface that allows it to read information from <a href="https://clinicaltrials.gov/" target="_blank" > ClinicalTrials.Gov</a> while maintaining tractability and reproducibility.
<b> <a href="https://simtk.org/plugins/simtk_news/index.php?group_id=1286" target="_blank"> PUBLICATIONS: </a> </b>
The Reference Model was created in 2012 and evolved since then. You can find key developments and publications by year in the <a href="https://simtk.org/plugins/simtk_news/index.php?group_id=1286" target="_blank"> news section </a>.
Here are some videos describing the Model:
This video gives a brief introduction
<iframe width="800" height="450" src="https://www.youtube.com/embed/s9L-qFF84Ew" title="The Reference Model for Disease Progression: Explaining COVID-19" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
This video will shows recent results of explaining COVID-19 using USA data:
<iframe width="800" height="450" src="https://www.youtube.com/embed/1M645o5gWrc" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
This video will show a breakthrough of becoming the first multiscale ensemble model for COVID-19:
<iframe width="800" height="450" src="https://www.youtube.com/embed/-z8N40TdKDk?start=1860" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
This video explains the model in a larger context as presented in AnacondaCon 2019:
<iframe width="800" height="450" src="https://www.youtube.com/embed/fQIYMf5wKGE" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
This video explains how human interpretation can be used as presented in the Multiscale Viral Pandemics working group webinar:
<iframe width="800" height="450" src="https://www.youtube.com/embed/aTB8-XEZheU" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
This video summarizes a decade of work as presented in PyTexas 2017:
<iframe width="800" height="450" src="https://www.youtube.com/embed/Pj_N4izLmsI?list=PL0MRiRrXAvRiwQUUwTTh5g8rhbQyYlubo" frameborder="0" gesture="media" allow="encrypted-media" allowfullscreen></iframe>
This describes the evolution of the model up to 2016 presented in PyTexas:
<iframe width="800" height="450" src="https://www.youtube.com/embed/htGRRjia-QQ" frameborder="0" allowfullscreen></iframe>
This describes the work presented in PyData in 2014:
<iframe width="800" height="450" src="https://www.youtube.com/embed/vyvxiljc5vA" frameborder="0" allowfullscreen></iframe> | |
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Registered: 2017-05-09 05:34 |
28 projects in result set. Displaying 20 per page. Projects sorted by alphabetical order.
<1> <2>