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261 projects in result set. Displaying 20 per page. Projects sorted by alphabetical order.
<1> <2> <3> <4> <5> <6> <7> <8> <9> <10> <11> <12> <13> <14>
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 |
Grand Challenge Competition to Predict In Vivo Knee Loads
- Knowledge of muscle and joint contact forces during gait is necessary to characterize muscle coordination and function as well as joint and soft-tissue loading. Musculoskeletal modeling and simulation is required to estimate muscle and joint contact forces, since direct measurement is not feasible under normal conditions. This project provides the biomechanics community with a unique and comprehensive data set to validate muscle and contact force estimates in the knee. This data set includes motion capture, ground reaction, EMG, tibial contact force, and strength data collected from a subject implanted with an instrumented knee prosthesis. | |
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Activity Percentile: 95.42 Registered: 2009-07-14 23:24 |
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 |
Full Body Model for use in Dynamic Simulations of Human Gait
- Our paper describes a full body OpenSim model with musculotendon parameters derived from experimental measurements of 21 cadaver lower limbs and magnetic resonance images of 24 young adult subjects. Our model is derived from the lower body model published by Arnold et al. (2010) and the tracking upper body by Hamner et al. (2013), but updates the muscle force distribution to reflect those of a young, healthy population, includes a new knee model to accurately represent internal forces, and simplified muscle wrapping surfaces to increase computation speed in CMC and other muscle-driven simulations. | |
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Activity Percentile: 93.51 Registered: 2012-06-11 22:52 |
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: 93.13 Registered: 2014-11-10 15:19 |
Simulations of Crouch Gait
- This research examined the <b>dynamics of crouch gait among children with cerebral palsy </b>. Specifically, our work examined individual muscles contribute to joint and mass center movement in children with cerebral palsy who walk with a crouch gait. In 2010, we created simulations of single-limb stance for 10 subjects with a mild crouch gait. In 2012-2013, we expanded this study to evaluate muscle contributions to gait during mild, moderate, and severe crouch gait. We also used these simulations to evaluate how muscle weakness may contribute to crouch gait and to examine knee contact force during crouch gait. In 2017, these simulations were also used to evaluate how passive or powered ankle foot orthoses may assist during crouch gait. Together this research has helped us understand the mechanisms that contribute to crouch gait and guide treatment planning to improve gait for children with cerebral palsy.
Please visit the <a href="https://nmbl.stanford.edu"> Neuromuscular Biomechanics Lab </a> and the <a href="depts.washington.edu/uwsteele/"> Ability & Innovation Lab </a> to learn more about our on-going research in this area.
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Activity Percentile: 92.37 Registered: 2010-05-18 22:21 |
Predicting Cell Deformation from Body Level Mechanical Loads
- This project is a NIBIB/NIH funded study (1R01EB009643-01) to establish models and computational platforms to predict cellular deformations from joint level mechanical loading.
Collaborators:
Ahmet Erdemir (PI), Amit Vasanji, Jason Halloran (Cleveland Clinic)
Cees Oomens, Frank Baaijens (Eindhoven University of Technology)
Jeff Weiss (University of Utah)
Farshid Guilak (Duke University)
Summary (from grant proposal):
Cells of the musculoskeletal system are known to have a biological response to deformation. Deformations, when abnormal in magnitude, duration, and/or frequency content, can lead to cell damage and possible disruption in homeostasis of the extracellular matrix. These mechanisms can be studied in an isolated fashion but connecting mechanical cellular response to organ level mechanics and human movement requires a multiscale approach. At the organ level, physicians perform surgical procedures, investigators try to understand risk of injury, and clinicians prescribe preventive and therapeutic interventions. Many of these operations are aimed at management and prevention of cell damage, and to associate joint level mechanical markers of failure to cell level failure mechanisms. Through human movement, one explores neuromuscular control mechanisms and the influence of physical activity on musculoskeletal tissue properties. At a lower level, mechanical sensation of cell deformations regulate movement control. Physical rehabilitation and exercise regimens are prescribed to promote tissue healing and/or strengthening through cellular regeneration. The knowledge of the mechanical pathway, through which the body level loads are distributed between organs, then within the tissues and further along the extracellular matrix and the cells, is critical for the success of various interventions. However, this information is not established. The goal of this research proposal is to portray that prediction of cell deformations from loads acting on the human body, therefore a clear depiction of the mechanical pathway, is possible, if a multiscale simulation approach is used. Multiresolution models of the knee joint, representative of joint, tissue and cell structure and mechanics, will be developed for this purpose. The knee endures high rates of traumatic injury to its soft tissue structures and it is predominantly affected by osteoarthritis, chronically induced by abnormalities in mechanical loading or how it is transferred to the cartilage. Through multiscale mechanical coupling of these models, a map of cellular deformation in cartilage, ligaments and menisci under a variety of tibiofemoral joint loads will be obtained. Comprehensive mechanical testing at joint, tissue and cell levels will be conducted for parameter estimation and validation, including in vitro loading of the knee joint representative of lifelike loading scenarios. In addition, imaging modalities will capture joint and tissue anatomy, and spatial and deformation related information from cell and extracellular matrix. Advanced computational approaches will be used to obtain model properties and to facilitate multiscale simulations. The approach will combine the expertise of many investigators experienced in biomechanical modeling and experimentation at various biological scales, some with clinical expertise. In future, the research team will utilize this platform to establish the relationship between the structural and loading state of the knee and chondrocyte stresses to explore potential mechanisms of cartilage degeneration. Through documented dissemination of data and models, simulations of other pathologies and translation of the methodology to other organs can be carried out by any interested investigator. | |
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Registered: 2009-07-23 17:33 |
Upper Extremity Kinematic Model
- The project holds all the files necessary for a SIMM-based kinematic musculoskeletal model of the human upper-extremity which can also be easily imported and used in OpenSIM. In order to respect the time and effort put in by the original developers please carefully read accompanying publications and cite appropriate references in future work. The links to the left contain all the files (Downloads) and documentation (Documents) related to the model.
<hr> </hr>
<b>Please cite the following paper:</b>
- Holzbaur KR, Murray WM, Delp SL.: A model of the upper extremity for simulating musculoskeletal surgery and analyzing neuromuscular control., Ann Biomed Eng. 2005 Jun;33(6):829-40. (2005)
<hr> </hr>
<b>About the model:</b>
This model of the upper extremity includes 15 degrees of freedom representing the shoulder, elbow, forearm, wrist, thumb, and index finger, and 50 muscle compartments crossing these joints. The kinematics of each joint and the force-generating parameters for each muscle were derived from experimental data. The model estimates the muscle–tendon lengths and moment arms for each of the muscles over a wide range of postures. Given a pattern of muscle activations, the model also estimates muscle forces and joint moments. The moment arms and maximum moment generating capacity of each muscle group (e.g., elbow flexors) were compared to experimental data to assess the accuracy of the model. These comparisons showed that moment arms and joint moments estimated using the model captured important features of upper extremity geometry and mechanics. The model also revealed coupling between joints, such as increased passive finger flexion moment with wrist extension.
<hr> </hr> | |
Registered: 2008-07-25 21:56 |
IA-FEMesh
- In an effort to facilitate anatomic FE model development, we introduce IA-FE Mesh (Iowa FE Mesh), a freely available software toolkit. IA-FEMesh employs a multiblock meshing scheme aimed at hexahedral mesh generation. An emphasis has been placed on making the tools interactive, in an effort to create a user-friendly environment. The goal is to provide an efficient and reliable method for model development, visualization, and mesh quality evaluation. While these tools have been developed, initially, in the context of skeletal structures, they can be applied to a virtually endless number of modeling applications. | |
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Activity Percentile: 89.31 Registered: 2008-08-29 02:59 |
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: 88.55 Registered: 2015-01-14 23:10 |
Full-body Musculoskeletal Model of the Lumbar Spine
- The full-body lumbar spine (FBLS) model was created by combining other previously developed OpenSim models (https://simtk.org/home/lumbarspine, https://simtk.org/home/runningsim, https://simtk.org/home/lowlimbmodel09). The purpose of developing this model was to provide users with a full-body model suited for investigations involving the trunk musculature and lumbar spine.
Briefly, this model consists of 21 segments, 29 degrees-of-freedom, and 324 musculotendon tendon actuators. The five lumbar vertebrae are modeled as individual bodies, each connected by a 6 degree-of-freedom joint. Net lumbar movement is described as flexion-extension, axial rotation, and lateral bending by imposing constraint functions to each individual lumbar vertebra. The eight main muscle groups of the lumbar spine are modeled, each consisting of multiple fascicles to allow the large muscles to act in multiple directions. These trunk muscles include: rectus abdominis, external obliques, internal obliques, erector spinae, multifidus, quadratus lumborum, psoas major, and latissimus dorsi.
This model is currently suitable for running Static Optimization but is not yet suited for Computed Muscle Control (CMC). A future release of the model will be suited for CMC.
This project page will make the model freely-available to OpenSim users and include information about model development and validation procedures. | |
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Activity Percentile: 86.26 Registered: 2015-06-24 18:25 |
Integrated Flux Balance Analysis Model of Escherichia coli
- This project includes several MATLAB scripts that simulate E. coli central metabolism and the effects of single gene deletions on metabolism using 3 approaches -- iFBA, rFBA, and ODE. The project also includes several MATLAB scripts that simulate biochemical networks using 1) integrated flux balance analysis (iFBA) -- a combined FBA, boolean regulatory, and ODE approach; 2) regulatory flux balance analysis (rFBA); and 3) ordinary differential equations (ODE). Additionally, the project includes several MATLAB and php scripts for visualizing metabolic simulations. | |
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Registered: 2008-06-11 23:27 |
Modeling, Evaluation, and Control Optimization of Exosuit with OpenSim
- This project tackles the challenges of developing wearable device using OpenSim simulation. Simulation can help developing wearable device as it can give an intuition on how wearable devices interact with human and how muscle activations change when a subject wear the device. We can also find the key features that one should account for when designing wearable device in order to make it efficient.
In this project, I focused on specific wearable device, called Harvard Exosuit. BioDesign group at Harvard University is developing this suit, and the main idea is to create a soft and deformable under-suit which can assists loaded walking.
My accomplishments through this project are
- Evaluate the effectiveness of wearing active actuators on metabolic cost reduction.
- Explain how Exosuit can help loaded gait
- Verify the impact of changes of design parameters
- Find optimal control inputs for active actuators
Here is a video clip for project overview:
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If you want more details of this project, please visit the project confluence webpage: <a href="http://simtk-confluence.stanford.edu:8080/display/OpenSim/Modeling%2C+Evaluation%2C+and+Control+Optimization+of+Exosuit+with+OpenSim"> Confluence page</a> | |
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Activity Percentile: 84.35 Registered: 2013-06-06 23:00 |
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 |
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 |
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 |
Upper and Lower Body Model
- This project provides a useful starting model to those interested in a full body model. In this project the lower limb model developed by Delp S.L. et al. ("Gait2354_Simbody") is combined with the upper limb model developed by Holzbaur K.R. et al. ("UpperExtremityModel") in order to create an almost full body model (the neck degrees of freedom are for example not included in the models of this project). | |
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Activity Percentile: 81.68 Registered: 2009-07-18 21:29 |
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 |
261 projects in result set. Displaying 20 per page. Projects sorted by alphabetical order.
<1> <2> <3> <4> <5> <6> <7> <8> <9> <10> <11> <12> <13> <14>