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70 projects in result set. Displaying 20 per page. Projects sorted by alphabetical order.
<1> <2> <3> <4>
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 |
Practical Annotation and Exchange of Virtual Anatomy
- Representation of anatomy in a virtual form is at the heart of clinical decision making, biomedical research, and medical training. Virtual anatomy is not limited to description of geometry but also requires appropriate and efficient labeling of regions - to define spatial relationships and interactions between anatomical objects; effective strategies for pointwise operations - to define local properties, biological or otherwise; and support for diverse data formats and standards - to facilitate exchange between clinicians, scientists, engineers, and the general public. Development of aeva, a free and open source software package (library, user interfaces, extensions) capable of automated and interactive operations for virtual anatomy annotation and exchange, is in response to these currently unmet requirements. This site serves for aeva outreach, including dissemination the software and use cases. The use cases drive design and testing of aeva features and demonstrate various workflows that rely on virtual anatomy.
aeva downloads:
Downloads (https://simtk.org/frs/?group_id=1767)
Kitware data repository (https://data.kitware.com/#folder/5e7a4690af2e2eed356a17f2)
aeva documentation:
Guides and tutorials (https://aeva.readthedocs.io)
aeva videos:
Short instructions (https://www.youtube.com/channel/UCubfUe40LXvBs86UyKci0Fw)
aeva source code:
Kitware source code repository (https://gitlab.kitware.com/aeva)
aeva forum:
Forums (https://simtk.org/plugins/phpBB/indexPhpbb.php?group_id=1767 ) | |
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Registered: 2019-08-28 01:27 |
Statistical analysis of conformational ensembles
- This project provides computational tools and methods to analyze conformational ensembles of biomolecules, as well as their assemblies, such as those obtained from molecular simulations.
(A) PROTEINS: The molecular understanding of the functional regulation of proteins requires assessment of various states, including active and inactive states, as well as their interdependencies. For several proteins, their various states can be distinguished from each other on the basis of their minimum energy 3D structures. For many other proteins, like GPCRs, PDZ domains, nuclear transcription factors, heat shock proteins, T-cell receptors and viral attachment proteins, their states can be distinguished categorically from each other only when their finite-temperature conformational ensembles are considered alongside their minimum-energy structures. We are developing tools/methods for:
(A1) Direct comparison of conformational ensembles - The traditional approach to compare two or more conformational ensembles is to compare their respective summary statistics. This approach is, however, prone to artifactual bias, as data is compared after dimensionality reduction. The proper way to compare ensembles is to compare them directly with each other and prior to any dimensionality reduction. g_ensemble_comp is a tool we have developed that does just that and reports the difference between ensembles in terms of a true metric defined by the zeroth law of thermodynamics.
(A2) Prediction of allosteric signaling networks - method under development.
(B) LIPID MEMBRANES: The surface area of a lipid bilayer is related fundamentally to many other observables, such as thermal phase transitions and domain formation in mixed lipid bilayers. We have developed g_tessellate_area to compute the 3D surface area of a bilayer using Delunay tessellation. | |
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Activity Percentile: 93.51 Registered: 2015-09-15 17:52 |
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 |
Musculoskeletal Model of the Lumbar Spine
- The work here features a number of different OpenSim models of the lumbar spine developed to study lumbar kinematics and dynamics.
Briefly, the models consist of the following bodies:
# rigid pelvis and sacrum
# five lumbar vertebrae (separated by joints with three rotational degrees of freedom)
# torso (thoracic spine + ribcage)
The motion of the individual joints are defined using constraint functions specifying the motion of the lumbar vertebra as functions of the net lumbar motion (flexion-extension, lateral bending and axial rotation). Future models will incorporate joints with stiffness properties to more accurately mimic the action of the intervertebral joints.
The most complex of these models also feature the 238 muscle fascicles associated with the 8 main muscle groups of the lumbar spine necessary to study the contribution of the lumbar spinal musculature to spinal motion. Simpler models incorporating two and seven of the main muscle groups of the lumbar spine are provided as well for completeness.
Read more about the model in the paper, freely downloadable at http://link.springer.com/article/10.1007%2Fs10237-011-0290-6.
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September 2011 Addendum
Click on the "Downloads" link to the left for downloads related to more recent work.
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September 2012 Addendum
The Constrained Lumbar Spine Model does not require any of the files uploaded after the creation of the Constrained Lumbar Spine Model project. The .vtp files (and descriptions) are included here for the benefit of those of you who wish to create your own model that has origins shifted to the center of the bones since this typically saves a number of transformations. Many apologies for any confusion(!).
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March 2014 Addendum
(1)
This model was build with OpenSim 2+. Version 3+ will not allow you to use periods (.) in your variable names. Unfortunately, a bunch of the variables used (muscles mainly) have periods in the names so it will throw an error if you try and run it in OpenSim version 3+. To fix this, either use version 2+, OR, rename the variables appropriately.
(2)
We have all graduated and are no longer actively working on this project (we haven't been working on it since the end of 2011 actually). At this point, you probably know more than us about OpenSim so we apologize in advance if our support is subpar.
(3)
The complex mode is not meant to be run straight out of the box. It has almost 250 muscles after all and unless you have a super computer, running CMC, or FD on it is going to bring up the rainbow ball of death on your computer.
Rather, it's meant to be a reference for those of you who intend to build up your own model. My advice would be to start with the simple 4 fascicle model, get it to work, then incrementally build up from there using the parameters provided in our model as a starting point. Copy-Paste is your friend here. :)
(4)
If this is your very first OpenSim project, I strongly _strongly_ *strongly* suggest that you go through the examples provided with the OpenSim version you just downloaded and understand how they work. This will save you months of pain down the road. | |
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Activity Percentile: 87.02 Registered: 2010-11-04 02:25 |
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: 86.64 Registered: 2008-08-29 02:59 |
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 |
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 |
SCONE: Open Source Software for Predictive Simulation
- If SCONE is helpful for your research, please cite the following paper:
Geijtenbeek, T (2019). SCONE: Open Source Software for Predictive Simulation of Biological Motion. Journal of Open Source Software, 4(38), 1421, https://doi.org/10.21105/joss.01421 | |
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Registered: 2016-10-27 13:07 |
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 |
Matlab MOtion data elaboration TOolbox for NeuroMusculoSkeletal apps (MOtoNMS)
- MOtoNMS processes experimental data from C3D files of different motion analysis devices and produces input data for OpenSim (.trc and .mot, OpenSim file formats). When available, EMG signals are also processed and can be exported in several formats (.mot, OpenSim motion, .sto, OpenSim Storage, and .txt, plain text format) compatible with the CEINMS toolbox (https://simtk.org/home/ceinms), and easily usable also by other applications.
Procedures implemented in MOtoNMS include: (i) computation of centers of pressure and torques for the most commonly available force platforms (types from 1 to 4, including Bertec, AMTI and Kistler); (ii) rotation of motion capture data between different coordinate systems (those of force platforms, laboratory and OpenSim); (iii) EMG filtering, maximum peak computation, and normalization; (iv) exportation of data ready to be used in OpenSim and CEINMS toolbox. Procedures are highly configurable through user-friendly graphical interfaces that setup XML files listing all the parameters of the execution.
The architecture has been designed to easily accommodate new contributions in instrumentations, protocols, and methodologies. Additionally, data management results in a clear organization of input data and an automatic generation of output directories with a uniquely defined structure.
The tool has been already tested on data from several laboratories with different instruments and procedures for the data collection.
MOtoNMS is released under GNU General Public Licence and freely available to the community without warranty. The software requires either Motion Labs C3D Server software or BTK (Biomechanical ToolKit).
A manual is included with the software, while a html version is always available from the GitHub Project Pages at http://rehabenggroup.github.io/MOtoNMS/. For doubts, suggestions, bugs please either use the MOtoNMS forum or send us an email. This is an ongoing project, any feedback is really appreciated.
When using MOtoNMS or our Test Data, please acknowledge the authors and cite our main publication:
Mantoan et al. Source Code for Biology and Medicine (2015) 10:12
DOI 10.1186/s13029-015-0044-4
http://www.scfbm.org/content/10/1/12 | |
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Activity Percentile: 75.95 Registered: 2014-02-16 11:33 |
Batch OpenSim Processing Scripts (BOPS)
- BOPS performs batch processing of common OpenSim procedures (Inverse Kinematics - IK, Inverse Dynamics - ID, Muscle Analysis - MA, Static Optimization - SO, and Joint Reaction Analysis - JRA) and stores output, logging information, setup files, and plots in an ordered structure of folders.
We implemented BOPS using OpenSim APIs, that receive the following information through setup files: (i) name and weight of each marker (IK); (ii) external loads (ID); (iii) muscles and moment arms of interest (MA); (iv) static optimization conditions, and muscle actuators loads (SO); (v) joints of interest (JRA). The user is in charge of defining the appropriate configuration for its data, but we already provide several templates for each setup file to speed up their customization.
A MATLAB Graphical User Interface (GUI) is available to simplify the execution of procedures. The use of the GUI is not limited to inputting the setup files. The user can also select: (i) the OpenSim procedures to execute, (ii) the trials to process, (iii) the OpenSim model to use on the simulations, (iv) the cut-off frequencies for the filtering, (v) the residual actuators, (vi) the output variables to plot and the x-axis label.
The software only requires to configure MATLAB for the use of OpenSim API (http://simtk-confluence.stanford.edu:8080/display/OpenSim/Scripting+with+Matlab), and it is based on the data folder organization provided by MOtoNMS software (https://simtk.org/home/motonms).
BOPS stores its outputs in folders that are automatically created and that integrate perfectly in the structure provided by MOtoNMS software (https://simtk.org/home/motonms). We designed the two tools to work in close cooperation to transform the data collected in a motion analysis laboratory into inputs for OpenSim and CEINMS (https://simtk.org/home/ceinms) tools.
BOPS is released under Apache v2.0 License and freely available to the community without warranty. Latest updates can be found on the GitHub repository (https://github.com/RehabEngGroup/BOPS).
Thanks to the recent join of the Human Movement Biomechanics Laboratory (University of Ottawa, Canada) to the project, the tool has been refined and extensively tested on data from several laboratories and with different combinations of procedures, setups and user choices. Their precious contribution has allowed also the addition of the JRA procedure to those already available and led to the release of v2.0, a definitely improved and more stable version.
A tutorial video exemplifying how to use BOPS v2.0 is available in the Documents section.
For any doubts, suggestions, bugs please either use the BOPS forum or send us an email.
This is an ongoing project, therefore any feedback is really appreciated.
When using BOPS or our Test Data, please acknowledge the authors and cite our main publication:
Bruno L. S. Bedo, Alice Mantoan, Danilo S. Catelli, Willian Cruaud, Monica Reggiani & Mario Lamontagne (2021): BOPS: a Matlab toolbox to batch musculoskeletal data processing for OpenSim, Computer Methods in Biomechanics and Biomedical Engineering
DOI: 10.1080/10255842.2020.1867978 | |
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Activity Percentile: 69.08 Registered: 2015-09-05 18:12 |
OpenSim Soccer Ball Kicking Example
- This project is for students and educators interested in how elements of a musculoskeletal model come together to generate simulations of human movement.
The soccer kick is meant to be compelling, challenging, and fun, allowing students to experiment with motor control strategies.
If you have questions, please feel free to contact us at opensim@stanford.edu.
To find out more about the OpenSim project, please visit our website at http://opensim.stanford.edu | |
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Registered: 2011-09-30 20:42 |
Stroke gait
- This project involves the generation of subject-specific simulations of a range of post-stroke hemiparetic gait patterns, contribution of parallel optimization techniques, comparison of control algorithms, and analysis of 2d and 3d results. | |
Activity Percentile: 62.60 Registered: 2006-08-23 17:28 |
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: 48.85 Registered: 2015-07-20 20:18 |
Motion Analyst Software Suite
- This project is a suite of motion analysis tools that use images from common video cameras to measure 2D and 3D motions. Locations of markers in 2D space can be tracked in time using MotionAnalyst2D. When interested in 3D reconstruction, 2D analysis needs to be completer using two cameras that simultaneously capture the images. By combining the two 2D results with the camera orientation calibration data, then 3D locations for those original markers can be reconstructed using MotionAnalyst3D. | |
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Activity Percentile: 47.71 Registered: 2011-12-01 21:24 |
Surrogate Contact Modeling Toolbox
- This opensource toolbox provides researchers with the capabilities to construct and use surrogate contact models. Some features are:
- Multiple domains for sampling including out-of-contact configurations
- A multi-threaded sampler that makes use of FEBio's contact modeling capabilities
- Flexible specification of surrogate model inputs and outputs, and architecture
- Parallelized training
- Testing module
- Surrogate models portable as DLLs
Operating System: Microsoft Windows.
Model fitting requires: Matlab's Neural Network Toolbox, and Matlab coder.
Sampling requires: FEBio. | |
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Activity Percentile: 27.48 Registered: 2014-10-01 18:56 |
Multicore parallel computing with OpenSim Moco
- In this project, we investigated the computational speed‐up obtained via multicore parallel computing relative to solving problems serially (i.e., using a single core) in optimal control simulations of human movement in OpenSim Moco. Simulations were solved using up to 18 cores with a variety of temporal mesh interval densities and using two different initial guess strategies. Considerable speed‐up can be achieved for some optimal control simulation problems in OpenSim Moco by leveraging the multicore processors often available in modern computers.
This work is described in the paper "Computational performance of musculoskeletal simulation in OpenSim Moco using parallel computing" which is available on the Publications page. Models and complete working examples are provided on the Downloads page. This project was supported by a Rackham Graduate Student Research Grant. | |
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Registered: 2023-08-21 23:33 |
An OpenSim plugin to minimize joint reaction forces and muscle activations
- This project provides an OpenSim analysis to minimize both joint reaction loads and muscle activations in a moving musculoskeletal model. The analysis, called JointLoadOptimization, is provided as an independent plugin that users can link with OpenSim. JointLoadOptimization is highly configurable version of static optimization, providing an xml interface for customizing the cost function. The cost function can include independently weighted components of the joint reaction force and moment for any joint in the model, as well as weighted muscle activations. | |
Activity Percentile: 18.70 Registered: 2012-05-10 19:00 |
70 projects in result set. Displaying 20 per page. Projects sorted by alphabetical order.
<1> <2> <3> <4>