Project Tree
Now limiting view to projects in the following categories:
All Topics :: Primary Content :: Applications [Remove This Filter]
All Topics > Primary Content > Models |
Browse By: |
96 projects in result set. Displaying 20 per page. Projects sorted by alphabetical order.
<1> <2> <3> <4> <5>
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> | |
|
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>.
| |
|
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. | |
|
Registered: 2012-01-24 03:21 |
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. | |
|
Activity Percentile: 93.13 Registered: 2014-11-10 15:19 |
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. | |
|
Registered: 2009-07-23 17:33 |
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. | |
|
Activity Percentile: 89.31 Registered: 2008-08-29 02:59 |
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. | |
|
Registered: 2008-06-11 23:27 |
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. | |
|
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> | |
|
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. | |
|
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. | |
|
Registered: 2015-08-24 12:54 |
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.
----------------------------------------------------------------
----------------------------------------------------------------
September 2011 Addendum
Click on the "Downloads" link to the left for downloads related to more recent work.
----------------------------------------------------------------
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(!).
-----------------------------------------------------------------
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. | |
|
Activity Percentile: 79.39 Registered: 2010-11-04 02:25 |
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 | |
|
Registered: 2016-10-27 13:07 |
Myosin Resources and Communication
- A public forum for the myosin community to post documents, engage in discussions and exchange background material.
Related projects: www.simtk.org/home/dwell. | |
Registered: 2005-09-02 21:04 |
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 | |
|
Registered: 2011-09-30 20:42 |
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
<object width="560" height="500"><param name="movie" value="//www.youtube.com/v/6OkaTvEmpWk?hl=en_US&version=3"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="//www.youtube.com/v/6OkaTvEmpWk?hl=en_US&version=3" type="application/x-shockwave-flash" width="560" height="500" allowscriptaccess="always" allowfullscreen="true"></embed></object> | |
|
Activity Percentile: 51.91 Registered: 2015-07-20 20:18 |
OpenSim 3D World Objects Library
- We have developed a library of 3D world objects which appear as colored solid bodies in OpenSim. The objects are formatted with color, texture, and correct geometries. We hope these objects both provide a visual context for simulations and also serve as a tool to analyze interactions of objects with musculoskeletal models. | |
Activity Percentile: 34.73 Registered: 2010-06-10 22:26 |
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! | |
|
Registered: 2011-12-20 17:04 |
Wrist Anatomy and Kinematics Data Collection
- <div align="justify">CT images of wrists from 90 healthy volunteers (43 males and 47 females) were acquired in various wrist positions. The outer cortical surfaces of the carpal bones, radius, and ulna in a 3D format, and each bone kinematics were calculated for each wrist position using a methodology described in the README file associated with the database. The database does not include soft tissue or the cartilage information of the wrist. Moreover, there is a MATLAB graphic user interface (GUI) available for you to observe the database. This dataset comes from four different NIH funding between 2001 and 2014.</div>
Please cite the work if you're using this database:
<div align="justify"><a href="https://onlinelibrary.wiley.com/doi/abs/10.1002/jor.24435">Akhbari, B., Moore, D. C., Laidlaw, D. H., Akelman, E., Weiss, A-P. C., Wolfe, S. W., Crisco, J. J., 2019. Predicting Carpal Bone Kinematics using an Expanded Digital Database of Wrist Carpal Bone Anatomy and Kinematics, Journal of Orthopaedic Research. DOI:10.1002/jor.24435</a></div>
If you want the pdf version of the manuscript, please send your request on <a href="http://bit.ly/2YU2tTh">ResearchGate</a>.
| |
|
Registered: 2019-02-25 19:48 |
The Fatigable Runner
- There has been an ongoing debate for a long time as to which running form is the optimal for performance for endurance, long distance running. Numerous personal accounts for improvement in performance has been reported by everyday athletes all the way to world champion triathletes describing a number of modified components to their running form that have helped in making them run faster and more efficiently. But none of which has really been well documented scientifically. Though this project is only a tiny step toward analyzing differences in running forms with preliminary data, it provides a platform for future biomechanists to examine the key differences in running forms of different individuals.
This is an extremely difficult question to answer since there is almost no way to experimentally test the differences between running forms. This is because it is impossible to have adequate controls. Every runner is different in height, weight, fitness level, muscular strength, etc. Every runner also runs differently. It’s not possible for one runner to replicate many different styles in an experiment as every runner has his/her own natural style. However, if different running motion kinematics can be replicated with one model of runner, the differences may be well observed.
Utilizing opensim software, simulations can be performed using the same runner and replicating different running styles. Computed muscle controls also allows muscle activations to be calculated and compared. An additional feature is the adding custom muscle model that fatigues to mimic an endurance running event. Since there has been no model with fatigable muscle implemented before, there are a lot of questions that can only be answered through simulation with fatigable muscles. Differences in running form may be analyzed without considering muscle fatigue, but inducing muscle fatigue may provide more insight. | |
Activity Percentile: 29.01 Registered: 2013-06-06 05:52 |
96 projects in result set. Displaying 20 per page. Projects sorted by alphabetical order.
<1> <2> <3> <4> <5>