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31 projects in result set. Displaying 20 per page. Projects sorted by alphabetical order.
<1> <2>
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 |
Simbios Dissemination
- Website for Simbios dissemination planning and distribution of materials. Videos and workshop material (slides, videos, handouts)are available through the Downloads link. The <a href="http://wiki.simtk.org/dissemination">wiki</a> describes the strategy and includes metrics being tracked for Simbios dissemination. | |
Registered: 2006-06-21 01:23 |
OpenSim Advanced Users Workshop, August 12-14, 2009
- This workshop covers advanced topics in OpenSim, an easy-to-use, extensible software for modeling, simulating, controlling, and analyzing the neuromusculoskeletal system. The workshop is an opportunity to learn more about how OpenSim works "under the hood" and get supervised, hands-on assistance with problems participants bring to the workshop. On the first day, a conceptual overview of OpenSim will be provided. The second and third days will be devoted to working on problems participants bring to the workshop. Participants have the opportunity to work in small breakout groups with OpenSim experts on their research problems. | |
Registered: 2009-08-07 22:39 |
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: 79.39 Registered: 2010-11-04 02:25 |
Computational Methods in Cardiovascular
Bioengineering Course (BioE484)
- This research PhD-level class was taught during Spring 2007 by Alberto Figueroa, from the Taylor lab. For their final project, students were organized into five teams and each team worked on a different cardiovascular research project.
The basic research tool the students used is the software SimVascular, which is a Cardiovascular Modeling and Simulation
application currently in the process of being open-sourced through http://Simbios.stanford.edu. This project presents a summary of the final projects. All presentations were taped and made available from the download section on the left menu. | |
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Registered: 2007-06-15 17:20 |
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 |
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 |
OpenMM Workshop February 2009
- Simbios is holding a two-day workshop on February 12 and 13 to introduce programmers and scientists to two important releases that will be made available mid January on Simtk.org by the Protein Folding group.
1) OpenMM, a high-performance, extensible library written in C++ for executing molecular dynamics (MD) simulations on high performance computer architectures, such as GPUs. Significant performance speed ups of over 100x were achived in some cases using OpenMM.*
Reference code for OpenMM was released in September 08. The January release includes a version of Gromacs that uses OpenMM and hence benefits from the speed-up afforded by executing portions of the code on recent versions of NVIDIA or ATI GPUs. The current release supports implicit solvent models, with explicit solvent models to be incorporated into the next release.
2) OpenMM Zephyr, an application that uses Gromacs with OpenMM, and is designed to allow MD novices run Molecular Dynamics simulations and visualize them with VMD.
At the workshop, you will hear from:
-Experts in molecular dynamics and
-Representatives from ATI and NVIDIA about their GPU architectures and future plans | |
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Registered: 2009-01-22 01:47 |
ACL Reconstruction Decision Support Through Personalized Simulation of the Lachm
- The objective of the proposed approach is to develop a clinical decision support system (DSS) that will help clinicians optimally plan the ACL reconstruction procedure in a patient specific manner.
Methods: A full body model is developed in this study with 23 degrees of freedom and 93 muscles. The knee ligaments are modeled as non-linear spring-damper systems and a tibiofemoral contact model was utilized. The parameters of the ligaments were calibrated based on an optimization criterion. Forward dynamics were utilized during simulation for predicting the model’s response to a given set of external forces, posture configuration and physiological parameters.
Results: The proposed model is quantified using MRI scans and measurements of the well-known Lachman test, on several patients with a torn ACL. The clinical potential of the proposed framework is demonstrated in the context of flexion-extension, gait and jump actions. The clinician is able to modify and fine tune several parameters such as number of bundles, insertion position on the tibia or femur and the resting length that correspond to the choices of the surgical procedure and study their effect on the biomechanical behavior of the knee.
Conclusion: Computational knee models can be used to predict the effect of surgical decisions and to give insight on how different parameters can affect the stability of the knee. Special focus has to be given in proper calibration and experimental validation.
<iframe width="560" height="315" src="https://www.youtube.com/embed/zgcq0c5_w3c" frameborder="0" allow="autoplay; encrypted-media" allowfullscreen></iframe> | |
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Activity Percentile: 46.95 Registered: 2015-08-31 08:55 |
Data for Exacycle GPCR paper on cloud-based simulations
- This project provides links to the GPCR trajectory data used for the analysis in the paper on cloud-based simulations on Google Exacycle. The data is available for download and can be used freely by anyone. | |
Activity Percentile: 37.40 Registered: 2013-12-13 19:27 |
Easy-to-use interactive musculoskeletal simulations and curriculum (OpenSim).
- This project brings "life" to the physical sciences. Its curriculum and simulations are correlated with National and State Standards for Physics and the Physical Sciences and helps high-school, college, and professionals combine biology with physics. | |
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Activity Percentile: 37.02 Registered: 2010-08-28 02:06 |
OpenMM March 2012 Workshop: Rapid MD Prototyping & Simulations on GPUs
- OpenMM is open-source software that enables molecular dynamics (MD) simulations to be accelerated on high performance computer architectures. It has demonstrated speed ups for both implicit solvent and explicit solvent simulations on graphics processing units (GPUs) (see benchmarks at http://wiki.simtk.org/openmm/Benchmarks).
With the new application layer in its recent 4.0 release, OpenMM allows non-programmers to easily and quickly run MD simulations and develop custom algorithms on GPUs, while continuing to enable programmers to integrate OpenMM into their own programs.
This workshop is designed for those interested in accelerating MD simulations on GPUs and/or developing new MD algorithms that can automatically be implemented and accelerated on GPUs. No programming background is required, though programming topics will also be covered for those who are interested in them.
During the workshop, participants will gain hands-on experience using OpenMM's new application layer and application programming interface (API). They will learn to:
<ul>
<li>Set up and run an MD simulation on a GPU using both PDB and AMBER files </li>
<li>Create a custom force to apply to their simulations </li>
<li>Customize simulations through Python scripting </li>
</ul>
They will also have time to work with the OpenMM development team on their own research project. | |
Registered: 2012-02-29 19:29 |
Data and Media Management for Biomechanics (DMMB)
- (written for biomechanics researchers interested in managing and distributing big data/ media)
This project will serve as a tool to help researchers categorize, organize, prioritize, and distribute big data collected specifically in biomechanical applications. Additionally, this project will serve as a project map a guide for how to streamline and distribute biomechanics-related media (photographs, videos, interactive modules, etc.). | |
Registered: 2014-02-04 18:53 |
Enhanced Model Assembly for Intervertebral Reaction Force Prediction
- This project provides a model, supplementary files, and corresponding documentation for the prediction of intervertebral joint reaction forces. | |
Activity Percentile: 32.44 Registered: 2015-01-28 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 |
Molecular Dynamics Workshop Series, May 23-24, 2011
- Simbios is excited to announce its Molecular Dynamics Workshop Series:
<b>Developing Molecular Dynamics (MD) on GPUs with OpenMM</b>
This first day is intended for those interested in developing MD simulations on graphics processing units (GPUs) and/or developing new MD algorithms that can automatically be implemented and accelerated on GPUs. A programming background is required. During the workshop, participants will:
<ul>
<li>Set up simulations using OpenMM, a freely downloadable library that enables MD simulations to run on high performance computer architectures. It has demonstrated significant speed ups for both implicit solvent and explicit solvent simulations on GPUs.</li>
<li>Learn about new features in OpenMM 3.0, such as its Python API, its serialization capabilities, and the integration of the AMOEBA polarizable force field.</li>
</ul>
<b>Introduction to Trajectory Analysis with Markov State Models</b>
This workshop is intended for researchers analyzing MD results in their research. During the workshop, participants will:
<ul>
<li>Learn different techniques for analyzing MD simulations, including Markov State Models and why they are suitable for this </li>
<li>Gain hands-on experience with the MSMBuilder software to automatically construct Markov State Models for trajectory analysis</li>
</ul> | |
Activity Percentile: 8.78 Registered: 2011-05-20 06:38 |
Cross-NCBC Dissemination
- The National Centers for Biomedical Computing (NCBCs) are intended to form the core infrastructure for biomedical computing in the nation. These are cooperative agreement awards funded under the NIH Roadmap for Bioinformatics and Computational Biology. There are seven funded Centers that cover systems biology, image processing, biophysical modeling, biomedical ontologies, information integration, and tools for gene-phenotype and disease analysis. This project is intended to coordinate joint dissemination activities across the seven centers. See the wiki for specific activities. | |
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Registered: 2009-02-24 01:07 |
Ayman s Private Project
- A private poject to maintain OpenSim related materials, presentations, bookKeeping. In case of a personal machine crash and to sync. up between my different computers/environments. | |
Activity Percentile: 0.00 Registered: 2007-10-19 19:22 |
Full Body Gait with Knee Contact Model
- This project aims to add a knee contact model to OpenSim in order to study knee forces in detail. | |
Activity Percentile: 0.00 Registered: 2008-05-06 05:27 |
Obese Locomotion Biomechanics
- We are in the process of designing and creating a number of obese specific musculoskeletal model templates that will account for changes in muscle properties and the adiposity distribution of obese body types. The refined model will not only provide more accurate scientific data on obese locomotion, but will also be used in combination with forward dynamic analyses as a predictive tool to analyze locomotion. These templates will also allow researchers to examine potential benefits of proper exercise prescription and targeted muscle strengthening, and to validate possible benefits of functional bracing and movement aiding exoskeletons.
Find more information here: http://pal.colostate.edu/ | |
Activity Percentile: 0.00 Registered: 2012-07-08 08:46 |
31 projects in result set. Displaying 20 per page. Projects sorted by alphabetical order.
<1> <2>