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30 projects in result set. Displaying 20 per page. Projects sorted by alphabetical order.
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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 |
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 |
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 |
Contact Modeling with OpenSim: a User’s Approach
- This project presents step-by-step tutorials on how to integrate contact elements within a OpenSim model. Contact modeling is performed by editing two *.osim files. The first tutorial covers the classic model of a bouncing sphere on an even plane (two cases will be considered: pure elastic contact; and dissipative contact). The second tutorial considers multiple contact interactions between a sphere, an ellipsoid and a plane. Contact forces are described with the Hunt & Crossley and the Elastic Foundation models. No friction forces are applied. The main motivation of this project is to provide easy to follow tutorials for contact modeling in OpenSim, therefore, complementing the current documentation on this topic. Musculoskeletal modelers or computational researchers that wish to incorporate surface contact elements within a multibody model will find this project of their interest.
<object width="420" height="315"><param name="movie" value="//www.youtube.com/v/BeOzPwoz1nk?version=3&hl=pt_PT"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="//www.youtube.com/v/BeOzPwoz1nk?version=3&hl=pt_PT" type="application/x-shockwave-flash" width="420" height="315" allowscriptaccess="always" allowfullscreen="true"></embed></object> | |
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Activity Percentile: 54.96 Registered: 2012-03-09 19:31 |
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 |
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 |
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 |
LoopTK: Protein Loop Kinematic Toolkit
- Analyzing the motion of flexible protein loops is becoming increasingly important in understanding the various roles that proteins play in human body. LoopTK is a C++ based object-oriented toolkit which models the kinematics of a protein chain and provides methods to explore its motion space. In LoopTK, a protein chain is modeled as a robot manipulator with bonds acting as arms and the dihedral degree of freedoms acting as joints.
LoopTK is designed specifically to model the kinematics of protein loops, but it can be used to analyze the motion of any part of the protein chain. LoopTK provides methods for sampling the conformation space of protein loops as well as the self motion space of a loop. Example applications for LoopTK include x-ray crystallography, homology modeling, and drug design.
LoopTK was developed in close collaboration with the Joint Center for Structural Genomics (JCSG) at the Stanford Linear Accelerator Center. Now a part of the JCSG's protein structure determination process, loopTK models missing protein fragments into experimental data (http://smb.slac.stanford.edu/XpleoServer/Xpleo.jsp).
This material is based upon work supported by the National Science Foundation under Grant No. 0443939. Any opinions, findings, and conclusions or recommendations expressed in the above material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. | |
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Activity Percentile: 0.00 Registered: 2007-05-13 22:32 |
Evaluation of In Vivo Knee Load Predictions Using Instrumented Implants
- This project seeks to advance the field of musculoskeletal modeling by critically evaluating muscle and contact force estimates at the knee during gait using data collected from patients with force-measuring knee implants. | |
Activity Percentile: 0.00 Registered: 2010-11-18 17:17 |
2007BioE215 Meyer
- This project is a collection of modules created for the Stanford University class Bioengineering 215. | |
Activity Percentile: 0.00 Registered: 2007-04-07 19:19 |
The Osteoporotic Virtual Physiological Human
- Nearly four million osteoporotic bone fractures cost the European health system more than 30 billion Euro per year. This figure could double by 2050. After the first fracture, the chances of having another one increase by 86%. We need to prevent osteoporotic fractures. The first step is an accurate prediction of the patient-specific risk of fracture that considers not only the
skeletal determinants but also the neuromuscular condition. The aim of VPHOP is to develop a multiscale modelling technology based on conventional diagnostic imaging methods that makes it possible, in a clinical setting, to predict for each patient the strength of his/her bones, how this strength is likely to change over time, and the probability that the he/she will overload his/her bones during daily life. With these three predictions, the evaluation of the
absolute risk of bone fracture will be much more accurate than any prediction based on
external and indirect determinants, as it is current clinical practice. These predictions will be used to: i) improve the diagnostic accuracy of the current clinical standards; ii) to provide the basis for an evidence-based prognosis with respect to the natural evolution of the disease, to pharmacological treatments, and/or to preventive interventional treatments aimed to selectively strengthen particularly weak regions of the skeleton. For patients at high risk of fracture, and for which the pharmacological treatment appears insufficient, the VPHOP system will also assist the interventional radiologist in planning the augmentation procedure.
The various modelling technologies developed during the project will be validated not only in vitro, on animal models, or against retrospective clinical outcomes, but will also be assessed in term of clinical impact and safety on small cohorts of patients enrolled at four different clinical institutions, providing the factual basis for effective clinical and industrial exploitations. | |
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Registered: 2010-03-08 08:57 |
2007BioE215 Eser
- BioE215 Coursework Spring 2007 | |
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Activity Percentile: 0.00 Registered: 2007-04-07 02:13 |
Shoulder mechanics: Undergrad research in muscle mechanics of the shoulder
- This project is a combination of experimental and computational approaches to understanding shoulder mechanics. We are investigating the role of muscle architecture in joint mechanics. | |
Registered: 2010-03-26 19:28 |
Sam's Simulations
- This project is intended to serve as a repository for software developed for physics-based simulation of human motion, as part of the work in the Neuromuscular Biomechanics Lab. | |
Activity Percentile: 0.00 Registered: 2007-09-28 18:32 |
2007BioE15 Bruns
- Project for class. Hey! Guess what! It is required to put a longer \"detailed\" description into this area by the set up form! The retarded error message just says \"longer\", so who knows how long I have to keep spitting up this junk to keep the darn thing happy? | |
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Activity Percentile: 0.00 Registered: 2007-04-11 01:29 |
Protein Engineering through Computational Design
- In recent years, computational methods have matured to a point at which it has become possible to equip protein structures with new functions. Computational ‘de-novo’ design has taken the approach of engineering entire active sites around a QM transition state and grafting these into stable protein scaffolds. While this lead to the production of new biocatalysts, we are far from achieving the level of specificity, turnover rates, and chemical sophistication that is evident from nature’s enzymes. We are working on significantly improving this by accounting for dynamic motions.
Over the past year, the focus of my research has been on methodological developments and on their applications towards biochemically relevant systems. More specifically, I have been working a) on a protocol for the automated and reliable setup of molecular dynamics (MD) simulations, b) on rapid ways of analyzing the vast amount of data that is generated in the course of such simulations, c) on applying both (a) and (b) towards the analysis and the redesign of a prenyltransferase (in collaboration with Prof. Chaitan Khosla at Stanford), and d) on the high-throughput screening and evaluation of computationally designed enzymes, binders, and structural proteins (in collaboration with Prof. David Baker at UW). | |
Activity Percentile: 0.00 Registered: 2013-03-04 19:00 |
Matt DeMers' project
- This is just a place for me to track, manage, and backup data for my ongoing projects. | |
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Activity Percentile: 0.00 Registered: 2009-07-31 22:54 |
Creating a Tensegrity Robot
- This project is to study the applicability of utilizing this program to create a tensegrity robot and a virtual environment for the tensegrity robot. | |
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Activity Percentile: 0.00 Registered: 2010-08-11 01:17 |
30 projects in result set. Displaying 20 per page. Projects sorted by alphabetical order.
<1> <2>