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27 projects in result set. Displaying 20 per page. Projects sorted by alphabetical order.
<1> <2>
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 |
MITK-GEM: Software pipeline to GEnerate Models from images
- An attempt to provide a software pipeline to interactively create finite element models from medical images. Primarily intended to model bone fracture risk.
An application with graphical user interface and image processing plugins is provided. The application is build using the MITK Workbench software framework. The following plugins are available: fast image segmentation using graph cut, volume meshing using tetgen and density to modulus conversion for bone material property assignment.
Documentation and tutorials are available on our <a href="http://araex.github.io/mitk-gem-site/">tutorial website</a>.
Along with pre-compiled executables available here, the source code is available on our <a href="https://github.com/araex/mitk-gem">github page</a>.
The graph cut segmentation plugin and the material mapping plugin were developed as part of research studies.
If you use the software or source code in your research, please cite the corresponding journal <a href="https://simtk.org/project/xml/publications.xml/?group_id=1063">publications</a>. | |
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Registered: 2015-12-23 02:46 |
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 |
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 |
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 |
Tim's OpenSim Utilities
- This project site is concerned with extending the functionality of OpenSim through the use of scripting tools and plugins.
Click on the downloads link to browse the set of freely available OpenSim tools for download.
*******************************************************
Previously delivered interactive webinars demonstrating
the use of the Pseudo-Inverse Induced Acceleration
plugin for OpenSim (IndAccPI).
http://www.stanford.edu/group/opensim/support/webinars.html
******************************************************* | |
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Registered: 2009-09-01 00:52 |
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 |
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 |
Neuromusculoskeletal Modeling (NMSM) Pipeline
- <div style="display:inline-block"><a href="https://nmsm.rice.edu"><img src="https://nmsm.rice.edu/img/nmsm-pipeline-social-card.jpg" style="float:left;max-width:calc(100% - 40px);"></a></div>
Full project information is available at: https://nmsm.rice.edu. Please direct any inquiries about the NMSM Pipeline to us by posting your questions on this SimTK project forum or emailing nmsm@rice.edu.
Neuromusculoskeletal Modeling (NMSM) Pipeline is a set of tools for personalizing models and designing treatments for movement impairments and other pathologies.
The NMSM Pipeline consists of two toolsets:
Model Personalization - Personalize joint, muscle-tendon, neural control, and ground contact model properties.
Treatment Optimization - Design treatments using personalized models and an optimal control methodology.
At this time, Treatment Optimization requires the use of <a href="https://www.gpops2.com/">GPOPS-II optimal control solver</a>.
The NMSM Pipeline is written in MATLAB to lower the barrier for entry and to facilitate accessibility to the core codebase. We encourage users to modify the code to meet their needs.
The core codebase and examples are available to download for use in research. At this time, we ask that you wait to publish any work that uses the NMSM Pipeline until the journal article reference for the software is available. Please get in touch with us if you have any questions.
If you need help or want to start a discussion, please use the SimTK forum for this project.
Note: This project is a living entity. Updates will be made available as the Pipeline, examples, and tutorials are developed further and improved. | |
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Registered: 2022-07-07 14:55 |
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 |
OpenMM September 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:
* Set up and run an MD simulation on a GPU using both PDB and AMBER files
* Create a custom force to apply to their simulations
* Customize simulations through Python scripting
They will also have time to work with the OpenMM development team on their own research project. | |
Activity Percentile: 0.00 Registered: 2012-08-23 17:52 |
OpenSim Developer Jamboree - July 12-14, 2010
- A Developer Jamboree covering advanced topics in OpenSim. This is an opportunity for software developers to learn more about how OpenSim works "under the hood" and get supervised, hands-on assistance with problems you bring to the workshop. A conceptual overview of the OpenSim API (Application Programming Interface) will be provided, followed by sessions where participants work on problems they bring to the workshop. Advanced OpenSim users may also attend and work on their research problems. For example, participants generate simulations from motion capture data collected in their lab, add arms to their gait model, or write a new muscle model or controller. Participants will have the opportunity to work in small breakout groups with OpenSim experts on these problems. | |
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Activity Percentile: 0.00 Registered: 2010-06-29 00:04 |
Molecular Dynamics Workshop Series, March 1-2, 2010
- Simbios is excited to announce its Molecular Dynamics Workshop Series. The series consists of two workshops. Materials from the workshops will be provided via this project.
<b>Running and Developing Molecular Dynamics (MD) Algorithms on GPUs with OpenMM</b>: The workshop is intended for those interested in running MD simulations on graphics processing units (GPUs) and/or developing new MD algorithms that can automatically be implemented and accelerated on GPUs. Some programming background is required.
During the workshop, participants will learn to:
- 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[1] and explicit solvent simulations[2] on GPUs.
- Use OpenMM's custom force options to design and test new MD algorithms
- Use PyOpenMM, the Python version of OpenMM that is ideal for rapid code development but still achieves high performance
<b>Introduction to Molecular Dynamics (MD) and Trajectory Analysis with Markov State Models</b>: This workshop is intended for researchers (including novices to MD) interested in using MD and/or analyzing MD results in their research. During the workshop, you will:
- Learn the theory behind MD
- Use the OpenMM Zephyr application, which makes it easy to run and visualize MD simulations. OpenMM Zephyr incorporates the OpenMM library, enabling acceleration of the simulations on GPUs.
- Learn different techniques for analyzing MD simulations, including Markov State Models and why they are suitable for this
- Gain hands-on experience with the MSMBuilder software[3] to automatically construct Markov State Models for trajectory analysis. | |
Activity Percentile: 0.00 Registered: 2010-02-19 23:07 |
Muscle function of overground running across a range of speeds
- This project is a repository of overground running data (3.5m/s 5.2m/s, 7.0m/s and 9.0m/s) along with a working musculoskeletal model to perform simulations and derive the function of individual muscles. | |
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Registered: 2011-08-07 14:01 |
Fiber Tractography for Finite-Element Modeling of Transversely Isotropic Tissues
- This project demonstrates the process for fiber tractography of complex biological tissues with transverse isotropy, such as tendon and muscle. This is important for finite element studies of these tissues, as the fiber direction must be specified in the constitutive model. This project contains code, models, and data that can be used to reproduce the results of our publication on this technique. The supplied instructional videos will enable researchers to easily and efficiently apply this method to a variety of other tissues. The software used in the fiber tractography process and demonstrated in this project is Matlab, Autodesk Inventor (free for educators), and Autodesk Simulation CFD (free for educators). Full demonstrations and process instructions can be found in the 7 videos posted at https://vimeo.com/album/3414604:
Contents:
Chapter 1: Introduction (2:35)
This video introduces the CFD fiber tractography software pipeline
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Chapter 2: Supplementary materials code, models and data (20:21)
This video shows the shared models, code, and data posted online at simtk.org/m3lab_cfd4fea.
Chapter 3: Finite element simulations (5:38)
This video shows finite element simulations using the fiber mapping process.
Chapter 4: Iliacus example walkthrough (21:38)
This video shows the step-by-step process for fiber mapping the iliacus muscle (a hip flexor).
Chapter 5: Bflh example walkthrough (12:09)
This video shows the step-by-step process for fiber mapping the biceps femoris longhead muscle (a hamstring).
Chapter 6: Autodesk Inventor segmentation (9:09)
This video shows how to do segmentation of medical images in Autodesk Inventor in order to simplify the solid model for the CFD and FEA software.
Chapter 7: Curved inlet surfaces (6:28)
This video shows how to create curved inlet surfaces for use in Autodesk Simulation CFD. | |
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Activity Percentile: 0.00 Registered: 2015-05-28 18:52 |
27 projects in result set. Displaying 20 per page. Projects sorted by alphabetical order.
<1> <2>