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20 projects in result set.
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 |
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. | |
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Registered: 2012-01-24 03:21 |
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 |
MIcro Simulation Tool - MIST
- The MIcro Simulation Tool is free software that allows the user to :
* Define state transition models with multiple processes
* Generate populations to match given statistics using Evolutionary Computation
* Run Simulations in High Performance Computing environment - including the cloud
* Analyze and Report the results
Below are some videos that describe MIST capabilities:
This video shows the basic ideas behind MIST
<iframe width="640" height="360" src="https://www.youtube.com/embed/AD896WakR94" frameborder="0" allowfullscreen></iframe>
This video shows some population generation capabilities using Evolutionary Computation:
<iframe width="640" height="360" src="https://www.youtube.com/embed/PPpmUq8ueiY" frameborder="0" allowfullscreen></iframe>
This video will show how MIST runs over the cloud:
<iframe width="640" height="360" src="https://www.youtube.com/embed/wpfw8POx-wI" frameborder="0" allowfullscreen></iframe>
This video will show how MIST modeled COVID19 in <a href="https://devpost.com/software/improved-disease-modeling-tools-for-populations">Pandemic Response Hackathon</a>
<iframe width="640" height="360" src="https://www.youtube.com/embed/0ElKy0Ysz3I" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
The Reference Model is one examples of use of MIST. It can be found in the following link:
https://simtk.org/projects/therefmodel
MIST version 0.92.5.0 is released to the public. It has limited capabilities. For later versions with enhanced capabilities, please contact the developer.
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Registered: 2014-08-21 20:53 |
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 |
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: 37.50 Registered: 2011-12-01 21:24 |
Simbiome - Resource Inventory System
- Simbiome is a trusted, online electronic resource management system that organizes and presents relevant resources for a center. Content in Simbiome is focused on physics-based simulation of biomedical structures and related entities in biology and life sciences. | |
Activity Percentile: 0.00 Registered: 2006-03-22 17:17 |
OpenSim Developer's Jamboree 2008
- This project will be a repository for the OpenSim Jamboree projects. | |
Registered: 2008-08-25 23:46 |
Computational Analysis of Kinase Selectivity using Structural Knowledge
- Here, we present a knowledge-based approach to profile kinase selectivity based on the similarity between drug binding microenvironments. To allow large-scale kinase site similarity profiling, we have created a kinome structure database consisting of 5000 inhibitor-binding pockets from 187 unique human kinase crystal structures. | |
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Registered: 2017-04-18 20:03 |
OpenSim Developers Jamboree - October 28-30, 2009
- The developer's jamboree covers the OpenSim 2.0 API (to be released). This an opportunity to learn about how OpenSim is constructed and how to build on this foundation to meet your research and laboratory goals. On the first day, a brief architectural overview of OpenSim and commonly used SimTK libraries (e.g., Simbody) will be provided. In particular, we will describe OpenSim model components such as bodies, joints, constraints, forces, and controllers and demonstrate how to assemble these components into working models in coding exercises in the form of small main programs. The second and third days will be devoted to building and interacting with models programmatically including the development of custom components and analysis plug-ins. | |
Registered: 2009-10-01 23:25 |
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 |
OpenSim for the Warrior Web
- Online support and resource portal for teams developing Warrior Web Technologies.
Access all of our OpenSim resources at the <br /><a href="http://www.stanford.edu/group/opensim/support/index.html"><b style="color:#900; font-size:16px;">Support Site</b></a>.
Also see the <br /><a href="http://simtk-confluence.stanford.edu:8080/display/OpenSim/Warrior+Web+Wiki"><b style="color:#900; font-size:16px;">Warrior Web Wiki</b></a>.
This project includes the following (see links at left):
1) A Team page, where you can see our team members and get in touch for support and questions.
2) A Downloads page, where you can find models, plug-ins, data, and other code and software for Warrior Web teams. Additional downloads are available on the main OpenSim Simtk project page.
3) A Documents page, where you can find handouts, slides, and links to relevant OpenSim resources and downloads.
4) A Public Forums page, a discussion forum for Warrior Web teams using OpenSim
5) Under the Advanced tab, you will find:
- A repository for uploading and sharing models and code
- A mailing list to receive OpenSim Warrior Web news and events | |
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Registered: 2012-05-31 00:39 |
Platform for Dynamic Simulation and Control of Movement based on OpenSim&MATLAB
- Numerical simulations are playing an increasingly important role in solving complex engineering problems, and have the potential to revolutionize medical decision making and treatment design. Musculoskeletal diseases cost the United States economy an estimated $849 billion a year (equal to 7.7% of the gross domestic product) and place great demands on the healthcare system. This research area could greatly benefit from computational tools that offer greater understanding of neuromuscular biomechanics, and predictive capabilities for optimal surgical and rehabilitation treatment planning.
The MATLAB®/Simulink® package is the world’s leading mathematical computing software for engineers and scientists in industry, government, and education. Although Simulink® extends MATLAB® with a graphical environment for rapid design, control, and simulation of complex dynamic systems, this powerful package has limited resources for simulations of neuromusculoskeletal systems. On the contrary, OpenSim is a popular open-source platform for modeling, simulating, and analyzing neuromusculoskeletal systems, but it is lacks the robust design and control tools of Simulink®.
This project is an interface between OpenSim and MATLAB®/Simulink® that combines relevant strengths (e.g., neuromusculoskeletal dynamics, rapid model-based design, control systems, and numerical simulation) of each individual software package. The foundation of this interface is a MATLAB® S-function (system-function) based on an OpenSim model as a Simulink® block written in C++ and compiled as a MEX-file using the MATLAB® mex utility. | |
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Activity Percentile: 0.00 Registered: 2012-07-26 21:40 |
Extracting conserved domains from cryo-EM maps.
- In our research, we are dealing with the problem of computationally identifying the domains of large macro-molecules (such as Chaperonin) that remain conserved upon conformation change, by comparing low-resolution volumetric electron microscopy (EM) maps. A simple instance of this problem can be shown to be NP-complete. As of now there is no computational tool to solve this problem efficiently or even approximately. We are developing the first method to do so.
Previous attempts have been for some simple instances of this problem, like identifying secondary structures in intermediate-resolution maps (helixhunter: http://ncmi.bcm.tmc.edu/software/AIRS/ssehunter/sse-help.htm) and docking a component of a bio-molecular assembly into latter's EM map. For intermediate resolution maps (<10A), one could use helixhunter to identify secondary structures and then use them to find conserved domains. But about 80% of the maps in EMDB database (http://www.ebi.ac.ac.uk/msd-srv/emsearch/) are of low resolution (>10A), where secondary structures "fuzz-out" beyond the recognition limits of helixhunter or even any manual technique. However, we believe that it should be still possible to extract motifs or domains which are bigger entities than secondary structures and could remain in the "detectable range" may be upto 20A resolution. | |
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Activity Percentile: 0.00 Registered: 2007-12-18 17:02 |
2007BioE215 Eser
- BioE215 Coursework Spring 2007 | |
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Activity Percentile: 0.00 Registered: 2007-04-07 02:13 |
NetworkPainter: Biological pathway animation
- NetworkPainter is a web-based program for drawing and painting signaling network diagrams with high-dimensional cytometry data. Two versions of NetworkPainter are available. The <a href="http://covert.stanford.edu/networkpainter">NetworkPainter stand-alone version</a> is capable of visualizing any uploaded cytometry data. NetworkPainter is also available through the <a href="http://www.cytobank.org/networkpainter.html">Cytobank</a> flow cytometry repository. This version is capable of analyzing flow and mass cytometry data stored in Cytobank. | |
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Registered: 2014-01-10 00:11 |
SimTK Planning Project
- This project collects general SimTK planning and scheduling documents, developer mailing lists, status reports, etc. It is intended primarily for use by SimTK staff and other developers of SimTK core software. | |
Activity Percentile: 0.00 Registered: 2005-07-21 17:02 |
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 |
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 |
BioGears: An open source mathematical model of the human physiology.
- BioGears is an open source, comprehensive, extensible human physiology engine that will drive medical education, research, and training technologies. BioGears enables accurate and consistent physiology simulation across the medical community. The engine can be used as a standalone application or integrated with simulators, sensor interfaces, and models of all fidelities. | |
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Activity Percentile: 0.00 Registered: 2014-10-09 18:12 |