Project Tree
Now limiting view to projects in the following categories:
All Topics :: Biocomputational Focus :: Experimental Analysis [Remove This Filter]
All Topics > Primary Content > Developer Tools |
Browse By: |
8 projects in result set.
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. | |
|
Registered: 2022-07-07 14:55 |
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
******************************************************* | |
|
Registered: 2009-09-01 00:52 |
Modeling kinematic and dynamic redundancy
- The coordination of the human musculoskeletal system is deeply influenced by its redundant structure, in both kinematic and dynamic terms. Noticing a lack of a relevant, thorough treatment in the literature, we formally address the issue in order to understand and quantify factors affecting the motor coordination. We employed well-established techniques from linear algebra and projection operators to extend the underlying kinematic and dynamic relations by modeling the redundancy effects in null space. We distinguish three types of operational spaces, namely task, joint and muscle space, which are directly associated with the physiological factors of the system. A method for consistently quantifying the redundancy on multiple levels in the entire space of feasible solutions is also presented. We evaluate the proposed muscle space projection on segmental level reflexes and the computation of the feasible muscle forces for arbitrary movements. The former proves to be a convenient representation for interfacing with segmental level models or implementing controllers for tendon driven robots, while the latter enables the identification of force variability and correlations between muscle groups, attributed to the system’s redundancy. Furthermore, the usefulness of the proposed framework is demonstrated in the context of estimating the bounds of the joint reaction loads, where we show that misinterpretation of the results is possible if the null space forces are ignored. This work presents a theoretical analysis of the redundancy problem, facilitating application in a broad range of fields related to motor coordination, as it provides the groundwork for null space characterization. The proposed framework rigorously accounts for the effects of kinematic and dynamic redundancy, incorporating it directly into the underlying equations using the notion of null space projection, leading to a complete description of the system.
https://github.com/mitkof6/musculoskeletal-redundancy
https://github.com/mitkof6/feasible_muscle_force_analysis | |
|
Registered: 2018-05-17 10:19 |
Application for the simulation of the prosthetic gait
- This application has a dataset belonging to macha prosthetic patterns , in which the angle of the socket and prosthetic foot is changed.
It focuses on patients with transtibial amputation and uses opensim in MATLAB libraries to link and generate a model for opensim , based on data captured from a measuring TECHNAID brand. | |
|
Registered: 2016-08-24 14:21 |
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. | |
|
Registered: 2017-04-18 20:03 |
C3D Extraction Toolbox
- This toolbox is of benefit to musculoskeletal modellers in the field of biomechanics / bioengineering to assist extracting kinematic, kinetic, and EMG information directly from a C3D file for Matlab manipulation or for input to OpenSim biosimulation software. The scripts can be configured for any laboratory configuration. This software is free without warranty but I do ask for acknowledgement if used in publications. Free download is available with documentation and two examples included.
Main features of this script include:
Custom markerset extraction
Foot-plate detection algorithm
Kinetic extraction (ground reaction forces / moments)
Center of pressure calculation
Transformation to customizable model coordinate system
Custom EMG acquisition & processing tools
XML file production (for OpenSim)
Lab customizable
The scripts require Motion Labs C3D Server software (freeware) and XML Toolbox (Marc Molinari)(freeware) which is included with the script download. Also requires Matlab 2008 or greater (32 bit only) with the Signal Processing Toolbox.
Additional C3D software may be useful and these are available at http://www.c3d.org/c3dapps.html. Review the included manual for version updates and additions. Please inform me of bugs / suggestions to improve as this will be an ongoing project. | |
|
Registered: 2008-10-03 01:17 |
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. | |
|
Registered: 2014-01-10 00:11 |
3D Numerical Investigation of Endothelial Shear Stress in Arteries
- 3D numerical investigation of endothelial shear stress in coronary arteries. | |
|
Activity Percentile: 0.00 Registered: 2015-11-30 13:34 |