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14 projects in result set.
Extendable OpenSim-Matlab Infrastructure Using Class Oriented C++ Mex Interface
- The objective of this project is to provide an alternative interface between OpenSim and Matlab®, based on an extended C++ mex interface. Despite the fact that there is a user friendly OpenSim interface for Matlab, it lacks the ability to extend new functionalities based on the Java API (e.g. custom controller). Inspired by the relative project “Dynamic Simulation of Movement Based on OpenSim and MATLAB®/Simulink®”, where the user can easily interface OpenSim with Simulink, the proposed framework moves one step further by providing new capabilities to link custom written C++ OpenSim extensions to Matlab and to harvest both the powerful OpenSim C++ API and Matlab functionalities. The implementation is based on Matlab mex interface, which is further extended to support more complex functionalities based on the project mexplus. The latter is a C++ Matlab mex development kit that contains a couple of C++ classes and macros to make mex development easy in Matlab.
An example project is provided in the download section with instructions on how-to use. | |
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Activity Percentile: 22.73 Registered: 2015-09-28 14:09 |
Modeling the Intervertebral Discs as a Stiffness Matrix: a SpineBushing element
- This project features a "SpineBushing" element that can be used to model the intervertebral disc as a 6x6 stiffness matrix. This permits the study of the disc's force-motion relationship for the case where the coordinates are coupled to each other.
The guiding equation is,
F_2 = -K * Delta_Q
where F_2 is the generalized 6x1 force vector acting on the upper vertebra, K is a stiffness matrix, and Delta_Q is the generalized 6x1 displacement vector specifying the change in position from neutral between the points of attachment of the stiffness element.
By Newton's 3rd law,
F_1 = - F_2.
The SpineBushing features two *key* differences from the existing bushing element:
(1) we incorporated a full 6x6 stiffness matrix instead of the current three translational and three rotational stiffnesses.
(2) the **change** in relative motion is used and not the relative motion itself. In 1-D, you can think of this as having a spring with a resting length equal to the distance between the specified attachment points on the two bodies in the neutral posture. (The typical bushing element, on the other hand would be analogous to a spring with zero resting length.)
Further details are provided in the accompanying documents. | |
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Activity Percentile: 3.03 Registered: 2011-10-12 05:41 |
SimTKcommon: essential objects for the SimTK Core toolkit
- SimTKcommon provides a gathering place for essential software that enables SimTK Core programming. This includes the basic objects of the SimTK architecture including the Simmatrix toolset, a Matlab-like ability to manipulate vectors and matrices from within a C++ program. Please see the Documents page for more information about Simmatrix. | |
Activity Percentile: 0.00 Registered: 2006-03-25 02:29 |
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 |
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 |
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 |
APPLICATION OF OPENSIM TO CLINICAL SIMULATIONS WITH TENSEGRITY OVERLAYS
- This project is an attempt to apply formal biomechanical research systems methods to the direct manual manipulation clinical methods used by Osteopathic physicians and physical therapists. We have been looking at designing interactive visualization models using IDL, 3D_SLICER, PARAVIEW and OSIRIX.
However, we are now looking into the efficacy of applying OpenSim to this effort.
The central problem: OMM is taught in detail to all first year DO students and requires the development of a profound store of anatomical knowledge involving complete academic didactic traing, dissection and physiology along with the other basic medical sciences.
The mainline textbooks of osteopathic medicine describe distinct diagnostic and treatment protocols for all regions of the body using clinical manipulation for abnormalities seen to be treatable by these methods. In doing so, the introductory information describes Fuller\'s et. al. biomechanical systems known as synergy and tensegrity to describing the general characteristics of the integrate human myofascial framework, but do not appear to apply it in training situations.
Our research team feels that developing 3D dynamic biomechanical anatomical visualizations that will react to external perturbation by instructor and student and have the cause-effect results demonstrated on top of the anatomical structures via vector diagrams would be a revolutionary educational breakthrough. We intend to proceed from simple didactic demonstration visualizations for a series of case studies towards a virtual simulation linking clinicial/student hand local pressure and movement to the internal anatomy of a given patient by first using the Visible Human dataset (male and female) as the standard model, having CT/MR sets of the local region generated for a given patient, registering the image sets and using the network of landmark points transferred to the patient\'s model from the gold standard VHM/F model to generate the superimposed tensegrity model.
Our task will be to either apply existing functions of OpenSim capable of achieving this, borrow functions from another SimTk project or develope our own under the SimTk framework.
Upon generating working and tested software, we will be testing it on experimental and control groups of students and instructors here at Des Moines University.
All results will be published and all resource sources from SimTk will be acknowledged as well as posting the software designs on the SimTk site. | |
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Activity Percentile: 0.00 Registered: 2007-11-18 04:59 |
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 |
2007BioE215 Eser
- BioE215 Coursework Spring 2007 | |
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Activity Percentile: 0.00 Registered: 2007-04-07 02:13 |
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 |
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 |
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 |
VTK Mac with Java Support
- Using Java with VTK on Mac OS X 10.3 and higher is basically broken. This project aims to correct these problems and provide a version of VTK on the Mac where Java (and C++) can be used. This code is based on the latest VTK 4.2 stable release. The changes made to VTK here have been submitted to the VTK organization, but these have not yet been integrated into their code repository. Also, the changes will probably never make it to their 4.2 code base, so we will provide this code until the next stable release of VTK comes out with proper Java Mac support.
Java VTK support on the Mac uses Cocoa. Tcl and Python wrappers currently do not work with Cocoa, so they are not supported with this modified version of VTK. Java and C++ are supported. | |
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Activity Percentile: 0.00 Registered: 2005-07-13 05:20 |
Wearable Sensor Glove to prove positive effect in stroke patients for rehab
- This project is going to allow physical therapists to better understand the positive affects of their physical therapy by witnessing positive movements from patients. A negative effect of a stroke is not just the initial neuro-muscular lose but also the over-compensation of the less impaired limb to take over space needed for the severely impaired limb to re-establish its neuro-muscular pathway. Although a full recovery can not be expected the severely impaired limb still has hope to fill the role of the less dominant hand. Not as focused on as the dominant hand, the role of the less dominant hand is unarguably important and necessary that is why we have two hands after all these years of selection. This project is a work compilation of 4 undergraduate students headed by the computer science student, Luke Greenleaf, under the advisement of Dr. Foulds and the Biomedical Engineering Department at NJIT. This summer we will be creating a prototype that will allow us to begin proving that we can collect continuous data and recreate the meaning of that data in order to understand the movement initiated for both hands and understand a patients use of their severely impaired limb. | |
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Activity Percentile: 0.00 Registered: 2012-06-05 22:01 |