Project Tree
Now limiting view to projects in the following categories:
All Topics :: Primary Content :: Models [Remove This Filter]
All Topics > Biocomputational Focus > Visualization |
Browse By: |
30 projects in result set. Displaying 20 per page. Projects sorted by alphabetical order.
<1> <2>
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. | |
|
Registered: 2012-01-24 03:21 |
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. | |
|
Activity Percentile: 92.80 Registered: 2014-11-10 15:19 |
Model of the Scapulothoracic Joint
- In this study, we developed a rigid-body model of a scapulothoracic joint to describe the kinematics of the scapula relative to the thorax. This model describes scapula kinematics with four degrees of freedom: 1) elevation and 2) abduction of the scapula on an ellipsoidal thoracic surface, 3) upward rotation of the scapula normal to the thoracic surface, and 4) internal rotation of the scapula to lift the medial border of the scapula off the surface of the thorax. The surface dimensions and joint axes can be customized to match an individual’s anthropometry. We compared the model to “gold standard” bone-pin kinematics collected during three shoulder tasks and found modeled scapula kinematics to be accurate to within 2 mm root-mean-squared error for individual bone-pin markers across all markers and movement tasks. As an additional test, we added random and systematic noise to the bone-pin marker data and found that the model reduced kinematic variability due to noise by 65% compared to Euler angles computed without the model. Our scapulothoracic joint model can be used for inverse and forward dynamics analyses and to compute joint reaction loads. The computational performance of the scapulothoracic joint model is well suited for real-time applications, is freely available as an OpenSim 3.2 plugin, and is customizable and usable with other OpenSim models. | |
|
Activity Percentile: 88.64 Registered: 2015-01-14 23:10 |
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 | |
|
Registered: 2016-10-27 13:07 |
A three-dimensional musculoskeletal model of the dog
- The domestic dog is interesting to investigate because of their wide range of body size, body mass, and physique. In the last several years, the number of clinical and biomechanical studies on dog locomotion has increased. However, the relationship between body structure and joint load during locomotion, as well as between joint load and degenerative diseases of the locomotor system (e.g. dysplasia), are not sufficiently understood. Collecting this data through in vivo measurements/records of joint forces and loads on deep/small muscles is complex, invasive, and sometimes unethical. The use of detailed musculoskeletal models may help fill the knowledge gap. We describe here the methods we used to create a detailed musculoskeletal model with 84 degrees of freedom and 134 muscles. Our model has three key-features: three-dimensionality, scalability, and modularity. We tested the validity of the model by identifying forelimb muscle synergies of a beagle at walk. We used inverse dynamics and static optimization to estimate muscle activations based on experimental data. We identified three muscle synergy groups by using hierarchical clustering. The activation patterns predicted from the model exhibit good agreement with experimental data for most of the forelimb muscles. We expect that our model will speed up the analysis of how body size, physique, agility, and disease influence neuronal control and joint loading in dog locomotion. | |
|
Registered: 2020-11-30 08:11 |
Musculoskeletal Representation of Large Repertoires of Hand Grasping in Primates
- The project aims to investigate and characterize the complex function of the primate hand at the musculoskeletal level. The OpenSim models used in this project enabled extracting joint angles from 27 degrees of freedom as well as length of 50 musculotendon units in the hand and upper extremity. Results demonstrated both a more compact representation and a higher decoding capacity of grasping tasks when movements were expressed in the muscle kinematics domain than when expressed in the joint kinematics domain. The OpenSim models in the project were adapted from the upper extremity model by Holzbaur et al., Ann.Biomed. Eng., 2005. | |
Activity Percentile: 65.91 Registered: 2015-02-10 15:59 |
Analysis of arm swing during human walking
- This project provides a simplified version of the UpperLowerBodySimple model from the ULB-project, which was adjusted with the purpose to decrease the run time of the simulations.
The adjusted model was used to determine arm swing kinematics (with and without muscle excitations) during human walking, with arm movements not exceeding 70 degrees of anteflexion or abduction. However, the adjusted_ULB model can be used for modeling and simulating kinematics and kinetics of all neuromusculoskeletal systems.
For an example of an arm swing simulation without muscle excitation we refer to the video below.
<object width="420" height="315"><param name="movie" value="//www.youtube.com/v/2C_SCeQS4ks?hl=en_US&version=3"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="//www.youtube.com/v/2C_SCeQS4ks?hl=en_US&version=3" type="application/x-shockwave-flash" width="420" height="315" allowscriptaccess="always" allowfullscreen="true"></embed></object> | |
|
Activity Percentile: 48.86 Registered: 2013-10-19 09:43 |
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
<!-- This version of the embed code is no longer supported. Learn more: https://vimeo.com/s/tnm --> <object width="500" height="281"><param name="allowfullscreen" value="true" /><param name="allowscriptaccess" value="always" /><param name="movie" value="https://vimeo.com/moogaloop.swf?clip_id=129107314&force_embed=vimeo.com&fullscreen=1" /><embed src="https://vimeo.com/moogaloop.swf?clip_id=129107314&force_embed=vimeo.com&fullscreen=1" type="application/x-shockwave-flash" allowfullscreen="true" allowscriptaccess="always" width="500" height="281"></embed></object>
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. | |
|
Activity Percentile: 35.23 Registered: 2015-05-28 18:52 |
Wrist Anatomy and Kinematics Data Collection
- <div align="justify">CT images of wrists from 90 healthy volunteers (43 males and 47 females) were acquired in various wrist positions. The outer cortical surfaces of the carpal bones, radius, and ulna in a 3D format, and each bone kinematics were calculated for each wrist position using a methodology described in the README file associated with the database. The database does not include soft tissue or the cartilage information of the wrist. Moreover, there is a MATLAB graphic user interface (GUI) available for you to observe the database. This dataset comes from four different NIH funding between 2001 and 2014.</div>
Please cite the work if you're using this database:
<div align="justify"><a href="https://onlinelibrary.wiley.com/doi/abs/10.1002/jor.24435">Akhbari, B., Moore, D. C., Laidlaw, D. H., Akelman, E., Weiss, A-P. C., Wolfe, S. W., Crisco, J. J., 2019. Predicting Carpal Bone Kinematics using an Expanded Digital Database of Wrist Carpal Bone Anatomy and Kinematics, Journal of Orthopaedic Research. DOI:10.1002/jor.24435</a></div>
If you want the pdf version of the manuscript, please send your request on <a href="http://bit.ly/2YU2tTh">ResearchGate</a>.
| |
|
Registered: 2019-02-25 19:48 |
Neuromuscular Models for the Predictive Treatment of Parkinson's Disease
- NoTremor aims to provide patient specific computational models of the coupled brain and neuromuscular systems that will be subsequently used to improve the quality of analysis, prediction and progression of Parkinson’s disease. In particular, it aspires to establish the neglected link between brain modelling and neuromuscular systems that will result in a holistic representation of the physiology for PD patients. | |
|
Activity Percentile: 10.23 Registered: 2014-06-18 13:56 |
C++ and Python code, distributed computing and OpenMM interfaces for simulations
- please cite: "Interplay of Protein and DNA Structure Revealed in Simulations of the lac Operon" (PLOS One 2013)
for any code related to protein-DNA modeling and
"Free Energy Monte Carlo Simulations on a Distributed Network" (Lecture Notes in Computer Science Journal for PARA 2010)
http://link.springer.com/chapter/10.1007%2F978-3-642-28145-7_1
for parallel client-server code, users of additional code should cite this web site. Code is provided as-is with no warranty and examples are provided to illustrate the usage of these modeling techniques with some sample systems. Code is the intellectual property of Luke Czapla, developer and biophysicist. Examples are provided in C/C++ and Python. | |
|
Activity Percentile: 0.00 Registered: 2014-02-01 22:32 |
NMBL Image to Model Pipeline
- The NMBL Pipeline is a version of NAMIC's (www.na-mic.org) 3D Slicer, adapted to the needs of the Neuromuscular Biomechanics Lab (NMBL) at Stanford University. Slicer is an open-source software tool for performing a diverse array of medical image processing activities within one freely available, easily extensible kit. NMBL Pipeline is intended to coincide with NAMIC's Slicer, and is developed along with 3D Slicer in full collaboration with NAMIC. The differences between NMBL Pipeline and Slicer will be minimal, and probably will include the absence of some of Slicer's modules in NMBL Pipeline, and perhaps some differences in default value settings. This project will continue to be developed for use by NMBL and other members of the general Slicer user community.
I intend to use SimTK.org in exactly those ways that are intended: namely to make my software available to SimTK users and provide users with documentation, while the users are encouraged to provide feedback to me for improvements. | |
|
Activity Percentile: 0.00 Registered: 2005-07-25 22:48 |
Spine Movement
- Generate Euler Angles and joint forces of vertebral bodies | |
Activity Percentile: 0.00 Registered: 2013-08-07 17:25 |
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. | |
|
Registered: 2010-03-08 08:57 |
3D visualization of spinal kinematics collected in 2D using Quantitative Fluoros
- 3D visualization of spinal kinematics collected in 2D using Quantitative Fluorosopy | |
Activity Percentile: 0.00 Registered: 2015-03-16 16:10 |
Acetaminophen Induced Liver Injury
- The AILI project is a type of In-Silico Liver (ISL) project, which consists of a body of Java code used and reused for exploring hypothetical liver mechanisms. For AILI, the liver mechanisms are those that cause cellular damage, specifically necrosis, because of exposure to acetaminophen. Moreover, the model, a mouse analog, is used for virtual experimentation to explore and explain AILI phenomena, analogous to wet-lab experimentation. A recent addition to this project is studying the disconnect between in vitro and in vivo wet-lab experiments by comparing and contrasting virtual Mouse and Culture Analogs. | |
|
Activity Percentile: 0.00 Registered: 2015-05-07 23:25 |
A Cell-centered, Agent-based Framework with flexible Granularity
- Mechanistic explanations of cell-level phenomena rarely study behavior from a cell's perspective. Agent-based models lend themselves to model from an individual's perspective, and we extend that with a framework which utilizes a cell's perspective in an off-lattice environment. We aim to help increase the understanding of biological phenomena through our Delaunay and Voronoi off-lattice agent-based, discrete event framework. We focus on biological cells and expand on existing cell- and agent-centered methods by offering a new perspective in an off-lattice environment. | |
|
Activity Percentile: 0.00 Registered: 2015-09-24 18:24 |
Proteolytic and non-proteolytic regulation of collective cell invasion
- Cancer cells manoeuvre through extracellular matrices (ECMs) using different invasion modes, including single cell and collective cell invasion. These modes rely on MMP-driven ECM proteolysis to make space for cells to move. How cancer-associated alterations in ECM influence the mode of invasion remains unclear. Further, the sensitivity of the two invasion modes to MMP dynamics remains unexplored. In this paper, we address these open questions using a multiscale hybrid computational model combining ECM density-dependent MMP secretion, MMP diffusion, ECM degradation by MMP and active cell motility. Our results demonstrate that in randomly aligned matrices, collective cell invasion is more efficient than single cell invasion. Although increase in MMP secretion rate enhances invasiveness independent of cell–cell adhesion, sustenance of collective invasion in dense matrices requires high MMP secretion rates. However, matrix alignment can sustain both single cell and collective cell invasion even without ECM proteolysis. Similar to our in-silico observations, increase in ECM density and MMP inhibition reduced migration of MCF-7 cells embedded in sandwich gels. Together, our results indicate that apart from cell intrinsic factors (i.e., high cell–cell adhesion and MMP secretion rates), ECM density and organization represent two important extrinsic parameters that govern collective cell invasion and invasion plasticity. | |
|
Activity Percentile: 0.00 Registered: 2016-03-07 06:05 |
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 |
CT-scan based extended dynamic foot model
- This project aims to develop a more realistic dynamic foot model, capturing the full complexity of the foot biomechanics. This model is constructed semi-automatically using CT images. In addition intrinsic foot muscles and ligaments were added. | |
|
Activity Percentile: 0.00 Registered: 2015-06-24 08:40 |
30 projects in result set. Displaying 20 per page. Projects sorted by alphabetical order.
<1> <2>