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24 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. | |
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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. | |
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Activity Percentile: 92.37 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. | |
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Activity Percentile: 88.17 Registered: 2015-01-14 23:10 |
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: 67.56 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.
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Activity Percentile: 57.25 Registered: 2013-10-19 09:43 |
Live Cell NF-κB
- This project provides data and visualization tools to explore single-cell NF-κB dynamics. To view the interactive figure, please see the Downloads section. | |
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Activity Percentile: 44.27 Registered: 2013-03-05 01:40 |
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: 36.64 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>.
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Registered: 2019-02-25 19:48 |
Finite Element Mesh Overclosure Reduction and Slicing (FEMORS)
- The code was developed with the project to make freely available 3D geometries of the lower limbs of the Visible Human Female and Visible Human Male. The FEMORS code was used to remove all overclosures between adjacent geometries. The VH 3D geometries are available at: https://simtk.org/projects/3d-vh-geometry
The code was implemented in MATLAB utilizing the Machine Learning Toolbox and is available free and open-source, but we ask that you cite the following two works:
Andreassen, T. E., Hume, D. R., Hamilton, L. D., Higinbotham, S. E. & Shelburne, K. B. "An Automated Process for 2D and 3D Finite Element Overclosure and Gap Adjustment using Radial Basis Function Networks". 1–13 (2022) https://doi.org/10.48550/arXiv.2209.06948
TE Andreassen, DR Hume, LD Hamilton, K Walker, SE Higinbotham, KB Shelburne, "Three-dimensional lower extremity musculoskeletal geometry of the Visible Human Female and Male,” Sci Data 10, 34 (2023). https://doi.org/10.1038/s41597-022-01905-2.
Adding changes to the code is encouraged and can be added to the repository by contacting the author. The author will check new or revised content for accuracy and completeness and add it to the repository.
Future/ongoing work aims to recreate the code using code that does not need the Machine Learning Toolbox, as well as implementing the code into a Python Toolbox for widespread use. | |
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Registered: 2023-03-27 19:58 |
scexpress: A visual aid to examine expression patterns within single cells
- We have designed SC Express, a bioinformatics tool that produces a three-dimensional shape that is reflective of the expression patterns of a single cell. The software package accepts tab delimited text files containing the relevant gene expression data and provides a graphical user interface that enables facile comparison of any two individual cell types on the same screen. | |
Activity Percentile: 0.00 Registered: 2011-03-05 14:54 |
Application of PCA and LASSO methods to visualize and quantify neurodegeneration
- This is a public data repository for the PLOS ONE (https://journals.plos.org/plosone/) publication entitled "Data-driven, voxel-based analysis of brain PET images: application of PCA and LASSO methods to visualize and quantify patterns of neurodegeneration". The repository contains imaging and clinical data from healthy controls and Parkinson's disease patients that is necessary to replicate the findings of the study. | |
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Registered: 2018-10-18 17:57 |
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 |
Tibial forces in independently ambulatory children with spina bifida
- Experimental motion capture and bone strength data and simulation results from 16 independently ambulatory children with spina bifida and 16 age- and sex-matched children with typical development. Additional motion capture and EMG data and simulation results for 6 independently ambulatory children with spina bifida and 1 child with typical development. Custom scripts were used to calculate joint kinematics, moments, and forces. Post-simulation analyses were conducted to compare these waveforms between the group with spina bifida and the group with typical development.
The manuscript using these data and simulations can be found here:
Lee MR, Hicks JL, Wren TAL, and Delp SL (2022). Independently ambulatory children with spina bifida experience near-typical knee and ankle joint moments and forces during walking. Gait and Posture, 99:1-8. https://doi.org/10.1016/j.gaitpost.2022.10.010 | |
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Registered: 2022-06-01 20:00 |
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. | |
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Activity Percentile: 0.00 Registered: 2015-05-07 23:25 |
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. | |
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Activity Percentile: 0.00 Registered: 2016-03-07 06:05 |
Total Wrist Arthroplasty Biomechanics
- Total Wrist Arthroplasty (TWA) biomechanics was assessed using a biplane videoradiography (BVR) system at the <a href="https://www.xromm.org/">XROMM facility</a>, at Brown University.
This database will include:
1) Videoradiographs from 2 X-ray Sources
2) Tracked Implants in Radiographs
3) Matlab Codes for Processing the Tracked Data
4) Contact Calculation for Implants
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Registered: 2021-02-22 19:30 |
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. | |
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Registered: 2016-08-24 14:21 |
CFD analysis of Arterial flow in Thromboembolism
- To evaluate "52" dimensionless CFD numbers (akin to 'deck' of French-Playing cards):-
# Reynolds number,
# Sherwood number,
# Schimdt number,
# Rayleigh number,
# Weber number,
# Capillary number,
# Bond number,
# Froude number,
# Nusselt number,
# Peclet number (for Mass diffusivity),
# Peclet number (for Heat diffusivity),
# Prandtl number,
# Grashof number, and
# Brinkman number,
# Cavitation number,
# Stanton number,
# [Mass -Transfer] Stanton number,
# Eckert number,
# Knudsen number,
# Graetz number,
# Lewis number,
# Mach number,
# Poiseuille number,
# Rossby number,
# Strouhal number; and
# Taylor number,
# Archimedes number,
# Arrhenius number,
# Bingham number,
# Biot number,
# [Mass-Transfer] Biot number,
# Blake number,
# Bondenstein number,
# Cauchy number,
# Coefficient of Frication (dimensionless number),
# Condensation number,
# Dean number,
# Drag-coefficient (dimensionless number),
# Elasticity number,
# Etovos number,
# Euler number,
# Fourier number,
# [Mass-Transfer] Fourier number,
# Friction factor (dimensionless number),
# Galileo number,
# Colburn "j" (Heat) factor,
# Colburn "j" (Mass) factor,
# Hodgson number,
# Jakob number,
# Ohnesorge number,
# Pipeline parameter (dimensionless number),
# Power number [possibly of 3D-printed Thrombotic human heart].
Ideally, we would very much like to Extend this "Wolfram Mathematica-11 Demonstration" under the simplistic consideration of a Single "Spherical Thromb", merely beyond the Re= Reynolds number - to ALL of the "52" CFD-'deck' numbers immediately post-Plaque Fissure around the instance of "Thrombotic-Thrombolytic Equilibrium" involved in Coronary Arterial flow.
DEMO:
- Mikhail Dimitrov Mikhailov
"Flow around a Sphere at Finite Reynolds Number by Galerkin Method"
http://demonstrations.wolfram.com/FlowAroundASphereAtFiniteReynoldsNumberByGalerkinMethod/
Wolfram Demonstrations Project
Published: January 2, 2013
REFERENCES:
[0] Coronary Plaque Disruption
Erling Falk, Prediman K. Shah, Valentin Fuster
https://doi.org/10.1161/01.CIR.92.3.657
Circulation. 1995;92:657-671
Originally published August 1, 1995.
[1] Lagrangian wall shear stress structures and near-wall transport in high-Schmidt-number aneurysmal flows.
Amirhossein Arzani (a1), Alberto M. Gambaruto (a2), Guoning Chen (a3) and Shawn C. Shadden (a1)
(a1) Mechanical Engineering, University of California Berkeley, Berkeley, CA 94720, USA
(a2) Mechanical Engineering, University of Bristol, University Walk, Bristol BS8 1TR, UK
(a3) Computer Science, University of Houston, Houston, TX 77204, USA
https://doi.org/10.1017/jfm.2016.6
[2] A reduced-dimensional model for near-wall transport in cardiovascular flows.
Kirk B. Hansen* , Shawn C. Shadden*
*Department of Mechanical Engineering, University of California, Berkeley, CA, USA.
PMID: 26298313 PMCID: PMC4764478 DOI: 10.1007/s10237-015-0719-4
^WIKI:
https://en.wikipedia.org/wiki/Dimensionless_numbers_in_fluid_mechanics
$OPEN ACCESS IMAGING DATASETS:
https://grand-challenge.org/
@OUR LAB HOMEPAGE:
http://www.triindia.org/
%RESOURCES:
http://www.cfd.life/
https://cfd.direct/
+CERTIFICATIONS:
https://onlinecourses.nptel.ac.in/noc17_ee01/preview
https://onlinecourses.nptel.ac.in/noc17_ch01/preview
~Inspiration: "CAF" (Cellular Automaton Fluids: Wolfram, 1986).
http://www.stephenwolfram.com/publications/cellular-automata-complexity/pdfs/cellular-automaton-fluids-theory.pdf | |
Registered: 2017-01-23 13:42 |
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. | |
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Activity Percentile: 0.00 Registered: 2014-02-01 22:32 |
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. | |
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Activity Percentile: 0.00 Registered: 2015-06-24 08:40 |
24 projects in result set. Displaying 20 per page. Projects sorted by alphabetical order.
<1> <2>