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19 projects in result set.
SimVascular: Cardiovascular Modeling and Simulation
- SimVascular is an open source software suite for cardiovascular simulation, providing a complete pipeline from medical image data to 3D model construction, meshing, and blood flow simulation. SimVacular represents the state of the art in cardiovascular simulation, including advanced tools for physiologic boundary conditions, fluid structure interaction, and an accurate and efficient finite element Navier-Stokes solver. SimVascular integrates custom code with best-in-class open source packages to support clinical and basic science research.
DOCUMENTATION and CLINICAL EXAMPLES are available on the main project website at:
http://www.simvascular.org
Demo projects and examples for SimVascular can be downloaded at:
https://simtk.org/projects/sv_tests
Interested users should join the mailing list for the SimVascular project on simtk.org to be notified about upcoming releases and workshop announcements.
<b>If you use SimVascular for your work, please cite the following publication:</b>
Updegrove, A., Wilson, N., Merkow, J., Lan, H., Marsden, A. L. and Shadden, S. C., <a href="http://link.springer.com/article/10.1007/s10439-016-1762-8">SimVascular - An open source pipeline for cardiovascular simulation</a>, <em>Annals of Biomedical Engineering</em> (2016). DOI:10.1007/s10439-016-1762-8
The SimVascular project is funded by the NSF SSI program under Program Officers Rajiv Ramnath (ACI) and Sumanta Acharya (CBET). | |
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Registered: 2007-03-13 21:42 |
Practical Annotation and Exchange of Virtual Anatomy
- Representation of anatomy in a virtual form is at the heart of clinical decision making, biomedical research, and medical training. Virtual anatomy is not limited to description of geometry but also requires appropriate and efficient labeling of regions - to define spatial relationships and interactions between anatomical objects; effective strategies for pointwise operations - to define local properties, biological or otherwise; and support for diverse data formats and standards - to facilitate exchange between clinicians, scientists, engineers, and the general public. Development of aeva, a free and open source software package (library, user interfaces, extensions) capable of automated and interactive operations for virtual anatomy annotation and exchange, is in response to these currently unmet requirements. This site serves for aeva outreach, including dissemination the software and use cases. The use cases drive design and testing of aeva features and demonstrate various workflows that rely on virtual anatomy.
aeva downloads:
Downloads (https://simtk.org/frs/?group_id=1767)
Kitware data repository (https://data.kitware.com/#folder/5e7a4690af2e2eed356a17f2)
aeva documentation:
Guides and tutorials (https://aeva.readthedocs.io)
aeva videos:
Short instructions (https://www.youtube.com/channel/UCubfUe40LXvBs86UyKci0Fw)
aeva source code:
Kitware source code repository (https://gitlab.kitware.com/aeva)
aeva forum:
Forums (https://simtk.org/plugins/phpBB/indexPhpbb.php?group_id=1767 ) | |
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Registered: 2019-08-28 01:27 |
Statistical analysis of conformational ensembles
- This project provides computational tools and methods to analyze conformational ensembles of biomolecules, as well as their assemblies, such as those obtained from molecular simulations.
(A) PROTEINS: The molecular understanding of the functional regulation of proteins requires assessment of various states, including active and inactive states, as well as their interdependencies. For several proteins, their various states can be distinguished from each other on the basis of their minimum energy 3D structures. For many other proteins, like GPCRs, PDZ domains, nuclear transcription factors, heat shock proteins, T-cell receptors and viral attachment proteins, their states can be distinguished categorically from each other only when their finite-temperature conformational ensembles are considered alongside their minimum-energy structures. We are developing tools/methods for:
(A1) Direct comparison of conformational ensembles - The traditional approach to compare two or more conformational ensembles is to compare their respective summary statistics. This approach is, however, prone to artifactual bias, as data is compared after dimensionality reduction. The proper way to compare ensembles is to compare them directly with each other and prior to any dimensionality reduction. g_ensemble_comp is a tool we have developed that does just that and reports the difference between ensembles in terms of a true metric defined by the zeroth law of thermodynamics.
(A2) Prediction of allosteric signaling networks - method under development.
(B) LIPID MEMBRANES: The surface area of a lipid bilayer is related fundamentally to many other observables, such as thermal phase transitions and domain formation in mixed lipid bilayers. We have developed g_tessellate_area to compute the 3D surface area of a bilayer using Delunay tessellation. | |
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Activity Percentile: 94.66 Registered: 2015-09-15 17:52 |
SimVascular: Examples and Clinical Cases
- We invite you to download and try these examples and clinical case projects, which are all compatible with the open source SimVascular cardiovascular modeling software package. Each case includes image data of a healthy or diseased individual, a 3D anatomic model created from the image data, and simulation job files which specify initial conditions, boundary conditions and various parameters required to run the simulation. Many of the cases are already organized as SV projects, which means you can easily load them into SimVascular and view or try out various project components. Following the guides in the SimVascular documentation website, you can also create new models and run simulations with different conditions, based on these example cases.
You are free to download the examples and cases provided that you properly reference the source. The cases are part of the academic output of the researcher cited and should be referred to as such. Permission is granted to use these cases for research purposes, but for commercial use please contact the director of the Cardiovascular Biomechanics Computation Lab, Alison Marsden (amarsden@stanford.edu).
The examples and clinical cases included are:
Example: Demo Project
Example: Cylinder Project (no image, for simulation)
Clinical Case: Coronary Normal
Clinical Case: Aortofemoral Normal 1
Clinical Case: Aortofemoral Normal 2
Clinical Case: Healthy Pulmonary
SimVascular is available for download at our project website at:
https://simtk.org/projects/simvascular
Comprehensive documentation is available on the SimVascular website at:
http://www.simvascular.org
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Activity Percentile: 93.13 Registered: 2014-03-14 20:12 |
Computational Methods in Cardiovascular
Bioengineering Course (BioE484)
- This research PhD-level class was taught during Spring 2007 by Alberto Figueroa, from the Taylor lab. For their final project, students were organized into five teams and each team worked on a different cardiovascular research project.
The basic research tool the students used is the software SimVascular, which is a Cardiovascular Modeling and Simulation
application currently in the process of being open-sourced through http://Simbios.stanford.edu. This project presents a summary of the final projects. All presentations were taped and made available from the download section on the left menu. | |
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Registered: 2007-06-15 17:20 |
Normal human left ventricular myofiber stress
- Ventricular wall stress is believed to be responsible for many physical mechanisms taking place in the human heart, including ventricular remodeling, which is frequently associated with heart failure. Therefore, normalization of ventricular wall stress is the cornerstone of many existing and new treatments for heart failure. In this paper, we sought to construct reference maps of normal ventricular wall stress in humans that could be used as a target for in silico optimization studies of existing and potential new treatments for heart failure. To do so, we constructed personalized computational models of the left ventricles of five normal human subjects using magnetic resonance images and the finite element method. These models were calibrated using left ventricular volume data extracted from magnetic resonance imaging (MRI) and validated through comparison with strain measurements from tagged MRI (950 ± 170 strain comparisons/subject). The calibrated passive material parameter values were C0 = 0.115 ± 0.008 kPa and B0 = 14.4 ± 3.18; the active material parameter value was Tmax = 143 ± 11.1 kPa. These values could serve as a reference for future construction of normal human left ventricular computational models. The differences between the predicted and the measured circumferential and longitudinal strains in each subject were 3.4% ± 6.3% and 0.5% ± 5.9%, respectively. The predicted end-diastolic and end-systolic myofiber stress fields for the five subjects were 2.21 ± 0.58 kPa and 16.54 ± 4.73 kPa, respectively. Thus, these stresses could serve as targets for in silico design of heart failure treatments. | |
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Registered: 2014-06-04 18:58 |
Life in Motion -- the annual 2007 Bio-X symposium co-organized by Simbios
- Life in Motion is part of the annual Bio-X Symposium at Stanford University. In 2007, Bio-X, Stanford's interdisciplinary life sciences initiative, teamed up with Simbios to hold a symposium entitled: "Life in Motion". The goal of this symposium is to educate students and scientists from different disciplines about the exciting uses of simulations in the life sciences driven by the laws of physics and mechanics across a range of scales, from molecules to organisms.
Life in Motion was held on October 25th 2007 in the Clark Center at Stanford University. The POSTER ANNOUNCING THE SYMPOSIUM and The PROGRAM are available by selecting the Downloads TAB ON THE LEFT MENU. | |
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Registered: 2007-06-06 01:20 |
Infarcted human left ventricular myofiber stress
- Heart failure is increasing at an alarming rate, making it a worldwide epidemic. As the population ages and life expectancy increases, this trend is not likely to change. Myocardial infarction (MI)-induced adverse left ventricular (LV) remodeling is responsible for nearly 70% of heart failure cases. The adverse remodeling process involves an extension of the border zone (BZ) adjacent to an MI, which is normally perfused but shows myofiber contractile dysfunction. To improve patient-specific modeling of cardiac mechanics, we sought to create a finite element model of the human LV with BZ and MI morphologies integrated directly from delayed-enhancement magnetic resonance (DE-MR) images. Instead of separating the LV into discrete regions (e.g., the MI, BZ, and remote regions) with each having a homogeneous myocardial material property, we assumed a functional relation between the DE-MR image pixel intensity and myocardial stiffness and contractility--we considered a linear variation of material properties as a function of DE-MR image pixel intensity, which is known to improve the accuracy of the model''''s response. The finite element model was then calibrated using measurements obtained from the same patient--namely, 3D strain measurements-using complementary spatial modulation of magnetization magnetic resonance (CSPAMM-MR) images. This led to an average circumferential strain error of 8.9% across all American Heart Association (AHA) segments. We demonstrate the utility of our method for quantifying smooth regional variations in myocardial contractility using cardiac DE-MR and CSPAMM-MR images acquired from a 78-yr-old woman who experienced an MI approximately 1 yr prior. We found a remote myocardial diastolic stiffness of C(0) = 0.102 kPa, and a remote myocardial contractility of T(max) = 146.9 kPa, which are both in the range of previously published normal human values. Moreover, we found a normalized pixel intensity range of 30% for the BZ, which is consistent with the literature. Based on these regional myocardial material properties, we used our finite element model to compute patient-specific diastolic and systolic LV myofiber stress distributions, which cannot be measured directly. One of the main driving forces for adverse LV remodeling is assumed to be an abnormally high level of ventricular wall stress, and many existing and new treatments for heart failure fundamentally attempt to normalize LV wall stress. Thus, our noninvasive method for estimating smooth regional variations in myocardial contractility should be valuable for optimizing new surgical or medical strategies to limit the chronic evolution from infarction to heart failure. | |
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Activity Percentile: 0.00 Registered: 2015-04-16 18:15 |
Optimal Control Workshop
- This project provides files distributed at the NSF-funded Optimal Control Workshop held on July 9, 2015 at the University of Edinburgh as part of the XV International Symposium on Computer Simulation in Biomechanics. The workshop material was organized into three sections: 1) Motivational material, 2) Technical material, and 3) Tutorial material. Slides from each section, along with all tutorial material (requires a license of GPOPS-II optimal control software), are included. | |
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Activity Percentile: 0.00 Registered: 2015-08-01 16:35 |
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 |
Purkinje Network Generation with Fractal Trees
- This project is a tool to generate Purkinje networks in realistic representations of the ventricles. Using fractal trees, our method provides an anatomically based approximation to the network. The input consist of a surface discretized with triangles and the output consist of a finite element mesh, suitable for simulations.
The source code is available in this repository and in <a href="https://www.github.com/fsahli/fractal-tree/">GitHub</a>. The documentation can be found in <a href="https://fractal-tree.readthedocs.org">fractal-tree.readthedocs.org</a>. | |
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Activity Percentile: 0.00 Registered: 2015-11-25 00:10 |
Investigating the effects of pelvic floor muscles during pregnancy
- Developing a risk predictive Model about how the pelvic floor muscles change during pregnancy and how they stretch during the delivery in order to identify and discover knowledge about these muscles to avoid damage during delivery. Which damage increases the risk of urinary incontinence or pelvic organ prolapse later in life. | |
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Registered: 2016-11-22 20:54 |
3D Numerical Investigation of Endothelial Shear Stress in Arteries
- 3D numerical investigation of endothelial shear stress in coronary arteries. | |
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Activity Percentile: 0.00 Registered: 2015-11-30 13:34 |
SimVascular: Third-party open source software.
- Third party open source software needed by internal developers of the new SimVascular project. | |
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Registered: 2013-12-10 23:33 |
Biosimulation Education and Training
- Biosimulation education and training resources for Neuromuscular Biomechanics, RNA folding, Cardiovascular Dynamics, and Myosin Dynamics.
Course material can be found by clicking the documents link on the left menu. | |
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Activity Percentile: 0.00 Registered: 2006-08-02 20:35 |
Finite element method for nonlinear solid mechanics with discontinuous Galerkin
- The library is written in C,C++, and Fortran. Thus far, it has only been tested on a linux cluster consisting of 92 Intel processors. For use of this library, the user must create a C++ driver application that will supply C style arrays containing the mesh data for the biological model. These include the standard connectivity, coordinate, and boundary data arrays. These can be given in the form of a conforming finite element mesh, since the library has a utility that will convert this data into a discontinuous finite element mesh. The user will need to decide the most appropriate way to analyze the results. Presently there is a utility that will create output files for the TecPlot visualization package.
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Activity Percentile: 0.00 Registered: 2005-08-24 19:38 |
IMAG/MSM Biomechanics Working Group (Demo)
- <iframe width="560" height="315" src="https://www.youtube.com/embed/n_3vxZMtae0" frameborder="0" allowfullscreen></iframe>
<i>Example of multiscale modeling in biomechanics</i>
<b>Goals and Objectives</b>
Through interactions within members and with other working groups, the goals of the Biomechanics Working Group are:
• to establish a cross-discipline discussion platform for multiscale modeling and analysis issues in the general area of biomechanics
• to identify computational infrastructure needs for multiscale biomechanical simulations
• to establish pathways for experimental data and validation to support multiscale modeling and simulation in biomechanics
• to increase awareness to the role of multiscale analysis in biomechanics and simulation-based medicine
• to promote the role of dissemination to accelerate multiscale analysis in biomechanics
<b>History</b>
The Biomechanics Working Group has started in November 2010 following working group related discussions at the <a href="http://nibibwiki2.nih.gov/mediawiki/index.php?title=2010_MSM_CONSORTIUM_MEETING">2010 MSM CONSORTIUM MEETING</a>. Founding co-leads of the working group were Jay Humphrey of Yale University and Ahmet Erdemir of Cleveland Clinic. The working group inherited the <a href="http://nibibwiki2.nih.gov/mediawiki/index.php?title=Working_Group_6">Working Group 6 - Tissue Mechanics</a>, which was started by Trent Guess of University of Missouri, Kansas City.
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Registered: 2007-10-09 17:52 |
Blood vessel micromechanics
- This project is a parallel finite element analysis (FEA) tool for nonlinear solid mechanics. The FEA tool uses discontinuous Galerkin which specifically designed for nearly incompressible materials such as biological tissue. In addition to the FEA libraries, the project also includes a set of binaries which describe the geometry of the elastin microstructure in rat aorta. The geometry was obtained from high resolution electron microscopy. | |
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Activity Percentile: 0.00 Registered: 2008-09-10 20:37 |
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 |