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16 projects in result set.
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: 93.51 Registered: 2015-09-15 17:52 |
IA-FEMesh
- In an effort to facilitate anatomic FE model development, we introduce IA-FE Mesh (Iowa FE Mesh), a freely available software toolkit. IA-FEMesh employs a multiblock meshing scheme aimed at hexahedral mesh generation. An emphasis has been placed on making the tools interactive, in an effort to create a user-friendly environment. The goal is to provide an efficient and reliable method for model development, visualization, and mesh quality evaluation. While these tools have been developed, initially, in the context of skeletal structures, they can be applied to a virtually endless number of modeling applications. | |
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Activity Percentile: 86.64 Registered: 2008-08-29 02:59 |
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 |
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 |
NIH monthly Tcons
- Regularly scheduled Tcon, focused on RNA DBP for March 19th | |
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Activity Percentile: 0.00 Registered: 2010-03-19 16:17 |
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 |
Python tools for Markov state models
- This project is a collection of Python modules for generating, analyzing, and interpreting Markov state models. Some features: objects to represent and sample from transition matrices, Singhal's sensitivity analysis, clustering on arbitrary data objects. | |
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Activity Percentile: 0.00 Registered: 2007-12-19 01:22 |
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 |
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 |
Biomechanics of Growth Directory
- This project provides a simple but yet very illustrative tool how changes in the mechanical environment effect biological structure, density and volume. The simulation is based on three dimensional geometrically nonlinear finite elements. The code is developed in matlab and very basic. The project has been developed and used in class (ME337, "Mechanics of Growth"). | |
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Activity Percentile: 0.00 Registered: 2007-10-24 04:05 |
2007BioE215 Jonikas
- In progress and completed assignments for BioE 215. | |
Activity Percentile: 0.00 Registered: 2007-03-26 19:09 |
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 |
Open MM and Zephyr applications to XBOX360 platform.
- This project is intended to use the OpenMM and Zephyr source code for compilation upon the XBOX 360 platforms. An executable with the functionality of Zephyr is desired. | |
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Activity Percentile: 0.00 Registered: 2009-12-25 17:02 |
Hierarchical Human Biomechanics Framework
- This project intends to build a virtual anatomical object library to hierarchiclally implement human biomechanics simulators used to improve clinical approaches and human biotech products. | |
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Activity Percentile: 0.00 Registered: 2008-04-25 12:23 |
PySimTK: SimTK core multibody dynamics tool kit in python
- This project creates an easier to use python API for the SimTK core multibody mechanics simulation tool kit. | |
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Registered: 2009-07-29 17:59 |