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25 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 |
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 |
MITK-GEM: Software pipeline to GEnerate Models from images
- An attempt to provide a software pipeline to interactively create finite element models from medical images. Primarily intended to model bone fracture risk.
An application with graphical user interface and image processing plugins is provided. The application is build using the MITK Workbench software framework. The following plugins are available: fast image segmentation using graph cut, volume meshing using tetgen and density to modulus conversion for bone material property assignment.
Documentation and tutorials are available on our <a href="http://araex.github.io/mitk-gem-site/">tutorial website</a>.
Along with pre-compiled executables available here, the source code is available on our <a href="https://github.com/araex/mitk-gem">github page</a>.
The graph cut segmentation plugin and the material mapping plugin were developed as part of research studies.
If you use the software or source code in your research, please cite the corresponding journal <a href="https://simtk.org/project/xml/publications.xml/?group_id=1063">publications</a>. | |
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Registered: 2015-12-23 02:46 |
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 | |
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Registered: 2016-10-27 13:07 |
BlurLab -- 3D Microscopy Simulation Package
- BlurLab is an easy to use platform for generating simulated fluorescence microscopy data for use in mechanistic modeling visualization, image comparison, and hypothesis testing. The software accepts the 3D positions, intensities and labels of fluorescing objects that are produced by an underlying mechanistic model and transforms them into high quality simulated images. The program includes full 3D convolution with realistic (or even measured) point spread functions; inclusion of thermal, shot and custom noise spectra; simulations of mean and fully stochastic photobleacing; the ability to view scenes in wide-field and TIRF, and perform Z-slicing; and the ability to simulate FRAP experiments.
The software provides a platform for adjusting and saving these simulated images, as well as a number of helpful, semi-automated features to make image simulation easy and less error prone. | |
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Activity Percentile: 77.27 Registered: 2011-08-05 01:17 |
Simbody: Multibody Physics API
- This project is a SimTK toolset providing general multibody dynamics capability, that is, the ability to solve Newton's 2nd law F=ma in any set of generalized coordinates subject to arbitrary constraints. (That's Isaac himself in the oval.) Simbody is provided as an open source, object-oriented C++ API and delivers high-performance, accuracy-controlled science/engineering-quality results.
Simbody uses an advanced Featherstone-style formulation of rigid body mechanics to provide results in Order(<em>n</em>) time for any set of <em>n</em> generalized coordinates. This can be used for internal coordinate modeling of molecules, or for coarse-grained models based on larger chunks. It is also useful for large-scale mechanical models, such as neuromuscular models of human gait, robotics, avatars, and animation. Simbody can also be used in real time interactive applications for biosimulation as well as for virtual worlds and games.
This toolset was developed originally by Michael Sherman at the Simbios Center at Stanford, with major contributions from Peter Eastman and others. Simbody descends directly from the public domain NIH Internal Variable Dynamics Module (IVM) facility for molecular dynamics developed and kindly provided by Charles Schwieters. IVM is in turn based on the spatial operator algebra of Rodriguez and Jain from NASA's Jet Propulsion Laboratory (JPL), and Simbody has adopted that formulation.
<b>SOURCE CODE:</b> Simbody is distributed in source form. The source code is maintained at <a href="https://www.github.com/simbody">GitHub</a>. You can get a zip of the latest stable release <a href="https://github.com/simbody/simbody/releases">here</a>, then build it on your Windows, Mac OSX, or Linux machine (you will need CMake and a compiler).
You can also clone the git repository and build the latest development version <a href="https://github.com/simbody/simbody">here</a>; the repository URL is https://github.com/simbody/simbody.git. If you would like to contribute bug fixes, new code, documentation, examples, etc. to Simbody (and we hope you will!), please fork the repository on GitHub and send pull requests.
If you are new to git, you may want to start with GitHub's <a href="https://help.github.com/categories/54/articles">Bootcamp tutorial</a>. | |
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Registered: 2005-07-26 19:52 |
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: 55.30 Registered: 2013-03-05 01:40 |
ViewCommonPaths Application
- The ViewCommonPaths program helps to simultaneously visualize a set of numeric sequences that have the same start and end elements by drawing them into a common directed acyclic graph (DAG). In particular, ViewCommonPaths helps to simultaneously visualize a set of allosteric communication paths with the same start and end residues. Given a set of allosteric paths (each a sequence of residues), ViewCommonPaths creates a DAG from the set of individual pathways and allows a quick visual analysis of these pathways and the relationships among the residues along these paths. | |
Activity Percentile: 30.68 Registered: 2008-09-16 04:02 |
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. | |
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Activity Percentile: 10.23 Registered: 2014-06-18 13:56 |
A Visualization Tool for OpenSim
- This project is a visualization tool for OpenSim. It allows the visualization of musculoskeletal data or simulation results within the GUI of OpenSim. It currently includes 7 modes of visualization :
1) Error from an IK process as streamlines for each marker
2) Muscular activation or forces from CMC/SO as color/opacity mapping on 3D meshes
3) MR Images viewer and alignment with the musculoskeletal model
4) Moments from ID as arrows located at joint positions
5) Finite Element simulations from FEBio as color coded time-dependent 3D meshes
6) EMG comparison to muscle activation as color/opacity mapping on 3D meshes
7) Multi-simulation visualization as 3D volume rendering
This project was initiated by EPFL-VRLab (Switzerland) within the framework of the Marie-Curie european project 3D Anatomical Human (http://3dah.miralab.ch/). It is now developed within the Games and Virtual Groups of Utrecht University (The Netherlands).
Module, documentation and test samples are available in the download section. | |
Registered: 2010-04-12 14:23 |
BPPalign: Aligning RNA secondary structure probabilities to discover new motifs
- This tool provides basic scripts to run the partition executable RNAstructure on hundreds of homolog sequences from RFAM, and to then visualize the results by averaging across these matrices. Examples from purine-binding and double glycine-binding riboswitches are included. | |
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Activity Percentile: 0.00 Registered: 2011-09-18 05:31 |
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 |
MSMExplorer: A Visualization Application for Markov State Models for Folding
- A java-based visualization application for Markov State Models for folding simulations. The programs is designed as a gui interface for viewing and interacting with MSMs constructed by MSMBuilder.
SOURCE CODE NOTICE:
for up-to-date source code access please visit:
http://github.com/brycecr/msmexplorer
Similarly, Up-to-date distributions can be downloaded from
https://github.com/brycecr/msmexplorer/downloads
but periodic major releases (considered "stable") will still be uploaded to simtk.
In the Documents section of this site, you'll find an illustrated Reference and Tutorial PDF and a short tutorial video. | |
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Activity Percentile: 0.00 Registered: 2010-06-15 00:10 |
NMWiz: Normal Mode Animation, Visualization, and Plotting
- NMWiz is a VMD plug-in for animating, visualizing, and plotting normal modes. User can make a comparative analysis of modes from different models and sources.
Normal mode data may come from an elastic network model, a force field based atomistic model, or essential dynamics analysis of a structural ensemble. NMWiz recognizes coordinate and normal mode data in a simple format, called Normal Mode Data (NMD) format.
See the NMWiz main page for more details:
http://www.csb.pitt.edu/NMWiz/
**ANM Server**
ANM data can be downloaded in NMD format from the ANM Server (Thanks to Dr. Eran Eyal). After your calculation is performed, go to "Download Files" page using the link in the lower left corner of the page. The last output file is for NMWiz. You can use it in VMD with NMWiz to prepare publication quality images.
http://www.csb.pitt.edu/ANM/
Acknowledgements:
Developers thank Dr. Timothy Lezon for his useful suggestions and Dr. Eran Eyal for his effort to make ANM server compatible with NMWiz. | |
Activity Percentile: 0.00 Registered: 2010-07-24 02:19 |
Biomechanics in Product Design
- This project provides methods and tools to conduct biomechanical analyses of human-artifact interaction. The objective is to facilitate the creation of models to predict the effects of interaction processes on the human musculoskeletal system. Designers gain valuable insights on how to improve the ergonomic quality of consumer products and workplaces. Our research currently focuses on the integration of OpenSim into CAD environments as well as the prediction of human motion based on interaction goals. | |
Activity Percentile: 0.00 Registered: 2014-07-02 08:11 |
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 |
Muscle Fiber Analysis and Visualization with Diffusion Tensor Imaging
- This software allows users to attain functionally pertinent biological information about the fibrous structure of living muscle tissue using Diffusion Tensor Images (DTI). | |
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Activity Percentile: 0.00 Registered: 2006-04-10 22:45 |
FEBio: Finite Elements for Biomechanics
- FEBio is a nonlinear finite element solver that is specifically designed for biomechanical applications. It offers modeling scenarios, constitutive models, and boundary conditions that are relevant to many research areas in biomechanics and biophysics. All features can be used together seamlessly, giving the user a powerful tool for solving 3D problems in computational biomechanics. The software is open-source, and pre-compiled executables for Windows, Mac OS X and Linux platforms are available.
Current modeling capabilities include:
* Large deformation quasi-static and dynamic structural mechanics analysis.
* Modeling of complex structures that contain a combination of deformable and rigid parts.
* Multiphasic modeling, where the solvent can contain any number of solutes that may undergo chemical reactions.
* Fluid mechanics analysis, both steady-state and transient
* Fluid-solid interaction (FSI), which combines the powerful solid and fluid solvers.
FEBio also supports a plugin framework that can be used to easily develop new features for FEBio, including new constitutive models, boundary conditions, and even entire new physics solvers.
For more information check out the FEBio website at http://www.febio.org | |
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Registered: 2007-09-14 16:08 |
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 |
25 projects in result set. Displaying 20 per page. Projects sorted by alphabetical order.
<1> <2>