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120 projects in result set. Displaying 20 per page. Projects sorted by alphabetical order.
<1> <2> <3> <4> <5> <6>
OpenSim
- OpenSim is a freely available, user extensible software system that lets users develop models of musculoskeletal structures and create dynamic simulations of movement.
Find out how to join the community and see the work being performed using OpenSim at <a href="http://opensim.stanford.edu">opensim.stanford.edu</a>.
Access all of our OpenSim resources at the new <br /><a href="http://opensim.stanford.edu/support/index.html"><b style="color:#900; font-size:16px;">Support Site</b></a>.
Watch our <a href="http://www.youtube.com/watch?v=ME0VHfCtIM0">Introductory Video</a> get an overview of the OpenSim project and see how modeling can be used to help plan surgery for children with cerebral palsy.
<iframe width="560" height="315" src="https://www.youtube.com/embed/ME0VHfCtIM0" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe> | |
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Registered: 2006-03-23 18:48 |
OpenMM
- OpenMM is a toolkit for molecular simulation. It can be used either as a stand-alone application for running simulations, or as a library you call from your own code. It
provides a combination of extreme flexibility (through custom forces and integrators), openness, and high performance (especially on recent GPUs) that make it truly unique among simulation codes.
<b>NEED HELP?</b> Check out the discussion forums under <a href="https://simtk.org/forums/viewforum.php?f=161">Public Forums</a> and the material from our workshops under <a href="https://simtk.org/project/xml/downloads.xml?group_id=161">Downloads</a>.
<b>GET STARTED QUICKLY:</b> Tutorials and sample scripts to run OpenMM are available in the <a href="http://wiki.simtk.org/openmm/VirtualRepository">OpenMM Code Repository</a>.
<b>SOURCE CODE:</b> The source code for OpenMM is available under <a href="https://simtk.org/project/xml/downloads.xml?group_id=161">Downloads</a> and also from the <a href="http://www.github.com/SimTk/openmm">Github Source Code Repository</a>.
<b>BENCHMARKS:</b> A collection of <a href="http://wiki.simtk.org/openmm/Benchmarks">benchmarks</a> is available to show the performance of OpenMM simulating a variety of molecular systems.
<b>CITING OPENMM:</b> Any work that uses OpenMM should cite the papers listed on the <a href="https://simtk.org/project/xml/publications.xml/?group_id=161">Publications</a> page. | |
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Registered: 2006-11-16 18:27 |
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 |
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: 93.89 Registered: 2015-09-15 17:52 |
Upper Extremity Dynamic Model
- The project releases the MoBL-ARMS dynamic musculoskeletal model of the human upper extremity, implemented in SIMM/SDFast and OpenSIM. Please see the model summary for details of the new model and its use.
New! We have released a new version of the OpenSim models and tutorial, now compatible with releases 3.2 and later. See download page for release and more information. | |
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Activity Percentile: 91.98 Registered: 2011-08-02 19:56 |
Predicting Cell Deformation from Body Level Mechanical Loads
- This project is a NIBIB/NIH funded study (1R01EB009643-01) to establish models and computational platforms to predict cellular deformations from joint level mechanical loading.
Collaborators:
Ahmet Erdemir (PI), Amit Vasanji, Jason Halloran (Cleveland Clinic)
Cees Oomens, Frank Baaijens (Eindhoven University of Technology)
Jeff Weiss (University of Utah)
Farshid Guilak (Duke University)
Summary (from grant proposal):
Cells of the musculoskeletal system are known to have a biological response to deformation. Deformations, when abnormal in magnitude, duration, and/or frequency content, can lead to cell damage and possible disruption in homeostasis of the extracellular matrix. These mechanisms can be studied in an isolated fashion but connecting mechanical cellular response to organ level mechanics and human movement requires a multiscale approach. At the organ level, physicians perform surgical procedures, investigators try to understand risk of injury, and clinicians prescribe preventive and therapeutic interventions. Many of these operations are aimed at management and prevention of cell damage, and to associate joint level mechanical markers of failure to cell level failure mechanisms. Through human movement, one explores neuromuscular control mechanisms and the influence of physical activity on musculoskeletal tissue properties. At a lower level, mechanical sensation of cell deformations regulate movement control. Physical rehabilitation and exercise regimens are prescribed to promote tissue healing and/or strengthening through cellular regeneration. The knowledge of the mechanical pathway, through which the body level loads are distributed between organs, then within the tissues and further along the extracellular matrix and the cells, is critical for the success of various interventions. However, this information is not established. The goal of this research proposal is to portray that prediction of cell deformations from loads acting on the human body, therefore a clear depiction of the mechanical pathway, is possible, if a multiscale simulation approach is used. Multiresolution models of the knee joint, representative of joint, tissue and cell structure and mechanics, will be developed for this purpose. The knee endures high rates of traumatic injury to its soft tissue structures and it is predominantly affected by osteoarthritis, chronically induced by abnormalities in mechanical loading or how it is transferred to the cartilage. Through multiscale mechanical coupling of these models, a map of cellular deformation in cartilage, ligaments and menisci under a variety of tibiofemoral joint loads will be obtained. Comprehensive mechanical testing at joint, tissue and cell levels will be conducted for parameter estimation and validation, including in vitro loading of the knee joint representative of lifelike loading scenarios. In addition, imaging modalities will capture joint and tissue anatomy, and spatial and deformation related information from cell and extracellular matrix. Advanced computational approaches will be used to obtain model properties and to facilitate multiscale simulations. The approach will combine the expertise of many investigators experienced in biomechanical modeling and experimentation at various biological scales, some with clinical expertise. In future, the research team will utilize this platform to establish the relationship between the structural and loading state of the knee and chondrocyte stresses to explore potential mechanisms of cartilage degeneration. Through documented dissemination of data and models, simulations of other pathologies and translation of the methodology to other organs can be carried out by any interested investigator. | |
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Registered: 2009-07-23 17:33 |
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 |
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: 89.31 Registered: 2008-08-29 02:59 |
Force Field X
- Force Field X is a group of open source (GPL v. 3), platform independent (Java Runtime Environment) modules for molecular biophysics. Key methods include:
Polarizable AMOEBA force fields
Particle-mesh Ewald electrostatics
Generalized Kirkwood continuum electrostatics
X-ray and neutron crystallography refinement
Real space refinement for CryoEM
Methods for structure based drug design
for more information, see http://ffx.kenai.com | |
Activity Percentile: 86.64 Registered: 2012-02-04 21:49 |
Integrated Flux Balance Analysis Model of Escherichia coli
- This project includes several MATLAB scripts that simulate E. coli central metabolism and the effects of single gene deletions on metabolism using 3 approaches -- iFBA, rFBA, and ODE. The project also includes several MATLAB scripts that simulate biochemical networks using 1) integrated flux balance analysis (iFBA) -- a combined FBA, boolean regulatory, and ODE approach; 2) regulatory flux balance analysis (rFBA); and 3) ordinary differential equations (ODE). Additionally, the project includes several MATLAB and php scripts for visualizing metabolic simulations. | |
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Registered: 2008-06-11 23:27 |
Matlab-Opensim Interfaces
- Matlab is a common analysis tool used for data manipulation, signal processing and function integration. These features can be used in conjunction with simulation tools provided by the Opensim interface.
This project provides tools for using different aspects of Opensim within the Matlab environment. This includes 1) using the command line tools by generating XML setup files etc (Scaling, Inverse Kinematics, Inverse Dynamics, Forward Dynamics) 2) using the Java classes that the Opensim GUI is built on to access aspects of the Opensim API.
Provided in this project are -
1) Tools for taking motion capture data from C3D files and generating the required input files (marker files {*.trc} motion files {*.mot}, GRF xml files {*.xml}) as well as setup files for each of the different tools that can be called from the command line. Example data from different models and data sets are provided including example pipelines to analyse data using Opensim. Some of this implementation has taken inspiration from Tim Dorn's excellent GaitExtract toolbox. A new page with more up-to-date tools can be found here - http://simtk-confluence.stanford.edu:8080/display/OpenSim/Tools+for+Preparing+Motion+Data
2)Matlab functions and example scripts for accessing the Opensim API through Matlab. This utilises the Java wrapping classes that the Opensim GUI is built on. Examples are shown to open and edit models as well as perform a 'Muscle Analysis'. Please now use the inbuilt support from Opensim rather than this toolbox! (http://simtk-confluence.stanford.edu:8080/display/OpenSim/Scripting+with+Matlab) | |
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Activity Percentile: 85.11 Registered: 2011-08-06 20:22 |
MMB (MacroMoleculeBuilder)
- MMB (a contraction of MacroMolecule Builder) was previously known as RNABuilder. The latter is available up to revision 2.2. We renamed the software since even some longtime users were unaware that the package now handles protein and DNA and protein as well as RNA. You can use MMB for morphing, homology modeling, folding (e.g. using base pairing contacts), redesigning complexes, fitting to low-resolution density maps, predicting local rearrangements upon mutation, and many other applications limited mostly by your imagination.
MMB was written by Samuel Coulbourn Flores at the Stanford Simbios Center. It is currently maintained by the same person, now as Dean of the Swedish National Graduate School in Medical Bioinformatics, based at Stockholm University, Sweden. | |
Registered: 2008-12-05 00:15 |
Topological Methods for Exploring Low-density States in Folding Pathways
- In this paper, we develop a computational approach to explore the relatively low populated transition or intermediate states in biomolecular folding pathways based on a topological data analysis tool, Mapper. We applied Mapper to simulation data from large-scale distributed computing to provide structural evidence on multiple intermediate states of the unfolding and refolding of an RNA hairpin with a GCAA tetraloop. This project contains Mapper, the RNA conformations (in contact map format), and instructions to reproduce results from this paper.
<b> Motivation: </b> Characterization of transient intermediate or transition states is crucial for the description of biomolecular folding pathways, which is however difficult in both experiments and computer simulations. Such transient states are typically of low population in simulation samples. Even for simple systems such as RNA hairpins, recently there are mounting debates over the existence of multiple intermediate states.
<b> More about Mapper and the computational approach </b> The method is inspired by the classical Morse theory in mathematics which characterizes the topology of high dimensional shapes via some functional level sets. In this paper we exploit a conditional density filter which enables us to focus on the structures on pathways, followed by clustering analysis on its level sets, which helps separate low populated intermediates from high populated uninteresting structures.
The method is effective in dealing with high degree of heterogeneity in distribution, capturing structural features in multiple pathways, and being less sensitive to the distance metric than nonlinear dimensionality reduction or geometric embedding methods. The methodology described in this paper admits various implementations or extensions to incorporate more information and adapt to different settings, which thus provides a systematic tool to explore the low density intermediate states in complex biomolecular folding systems. | |
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Activity Percentile: 83.97 Registered: 2008-12-10 00:53 |
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: 80.15 Registered: 2011-08-05 01:17 |
MB Knee: Multibody Models of the Human Knee
- The purpose of this site is to disseminate geometry and modeling information for development of knee models, primarily in the multibody framework. MBKnee_4 is based on in vivo measurements from a 29 year old female while MBKnee_1, MBKnee_2, and MBKnee_3 are based on cadaver knees that were physically tested in a dynamic knee simulator. Knee geometries (bone, cartilage, and mensici) were derived from Magnetic Resonance Imaging (MRI) and ligament insertions come from MRI, the literature, and probing the cadaver knees. The site also contains information on ligament modeling, such as bundle insertion locations and zero load lengths. Examples of knee models are also provided in the form of ADAMS command files. MBKnee_4 is the most recent model and it includes representation of the medial and lateral menisci, wrapping around bone and cartilage of the meniscal horn attachments, attachments of the deep medial collateral ligament and the anterolateral ligament to the menisci, representation of the posterior oblique ligament and the anterolateral ligament, ligament zero load lengths (or reference strain) determined from experimental laxity measurements, and measured motion to deep flexion.
Funding for this work was provided by the National Institute of Arthritis an Musculoskeletal and Skin Diseases (RAR061698) and by the National Science Foundation (CMS-0506297). | |
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Activity Percentile: 79.77 Registered: 2012-05-25 17:31 |
Lee-Son's Toolbox: a Toolbox that Converts VICON Mocap Data into OpenSim Inputs
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This toolbox converts VICON motion capture data into OpenSim inputs. Using this, you can easily and quickly obtain *.trc (marker trajectories) and *.mot (force plate data) files which can be used directly in OpenSim.
This toolbox automatically adapt to the number of markers, the name of markers, and the number of force plates that you used. Also, you can choose your VICON global coordinates.
This toolbox is free without warranty but we do ask for acknowledgement if used in publications. If you have any questions, please contact us by e-mail or public forums. | |
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Registered: 2011-08-30 02:08 |
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 |
Batch OpenSim Processing Scripts (BOPS)
- BOPS performs batch processing of common OpenSim procedures (Inverse Kinematics - IK, Inverse Dynamics - ID, Muscle Analysis - MA, Static Optimization - SO, and Joint Reaction Analysis - JRA) and stores output, logging information, setup files, and plots in an ordered structure of folders.
We implemented BOPS using OpenSim APIs, that receive the following information through setup files: (i) name and weight of each marker (IK); (ii) external loads (ID); (iii) muscles and moment arms of interest (MA); (iv) static optimization conditions, and muscle actuators loads (SO); (v) joints of interest (JRA). The user is in charge of defining the appropriate configuration for its data, but we already provide several templates for each setup file to speed up their customization.
A MATLAB Graphical User Interface (GUI) is available to simplify the execution of procedures. The use of the GUI is not limited to inputting the setup files. The user can also select: (i) the OpenSim procedures to execute, (ii) the trials to process, (iii) the OpenSim model to use on the simulations, (iv) the cut-off frequencies for the filtering, (v) the residual actuators, (vi) the output variables to plot and the x-axis label.
The software only requires to configure MATLAB for the use of OpenSim API (http://simtk-confluence.stanford.edu:8080/display/OpenSim/Scripting+with+Matlab), and it is based on the data folder organization provided by MOtoNMS software (https://simtk.org/home/motonms).
BOPS stores its outputs in folders that are automatically created and that integrate perfectly in the structure provided by MOtoNMS software (https://simtk.org/home/motonms). We designed the two tools to work in close cooperation to transform the data collected in a motion analysis laboratory into inputs for OpenSim and CEINMS (https://simtk.org/home/ceinms) tools.
BOPS is released under Apache v2.0 License and freely available to the community without warranty. Latest updates can be found on the GitHub repository (https://github.com/RehabEngGroup/BOPS).
Thanks to the recent join of the Human Movement Biomechanics Laboratory (University of Ottawa, Canada) to the project, the tool has been refined and extensively tested on data from several laboratories and with different combinations of procedures, setups and user choices. Their precious contribution has allowed also the addition of the JRA procedure to those already available and led to the release of v2.0, a definitely improved and more stable version.
A tutorial video exemplifying how to use BOPS v2.0 is available in the Documents section.
For any doubts, suggestions, bugs please either use the BOPS forum or send us an email.
This is an ongoing project, therefore any feedback is really appreciated.
When using BOPS or our Test Data, please acknowledge the authors and cite our main publication:
Bruno L. S. Bedo, Alice Mantoan, Danilo S. Catelli, Willian Cruaud, Monica Reggiani & Mario Lamontagne (2021): BOPS: a Matlab toolbox to batch musculoskeletal data processing for OpenSim, Computer Methods in Biomechanics and Biomedical Engineering
DOI: 10.1080/10255842.2020.1867978 | |
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Activity Percentile: 71.76 Registered: 2015-09-05 18:12 |
120 projects in result set. Displaying 20 per page. Projects sorted by alphabetical order.
<1> <2> <3> <4> <5> <6>