Project Tree
Now limiting view to projects in the following categories:
All Topics :: Primary Content :: Software Libraries [Remove This Filter]
All Topics > Primary Content > Developer Tools |
Browse By: |
81 projects in result set. Displaying 20 per page. Projects sorted by alphabetical order.
<1> <2> <3> <4> <5>
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> | |
|
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. | |
|
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. | |
|
Registered: 2012-01-24 03:21 |
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>. | |
|
Registered: 2015-12-23 02:46 |
DeepCell: Deep convolutional neural networks for image segmentation
- The assignment of a cellular identity to individual pixels in microscopy images is a key technical challenge for many live-cell experiments. Traditional approaches to this image segmentation problem have relied on standard computer vision techniques, such as thresholding, morphological operations, and the watershed transform. While these approaches have enabled the analysis of numerous experiments, they are limited in their robustness and in applicability. Here, we show that deep convolutional neural networks, a supervised machine learning method, can robustly segment the cytoplasms of individual bacterial and mammalian cells. This approach automates the analysis of thousands of bacterial cells and leads to more accurate quantification of localization based fluorescent reporters in mammalian cells. In addition, this approach can also simultaneously segment and identify different mammalian cell types in co-cultures. Deep convolutional neural networks have had a transformative impact on the problem of image classification, and we anticipate that they will have a similar impact for live-cell imaging experiments.
Visit our webpage at http://covertlab.github.io/DeepCell | |
|
Activity Percentile: 84.73 Registered: 2015-11-16 19:58 |
Lee-Son's Toolbox: a Toolbox that Converts VICON Mocap Data into OpenSim Inputs
-
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. | |
|
Registered: 2011-08-30 02:08 |
Simulation of Constrained Musculoskeletal Systems in Task Space
- Objective: This work proposes an operational task space formalization of constrained musculoskeletal systems, motivated by its promising results in the field of robotics.
Methods: The change of representation requires different algorithms for solving the inverse and forward dynamics simulation in the task space domain. We propose an extension to the Direct Marker Control and an adaptation of the Computed Muscle Control algorithms for solving the inverse kinematics and muscle redundancy problems respectively.
Results: Experimental evaluation demonstrates that this framework is not only successful in dealing with the inverse dynamics problem, but also provides an intuitive way of studying and designing simulations, facilitating assessment prior to any experimental data collection.
Significance: The incorporation of constraints in the derivation unveils an important extension of this framework towards addressing systems that use absolute coordinates and topologies that contain closed kinematic chains. Task space projection reveals a more intuitive encoding of the motion planning problem, allows for better correspondence between observed and estimated variables, provides the means to effectively study the role of kinematic redundancy and, most importantly, offers an abstract point of view and control, which can be advantageous towards further integration with high level models of the precommand level.
Conclusion: Task-based approaches could be adopted in the design of simulation related to the study of constrained musculoskeletal systems.
The source code of the project can be found at: https://github.com/mitkof6/opensim-task-space.git
The new API of task space and constraint projection for OpenSim V4.0 is available at: https://github.com/mitkof6/task-space
<iframe width="560" height="315" src="https://www.youtube.com/embed/jfE14iWRZDs" frameborder="0" allow="autoplay; encrypted-media" allowfullscreen></iframe> | |
|
Registered: 2017-08-28 12:06 |
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) | |
|
Activity Percentile: 79.39 Registered: 2011-08-06 20:22 |
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: 75.19 Registered: 2012-02-04 21:49 |
MIcro Simulation Tool - MIST
- The MIcro Simulation Tool is free software that allows the user to :
* Define state transition models with multiple processes
* Generate populations to match given statistics using Evolutionary Computation
* Run Simulations in High Performance Computing environment - including the cloud
* Analyze and Report the results
Below are some videos that describe MIST capabilities:
This video shows the basic ideas behind MIST
<iframe width="640" height="360" src="https://www.youtube.com/embed/AD896WakR94" frameborder="0" allowfullscreen></iframe>
This video shows some population generation capabilities using Evolutionary Computation:
<iframe width="640" height="360" src="https://www.youtube.com/embed/PPpmUq8ueiY" frameborder="0" allowfullscreen></iframe>
This video will show how MIST runs over the cloud:
<iframe width="640" height="360" src="https://www.youtube.com/embed/wpfw8POx-wI" frameborder="0" allowfullscreen></iframe>
This video will show how MIST modeled COVID19 in <a href="https://devpost.com/software/improved-disease-modeling-tools-for-populations">Pandemic Response Hackathon</a>
<iframe width="640" height="360" src="https://www.youtube.com/embed/0ElKy0Ysz3I" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
The Reference Model is one examples of use of MIST. It can be found in the following link:
https://simtk.org/projects/therefmodel
MIST version 0.92.5.0 is released to the public. It has limited capabilities. For later versions with enhanced capabilities, please contact the developer.
| |
|
Registered: 2014-08-21 20:53 |
OpenSim Moco
- OpenSim Moco is a software toolkit to solve optimal control problems with musculoskeletal models defined in OpenSim, including those with kinematic constraints. Using the direct collocation method, Moco can solve a wide range of problems, including motion tracking, motion prediction, and parameter optimization. The design of Moco focuses on ease-of-use, customizability, and extensibility. Just like OpenSim itself, Moco has interfaces in XML/command-line, Matlab, Python, Java, and C++.
<ul style="line-height: 100%;">
<li><a href="https://opensim.stanford.edu/moco">Read the <b>documentation</b></a></li>
<li><a href="https://github.com/opensim-org/opensim-moco">View the source code, report bugs, suggest features, or contribute on <b>GitHub</b></a></li>
<li><a href="https://www.biorxiv.org/content/10.1101/839381v1">Read the Moco preprint on <b>bioRxiv</b></a></li>
<li><a href="https://github.com/stanfordnmbl/mocopaper">Obtain the models, data, and code used to produce the Moco preprint</a></li>
<li><a href="https://opensim.stanford.edu/support/event_details.php?id=236&title=Webinar-OpenSim-Moco-Software-to-optimize-the-motion-and-control-of-OpenSim-models">Watch the recording of the Moco <b>webinar</b> from November, 2019</a></li>
</ul> | |
|
Registered: 2019-11-03 22:27 |
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>. | |
|
Registered: 2005-07-26 19:52 |
MSMBuilder
- MSMBuilder is an open source software package for automating the construction and analysis of Markov state models (MSMs). It is primarily written in the python programming language with C extensions for the most time consuming routines.
MSMs are a powerful means of modeling the structure and dynamics of molecular systems, like proteins. An MSM is essentially a map of the conformational space a molecule explores. Such models consist of a set of states and a matrix of transition probabilities (or, equivalently, transition rates) between each pair of states. Intuitively, the states in an MSM can be thought of as corresponding to local minima in the free energy landscape that ultimately determines a molecule’s structure and dynamics.
MSMBuilder includes tools for
- Constructing an MSM from a set of computer simulations (typically molecular dynamics simulations in standard formats like xtc, dcd, and pdb)
- Validating statistical properties of MSMs
- Mimicking various experimental protocols to allow a quantitative comparison with experiments
- Driving efficient simulations via adaptive sampling (which decides where new simulations should be run to minimize statistical uncertainty in a model)
<p style="font-size:20px">For more information, including the latest releases, see our website at</p><p style="font-size:20px; text-align:center; font-weight:600;"><a href="http://msmbuilder.org">MSMBuilder.org</a></p> | |
|
Registered: 2008-11-26 04:53 |
Neuromusculoskeletal Modeling (NMSM) Pipeline
- <div style="display:inline-block"><a href="https://nmsm.rice.edu"><img src="https://nmsm.rice.edu/img/nmsm-pipeline-social-card.jpg" style="float:left;max-width:calc(100% - 40px);"></a></div>
Full project information is available at: https://nmsm.rice.edu. Please direct any inquiries about the NMSM Pipeline to us by posting your questions on this SimTK project forum or emailing nmsm@rice.edu.
Neuromusculoskeletal Modeling (NMSM) Pipeline is a set of tools for personalizing models and designing treatments for movement impairments and other pathologies.
The NMSM Pipeline consists of two toolsets:
Model Personalization - Personalize joint, muscle-tendon, neural control, and ground contact model properties.
Treatment Optimization - Design treatments using personalized models and an optimal control methodology.
At this time, Treatment Optimization requires the use of <a href="https://www.gpops2.com/">GPOPS-II optimal control solver</a>.
The NMSM Pipeline is written in MATLAB to lower the barrier for entry and to facilitate accessibility to the core codebase. We encourage users to modify the code to meet their needs.
The core codebase and examples are available to download for use in research. At this time, we ask that you wait to publish any work that uses the NMSM Pipeline until the journal article reference for the software is available. Please get in touch with us if you have any questions.
If you need help or want to start a discussion, please use the SimTK forum for this project.
Note: This project is a living entity. Updates will be made available as the Pipeline, examples, and tutorials are developed further and improved. | |
|
Registered: 2022-07-07 14:55 |
EMG-informed Computed Muscle Control for Dynamic Simulations of Movement
- This project is an EMG-informed control plug-in that interfaces with OpenSim to provide robust estimates of muscles activation patterns. | |
Activity Percentile: 59.16 Registered: 2009-04-08 13:49 |
Tim's OpenSim Utilities
- This project site is concerned with extending the functionality of OpenSim through the use of scripting tools and plugins.
Click on the downloads link to browse the set of freely available OpenSim tools for download.
*******************************************************
Previously delivered interactive webinars demonstrating
the use of the Pseudo-Inverse Induced Acceleration
plugin for OpenSim (IndAccPI).
http://www.stanford.edu/group/opensim/support/webinars.html
******************************************************* | |
|
Registered: 2009-09-01 00:52 |
MemtestG80 and MemtestCL: Memory Testers for CUDA- and OpenCL-enabled GPUs
- MemtestG80 and MemtestCL are a software-based testers to test for "soft errors" in GPU memory or logic for NVIDIA CUDA-enabled or OpenCL-enabled (of any manufacturer) GPUs. They use a variety of proven test patterns (some custom and some based on Memtest86) to verify the correct operation of GPU memory and logic. They are useful tools to ensure that given GPUs do not produce "silent errors" which may corrupt the results of a computation without triggering an overt error.
For the latest code, please visit http://github.com/ihaque/memtestCL.
Haque IS and Pande VS. Hard Data on Soft Errors: A Large-Scale Assessment of Real-World Error Rates in GPGPU. In Proceedings of 10th IEEE/ACM International Conference on Cluster, Cloud, and Grid Computing (CCGrid 2010), pp 691-696. | |
Activity Percentile: 56.49 Registered: 2009-04-05 22:57 |
PAPER Accelerates Parallel Evaluations of ROCS
- PAPER is a program to calculate optimal molecular overlays, based on the Gaussian model of molecular shape (as used, for example, in OpenEye ROCS). It accelerates large screening experiments by evaluating multiple overlays in parallel on NVIDIA GPUs. | |
Registered: 2008-09-26 20:01 |
OpenSim plugin to extract the muscle lines of action
- The OpenSim plugin made available with this project extends the functionality of OpenSim and allows the user to extract the directionality of the muscle lines of action for a given kinematics. Also the muscle attachments can be exported if required by the user.
With this information it is generally possible to define loads representative of the muscle forces in finite element models of bone structures.
| |
|
Registered: 2012-04-22 20:49 |
Motion Analyst Software Suite
- This project is a suite of motion analysis tools that use images from common video cameras to measure 2D and 3D motions. Locations of markers in 2D space can be tracked in time using MotionAnalyst2D. When interested in 3D reconstruction, 2D analysis needs to be completer using two cameras that simultaneously capture the images. By combining the two 2D results with the camera orientation calibration data, then 3D locations for those original markers can be reconstructed using MotionAnalyst3D. | |
|
Activity Percentile: 34.73 Registered: 2011-12-01 21:24 |
81 projects in result set. Displaying 20 per page. Projects sorted by alphabetical order.
<1> <2> <3> <4> <5>