Project Tree
Now limiting view to projects in the following categories:
All Topics :: Primary Content :: Data Sets [Remove This Filter]
All Topics > Primary Content > Developer Tools |
Browse By: |
28 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. | |
|
Registered: 2012-01-24 03:21 |
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
| |
|
Activity Percentile: 94.70 Registered: 2014-03-14 20:12 |
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 |
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: 80.30 Registered: 2015-11-16 19:58 |
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: 74.62 Registered: 2012-02-04 21:49 |
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 |
Fiber Tractography for Finite-Element Modeling of Transversely Isotropic Tissues
- This project demonstrates the process for fiber tractography of complex biological tissues with transverse isotropy, such as tendon and muscle. This is important for finite element studies of these tissues, as the fiber direction must be specified in the constitutive model. This project contains code, models, and data that can be used to reproduce the results of our publication on this technique. The supplied instructional videos will enable researchers to easily and efficiently apply this method to a variety of other tissues. The software used in the fiber tractography process and demonstrated in this project is Matlab, Autodesk Inventor (free for educators), and Autodesk Simulation CFD (free for educators). Full demonstrations and process instructions can be found in the 7 videos posted at https://vimeo.com/album/3414604:
Contents:
Chapter 1: Introduction (2:35)
This video introduces the CFD fiber tractography software pipeline
<!-- This version of the embed code is no longer supported. Learn more: https://vimeo.com/s/tnm --> <object width="500" height="281"><param name="allowfullscreen" value="true" /><param name="allowscriptaccess" value="always" /><param name="movie" value="https://vimeo.com/moogaloop.swf?clip_id=129107314&force_embed=vimeo.com&fullscreen=1" /><embed src="https://vimeo.com/moogaloop.swf?clip_id=129107314&force_embed=vimeo.com&fullscreen=1" type="application/x-shockwave-flash" allowfullscreen="true" allowscriptaccess="always" width="500" height="281"></embed></object>
Chapter 2: Supplementary materials code, models and data (20:21)
This video shows the shared models, code, and data posted online at simtk.org/m3lab_cfd4fea.
Chapter 3: Finite element simulations (5:38)
This video shows finite element simulations using the fiber mapping process.
Chapter 4: Iliacus example walkthrough (21:38)
This video shows the step-by-step process for fiber mapping the iliacus muscle (a hip flexor).
Chapter 5: Bflh example walkthrough (12:09)
This video shows the step-by-step process for fiber mapping the biceps femoris longhead muscle (a hamstring).
Chapter 6: Autodesk Inventor segmentation (9:09)
This video shows how to do segmentation of medical images in Autodesk Inventor in order to simplify the solid model for the CFD and FEA software.
Chapter 7: Curved inlet surfaces (6:28)
This video shows how to create curved inlet surfaces for use in Autodesk Simulation CFD. | |
|
Activity Percentile: 35.23 Registered: 2015-05-28 18:52 |
Modeling the Intervertebral Discs as a Stiffness Matrix: a SpineBushing element
- This project features a "SpineBushing" element that can be used to model the intervertebral disc as a 6x6 stiffness matrix. This permits the study of the disc's force-motion relationship for the case where the coordinates are coupled to each other.
The guiding equation is,
F_2 = -K * Delta_Q
where F_2 is the generalized 6x1 force vector acting on the upper vertebra, K is a stiffness matrix, and Delta_Q is the generalized 6x1 displacement vector specifying the change in position from neutral between the points of attachment of the stiffness element.
By Newton's 3rd law,
F_1 = - F_2.
The SpineBushing features two *key* differences from the existing bushing element:
(1) we incorporated a full 6x6 stiffness matrix instead of the current three translational and three rotational stiffnesses.
(2) the **change** in relative motion is used and not the relative motion itself. In 1-D, you can think of this as having a spring with a resting length equal to the distance between the specified attachment points on the two bodies in the neutral posture. (The typical bushing element, on the other hand would be analogous to a spring with zero resting length.)
Further details are provided in the accompanying documents. | |
|
Activity Percentile: 3.03 Registered: 2011-10-12 05:41 |
LiFFT: Likelihood-based Fits of Footprinting Transitions
- This analysis tool will allow researchers to analyze their entire footprinting dataset, without filtering out noisy lanes and residues, or heuristic normalization, by employing a likelihood-based model fitting approach. This methodology allows for the rigorous estimation of parameters and parameter confidence intervals, to fit footprinting data to real physical models. | |
Activity Percentile: 0.00 Registered: 2012-01-26 22:35 |
Thermodynamics and Kinetics of Biomolecular Folding
- SimTK RNA_Fold project aims to understand the accurate folding pathways of RNA molecules. Free energy landscape of RNA folding will be studied for all atom model or physical based coarse graining model. Replica exchange Molecular Dynamics, simulated tempering and other sampling methods will be used to enhance sampling. Folding@Home distributed computing will be used due to its big computing power. | |
|
Activity Percentile: 0.00 Registered: 2006-08-29 18:41 |
Supplemental data and scripts for Nicholas Tatonetti's PhD Dissertation
- The data files and scripts used for the analysis presented in the dissertation. | |
Activity Percentile: 0.00 Registered: 2012-05-21 16:51 |
Creating a Tensegrity Robot
- This project is to study the applicability of utilizing this program to create a tensegrity robot and a virtual environment for the tensegrity robot. | |
|
Activity Percentile: 0.00 Registered: 2010-08-11 01:17 |
OpenSim for the Warrior Web
- Online support and resource portal for teams developing Warrior Web Technologies.
Access all of our OpenSim resources at the <br /><a href="http://www.stanford.edu/group/opensim/support/index.html"><b style="color:#900; font-size:16px;">Support Site</b></a>.
Also see the <br /><a href="http://simtk-confluence.stanford.edu:8080/display/OpenSim/Warrior+Web+Wiki"><b style="color:#900; font-size:16px;">Warrior Web Wiki</b></a>.
This project includes the following (see links at left):
1) A Team page, where you can see our team members and get in touch for support and questions.
2) A Downloads page, where you can find models, plug-ins, data, and other code and software for Warrior Web teams. Additional downloads are available on the main OpenSim Simtk project page.
3) A Documents page, where you can find handouts, slides, and links to relevant OpenSim resources and downloads.
4) A Public Forums page, a discussion forum for Warrior Web teams using OpenSim
5) Under the Advanced tab, you will find:
- A repository for uploading and sharing models and code
- A mailing list to receive OpenSim Warrior Web news and events | |
|
Registered: 2012-05-31 00:39 |
Platform for Dynamic Simulation and Control of Movement based on OpenSim&MATLAB
- Numerical simulations are playing an increasingly important role in solving complex engineering problems, and have the potential to revolutionize medical decision making and treatment design. Musculoskeletal diseases cost the United States economy an estimated $849 billion a year (equal to 7.7% of the gross domestic product) and place great demands on the healthcare system. This research area could greatly benefit from computational tools that offer greater understanding of neuromuscular biomechanics, and predictive capabilities for optimal surgical and rehabilitation treatment planning.
The MATLAB®/Simulink® package is the world’s leading mathematical computing software for engineers and scientists in industry, government, and education. Although Simulink® extends MATLAB® with a graphical environment for rapid design, control, and simulation of complex dynamic systems, this powerful package has limited resources for simulations of neuromusculoskeletal systems. On the contrary, OpenSim is a popular open-source platform for modeling, simulating, and analyzing neuromusculoskeletal systems, but it is lacks the robust design and control tools of Simulink®.
This project is an interface between OpenSim and MATLAB®/Simulink® that combines relevant strengths (e.g., neuromusculoskeletal dynamics, rapid model-based design, control systems, and numerical simulation) of each individual software package. The foundation of this interface is a MATLAB® S-function (system-function) based on an OpenSim model as a Simulink® block written in C++ and compiled as a MEX-file using the MATLAB® mex utility. | |
|
Activity Percentile: 0.00 Registered: 2012-07-26 21:40 |
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? | |
|
Activity Percentile: 0.00 Registered: 2007-04-11 01:29 |
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. | |
|
Activity Percentile: 0.00 Registered: 2014-02-01 22:32 |
Biomechanics of Golf
- Develop an integrated model of the golfer and club to simulate the biomechanics of the golf swing. Primary objectives are to gain insight into optimizing swing mechanics for distance and control, and identify appropriate physical training to improve skill level. | |
Activity Percentile: 0.00 Registered: 2011-01-08 20:38 |
Reserved for Simbios Center use
- This project is reserved for use by the Simbios center for centralized commentary on its various software offerings, consisting of SimTK (a toolkit for developers of biosimulation applications) and Simbios Applications (a collection of such applications produced by or in collaboration with Simbios). | |
Activity Percentile: 0.00 Registered: 2009-06-11 17:16 |
Computational Analysis of Kinase Selectivity using Structural Knowledge
- Here, we present a knowledge-based approach to profile kinase selectivity based on the similarity between drug binding microenvironments. To allow large-scale kinase site similarity profiling, we have created a kinome structure database consisting of 5000 inhibitor-binding pockets from 187 unique human kinase crystal structures. | |
|
Registered: 2017-04-18 20:03 |
Matt DeMers' project
- This is just a place for me to track, manage, and backup data for my ongoing projects. | |
|
Activity Percentile: 0.00 Registered: 2009-07-31 22:54 |
28 projects in result set. Displaying 20 per page. Projects sorted by alphabetical order.
<1> <2>