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49 projects in result set. Displaying 20 per page. Projects sorted by alphabetical order.
<1> <2> <3>
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 |
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 |
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> | |
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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) | |
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Activity Percentile: 76.52 Registered: 2011-08-06 20:22 |
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 |
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> | |
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Registered: 2019-11-03 22:27 |
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
******************************************************* | |
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Registered: 2009-09-01 00:52 |
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: 59.85 Registered: 2009-04-08 13:49 |
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. | |
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Registered: 2022-07-07 14:55 |
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.
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Registered: 2012-04-22 20:49 |
Predictive Simulation of Standing Long Jumps
- This project is aimed at creating a predictive simulation framework for standing long jumps and studying how using a how such a framework can be used to study performance differences due to various perturbations.
In particular, we have used this framework to study how simulation can be used to aid in device design. In our publication, we first show that the framework could generate a simulation that captured salient features of a standing long jump, including kinematics and kinetics. We then used the framework to design active and passive devices to increase simulated jump performance. | |
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Registered: 2014-01-30 23:21 |
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. | |
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Activity Percentile: 37.50 Registered: 2011-12-01 21:24 |
OpenSim Utilities
- <i>This collection is no longer being maintained through this project. To find OpenSim utilities, you now have two options:
1) Visit the summary table on the OpenSim documentation pages (http://simtk-confluence.stanford.edu:8080/display/OpenSim/Tools+for+Preparing+Motion+Data)
2) Conduct a search on SimTK. Click here (https://simtk.org/search/search.php?srch=opensim&type_of_search=soft) and then narrow your search to "Scripts, Plug-Ins, and Other Utilities" by checking the box on the left.</i>
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A repository of tools written by members of the OpenSim community to support their usage of the software.
<hr> </hr><b>Please respect your fellow OpenSim Users.</b>
In using these utilities we ask that you respect the hard work of your fellow researchers by citing their work appropriately. When you go to the Download section you will be directed to individual project pages for each model which contain all of the files and documentation. Please carefully review the publications and cite the references in your future papers, presentations, grant applications, etc.
<hr> </hr><b>Have a utility to contribute?</b>
Do you have a utility which you would like to make available through this library? Providing others with access to your tools and utiities can stimulate future studies, provide a foundation for young researchers, and maximize the impact of your work. It’s easy to set up a project page to post your work. This will allow you to track who is using your utilities and be in contact with them. Please consider contributing! If you would like to have your project included on this site, please contact Jennifer Hicks, listed as one of the Project Leads.
<hr> </hr>
No guarantees about quality, correctness or support are provided by the SimTK team or OpenSim team. Use at your own risk.
<hr> </hr>
To find out more about the OpenSim project, please visit <a href="http://opensim.stanford.edu">http://opensim.stanford.edu</a> | |
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Registered: 2007-09-17 21:53 |
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
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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. | |
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Activity Percentile: 35.23 Registered: 2015-05-28 18:52 |
Extendable OpenSim-Matlab Infrastructure Using Class Oriented C++ Mex Interface
- The objective of this project is to provide an alternative interface between OpenSim and Matlab®, based on an extended C++ mex interface. Despite the fact that there is a user friendly OpenSim interface for Matlab, it lacks the ability to extend new functionalities based on the Java API (e.g. custom controller). Inspired by the relative project “Dynamic Simulation of Movement Based on OpenSim and MATLAB®/Simulink®”, where the user can easily interface OpenSim with Simulink, the proposed framework moves one step further by providing new capabilities to link custom written C++ OpenSim extensions to Matlab and to harvest both the powerful OpenSim C++ API and Matlab functionalities. The implementation is based on Matlab mex interface, which is further extended to support more complex functionalities based on the project mexplus. The latter is a C++ Matlab mex development kit that contains a couple of C++ classes and macros to make mex development easy in Matlab.
An example project is provided in the download section with instructions on how-to use. | |
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Activity Percentile: 22.73 Registered: 2015-09-28 14:09 |
Modeling kinematic and dynamic redundancy
- The coordination of the human musculoskeletal system is deeply influenced by its redundant structure, in both kinematic and dynamic terms. Noticing a lack of a relevant, thorough treatment in the literature, we formally address the issue in order to understand and quantify factors affecting the motor coordination. We employed well-established techniques from linear algebra and projection operators to extend the underlying kinematic and dynamic relations by modeling the redundancy effects in null space. We distinguish three types of operational spaces, namely task, joint and muscle space, which are directly associated with the physiological factors of the system. A method for consistently quantifying the redundancy on multiple levels in the entire space of feasible solutions is also presented. We evaluate the proposed muscle space projection on segmental level reflexes and the computation of the feasible muscle forces for arbitrary movements. The former proves to be a convenient representation for interfacing with segmental level models or implementing controllers for tendon driven robots, while the latter enables the identification of force variability and correlations between muscle groups, attributed to the system’s redundancy. Furthermore, the usefulness of the proposed framework is demonstrated in the context of estimating the bounds of the joint reaction loads, where we show that misinterpretation of the results is possible if the null space forces are ignored. This work presents a theoretical analysis of the redundancy problem, facilitating application in a broad range of fields related to motor coordination, as it provides the groundwork for null space characterization. The proposed framework rigorously accounts for the effects of kinematic and dynamic redundancy, incorporating it directly into the underlying equations using the notion of null space projection, leading to a complete description of the system.
https://github.com/mitkof6/musculoskeletal-redundancy
https://github.com/mitkof6/feasible_muscle_force_analysis | |
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Registered: 2018-05-17 10:19 |
SimTK Core Toolset (obsolete project)
- Prior to June, 2011 this project was used to distribute the Simbios-developed Simbody and Molmodel packages in the SimTK biosimulation toolkit. These are now distributed separately from the Simbody and Molmodel projects (https://simtk.org/home/simbody, https://simtk.org/home/molmodel). Please use those projects instead of this one.
The other major component of SimTK is the GPU-accelerated molecular dynamics package OpenMM, see https://simtk.org/home/openmm if you are interested.
<b>The text below refers to the pre-June, 2011 packaging and has been superseded as described above.</b>
<b><i>SimTK Core subprojects</i></b> This SimTK Core project collects together all the binaries needed for the various SimTK Core subprojects. These include Simbody, Molmodel, Simmath (including Ipopt), Simmatrix, CPodes, SimTKcommon, and Lapack. See the individual projects for descriptions.
<b><i>SimTK overview</i></b>
SimTK brings together in a robust, convenient, open source form the collection of highly-specialized technologies necessary to building successful physics-based simulations of biological structures. These include: strict adherence to an important set of abstractions and guiding principles, robust, high-performance numerical methods, support for developing and sharing physics-based models, and careful software engineering.
<b><i>Accessible High Performance Computing</i></b><br/>
We believe that a primary concern of simulation scientists is performance, that is, speed of computation. We seek to build valid, approximate models using classical physics in order to achieve reasonable run times for our computational studies, so that we can hope to learn something interesting before retirement. In the choice of SimTK technologies, we are focused on achieving the best possible performance on hardware that most researchers actually have. In today's practice, that means commodity multiprocessors and small clusters.
The difference in performance between the best methods and the do-it-yourself techniques most people use can be astounding—easily an order of magnitude or more. The growing set of SimTK Core libraries seeks to provide the best implementation of the best-known methods for widely used computations such as:
Linear algebra, numerical integration and Monte Carlo sampling, multibody (internal coordinate) dynamics, molecular force field evaluation, nonlinear root finding and optimization. All SimTK Core software is in the form of C++ APIs, is thread-safe, and quietly exploits multiple CPUs when they are present.
The resulting pre-built binaries are available for download and immediate use.
<b><i>Citation:</i></b> Any work that uses SimTK Core (including Simbody) should cite the following paper: Jeanette P. Schmidt, Scott L. Delp, Michael A. Sherman, Charles A. Taylor,Vijay S. Pande, Russ B. Altman, "The Simbios National Center: SystemsBiology in Motion", Proceedings of the IEEE, special issue on Computational System Biology. Volume 96, Issue 8:1266 - 1280. (2008) | |
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Registered: 2006-04-04 20:03 |
Stiffness Modulation of Redundant Musculoskeletal Systems
- This work presents a framework for computing the limbs' stiffness using inverse methods that account for the musculoskeletal redundancy effects. The musculoskeletal task, joint and muscle stiffness are regulated by the central nervous system towards improving stability and interaction with the environment during movement. Many pathological conditions, such as Parkinson's disease, result in increased rigidity due to elevated muscle tone in antagonist muscle pairs, therefore the stiffness is an important quantity that can provide valuable information during the analysis phase. Musculoskeletal redundancy poses significant challenges in obtaining accurate stiffness results without introducing critical modeling assumptions. Currently, model-based estimation of stiffness relies on some objective criterion to deal with muscle redundancy, which, however, cannot be assumed to hold in every context. To alleviate this source of error, our approach explores the entire space of possible solutions that satisfy the action and the physiological muscle constraints. Using the notion of null space, the proposed framework rigorously accounts for the effect of muscle redundancy in the computation of the feasible stiffness characteristics. To confirm this, comprehensive case studies on hand movement and gait are provided, where the feasible endpoint and joint stiffness is evaluated. Notably, this process enables the estimation of stiffness distribution over the range of motion and aids in further investigation of factors affecting the capacity of the system to modulate its stiffness. Such knowledge can significantly improve modeling by providing a holistic overview of dynamic quantities related to the human musculoskeletal system, despite its inherent redundancy.
https://github.com/mitkof6/musculoskeletal-stiffness | |
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Registered: 2018-11-12 13:00 |
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. | |
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Activity Percentile: 3.03 Registered: 2011-10-12 05:41 |
Full Body Gait with Knee Contact Model
- This project aims to add a knee contact model to OpenSim in order to study knee forces in detail. | |
Activity Percentile: 0.00 Registered: 2008-05-06 05:27 |
49 projects in result set. Displaying 20 per page. Projects sorted by alphabetical order.
<1> <2> <3>