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92 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> | |
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Registered: 2006-03-23 18:48 |
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: 93.51 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: 91.60 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 |
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: 86.64 Registered: 2008-08-29 02:59 |
Specimen-Specific Models of the Healthy Knee
- As part of research funded by the National Institutes of Health, National Institute of Biomedical Imaging and Bioengineering (NIBIB), investigators at the University of Denver Center for Orthopaedic Biomechanics have made available a repository of experimental, image, and computational modeling data from mechanical testing of natural human knee biomechanics. It is uncommon for such a comprehensive dataset to be obtained. Therefore, we have made this repository available to assist the greater research community interested in the complexities and pathologies of knee health and mechanical function. Data are provided for 7 human knees (5 cadaveric subjects) and fall under two categories:
Image Data and Experimental & Computational Modeling Data.
Additional details about the data can be found at:
http://ritchieschool.du.edu/research/centers-institutes/orthopaedic-biomechanics/downloads/natural-knee-data/
This repository of natural knee data has been made available thanks to funding from the National Institutes of Health through National Institute of Biomedical Imaging and Bioengineering R01-EB015497. | |
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Registered: 2008-06-12 23:15 |
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 |
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: 83.97 Registered: 2011-08-06 20:22 |
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 |
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 |
Calibrated EMG-Informed Neuromusculoskeletal Modelling Toolbox (CEINMS)
- The software permits the simulation of all the transformations that take place from the onset of muscle excitation to the generation of force in 34 musculotendon units and the resulting moments about six degrees of freedom (DOFs) in the lower extremity. The selected DOFs include: hip flexion-extension, hip adduction-abduction, hip internal-external rotation, knee flexion-extension, ankle plantar-dorsi flexion, and ankle subtalar angle.
Experimentally recorded electromyography (EMG) signals and three-dimensional joint angles can be used to determine the neural drive and the instantaneous kinematics for the multiple musculotendon units being modelled. Furthermore, the CEINMS software can estimate the excitation patterns for musculotendon units from which EMGs cannot be experimentally measured and adjust the EMG linear envelopes that may be subject to measurement errors and uncertainties, while ensuring dynamical consistency in the predicted joint moments.
Finally, the CEINMS software allows automatically identification of a number of parameters that determine the way musculotendon units activate and contract, which vary non-linearly across individuals. This is done via an optimization-based calibration procedure that adjusts the internal parameters to best reflect the anatomy and physiology of an individual. | |
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Activity Percentile: 72.14 Registered: 2013-02-19 05:59 |
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: 69.08 Registered: 2015-09-05 18:12 |
Stroke gait
- This project involves the generation of subject-specific simulations of a range of post-stroke hemiparetic gait patterns, contribution of parallel optimization techniques, comparison of control algorithms, and analysis of 2d and 3d results. | |
Activity Percentile: 62.60 Registered: 2006-08-23 17:28 |
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 |
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 |
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: 59.16 Registered: 2012-05-25 17:31 |
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 |
Real-time OpenSim extension
- RTOSIM is a set of efficient and extensible C++ libraries to connect OpenSim with different devices. RTOSIM can use data provided by motion capture systems to solve OpenSim inverse kinematics and inverse dynamics on a frame-by-frame basis. Multiple threads operate concurrently to remove idle times due to communications with input and output devices, and the data flow is automatically managed by RTOSIM in order to preserve data integrity and avoid race conditions.
The inverse kinematics throughput is also enhanced by the use of multiple threads. From our tests, full-body inverse kinematics using the gait2392 can be solved up to 2000fps using 10+ cores.
RTOSIM source code is available on GitHub (see Downloads section). | |
Registered: 2016-05-24 07:56 |
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: 54.58 Registered: 2009-04-08 13:49 |
92 projects in result set. Displaying 20 per page. Projects sorted by alphabetical order.
<1> <2> <3> <4> <5>