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OpenSim Workshop for Pilot Awardees We held an OpenSim (http://simtk.org/home/opensim) Workshop from March 25-27, 2013 on the Stanford University campus for winners of Outstanding Researcher awards from the NCSRR Pilot Project Program (http://opensim.stanford.edu). Participants had the opportunity to work in small breakout groups with OpenSim experts on their research problems. All the teams made excellent progress toward their research goals. You can read more in the Workshop Wiki page located at http://simtk-confluence.stanford.edu:8080/display/OpenSim/Advanced+User+Workshop+March+2013. November 7, 2011 OpenSim at the American Academy for Cerebral Palsy and Developmental Medicine Annual Meeting A hands-on session entitled "Simulation of Human Movement and Gait Pathology - An Introduction to OpenSim for the Clinician" was held earlier this month at the Annual Meeting of the American Academy for Cerebral Palsy and Developmental Medicine. Twenty surgeons, physical therapists, and other clinicians learned how OpenSim can be used to help plan surgery for children with cerebral palsy. The OpenSim team encountered lots of enthusiasm and interest at the workshop, which was their first time introducing simulation to this clinical conference. Visit the workshop's website (http://www.stanford.edu/group/opensim/support/event_details.html?id=27%26title=Instructional-Course-at-AACPDM) to download slides and handouts from the workshop. October 20, 2011 Fall Issue of Biomedical Computation Review Now Available Announcing the Fall issue of the Biomedical Computation Review. Feature Stories: Error! What biomedical computating can learn from its mistakes; Dogs, Doses and Devices: The FDA's ambitious plans for computational modeling plus computing gene interactions, simulating cells in context, de novo protein design and more....Read the full issue at http://biomedicalcomputationreview.org/7/2/index.html. October 20, 2011 OpenSim 2.4 Released We are excited to announce the release of OpenSim 2.4, a robust and flexible software package for modeling and simulation of the musculoskeletal system. OpenSim 2.4 includes faster and more robust tools for Inverse Dynamics and Inverse Kinematics, new visualization tools, enhanced access for API users, and several usability improvements. In addition, we've verified that the results of Computed Muscle Control now match or exceed the quality of those achieved in OpenSim version 1.9.1. We've added documentation of Induced Acceleration Analysis, application of external loads and several examples. We encourage you to download the software and review the full list of new features on the OpenSim project's download page:https://simtk.org/project/xml/downloads.xml?group_id=91 October 20, 2011 OpenSim Video and Interactive Soccer Activity at The Leonardo Museum We've created a new video to educate people of all ages and backgrounds about the OpenSim project. The short movie describes how and why we simulate movement and demonstrates how modeling is being applied to help plan surgery for children with cerebral palsy (http://opensim.stanford.edu/work/index.html). The video is featured as part of an exhibit on understanding human movement at The Leonardo, a new art, science, and technology museum in Salt Lake City. The exhibit also has an interactive soccer ball kicking "game", where the real-life player tries to score a goal in OpenSim by adjusting the virtual player's muscle forces. If you are in Salt Lake City, we encourage you to visit the museum: http://www.theleonardo.org/. If you can't make it to Utah, you can download the example from SimTK.org: https://simtk.org/home/soccerkickmodel October 19, 2011 OpenSim at the HYPER Summer School on Neurorehabilitation Members of the OpenSim team traveled to La Alberca, Spain to give an OpenSim workshop at the HYPER Summer School on Neurorehabilitation. Jeff Reinbolt, from the University of Tennesse, and Jennifer Hicks, from Stanford, introduced 50 rehabilitation engineers to the OpenSim software package (http://opensim.stanford.edu). Students got hands-on practice using the OpenSim pipeline and a new interface with Matlab/Simulink, which is set to be released by Reinbolt in the coming months. Check out the workshop materials at http://www.stanford.edu/group/opensim/support/event_details.html?id=25&title=Workshop-at-HYPER-Summer-School-on-Neurorehabilitation. September 2, 2011 OpenMM 3.1.1 Released We are pleased to announce the release of version 3.1.1 of OpenMM. OpenMM is an extensible library that enables accelerated calculations for molecular dynamics on high-performance computer architectures, such as GPU cards. In this release, the ability to parallelize calculations across multiple GPUs has been added for the OpenCL platform. There have also been large performance improvements, especially to the AMOEBA plugin. Benchmarks for OpenMM and the AMOEBA plugin are now available at http://wiki.simtk.org/openmm/Benchmarks. Additional features include support of the direct polarization model for the AMOEBA plugin and the GB/VI force [1]. Download the latest version of OpenMM from http://simtk.org/home/openmm. [1] Labute P, The generalized Born/volume integral implicit solvent model: Estimation of the free energy of hydration using London dispersion instead of atomic surface area, J Comput Chem (2008), 29(10): 16931698. August 18, 2011 Vijay Pande receives the 2012 Barany Award We are pleased to announce that Simbios co-PI Vijay Pande has been selected to receive the Biophysical Societys Michael and Kate Barany Award for Young Investigators for 2012. July 15, 2011 OpenSim's Strong Showing at the ISB Conference The OpenSim team had a strong showing during the recent International Society of Biomechanics (ISB) Congress in Brussels. The first event was a workshop organized for over 50 participants during the ISB Technical Group on Computer Simulation (TGCS) Symposium. The new hands-on, group-oriented exercises taught participants how to work through common errors made when using OpenSim for research. Also encouraging was the large number of research talks and posters during TGCS and the general ISB meeting that used OpenSim. Other activities during ISB included a special OpenSim demo that was hosted through our NMS Physiome (http://www.nmsphysiome.eu/) collaboration and attended by over 50 researchers, many new to OpenSim (http://simtk.org/home/opensim). July 15, 2011 SimTK Workshops in the Land of the Midnight Sun Simbios staff Peter Eastman and Michael Sherman traveled to Sweden last month to host workshops on our OpenMM (http://simtk.org/home/openmm), Simbody (http://simtk.org/home/simbody), and Molmodel (http://simtk.org/home/molmodel) software as part of the Stanford-Sweden Multiresolution Molecular Simulation Workshop at Uppsala University. May 24, 2011 OpenMM/MSMBuilder Workshop Held at Stanford Simbios held a molecular dynamics workshop on May 23-24, 2011 at Stanford University. Participants learned to use OpenMM, a software library that enables molecular dynamics (MD) simulations to be accelerated on GPUs, and MSMBuilder (http://simtk.org/home/msmbuilder), a tool for automatically generating Markov State Models for MD trajectory analysis. New features highlighted during the event included the OpenMM Python API and the AMOEBA plug-in. Slides and videos from the workshop will be available from the workshop website (http://simtk.org/home/mdseriesmay2011). April 15, 2011 Spring Issue of Biomedical Computation Review Now Available Announcing the Spring 2011 issue of the Biomedical Computation Review. Feature Story: Profiles in Computer Science Courage - Reflections on the rewards of plunging into biomedicine. Also: Computational Drug Design - Old drugs learn new tricks, Biosurveillance, and more ... April 15, 2011 OpenSim Advanced Users and Developers Workshop Held From March 16-18, 2011 over 20 researchers, from students to professors, participated in an OpenSim workshop for advanced users and developers on the Stanford University campus. The participants worked closely with the OpenSim team at Stanford to make progress on their research projects. Project topics ranged from studying control of postural stability to implementing new contact models. See photos and learn more about OpenSim workshops at http://opensim.stanford.edu/support/workshops.html. April 12, 2011 Release of OpenSim 2.2.1 OpenSim version 2.2.1 is now available for download. The OpenSim software enables computer modeling and dynamic simulations of movement. The new version contains enhancements to the user interface to show the XML representation of available objects, the ability to set bounds on activations of muscles and various actuators when solving static optimization, and updates to the Joint Reaction analysis. The release includes example setup files to run Static Optimization and Joint Reaction analyses. The release is available on the downloads page of the OpenSim project website: https://simtk.org/home/opensim. April 4, 2011 OpenMM 3.0 Released We are pleased to announce this major update to the OpenMM platform. OpenMM is an extensible library that enables accelerated calculations for molecular dynamics on high-performance computer architectures, such as GPU cards. New features include support for the AMOEBA polarizable force field, energy minimization, performance improvements, and much more. Visit http://simtk.org/home/openmm for more information and to download. November 16, 2010 $10.6 Million Grant Awarded to Simbios The National Institutes of Health has awarded $10.6 million to renew the Simbios grant. During this next period, Simbios will focus on using simulations to advance drug discovery and neuroprosthetics research and help develop Domain Specific Languages to accelerate biosimulation software development for high-performance computers. Read more about Simbios' plans in the full press release at http://simbios.stanford.edu/PressReleases/2010nov_grantrenewal.htm. October 1, 2010 Openings for Distinguished Postdoctoral Fellows Simbios has just begun its search for several new Distinguished Postdoctoral Fellows. For more details, see our job announcement at http://simbios.stanford.edu/Jobs/PostDocAd2010.pdf. September 16, 2010 OpenMM Zephyr 2.0 Released We're excited to announce the release of OpenMM Zephyr 2.0, based on the most recent release of OpenMM. OpenMM Zephyr is a freely available molecular simulation application with an easy-to-use graphical user interface and GPU-acceleration capabilities. In this new version, you are able to run explicit solvent simulations from the graphical user interface. In addition to NVIDIA GPUs, OpenMM Zephyr now also supports OpenCL on all platforms, including ATI GPU boards. You can download the latest version from http://simtk.org/home/zephyr. August 26, 2010 SimTK Core 2.1 Released We are pleased to announce release 2.1 of the SimTK Core, now available for download at https://simtk.org/home/simtkcore. SimTK Core is an open-source toolkit providing high-performance numerical methods for biosimulations. This release increases the robustness and usability of SimTK Core, incorporating numerous improvements in reliability, functionality, performance, and documentation. It also provides built-in support for high-speed inverse kinematics (motion tracking) via the newly incorporated Assembler solver (available through the Simbody component) and includes several experimental features that may be adopted in a future release... August 20, 2010 Simbios Presentation at RosettaCon Simbios staff member Peter Eastman presented his invited talk "Accelerating Rosetta with OpenMM" at the recent RosettaCon in Washington (August 3-6). OpenMM (http://simtk.org/home/openmm) is an open-source library that enables hardware acceleration of molecular modeling codes (e.g., on graphics processing units, GPUs), and the Rosetta software suite, developed by David Baker's lab, is used to predict and design protein structures. Eastman's presentation generated excitement among the hundred or so individuals in attendance, as running an accelerated version of Rosetta on GPUs could open new doors in research. July 15, 2010 OpenMM 2.0 Enables Molecular Dynamics Acceleration on ATI and NVIDIA GPUs Simbios is excited to announce the release of OpenMM 2.0, a major update of this library for accelerating molecular dynamics. This version supports accelerated calculations on NVIDIA GPU cards (using either CUDA or OpenCL), as well as ATI GPU cards (using OpenCL). It also includes pressure coupling, more custom force types, and significant performance increases. You can download OpenMM from http://simtk.org/home/openmm. OpenMM 2.0 has been made available to GROMACS users (via OpenMM-Accelerated GROMACS) and to AMBER users (via an AMBER/Sander-compatible interface to OpenMM, available at http://simtk.org/home/sander_openmm). July 15, 2010 OpenSim Jamboree Brings Together Researchers from Around the World The OpenSim Developer Jamboree, held from July 12-14, was an intense working session that brought together researchers from 14 institutions around the world. The OpenSim software enables computer modeling and dynamic simulations of movement. During these three days, participants worked with the newest version of OpenSim and received help from the OpenSim team on individual research projects. Exciting progress was made on biomechanical research questions and useful plugins for the OpenSim community. In addition, participants were introduced to a Matlab/Simulink interface to OpenSim, developed by Prof. Reinbolt as part of a Simbios seed grant. OpenSim is available at http://simtk.org/home/opensim. July 12, 2010 EU Collaborators Announce PhysiomeSpace: Share Biomedical Data Freely and Easily News from our EU Neuro-Musculo-Skeletal Physiome collaborators: B3C announces the release of an interactive digital library service, called PhysiomeSpace, designed to manage and share a large collection of heterogeneous biomedical data, such as medical imaging, motion capture, biomedical instrumentation signals, finite element models, etc... July 12, 2010 EU Collaborators Announce Availability of a Complete 3D Human Skeleton Model on PhysiomeSpace News from our EU Neuro-Musculo-Skeletal Physiome collaborators: Super Computing Solutions (SCS) and the Computational Bioengineering Lab (BIC) at the Istituto Ortopedico Rizzoli in Bologna (Italy) are happy to announce the release of the first dataset that composes the Living Human Digital Library (LHDL) multiscale musculoskeletal data collection. The data represent the three-dimensional skeletal anatomy from the cadaver of a 78-year-old woman with normal morphology... June 17, 2010 Summer Issue of Biomedical Computation Review Now Available Announcing the Summer 2010 issue of the Biomedical Computation Review (http://www.biomedicalcomputationreview.org). Features: (1) The Physiome: A Mission Imperative; (2) The Epigenome: A New View Into the Book of Life April 22, 2010 Simtk.org has over 10,000 members As of today April 22, 2010, Simtk.org, Simbios' software and data dissemination site has over 10,000 members. Most of the members join to download software. Software offerings include applications in Neuromuscular Biomechanics, RNA and Protein Folding and Cardiovascular Dynamics and a simulation toolkit used at all scales. March 30, 2010 Simbios and the European VPHOP announce collaboration: NMS Physiome kicks off Neuro-Musculo-Skeletal Physiome, or NMS Physiome for short, officially started on January 27th, 2010. This is a collaborative project between VHPOP and Simbios. VPHOP (http://www.vphop.eu) is a Collaborative Integrated Project that is developing simulation-based technology to predict the risk of bone fracture in osteoporosis patients. VPHOP and Simbios are two of the largest research projects worldwide developing technology for personalised, predictive, and integrative musculoskeletal medicine. These two projects are targeting the same strategic objective and developing highly complementary technologies. This unique condition creates a compelling opportunity for international collaboration, which would dramatically increase the international impact of the work being done by both the VPHOP and the Simbios project. Please also see the announcement at http://www.biomedtown.org/biomed_town/vphop/reception/news/nms. (NMS Physiome News) March 29, 2010 Spring Issue of Biomedical Computation Review Now Available Announcing the Spring 2010 issue of the Biomedical Computation Review (http://www.biomedicalcomputationreview.org/). Features: (1) More Than Fate: Computation Addresses Hot Topics in Stem Cell Research; (2) The Cell In 2010: A Modeling Odyssey March 29, 2010 Greg Bowman awarded the 2010 Kuhn Paradigm Shift Award The Thomas Kuhn Paradigm Shift Award is given by the American Chemical Society (ACS) in honor of researchers who have changed the way we look at scientific problems. Greg Bowman was one of five researchers in the world competing for the award at the March 2010 ACS meeting. He was awarded the Thomas Kuhn Paradigm Shift Award for his talk on two paradigm shifts. 1) Moving from an anecdotal approach to simulation to a statistical approach using Markov State Models and Adaptive Sampling. 2) Attaining quantitative agreement between theory and experiment using this approach, and generating testable hypothesis about the nature of folding and the unfolded state. The MSM Builder software was instrumental for both of these scientific breakthroughs, which are also used by Folding@home (http://folding.stanford.edu/) to simulate protein folding. February 18, 2010 OpenSim 2.0.1 Now Available OpenSim 2.0.1 (http://simtk.org/home/opensim) was released on February 9th. The OpenSim software is freely available to the biomechanics research community and enables computer modeling and simulation of human and animal movement. This version includes... February 18, 2010 OpenMM 1.1 Released OpenMM 1.1 (http://simtk.org/home/openmm) was released on February 12th. OpenMM is an extensible library that enables accelerated calculations for molecular dynamics on high-performance computer architectures, such as GPU cards. This release adds custom forces for angles and torsions. It also has enhancements to the OpenCL platform and includes several bug fixes. February 10, 2010 First Stage of Grand Challenge Competition to Predict In Vivo Knee Loads Completed The abstract submission process for the first known grand challenge competition within the musculoskeletal modeling community has just closed. The grand challenge, which used simtk.org as its web portal, provided a comprehensive data set (available via http://simtk.org/home/kneeloads) to which researchers were challenged to apply computational methods of their choice to predict the internal knee loads. B.J. Fregly, Darryl D'Lima and Thor Besier organized the competition, which will conclude with a special session at this year's ASME Summer Bioengineering Conference in Naples, Florida... January 20, 2010 OpenMM 1.0 Released Today We are excited to announce the release of OpenMM 1.0. OpenMM (http://simtk.org/home/openmm) is a freely available, extensible library that enables accelerated calculations for molecular dynamics on high-performance computer architectures, such as GPU cards. This release marks a major milestone... January 13, 2010 Simbios Organizes "Multi-resolution Modeling of Biological Macromolecules" Session at PSB 2010 Simbios postdocs Xuhui Huang and Samuel Flores, along with 3 other co-chairs, organized and ran a special session on "Multi-resolution Modeling of Biological Macromolecules" at last week's Pacific Symposium on Biocomputing 2010 in Hawaii... January 13, 2010 Winter Issue of Biomedical Computation Review Now Available Announcing the Winter 2009/2010 issue of the Biomedical Computation Review (http://www.biomedicalcomputationreview.org/). Features: (1) Structural Genomics: Exploring the 3D Protein Landscape; (2) Clinical Decision Support: Providing Quality Healthcare with Help from a Computer January 7, 2010 SimTK 2.0 Now Available Simbios is pleased to announce the release of SimTK 2.0. SimTK (available from http://simtk.org/home/simtkcore) is an open-source biosimulation toolkit providing access to high performance computational tools, such as multibody dynamics (Simbody), LAPACK, and numerical integrators. This latest version adds a host of new features including: generalized contact modeling and reversible mobilizers for Simbody... January 4, 2010 Collaborative Project with EU's VPHOP Launched January 1st marked the beginning of the Simbios collaborative grant with the EU's Osteoporotic Virtual Physiological Human project (VPHOP). The three-year project is devoted to the development of tools for the NeuroMusculoSkeletal Physiome... December 31, 2009 OpenSim 2.0 Released Simbios is excited to announce the release of OpenSim 2.0 (http://simtk.org/home/opensim). An open-source application for simulating movement, OpenSim now provides a well-designed application programming interface (API) that allows researchers access to core OpenSim functionality, enabling them to extend and integrate algorithms within the OpenSim framework. Version 2.0 also features new functionality, such as contact models for modeling the behavior of two bodies, such as bones, when they come together, and a faster, more robust integrator. November 23, 2009 Simtk.org Membership Reaches 8000 The Simtk.org (http://simtk.org) website membership reached the 8000 mark today. Simbios launched Simtk.org in 2005 as a means to share and collaborate on the development of software and data for physics-based simulation of biological structures. Since then, Simtk.org has seen tremendous growth, at least doubling its member growth rate each year. Today, it hosts nearly 380 projects. November 11, 2009 Simbios Participates in 10th Annual BCATS Simbios post-doctoral fellows Samuel Flores and Kai Kohlhoff participated in the 10th annual symposium on Biomedical Computation at Stanford (BCATS) this past Saturday, November 7th. This year, the student-run one-day symposium on computational biology and medicine featured over 60 posters and 13 presentations from students and post-docs around the San Francisco Bay Area. Kohlhoff showcased his work on "Using graphics processors for clustering of biological data sets" and Flores shared his work on "Modeling RNA structure from experimental results" using his freely available tool RNABuilder (http://simtk.org/home/rnatoolbox). Simbios was a sponsor of the event. |
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