- July 12, 2013
OpenSim/NCSRR Pilot Project Program Call for Proposals
The National Center for Simulation in Rehabilitation Research (NCSRR) and OpenSim project at Stanford seek proposals for our pilot project program. The program awards seed grants to innovative and meritorious projects that will accelerate the use of simulation in rehabilitation research. Our intent is to engage rehabilitation research experts to demonstrate the use of biomechanical simulations in novel areas and to help enhance the OpenSim software for rehabilitation science. Pilot project awardees may request funding (up to $25,000) for their research.
- July 12, 2013
Registration Now Open for OpenSim Advanced User Workshop
An OpenSim Workshop will be held August 28-30, 2013 on the Stanford University campus for advanced users to work on their OpenSim projects. This workshop is intended for advanced OpenSim users and developers who want to work directly with the OpenSim staff on specific research projects.
- July 12, 2013
Webinar: All Models are NOT wrong...
All Models Are NOT Wrong (Contrary to Popular Belief), will be presented by Dr. Wendy Murray of Northwestern University, on Tuesday, July 16, 2013 at 9:30 a.m. PDT. In this webinar, Dr. Murray will highlight two recent studies in which biomechanical simulation was used to gain important insights that would have been difficult (or impossible) to derive from the existing experimental data alone. In doing so, she hopes to highlight the value of simulation studies and advocate for well-designed, simulation approaches to advance our understanding of human movement. Participation is free, but you must register in advance.
- July 12, 2013
Registration Open for OpenMM Jamboree
Join OpenMM developers and other OpenMM users on August 22-23, 2103 at Stanford University for 2 intense days of work on your OpenMM project. The OpenMM Jamboree is a unique event where participants have the opportunity to engage deeply with OpenMM experts and developers on their particular OpenMM project for two solid days. The stimulating environment and access to OpenMM experts enable you to accelerate the progress on your project.
- March 29, 2013
OpenSim Workshop for Pilot Awardees
We held an OpenSim Workshop from March 25-27, 2013 on the Stanford University campus for winners of Outstanding Researcher awards from the NCSRR Pilot Project Program. 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 on the Workshop Wiki page.
- 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 at the 65th Annual Meeting of the American Academy for Cerebral Palsy and Developmental Medicine, in Las Vegas, Nevada, October 12-15, 2011. 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 to download slides and handouts from the workshop.
- 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
Fall 2011 Issue of Biomedical Computation Review Now Available
Announcing the Fall 2011 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.
- 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. 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. 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 Tennessee, and Jennifer Hicks, from Stanford, introduced 50 rehabilitation engineers to the OpenSim software package. 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 here.
- 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 . Download the latest version of OpenMM from http://simtk.org/home/openmm.
 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
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, Simbody, and Molmodel software as part of the Stanford-Sweden Multiresolution Molecular Simulation Workshop at Uppsala University.
- 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, Belgium. 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 collaboration and attended by over 50 researchers, many new to OpenSim.
- 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, 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 are available from the workshop website at http://simtk.org/home/mdseriesmay2011.
- 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 15, 2011
Spring 2011 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 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.
- 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. OpenMM Zephr 2.0 can be downloaded 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 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
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. Jeff Reinbolt as part of a Simbios seed grant. OpenSim is available at http://simtk.org/home/opensim.
- 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. OpenMM can be downloaded 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 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.
- 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.
- June 17, 2010
Summer 2010 Issue of Biomedical Computation Review Now Available
Announcing the Summer 2010 issue of the Biomedical Computation Review. Featured articles: (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 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 biomedTown.
- 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, and 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 to simulate protein folding.
- March 29, 2010
Spring 2010 Issue of Biomedical Computation Review Now Available
Announcing the Spring 2010 issue of the Biomedical Computation Review. Feature Articles: (1) More Than Fate: Computation Addresses Hot Topics in Stem Cell Research; (2) The Cell In 2010: A Modeling Odyssey.
- February 18, 2010
OpenMM 1.1 Released
OpenMM 1.1 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 18, 2010
OpenSim 2.0.1 Now Available
OpenSim 2.0.1 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.
- 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 2010 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 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
Winter 2009/2010 Issue of Biomedical Computation Review Now Available
Announcing the Winter 2009/2010 issue of the Biomedical Computation Review. Feature Articles: (1) Structural Genomics: Exploring the 3D Protein Landscape; (2) Clinical Decision Support: Providing Quality Healthcare with Help from a Computer.
- 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 7, 2010
SimTK 2.0 Now Available
Simbios is pleased to announce the release of SimTK 2.0. SimTK 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. 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 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. Simbios was a sponsor of the event.
- November 5, 2009
OpenMM 1.0 Beta Just Released
Simbios is excited to announce the release of OpenMM 1.0 Beta. OpenMM is an extensible library that enables accelerated calculations for molecular dynamics on high-performance computer architectures, such as GPU cards. This release enables users to include Particle Mesh Ewald and custom non-bonded interactions in their simulations. It also provides preliminary support for the new cross-platform, parallel programming standard OpenCL. OpenMM is freely downloadable from http://simtk.org/home/openmm.
- November 2, 2009
First OpenSim Developers Workshop Held
The OpenSim team hosted a successful first Developers Workshop from October 28-30, 2009 at Stanford University. The workshop introduced participants to OpenSim as a software development tool, describing its software architecture and specific functions of the OpenSim components. During the workshop, participants were able to accelerate work on their own research problems, receiving one-on-one assistance from OpenSim team members as needed, and had the opportunity to work with the new OpenSim API, to be released as part of OpenSim 2.0.
- October 7,2009
Simbios Participates in the NIH Protein Folding Machinery 4th Annual Meeting
Simbios postdoctoral fellow Martin Stumpe and research associate Xuhui Huang gave invited talks at the NIH Protein Folding Machinery 4th Annual Meeting on September 29-30, 2009 in Woodside, California. The meeting brought together about 80 researchers working on chaperonins with interdisciplinary approaches ranging from in vivo and wet lab experiments to simulation and theory, and helped to further a common roadmap for future research in the NIH Nanomedicine Center for Protein Folding Machinery.
- October 5, 2009
Fall 2009 Issue of Biomedical Computation Review Now Available
Announcing the Fall 2009 issue of the Biomedical Computation Review. This special issue is devoted to the publishers of the magazine, Simbios. Along with our regular NewsBytes, this issue features the article Simbios: Bringing Biomedical Simulation to Your Fingertips.
- September 28, 2009
New Version of OpenMM Zephyr Now Available
With version 0.9.2, OpenMM Zephyr makes it even easier to run molecular dynamics simulations. OpenMM Zephyr is a freely available molecular simulation application with an easy-to-use graphical user interface and GPU-acceleration capabilities on both NVIDIA and ATI GPUs. This latest version of OpenMM Zephyr has automated many of the steps for converting PDB molecule files into the format required for the simulations. OpenMM Zephyr runs on Windows, Mac OSX, and Linux (32-bit, and with this release, also 64-bit). It can be freely downloaded from http://simtk.org/home/zephyr.
- September 3, 2009
OpenSim 1.9.1 Just Released
OpenSim version 1.9.1 is now available for download. The OpenSim software (https://simtk.org/home/opensim) is freely available to the biomechanics research community and enables computer modeling and simulation of human and animal movement. It has been downloaded by over 3000 users to-date. This new version of OpenSim enables users to preview motion capture data. It also adds a new analysis to compute joint reactions and includes many other enhancements.
- August 31, 2009
Preview Release 4 of OpenMM
Simbios is pleased to announce Preview Release 4 of OpenMM, an open-source library that enables molecular dynamics (MD) simulations to be accelerated on high performance computer architectures, such as GPUs. This release adds support for energy computations on GPUs, Ewald summation, a complete set of C and Fortran wrappers and several other enhancements. Download the latest version of OpenMM from http://simtk.org/home/openmm.
- August 18, 2009
OpenSim Advanced User Workshop Held
An OpenSim advanced user workshop was held on Aug. 12-14th. Fifteen users from 14 institutions around the world came to Stanford campus for the event. They brought their own projects and datasets to work on, and with the help of the OpenSim team, all were able to make progress on their research during the 3 days. A pre-release version of OpenSim 1.9 that contains a mocap data previewer and reaction forces computation was used in the workshop. Materials from the workshop are available here.
- July 9, 2009
Well-attended OpenSim Workshop Held at International Society of Biomechanics Meeting
The OpenSim team held an introductory workshop to OpenSim at the XXII Congress of the International Society of Biomechanics Meeting in Cape Town, South Africa on July 5, 2009. Over 120 people attended the session, generating interest in OpenSim and the more advanced workshops being offered later this year.
- July 9, 2009
Molecular Dynamics Workshop Series Showcases Three Simbios Tools
Simbios held a molecular dynamics (MD) workshop series at Stanford University from June 24-26, 2009. Each day of the workshop featured a different Simbios tool, geared at a different level of MD user.
- July 7, 2009
First 3D RNA Modeling Workshop Held
Simbios hosted its first 3D RNA Modeling workshop on June 19th at Stanford University. Three different Simbios tools useful in the 3D RNA modeling process were presented.
- June 24, 2009
Summer 2009 Issue of Biomedical Computation Review Now Available
Announcing the Summer 2009 issue of the Biomedical Computation Review. Feature Articles: (1) From SNPs to Prescriptions: Can Genes Predict Drug Response?; (2) Evolution and HIV: Using Computational Phylogenetics to Close In On a Killer
- June 24, 2009
New Release of OpenMM Zephyr Supports Mac OSX
OpenMM Zephyr 0.8.3 is now available. OpenMM Zephyr is a freely available molecular simulation application with an easy-to-use graphical user interface. It is built on top of the visualization tool VMD and a special version of the molecular dynamics code GROMACS. This version of GROMACS uses the OpenMM API for GPU-accelerated molecular simulations. The new release is able to run on Mac OSX and further simplifies the installation process. Go to http://simtk.org/home/zephyr to see a list of other features that were added and to download.
- June 24, 2009
Simbios Organizes 3D RNA Modeling Panel at RNA Society Annual Meeting
At the recent RNA Society Annual Meeting in Madison, Wisconsin, Simbios organized a well-attended panel discussion on RNA 3D Modeling. During the session, the panelists each introduced a software tool for modeling the 3D structure of RNA, followed at the end by a discussion of the capabilities and limitations of the tools. Feedback from attendees indicated that they found the session extremely helpful. Panelists included Samuel Flores (RNABuilder), Magdalena Jonikas (NAST/C2A), Francois Major (MC-Pipeline), John SantaLucia (RNA-123), and Eric Westhof (ASSEMBLE). Alain Laederach was the moderator.
- April 15, 2009
Spring Issue of Biomedical Computation Review Now Available
Announcing the Spring 2009 issue of the Biomedical Computation Review
- Reverse Engineering the Brain
- Bringing the Fruits of Computation to Bear on Human Health: It's a Tough Job but the NIH Has to Do It
- April 6, 2009
Invited Talk Given at NCSA "Path to Petascale" Workshop
Simbios staff member Peter Eastman gave an invited talk at the "Path to Petascale: Adapting GEO/CHEM/ASTRO Applications for Accelerators and Accelerator Clusters" workshop held at the University of Illinois, Urbana-Champaign from April 1-3, 2009. The event, sponsored by the National Science Foundation and the National Center for Supercomputing Applications, featured domain-specific breakout sessions, including one in computational chemistry chaired by Todd Martinez with approximately 40 registrants. Eastman's presentation on Simbios' OpenMM library, which enables molecular dynamics simulations to run on GPUs, was part of that breakout session.
- April 3, 2009
Invited Talk Given at USA-Mexico Protein Folding Workshop
Simbios research associate Xuhui Huang gave an invited presentation on OpenMM at the USA-Mexico Workshop in Biological Chemistry: Multidisciplinary Approaches to Protein Folding, held in Mexico City from March 25-27, 2009. The workshop provided an international forum for a multidisciplinary discussion of the protein folding problem, bringing together more than 70 researchers from the U.S., Mexico and Argentina.
- April 2, 2009
RSS Feed and Google Calendar of Events Now Available for Keeping Informed about Simbios
Keep up with Simbios' latest news and event announcements. Subscribe to our RSS feed or add our Google calendar of events to your calendar (also available in iCalendar format). This calendar is part of a larger calendar of events for all 7 National Centers of Biomedical Computing available at http://ncbcs.org/cal.html.
- March 16, 2009
OpenSim Workshop at the Gait and Clinical Movement Analysis Society Annual Meeting
The OpenSim team gave an introductory OpenSim workshop at the Gait and Clinical Movement Analysis Society's annual meeting in Denver, Colorado on March 10, 2009. It was attended by approximately 80 individuals and was an excellent opportunity to introduce OpenSim to a clinical audience (over half the attendees were clinical - surgeons, physical therapists, etc.).
- March 12, 2009
Simbios Faculty/Staff Give Invited Talks at OpenEye's CUP X Conference
Vijay Pande and Michael Sherman gave invited talks at the 10th anniversary CUP Conference, sponsored by OpenEye in Santa Fe, New Mexico earlier this week (March 8-11, 2009). Several members of Dr. Pande's lab also presented their work at the conference. The conference combined the user group meeting for OpenEye software with scientific presentations on computational drug discovery, including a keynote speech by Barry Honig. Attended by some of the top researchers in molecular electrostatics and researchers and active practitioners of computational drug design, the CUP Conference provided a stimulating environment for exploring new ideas.
- March 12, 2009
OpenSim Presentation to the IMAG/MSM Consortium
Scott Delp gave a presentation on OpenSim to the IMAG/MSM Consortium on March 3, 2009. The talk, titled "OpenSim - an Open-Source Application for Musculoskeletal Modeling and Movement Simulations," generated interest in OpenSim, both as a simulation tool for movement and as an open-source application that coordinates contributions from others. Slides from the talk are available here.
- February 17, 2009
First OpenMM Workshop/MD Symposium Held at Stanford
Simbios held its first workshop on OpenMM on February 12-13, 2009 at Stanford University. Participants learned to use OpenMM, a software library that enables molecular dynamics (MD) simulations to be accelerated on GPUs, and OpenMM Zephyr, an easy-to-use application built on top of OpenMM, GROMACS (a widely used MD package), and VMD (a popular molecular visualization tool). Many of the participants expressed excitement about what OpenMM and Zephyr might enable them to do. The workshop was filled within a week after registration opened. Another workshop is planned for later this year. Slides and videos from the workshop are available from the OpenMM project (click on Documents).
- February 9, 2009
Simbios High School Intern Semi-Finalist in National Science Competitions
We're proud to announce that Dominique Dabija, a senior at the Harker School in San Jose, CA and an intern at Simbios last summer, was named a semi-finalist in both the Intel Science Talent Search and the
Siemens Competition in Math, Science, and Technology. These national contests are highly competitive and prestigious. Dominique's entry was based on her research project at Simbios: Computational Methods for Identifying Functionally Important Residues Involved in Allosteric Communication Pathways.
- February 9, 2009
New Release of OpenMM Available
We are excited to announce the release of OpenMM, software that enables molecular dynamics (MD) simulations to be accelerated on high performance computer architectures, such as GPUs. This release includes a version of the MD package GROMACS that uses OpenMM and can run on GPUs, achieving speed ups of over 100 times in some cases. A related publication was just posted online in the Journal of Computational Chemistry. The full press release can be read here. Download
- January 22, 2009
OpenSim 1.8 Released
We are pleased to announce the release of OpenSim 1.8. OpenSim is an open-source software system for developing models of musculoskeletal structures and creating dynamic simulations
of movement. This release makes it possible to build and load in plug-ins. Other features include a simplified model file format, a new marker editor, the ability to do live plotting of residuals...You can download
OpenSim from http://simtk.org/home/opensim.
- January 22, 2009
Praise and Appreciation for Last Week's OpenSim Developers' Jamboree
The 2nd OpenSim Developers' Jamboree was held at Stanford University from January 14-16, 2009. As with the first jamboree, the
workshop participants were enthusiastic about the experience, expressing thanks to the OpenSim team and displaying excitement about the progress
they had made during the workshop. Registration was limited to fifteen participants, and those spots were filled within two days
of the jamboree announcement. The next OpenSim Jamboree is planned for Summer 2009.
- December 19, 2008
Winter Issue of Biomedical Computation Review Now Available
Announcing the Winter 2008/2009 issue of the Biomedical Computation Review
- NCBC Update: Shedding New Light on Biological Complexity
- Tool Dissemination - Doing it Right
- November 18, 2008
Simtk.org Now Supports Publication Projects
You can now link the software and data you share on Simtk.org to a given publication by creating a publication project. These publication projects highlight the publication
and are intended to facilitate replication of the published results, which can be extremely difficult to do in biocomputations due to
limited access to working, documented software, and/or key data sets and models. Here is just one example of a
publication project: Predicting allosteric communication in myosin.
- November 17, 2008
Simbios Exhibit at Supercomputing 2008
Simbios is highlighting its OpenMM project at the Stanford University exhibit booth at Supercomputing 2008 in Austin, Texas,
this week. The Simbios video being shown there demonstrates the significant speed-up of molecular dynamics (MD) simulations that is possible using OpenMM,
which enables MD code to run on GPUs with minimal extra coding.
- November 14, 2008
Simbios Participates in the First Stanford Open Source Lab (un)Conference
Simbios presented its efforts to encourage biocomputational researchers to share their software and data at the first Stanford Open Source Lab
Highlights of the talk included an overview of Simtk.org, Simbios software such as
OpenMM and OpenSim and biositemaps, a joint effort by the seven
National Centers for Biomedical Computing to help people find
biocomputational tools. Slides from the presentation can be found here.
- October 27, 2008
Simbios Research Highlighted at BCATS Conference
The 9th annual Biomedical Computation at Stanford conference (BCATS) took place on October 25, 2008. Several hundred people registered for this student-run
event where local students and post-docs share their latest work in computational biology and medicine. This year Simbios had 6 poster presentations
there (out of 57) and Mitul Saha, a Simbios post-doc, was selected to give one of 10 student talks. Jeff Reinbolt, another Simbios post-doc, and Melanie
Fox received the "Best Poster Award" for their poster on "Mechanism of Improved Knee Flexion after Rectus Femoris Transfer Surgery."
- October 1, 2008
Fall Issue of Biomedical Computation Review Now Available
Announcing the Fall 2008 issue of the Biomedical Computation Review
- The Golden Age of Public Databases: Speeding Biomedical Discovery
- Simulated Metabolism - A First Step Towards Simulated Cells
- September 29, 2008
Well-Received SimTK Core Workshop Held Last Week
We held a successful, productive workshop for SimTK 1.5 at Stanford on September 25-26, 2008. It was attended by individuals from both industry and academic,
with interests in musculoskeletal as well as molecular applications. The workshop slides and video are available via the Documents link from
- September 9, 2008
OpenMM Preview Release Now Available
We're excited to announce that the OpenMM preview release is now available for download. OpenMM
is an API written in C++ for executing molecular dynamics simulations on high performance computer architectures, such as GPUs or computer clusters
communicating over a network. It will make it easier for molecular dynamics code to benefit from hardware acceleration, such as with GPUs. This release
provides reference code only (no GPU code is included yet). It is intended to give people a first look at the API and to solicit feedback.
Gromacs code code using this API will be released on December 1, 2008.
- September 4, 2008
OpenSim Simulation Appears on Computing Life Website
A walking simulation created in OpenSim is featured on the Computing Life website. Computing Life is a
resource developed by the National Institutes of Health to show how computers can advance our understanding of biology and human health. (The article can be directly accessed from here.)
- September 4, 2008
OpenSim Featured on the Stanford Website
In recognition of OpenSim's one-year anniversary, the Stanford School of Engineering website is featuring OpenSim.
Read about how much OpenSim and its community has grown since it was first released in August 2007. (The full article can be directly accessed from here.)
- August 27, 2008
First OpenSim Developers' Jamboree Starts Today
The OpenSim team is hosting its first ever developers' jamboree from August 27-29, 2008 at Stanford University. 24 participants are attending, representing universities and companies from around the world (9 of the 24 are from outside the United States). This workshop is aimed at the expert user and provides them the opportunity to work on their own projects with face-to-face assistance from the OpenSim developers.
- August 15, 2008
National Centers for Biomedical Computing (NCBC)
All-Hands Meeting Takes Place at the NIH
Simbios and the six other NCBCs met at the NIH on August 13-14, 2008 to report on and demonstrate their latest research and software. Representatives from the centers and from NIH also discussed cross-center projects that will impact the field of biomedical computing. Details about the meeting can be found here.
- August 15, 2008
Dariya Glazer's Work Receives "Outstanding Poster Award" at ISMB
Congratulations to Dariya Glazer! Her poster, titled "Clustering across Space and Time," was awarded the Outstanding Poster Award at the recent Intelligent Systems for Molecular Biology (ISMB)
conference in Toronto. Dariya is a graduate student in genetics at Stanford, whose work is partially funded by Simbios. Her research demonstrated that combining molecular
dynamics simulations with structure-based function prediction algorithms markedly improved the performance of these algorithms.
- August 8, 2008
Release of SimTKCore 1.5
SimTKCore 1.5 was released today. This new release contains significant improvement in performance, including utility classes for multithreading calculations, as well as new capabilities, including:
A workshop for SimTKCore 1.5 is being held on September 25-26. Registration is free but required and spaces are limited.
- The ability to fit splines to data
- An API for creating new MobilizedBody types
- The ability to calculate mobilizer reaction forces
- The ability to view molecular simulations live in VMD
- Improved support for loading PDB files
- August 6, 2008
Well-attended, Successful OpenSim Workshop at NACOB
The OpenSim team hosted a very successful, well-received workshop at the North American Congress on Biomechanics in Ann Arbor, Michigan on August 5th.
Scott Delp, the PI behind OpenSim, and his team introduced approximately 100 conference attendees to some of the many musculoskeletal simulation and analysis tools
available within OpenSim. Videos and handouts from the workshop
are posted under the Documents link from the OpenSim home page.
- August 6, 2008
Simbios Participates at the SIAM Life Sciences Conference
with other IMAG/MSM Consortium Members
Simbios joined other IMAG/MSM Consortium members at the SIAM Life Sciences conference held in Montreal from August 4-7.
The IMAG/MSM members organized 8 mini-symposia and two special panels for the conference. Our Director of Dissemination, Joy Ku, participated in
an animated discussion on model sharing with Professor Trent Guess from the University of Missouri - Kansas City, a user of our research project repository
Simtk.org (http://simtk.org). And Alberto Figueroa, a research associate
actively involved in our cardiovascular driving biological project (DBP), presented the latest results of his work on fluid-solid growth, which has been incorporated into the
cardiovascular simulation software SimVascular.
- July 31, 2008
Successful "Fast Molecular Dynamics" Demo at ISMB
The software we are developing to improve the performance of molecular dynamics simulations was showcased at the Intelligent Systems for Molecular Biology (ISMB) conference held in Toronto, Canada July 19-23, 2008. Our demo "Fast Molecular Dynamics Calculations on Your Laptop" highlighted two sets of code released or to be released this year:
- OpenMM is an open-source application programming interface that will accelerate molecular dynamics, such as Gromacs, via GPUs (for more information, see the article in Biomedical Computation Review)
- Molmodel provides C++ libraries for molecular modeling. It takes advantage of Simbody, a library for multibody dynamics that allows mechanical systems, such as molecules and joints, to be modeled and simulated more easily (see the article in Biomedical Computation Review).
Molmodel can be downloaded as part of the SimTK Core.
- July 8, 2008
Dr. Jung-Chi Liao Moves to Columbia University
Congratulations to Dr. Jung-Chi Liao on his appointment as an assistant professor at Columbia University. Dr. Liao was the research associate for Simbios' myosin DBP (driving biological project), developing tools for analyzing single molecule dwell-time distributions, computing allosteric pathways, and understanding the structure of myosin VI. We wish him the best of luck in his new position.
- July 2, 2008
The Program announcement for Collaborations with National Centers for Biomedical Computing (R01 and R01) was re-issued on June 24, 2008. Please consult the R01 and R21 program announcements as well as our process described under "collaborating with Simbios".
- June 24, 2008
Announcing the Summer 2008 issue of the Biomedical Computation Review
- Mining Biomedical Literature
- Successful Collaborations
- June 20, 2008
Prof. Charles Taylor ran a cardiovascular course for about 70 participants from industry and academia from June 17-20, 2008. Attendees learned about cardiovascular physiology and pathophysiology, and gained first-hand experience working with data and tools developed with support from Simbios. SimVascular, a version of the cardiovascular simulation tool developed by Prof. Taylor's lab, is available on https://simtk.org.
- May 8, 2008
Simbios has just begun its search for a new Distinguished Postdoctoral Fellow. For more details, see our job announcement.
- April 1, 2008
New Driving Biological Problem (DBP) launched
Simbios is excited to announce the launch of the new "Protein Folding" DBP. For more information please visit the Protein Folding DBP page on simtk.org.
- March 31, 2008
Annnouncing the Spring 2008 issue of the Biomedical Computation Review
- Assembling the Aging Puzzle: Computation Helps Connect the Pieces
- On Simulating Growth and Form
- March 10, 2008
SimTK 1.0 released
The Simbios staff is excited to announce the release of SimTK 1.0. SimTK 1.0 provides a one step install to many components needed for the simulation of biological structures including: Linear Algebra, root finding, vector systems, rotations and the expression of directions, optimization, numerical differentiation and integration, as well as Simbody: a system for rigid multi-body dynamics. A 2-day workshop (http://simbios.stanford.edu/workshop.htm) will be held on March 20-21 to introduce programmers and modelers to the essential features of the toolkit.
- January 9, 2008
Annnouncing the 11th issue of the Biomedical Computation Review
- Life in Motion:
Simulation from Particles to People
- November 12-15, 2007
Simbios joined other Stanford groups to present a unique exhibit at Supercomputing ’07, the international conference for high performance computing, networking, storage and analysis. The exhibit included extremely high-resolution animations and images from Simbios researchers displayed on a 5x5 monitor display floor, and a demonstration of Folding@Home, a distributed computing project for protein-folding simulations, running on a Sony Playstation3 (http://folding.stanford.edu/).
- Read more about the event at http://today.slac.stanford.edu/a/2007/11-27.htm.
- Photos from the event can be viewed at http://picasaweb.google.com/preese/SC07Public.
- October 27, 2007
Biomedical Computation at Stanford Symposium (BCATS)
Simbios is proud to support the Biomedical Computation Symposium at Stanford, which was held at Cubberley Auditorium at Stanford University. This is not your usual biomedical computation conference. Stanford students organize this annual conference, where students and post-doctoral fellows share their latest research in the field of biomedical computation. The quality and breadth of the research represented at BCATS draw hundreds of individuals from across the campus and the community. BCATS had four keynote speakers, ten student speakers and 51 poster presenters.
- October 25, 2007
Bio-X, Stanford's interdisciplinary life sciences initiative, teamed up with Simbios to hold a memorable symposium entitled: "Life in Motion". This full day Symposium featured ten speakers that presented physics-based simulation research from molecules to organisms. Our latest edition of the Biomedical Computation Review includes interviews with the speakers and summarizes this memorable event.
- October 5, 2007
Annnouncing the tenth issue of the Biomedical Computation Review
- Computing the Ravages of Time: Using Algorithms To Tackle Alzheimer's Disease
- Genetic Variants and Ill Health: Scanning 500,000 SNPs Yields Gene-Disease Connections
- August 27-31, 2007
A SimVascular short course was held at the Clark Center at Stanford University.
SimVascular is Simbios's open source release of tools for cardiovascular simulation. It includes code for reading 3D images, segmenting structures, generating models and meshes, and modeling blood flow in deformable vessels.
- August 22, 2007
We are delighted to announce the OpenSim version 1.0 release. View pictures taken at the event and go to Simtk.org/home/opensim to get the newest release.
OpenSim is a freely available software system that allows you to build, exchange, and analyze musuloskeletal models and dynamic simulations of movement.
- June 25, 2007
Annnouncing the ninth issue of the Biomedical Computation Review
- Imaging Collections: How They're Stacking Up
- Dock This: In Silico Drug Design Feeds Drug Development
- April 4, 2007
Announcing the eighth issue of the Biomedical Computation Review
- Biocomputation Startups: Where does value lie?
- Modeling Cancer Biology: How mathematical models are transforming the fight agaist cancer
- January 19, 2007
Announcing the seventh issue of the Biomedical Computation Review
- Computational Biomechanics: Making strides toward patient care
Biologically Inspired Computation: Algorithms that mimic nature's tricks
- October 5, 2006
Announcing the sixth issue of the Biomedical Computation Review
- Microarrays: The search for meaning in a vast sea of data
Bringing Supercomputers to Life (Siences)
- July 17, 2006
Announcing the fifth issue of the Biomedical Computation Review
- Human Versus Machine: Biomedical expertise meets computer automation
Computational Biology Catches the Flu: Modeling the bug, the host, the world
- May 5, 2006
Science Magazine (www.sciencemag.org) featured SimTK in its NetWatch article on May 5, 2006. Titled "Bodily Functions", Science introduced SimTK's algorithms, applications, and resources that simulate how force and motion affect biology - from molecules to man.
Science highlighted aortic blood flow by Charley Taylor and Chris Zarins, gait analysis by Scott Delp, and RNA folding by Russ Altman and Dan Herschlag.
April 4, 2006
Simbios announces source code distribution rights for the TAO Dynamics Engine at https://simtk.org/home/tao_de
. Under MIT license
, TAO provides an intuitive, efficient, commercial, rigid-body dynamics library for modeling, control, and simulation of articulated branching structures.
- April 4, 2006
Announcing the release of the new simtk.org web site.
Simtk.org deploys new resources, algorithms, and applications at simtk.org.
- April 3, 2006
Announcing the fourth issue of the Biomedical Computation Review
-The Female Factor: Is the gender gap in computer science carrying over to biomedical computing?
-Ramping Up to Multiscale: Taking Biomedical Modeling to a New Level
- March 16, 2006
- January 5, 2006
Announcing the third issue of the Biomedical Computation Review
-Three New Building Blocks: Ontologies, cellular and genomic data integration featured at new national centers
-From Sight To Insight: Visualization tools yield biomedical success stories
- December 7, 2005
Welcome to our new Lead Science Officer.
On December 7th, Dr. Jennie Larkin (NHLBI) was named Lead Science Officer for Simbios.
- November 22, 2005
On November 22nd 2005 Simbios held a retreat that all simbios faculty, staff, postdocs, students, NIH Program Officer Peter Lyster and NIH Lead Science Officer Peter Highnam attended.
- October 2005
Announcing the second issue of the Biomedical Computation Review
-Packing It All In: Curricula for Biomedical Computing
-The Dawn of Brain-Machine Interfaces
- August, 2005
Announcing the start of the Cardiovascular Driving Biological Problem
- July 14, 2005
Announcing SimTK 0.5
SimTK 0.5 is our pre-release of SimTK. Please browse Simtk.org for new projects, view our July 14th presentation detailing some of the features and capabilities of SimTK 0.5. and create your own project to take advantage of the SimTK infrastructure. To view the presentation go to http://simbios.stanford.edu/Presentations/SimTK0.5.ppt
- July 8, 2005
Biomedical Computation Review goes live
- June 8, 2005
Biomedical computation magazine to make its debut
- April 18, 2005
Collaborating with National Centers for Biomedical Computing
For prospective applicants to the NIH Roadmap Related PAR-05-063 Collaborating with National Centers for Biomedical Computing. If you are interested in a collaborative project with the Simbios Center please contact us.
In addition to contacting the center, you are encouraged to contact the NIH Program Officer Peter Lyster, Ph.D. (NIGMS) or the Lead Science Officer Peter Highnam, Ph.D. (NCRR) for Simbios.
- April 1, 2005
- November 2004
$20 million launches Center for biological software
- September 29, 2004
Researchers establish national center for biological simulation