|
|
|
- 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. Stumpe's work relating chaperonin structure and function contributes to our understanding of chaperonins on the molecular level and could be a key step in the effort to design chaperonins with increased folding activity. Huang discussed his recent work on using computer simulations to study the thermodynamics of the headpiece of the hungtingtin protein and its implications on hungtingtin aggregation, hypothesized to be the cause of Huntington's disease.
- October 5, 2009
Special Fall 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
OpenMM Preview Release 4 Now Available
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. Material from the workshop are available here: https://simtk.org/home/opensimws_aug09.
- 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. The first day featured OpenMM, a library for MD developers to speed up their own MD codes on GPUs. The second day featured MSM Builder, software for researchers to automatically construct Markov State Models to analyze their MD simulations. And the last day introduced researchers to MD through OpenMM Zephyr. 25 individuals attended the workshop series, representing 12 different institutions, from industry to government to universities. Slides, videos, and handouts from the workshop are available here.
- 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: RNABuilder constructs structural models of RNA by enforcing user-provided base pairing interactions and other structural constraints; NAST/C2A generates a diverse set of plausible 3D structures based on user-provided primary sequence and secondary structure (and optionally, tertiary contacts) information; and OpenMM Zephyr which provides an easy-to-use graphical user interface for conducting molecular dynamics simulations. Slides and videos from the workshop will be available here.
- June 24, 2009
Summer Issue of Biomedical Computation Review Now Available
Announcing the Summer 2009 issue of the Biomedical Computation Review
Features:
- From SNPs to Prescriptions: Can Genes Predict Drug Response?
- 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. See the Zephyr website 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.
More News... |
|
RSS Feed