- 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