Alain Laederach of the Wadsworth Center counts on Simtk.org as a long term software and data repository and says Simbios’ dissemination efforts will pay off.
from http://biomedicalcomputationreview.org/content/simbios-bringing-biomedical-simulation-your-fingertips
Alain Laederach, PhD, a research scientist at the Wadsworth Center and an assistant...
Oct, 01, 2009
And people are starting to notice
In 1991, a prescient editorial in Nature by Harvard’s Walter Gilbert, PhD, (“Towards a paradigm shift in biology”) included these observations on the utility and impact of computing...
Apr, 01, 2006
Like humans, cells are affected by their physical environment, their neighbors, the context in which they exist. Much research has focused on the chemical signals that control cell behavior. But...
Sep, 01, 2011
Erik Lindahl of Stockholm University uses OpenMM to speed up molecular simulations of membrane proteins and takes inspiration from Simbios’ professional approach to software development as he continues developing and maintaining GROMACS.
from http://biomedicalcomputationreview.org/content/simbios-bringing-biomedical-simulation-your-fingertips
Simbios provides two key benefits to Erik Lindahl, PhD, associate professor of...
Oct, 01, 2009
Researchers are not simply retrieving and repackaging what is already known, but are also deriving new knowledge by discovering connections that were previously unnoticed.
Not long ago, reading biomedical literature involved hours in the library combing through rows of dusty periodicals—not to mention pocketfuls of change for the copy machine. Now, although the...
Jul, 01, 2008
Making reproducible research accessible to people who don’t write code
A particular mashup of data and tools produces the unique results found in each computational biology publication. Now, researchers have developed a model system that gives readers—especially...
Apr, 01, 2010
Columbia’s Jung-Chi Liao seeks pathways within proteins using AlloPathFinder, a Simbios tool he co-developed while at Stanford.
from http://biomedicalcomputationreview.org/content/simbios-bringing-biomedical-simulation-your-fingertips
As a Simbios post-doc, Jung-Chi Liao, PhD, sought to understand how a conformational...
Oct, 01, 2009
University of California, San Diego’s Alison Marsden uses SimVascular to do patient-specific modeling of blood flow for surgical applications.
from http://biomedicalcomputationreview.org/content/simbios-bringing-biomedical-simulation-your-fingertips
Alison Marsden, PhD, an assistant professor of mechanical and aerospace engineering...
Oct, 01, 2009
Kim Branson of Vertex Pharmaceuticals uses OpenMM as the GPU accelerator for Yank, a program for quickly estimating molecular binding affinities that he’s building with collaborators from Pande’s lab.
from http://biomedicalcomputationreview.org/content/simbios-bringing-biomedical-simulation-your-fingertips
Kim Branson, PhD, a research scientist in the modeling and simulation group at Vertex...
Oct, 01, 2009
In the world of molecular dynamics (MD), researchers often need to analyze and extract meaningful results from millions of conformations. Existing software for accomplishing this task focuses on...
Oct, 01, 2009