Category: Life Science
Realtime Computer Vision with OpenCV
OpenCV have made it easier for application developers to use computer vision. They are well-documented and vibrant open source projects that keep growing, and they are being adapted to new computing technologies
Smoldyn on Graphics Processing Units: Massively Parallel Brownian Dynamics Simulations
In this paper, we analyze Smoldyn, a widely diffused algorithm for stochastic simulation of chemical reactions with spatial resolution and single molecule detail, and we propose an alternative, innovative implementation that exploits the parallelism of GPU
Fast Parallel Markov Clustering in Bioinformatics Using Massively Parallel Computing on GPU with CUDA and ELLPACK-R Sparse Format
Thus, large-scale parallel computation on off-the-shelf desktop-machines, that were previously only possible on supercomputing architectures, can significantly change the way bioinformaticians and biologists deal with their data
Optimizing ion channel models using a parallel genetic algorithm on graphical processors
We substantially reduced computing time by solving the ODEs so as to massively reduce memory transfers to and from the GPU.
SOAP3: Ultra-fast GPU-based parallel alignment tool for short reads
SOAP3 is the first short read alignment tool that leverages the multi-processors in a graphic processing unit (GPU) to achieve a drastic improvement in speed
Multiscale model of fibrin accumulation on the blood clot surface and platelet dynamics
A multiscale computational model of thrombus (blood clot) development is extended by incorporating a submodel describing formation of fibrin network through “fibrin elements” representing regions occupied by polymerized fibrin.
Accelerating knowledge-based energy evaluation in protein structure modeling with GPU
We present an efficient implementation of knowledge-based energy functions by taking advantage of the recent Graphics Processing Unit (GPU) architectures
Drew Berry: Astonishing Molecular Machines
Drew Berry is a biomedical animator whose scientifically accurate and aesthetically rich visualizations reveal the microscopic world inside our bodies to a wide range of audiences. He delivered this speech at TEDxSydney last year.
DMD: An Efficient and Versatile Simulation Method for Fine Protein Characterization
We enhance the computational performance by parallelizing the DMD algorithm. Using a small number of commodity computers, we achieve sampling quality and folding accuracy comparable to the explicit-solvent simulations performed on high-end hardware.
BEAGLE: An Application Programming Interface and HPC Library for Statistical Phylogenetics
BEAGLE is an API and library for high-performance evaluation of phylogenetic likelihoods. The API provides a uniform interface for performing calculations on an expanding variety of computer hardware platforms including GPUs, multicore CPUs, and SSE vectorization.
