“…This software incorporates an efficient approximation of the Chemical Master Equation as well as a stochastic simulation algorithm—both with GPU and CPU implementations—combined with global optimization algorithms capable of solving Mixed Integer Nonlinear Programming problems. …”
Enlace del recurso
Enlace del recurso
Enlace del recurso

“…By converting oligonucleotides to integers hashed in RAM, xMAN can scan through genomes using bit shifting operation and achieve at least one order of magnitude speed increase over existing tools. xMAN can map the 42 million 25-mer probes on the Affymetrix whole human genome tiling arrays to the entire genome in less than 6 CPU hours. CONCLUSIONS: In addition to the speed advantage, we found the probe mapping of xMAN to substantially improve the final analysis results in both a spike-in experiment on ENCODE tiling arrays and an estrogen receptor ChIP-chip experiment on whole human genome tiling arrays. …”
Enlace del recurso
Enlace del recurso
Enlace del recurso

“…We also show that swps3 on this CPU is faster than a recent GPU implementation. …”
Enlace del recurso
Enlace del recurso
Enlace del recurso

“…However, for many of these cases, ‘de novo phasing with de novo models’ requires significant investment of computational power, much greater than 10(3) CPU days per target. Improvements in conformational search methods will be necessary if molecular replacement with de novo models is to become a practical tool for targets without homology to previously solved protein structures.…”
Enlace del recurso
Enlace del recurso
Enlace del recurso

“…Furthermore, hydrogen atoms placed by HAAD have more matches with the NOE restraints and fewer clashes with heavy atoms. The average CPU cost by HAAD is 18 and 8 times lower than that of CHARMM and REDUCE, respectively. …”
Enlace del recurso
Enlace del recurso
Enlace del recurso

“…CONCLUSION: RAMMCAP is a very fast method that can cluster and annotate one million metagenomic reads in only hundreds of CPU hours. It is available from .…”
Enlace del recurso
Enlace del recurso
Enlace del recurso

“…The filter does not affect the outcome of standard downstream chemometric analysis methods, such as principal component analysis, but use of the filter significantly reduces memory requirements and CPU time for such analyses. We demonstrate the utility of the filter for urinary metabolite profiling using direct infusion electrospray ionization and a 15 tesla FTICR mass spectrometer. …”
Enlace del recurso
Enlace del recurso
Enlace del recurso

“…The Grid program is automated and scalable to millions of dose-response curves, and it is able to process 100,000 dose-response curves from high throughput screening experiment per CPU hour. The Grid program has the potential of greatly increasing the productivity of large-scale dose-response data analysis and early drug discovery processes, and it is also applicable to many other curve fitting problems in chemical, biological, and medical sciences.…”
Enlace del recurso
Enlace del recurso
Enlace del recurso

“…It took 295 seconds to estimate variance components and 70 seconds to perform the genome scan on an Linux machine equipped with a 2.40GHz Intel(R) Core(TM)2 Quad CPU. CONCLUSIONS: QTLRel provides a toolkit for genome-wide association studies that is capable of calculating genetic incidence matrices from pedigrees, estimating variance components, performing genome scans, incorporating interactive covariates and genetic and non-genetic variance components, as well as other functionalities such as multiple-QTL mapping and genome-wide epistasis.…”
Enlace del recurso
Enlace del recurso
Enlace del recurso

“…We also achieve the speedup of three orders of magnitudes compared to a CPU reference implementation, making it possible to use the technique in time-critical applications.…”
Enlace del recurso
Enlace del recurso
Enlace del recurso

“…Without requiring prior knowledge of DNA length and sequence, and within <2 h per target on a standard 2.0 GHz single processor CPU, ParaDock offers a fast ab initio docking solution.…”
Enlace del recurso
Enlace del recurso
Enlace del recurso

“…The results show that the architecture presented in this paper significantly decreases the consumption of resources (memory, CPU and battery) without a substantial decrease in the accuracy of the inferred values.…”
Enlace del recurso
Enlace del recurso
Enlace del recurso

“…This prototype system is composed of remote on-line classification platform (ROCP), which uses a digital signal processor (DSP) as a core CPU, and a host control platform (HCP). The ROCP is in charge of acquiring the pest image, extracting image features and detecting the class of pest using an Artificial Neural Network (ANN) classifier. …”
Enlace del recurso
Enlace del recurso
Enlace del recurso

“…Furthermore, our aligner shows good parallel scalability with respect to the number of CPU threads. Availability: CUSHAW2, written in C++, and all simulated datasets are available at http://cushaw2.sourceforge.net Contact: liuy@uni-mainz.de; bertil.schmidt@uni-mainz.de Supplementary information: Supplementary data are available at Bioinformatics online.…”
Enlace del recurso
Enlace del recurso
Enlace del recurso

“…There are two major issues in this pathway optimization: i) excessive CPU time requirements and ii) loosely constrained optimization problem due to lack of data with respect to large signaling pathways. …”
Enlace del recurso
Enlace del recurso
Enlace del recurso

“…In addition, JBioWH can be tailored for use in specific circumstances, including the handling of massive queries for high-throughput analyses or CPU intensive calculations. The framework is provided with complete documentation and application examples and it can be downloaded from the Project Web site at http://code.google.com/p/jbiowh. …”
Enlace del recurso
Enlace del recurso
Enlace del recurso

“…Experiments on three popular benchmarks (BAliBASE, PREFAB, OXBench-X) on quad-core PC equipped with high-end graphics card show QuickProbs to be 5.7 to 9.7 times faster than original CPU-parallel MSAProbs. Additional tests performed on several protein families from Pfam database give overall speed-up of 6.7. …”
Enlace del recurso
Enlace del recurso
Enlace del recurso

“…The computation time of the algorithm on host CPU and the GPU system is presented for C and Matlab implementations. …”
Enlace del recurso
Enlace del recurso
Enlace del recurso

“…The GPU implementation shows an excellent acceleration ratio of more than 100 compared with CPU computation without losing numerical accuracy. …”
Enlace del recurso
Enlace del recurso
Enlace del recurso

“…The multicore version of the cache efficient single core algorithm provides a speedup, relative to the naive single core algorithm, between 7.5 and 14.0 on a 6 core hyperthreaded CPU. Our GPU algorithm for the NVIDIA C2050 is up to 1582 times as fast as the naive single core algorithm and between 5.1 and 11.2 times as fast as the fastest previously known GPU algorithm for Nussinov RNA folding.…”
Enlace del recurso
Enlace del recurso
Enlace del recurso