“…We used three GWAS models, namely, general linear model (GLM), mixed linear model (MLM), and Fixed and Random model Circulating Probability Unification (FarmCPU) model. We observed significant genetic variation among the DH lines and their derived testcrosses. …”
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“…Phenotypic data were analyzed along with 854,832 SNPs using three statistical models: mixed linear model (MLM), multi-locus mixed model (MLMM), and fixed and random model circulating probability unification (FarmCPU). Significant variations in HRP and CGP were observed between rice accessions. …”
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“…RESULTS: Parameters for genome scans are entered using a Java-based GUI interface and backend scripts in Perl. Multi-processor CPU load-sharing minimized the average response time for scans of different chromosomes. …”
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“…RESULTS: We have developed a tool, GENe AnaloGue FINdEr (ENGINE) that parallelizes the search process and distributes the calculation and data over the computational GRID, splitting the process into many sub-processes and joining the calculation and the data on the same machine and therefore completing the whole search in about 3 days instead of occupying one single machine for more than 5 CPU years. The results of the functional comparison contain potential functional analogues for more than 79000 gene products from the most important species. 46% of the analyzed gene products are well enough described for such an analysis to individuate functional analogues, such as well-known members of the same gene family, or gene products with similar functions which would never have been associated by standard methods. …”
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“…SE also used considerably less CPU time than DP. CONCLUSION: The Seed Extension algorithm is fast and, without using a gap penalty, produces more accurate sequence alignments from superimposed structures than three other programs tested that use dynamic programming algorithm.…”
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“…In its current form, Motmot allows for: (1) image acquisition from a variety of camera interfaces (package motmot.cam_iface), (2) the display of these images with minimal latency and computer resources using wxPython and OpenGL (package motmot.wxglvideo), (3) saving images with no compression in a single-pass, low-CPU-use format (package motmot.FlyMovieFormat), (4) a pluggable framework for custom analysis of images in realtime and (5) firmware for an inexpensive USB device to synchronize image acquisition across multiple cameras, with analog input, or with other hardware devices (package motmot.fview_ext_trig). …”
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“…The toolkit uses efficient processes for specifying the parameterisation of statistical models, and implements numerous optimisations that make highly parameter rich likelihood functions solvable within hours on multi-cpu hardware. PyEvolve can be readily adapted in response to changing computational demands and hardware configurations to maximise performance. …”
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“…This is especially relevant on modern supercomputers such as the Blue Gene/P architecture where the available working memory per CPU core is rather limited. We develop a simple linear model to analyze the memory consumption of the constituent components of neuronal simulators as a function of network size and the number of cores used. …”
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“…The TriAnnot pipeline is parallelized on a 712 CPU computing cluster that can run a 1-Gb sequence annotation in less than 5 days. …”
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“…Crossbow is a software tool that can detect single nucleotide polymorphisms (SNPs) in whole-genome sequencing (WGS) data from a single subject; however, Crossbow has a number of limitations when applied to multiple subjects from large-scale WGS projects. The data storage and CPU resources that are required for large-scale whole genome sequencing data analyses are too large for many core facilities and individual laboratories to provide. …”
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“…The proposed algorithm allows to obtain reproducible results fully automatically at a time of 5 s per patient using the Core i5 CPU M460 @ 2.5GHz 4GB of RAM. CONCLUSIONS: The paper presents the possibility of using a profiled algorithm of image analysis, proposed by the authors, to measure additional cornea deformation parameters. …”
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“…Each image in a sequence was analysed in this way in no more than 100 ms using Intel Core i5 CPU M460 @2.5 GHz 4 GB RAM.…”
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“…As a result, RNA-Skim uses <4% of the k-mers and <10% of the CPU time required by Sailfish. It is able to finish transcriptome quantification in <10 min per sample by using just a single thread on a commodity computer, which represents >100 speedup over the state-of-the-art alignment-based methods, while delivering comparable or higher accuracy. …”
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“…These reference-based methods have been shown to compress better than reference-free schemes, but the alignment step they require demands several hours of CPU time on a typical dataset, whereas reference-free methods can usually compress in minutes. …”
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“…For a few segmented areas, the analysis time using Intel Core i5 CPU RAM M460@2.5GHz 4GB does not exceed 10 s. CONCLUSIONS: The obtained results confirm the usefulness of the applied method for image analysis and processing in dermatological practice. …”
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“…Realignment time was about 16 seconds per case, using a 2.5 GHz CPU desktop with obvious elimination of the distortion in the reconstructed model. …”
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“…We conclude that HLA*PRG for the first time achieves accuracies comparable to gold-standard reference methods from standard whole-genome sequencing data, though high computational demands (currently ~30–250 CPU hours per sample) remain a significant challenge to practical application.…”
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“…The analysis was performed on a PC with Intel(®) Xeon(®) X5680 3.33 GHz CPU in Matlab(®) Version 7.11.0.584 (R2010b) with Signal Processing Toolbox Version 7.1 (R2010b), Neural Network Toolbox 7.0 (R2010b) and Statistics Toolbox (R2010b). …”
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“…By using the 2,271,584 single nucleotide polymorphisms (SNPs) on the panel from previous studies, and genome-wide association studies by using FarmCPU R package to identify 17 genetic loci associated with cold tolerance. …”
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“…Marker-trait associations were identified using the FarmCPU R package. Principal component analysis was directly and a kinship matrix was indirectly used to account for population structure. …”
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