The use of a ram drive or SSD does not influence the calculation time more than a few percent. This allows the program to efficiently use all available processors and cores. Therefore the part of the alignment which is multi-threaded will have a smaller overhead time compared to the processing time when aligning far more than 16 data sets. Clearly PC4 as the most recently purchased PC is the fastest on one core. Concluding remarks The new version of metAlign is shown to increase the speed of processing considerably. Factors influencing the performance enhancement are discussed. Barbarea vulgaris linkage map and quantitative trait loci for saponins, glucosinolates, hairiness and resistance to the herbivore Phyllotreta nemorum.
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For PC4 with only four cores using four threads therefore is obviously still advantageous. Since the publication of metAlign in the standard consumer desktop PC configuration has changed.
This is also the case for the previous version of metAlign, which consists of multiple separate 32 bits programs which are run in a batch through an interface using one thread on one core. Received Aug 19; Accepted Sep An untargeted multi-technique metabolomics approach to studying intracellular metabolites of HepG2 cells exposed to 2,3,7,8-tetrachlorodibenzop-dioxin. Considering the fact that a few years back the available memory was limiting, this part of the program used to require pointers in multiple opened files to be continuously moved.
The same test calculations were done on one core on different PCs using different drives.
AIoutput 32 bit for Shimadzu. Our observations show that performance scales with the increase in processor core numbers we currently see in consumer PC hardware development.
MetAlign performance enhancement by efficient use of advances in computer hardware
Open Access This article is distributed under the terms of the Creative Commons Attribution Noncommercial License which permits any noncommercial use, distribution, and reproduction in any medium, provided the original author s and source are credited. The dependence on the number of threads is skewed. Dividing parts of the alignment into smaller pieces may make it possible to use the available RAM more efficiently for PC8 and therefore speed up alignment. Concluding remarks The new version of metAlign is shown to increase the speed of processing considerably.
Especially when using high numbers of threads the relative speed increase is not linearly correlated to the number of available threads any more.
As mentioned in Sect. The alignment was 5—10 fold faster.
The impact of the absence of aliphatic glucosinolates on insect herbivory in Arabidopsis. For example, creating one file from all pre-processed data sets requires the use of one thread, since the resulting overall file is not shared in the memory. Threads will be waiting for each other to free up RAM and the OS will start using the swap space on disk; this evidently decreases the performance. Although CPU speed and the number of cores play a significant role in processing time, it should be noted that setting parameters correctly for baseline correction will also greatly influence performance.
The current version of metAlign available as a free download at www. Although the above account is on accurate mass processing, it is also possible to process accurate mass data as nominal mass data using metAlign. In general the performance increases with the number of threads used.
This new version was tested softawre three different multi-core PCs with different operating systems. The number of threads, the number of data files and the storage medium used i.
MetAlign 3.0: performance enhancement by efficient use of advances in computer hardware
Data were exported as netCDF and were ca. The program starts with data conversion of all data sets to netCDF, continues with processing of all netCDF files and then ends with a conversion back to a desired format.
Alignment and statistical difference analysis of complex peptide data sets generated by multidimensional LC-MS. A thread of execution is the smallest unit of processing that can be scheduled by an OS. MetAlign acts as if it is running on multiple single core PCs at the same time but within one hardware system.
Metabolomics approach to anabolic steroid urine profiling of bovines treated with prohormones.
MetAlign – BioAssist
Barbarea vulgaris linkage map and quantitative trait loci for saponins, glucosinolates, hairiness and resistance to the herbivore Phyllotreta nemorum. Factors influencing the performance enhancement are discussed. This is more or less the case for all thread numbers in which the number of data sets i. Large random access memory RAM is common and now also accessible, due to the appearance of mainstream bit operating systems like for instance Windows 7.