Dataset Information

Comparison of Acceleration Techniques for Selected Low-Level Bioinformatics Operations.

ABSTRACT: Within the recent years clock rates of modern processors stagnated while the demand for computing power continued to grow. This applied particularly for the fields of life sciences and bioinformatics, where new technologies keep on creating rapidly growing piles of raw data with increasing speed. The number of cores per processor increased in an attempt to compensate for slight increments of clock rates. This technological shift demands changes in software development, especially in the field of high performance computing where parallelization techniques are gaining in importance due to the pressing issue of large sized datasets generated by e.g., modern genomics. This paper presents an overview of state-of-the-art manual and automatic acceleration techniques and lists some applications employing these in different areas of sequence informatics. Furthermore, we provide examples for automatic acceleration of two use cases to show typical problems and gains of transforming a serial application to a parallel one. The paper should aid the reader in deciding for a certain techniques for the problem at hand. We compare four different state-of-the-art automatic acceleration approaches (OpenMP, PluTo-SICA, PPCG, and OpenACC). Their performance as well as their applicability for selected use cases is discussed. While optimizations targeting the CPU worked better in the complex k-mer use case, optimizers for Graphics Processing Units (GPUs) performed better in the matrix multiplication example. But performance is only superior at a certain problem size due to data migration overhead. We show that automatic code parallelization is feasible with current compiler software and yields significant increases in execution speed. Automatic optimizers for CPU are mature and usually no additional manual adjustment is required. In contrast, some automatic parallelizers targeting GPUs still lack maturity and are limited to simple statements and structures.

SUBMITTER: Langenkamper D

PROVIDER: S-EPMC4748744 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Comparison of Acceleration Techniques for Selected Low-Level Bioinformatics Operations.

Langenkämper Daniel D Jakobi Tobias T Feld Dustin D Jelonek Lukas L Goesmann Alexander A Nattkemper Tim W TW

Frontiers in genetics 20160210

Within the recent years clock rates of modern processors stagnated while the demand for computing power continued to grow. This applied particularly for the fields of life sciences and bioinformatics, where new technologies keep on creating rapidly growing piles of raw data with increasing speed. The number of cores per processor increased in an attempt to compensate for slight increments of clock rates. This technological shift demands changes in software development, especially in the field of ...[more]

PMID: 26904094

Similar Datasets

Project description:BACKGROUND:Polycystic ovary syndrome (PCOS), the commonest endocrine disorder affecting young women, appears to be a multigenic trait with contributing genes being unclear. Hence, analysis of polymorphisms in multiple candidate genes is required. Currently available genotyping methods are expensive, time-consuming with limited analytical sensitivity. AIM:(i) Develop and validate high resolution melting (HRM) assay and allele-specific real-time quantitative PCR (AS-qPCR) for genotyping selected SNPs associated with PCOS. (ii) Identify selected SNPs and their association with a Sri Lankan cohort of well-characterized PCOS. METHODS:DNA was extracted from women with well-characterized PCOS from adolescence (n = 55) and ethnically matched controls (n = 110). FTO (Fat mass and obesity associated gene; rs9939609), FSHB (Follicle stimulating hormone beta subunit; rs6169), FSHR (Follicle stimulating hormone receptor; rs6165/rs6166), and INSR (Insulin receptor; rs1799817) genes were genotyped using HRM assay. GnRH1 (Gonadotropin releasing hormone; rs6185), LHB (Luteinizing hormone beta subunit; rs1800447/rs34349826) and LHCGR (Luteinizing hormone/choriogonadotropin receptor; rs2293275) genes were genotyped using AS-qPCR method. Genotyping results were validated using Sanger sequencing. RESULTS:A significant association was observed within FTO gene polymorphism (rs9939609) and PCOS. Genotype frequency of FTO gene (rs9939609)-cases versus controls were TT-36.4% vs.65.4% (p<0.05), AT-23.6% vs.20.9%, AA-40% vs.13.6% (p<0.05). Genotype frequencies of the SNPs GnRH1 (rs6185), FSHB (rs6169), FSHR (rs6165 & rs6166), LHB (rs1800447 & rs34349826), LHCGR (rs2293275) and INSR (rs1799817) were not significantly different between cases and controls (p>0.05). Only the mutant alleles were observed for LHB rs1800447 and rs34349826 SNPs in both groups. The HRM and AS-qPCR assay results had 100% concordance with sequencing results. CONCLUSIONS:FTO gene rs9939609 polymorphism is significantly more prevalent among Sri Lankan PCOS subjects while the other selected SNPs of HPG axis genes and INSR gene showed no association. HRM and AS-qPCR assays provide a reliable, fast and user-friendly genotyping method facilitating wider implication in clinical practice.

Project description:Background and objectives Recently, both surgical and non-surgical interventions have gained popularity in accelerating orthodontic tooth movement, but there is no randomized controlled trial (RCT) comparing both modalities in terms of patient-reported outcome measures (PROMs) during maxillary canine retraction. Therefore, this trial aimed to assess the PROMs associated with either low-level laser therapy (LLLT) or piezocision-assisted acceleration in the context of maxillary canine retraction. Materials and methods This was a single-blinded, single-center, three-arm RCT. A total of 54 patients (12 males, 42 females, mean age 20.65 ± 2.85) whose treatment needed upper-first-premolar extraction to facilitate canine retraction were enrolled and randomly divided into three groups: piezocision group (PG), LLLT group (LLLTG), and the control group (CG). Standardized questionnaires using a visual analog scale were distributed to patients at five assessment times: 1 (T1), 3 (T2), 7 (T3), 14 (T4), and 28 days following the canine retraction initiation (T5). The patients' pain, discomfort, swelling, chewing difficulty, satisfaction, and acceptance were recorded. Results Regarding pain and discomfort, the levels were significantly lower in the LLLTG during the first two weeks of canine retraction compared to the other two groups (p<0.017). At the same time, these levels were significantly greater in the PG than the CG in the first week of canine retraction (p<0.017). Patients in the PG had a "mild to moderate" perception of swelling at T1 and T2, which was significantly different than that of the other two groups (p<0.001). Regarding chewing difficulty, the levels in the LLLTG were significantly lower than those in PG at the first three assessment times (p<0.017). Patients' satisfaction with canine speed was significantly greater in the intervention groups compared to the CG (p<0.001). In contrast, no statistically significant differences were found between the three groups regarding satisfaction with gum appearance surrounding the canine (p=0.061) and acceptance (p=0.125). Conclusion The LLLT-assisted canine retraction was associated with significantly lower negative patient-reported outcomes during the first two weeks of retraction than piezocision-assisted retraction. However, the levels of pain and discomfort were significantly greater in the piezocision-assisted retraction group than those in the conventional canine retraction group, which in turn were greater than those with the LLLT-assisted canine retraction group during the first week of retraction. Patient satisfaction and acceptance were high with both piezocision and LLLT interventions.

Project description:Campylobacter, a major foodborne pathogen, is increasingly resistant to macrolide antibibotics. Previous findings suggeted that development of macrolide resistance in campylobacter requires a multi-step process, but the molecular mechanisms involved in the process are not known. In our study, multiple series of macrolide-resistant C. jejuni mutants were selected in vitro by stepwise exposure of C. jejuni NCTC11168 to increasing concentrations of erythromycin and tylosin. A set of the selected resistance were subjected to microarray and the the global transcriptional profile was analyzed. In this sery, DNA microarray was used to compare the gene expression profiles of macrolide resistant strains (68E1, 68E8 and 68E64) with its parent wild-type strain NCTC11168. The assay identified a small number of genes that showed significant changes (q-value<0.1) in expression in the low-level macrolide resistant strain 68E1, while a large number of gene showing significant changes in intermedia-level resistant stran 68E8 and high-level resistant strain 68 E64. The up-regulated genes in the resistant strains are involved in miscellaneous periplasmic proteins, efflux protienand putative aminotransferase, while the majority of the down-regulated genes are involved in electron transport,lipoprotein, heat shock protein and unknown function proteins. These findings suggest that there is not much change in low-level macrolide resistant C. jejuni strain. The over-expression of efflux pump and periplasmic protein was involved in the development of resistance to macrolide in C. jejuni. Keywords: macrolide resistant C. jejuni selected from NCTC 11168 step-wise selection. The design utilized an available two color microarray slide for the entire transcriptome of Campylobacter jejuni. Four hybridizations were performed each with independently extracted samples of either macrolide susceptible C. jejuni NCTC11168 cDNA samples or macrolide resistant C.jejuni cDNA samples. A dye swap was utilized to help minimize dye dependent bias. Thus, there were four biological replicates of each sample.

Dataset Information

Comparison of Acceleration Techniques for Selected Low-Level Bioinformatics Operations.

Publications

Comparison of Acceleration Techniques for Selected Low-Level Bioinformatics Operations.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets