1.How Big Data and High-performance Computing Drive Brain Science
Chen SHANYU ; He ZHIPENG ; Han XINYIN ; He XIAOYU ; Li RUILIN ; Zhu HAIDONG ; Zhao DAN ; Dai CHUANGCHUANG ; Zhang YU ; Lu ZHONGHUA ; Chi XUEBIN ; Niu BEIFANG
Genomics, Proteomics & Bioinformatics 2019;17(4):381-392
Brain science accelerates the study of intelligence and behavior, contributes fundamental insights into human cognition, and offers prospective treatments for brain disease. Faced with the challenges posed by imaging technologies and deep learning computational models, big data and high-performance computing (HPC) play essential roles in studying brain function, brain diseases, and large-scale brain models or connectomes. We review the driving forces behind big data and HPC methods applied to brain science, including deep learning, powerful data analysis capabilities, and computational performance solutions, each of which can be used to improve diagnostic accuracy and research output. This work reinforces predictions that big data and HPC will continue to improve brain science by making ultrahigh-performance analysis possible, by improving data standardization and sharing, and by providing new neuromorphic insights.
2.Gclust:A Parallel Clustering Tool for Microbial Genomic Data
Li RUILIN ; He XIAOYU ; Dai CHUANGCHUANG ; Zhu HAIDONG ; Lang XIANYU ; Chen WEI ; Li XIAODONG ; Zhao DAN ; Zhang YU ; Han XINYIN ; Niu TIE ; Zhao YI ; Cao RONGQIANG ; He RONG ; Lu ZHONGHUA ; Chi XUEBIN ; Li WEIZHONG ; Niu BEIFANG
Genomics, Proteomics & Bioinformatics 2019;17(5):496-502
The accelerating growth of the public microbial genomic data imposes substantial bur-den on the research community that uses such resources. Building databases for non-redundant ref-erence sequences from massive microbial genomic data based on clustering analysis is essential. However, existing clustering algorithms perform poorly on long genomic sequences. In this article, we present Gclust, a parallel program for clustering complete or draft genomic sequences, where clustering is accelerated with a novel parallelization strategy and a fast sequence comparison algo-rithm using sparse suffix arrays (SSAs). Moreover, genome identity measures between two sequences are calculated based on their maximal exact matches (MEMs). In this paper, we demon-strate the high speed and clustering quality of Gclust by examining four genome sequence datasets. Gclust is freely available for non-commercial use at https://github.com/niu-lab/gclust. We also introduce a web server for clustering user-uploaded genomes at http://niulab.scgrid.cn/gclust.