Implementation and optimization of SpMV algorithm based on SW26010P many-core processor and stored in BCSR format.

The irregular distribution of non-zero elements of large-scale sparse matrix leads to low data access efficiency caused by the unique architecture of the Sunway many-core processor, which brings great challenges to the efficient implementation of sparse matrix-vector multiplication (SpMV) computing by SW26010P many-core processor. To address this problem, a study of SpMV optimization strategies is carried out based on the SW26010P many-core processor. Firstly, we design a memorized data storage transformation strategy to transform the matrix in CSR storage format into BCSR (Block Compressed Sparse Row) storage. Secondly, the dynamic task scheduling method is introduced to the algorithm to realize the load balance between slave cores. Thirdly, the LDM memory is refined and designed, and the slave core dual cache strategy is optimized to further improve the performance. Finally, we selected a large number of representative sparse matrices from the Matrix Market for testing. The results show that the scheme has obviously speedup the processing procedure of sparse matrices with various sizes and sizes, and the master-slave speedup ratio can reach up to 38 times. The optimization method used in this paper has implications for other complex applications of the SW26010P many-core processor.

EDomics: a comprehensive and comparative multi-omics database for animal evo-devo.

Evolutionary developmental biology (evo-devo) has been among the most fascinating interdisciplinary fields for decades, which aims to elucidate the origin and evolution of diverse developmental processes. The rapid accumulation of omics data provides unprecedented opportunities to answer many interesting but unresolved evo-devo questions. However, the access and utilization of these resources are hindered by challenges particularly in non-model animals. Here, we establish a comparative multi-omics database for animal evo-devo (EDomics, http://edomics.qnlm.ac) containing comprehensive genomes, bulk transcriptomes, and single-cell data across 40 representative species, many of which are generally used as model organisms for animal evo-devo study. EDomics provides a systematic view of genomic/transcriptomic information from various aspects, including genome assembly statistics, gene features and families, transcription factors, transposable elements, and gene expressional profiles/networks. It also exhibits spatiotemporal gene expression profiles at a single-cell level, such as cell atlas, cell markers, and spatial-map information. Moreover, EDomics provides highly valuable, customized datasets/resources for evo-devo research, including gene family expansion/contraction, inferred core gene repertoires, macrosynteny analysis for karyotype evolution, and cell type evolution analysis. EDomics presents a comprehensive and comparative multi-omics platform for animal evo-devo community to decipher the whole history of developmental evolution across the tree of life.

Constructing marine expert management knowledge graph based on Trellisnet-CRF.

Creating and maintaining a domain-specific database of research institutions, academic experts and scholarly literature is essential to expanding national marine science and technology. Knowledge graphs (KGs) have now been widely used in both industry and academia to address real-world problems. Despite the abundance of generic KGs, there is a vital need to build domain-specific knowledge graphs in the marine sciences domain. In addition, there is still not an effective method for named entity recognition when constructing a knowledge graph, especially when including data from both scientific and social media sources. This article presents a novel marine science domain-based knowledge graph framework. This framework involves capturing marine domain data into KG representations. The proposed approach utilizes various entity information based on marine domain experts to enrich the semantic content of the knowledge graph. To enhance named entity recognition accuracy, we propose a novel TrellisNet-CRF model. Our experiment results demonstrate that the TrellisNet-CRF model reached a 96.99% accuracy rate for marine domain named entity recognition, which outperforms the current state-of-the-art baseline. The effectiveness of the TrellisNet-CRF module was then further demonstrated and confirmed on entity recognition and visualization tasks.

ConoMode, a database for conopeptide binding modes.

ConoMode is a database for complex three-dimensional (3D) structures of conopeptides binding with their target proteins. Conopeptides, a large family of peptides from the venom of marine snails of the Conus genus, have exceptionally diverse sequences, and their high specificity to block ion channels makes them crucial as drug leads and tools for physiological studies. ConoMode is a specialized archive for the collection of 3D coordinate data for the conopeptides and their binding target proteins from published literature and the Protein Data Bank. These 3D structures can be determined using experimental methods such as X-ray crystallography and electron microscopy and computational methods including docking, homology modeling and molecular dynamics simulations. The binding modes for the conopeptides determined using computational modeling must be validated based on experimental data. The 3D coordinate data from ConoMode can be searched, visualized, downloaded and uploaded. Currently, ConoMode manages 19 conopeptide sequences (from 10 Conus species), 15 protein sequences and 37 3D structures. ConoMode utilizes a modern technical framework to provide a good user experience on mobile devices with touch interaction features. Furthermore, the database is fully optimized for unstructured data and flexible data models. Database URL: http://conomode.qnlm.ac/conomode/conomode/index.

A high-resolution Asia-Pacific regional coupled prediction system with dynamically downscaling coupled data assimilation.

A regional coupled prediction system for the Asia-Pacific (AP-RCP) (38°E-180°, 20°S-60°N) area has been established. The AP-RCP system consists of WRF-ROMS (Weather Research and Forecast, and Regional Ocean Model System) coupled models combined with local observational information through dynamically downscaling coupled data assimilation (CDA). The system generates 18-day forecasts for the atmosphere and ocean environment on a daily quasi-operational schedule at Pilot National Laboratory for Marine Science and Technology (Qingdao) (QNLM), consisting of 2 different-resolution coupled models: 27 km WRF coupled with 9 km ROMS, 9 km WRF coupled with 3 km ROMS, while a version of 3 km WRF coupled with 3 km ROMS is in a test mode. This study is a first step to evaluate the impact of high-resolution coupled model with dynamically downscaling CDA on the extended-range predictions, focusing on forecasts of typhoon onset, improved precipitation and typhoon intensity forecasts as well as simulation of the Kuroshio current variability associated with mesoscale oceanic activities. The results show that for realizing the extended-range predictability of atmospheric and oceanic environment characterized by statistics of mesoscale activities, a fine resolution coupled model resolving local mesoscale phenomena with balanced and coherent coupled initialization is a necessary first step. The next challenges include improving the planetary boundary physics and the representation of air-sea and air-land interactions to enable the model to resolve kilometer or sub-kilometer processes.

Pro-arrhythmic Effects of Hydrogen Sulfide in Healthy and Ischemic Cardiac Tissues: Insight From a Simulation Study.

Hydrogen sulfide (H2S), an ambient air pollutant, has been reported to increase cardiac events in patients with cardiovascular diseases, but the underlying mechanisms remain not elucidated. This study investigated the pro-arrhythmic effects of H2S in healthy and ischemic conditions. Experimental data of H2S effects on ionic channels (including the L-type Ca2+ channel and ATP-sensitive K+ channel) were incorporated into a virtual heart model to evaluate their integral action on cardiac arrhythmogenesis. It was shown that H2S depressed cellular excitability, abbreviated action potential duration, and augmented tissue's transmural dispersion of repolarization, resulting in an increase in tissue susceptibility to initiation and maintenance of reentry. The observed effects of H2S on cardiac excitation are more remarkable in the ischemic condition than in the healthy condition. This study provides mechanistic insights into the pro-arrhythmic effects of air pollution (H2S), especially in the case with extant ischemic conditions.