Dataset Information

PreCICE v2: A sustainable and user-friendly coupling library.

ABSTRACT: preCICE is a free/open-source coupling library. It enables creating partitioned multi-physics simulations by gluing together separate software packages. This paper summarizes the development efforts in preCICE of the past five years. During this time span, we have turned the software from a working prototype -- sophisticated numerical coupling methods and scalability on ten thousands of compute cores -- to a sustainable and user-friendly software project with a steadily-growing community. Today, we know through forum discussions, conferences, workshops, and publications of more than 100 research groups using preCICE. We cover the fundamentals of the software alongside a performance and accuracy analysis of different data mapping methods. Afterwards, we describe ready-to-use integration with widely-used external simulation software packages, tests, and continuous integration from unit to system level, and community building measures, drawing an overview of the current preCICE ecosystem.

SUBMITTER: Chourdakis G

PROVIDER: S-EPMC10446068 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

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preCICE v2: A sustainable and user-friendly coupling library.

Chourdakis Gerasimos G Davis Kyle K Rodenberg Benjamin B Schulte Miriam M Simonis Frédéric F Uekermann Benjamin B Abrams Georg G Bungartz Hans-Joachim HJ Cheung Yau Lucia L Desai Ishaan I Eder Konrad K Hertrich Richard R Lindner Florian F Rusch Alexander A Sashko Dmytro D Schneider David D Totounferoush Amin A Volland Dominik D Vollmer Peter P Koseomur Oguz Ziya OZ

Open research Europe 20220930

preCICE is a free/open-source coupling library. It enables creating partitioned multi-physics simulations by gluing together separate software packages. This paper summarizes the development efforts in preCICE of the past five years. During this time span, we have turned the software from a working prototype -- sophisticated numerical coupling methods and scalability on ten thousands of compute cores -- to a sustainable and user-friendly software project with a steadily-growing community. Today, ...[more]

PMID: 37645328

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Project description:BackgroundGenotyping by re-sequencing has become a standard approach to estimate single nucleotide polymorphism (SNP) diversity, haplotype structure and the biodiversity and has been defined as an efficient approach to address geographical population genomics of several model species. To access core SNPs and insertion/deletion polymorphisms (indels), and to infer the phyletic patterns of speciation, most such approaches map short reads to the reference genome. Variant calling is important to establish patterns of genome-wide association studies (GWAS) for quantitative trait loci (QTLs), and to determine the population and haplotype structure based on SNPs, thus allowing content-dependent trait and evolutionary analysis. Several tools have been developed to investigate such polymorphisms as well as more complex genomic rearrangements such as copy number variations, presence/absence variations and large deletions. The programs available for this purpose have different strengths (e.g. accuracy, sensitivity and specificity) and weaknesses (e.g. low computation speed, complex installation procedure and absence of a user-friendly interface). Here we introduce Altools, a software package that is easy to install and use, which allows the precise detection of polymorphisms and structural variations.ResultsAltools uses the BWA/SAMtools/VarScan pipeline to call SNPs and indels, and the dnaCopy algorithm to achieve genome segmentation according to local coverage differences in order to identify copy number variations. It also uses insert size information from the alignment of paired-end reads and detects potential large deletions. A double mapping approach (BWA/BLASTn) identifies precise breakpoints while ensuring rapid elaboration. Finally, Altools implements several processes that yield deeper insight into the genes affected by the detected polymorphisms. Altools was used to analyse both simulated and real next-generation sequencing (NGS) data and performed satisfactorily in terms of positive predictive values, sensitivity, the identification of large deletion breakpoints and copy number detection.ConclusionsAltools is fast, reliable and easy to use for the mining of NGS data. The software package also attempts to link identified polymorphisms and structural variants to their biological functions thus providing more valuable information than similar tools.

Dataset Information

PreCICE v2: A sustainable and user-friendly coupling library.

Publications

preCICE v2: A sustainable and user-friendly coupling library.

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