Development of Bioinformatics Infrastructure for Genomics Research.
Development of Bioinformatics Infrastructure for Genomics Research.
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DOI：
10.1016/j.gheart.2017.01.005
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发表时间：
2017-06
期刊：
影响因子：
3.7
通讯作者：
H3ABioNet Consortium, as members of the H3Africa Consortium
中科院分区：
文献类型：
--
作者：
Mulder NJ;Adebiyi E;Adebiyi M;Adeyemi S;Ahmed A;Ahmed R;Akanle B;Alibi M;Armstrong DL;Aron S;Ashano E;Baichoo S;Benkahla A;Brown DK;Chimusa ER;Fadlelmola FM;Falola D;Fatumo S;Ghedira K;Ghouila A;Hazelhurst S;Isewon I;Jung S;Kassim SK;Kayondo JK;Mbiyavanga M;Meintjes A;Mohammed S;Mosaku A;Moussa A;Muhammd M;Mungloo-Dilmohamud Z;Nashiru O;Odia T;Okafor A;Oladipo O;Osamor V;Oyelade J;Sadki K;Salifu SP;Soyemi J;Panji S;Radouani F;Souiai O;Tastan Bishop Ö;H3ABioNet Consortium, as members of the H3Africa Consortium
虽然非洲已发展出一些生物信息学方面的卓越成果，但一般而言，大规模的基因组数据分析受到专门知识和基础设施的限制。H3ABioNet是一个泛非生物信息学网络，建立该网络的目的是专门建设能力，使H3Africa研究人员能够分析其在非洲的数据。自H3Africa倡议启动以来，H3ABioNet的作用随着联盟和非洲生物信息学界不断变化的需求而不断演变。该网络着手在数据收集、转移、储存和分析等各个方面发展核心生物信息学基础设施和基因组学研究能力。已经开发了各种资源，以满足H3Africa研究人员和非洲大陆其他科学界的基因组数据管理和分析需求。开发了NetMap，用于准确了解非洲内部以及非洲与世界其他地区之间的网络运行情况，并推出了Globus Online，以便利数据传输。开发了一个参与者征聘数据库，以监测参与者的登记情况，目前正在通过使用本体和受控词汇统一数据。将整合标准化元数据，为H3非洲数据和生物标本提供搜索设施。由于H3非洲项目正在产生大规模的基因组数据，因此分析和解释的设施至关重要。H3ABioNet正在实施几个数据分析平台，提供大量的生物信息学工具或工作流程，如Galaxy，作业管理系统和eBiokits。一组可复制、可移植和云可扩展的管道，以支持多种H3Africa数据类型，也正在开发和对接，以实现在多个计算基础设施上的执行。此外，还开发了新的工具，用于分析非洲独特的差异性数据，并用于对优先变量进行下游解释。为了支持这些和其他生物信息学查询，建立了一个由广泛的联盟专门知识支持的在线生物信息学帮助台。通过各种生物信息学培训模式提供进一步的支持。过去4年来，通过H3ABioNet发展基础设施支助和人力资源能力，为建立非洲科学网络、数据分析设施和培训方案作出了重大贡献。在这里，我们描述了基础设施以及它如何影响非洲的基因组学和生物信息学研究。
Although pockets of bioinformatics excellence have developed in Africa, generally, large-scale genomic data analysis has been limited by the availability of expertise and infrastructure. H3ABioNet, a Pan African bioinformatics network, was established to build capacity specifically to enable H3Africa researchers to analyse their data in Africa. Since the inception of the H3Africa initiative, H3ABioNet’s role has evolved in response to changing needs from the consortium and the African bioinformatics community. The network set out to develop core bioinformatics infrastructure and capacity for genomics research in various aspects of data collection, transfer, storage and analysis. Various resources have been developed to address genomic data management and analysis needs of H3Africa researchers and other scientific communities on the continent. NetMap was developed and used to build an accurate picture of network performance within Africa and between Africa and the rest of the world, and Globus Online has been rolled out to facilitate data transfer. A participant recruitment database was developed to monitor participant enrolment, and data is being harmonized through the use of ontologies and controlled vocabularies. The standardized metadata will be integrated to provide a search facility for H3Africa data and biospecimens. Since H3Africa projects are generating large-scale genomic data, facilities for analysis and interpretation are critical. H3ABioNet is implementing several data analysis platforms that provide a large range of bioinformatics tools or workflows, such as Galaxy, the Job Management System and eBiokits. A set of reproducible, portable and cloud scalable pipelines to support the multiple H3Africa data types are also being developed and dockerized to enable execution on multiple computing infrastructures. In addition, new tools have been developed for analysis of the uniquely divergent African data and for downstream interpretation of prioritized variants. To provide support for these and other bioinformatics queries, an online bioinformatics helpdesk backed by broad consortium expertise has been established. Further support is provided by means of various modes of bioinformatics training. For the past 4 years, the development of infrastructure support and human capacity through H3ABioNet, have significantly contributed to the establishment of African scientific networks, data analysis facilities and training programmes. Here, we describe the infrastructure and how it has impacted genomics and bioinformatics research in Africa.
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影响因子：
5.8
作者：
Horridge, Matthew;Tudorache, Tania;Musen, Mark A.
通讯作者：
Musen, Mark A.
影响因子：
14.9
作者：
Hubbard, T;Barker, D;Clamp, M
通讯作者：
Clamp, M
影响因子：
30.8
作者：
Lappalainen I;Almeida-King J;Kumanduri V;Senf A;Spalding JD;Ur-Rehman S;Saunders G;Kandasamy J;Caccamo M;Leinonen R;Vaughan B;Laurent T;Rowland F;Marin-Garcia P;Barker J;Jokinen P;Torres AC;de Argila JR;Llobet OM;Medina I;Puy MS;Alberich M;de la Torre S;Navarro A;Paschall J;Flicek P
通讯作者：
Flicek P
影响因子：
7
作者：
Mulder NJ;Adebiyi E;Alami R;Benkahla A;Brandful J;Doumbia S;Everett D;Fadlelmola FM;Gaboun F;Gaseitsiwe S;Ghazal H;Hazelhurst S;Hide W;Ibrahimi A;Jaufeerally Fakim Y;Jongeneel CV;Joubert F;Kassim S;Kayondo J;Kumuthini J;Lyantagaye S;Makani J;Mansour Alzohairy A;Masiga D;Moussa A;Nash O;Ouwe Missi Oukem-Boyer O;Owusu-Dabo E;Panji S;Patterton H;Radouani F;Sadki K;Seghrouchni F;Tastan Bishop Ö;Tiffin N;Ulenga N;H3ABioNet Consortium
通讯作者：
H3ABioNet Consortium
影响因子：
14.9
作者：
UniProt Consortium
通讯作者：
UniProt Consortium