H3ABioNet: informatics solutions for H3Africa

H3ABioNet：H3Africa 的信息学解决方案

• 批准号: 10217222
• 负责人: Nicola Mulder
• 金额: $ 245.43万
• 依托单位: UNIVERSITY OF CAPE TOWN
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-08-15 至 2024-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10217222
• 关键词: Address; Africa; African; Archives; Bioinformatics; Biological; Clinical; Clinical Data; Communities; Complex; Consent; Country; Data; Data Analyses; Data Collection; Data Coordinating Center; Data Set; Databases; Development; Disease; Ensure; Environment; European; Fostering; Funding; Future; Generations; Genetic; Genome; Genomics; Goals; Grant; Head; Health; Health Benefit; Health care facility; Informatics; Infrastructure; International; Internet; Lead; Link; Management Information Systems; Maps; Meta-Analysis; Monitor; Ontology; Outcome; Ownership; Participant; Patients; Phase; Policy Maker; Process; Public Health Informatics; Quality Control; Research; Research Personnel; Resource Development; Resources; Scientist; Standardization; Structure; System; Training; Training Programs; Transferable Skills; Translating; Translational Research; Translations; Variant; Vision; Work; analysis pipeline; bioinformatics network; burden of illness; career; dashboard; data archive; data integration; data quality; data resource; data standards; data tools; experience; falls; genome wide association study; genomic data; genomic tools; improved; informatics infrastructure; informatics training; innovation; interoperability; member; multidisciplinary; network informatics; next generation; novel; outreach; phenome; precision medicine; public repository; skills; success; tool; tool development; trend

H3ABioNet Project Summary H3ABioNet, a pan African bioinformatics network for H3Africa, had the enormous task of building bioinformatics capacity for genomics research against a backdrop of high disease burden, limited resources, poor internet and a large gap in bioinformatics skills in Africa. Despite these challenges, the network achieved a number of successes by building computing infrastructure and associated skills, developing and facilitating access to analysis tools, and implementing a comprehensive training programme. In the next phase, H3ABioNet will extend these activities more broadly to develop a robust and innovative informatics network that addresses the complex needs of genomics researchers from clinical and biological data collection to genomic data generation and analysis and ultimately to impactful translation health research. The network will be the H3Africa data coordinating centre, hosting the data prior to submission to public repositories and providing access to data in line with the needs and consent of PIs and participants. It will ensure that data is quality controlled, standardized and interoperable. In order to facilitate adequate exploitation of genomic data, H3ABioNet will improve the user experience with genomics tools, adapting them, where necessary, for African data. The network will also go beyond this by seeking innovative data integration and translational solutions to enable comprehensive systems level analysis of diseases to ensure African scientists not only remain internationally competitive, but lead the way in translational research with tangible benefits for patients. The informatics infrastructure will be implemented through eight work packages: 1) Health Informatics; 2) Data and standards; 3) Databases and resources; 4) Pipelines and Computing; 5) Tool Development; 6) Integration; 7) Training; and 8) Sustainability, Outreach and Development. A ninth, cross-cutting activity, will be H3Africa project and Coordinating Center support in data analysis and the use of the infrastructure developed. H3ABioNet will reach out to all members of the H3Africa consortium and beyond to ensure maximum utilization of our resources and to transfer skills across the continent. It will develop the next generation of African scientists who have multidisciplinary skills and the capacity to successfully attract research funding. Links with national and international organisations and networks will ensure that these scientists remain on the cutting edge of genomics and are well placed for future realisation of precision medicine.

H3ABioNet项目摘要 H3ABioNet，一个面向H3Africa的泛非洲生物信息学网络，面临着巨大的任务 在高疾病背景下建设基因组学研究的生物信息学能力 负担、有限的资源、糟糕的互联网以及非洲生物信息学技能的巨大差距。 尽管面临这些挑战，该网络还是通过构建计算能力取得了一些成功 基础设施和相关技能，开发和便利使用分析工具，以及 实施全面的培训方案。在下一阶段，H3ABioNet将扩展 这些活动范围更广，以发展一个强大和创新的信息学网络， 从临床和生物学数据解决基因组研究人员的复杂需求 从收集到基因组数据的生成和分析，最终到有效的翻译 健康研究。该网络将成为H3非洲数据协调中心，负责托管数据 在提交到公共存储库之前，并根据需要提供对数据的访问 并征得私人投资者和参与者的同意。它将确保数据得到质量控制、标准化 并且可以互操作。为了促进充分利用基因组数据，H3ABioNet将 使用基因组学工具改善用户体验，必要时对其进行调整以适应非洲 数据。网络还将超越这一点，寻求创新的数据集成和 翻译解决方案，以实现对疾病的全面系统级别分析，以确保 非洲科学家不仅保持着国际竞争力，而且在翻译方面处于领先地位 为患者带来实实在在好处的研究。将实施信息学基础设施 通过八个工作包：1)卫生信息学；2)数据和标准；3)数据库和 资源；4)管道和计算；5)工具开发；6)集成；7)培训；以及 8)可持续性、外展和发展。第九个交叉活动将是H3非洲 项目和协调中心在数据分析和基础设施使用方面的支持 发展起来的。H3ABioNet将与H3Africa财团的所有成员及其他成员进行接触 以确保最大限度地利用我们的资源，并在整个大陆转让技能。它 将培养下一代具有多学科技能的非洲科学家 成功吸引研究资金的能力。与国内和国际的联系 组织和网络将确保这些科学家保持在 基因组学，为未来实现精确医学奠定了良好的基础。

项目成果

Integrated molecular characterisation of the MAPK pathways in human cancers reveals pharmacologically vulnerable mutations and gene dependencies.

• DOI: 10.1038/s42003-020-01552-6
• 发表时间: 2021-01-04
• 期刊: Communications biology
• 影响因子: 5.9
• 作者: Sinkala M;Nkhoma P;Mulder N;Martin DP
• 通讯作者: Martin DP

MDM-TASK-web: MD-TASK and MODE-TASK web server for analyzing protein dynamics.

• DOI: 10.1016/j.csbj.2021.08.043
• 发表时间: 2021
• 期刊: Computational and structural biotechnology journal
• 影响因子: 6
• 作者: Sheik Amamuddy O;Glenister M;Tshabalala T;Tastan Bishop Ö
• 通讯作者: Tastan Bishop Ö

TBDBT: A TB DataBase Template for collection of harmonized TB clinical research data in REDCap, facilitating data standardisation for inter-study comparison and meta-analyses.

• DOI: 10.1371/journal.pone.0249165
• 发表时间: 2021
• 期刊: PloS one
• 影响因子: 3.7
• 作者: Allie T;Jackson A;Ambler J;Johnston K;Du Bruyn E;Schultz C;Boloko L;Wasserman S;Davis A;Meintjes G;Wilkinson RJ;Tiffin N
• 通讯作者: Tiffin N

Equity, diversity, and inclusion at the Global Alliance for Genomics and Health.

• DOI: 10.1016/j.xgen.2023.100386
• 发表时间: 2023-10-11
• 期刊: CELL GENOMICS
• 作者: Skantharajah, Neerjah;Baichoo, Shakuntala;Boughtwood, Tiffany F.;Casas-Silva, Esmeralda;Chandrasekharan, Subhashini;Dave, Sanjay M.;Fakhro, Khalid A.;de Vargas, Aida B. Falcon;Gayle, Sylvia S.;Gupta, Vivek K.;Hendricks-Sturrup, Rachele;Hobb, Ashley E.;Li, Stephanie;Llamas, Bastien;Lopez-Correa, Catalina;Machirori, Mavis;Melendez-Zajgla, Jorge;Millner, Mareike A.;Page, Angela J. H.;Pagilone, Laura D.;Raven-Adams, Maili C.;Smith, Lindsa;Thomas, Ericka M.;Kumthini, Judi;Corpas, Manuel
• 通讯作者: Corpas, Manuel

Targeted Sanger sequencing to recover key mutations in SARS-CoV-2 variant genome assemblies produced by next-generation sequencing.

• DOI: 10.1099/mgen.0.000774
• 发表时间: 2022-03
• 期刊: MICROBIAL GENOMICS
• 影响因子: 3.9
• 作者: Singh, Lavanya;San, James E.;Tegally, Houriiyah;Brzoska, Pius M.;Anyaneji, Ugochukwu J.;Wilkinson, Eduan;Clark, Lindsay;Giandhari, Jennifer;Pillay, Sureshnee;Lessells, Richard J.;Martin, Darren Patrick;Furtado, Manohar;Kiran, Anmol M.;de Oliveira, Tulio
• 通讯作者: de Oliveira, Tulio