Maintenance and Extension of a Central Project Knowledge Base (CPKB), systems biomedicine and statistics pipeline

中央项目知识库（CPKB）、系统生物医学和统计管道的维护和扩展

• 批准号: 318861229
• 负责人: Professor Dr. Hauke Busch
• 金额: --
• 依托单位: Institut für Medizinische Biometrie und Statistik
• 依托单位国家: 德国
• 项目类别: Research Units
• 资助国家: 德国
• 项目状态: 未结题
• 来源: https://gepris.dfg.de/gepris/projekt/318861229?language=en
• 关键词: Maintenance; Extension; Central; Project; Knowledge

The goals of the INF project in the second funding period of ProtectMove are three-fold. The first is to maintain and develop a Central Project Knowledge Base (CPKB) that supports team communication, provides a regulatory framework for data management and enables its long-term storage. The second is to operate a Systems Biomedicine Core which provides bioinformatics and modeling support for all projects. Activities will be pursued by groups at the two UKSH campuses at Lübeck and Kiel and the Bioinformatics Core at the University of Luxembourg. The third goal is to provide Biostatistics support for high-level statistical expertise with respect to study design and analysis. The CPKB will continue to be responsible for the long-term management, storage and governance of all data generated by ProtectMove subprojects. It will facilitate internal communication within the research group by developing further a group-wide research Wiki. A focus will be to align IT activities for ProtectMove with current data integration at UKSH in Lübeck/Kiel. The Biostatistics pipeline will provide state-of-the-art biometric support including study design, genetic epidemiological, classical statistical, and machine learning approaches. These will optimize experimental and human studies and strengthen the integrity and reproducibility of results. The Systems Medicine Core will provide comprehensive analyses of genome, transcriptome, epigenome, metabolome and phenome data. Data analysis will be pursued to variable depth according to the needs and wants of the project partners, ranging from experimental design, quality control, normalization and data annotation to integrative OMICs analysis using unsupervised or supervised methods and detailed modeling of molecular pathways. Data will be processed using standardized, yet adaptive workflows that will run reproducibly as singularity containers in a high-performance computing environment on the Lübeck campus.All PIs have extensive experience in leading and coordinating informatics support projects in medical research networks. The Krawczak group has been involved in implementing and operating the P2N biobank network at Kiel University and is participating in the integration of patient- centered research and clinical care data. The Erdmann group has world-leading expertise in complex genetics with a main focus on cardio-genetics. The König group has long-standing expertise in large scale genetic epidemiological studies, clinical trials, prognostic modeling, and development of machine learning methods. The Busch group heads a systems biology core unit at Lübeck University, develops the HPC infrastructure on campus and is experienced in bioinformatics analysis of various data types. The May group has established a data-hub for Parkinson’s disease (PD) sequencing data, is involved in international multi-omics projects on epilepsy, microbiome and PD research and hosts the ELIXIR node for Translational Medicine.

在“保护行动”第二个筹资期，INF项目的目标有三个方面。第一个是维护和开发一个中央项目知识库（Central Project Knowledge Base， CPKB），该知识库支持团队通信，为数据管理提供一个规范框架，并支持其长期存储。二是运营系统生物医学核心，为所有项目提供生物信息学和建模支持。活动将由位于l<s:1>贝克和基尔的两个UKSH校区以及卢森堡大学生物信息学核心的小组进行。第三个目标是为研究设计和分析方面的高级统计专家提供生物统计学支持。CPKB将继续负责ProtectMove子项目生成的所有数据的长期管理、存储和治理。它将通过进一步发展全组范围的研究Wiki来促进研究小组内部的交流。重点将是使ProtectMove的IT活动与位于莱尔贝克/基尔的UKSH当前的数据集成保持一致。生物统计学管道将提供最先进的生物统计学支持，包括研究设计、遗传流行病学、经典统计学和机器学习方法。这将优化实验和人体研究，并加强结果的完整性和可重复性。系统医学核心将提供基因组、转录组、表观基因组、代谢组和表型组数据的综合分析。数据分析将根据项目合作伙伴的需求进行不同深度的研究，从实验设计、质量控制、规范化和数据注释，到使用无监督或有监督方法的综合组学分析，以及分子途径的详细建模。数据将使用标准化的自适应工作流进行处理，这些工作流将作为奇点容器在l<s:1>贝克校区的高性能计算环境中可重复运行。所有pi在领导和协调医学研究网络中的信息学支持项目方面都有丰富的经验。Krawczak团队参与了基尔大学P2N生物银行网络的实施和运营，并参与了以患者为中心的研究和临床护理数据的整合。厄德曼集团在复杂遗传学方面拥有世界领先的专业知识，主要专注于心脏遗传学。König小组在大规模遗传流行病学研究、临床试验、预后建模和机器学习方法开发方面拥有长期的专业知识。Busch团队在l<s:1>贝克大学领导一个系统生物学核心部门，在校园开发高性能计算基础设施，并在各种数据类型的生物信息学分析方面经验丰富。May团队已经建立了帕金森病（PD）测序数据中心，参与了癫痫、微生物组和PD研究的国际多组学项目，并主持了ELIXIR转化医学节点。