DMMCore: Data and Model Management Core for ERASysAPP & Europe

DMMCore：ERASysAPP 的数据和模型管理核心

• 批准号: BB/M013189/1
• 负责人: Carole Goble
• 金额: $ 129.43万
• 依托单位: University of Manchester
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2014
• 资助国家: 英国
• 起止时间: 2014 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FM013189%2F1
• 关键词: DMMCore; Data; Model; Management; Core

This project, in partnership with colleagues in HITS, Heidelberg and Sybit, Switzerland, aims at establishing an internationally sustained Data and Model Management service to the European Systems Biology community. Many projects in Systems Biology have been funded worldwide. However, it is often not clear how the results are made available to further research. Some result data sets or models are stored in public resources, but not all. Other repositories are ripe for a greater exploitation world-wide. Funding agencies now expect new projects to publish their results using open access and to provide a data management and data sustainability plan to assure that their investment has the desired impact. However, the researchers often have neither the means nor the knowledge necessary to publish and maintain their results according to the necessary standards so that they remain available beyond the end of their project. The results as requested by the publishers are often insufficient to be able to reliably reproduce results. Models and standard operating procedures are often not available or are not sufficiently described to be reproducible. This introduces inefficiencies, as the limited reusability and impact of project results on future projects leads to reinventions of methods and tools and slows the pace of scientific progress. Systems Biology projects often have large and heterogeneous data sets, always have mathematical models based on experimental data. Such projects usually have researchers from various disciplines at many locations collaborating, where direct communication is often difficult not just because of the locality but also due to different semantics among disciplines. A shared software interface with transparent data and links to models is essential to allow for interdisciplinary research and to interact among research groups in Systems Biology. The iterative cycle between experiment and models that is typical in System Biology projects, mandates a good versioning system for experiment and model versions as well as investigation-study organisational structures such that the project workflow is clear and reproducible. Furthermore, a strict adherence to community standards and standard operating procedures is important for linking data and models created by different project members. A management platform needs to support experimental workflows and model and data linkages, with good tools for data and model annotation and adherence to standard formats of representation. In order to have all the information for a reproducible scientific process, data for model construction and model validation need to be clearly separated and all data, models and Standard Operating Procedures must be made available for download. Dedicated software platforms and tools are necessary to lift scientific research in Systems Biology up to industrial standards of reproducibility and quality control. In this project we will establish a sustainable European data and model e-infrastructure for the European systems biology community with a long-term business model. We will found a European wide Data & Model Management Network to support and promote data and model management and capacity building, using the EraSysAPP ERANet as a seed. We will disseminate knowledge and standards, coordinating with related e-infrastructures such as ELIXIR and ISBE, and interacting with community related policy and standards settings. We will develop the necessary toolset and set up a data and model management platform for Systems Biology projects by combining and further developing/improving the well-proven software platforms SEEK and openBIS with a pool of public tools and resources, working closely with both the user and the developer communities. Finally, we will establish a sustainable training programming on the use and development of the platform and on data/model management practices for Systems Biology.

该项目与HITS，海德堡和瑞士Sybit的同事合作，旨在为欧洲系统生物学社区建立国际持续的数据和模型管理服务。系统生物学的许多项目都得到了世界各地的资助。然而，通常不清楚如何将结果提供给进一步的研究。一些结果数据集或模型存储在公共资源中，但不是全部。其他的知识库已经成熟，可以在世界范围内进行更大的开发。资助机构现在希望新项目使用开放获取发布其结果，并提供数据管理和数据可持续性计划，以确保其投资产生预期的影响。然而，研究人员往往既没有必要的手段，也没有必要的知识来根据必要的标准发表和维护他们的结果，以便他们在项目结束后仍然可以使用。出版商要求的结果往往不足以可靠地复制结果。模型和标准操作程序往往不可用，或没有充分说明可复制性。这导致了效率低下，因为项目成果的可重用性和对未来项目的影响有限，导致方法和工具的重新发明，减缓了科学进步的步伐。系统生物学项目通常具有大型和异构的数据集，总是有基于实验数据的数学模型。这些项目通常有来自许多地方的不同学科的研究人员进行合作，直接沟通往往很困难，不仅因为地点，而且还因为学科之间的语义不同。具有透明数据和模型链接的共享软件接口对于跨学科研究和系统生物学研究小组之间的互动至关重要。系统生物学项目中典型的实验和模型之间的迭代循环要求实验和模型版本以及调查研究组织结构具有良好的版本控制系统，以便项目工作流程清晰且可重现。此外，严格遵守社区标准和标准操作程序对于连接不同项目成员创建的数据和模型非常重要。管理平台需要支持实验工作流程以及模型和数据链接，并提供良好的数据和模型注释工具，并遵守标准的表示格式。为了获得可重复的科学过程的所有信息，模型构建和模型验证的数据需要明确分开，所有数据，模型和标准操作程序必须可供下载。专用的软件平台和工具是必要的，以提升系统生物学的科学研究达到再现性和质量控制的工业标准。在这个项目中，我们将为欧洲系统生物学社区建立一个可持续的欧洲数据和模型电子基础设施，并提供长期的商业模式。我们将建立一个欧洲范围的数据和模型管理网络，以支持和促进数据和模型管理以及能力建设，使用EraSysAPP ERANet作为种子。我们将传播知识和标准，与相关的电子基础设施，如ELIXIR和ISBE协调，并与社区相关的政策和标准设置互动。我们将开发必要的工具集，并通过结合和进一步开发/改进成熟的软件平台SEEK和openBIS与公共工具和资源池，与用户和开发人员社区密切合作，为系统生物学项目建立数据和模型管理平台。最后，我们将建立一个可持续的培训计划的使用和开发平台和系统生物学的数据/模型管理实践。

项目成果

FAIRDOM approach for semantic interoperability of systems biology data and models

用于系统生物学数据和模型语义互操作性的 FAIRDOM 方法

• 发表时间: 2016
• 期刊: CEUR Workshop Proceedings
• 作者: Krebs O.

An automated Design-Build-Test-Learn pipeline for enhanced microbial production of fine chemicals.

• DOI: 10.1038/s42003-018-0076-9
• 发表时间: 2018
• 期刊: Communications biology
• 影响因子: 5.9
• 作者: Carbonell P;Jervis AJ;Robinson CJ;Yan C;Dunstan M;Swainston N;Vinaixa M;Hollywood KA;Currin A;Rattray NJW;Taylor S;Spiess R;Sung R;Williams AR;Fellows D;Stanford NJ;Mulherin P;Le Feuvre R;Barran P;Goodacre R;Turner NJ;Goble C;Chen GG;Kell DB;Micklefield J;Breitling R;Takano E;Faulon JL;Scrutton NS
• 通讯作者: Scrutton NS

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

21 世纪的标识符：如何设计、提供和重用持久标识符以最大限度地提高生命科学数据的效用和影响

• DOI: 10.1101/117812
• 发表时间: 2017
• 作者: McMurry J

Studying Glycolytic Oscillations in Individual Yeast Cells by Combining Fluorescence Microscopy with Microfluidics and Optical Tweezers.

通过将荧光显微镜与微流体和光镊相结合来研究单个酵母细胞中的糖酵解振荡。

• DOI: 10.1002/cpcb.70
• 发表时间: 2019
• 期刊: Current protocols in cell biology
• 作者: Gustavsson AK

COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project.

• DOI: 10.1186/s12859-014-0369-z
• 发表时间: 2014-12-14
• 期刊: BMC bioinformatics
• 影响因子: 3
• 作者: Bergmann FT;Adams R;Moodie S;Cooper J;Glont M;Golebiewski M;Hucka M;Laibe C;Miller AK;Nickerson DP;Olivier BG;Rodriguez N;Sauro HM;Scharm M;Soiland-Reyes S;Waltemath D;Yvon F;Le Novère N
• 通讯作者: Le Novère N