SysMO-DB2

系统管理数据库2

• 批准号: BB/I004637/1
• 负责人: Carole Goble
• 金额: $ 121.08万
• 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: 2010
• 资助国家: 英国
• 起止时间: 2010 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FI004637%2F1
• 关键词: SysMO; DB2

Systems biology is a biology-based inter-disciplinary study field combining experimental investigations and computational modeling to discover emergent properties of complex interactions in biological systems. SysMO is a European trans-national funding and research initiative on 'Systems Biology of Microorganisms'. The initiative's goal is to record and describe the dynamic molecular processes that occur in microorganisms in a comprehensive way and to present these processes in the form of computerized mathematical models. Each project is made up of a consortium of European institutions and each works towards different research outcomes on a variety of microorganisms, including bacteria, archaea (single-celled microorganisms) and yeast. The environmental conditions for each organism vary, growing in culture, soil, water and animal hosts. This diversity means that there are many different kinds of models and many different types of data collected. The SysMO initiative has been divided into two phases: SysMO1 funded eleven projects and 91 institutions; SysMO2 will fund seven projects, five of which are project continuations from phase 2 (so six projects are concluded) and two of which are new. The research outcomes (models, data, procedures), and the know-how and best practice developed by the scientists, are to be managed and pooled in order to: benefit the members of the programme during the running of the projects; disseminate and publish the results to the wider scientific community; and safeguard the results after the completion of the projects that maximises the 'shelf life' and utility of data generated by SysMO. SysMO-DB is a project to build and manage an incrementally developed web-based software platform to achieve this. SysMO-DB1, funded during the first phase, begun the development of a web-based platform - called the SEEK - for cataloguing the different outcomes of the projects, archiving data, procedures and models and integrating with the different project's local data management systems, including the standardisation of the information used to describe the data and models and the handling of project spreadsheets. The SEEK also includes a social network for the SysMO members and integrates with public repositories for data, models, analyses and publications such as JWS Online (for models); SABIO-RK (for data), myExperiment (for bioinformatics data analysis pipelines) and PubMed (for publications). SysMO-DB has also developed effective practices for working with SysMO scientists through the founding of a PALs focus group of researchers who shape the developments, data standards and protocols necessary for pooling and promote SEEK adoption in their own projects. The focus of SysMO-DB1 is on supporting the current projects. SysMO-DB2 continues and extends the work to cope with SysMO-phase changes and life after beyond and after SysMO: new and terminating projects, personnel change, publication outside the consortium and long-term preservation of results. SysMO-DB2 also plans to package up the software and methods so that they can be adopted and sustained by other programmes such as EraSysBio+. EraSysBio+ is a pan-European programme for 16 Systems Biology projects. It is similar in organisation to SysMO but radically different in terms of scope. Hence it differs in the data, model and process capabilities needed. As part of widening the adoption of the SysMO-DB approach the project will support EraSysBio+ in its first 18 months. The two projects from EraSysBio+ that focus on microorganisms will be fully integrated into the SysMO-DB work programme. For the full range of EraSysBio+ projects SysMO-DB2 will instantiate a new instance of the SEEK, provide advice and help launch a PALs scheme.

系统生物学是一个基于生物学的跨学科研究领域，结合了实验研究和计算建模，以发现生物系统中复杂相互作用的新兴特性。 Sysmo是一项欧洲跨国资金和研究计划，涉及“微生物系统生物学”。该计划的目标是以全面的方式记录和描述微生物中发生的动态分子过程，并以计算机化数学模型的形式介绍这些过程。每个项目均由欧洲机构组成，每项项目都为各种微生物的不同研究成果而组成，包括细菌，古细菌（单细胞微生物）和酵母。每种生物的环境条件在培养，土壤，水和动物宿主中都在变化。这种多样性意味着收集了许多不同类型的模型和许多不同类型的数据。 Sysmo倡议已分为两个阶段：SYSMO1资助了11个项目和91个机构； SYSMO2将资助七个项目，其中五个是第2阶段的项目延续（因此得出了六个项目），其中两个是新的。研究结果（模型，数据，程序）以及科学家开发的专有技术和最佳实践应进行管理和汇总，以使：在项目运行过程中使计划成员受益；将结果传播并发布给更广泛的科学界；并在完成最大化的“保质期”和Sysmo生成的数据的实用性的项目完成后维护结果。 Sysmo-DB是一个旨在构建和管理基于Web的软件平台以实现此目的的项目。在第一阶段资助的Sysmo -DB1开始开发一个基于网络的平台（称为Seek），用于对项目的不同结果，归档数据，程序和模型进行分类，并与不同项目的本地数据管理系统集成，包括用于描述项目电子表格的数据和模型的信息的标准化。 SEEK还包括一个针对Sysmo成员的社交网络，并与公共存储库集成了数据，模型，分析和出版物，例如JWS Online（用于模型）； SABIO-RK（用于数据），MySconperigent（用于生物信息学数据分析管道）和PubMed（用于出版物）。 Sysmo-DB还通过建立一个焦点的研究人员组成的研究人员，他们塑造了在自己的项目中汇总和促进寻求收养所必需的发展，与SYSMO科学家合作开发了有效的实践。 Sysmo-DB1的重点是支持当前项目。 Sysmo-DB2继续进行并扩展工作，以应对SYSMO相变的变化和生命，之后和之后的Sysmo之后：新的和终止的项目，人员变革，财团以外的出版物以及结果的长期保存。 Sysmo-DB2还计划包装软件和方法，以便可以由其他程序（例如Erasysbio+）采用和维持。 Erasysbio+是16个系统生物学项目的泛欧洲计划。它在组织中与sysmo相似，但在范围方面截然不同。因此，它在需要的数据，模型和过程功能上有所不同。作为扩大SYSMO-DB方法采用的一部分，该项目将在最初的18个月内支持Erasysbio+。来自Erasysbio+的两个项目，重点是微生物，将完全集成到Sysmo-DB工作计划中。对于Erasysbio+ Projects的全部范围，Sysmo-DB2将实例化搜索的新实例，提供建议并帮助启动PALS计划。

项目成果

Phosphoglycerate kinase acts as a futile cycle at high temperature.

磷酸甘油酸激酶在高温下充当无效循环。

• DOI: 10.1099/mic.0.000542
• 发表时间: 2017
• 期刊: Microbiology (Reading, England)
• 作者: Kouril T

Determining enzyme kinetics for systems biology with nuclear magnetic resonance spectroscopy.

• DOI: 10.3390/metabo2040818
• 发表时间: 2012-11-06
• 期刊: Metabolites
• 影响因子: 4.1
• 作者: Eicher JJ;Snoep JL;Rohwer JM
• 通讯作者: Rohwer JM

Why linked data is not enough for scientists

• DOI: 10.1016/j.future.2011.08.004
• 发表时间: 2013-02-01
• 期刊: FUTURE GENERATION COMPUTER SYSTEMS-THE INTERNATIONAL JOURNAL OF ESCIENCE
• 影响因子: 7.5
• 作者: Bechhofer, Sean;Buchan, Iain;Goble, Carole
• 通讯作者: Goble, Carole

The evolution of standards and data management practices in systems biology.

• DOI: 10.15252/msb.20156053
• 发表时间: 2015-12-23
• 期刊: Molecular systems biology
• 影响因子: 9.9
• 作者: Stanford NJ;Wolstencroft K;Golebiewski M;Kania R;Juty N;Tomlinson C;Owen S;Butcher S;Hermjakob H;Le Novère N;Mueller W;Snoep J;Goble C
• 通讯作者: Goble C

Toward interoperable bioscience data.

• DOI: 10.1038/ng.1054
• 发表时间: 2012-01-27
• 期刊: NATURE GENETICS
• 影响因子: 30.8
• 作者: Sansone, Susanna-Assunta;Rocca-Serra, Philippe;Field, Dawn;Maguire, Eamonn;Taylor, Chris;Hofmann, Oliver;Fang, Hong;Neumann, Steffen;Tong, Weida;Amaral-Zettler, Linda;Begley, Kimberly;Booth, Tim;Bougueleret, Lydie;Burns, Gully;Chapman, Brad;Clark, Tim;Coleman, Lee-Ann;Copeland, Jay;Das, Sudeshna;de Daruvar, Antoine;de Matos, Paula;Dix, Ian;Edmunds, Scott;Evelo, Chris T.;Forster, Mark J.;Gaudet, Pascale;Gilbert, Jack;Goble, Carole;Griffin, Julian L.;Jacob, Daniel;Kleinjans, Jos;Harland, Lee;Haug, Kenneth;Hermjakob, Henning;Sui, Shannan J. Ho;Laederach, Alain;Liang, Shaoguang;Marshall, Stephen;McGrath, Annette;Merrill, Emily;Reilly, Dorothy;Roux, Magali;Shamu, Caroline E.;Shang, Catherine A.;Steinbeck, Christoph;Trefethen, Anne;Williams-Jones, Bryn;Wolstencroft, Katherine;Xenarios, Ioannis;Hide, Winston
• 通讯作者: Hide, Winston