MultiMod, flexible management for multi-scale multi-approach models in biology

MultiMod，生物学中多尺度多方法模型的灵活管理

• 批准号: BB/N019474/1
• 负责人: Simon Andrews
• 金额: $ 35.25万
• 依托单位: Babraham Institute
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2016
• 资助国家: 英国
• 起止时间: 2016 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FN019474%2F1
• 关键词: MultiMod; flexible; management; multi; scale

Even the simplest living organisms perform a huge number of different processes, which are interconnected in complex ways to ensure that the organism responds appropriately to its environment. One of the ways of ensuring that we really understand how these processes fit together is to build quantitative mathematical models of them which can be simulated using computers. This approach is known as "Computational Systems Biology". As in most domains of science, databases are essential to allow the proverbial "standing on the shoulders of giants". BioModels provides access to quantitative biology models that have been published in the scientific literature, and verified to be accurate. For instance, in order to develop a quantitative model of cell tumorigenesis, one may choose a suitable model of cell-cycle, and attempt to merge it with models of relevant cell signalling pathways such as the MAP kinase cascade. Since its creation at EMBL-EBI in 2005 - and supported by the BBSRC since 2008 - BioModels has undergone an exponential growth to become the worldwide reference for quantitative models of biological processes. Deposition of models upon publication is advised by several hundred scientific journals, and the resource receives around a million page requests a year from around 65 000 distinct users.Over the recent years, mathematical models of biological processes have become larger and more complex. To be able to represent more accurately living structures, multi-scale models are developed, with processes taking place at different scales described by components coupled together. Because of the nature of the processes as well as the experimental information available, a variety of modelling approaches are use. In 2012, a landmark publication described the first such model of a bacterium (Mycoplasma genitalium) that accounts for all of its components and their interactions. Multi-scale models of organs and organisms (for instance the BBSRC-funded model of Arabidopsis) are now available. Those models must be made available, regardless of their structure, the modelling approach used and the formats they are encoded with.The MultiMod project, developed in collaboration by the Babraham Institute and EMBL-EBI, will extend BioModels coverage considerably, to support a large variety of mathematical models developed in the biosciences. This will be achieved by accepting more file formats, improving support for standard formats and expanding the information distributed (for instance including necessary experimental datasets, simulation descriptions etc). We will also expand the spectrum of models we verify by reproducing published results. Such an increase in scope will be accompanied by an improvement of the software and hardware infrastructure underlying the resource. To make the resource more useful we will develop better browsing, search and download capabilities. Finally, we will improve and further develop our documentation and training offer, including online and in person tutorial and courses. We expect that MultiMod will improve the user experience significantly, increase the number of users and the communities using the resource, and make it more useful for the UK biosciences.

即使是最简单的生物体也会执行大量不同的过程，这些过程以复杂的方式相互关联，以确保生物体对其环境做出适当的反应。确保我们真正理解这些过程如何结合在一起的方法之一是建立可以用计算机模拟的定量数学模型。这种方法被称为“计算系统生物学”。正如在大多数科学领域一样，数据库对于实现“站在巨人的肩膀上”至关重要。BioModels提供了对已在科学文献中发表并经验证准确的定量生物学模型的访问。例如，为了开发细胞肿瘤发生的定量模型，可以选择合适的细胞周期模型，并尝试将其与相关细胞信号传导途径（如MAP激酶级联）的模型合并。自2005年在EMBL-EBI创建以来-并自2008年以来得到BBSRC的支持- BioModels经历了指数增长，成为生物过程定量模型的全球参考。数百种科学期刊建议在出版时存放模型，该资源每年收到来自约65000个不同用户的约100万页的请求。近年来，生物过程的数学模型变得更大更复杂。为了能够更准确地表示生命结构，开发了多尺度模型，其中通过耦合在一起的组件描述在不同尺度下发生的过程。由于过程的性质以及可用的实验信息，使用了各种建模方法。2012年，一份具有里程碑意义的出版物描述了第一个这样的细菌模型（生殖支原体），该模型解释了其所有组分及其相互作用。器官和生物体的多尺度模型（例如BBSRC资助的拟南芥模型）现在可用。这些模型必须提供，无论其结构如何，使用的建模方法和编码格式如何。由Babraham研究所和EMBL-EBI合作开发的MultiMod项目将大大扩展BioModels的覆盖范围，以支持生物科学中开发的各种数学模型。这将通过接受更多的文件格式，改进对标准格式的支持以及扩展分发的信息（例如包括必要的实验数据集，模拟描述等）来实现。我们还将通过复制已发表的结果来扩展我们验证的模型的范围。在扩大范围的同时，还将改善作为资源基础的软件和硬件基础设施。为了使资源更有用，我们将开发更好的浏览，搜索和下载功能。最后，我们将改进和进一步开发我们的文档和培训服务，包括在线和面对面的教程和课程。我们预计MultiMod将显著改善用户体验，增加使用该资源的用户和社区数量，并使其对英国生物科学更有用。

项目成果

Reproducibility in systems biology modelling.

• DOI: 10.15252/msb.20209982
• 发表时间: 2021-03
• 期刊: Molecular systems biology
• 影响因子: 9.9
• 作者: Tiwari K;Kananathan S;Roberts MG;Meyer JP;Sharif Shohan MU;Xavier A;Maire M;Zyoud A;Men J;Ng S;Nguyen TVN;Glont M;Hermjakob H;Malik-Sheriff RS
• 通讯作者: Malik-Sheriff RS

Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology.

• DOI: 10.1093/bib/bbac212
• 发表时间: 2022-07-18
• 期刊: Briefings in bioinformatics
• 影响因子: 9.5

BioModels Parameters: a treasure trove of parameter values from published systems biology models.

• DOI: 10.1093/bioinformatics/btaa560
• 发表时间: 2020-11-01
• 期刊: Bioinformatics (Oxford, England)
• 作者: Glont M;Arankalle C;Tiwari K;Nguyen TVN;Hermjakob H;Malik-Sheriff RS
• 通讯作者: Malik-Sheriff RS

A brief history of COMBINE

COMBINE 简史

• 发表时间: 2017
• 作者: Myers C

BioModels: expanding horizons to include more modelling approaches and formats.

• DOI: 10.1093/nar/gkx1023
• 发表时间: 2018-01-04
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Glont M;Nguyen TVN;Graesslin M;Hälke R;Ali R;Schramm J;Wimalaratne SM;Kothamachu VB;Rodriguez N;Swat MJ;Eils J;Eils R;Laibe C;Malik-Sheriff RS;Chelliah V;Le Novère N;Hermjakob H
• 通讯作者: Hermjakob H