BioLayout Express3D: A Community Resource for the Network Visualisation and Analysis of Biological Data and Pathways

BioLayout Express3D：生物数据和通路的网络可视化和分析的社区资源

• 批准号: BB/I001107/1
• 负责人: Tom Freeman
• 金额: $ 44.41万
• 依托单位: University of Edinburgh
• 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%2FI001107%2F1
• 关键词: BioLayout; Express3D; Community; Resource; Network

Biological data is increasingly complex and large-scale. Genome sequencing and other high-throughput technologies have provided us with a parts-list of life, together with a wealth of information about how these components interact with each other. Humans are inherently visual and representing this information in the form of graphs and graphics is an extremely useful aid to our understanding of its innate complexity. Tools that assist biologists in their ability to visualise, analyse and interpret biological systems are therefore potentially of great utility. Both applicants have a long-standing interest in the analysis of biological data and have been involved in the development of computer programs for its visualisation and analysis. In particular, with support from the BBSRC and Wellcome Trust, we have co-developed a powerful network analysis tool, BioLayout Express3D. This software has proved highly useful to applicant's research and also popular with the wider academic community. We therefore seek to continue to expand its functionality into new areas, thereby maintaining its position at the cutting-edge of the visualisation and interpretation of biological systems. This project capitalises on the existing collaborative work and aims to explore new areas of computation, biology and visualisation with both participating laboratories scoping, testing and validating developments prior to their release to the wider community. Our first aim is to refine and expand the existing interface of BioLayout Express3D to enable it to read and process biological data from a wide variety of sources. We also seek to improve the quality of the user interface and its analytical potential, as well as to provide improved support and training its users. Secondly we aim to develop its capabilities to be deployed for the visualisation and analysis of data derived from other sources e.g. EBI databases, and for providing access to networks of analysed data. Thirdly, we wish to further explore the potential to use this tool for the modelling and visualisation of biological pathways. Finally, with the rapid pace of development of programming languages and advanced computer hardware, we will explore the potential to harness the power these developments for improving the power and speed of network analyses. We believe that the proposed project will allow us to deliver a cutting-edge tool addressing the shortcomings of currently available commercial and academic systems. The rapid growth of 3D graphics hardware and computer speed allows us to develop these tools for regular desktop computers, yet still allow the analysis of datasets an order of magnitude larger than other systems. BioLayout Express3D will allow biologists to contextualise and visualise their data in an unprecedented manner and we hope it will be a significant boon to the wider academic community.

生物数据越来越复杂，规模越来越大。基因组测序和其他高通量技术为我们提供了生命的部件列表，以及关于这些部件如何相互作用的丰富信息。人类天生是视觉的，以图表和图形的形式表示这些信息对我们理解其内在的复杂性非常有用。因此，帮助生物学家可视化、分析和解释生物系统的工具可能具有很大的实用性。两个申请人都对生物数据的分析有着长期的兴趣，并参与了用于其可视化和分析的计算机程序的开发。特别是，在BBSRC和Wellcome Trust的支持下，我们共同开发了一个强大的网络分析工具BioLayout 3D。该软件已被证明对申请人的研究非常有用，也受到更广泛的学术界的欢迎。因此，我们寻求继续将其功能扩展到新的领域，从而保持其在生物系统可视化和解释方面的前沿地位。该项目利用现有的合作工作，旨在探索计算，生物学和可视化的新领域，参与实验室在向更广泛的社区发布之前对开发进行范围界定，测试和验证。我们的首要目标是改进和扩展BioLayout 3D的现有界面，使其能够读取和处理来自各种来源的生物数据。我们还力求提高用户界面的质量及其分析潜力，并改进对用户的支持和培训。其次，我们的目标是开发其能力，用于可视化和分析来自其他来源的数据，例如EBI数据库，并提供对分析数据网络的访问。第三，我们希望进一步探索使用该工具对生物途径进行建模和可视化的潜力。最后，随着编程语言和先进计算机硬件的快速发展，我们将探索利用这些发展来提高网络分析的能力和速度的潜力。我们相信，拟议的项目将使我们能够提供一个尖端的工具，解决目前可用的商业和学术系统的缺点。3D图形硬件和计算机速度的快速增长使我们能够为常规台式计算机开发这些工具，但仍然允许分析比其他系统大一个数量级的数据集。BioLayout 3D将使生物学家能够以前所未有的方式将他们的数据背景化和可视化，我们希望它将成为更广泛的学术界的一个重大布恩。

项目成果

A high resolution atlas of gene expression in the domestic sheep (Ovis aries).

• DOI: 10.1371/journal.pgen.1006997
• 发表时间: 2017-09
• 期刊: PLoS genetics
• 影响因子: 4.5
• 作者: Clark EL;Bush SJ;McCulloch MEB;Farquhar IL;Young R;Lefevre L;Pridans C;Tsang HG;Wu C;Afrasiabi C;Watson M;Whitelaw CB;Freeman TC;Summers KM;Archibald AL;Hume DA
• 通讯作者: Hume DA

Oncogenic properties of apoptotic tumor cells in aggressive B cell lymphoma.

• DOI: 10.1016/j.cub.2014.12.059
• 发表时间: 2015-03-02
• 期刊: CURRENT BIOLOGY
• 影响因子: 9.2
• 作者: Ford, Catriona A.;Petrova, Sofia;Pound, John D.;Voss, Jorine J. L. P.;Melville, Lynsey;Paterson, Margaret;Farnworth, Sarah L.;Gallimore, Awen M.;Cuff, Simone;Wheadon, Helen;Dobbin, Edwina;Ogden, Carol Anne;Dumitriu, Ingrid E.;Dunbar, Donald R.;Murray, Paul G.;Rucker, Dominik;Allen, Judith E.;Hume, David A.;van Rooijen, Nico;Goodlad, John R.;Freeman, Tom C.;Gregory, Christopher D.
• 通讯作者: Gregory, Christopher D.

Reciprocal regulation of lymphoid tissue development in the large intestine by IL-25 and IL-23.

• DOI: 10.1038/mi.2014.90
• 发表时间: 2015-05
• 期刊: Mucosal immunology
• 影响因子: 8

Coexpression analysis of large cancer datasets provides insight into the cellular phenotypes of the tumour microenvironment.

• DOI: 10.1186/1471-2164-14-469
• 发表时间: 2013-07-11
• 期刊: BMC genomics
• 影响因子: 4.4
• 作者: Doig TN;Hume DA;Theocharidis T;Goodlad JR;Gregory CD;Freeman TC
• 通讯作者: Freeman TC

Distribution of Misfolded Prion Protein Seeding Activity Alone Does Not Predict Regions of Neurodegeneration.

• DOI: 10.1371/journal.pbio.1002579
• 发表时间: 2016-11
• 期刊: PLoS biology
• 影响因子: 9.8
• 作者: Alibhai J;Blanco RA;Barria MA;Piccardo P;Caughey B;Perry VH;Freeman TC;Manson JC
• 通讯作者: Manson JC