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

生物数据日益复杂和大规模。基因组测序和其他高通量技术为我们提供了一份生命的组成部分清单，以及关于这些组成部分如何相互作用的丰富信息。人类天生就是可视的，以图形和图形的形式表示这种信息对于我们理解其固有的复杂性是非常有用的。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会非常有用。这两位申请者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，我们共同开发了强大的网络分析工具BioLayout Express3D。事实证明，该软件对申请者的研究非常有用，也受到了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，在向更广泛的社区发布之前，与两个参与的实验室一起确定开发的范围、测试和验证。我们的第一个目标是改进和扩展BioLayout Express3D的现有接口，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，并提供更好的支持和培训其用户。其次，我们的目标是发展其能力，以便对来自其他来源的数据进行可视化和分析，例如EBI数据库，并提供进入分析数据网络的途径。第三，我们希望进一步探索利用这一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的潜力来提高网络分析的能力和速度。我们相信，拟议的项目将使我们能够提供一种尖端工具，解决目前现有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 Express3D将允许生物学家以一种前所未有的方式将他们的数据联系起来并可视化，我们希望这将是更广泛的学术界的重大恩惠。

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.