GenomeSpace: community web environment for analysis across diverse genomic tools

基因组学研究界正在处理来自不断改进的技术平台的越来越多的数据。这些不同的数据类型(序列、表达、表观遗传学、RNAi屏幕等)提供了整合生物状态的不同观点以获得更深层次的机制理解的前景。然而，这种集成需要使用多种复杂的计算方法和工具。对于大多数生物学家来说，在数量迅速增加的可用工具中找到合适的工具，然后让它们一起工作是遥不可及的。因此，许多生物学家依赖于他们已经熟悉的少数工具，但无法利用可能改变生物医学研究的更先进的方法。 GenomeSpace通过为生物学家提供一个轻量级的互操作性环境来应对这一挑战，在这个环境中，各种分析方法、工具和基因组学资源可以无缝地协同工作，同时保留他们独立的开发努力和自己的外观。这项提议的目标是将基因组空间转换和扩展为生物医学研究界更全面的研究资源，重点是开发、传播和分享“分析处方”(目标1)。GenomeSpace配方集将为板凳生物学家用户揭开综合计算基因组学的神秘面纱，提供高需求、高实用的用例，展示如何利用和无缝结合环境中可用的多种工具来推进他们的工作。为了支持这一资源的成功，我们将进一步增强用户的体验和能力(目标2)；扩大基因空间的工具和数据范围(目标3)；建立和支持一个庞大的用户和开发人员社区(目标4)；以及完善和加强基因空间的基础设施和接口(目标5)。我们对GenomeSpace的全面实施和社区接纳的愿景确保了我们将使其成为研究界和生物最终用户的成功和关键资源。

The genomics research community is tackling increasing amounts of data from ever improving technology platforms. These diverse data types (sequence, expression, epigenetic, RNAi screens, etc.) offer the prospect of integrating different views of biological states to derive deeper mechanistic understanding. However, such integration requires using multiple sophisticated computational methods and tools. Finding the right tools among a rapidly increasing number of available ones, and then getting them to work together, is out of reach for most biologists. As a result, many biologists rely on the few tools with which they are already acquainted, but are unable to take advantage of more advanced approaches that could transform biomedical research. GenomeSpace addresses this challenge by providing biologists with a lightweight interoperability environment, where a wide range of analytical methods, tools, and genomics resources can seamlessly work together, while retaining their independent development efforts and own look and feel. The goal of this proposal is to convert and expand GenomeSpace to a fuller research resource for the biomedical research community, focused around the development, dissemination, and sharing of 'Analysis Recipes' (Aim 1). The GenomeSpace recipe collection will demystify integrative computational genomics for bench biologist users by providing high-demand, high-utility use cases that demonstrate how to leverage and seamlessly combine the multiple tools available in the environment to further their work. Supporting the success of this resource, we will further enhance the user's experience and power (Aim 2); broaden the scope of tools and data in GenomeSpace (Aim 3); build and support a large community of users and developers (Aim 4); and perfect and enhance the GenomeSpace infrastructure and interface (Aim 5). Our vision for GenomeSpace's full implementation and community uptake ensure that we will make it a successful and critical resource for the research community and biological end user.