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.
The GenomeSpace community resource puts the universe of diverse genomic analysis tools within the reach of all biomedical researchers. Through the integrative analysis of genomic data from diverse sources and types, GenomeSpace users will be able to address a variety of problems at the forefront of biomedical research including patient diagnosis and prognosis, identification of new drug targets, and understanding biological mechanisms.
| Qu, Kun; Garamszegi, Sara; Wu, Felix et al. (2016) Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace. Nat Methods 13:245-247 |
| Lu, Zhipeng; Zhang, Qiangfeng Cliff; Lee, Byron et al. (2016) RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure. Cell 165:1267-1279 |
| Demchak, Barry; Hull, Tim; Reich, Michael et al. (2014) Cytoscape: the network visualization tool for GenomeSpace workflows. F1000Res 3:151 |
