Genome Browser Grant Proposal for 2017-2022

In September 2016, we submitted a grant to NHGRI to continue our work on the Genome Browser. We requested 5 years of additional funding for our project: 7/1/2017 - 6/30/2022. We typically hear a decision in late Spring of the grant start year (so May-ish of 2017). Read the details of the funding opportunity to which we applied here.

The guidelines for this grant required us to split our Research Plan (where we describe the work we intend to do) into 4 sections as follows:

• Overall
  • This section is a high-level overview of what we plan to do.
  • Doc: File:GrantOverallComponent.pdf
  • References: File:GrantOverallRefs.pdf
  • Appendices
    • Appendix 1 File:Appendix1 UCSC Genome Browser resources.pdf
    • Appendix 2 File:Appendix2 User Survey results.pdf
    • Appendix 3 File:Appendix3 Training and Outreach resources.pdf
    • Appendix 4 File:Appendix4 Workshop Survey Results.pdf

• Project
  • This section describes our plans to develop, maintain, and extend the UCSC Genome Browser software, build and maintain genome browsers and annotations for species of biomedical interest, and integrate data from the scientific community that help interpret the functions of various genome regions.
  • Doc: File:GrantProjectComponent.pdf
  • References: File:GrantProjectRefs.pdf
  • Aims
    • Aim 1. Develop, maintain, and extend software for the display and analysis of genomics resources.
    • Aim 2. Build and maintain genome browsers and related resources for species of biomedical interest.
    • Aim 3. Integrate data from the scientific community that help interpret the functions of various genome regions.

• Core
  • This section describes our plans to enhance the interconnectivity of the UCSC Genome Browser and related databases with other computational groups and tools in the scientific community, maintain the high quality of the Genome Browser software and data, and provide a robust computing environment capable of supporting our developers and users.
  • Doc: File:GrantCoreComponent.pdf
  • References: File:GrantCoreRefs.pdf
  • Aims
    • Aim 1. Develop, use, and extend data exchange standards such as file formats, APIs, and controlled vocabularies.
    • Aim 2. Assure the quality and understandability of genomics data sets as they are imported.
    • Aim 3. Maintain software quality through a combination of automated and manual testing and best practices.
    • Aim 4. Provide a fast, stable computer hardware environment for Genome Browser developers and users.

• Admin-Core
  • This section describes our plans for the scientific, project, and personnel management of the UCSC Genome Browser team and resource, the dissemination of our software and data, and the training of our users.
  • Doc: File:GrantAdminCoreComponent.pdf
  • Doc: File:GrantAdminCoreRefs.pdf
  • Aims
    • Aim 1. Provide effective scientific, project, and personnel management.
    • Aim 2. Broadly disseminate the software tools, libraries, source code and data.
    • Aim 3. Train users with online documentation, videos, workshops, courses, email and social media.