Roadmap

Specific features planned for upcoming releases:

1. Natural language query interface for ENA with automatic Galaxy integration
2. Embedded Galaxy Pages (notebook-like documents containing workflow results) in relevant BRC Analytics pages
3. Gene pages and gene sets with meaningful query and comparison capabilities
4. Enhanced Galaxy workflows for comparative genomics and other analyses
5. Priority pathogens/outbreaks tab highlighting specific organisms and relevant resources
6. Integration with specialized tools like hgPhyloPlace from UCSC for phylogenetic analysis
7. Importing gene model data from VEuPathDB
8. Access to Galaxy's MCP server to provide a natural language interface to Galaxy itself

In building a collaborative environment where researchers can share insights and analyses, we aim to:

1. Embed results of Galaxy analyses directly in the BRC Analytics site for community reference
2. Empower users to self-curate organism knowledge bases through peer review
3. Establish community forums for discussing research questions and methodologies
4. Enable contribution of custom workflows, analysis pipelines and visualizations tailored to specific organisms

We recognize that each organism is different, with unique biology, research communities, and funding landscapes that drive diverse analytical needs. To address this, we intend to:

1. Build a flexible platform that can adapt to the specific requirements of different organisms
2. Accommodate varying levels of genomic resources, from well-studied model organisms to neglected pathogens
3. Enable communities to prioritize the data types and analyses most relevant to their organism of interest
4. Design adaptable interfaces that can evolve as research interests and priorities shift over time
5. Support both emerging and established research communities with appropriate tools

While maintaining this flexibility, we will give special attention to NIAID-designated prototype pathogen viral families, biodefense priorities, and emerging threats.

We aim to create a unified experience that brings together diverse data sources and analysis capabilities. Our goals include:

1. Automatically manage reference genomes and annotations from NCBI
2. Provide an integrated and intuitive interface for ENA with automatic upload to Galaxy
3. Import gene models and other data from public resources (e.g. VEuPathDB)
4. Pre-build essential bioinformatics resources (indices, etc.) for supported organisms
5. Create a comprehensive resource that reduces the need to navigate between multiple platforms
6. Embed a wide diversity of analysis results from Galaxy as essential context for research on supported organisms
7. Build a flexible system that can be extended to support additional organisms, data sources and analysis tools quickly

In order to make complex analyses accessible to researchers with varying computational expertise, we will:

1. Leverage Galaxy's GUI-based platform, pre-built workflows and in-development MCP server, eliminating the need to learn command-line interfaces
2. Utilize TACC's compute resources, removing the need for institutional or paid hardware and associated configuration
3. Integrate curated, community-developed Galaxy workflows from the Intergalactic Workflow Commission (IWC)
4. Create intuitive interfaces that bring together multiple resources in a single, unified experience
5. Build on Galaxy team's strengths in tutorials and training networks to provide comprehensive educational resources
6. Gather dedicated resources for priority pathogens in one place for streamlined research
7. Implement LLM-powered natural language queries of data sources with automatic data upload to Galaxy