Vectorbase and Galaxy Jarek Nabrzyski On behalf of VectorBase Center for Research Computing University of Notre Dame VectorBase Bioinformatics Resource.

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Presentation transcript:

Vectorbase and Galaxy Jarek Nabrzyski On behalf of VectorBase Center for Research Computing University of Notre Dame VectorBase Bioinformatics Resource for Invertebrate Vectors of Human Pathogens

What is VectorBase?

VectorBase is... A bioinformatics resource center (BRC) A genome resource for invertebrate vectors of human pathogens VectorBase Bioinformatics Resource for Invertebrate Vectors of Human Pathogens

VectorBase is... Virtual Organization!

Virtual Organization

VectorBase is... A website (

Full release Pre-released* Organism pages Raw GenBank data from sequencing centers VectorBase is a collator of genome data * 3 * * * (our) Annotation

VectorBase is... A service providing tools for browsing and mining vector “-omics” data A content generator (genome annotation) A help desk to help our community on genome informatics Committed to regular releases (5-6 a year)

VectorBase is... A successful science gateway! Funding/Longevity Users & User-generated data ~175k unique visitors 27% returning

Vectorbase Ecosystem

Keys to Success 1. Virtual organizational structure 2. Integration of data and tools 3. Community involvement and outreach Cyberinfrastructure is CRITICAL for each

Data & Tools

Data is just as diverse!

Integrating Data & Tools Usability of software "After all, usability really just means that making sure that something works well: that a person … can use the thing - whether it's a Web site, a fighter jet, or a revolving door - for its intended purpose without getting hopelessly frustrated." (Steve Krug in “Don't make me think!: A Common Sense Approach to Web Usability”, 2005)

Integrating Data & Tools PopBio Browser BlastSearch...

Summary VectorBase has been successful by: acting as a Virtual Organization integrating data & tools engaging the community it serves All made possible by cyberinfrastructure

But… Users want more: - Run more complex workflows on VB data with Galaxy on various DCIs (local campus infrastructures, regional, national, etc.) - Potential use cases: - metagenomics analyses of various species - workflows that could design primers for specific species or subgroups of species

Acknowledgements National Institutes of Health/ National Institute of Allergy and Infectious Disease (Contract No. HHSN C) VectorBase colleagues: