Transcript VectorBase-Galaxy

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
(https://www.vectorbase.org)
VectorBase is a collator of genome data
Pre-released* Full release
Organism pages
(our) Annotation
Raw GenBank data
from sequencing centers
*
*
*
*
3
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
Biological Data
Genomic Sequences, Microarray Data,
Annotations (meta-data), Reports/WhitePapers, Images, Links, Post-Genomic Data
Users of VectorBase
Vector Biologists, Parasitologists,
Epidemiologists, Public Health
Scientists, Students
The VectorBase
Bioinformatics
Resource Center
Enabling
Data-Driven Science
Cyberinfrastucture
Data, Computation, Cyber Services,
Virtual Organization, Communications,
Learning
VectorBase Team
A Virtual Organization of PIs,
Developers, Bioinformaticians,
Managers, Biologists, Computer
Scientists
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 &
Tools
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
...
...
...
...
Blast
Search
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.
HHSN272200900039C)
• VectorBase colleagues: