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BIOMART IMPLEMENTATION OF SP_BASE

BIOMART IMPLEMENTATION OF SP_BASE. Mentors : Andrew Cameron Peer Mentor:Emmanuella Morin PI: Eric Davidson Intern:Steven Hobbs. Outline. Background The Project Methods/Approach Future directions. Biological significance.

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BIOMART IMPLEMENTATION OF SP_BASE

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  1. BIOMART IMPLEMENTATION OF SP_BASE Mentors : Andrew Cameron Peer Mentor:Emmanuella Morin PI: Eric Davidson Intern:Steven Hobbs

  2. Outline • Background • The Project • Methods/Approach • Future directions

  3. Biological significance • The Strongylocentrotus purpuratus is currently a widely used as research model in developmental biology • Sea urchin embryos offer the ability for: • The study of cis-regulatory systems • Transcription factor isolation • Exploration of gene networks

  4. GMOD • What is GMOD? • Generic Model Organism Database • a collection of software tools for creating and managing genome-scale biological databases

  5. Goals • Complete a working online version of Biomart to be used for the purple sea urchin genome • Setup a working public website so that researchers can have easy access to the data

  6. Methods for building a Biomart database 1. Build a relational database to hold the primary data 2. Alter the database to work with Biomart suite 3. Setup a working public website using Apache that links the Biomart software to the web 4. Alter and maintain the website to be as user-friendly as possible

  7. Desktop GUI Command line Web GUI DAS Web Service Data Flow Mart runner JAVA Mart builder Mart PERL Mart editor Source data Mart view

  8. Desktop GUI Command line Web GUI DAS Web Service Data Flow Mart runner JAVA Mart builder Mart PERL Mart editor Source data Mart view

  9. Desktop GUI Command line Web GUI DAS Web Service Data Flow Mart runner JAVA Mart builder Mart PERL Mart editor Source data Mart view

  10. Desktop GUI Command line Web GUI DAS Web Service Data Flow Mart runner JAVA Mart builder Mart PERL Mart editor Source data Mart view

  11. What is Mart Builder ? • A program that takes the source data in the form of a database and configures it to be used in other Biomart applications

  12. Mart Builder

  13. Mart editor • OUTPUT • Mart Editor

  14. Mart view

  15. Example demo • http://www.biomart.org/biomart/martview/e610930b9538b264df6f3467b341a3bf

  16. Future work • Linking to other parts of GMOD such as Gbrowse • Connecting to Chado Schema databases

  17. Acknowledgements: SP_base project team CalState LA /SoCal BSI Davidson Lab at Caltech Andrew Cameron, Ph.D Funding was provided by: NSF(National Science foundation) NIH(National institute of Health) Economic & Workforce development

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