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

Outline  Background  The Project  Methods/Approach  Future directions  Background  The Project  Methods/Approach  Future directions

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  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

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

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  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

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 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

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

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

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

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

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

Mart Builder

Mart editor  OUTPUT  Mart Editor

Mart view

Example demo  w/e610930b9538b264df6f3467b341a3b f w/e610930b9538b264df6f3467b341a3b f  w/e610930b9538b264df6f3467b341a3b f w/e610930b9538b264df6f3467b341a3b f

Future work  Linking to other parts of GMOD such as Gbrowse  Connecting to Chado Schema databases  Linking to other parts of GMOD such as Gbrowse  Connecting to Chado Schema databases

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 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