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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
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Outline Background The Project Methods/Approach Future directions Background The Project Methods/Approach Future directions
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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
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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
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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
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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
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Data Flow Mart JAVA PERL Source data DAS Web GUI Command line Desktop GUI Web Service Mart builder Mart editor Mart runner Mart view
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Data Flow Mart JAVA PERL Source data DAS Web GUI Command line Desktop GUI Web Service Mart builder Mart editor Mart runner Mart view
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Data Flow Mart JAVA PERL Source data DAS Web GUI Command line Desktop GUI Web Service Mart builder Mart editor Mart runner Mart view
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Data Flow Mart JAVA PERL Source data DAS Web GUI Command line Desktop GUI Web Service Mart builder Mart editor Mart runner Mart view
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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
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Mart Builder
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Mart editor OUTPUT Mart Editor
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Mart view
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Example demo http://www.biomart.org/biomart/martvie w/e610930b9538b264df6f3467b341a3b f http://www.biomart.org/biomart/martvie w/e610930b9538b264df6f3467b341a3b f http://www.biomart.org/biomart/martvie w/e610930b9538b264df6f3467b341a3b f http://www.biomart.org/biomart/martvie w/e610930b9538b264df6f3467b341a3b f
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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
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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
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