biomart implementation of sp_base mentors : andrew cameron peer mentor:emmanuella morin pi: eric...
Post on 20-Dec-2015
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BIOMART IMPLEMENTATION OF
SP_BASE
BIOMART IMPLEMENTATION OF
SP_BASEMentors : 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 Outline
Background The Project Methods/Approach Future directions
Background The Project Methods/Approach Future directions
Biological significanceBiological 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
GMODGMOD
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
GoalsGoals
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 databaseMethods for building a Biomart database1. 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 FlowData Flow
MartJAVA
PERL
Source data
DAS
WebGUI
Commandline
Desktop GUI
WebService
Mart builder
Mart editor
Mart runner
Mart view
Data FlowData Flow
MartJAVA
PERL
Source data
DAS
WebGUI
Commandline
Desktop GUI
WebService
Mart builder
Mart editor
Mart runner
Mart view
Data FlowData Flow
MartJAVA
PERL
Source data
DAS
WebGUI
Commandline
Desktop GUI
WebService
Mart builder
Mart editor
Mart runner
Mart view
Data FlowData Flow
MartJAVA
PERL
Source data
DAS
WebGUI
Commandline
Desktop GUI
WebService
Mart builder
Mart editor
Mart runner
Mart view
What is Mart Builder ?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
A program that takes the source data in the form of a database and configures it to be used in other Biomart applications
Mart BuilderMart Builder
Mart editor Mart editor
OUTPUT OUTPUTMart EditorMart Editor
Mart viewMart view
Example demoExample demo
http://www.biomart.org/biomart/martview/e610930b9538b264df6f3467b341a3bf
http://www.biomart.org/biomart/martview/e610930b9538b264df6f3467b341a3bf
Future workFuture 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: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