1 popcorn: project portal for corn a set of project and sequence-indexed data searching resources

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POPcorn: Project Portal for corn www.maizegdb.org/POPcorn

http://www.maizegdb.org/POPcorn/http://www.maizegdb.org/POPcorn/

A set of project and sequence-indexed data searching resources

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Project Objectives:

• Difficult to find all online resources relevant to one’s research• Project Search

Project Objectives:


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Project Objectives:


• Repeated BLAST searches at multiple sites• POPcorn BLAST

Project Objectives:



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Project Objectives:



• Sequence-indexed data can be challenging to search• Sequence-Indexed Data Search

Project Objectives:




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Project Objectives:




• Data and web resources can disappear after project completion• Processes and scripts to migrate data to MaizeGDB

Project Objectives:




• Data and web resources can disappear after project completion• Processes and scripts to migrate data to MaizeGDB

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Project Search• Status: available since April ‘09• Database of maize research projects and online resources• Hand-curated and updated monthly; 73 projects, 113 resources

Project Search• Status: available since April ‘09• Database of maize research projects and online resources• Hand-curated and updated monthly; 73 projects, 113 resources

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Project Search• Status: available since April ‘09• Database of maize research projects and online resources• Hand-curated and updated monthly; 73 projects, 113 resources• We need your help!

• submit projects not in our database• send us corrections

Project Search• Status: available since April ‘09• Database of maize research projects and online resources• Hand-curated and updated monthly; 73 projects, 113 resources• We need your help!


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Project Search• Status: available since April ‘09• Database of maize research projects and online resources• Hand-curated and updated monthly; 73 projects, 113 resources• Information presented for each project and resource• We need your help!


• Types of projects and resources: • just about everything that is relevant to maize• … except historic, archeological and educational; those go into PGROP at PlantGDB (http://www.plantgdb.org/PGROP/)

Project Search• Status: available since April ‘09• Database of maize research projects and online resources• Hand-curated and updated monthly; 73 projects, 113 resources• Information presented for each project and resource• We need your help!


• Types of projects and resources: • just about everything that is relevant to maize• … except historic, archeological and educational; those go into PGROP at PlantGDB (http://www.plantgdb.org/PGROP/)

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• Status: in development• BLAST against target sequence at multiple websites using Web Services• Status: in development• BLAST against target sequence at multiple websites using Web Services

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• Status: in development• BLAST against target sequence at multiple websites using Web Services• BLAST targets are explained and credited

• Status: in development• BLAST against target sequence at multiple websites using Web Services• BLAST targets are explained and credited

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• Status: in development• BLAST against target sequence at multiple websites using Web Services• BLAST targets are explained and credited• Contact us to add your target sequence or to set up a similar service

• Status: in development• BLAST against target sequence at multiple websites using Web Services• BLAST targets are explained and credited• Contact us to add your target sequence or to set up a similar service

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An example: find UniformMu stock containing a given mutation

1. BLAST query sequence against NCBI GSS 2. Parse definition line to get UniformMu locus name3. Get LOCUS record at MaizeGDB4. Get VARIATION records for that LOCUS at MaizeGDB5. Get UniformMu STOCK records for each VARIATION at MaizeGDB6. Construct links to MGC Stock Center for each stock found.

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An example: find UniformMu stock containing a given mutation

1. BLAST query sequence against NCBI GSS 2. Parse definition line to get UniformMu locus name3. Get LOCUS record at MaizeGDB4. Get VARIATION records for that LOCUS at MaizeGDB5. Get UniformMu STOCK records for each VARIATION at MaizeGDB6. Construct links to MGC Stock Center for each stock found.

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• Status: in development• Carries out complex searches• One or more searches at once

• Status: in development• Carries out complex searches• One or more searches at once

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• Status: in development• Carries out complex searches• One or more searches at once• Description provided for each search

• Status: in development• Carries out complex searches• One or more searches at once• Description provided for each search

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• Status: in development• Carries out complex searches• One or more searches at once• Description provided for each search• Please let us know if you would like a search added

• Status: in development• Carries out complex searches• One or more searches at once• Description provided for each search• Please let us know if you would like a search added

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Strategy for 2010•January: Hire a second full-time programmer•February: Release POPcorn BLAST and Sequence-Indexed Data Search for public comment•April-June: Release beta versions of the new tools•June-July: Develop and implement a curation tool to give collaborators control over BLAST access and descriptions.

Expand number of collaborator websites and databases, continue to add BLAST targets, and implement additional multi-step searches.

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POPcornPrincipal Investigator: Carolyn LawrenceCo-Principal Investigator: Taner SenSolution/Application Architect: Ethy CannonUndergraduate Programmer: Scott Birkett

POPcornPrincipal Investigator: Carolyn LawrenceCo-Principal Investigator: Taner SenSolution/Application Architect: Ethy CannonUndergraduate Programmer: Scott Birkett

MaizeGDB/POPcorn team

MaizeGDB

Director: Carolyn LawrenceComputational biologist: Taner SenWeb programmer: Carson AndorfDatabase administrator: Darwin CampbellCurators: Mary Schaeffer, Lisa Harper

MaizeGDB

Director: Carolyn LawrenceComputational biologist: Taner SenWeb programmer: Carson AndorfDatabase administrator: Darwin CampbellCurators: Mary Schaeffer, Lisa Harper

1 popcorn: project portal for corn a set of project and sequence-indexed data searching resources

Documents

project portal

set of project

maizegdb project objectives

online resources relevant

project completion processes

online resources hand

web resources

maizegdb slide