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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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POPcorn: Project Portal for corn www.maizegdb.org/POPcorn
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POPcorn: Project Portal for corn www.maizegdb.org/POPcorn
Project Objectives:
• Difficult to find all online resources relevant to one’s research• Project Search
Project Objectives:
• Difficult to find all online resources relevant to one’s research• Project Search
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POPcorn: Project Portal for corn www.maizegdb.org/POPcorn
Project Objectives:
• Difficult to find all online resources relevant to one’s research• Project Search
• Repeated BLAST searches at multiple sites• POPcorn BLAST
Project Objectives:
• Difficult to find all online resources relevant to one’s research• Project Search
• Repeated BLAST searches at multiple sites• POPcorn BLAST
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POPcorn: Project Portal for corn www.maizegdb.org/POPcorn
Project Objectives:
• Difficult to find all online resources relevant to one’s research• Project Search
• Repeated BLAST searches at multiple sites• POPcorn BLAST
• Sequence-indexed data can be challenging to search• Sequence-Indexed Data Search
Project Objectives:
• Difficult to find all online resources relevant to one’s research• Project Search
• Repeated BLAST searches at multiple sites• POPcorn BLAST
• Sequence-indexed data can be challenging to search• Sequence-Indexed Data Search
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POPcorn: Project Portal for corn www.maizegdb.org/POPcorn
Project Objectives:
• Difficult to find all online resources relevant to one’s research• Project Search
• Repeated BLAST searches at multiple sites• POPcorn BLAST
• Sequence-indexed data can be challenging to search• Sequence-Indexed Data Search
• Data and web resources can disappear after project completion• Processes and scripts to migrate data to MaizeGDB
Project Objectives:
• Difficult to find all online resources relevant to one’s research• Project Search
• Repeated BLAST searches at multiple sites• POPcorn BLAST
• Sequence-indexed data can be challenging to search• Sequence-Indexed Data Search
• Data and web resources can disappear after project completion• Processes and scripts to migrate data to MaizeGDB
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POPcorn: Project Portal for corn www.maizegdb.org/POPcorn
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POPcorn: Project Portal for corn www.maizegdb.org/POPcorn
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POPcorn: Project Portal for corn www.maizegdb.org/POPcorn
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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POPcorn: Project Portal for corn www.maizegdb.org/POPcorn
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!
• submit projects not in our database• send us corrections
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POPcorn: Project Portal for corn www.maizegdb.org/POPcorn
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!
• submit projects not in our database• send us corrections
• 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!
• submit projects not in our database• send us corrections
• 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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POPcorn: Project Portal for corn www.maizegdb.org/POPcorn
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POPcorn: Project Portal for corn www.maizegdb.org/POPcorn
• 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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POPcorn: Project Portal for corn www.maizegdb.org/POPcorn
• 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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POPcorn: Project Portal for corn www.maizegdb.org/POPcorn
• 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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POPcorn: Project Portal for corn www.maizegdb.org/POPcorn
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POPcorn: Project Portal for corn www.maizegdb.org/POPcorn
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POPcorn: Project Portal for corn www.maizegdb.org/POPcorn
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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POPcorn: Project Portal for corn www.maizegdb.org/POPcorn
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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POPcorn: Project Portal for corn www.maizegdb.org/POPcorn
• 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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POPcorn: Project Portal for corn www.maizegdb.org/POPcorn
• 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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POPcorn: Project Portal for corn www.maizegdb.org/POPcorn
• 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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POPcorn: Project Portal for corn www.maizegdb.org/POPcorn
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
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