1 POPcorn: Project Portal for corn A set of project and sequence-indexed data searching resources

2 POPcorn: Project Portal for corn

3 Project Objectives: Difficult to find all online resources relevant to ones research Project Search Project Objectives: Difficult to find all online resources relevant to ones research Project Search

4 POPcorn: Project Portal for corn Project Objectives: Difficult to find all online resources relevant to ones research Project Search Repeated BLAST searches at multiple sites POPcorn BLAST Project Objectives: Difficult to find all online resources relevant to ones research Project Search Repeated BLAST searches at multiple sites POPcorn BLAST

5 POPcorn: Project Portal for corn Project Objectives: Difficult to find all online resources relevant to ones 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 ones research Project Search Repeated BLAST searches at multiple sites POPcorn BLAST Sequence-indexed data can be challenging to search Sequence-Indexed Data Search

6 POPcorn: Project Portal for corn Project Objectives: Difficult to find all online resources relevant to ones 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 ones 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

7 POPcorn: Project Portal for corn

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9 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

10 POPcorn: Project Portal for corn 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

11 POPcorn: Project Portal for corn 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 ( 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 (

12 POPcorn: Project Portal for corn

13 POPcorn: Project Portal for corn 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

14 POPcorn: Project Portal for corn 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

15 POPcorn: Project Portal for corn 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

16 POPcorn: Project Portal for corn

17 POPcorn: Project Portal for corn

18 POPcorn: Project Portal for corn An example: find UniformMu stock containing a given mutation 1.BLAST query sequence against NCBI GSS 2.Parse definition line to get UniformMu locus name 3.Get LOCUS record at MaizeGDB 4.Get VARIATION records for that LOCUS at MaizeGDB 5.Get UniformMu STOCK records for each VARIATION at MaizeGDB 6.Construct links to MGC Stock Center for each stock found.

19 POPcorn: Project Portal for corn An example: find UniformMu stock containing a given mutation 1.BLAST query sequence against NCBI GSS 2.Parse definition line to get UniformMu locus name 3.Get LOCUS record at MaizeGDB 4.Get VARIATION records for that LOCUS at MaizeGDB 5.Get UniformMu STOCK records for each VARIATION at MaizeGDB 6.Construct links to MGC Stock Center for each stock found.

20 POPcorn: Project Portal for corn 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

21 POPcorn: Project Portal for corn 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

22 POPcorn: Project Portal for corn 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

23 POPcorn: Project Portal for corn 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.

24 POPcorn Principal Investigator: Carolyn Lawrence Co-Principal Investigator: Taner Sen Solution/Application Architect: Ethy Cannon Undergraduate Programmer: Scott Birkett POPcorn Principal Investigator: Carolyn Lawrence Co-Principal Investigator: Taner Sen Solution/Application Architect: Ethy Cannon Undergraduate Programmer: Scott Birkett MaizeGDB/POPcorn team MaizeGDB Director: Carolyn Lawrence Computational biologist: Taner Sen Web programmer: Carson Andorf Database administrator: Darwin Campbell Curators: Mary Schaeffer, Lisa Harper MaizeGDB Director: Carolyn Lawrence Computational biologist: Taner Sen Web programmer: Carson Andorf Database administrator: Darwin Campbell Curators: Mary Schaeffer, Lisa Harper