1 / 11

The Ionomics Atlas  Progress Report

Mourad Ouzzani David Salt Nabeel Mohamed. The Ionomics Atlas  Progress Report. Goal of the project. Develop a Google Map based intuitive graphical user interface that allows to access, analyze, interpret and find correlations among the following three properties in plant populations.

octavius-buchanan
Download Presentation

The Ionomics Atlas  Progress Report

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Mourad Ouzzani David Salt Nabeel Mohamed The Ionomics Atlas Progress Report

  2. Goal of the project • Develop a Google Map based intuitive graphical user interface that allows to access, analyze, interpret and find correlations among the following three properties in plant populations. • Ionomic information • Genetic information • Environmental information

  3. Tasks • Requirement analysis [DONE] • Understand the project proposal • Decide the functional requirements  • Understand Piims and related data sources [DONE] • Understand and gather input data [DONE - ionomic and genetic info; TODO - environmental info] • Database design [DONE] • System design [DONE] • Front-end design [IN PROGRESS] • Query mode [IN PROGRESS] • Browsing mode [IN PROGRESS] • Populate database [DONE - ionomic/genetic, TODO - environmental] • Implementation [IN PROGRESS]

  4. Input Data • Ionomic information: The project utilizes 360 different populations of the plant Arabidopsis thaliana. Each accession has the corresponding GIS information and ionomics information available through PiiMS database.  • Genetic information: For each accession, genotype information available in a compact representation containing 250,000 sub-sequences.   • Environmental information: The project utilizes the environmental information such as geographic location, altitude, climate (rainfall, temperature), soil properties, etc. Such environmental information are retrieved from public European databases.

  5. Ionomic/Genetic/Environmental data • There were some data quality issues with the input data we received. • Following are the main inconstancies: • Encoding errors • Formatting errors • Missing data •  Cleaned the data programmatically as well as manually

  6. Arabidopsis thaliana data • 360 accessions in total, we currently have • ionomic information for 350 accessions • genetic information for 337 accessions • GIS information for all 360 accessions

  7. Technologies • Database - Postgresql • Application server - Tomcat (back-end in Java) • Web technologies - GWT - Google Web Toolkit which supports AJAX based web pages (javascripts), JSP • Map - Google Maps along with free libraries to create overlays

  8. Database design

  9. Simple system architecture

  10. Initial front-end layout • The web page consists of two frames • Filters and output options • Google map overlaying accessions

  11. A screen shot of work-in-progress front end • Initially, all the 360 accessions are displayed  • Depending on the filters, only the relevant accessions are shown (back-end functionality for filtering is in-progress)

More Related