Cyber-infrastructure to Support Information Sharing, Analysis,
and Visualization Using a Fungal Plant Pathogen Database

The main objective of this inter-disciplinary project is to establish a cohesive computational environment (cyber-infrastructure) to support the capture, integration, exploration, analysis and dissemination of data, methods and research outcomes from studies on the genetic and phenotype diversity of fungal plant pathogens, at both the species and population levels. Our proposal weaves together two disparate threads: (i) the emerging computational tools and protocols that enable distributed teams of researchers to collaborate more closely and leverage each other’s work and (ii) the urgent need to better catalog, analyze and communicate the nature and threats posed by fungal diseases to agriculture.

The objectives of this project, therefore, are to create a cohesive computational environment for fungal data management, analysis and visualization that:

  • Supports a systematic approach to creating and maintaining databases of genotypes (genetic barcodes) of fungal collections and related (e.g. environmental, phenotype) information.
  • Provides distributed, community-wide access to these databases and associated computational analysis and visualization tools.
  • Hides many of the information science challenges that currently impede the progress of collaborative research into molecular systematics and population genetics of plant pathogenic fungi.
  • Is customizable to the emerging needs of the plant pathology/mycology/ecology research communities.

flow diagram
Schematic diagram of the components and processes involved in the proposed web portal interface and the database.

 

The computational tools and proposed fungal database will aid researchers in understanding the temporal, spatial, and evolutionary structure and dynamics of fungal pathogens, via an array of tools for information capture, management and integration, in addition to analysis and exploratory visualization apparatus. The combined computation environment (cyber-infrastructure), complete with database and analysis tools, will be packaged as community resources accessed by web portal technology. Using the portal, researchers will see a single interface with genetic logging, search, analysis, and visualization tools ready for their immediate use, and available from wherever they happen to be. Our vision is that the infrastructure we build will help pave the way for a greater degree of sharing and collaboration by the larger community of scientists doing DNA-based species/strain identification.

 

For more information see the plant pathology page at: http://posnania.biotec.psu.edu/research/plant_pathogen.html

 

 
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