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Coordination Site for PhytoBisque Project


A major goal in plant biology is to learn how the genome produces and controls the functions of an organism. Phenotypes due to induced mutations or natural genetic variation are rich sources of information about the genomic basis of form and function. This decade and the one previous brought enormous, transformative progress in the way genomes and their proximate levels of expression are characterized and manipulated. The next decade will bring more of the same. On the other side of the equation, organism form and function, the methods of study have not undergone a similar transformation in precision or capacity. Thus, there exists today a large imbalance between the sophistication with which genotypes and phenotypes are quantified. Making progress on the phenotype side of the equation will result in better use of the genotype information, and most efficient progress toward the overall goal will be made when the two sides of the equation are in a technological balance.


The Phytomorph project at the University of Wisconsin (; PI Edgar Spalding) focuses on enabling plant research by creating and disseminating tools for quantifying plant phenotypes in popular experimental systems, mostly Arabidopsis and maize. The emphasis has been on the early stages of seedling development. The Bisque project at the University of California, Santa Barbara (; PI B.S. Manjunath) presents and advances a sophisticated database environment for storing and manipulating biological images. At its core is a flat-structured database designed for images and metadata. The key feature of Bisque is that it can incorporate analysis-specific algorithms to create a workflow that takes images and the metadata and returns processed results required by the biologist. The objective of this collaboration is to integrate aspects of the two projects into a cyberinfrastructure-based tool taking the shape of a portal that enables the plant biologist to perform quantitative, image-based phenotype studies. The longer-term vision is to integrate the output of a Bisque-based image analysis pipeline with the outputs of activities closer to the genotype side so that plant biology research begins to build true multi-dimensional quantitative representations of the genotype-to-phenotype relationship.

Plans and Progress



2-3 Phytomorph algorithms incorporated in Bisque


Condor backend to Bisque


Condor-Bisque interface


Multi-dimensional image construction of 2D images sets in Bisque


Sample workflow (multi-tip analysis)

Spring 2011

Bisque relational database

Spring 2011

Analysis visualizations

Spring 2011

Support for new analysis modules

Spring 2011

Improved workflow support

Spring 2011



  • iPlant Support – assistance with credentials, issues with software or hardware infrastructure, virtual machines, etc
  • Image Analysis Working Group Home – documentation, discussion, working group meeting notes
  • Project JIRA – log in using your iPlant credentials
  • Subversion repositories
  • Development VM (Linux 2.6x, MatLab, GCC4.x, etc.)
    • authenticate using iPlant credentials
    • Desktop support via ssh -X and VNC port forwarding
    • MatLab: Version (R2010a) 64-bit (glnxa64)
    • OS: Linux 2.6.18-194.el5xen #1 SMP Tue Mar 16 22:01:26 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux
    • GCC: gcc version 4.1.2 20080704 (Red Hat 4.1.2-48)
  • Image Analysis Mailing List
  • Twiddla – interactive whiteboard. If you have an .edu address, you can get a free professional account from the company.

Guidance Documents

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