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iPlant

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Conifer Genome Network PineRefSeq Project SMarTForests Project Conifer Translational Genomics Network TreeGenes Database Dendrome Plone Forestry Careers and Education Resource

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treegenesdb@gmail.com


iPlant

Overview Members

The Tree Biology Seed project is an iPlant initiated seed project with the goal to address an iPlant Grand Challenge question. This project intends to address the integration disparity between databases by implementing iPlant's Simple Semantic Web Architecture and Protocol (SSWAP) to make databases interoperable. For the prototype seed project, there will be development to bring in Tree Biology data from genetic, ecological, and physiological data sources. The goal of the project is to create a system to allow Tree Biologists query geographic locals based on geo-referenced coordinates. The Tree Biologists will then be able to explore genetic, physiological, and ecological data sources based on this location to potentially perform an association study by bringing in other data types.

Currently, the seed project plans to prototype access to TreeGenes and DiversiTree for genetic data, AmeriFlux and WorldClim for ecological data, and TRY-db for physiological data. Once a prototype system has been implemented, we hope to extend interoperability to Fluxnet, LTER, and NCEAS BIEN for ecological sources. Along these lines, we also hope to extend support to more genomic resources like Genome Database for Rosaceae and Fagaceae Genomics Web.

David Neale
Univ. of California, Davis

Hans Vasquez-Gross
Univ. of California, Davis

Missy Holbrook
Harvard Univ.

Jill Wegrzyn
Univ. of California, Davis

Daniel Kliebenstein
Univ. of California, Davis

Michael Dietze
Univ. of Illinois

Ram Oren
Duke Univ.

Ross Whetten
North Carolina State Univ.

Sally Aitken
Univ. of British Columbia

Sarah Mathews
Harvard Univ.
CartograTree
iPlant Information

The NSF's Plant Science Cyberinfrastructure Collaborative (PSCIC) program intended to create a new type of organization, a cyberinfrastructure collaborative for the plant sciences, that enables new conceptual advances through integrative, computational thinking. Thusly, the iPlant Collaborative was created to satisfy this need.

iPlant is a community of researchers, educators, and students working to enrich all plant sciences through the development of cyberinfrastructure - the physical computing resources, collaborative environment, virtual machine resources, and interoperable analysis software and data services that are essential components of modern biology. iPlant is of, by, and for the community; community driven questions and requirements shape and focus iPlant's mission.

Active Services

The active services link directly to the SSWAP services. Depending on your browser, running a service will generate a Resource Response Graph in XML format which will either be displayed in the browser or downloaded. This is written in a machine-readable format, but can also be read by humans. The best way to use these services is through the sswap pipeline system at http://sswap.info/ipc.

Resources

Reference CartograTree


Vasquez-Gross H.A., Yu J.J., Figueroa B., Gessler D.D.G., Neale D.B., and Wegrzyn J.L.
"CartograTree: connecting tree genomes, phenotypes, and environment",
Molecular Ecology Resources
In Press.

Collaborators





Icon 03 Updates

PineRefSeq project releases assembly (v2.0) of the Pinus taeda genome Walnut genome project releases assembly (v1.0) of the Juglans regia genome PineRefSeq project releases assembly (v1.0) of the Pseudotsuga menziesii genome PineRefSeq project releases assembly (v1.0) of the Pinus lambertiana genome CartograTree (v3.0), a map interface that works with DiversiTree to bring together genomics, ecological, and trait data is now live! PineRefSeq project releases assembly (v1.01) of the Pinus teada genome SMarTForests Project releases the third assembly of the Picea glauca genome

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