Building a Cyberinfrastructure for Plant Science Research with the iPlant Tree of Life Project and Toolkit
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The iPlant Tree of Life Project and Toolkit: Building a Cyberinfrastructure for Plant Science Research Given at Evolution 2011 An overview of the iPlant and iPToL project
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Building a Cyberinfrastructure for Plant Science Research with the iPlant Tree of Life Project and Toolkit
- 1. The iPlant Tree of Life Project and Toolkit: Building a Cyberinfrastructure for Plant Science Research Naim Matasci The iPlant Collaborative Evolution 2011 Jun 17-21, 2011
- 3. Discovery Environment NEW RELEASE COMING SOON! http://www.iplantcollaborative.org/discovery-environment-preview-access
- 14. iPlant Tree Viewer Prototype AVAILABLE NOW! http://portnoy.iplantcollaborative.org/
- 16. 1KP unexplored territory N(genes) dozens of species completed genomes N(species) dozens of genes PCR in 10 4 species
- 17. Broad phylogenetic coverage algae non-flowering flowering (angiosperm) on role of polyploidy in Darwin ’s “abominable mystery” Phylogenomics of 1000 species across plant taxa
- 19. Tree Reconciliation Gene family data courtesy John Bowers
- 24. AS SEEN IN NATURE! AVAILABLE NOW!
- 30. Community Integrated (2 ½ Days Workshop)
- 32. Collaborative Tool AVAILABLE NOW! NEW AND IMPROVED! http://my-plant.org/
Notas do Editor
- Bringing a culture of computing to the Plant Sciences.
- World class resources: Rocinante : 128 cores; 16 nodes; 64 GB node; 300 TB storage Corral : 1.7 PB storage + 20 PB archive Lonestar4 : 22,656 Intel Westmere cores; 40 GB QDR-IB; 1 PB storage; 44.3 TB RAM. Plus 1 TB RAM, GPU, and Cloud upgrades. Longhorn : 2048 Intel Nehalem cores. 512 NVIDIA Quadro FX 5800 GPU. 14.5 TB RAM. 1 PB storage. Ranger : 62976 AMD Opteron cores; 123 TB RAM; 32 GPUs. 1.7 PB storage.
- Large: >2 Gigs, where browsers fail
- Highest level of abstraction
- Distance matrix calculation compared to FASTREE
- BIEN: biological information and ecology network
- Provide the scientific community with a toolkit that will allow them to study the evolution of traits of interest Adaptation in response to past climate change Co-evolution of pollinators and flowers or hosts and parasites
- Contrast: Test for correlation of continuous traits, taking into account phylogeny DACE: Estimating the status of a discrete trait (e.g. presence/absence of fruit, color) in the ancestors of a group of taxa CACE: Estimating the value of a continuous trait (e.g. yield, hight) in the ancestors of a group of taxa