Data Assembly

General Data Assembly

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Tasks:

My-Plant/My-Crop

Deliverables:

Strategy:

Milestones:

1. Official launch 10Q3.

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Tasks:

Trait Evolution

Deliverables:

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Milestones:

1. Identified set of 5 components for integration:

2. Released 1st component (PIC) 10Q2.

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Tasks:

Tree Reconciliation and onekp

Deliverables:

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Milestones:

1.Bioinformatic pipeline for gene-species tree reconciliation completed and database populated with the reconciled trees, 10Q4;

2.Developer preview released with the following features, 11Q1:

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TR Tasks:

Onekp Tasks:

TNRS

Deliverables:

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Milestones:

  1. First release of the tool 10Q4;
  2. Completion of Phase 1/Scoping of Phase 2 11Q1;
  3. Support for Family and infraspecific epithets 11Q1.

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Tasks:

Big Trees

Deliverables:

NINJA/WINDJAMMER.

Strategy:

Milestones:

  1. Software rewritten from Java to C with an MPI;
  2. On-board distance matrix calculation added (K2P and Jukes Cantor for DNA; Blossum 42 for protein);
  3. Six day run time reduced 32-fold to 4.5 hours for 220K species data set;
  4. Two/three day run time reduced 1,800-fold to 2 minutes for distance matrix calculation on 220K set.

Status:

RAxML

Tasks:

Status:

Phylogenetics Workflow and Perpetually Updating Tree

Workflow

A Nascent workflow has been added to the the DNA subway as an education tool. This can serve as a model for integrating phylogenetic analysis tools to the DE.

Perpetually updated TOL
This is predicated on the completion of the infrastructure for data matrix assembly, RAxML-lite tree building, tree vizualization etc and is being scoped by the the iPlant scientific project Management team (Eric Lyons, Sheldon McKay, Matt Vaughn, Nicole Hopkins). Advice will be sought from the iPToL faculty regrading further requirements.

Tree Visualization

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