Data Assembly

General Data Assembly

Deliverables:

• An industrial strength pipeline for data assembly for very large data sets;
• Collaboration and Analysis Tools (contribute one's own data, download data, analyze data, keep data/results private) through the DE.

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• Robust data upload capability (IRODS; Rion Dooley, Nirav Merchant), late 11Q1?
• Meta-data management (Rion Dooley, Nirav Merchant, Sudha Ram), early 11Q2;
• Robust data storage and retrieval, collaboration tools in DE (iPlant-wide requirement; core software), 11Q2;
• Advanced collaboration tools (iPlant-wide requirement; core software), 11Q3;
• Input data validation (core software in collaboration with data integration ETAs);
• Multiple sequence alignment generation:
  • PHLAWD (John Cazes, Stephen Smith);
  • Gordon Burleigh's pipeline (John Cazes, Eric Lyons, Stephen Smith);
  • Muscle, other alignment strategies (John Cazes, Eric Lyons).
• Sequence database(s) bad GIs for PHLAWD, etc (Sheldon McKay and delegates), 11Q2.

My-Plant/My-Crop

Deliverables:

• My-Plant: Robust, widely used scientific collaboration network for the plant sciences based on a phylogeny metaphor;
• My-Crop: In support of integrated breeding platform, a scientific interaction site as well as data landing pad.

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• Refactor back-end for generic 'clade' structure to facilitate other display/organization paradigms (Matther Helmke), late 11Q1:
  • Node based;
  • Drupal core taxonomy.
• Implement Drupal module to ingest and provide basic search functionality for relevant literature citations from the user community and public databases (Steve Mock and delegates), 11Q2;
• Integration with Facebook and other similar sites. Initially with passive linkouts, possible later with Facebook page or app (Steve Mock and delegates), 11Q3;
• Integration (as consumer) of TNRS and iPlant tree viewer (Steve Mock; Matt Hanlon);
• My-Crop (different paradigm for display – also data repository):
  • scoping, early 11Q2;
  • early implementation, late 11Q2;
  • full implementation, early 11Q3.

Trait Evolution

Deliverables:

• An infrastructure for trait analysis and ancestral characters estimation.

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• Tool integration in DE-R scripts and command line tools (Naim Matasci and delegates), early 11Q2;
• Data uptake- files and external web based data from TreeBase (Sonya Lowry and delegates);
• Tree viz integration:
  • New visualization needs (Kris Urie), early 11Q2;
  • Call backs for new analyses (Adam Kubach, Sonya Lowry), mid 11Q2.
• DE integration:
  • Integration (Sonya Lowry and delegates), late 11Q2;
  • Metadata mapping (Naim Matasci), late 11Q2;
  • Analysis and viewer integration (Sonya Lowry and delegates), late 11Q2.
• Code and documentation release (Naim Matasci, Matthew Helmke), 11Q2.

Tree Reconciliation and onekp

Deliverables:

• Applications to perform, visualize and analyze the evolution of gene families from the onekp project with gene-species tree reconciliations.

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• Sequencing and transcript assemblies (onekp consortium; external);
• Gene cluster identification and alignment (Norm Wickett), ongoing;
• Continue to manage onekp data intake and tool implementation at TACC (Michael Gonzales, Sheldon McKay, Chris Jordan).

TNRS

Deliverables:

• A Taxonomic Name Resolution Service that:
  • will query taxonomic data from Tropics and other data services using GNI architecture and global names index allowing for different nomenclatures;
  • recover validated names names using exact and fuzzy matching algorithms;
  • inspect taxonomic status of validated names and convert synonyms where applicable.

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• UI redesign (Nicole Hopkins), 11Q1;
• Algorithm to handle synonyms (Jerry Lu), early 11Q2.

Big Trees

Deliverables:

• Computational infrastructure to build ToL.

NINJA/WINDJAMMER.

Strategy:

• Optimization of NINJA (neighbor joining implementation) for HPC.

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• Completed, minor tweaking of MPI.

RAxML

Tasks:

• Implement RAxMl-lite on Ranger, benchmark with various data sets (John Cazes), 11Q1;
• Implement web interface (relies on foundational API; Steve Mock and delegates), 11Q2.

Status:

• In progress

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.

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• The basic strategy is an automated workflow that will synch with GenBank or other data repository, build or iterate on on a chaacter matrix, re-run the tree building and update the Discovery Environment.

Tree Visualization

Deliverables:

• An interactive tree viewer that:
  • Makes possible to view large trees as a stand alone tool;
  • Makes the green plant ToL and sub-trees available in the iPlant DE;
  • Meets the visualization needs of Trait Evolution and Tree Reconciliation and of other applications in the Discovery Environment.

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