Completion of Integrating PhyloMetarep into CAMERA

Principal Investigator: 
Andrew Allen, J. Craig Venter Institute
Proposal Abstract: 

This project is a collaborative effort between UCSD and the J. Craig Venter Institute (JCVI), funded by the Gordon and Betty Moore Foundation (GBMF) as part of the GBMF Marine Microbiology Initiative. The PIs on this project are Andrew E. Allen (JCVI) and Eric E. Allen (SIO/UCSD).

The goal of the project is to transition a new software platform (PhyloMETAREP) developed at the JCVI for the analysis of genomic, metagenomic and transcriptomic sequence data into the Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis (CAMERA) resource. CAMERA is a UCSD-led project funded by the GBMF that has developed an advanced cyberinfrastructureincluding data repository and analysis functions to serve the bioinformatic needs of the global microbial ecology research community. The phyloMETAREP instance deployed on CAMERA will contain all data being generated as part of the GBMF-supported Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP) <>. This new analysis environment will allow the marine microbial ecology research community to access gene sequence information to compare and quantify the gene expression patterns of marine microeukaryotes.

Specific aims for this project include:

  1. Integration of the PhyloDB database with the CAMERA database
  2. Successful migration of the computational code base for the PhyloMETAREP software into the CAMERA infrastructure
  3. Recurrent bioinformatic analysis of transcriptome data as it becomes available from data providers at the National Center for Genome Resources (NCGR)
  4. Integration of the MMETSP data into the PhyloMETAREP instance deployed on CAMERA.

Successful completion of this project will be marked by the stable execution of PhyloMETAREP and its associated analysis functions through the CAMERA web portal.

Start and End Date: 
December 2012 to November 2013