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biocore / emp

Code repository of the Earth Microbiome Project.
http://www.earthmicrobiome.org
BSD 3-Clause "New" or "Revised" License
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website: Defining the Tasks #48

Open cuttlefishh opened 8 years ago

cuttlefishh commented 8 years ago

Need to update. Current text from 2012:

There will be four key output from the EMP:

  1. Gene Atlas (GA) is a centralized repository and database for all information acquired during this study. This resource will follow the KBASE initiative and provide a searchable format to hold all information regarding annotation, environmental metadata and sequence. This will be a repository for all information, both known and unknown, the latter is also known as Dark Matter.
  2. Earth Microbiome Assembled Genomes (EM-AG) will encompass all genomes assembled from EMP data, which will be annotated using an automated pipeline and provided in public repositories and a KBASE derived analytical platform. This will enable comparative genomic analysis against all known and EMP-derived genomes and metagenomes.
  3. Earth Microbiome Visualization Portal (EM-VIP) will engage with expert in interactive visualization software to synthesize our unique vision into a format accessible to all. In here we will view the earth in microbial space, describing environmental parameter space and genomic functional space, to allow the interrogation of EMP data and the discovery of new ecological theory.
  4. Earth Microbiome Metabolic Reconstruction (EMMR) will be based on metagenomic metabolome description and prediction software such as modelSEED and Relative Metabolic Flux (RMF) we will describe changes in metabolites and metabolite profiles through time and biogeographic space. This will be used to produce descriptions regarding metabolite production in specific biomes, providing another metric against which to refine biome descriptions.
cuttlefishh commented 8 years ago

EMP webpages are now editable in markdown format here

cuttlefishh commented 6 years ago

This section has been removed from the website, because the public EMP data is all 16S and is not appropriate for these tasks, which are metagenomic in nature. However, it is worth noting these tasks in considering the next steps (EMP500 and such).