Major milestone reached - minimum viable product - Ordination
We're coming up to the half-way point of the 10 month project and have achieved a major milestone, with a demonstrable minimal viable product, where we can perform an ordination analysis on continental-scale environmental metagenomics data.
Here's a short movie showing a Principal Component Analysis (plot by vegetation type) of samples containing Bacteroidetes that were collected from Forest or Grassland environments:
Supported ordination methods include DCA, CCA, RDA, NMDS, MDS, PCoA, DPCoA.
Note that this is currently deployed internally on our staging environments but will be released to the production environment as soon as we have performed thorough quality assurance.
Getting to this point has required us to focus on lots of unglamorous backend issues:
The great news is that now we have reached this critical point, the rest of the project can now be focussed on work that will get our users excited - incorporating many of the functions on the community wishlist, and streamlining the system to make it as usable as possible for a wide range of user types.
Here's a short movie showing a Principal Component Analysis (plot by vegetation type) of samples containing Bacteroidetes that were collected from Forest or Grassland environments:
After pressing play, change the view mode to 'Theater' or 'Full Screen'
mode and adjust the Quality to 720p HD)
Supported ordination methods include DCA, CCA, RDA, NMDS, MDS, PCoA, DPCoA.
Note that this is currently deployed internally on our staging environments but will be released to the production environment as soon as we have performed thorough quality assurance.
Getting to this point has required us to focus on lots of unglamorous backend issues:
- establishing support for BIOM format files (as well as OTU tables);
- ensuring the BPA Data Portal communicates with Galaxy Australia over the API;
- tools are prepared for use in the system (we've focussed so far on 'wrapping' R-based scripts from the Phyloseq package for the ordination functions into the Galaxy environment we use for analysis); and
- developing methods and processes to manage individual user accounts.
The great news is that now we have reached this critical point, the rest of the project can now be focussed on work that will get our users excited - incorporating many of the functions on the community wishlist, and streamlining the system to make it as usable as possible for a wide range of user types.
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