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GROWREC: a media recommendation platform for microbes

Here we provide GROWREC, a tool that allows users to upload a 16S rDNA sequence or a NCBI taxon ID for any organism, and get predictions of likely lab media that the organism can grow on (from the known catalogue from DSMZ). The tool is based on collaborative filtering, an algorithm that is popularly employed by Amazon.com, Inc., to recommend products to consumers, based on products known to have been purchased by other consumers with similar past buying habits. Similarly, given an input 'test' organism for which we aim to predict growth media, we first select a set of organisms from within KOMODO that are phylogenetically close to the 'test' organism (which is not required to be in KOMODO); next, we integrate the known medium preferences of those organisms into a 'collaborative score' indicating the likelihood that the test organism will grow on a given medium. Please see the Overview page for more details.

Please note: If you upload a 16S rDNA sequence for prediction by GROWREC, we perform a BLAST search to look for the closest species that are in our database, in order to do analysis. If you upload an NCBI taxon ID, then you will get the results of GROWREC exactly as they are described in the source paper (Oberhardt & Zarecki et al.).

Phylogenetic distance

GROWREC contains an option to determine a distance cutoff for how phylogenetically 'close' an organism must be to the test organism in order for its media preferences to be used in predicting those of the test organism. Based on some tuning we previously did, the default distance is 0.04. Distances can range from zero (no distance) to 1 (including any organism in the NCBI phylogenetic tree that is also in the DSMZ database). If no results come up with the default, you can try a higher distance cutoff to obtain more solutions. However, please note, the collab scores depend on the cutoff that is put in. In order to have collab scores that can be compared across organism predictions, use the same cutoff (or keep it as the default).

Example inputs

Click here to fill in an example input for the predictor. 

GROWREC media recommendation system
Please enter information on the organism for which you want media recommendation.
pressing the "Submit" will calculate the recommended media entries.
This operation may take a few minutes
Is organism Aerobic (Yes|No|Unknown):
Does Organism grow in Saltly Media (Yes|No|Unknown):
Maximal phylogenetic distance (range:0.0 - 1.0, default:0.04):
NCBI taxon ID (optional parameter - can be replaced by 16S data):
16S data (optional parameter - can be replaced by NCBI Taxon ID):
Blast 'Identities' Low Limit %

If you encounter problems please send their details to raphy.zarecki@gmail.com