diff --git a/paper-proposal.tex b/paper-proposal.tex index db26505..ce2f83a 100644 --- a/paper-proposal.tex +++ b/paper-proposal.tex @@ -11,7 +11,7 @@ % For web servers, or essentially similar web servers, that have been the subject of a previous publication, including publication in journals other than NAR, there is a minimum two-year interval before re-publication in the Web Server Issue. Our proposal covers an update to Superphy \citep{whiteside2016superphy}, an online predictive genomics platform targeting \textit{Escherichia coli}. The update, called Spfy, uses graph datastructures to store and retrieve results for computational workflows. -We demonstrate the ability of graph data structures to scale to the [approximate number, eg. greater than 50,000]l of whole-genome sequences accumulated so far, and show the ability to scale to X genomes. +We demonstrate the ability of graph data structures to scale to the [approximate number, eg. greater than 50,000]l of hole-genome sequences accumulated so far, and show the ability to scale to X genomes. Spfy provides real-time subtyping through a ReactJS-based website, where user-defined analyses options are selected. Analyses are run in parallel using task queues and Docker containerization, and the results are immediately displayed to the user following their completion. Subtyping options include O-antigen, H-antigen, Shiga-toxin 1 (Stx1), Shiga-toxin 2 (Stx2), and Intimin typing. Reference-lab type tests include virulence factor and anti-microbial resistance annotation. All genomes are analyzed withing the pan-genome framework of \textit{E. coli}.