A Technical details
A.1 Basic information
STRAF is hosted on an Amazon Web Services (AWS) server located in Ireland.
STRAF has 2 CPUs and 4 gigabytes of memory available on the server. It is enough for the vast majority of cases, but might not be enough if your dataset is too large (too many samples, or too many loci).
The web application is based on the R-Shiny framework. R is an open source programming language particularly popular in data science. Shiny is an open source R package that provides a web framework for building web applications using R.
Figure A.1: The R logo.
A.2 Understanding STRAF’s performance
When you open STRAF, a new session starts. When you close your browser or the tab, the session is closed and your data and computations are deleted.
STRAF can accept an unlimited number of user connections at the same time. However, the computational resources are shared between users. In other words, multiple users can connect at the same time, but computations will be ran one after the other. If you wait longer than usual for a given task, it is likely that someone else is using the server. Please keep this in mind and try to avoid unnecessary computations!
STRAF has limited resources, as described above, and this can be limiting if your dataset is too large because you have too many samples or loci. In that case, you could consider trying to run STRAF locally as outlined in Chapter 9. You could even host it on your own institution’s server, in that case feel free to contact us as we would be happy to help in the process.
A.3 External dependencies
STRAF wouldn’t exist without the amazing community of R developers who contributed great resources and packages.
The application uses several genetics packages:
genepopedegenethierfstatpegas
More generic data science packages are also used:
Shiny-related packages:
shiny,colourpicker,shinycssloaders,shinyWidgetsThe “tidyverse”:
dplyr,tidyr,ggplot2,magrittr,openxlsx,reshape2,ggrepel