2.1. IMPLEMENTATION
The Ocean Barcode Atlas web server is implemented through a classical
Model-View-Controller pattern architecture using the Laravel 5.4 PHP
framework. The application server communicates with the user through an
Apache HTTP server using HTML5, CSS3, JS, BLADE and AJAX to retrieve
user requests and display results. The PHP application server queries
abundance and environmental data stored in a mySQL relational database.
The amchart javascript library (https://www.amcharts.com/) was used to
build maps and bubble plots, whilst phylotree
(https://github.com/veg/phylotree.js/tree/master) and jstree
(https://www.jstree.com/) were used to draw phylogenetic trees and
choose a taxon respectively. The vegan R package was used for diversity
analysis (https://cran.ism.ac.jp/web/packages/vegan/vegan.pdf whilst the
ggplot R package
(https://cran.r-project.org/src/contrib/Archive/ggplot/) was used for
producing plots.