I keep returning to the problem of viewing large graphs and trees, which means my hard drive has accumulated lots of failed prototypes. Inspired by some recent discussions on comparing taxonomic classifications I decided to package one of these (wildly incomplete) prototypes up so that I can document the idea and put the code somewhere safe.

Notes to self on web map-style tree viewers. The basic idea is to use Google Maps or Leaflet to display a tree. Hence we need to compute tiles. One approach is to use a database that supports spatial queries to store the x,y coordinates of the tree. When we draw a tile we compute the coordinates of that tile, based on position and zoom level, do a spatial query to extract all lines that intersect with the rectangle for that tile, and draw those.

Inspired in part by the release of the draft tree of life (doi:10.1073/pnas.1423041112 by the Open Tree of Life, I've been revisiting (yet again) ways to visualise very big phylogenies (see Very large phylogeny viewer for my last attempt). My latest experiment uses Google Maps to render a large tree. Google Maps uses "tiles" to create a zoomable interface, so we need to create tiles for different zoom levels for the phylogeny.

For the last few weeks I've been working on a little project to display phylogenies on web-based maps such as OpenStreetMap and Google Maps. Below I'll sketch out the rationale, but if you're in a hurry you can see a live demo here: http://iphylo.org/~rpage/geojson-phylogeny-demo/, and some examples below.

Following on from earlier posts on annotating biodiversity data (Rethinking annotating biodiversity data and More on annotating biodiversity data: beyond sticky notes and wikis) I've started playing with user interfaces for editing data.

Following on from the previous post on putting GBIF data onto Google Maps, I'm now going to put DNA barcodes onto Google Maps. You can see the result at http://iphylo.org/~rpage/bold-map/, which displays around 1.2 million barcodes obtained from the International Barcode of Life Project (iBOL) releases.

As part of a project exploring GBIF data I've been playing with displaying GBIF data on Google Maps.

Robert M. Griffin (@GriffinEvo) has launched ProjectEvoMap. Rob explains: Below is a screen shot of part of the map. If you're working on evolutionary biology now is your chance to literally put your lab on the map.

Here's a quick demo of a 2D large tree viewer that I'm working on. The aim is to provide a simple way to view and navigate very large trees (such as the NCBI classification) in a web browser using just HTML and Javascript. At the moment this is simply a viewer, but the goal is to add the ability to show "tracks" like a genome browser.

In previous articles I've looked at how various apps display scientific articles. The apps I looked at were: PLoS Reader Nature Papers Mendeley So, where next? As Ian Mulvany noted in a comment on an earlier post, I haven't attempted to summarise the best user interface metaphors for navigation. Rather than try and do that in the abstract, I'd like to create some prototypes to play with various ideas.