Here are some tricks for scraping the web with R and Python.

This week version 2.0 of the V8 package has been released to CRAN. Go get it now! install.packages("V8") The V8 package provides an embedded JavaScript engine that can be used inside of R. You can use it interactively as a JavaScript console, but it is mostly useful for wrapping JavaScript libraries in R packages. Some cool examples include jsonld, jsonvalidate, and daff.

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.

Continuing my on-again off-again relationship with the Semantic Web, I stumbled across a cool approach to visualising the results of SPARQL queries.

ELNs (electronic laboratory notebooks) have been around for a long time in chemistry, largely of course due to the needs of the pharmaceutical industries. We did our first extensive evaluation probably at least 15 years ago, and nowadays there are many on the commercial market, with a few more coming from opensource communities. Here I thought I would bring to your attention the potential of an interesting new entrant from the open community.

A word of explanation about this test page for experimenting with JSmol. Many moons ago I posted about how to include a generated 3D molecular model in a blog post, and have used that method on many posts here ever since. It relied on Java as the underlying software (first introduced in 1996), or almost 20 years ago.

TL;DR By using bookmarklets and a central annotation store, we can build a system to annotate any biodiversity database, and display those annotations on those databases. A couple of weeks ago I was at GBIF meeting in Copenhagen, and there was a discussion about adding a new feature to the GBIF portal. The conversation went something like this: Resources are limited, and adding new features to a project can be difficult.

Spam just doesn’t die. Every major mail provider has really good spam filters in place, as do the common mail clients. Nontheless, there seem to be enough people reading – and acting on – spam mail to make it a profitable business. No matter how much we hate it, we need to deal with spam. Better than having a good spam filter is not to be spammed in the first place.

Spam just doesn’t die. Every major mail provider has really good spam filters in place, as do the common mail clients. Nontheless, there seem to be enough people reading – and acting on – spam mail to make it a profitable business. No matter how much we hate it, we need to deal with spam. Better than having a good spam filter is not to be spammed in the first place.

Say what you will about Elsevier, they are certainly exploring ways to re-imagine the scientific article. In a comment on an earlier post Fabian Schreiber pointed out that Elsevier have released an app to display phylogenies in articles they publish. The app is based on jsPhyloSVGand is described here.