When developing Citation.js, I needed to get a JavaScript Object from a string representing one. There are several methods for this, and the one that comes to mind first is JSON.parse(). However, this didn't work.

Last week I made Citation.js usable for the command line, with Node.js. First of all, the main file determines if it is being run with Node.js or in the browser, and switches to Browser or Nodejs mode based on that.

I made a test JavaScript file for NodeJS to practice working with it, and prepare more for the project.

Some time ago in academia we realized that it didn’t make sense for individual scientists or even entire departments to maintain their own high performance computing resources.

There is an excellent post on open science, prestige economies, and the social web over at Marciovm’s posterous*. For those of you who aren’t insanely nerdy** GitHub is… well… let’s just call it a very impressive collaborative tool for developing and sharing software***. But don’t worry, you don’t need to spend your days tied to a computer or have any interest in writing your own software to enjoy gems like: Thanks to Carl Boettiger

Advertisements for three exciting postdoctoral positions came out in the last week. Interface between ecology, evolution and mathematics The first is with Hélène Morlon’s group in Paris. Hélène and I were postdocs in Jessica Green’s lab at the same time. She is both very smart and extremely nice, oh, and did I mention, her lab is in PARIS. Here’s the ad. If it’s a good fit then you couldn’t go wrong with this postdoc.

If you use R (and it seems like everybody does these days) then you should check out RStudio – an easy to install, cross-platform IDE for R. Basically it’s a seamless integration of all of the aspects of R (including scripts, the console, figures, help, etc.) into a single easy to use package. For those of you are familiar with Matlab, it’s a very similar interface. It’s not a full blown IDE yet (no debugger;

For me one of the most frustrating things about online databases is that they often can't be edited. For example, I've recently created a version of the Australian Faunal Directory on CouchDB, which contains a list of all animals in Australia, and a fairly comprehensive bibliography of taxonomic publication on those animals. What I'd like to do is locate those publications online.

The Ecological Database Toolkit Large amounts of ecological and environmental data are becoming increasingly available due to initiatives sponsoring the collection of large-scale data and efforts to increase the publication of already collected datasets. As a result, ecology is entering an era where progress will be increasingly limited by the speed at which we can organize and analyze data.

I’ve recently started reading two scientific programming blogs that I think are well worth paying attention to, so I’m blogrolling them and offering a brief introduction here. Serendipity is Steve Easterbrook’s blog about the interface between software engineering and climate science. Steve has a realistic and balanced viewpoint regarding the reality of programming in scientific disciplines.