Archive for category: Computing tips

Paperpile: A new kid on the block

March 17th, 2010 by

The first public beta of Paperpile–the latest entry in the crowded arena of free reference management software–has been recently announced. As I write, a test version is available for Linux, but Mac and Windows versions should be released soon. From the screenshots gallery, it looks like Paperpile will feature a streamlined (although quite typical) 3-column interface, support for tags/labels as well as the standard Web import functionality from online bibliographic databases.

paperpile screenshot

It will be interesting to see how this software compares with cross-platform biggies such as Mendeley or established tools for specific environments such as BibDesk or JabRef.

Introducing citeproc-js

January 29th, 2010 by

Citation copy-editing is one of those deceptively small burdens that have a way of taking over the working day. If left untended, the task of tidying up casually scribbled references can snowball to crisis proportions as a submission deadline approaches. Similarly, when a submission to one publisher is unsuccessful, significant effort may be required to recast its citations in the format required by another. Collaboration outside of one’s own field can bring with it an unwelcome tangle of fresh style-guide quandaries to ponder and fight through. These are things that the machines, if they want to make themselves useful, should be doing for us.

There is plenty of collective experience in this line, and as fate would have it, there are also plenty of collective solutions. In the TeX/LaTeX world, authors and their editors can today choose between BibTeX and BibLaTeX — both of them excellent utilities — with the several variants of the former supported by no fewer than four separate versions of the BibTeX program. [1] Users of WYSIWYG word processors can look to the bibliographic support built into Word or Open Office, or they can turn to an external solution such as EndNote ™, ProCite ™, Reference Manager ™, or more recently Zotero or Mendeley. Migrating data between these environments is a process fraught with uncertainty, but it is sometimes unavoidable when you need this kind of output, and it can only be produced on that kind of system …


LaTeXSearch: 1M snippets in a searchable database

January 24th, 2010 by

Springer announced last week the launch of, a free online service allowing users to search a huge database of LaTeX snippets from Springer journals and publications. This follows the launch of a similar service, a few months ago exposing Springer’s database of scientific images (which suggests a precise strategy on how to build Web services on top of content in their publication database).

LaTeXSearch does what it promises, using similarity algorithms “to normalize and compare LaTeX strings so that, if similar equations are written slightly differently, the outputs are normalized and matched, granting you the broadest possible results set”. The only glitch is that snippets are not cached but generated on the fly, with the annoying result that it can take quite some time to display the rendered version of LaTeX formulas in search results.

Blog-sized lit reviews

November 6th, 2009 by

When I started my DPhil, I set myself assignments in order to cover the lit review in easy bite-sized chunks. This worked pretty well but the collated material was scattered across different Word documents, which meant that I couldn’t look at everything at one glance or search the content.

However at about the same time, I also started free-writing to generate ideas. If you’re not familiar with the technique, it’s simply writing for a fixed amount of time without stopping. You don’t delete anything on the fly and just go, writing down anything that comes to mind until the timer sounds or your wrists cramp up, whichever comes first.

Instead of putting this writing into Word documents though, I decided to set up a local installation of the blogging engine Movable Type. In retrospect, I think this was probably just an excuse to play with blogging software but it turned out to be a good decision. I could add content from any computer with access to the server, the basic input form meant that I focused on content not style, and of course, I had all the blogging bells-and-whistles attached. Comments could be added at a later date, the information sorted and searched, shared with my supervisor and so on.

I’m not sure why I didn’t think of it at the time but I would now recommend combining the two ideas: use a blog to write your lit review. (I say “write”, but I really mean “draft”. The structure of blog writing is quite different from academic writing and besides, you’ll want to tidy up references, tables, etc. for the final version. But a blog post is still big enough to cover the bulk of the material and help you organize your thoughts.)

The final stumbling block of course is how to get the content out of the blogging engine and into a presentable format. Fortunately, there’s a script called WPTEX that will convert your WordPress blog into a LaTeX document. I found this software about six months ago and it does what it says on the tin: give it some basic details and it will parse all of your posts, tidying up the code and creating LaTeX source files which you can then compile as a standalone PDF book or for inclusion as part of your thesis.

The script’s not perfect and I can think of several improvements, particularly in the way that it converts URLs for paper presentation. But if you’re starting a PhD, I’d recommend giving it a go. A blog-sized lit review is a great way to manage this difficult task and of course, if you make the blog public, you can engage with the wider community in your field, getting feedback and maybe even making a bit of a name for yourself. Happy blogging!

Literate programming for talks: Beamer, Sweave and LaTeX

August 25th, 2009 by

The summer conference season is slowly drawing to a close and we can all put our feet up, right? After all, the papers are done and presented and it’s a least a couple of months before organizers want your abstracts for next year. But before you kick back and relax, it’s worth pausing for a second to reflect on how things have gone and what you might want to do differently next year.

I gave a couple of talks this summer and while they went well, I wasn’t happy with the behind-the-scenes workflow. Some problems:

  • Creating figures in one piece of software, exporting to the right image format, inserting them into PowerPoint, discovering that you made a mistake, re-doing the figures…
  • Trying to shoe-horn a nice story about the results into 10 tight slides
  • PowerPoint, PowerPoint, PowerPoint – having to use someone else’s PowerPoint template, ugly text and math, big files, etc.

A lot of these issues can be fixed using tips here on the site. Outlining your talks for example helps get away from the staccato style of PowerPoint and as commenters have pointed out here, there are lots of ways to mix slides and narrative in one source file. But I want to go step further and show how you can combine narrative, slides and content (i.e. figure creation) in one file.