LaTeX tip: make your own styles

Last year I wrote a short post with some ideas on how to generate citation styles. The idea being that whilst there are many styles of referencing in different journals, there is a finite set of elements: plain, bold or italic; all authors or et al. after 3; volume + number or just volume and so on and so on. Computationally, it should be possible to construct a set of questions based on these elements and have a style pop out the other end.

Well, since then I’ve moved to LaTeX and of course, it does precisely this for you. Just “latex makebst”, answer a long series of questions and you’ve got a custom .bst file. More details are available at the LaTeX Bibliography Styles Database.

Organise your bioinformatics projects using Subversion and Trac: part 2

So – you’ve installed Subversion and Trac on your server, everything works and you’re ready to start managing your projects. In this post, I’d like to focus less on the technical details of using SVN/Trac and more on how they can be useful to bioinformaticians. Trac in particular is highly configurable and I think there are some exciting ways to use it. These include managing your data, sharing it with collaborators and even using it as an open notebook system.
Read the rest…

Organise your bioinformatics projects using Subversion and Trac: part 1

Like most people with computer-related jobs, I work on numerous machines. At work, there’s the all-purpose server, the personal desktop machine, a second server for testing/backup and should I need it, a Linux cluster. At home there’s the desktop/server and laptop. In general, I use the work server as the “working machine”, with an NFS mount to the desktop and backups using rsync to the second work server and the home server. The laptop is, as much as possible, a dumb terminal for SSH to other places.

I imagine that I’m not alone in having a directory under my home directory named “projects/”, with a hierarchy of project directories below that and directories below them named “perl”, “fasta”, “gnuplot” and so on. This is all very well, until I’m sat at one or the other of the machines and decide to do some work. Pretty soon, confusion reigns as I try to recall in which direction I should rsync the altered files. What I really need is a master repository from which I make working copies that I can synchronise with the master from any location. In other words – revision control.

I’ve been using CVS for a few years just for code and found it to be very beneficial and quite easy to use, especially from within emacs. However, people kept telling me that Subversion (SVN), the CVS alternative, was far superior. Then I came across a project management system called Trac, which is used by the bioinformatics guys at the IMB on our campus and interfaces with SVN. So I thought – how about using SVN + Trac to handle all of my bioinformatics project files – not just the code?

It turns out that this is a great way to organise and maintain files and share them with other people. This post explains how I set up SVN + Trac; the next post looks at some ways to use them for bioinformatics projects.
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Random conference thoughts

When my mind wanders during a conference talk, I often find that short sentences summarising how I feel about work come into my head. Here’s what I scribbled in my notepad during the ComBio meeting this week:

Information relevant to me is communal, not owned by individuals
I wrote that down when thinking about how biologists interact (or not) at meetings. As a computational biologist, most of my day-to-day problems are programming and software issues. If I need information, I go straight to the Web. However, wet-lab biologists seem to get much more of their information by talking to other biologists. If you’re interested in an organism, a model system, a laboratory technique or if you just want to get your hands on a plasmid, you talk to someone who works on it. It strikes me that a lot of wet-lab group leaders claim some sort of ownership over the information that their lab generates, resulting in the “so-and-so is the world expert in system X, you should talk to him” mentality. On the other hand, the idea of schmoozing with “the Perl expert” is a tad silly.
That, at least, is my excuse for not networking much at biological conferences ;)

Bioinformaticians need to be free
We (or at least, I) are happiest when working on a range of problems. A main project and a bunch of fun, side projects with plenty of variety is the key to a happy bioinformatician. Conversely, getting bogged down for months or years on a single project, particularly one on which you work largely alone with little external input makes for a sad bioinformatician.
Much has been written about Google’s 20% time, where employees are encouraged to spend 20% of their time on projects that they think are fun, cool and interesting. I think this would be a great policy to implement for bioinformaticians, computational biologists and other researchers in academia.

Google Docs now with Presentations

The title of the post says it all, really. The news is slowly making its way through the tech blogs.

I just tried uploading a file saved as Powerpoint (ugh) from OpenOffice. First attempt – server error. Second attempt – success. On the whole, the import preserved formatting pretty well, except for some text formatting (spacing changes, tab stops vanish). Two attempts to display the online slideshow have resulted in a black window with no slides. Oh, and you can only save as zipped HTML.

Early days – let’s hope they iron out the bugs and introduce OpenOffice import/export soon.


mal·aise (n.)

  1. a vague or unfocused feeling of mental uneasiness, lethargy, or discomfort
  2. a general sense of depression or unease

It’s good to know that you’re not alone, but this blogosphere synchronicity is a little un-nerving.

Google Docs: now officially impressed

A while ago, I asked for suggestions about how a research group could collaboratively edit documents. More than one person suggested that I try Google Docs and Spreadsheets. I signed up, uploaded a file or two, played around with the editor and didn’t take it much further.

I went back to it this week and now I get it. On your own, it serves as little more than a backup or a way to publish on the web. It’s the collaborative features that make it shine. Your documents can be private, open by invitation or public. Invitees (up to 200 of them) can be “view only” or collaborators (editors). Several people can work on a document simultaneously (up to 50 for docs, 10 for spreadsheets). There’s a very nice revisions feature where you can view differences between versions, colour-coded by author. You can upload and download in all the common formats that people are likely to use and convert to PDF. This means that I can work on my documents in LaTeX, run them through latex2rtf, upload the RTF and let other people work on them in a format with which they’re comfortable.

As usual, now all I have to do is convince my colleagues to stop bouncing documents around by email and use this far-superior tool instead.

From the Zotero blog

I’m a big fan of the Zotero extension for Firefox. Old news from their blog earlier this year:

Currently there are several teams of developers working to integrate Zotero with popular social bookmarking sites like and reference management sites like Connotea.

This is tremendously exciting. You’d be able to search PubMed, one-click save using Zotero, sync your references to a shared, online resource and grab them back for citation in various formats. That’s pretty much the holy grail of reference management and bibliography as far as I’m concerned.