Suburban rainbow Non-science random thoughts this weekend:

  • On this last day of March – 16.8 mm of rain for the month. March average = 139.5 mm. See some Brisbane climate stats.
  • First weekend of the AFL season! Deep sadness as I realise that the first Swans game won’t be on TV here as it clashes with the Lions. Surely the great Grand Final rematch should be free to air in all states.
  • Wonder how the Pixies sound after all these years? Looking forward to reports from the V Festival.

Zen of LaTeX

Zen moments are common if you use a lot of open-source software. Sometimes you download software, work your way through some tutorials and how-tos and scan mailing lists, but you don’t quite see what all the fuss is about. Then one day you have your zen moment – “Aaah!” – when you get it.

It’s taken way too many years but this week, I finally had my LaTeX zen moment.
Read the rest…

A weekend of plugins

Plugins.  Add-ons.  Extensions.  You know, those things that make Firefox even better. Here are my latest favourites.

  • Google Reader Notifier
    Sits unobtrusively in the status bar and indicates the number of unread Reader items. Hover over it to see categories; click it to go to Reader, set preferences or update count. Clean and simple.
  • Gmail Space
    Presents you with an FTP-like interface to your Gmail account. You can then use your Gmail space to backup local files – they appear as a new email with the file as attachment. Very nice.
  • DapperFox
    Presents an icon in the URL bar which lets you create a Dapper feed or see Dapper feeds created by other people. I’m not yet 100% convinced by Dapper but this is a good utility if you use it.
  • ScribeFire
    Previously known as Performancing, this is an integrated blog editor. Works nicely with Seems a little pointless given that if I’m in my browser, I can blog at the WordPress site but some people claim that ScribeFire is quicker and full-featured. I’m giving it a go for this post.

On the Ubuntu front – ‘sudo apt-get install checkgmail’ for a system tray Gmail notifier.

Does anyone not like GTDGmail?

Check out the comments for the GTDGmail extension. It’s some kind of internet love-fest. No wonder that some suggest GTD is a cult.
FWIW, I installed it and found that I could no longer edit my Gmail contacts – clicking a contact just reloaded the page. I wasn’t impressed and promptly uninstalled.

update: seems that particular machine has Firefox javascript issues and this is not a general GTDGmail problem

GFF3 and the SO

I like GFF file format. Plain old ASCII text, human and machine-readable, simple yet full-featured and good BioPerl support.

I’m planning to use it in a project and browsing the GFF3 specs, I discovered that column 3 “type” should be a SOFA term – SOFA being part of the Sequence Ontology Project. All well and good, except:

  • The features that I would like to annotate are transmembrane helices (and the loops between them), as predicted using TMHMM. There does not seem to be a “TM helix” feature in the SO, which I think is a rather major omission.
  • It’s not clear to me if the SO project is still actively maintained. A lot of their SourceForge pages seem to be slow, broken or not updated for some time. The Term Tracker mechanism for suggesting new terms seems to be non-functional.

If anyone knows the current status of the SO, I’d like to hear about it. I’d also suggest that terms to describe both transmembrane helices and the extramembrane regions connected to them would be rather useful.

Science roundup

In the weekly battle for my attention that is Nature versus Science, the latter wins for me this week:

Google everything

Over the past couple of months I’ve tried out most Google services in the quest for research efficiency. Ratings, in no particular order:

  • Gmail: I use it but admit that I don’t yet “get it”. I expect to experience Gmail epiphany some day soon.
  • Docs/Spreadsheets: Nice idea but needs more features to convince me fully.
  • Notebook: probably my favourite. Simple and cleanly executed, makes gathering notes from the web a snap.
  • Web albums: not bad. I can see their potential for sharing e.g. gel photos. For non-work related photography, Flickr all the way.
  • Reader: also not bad and good for sharing feeds, but I prefer a standalone such as Liferea.
  • Groups: useful but not one of their better offerings. Needs work and better features.
  • Calendar: barely used it so can’t comment much. I don’t do a lot of scheduling, probably useful for those who do.

On the topic of Google Groups – our lab has set up a couple of private groups, one for general lab stuff and one for a specific project. This is working quite well but there are a few annoyances. In particular:

  • Registering users who have a Gmail address but would prefer to use an alternative address. Basically, they can’t.
  • Calendar integration would be really, really useful for group event reminders.
  • Page creation is extremely limited. It would be great if you could add e.g. the code that generates an RSS feed summary from Google Reader, or gadgets, to a Groups page.

Criticisms aside, I’m a big fan of Google services on the whole and recommend that everyone give them a go and provide feedback to Google.