Australiana

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.

Semi-identical twins

This is interesting. Two ova + two sperm = fraternal twins. One ovum + one sperm + splitting = identical twins. Now there’s a new twist in the tale: two sperm + one ovum + splitting = semi-identical twins.

I’m a little surprised that this hasn’t been described before – perhaps it has for other animals?

In other biology news, a monster cane toad. Who can tell me the error in the first paragraph?

Young scientists versus drugs giant

This one is off to court tomorrow, so we should perhaps wait for the verdict. In the meantime, satisfy your curiosity with these searches at Google News, Google blog search or Technorati that use the term ‘ribena and “new zealand”‘. Rumour has it that it’s not packed with vitamin C after all. I’ll point you to one specific blog post, just because I love the blog’s tagline.

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 WordPress.com. 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:

• Physicists’ Nightmare Scenario: The Higgs and Nothing Else
  Physicists are apparently terrified that their new multi-million dollar toy will generate the result that they want…
• Comparing Neanderthal and Human Genomes
  Interesting debate on the Letters page on whether whole-genome analysis is hypothesis-driven science. “Of course it is!”, shout myself and Jonathan.
• CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes
  I have a fondness for CRISPRs. They are a type of repeat region, associated with specific genes (called cas genes) and occur widely in bacterial and archaeal genomes. I found some a couple of years ago in a genome that I used to work on. Since then I’ve noted several bioinformatic and microbiological studies of CRISPRs. It’s one of those times when you wonder if you discovered a hot topic and just missed the boat (or is that bandwagon).

More on RSS-ification

As I mentioned Pedro’s post on openkapow, I should point you to Andrew’s experiments using Dapper towards a similar end. By all accounts Dapper is somewhat simpler but less powerful than openkapow. It’s just great to see people using this stuff and posting their findings.

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.