Monthly Archives: October 2007

ATI 8.42.3

Just a quick and boring hardware post for those Linux users stuck with ATI video cards. Release 8.42.3 of the proprietary fglrx driver now supports AIGLX and the composite extension (which means compiz-fusion and cool desktop effects without the need for Xgl).

My own experience on Ubuntu 7.10:

  • Installation relatively painless using any of these guides: one, two, three
  • Performance reasonable except that (1) cube rotation a little choppy, (2) 3D GL apps flicker terribly (fix: turn off compiz)
  • Much less CPU/RAM usage than when running Xgl

If you´re happy with the Xgl solution, stick with it until things improve. Some progress, at least.

Bioinformatics Australia 2007: day 2 and round-up

Some more brief notes and hyperlinks from day 2 of the Bioinformatics Australia 2007 meeting.

I enjoyed this meeting. Nothing earth-shattering, but a lot of good talks with themes that interest me: genomics, data management, data integration, bringing bioinformatics to bench biologists. I’d definitely attend again. The organisers hope that this meeting will become a major event in the Australian bioinformatics calendar, reaching into the Asia-Pacific region and attracting more interest. Bioinformaticians who fancy a trip to Australia should keep an eye on the event and wangle themselves an invitation.
Read the rest…

Bioinformatics Australia 2007: day 1

This week, I attended Bioinformatics Australia 2007 here in Brisbane. It’s a small meeting; about 100 participants, 2 plenary talks, 2 discussion forums and 22 symposium talks (including myself), plus a smattering of posters. As the name suggests it’s a local meeting, although there are a few participants from overseas.

I enjoyed day 1 on the whole; here’s a brief round up with hyperlinks.
Read the rest…

Plenty of time for Bio::Blogs #16 submissions

Bio::Blogs, the monthly bioinformatics blog journal will be hosted at Freelancing science on November 1.

You know what to do and you’ve plenty of time to do it. Send links to posts (your own or others) to the email addresses in Pawel’s post. Email bioblogs at gmail dot com if you’d like to host an edition – it’s easy, fun and the appreciation from the community will make you warm and fuzzy.

Does bioinformatics have protocols?

Continuing with my “get involved at Nature Network” theme: Bronwen Dekker has started a thread in the bioinformatics forum. She is interested in compiling protocols for bioinformatics and is looking for a way into the seemingly-infinite mass of available software tools.

I’ve posted a few thoughts there concerning workflows, categories of data and whether bioinformatics even has protocols in the traditional sense. I think that this is an important topic, so go there and contribute to the discussion if you can.

Feisty to Gutsy: things that I should know by now

  1. Never attempt to upgrade an Ubuntu distribution on the day of the new release
  2. If you do, don’t use your primary desktop machine
  3. Complex tasks that can trash a machine should not be performed after midnight

I only have myself to blame but still: I didn’t expect the upgrade manager to simply vanish midway through the procedure, leaving an unusable system. One thing that I have learned is not to panic. Provided /home is on a separate partition, you can always do a clean install from CD and restore your packages pretty quickly.

Not sure why I’m experiencing zen-like calm rather than seething rage – must be Friday.

Ask a bioinformatician?

Admins of the Bioinformatics group at Nature Network received an email from Corie Lok today:

Just wanted to let you know that membership of your bioinformatics group has broken 400, making it by far the biggest group on Nature Network! Congratulations.

With such a large membership, I thought the time is right to do something in the group to stimulate more discussion in the group’s forum. Do you have any thoughts on how we can do that? What kinds of conversations lend themselves to an online forum that would be important for bioinformaticians? Are there any key people in the field, or authors of recent important papers, that the 400 group members would want to talk to in the forum? Perhaps we can invite them to join the forum, say a few words, and then offer to answer people’s questions on a specific topic.

I like this idea. If you have any suggestions or other thoughts on how to stimulate discussion at NN, visit the group, let Corie know or leave a comment here.

Note to self

Never blog at the end of a long, difficult week when tiredness and cynicism have won out against raw enthusiasm.

My thoughts yesterday on JournalFire, an online journal club to promote science discussion, were not at all coherent or insightful, so I took the unusual step of deleting a post. Web initiatives by bright, enthusiastic people should always be welcomed and I hope each and every one of them finds an audience and makes a mark.

Normal service will resume next week.

Bad reporting

Last week, I am creating artificial life, declares US gene pioneer went into my Google Starred list. “Craig Venter, the controversial DNA researcher, is poised to announce the creation of the first new artificial life form on Earth”, stated the Guardian article.

Maybe the reporter was over-excited, maybe the researchers did a bad job. Either way, “poised to announce” is incorrect. You can trust a professional science writer in the form of Carl Zimmer to clarify the story.

Ig Nobels 2007

Can it really be Ig Nobel time again?

Details of the 2007 ceremony are not yet up at the official site; also check these news sites:

Good to see an Australian contribution:

Literature – Glenda Browne of Blue Mountains, Australia, for her study of the word “the”, and how it can flummox those trying to put things into alphabetical order.