Research thoughts for the day

Spent much of the day pondering HMMER, weak motifs and extraction of information from HMMER alignments to Pfam models. Many proteins contain short, weakly-conserved motifs. One that I’m working on at the moment contains a “GEL” motif, actually 6 residues that often, but not always, begin “GEL”.
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Some comments welcome

The comment spam has started. Sigh. This means that you now need a previously-approved comment before your comments are automatically posted. Which means more admin for me. Sigh. I did try a few Captcha-type WP plugins but unsurprisingly, they’re broken with the JD-WP Joomla-integrated WP.

Project management/notebook apps for bioinformaticians

At work recently, we’ve been discussing electronic notebooks, project management tools and so on. Here’s the problem: like other researchers, computational biologists would like to keep some record of what they’ve done during their working day. This is necessary so as to keep track of your progress, to reassure your boss that you really are working and possibly (though rarely), if legal issues like IP ever come up. Of course people like us refuse to maintain a paper notebook, so what do we do?
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User Agent Switcher

There are websites that do things which you don’t want, based on detection of your browser. I’m working on one at the moment – my predecessor has left me 1750 lines of javascript which starts off by checking if you use Internet Explorer and refusing to proceed if not. Uurgh.
Firefox users in this predicament – grab yourself a copy of the User Agent Switcher Extension. It gives you a Menu->Tools item that allows you to change your apparent browser ID. Now, the Firefox people just have to figure out how to avoid a browser restart after installing extensions. It’s kind of annoying when you have 10 tabs open.

Making do

Another in the mini-series “surviving the first weeks in a new job” – what to do whilst awaiting delivery of your promised new computer?

Go to a bioinformatics conference and you’ll see two types of bioinformatician: those with the latest swanky model of slimline, powerful laptops and those without. I fall into the latter category. To be precise, I own a Dell Inspiron 7000, circa 1997. At the time this was a state of the art “desktop replacement”, meaning that it weighs several kilos and the base alone is about three times the thickness of todays laptops. Some of the keys are becoming temperamental, the screen latches and PCMCIA slot covers are long gone and it boasts a PII 400 MHz CPU, 256 MB RAM, a 20 GB HDD and a whopping 8 MB video RAM. So what can you do with it?
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Back to work

It’s been a hectic 3 weeks – moved cities, found a place to live, started new job, but I’m starting to feel settled in my new home and workplace. No work machine to call my own as yet but my ancient laptop is networked, which I count as the official start of work.
For those interested, I’m now at the University of Queensland in the School of Molecular and Microbial Sciences. My new position is computational biologist to the Kobe group, where I’ll be working on computational analysis of protein structure, function and interaction, particularly of protein kinases and their substrates.
One of my first tasks will be to take 1750 lines of javascript and convert it to a real language as part of a website overhaul. My new colleagues are also expressing interest in MamboLIMS, so that should inspire me to make some long-overdue improvements to the package. Note to self: web development is fun but ultimately unproductive in terms of publications. Get it out of the way, get down to real work.

Woodpecker confusion

Is that recently rediscovered ivory-billed woodpecker merely a common pileated woodpecker? I do hope not.

I’d like to have posted a woodpecker picture – spent much of today playing with gallery and image plugins for WordPress, none of which worked very well, perhaps due to this being a Joomla-integrated version of WP. I’m considering turning the whole site over to WP and dropping the Joomla.