Darkly Colored Felines of Fury

Darkly Colored Felines of Fury » science http://blackcat.ca Personal site for Patrick Audley and Blackcat Systems. Mon, 31 Jan 2011 05:11:30 +0000 en hourly 1 http://wordpress.org/?v=3.3.1 My First Paper http://blackcat.ca/work/paper01 http://blackcat.ca/work/paper01#comments Fri, 21 Nov 2003 16:20:23 +0000 Patrick Audley http://blackcat.ca/work/paper01 This paper has been years in the making, and though I was only involved towards the end it was still a lot of fun. The paper evaluates several different methods for performing multiple sequence alignments (MSA). MSAs are used in biology to determine how similar several genes or proteins are. This is useful, for instance, to determine how closely related genes are among different species. Alternatively, MSAs can be used to compare different genes or proteins within a single species to find similar functions. MSAs are useful in other scientific fields, such as linguistics, where you need to determine the similarity between a number of sequences of things (like sentences of words).

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]]> http://blackcat.ca/work/paper01/feed/ 0 Pitlochry Symposium 2003 http://blackcat.ca/work/bioinform004 http://blackcat.ca/work/bioinform004#comments Mon, 31 Mar 2003 15:47:11 +0000 Patrick Audley http://blackcat.ca/work/bioinform004 What a BLAST! We both had a really great time at the Symposium. The lectures were great (even if they were a little too kinase heavy) and it was really fun to hang out in a social setting with people I work near everyday. Hearing everyone talk about their work during the lectures was really great too. On Saturday, Elizabeth and I took a hike in the wilderness and met a very cool retiree who belongs to the clan that owns all the land around Pitlochry. We chatted for the better part of a half hour as we walked back together and had a most enjoyable time. That night was the Ceilidh, a Scottish dance that resembles square dancing. Afterwards came the quiz session; a cross between a drunken game show and a game of Trivial Pursuit. We came in 5th but still had a great time! All in all a really good weekend. The only thing it lacked was sleep *lol*

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September 20, 2011, Andy Sokolov-Gorsky writes: Thank you for the nice fotoes! I would like to place the picture of Dr Sir Phillip Cohen on my website devoted to the treatment of Cancer and other fatal diseases science-for-life.ru The site is in Russian. Could you please confirm that I can do it. Thank you! With best wishes, Andy

]]> http://blackcat.ca/work/bioinform004/feed/ 1 Bioinformatics Feb. 2003 http://blackcat.ca/work/bioinform002 http://blackcat.ca/work/bioinform002#comments Sun, 16 Feb 2003 01:56:29 +0000 Patrick Audley http://blackcat.ca/work/bioinform002 It's been a fun month at work! Below is a picture of my new Cisco 6509. It's been a blast to play with and poke around. It's nice to have good hardware to use and network planning is always. On the software side I've been writing two software packages that shall be appearing in my code gallery soon. Submit_All is a package that allows biologists to submit a protein or DNA sequence and have it analysed by many programs at once on our cluster. The results are presented on a unified page and are cross-referenced. The second thing that I've been working on lately is a program to display sequences aligned with graphs and annotations. Good looking sequence displays are very lacking at the moment so I wanted to made something that will look pretty (hence the name Pretty_Seq *grin*). You can have a look below at the image of Pretty_Seq and the archive of Submit_All and see how I'm doing. [CALLAN,Chris Allan] who I worked with at [GT003,Group Telecom] has come out to join the University working as a guru in the Light Microscopy lab. It's cool to have someone from home to go out with. He's been staying with Elizabeth and I for the last few weeks until he gets a place. Canadian world domination proceeds a pace... This month promises to be fun at work!

]]> http://blackcat.ca/work/bioinform002/feed/ 0 Careers: Academia http://blackcat.ca/work/academia http://blackcat.ca/work/academia#comments Wed, 01 Jan 2003 20:55:40 +0000 Patrick Audley http://blackcat.ca/work/academia Working in Academia was more satisfying in many ways than working in [STARTUPS,startups]. Most of the people who work in research were smart, well informed, and enjoy their work (Elizabeth and I thought this was because the pay was half that of the private sector, so anyone who doesn't like it gets a job there elsewhere).

I really enjoyed working in the [BIOINFORM001,Bioinformatics Dept.] and had great coworkers. This was the first time in all my career when I could truly say that I enjoyed everyone I worked with. Seminars were particularly enjoyable and it was always easy to find people talking passionately about things they love.

]]> http://blackcat.ca/work/academia/feed/ 0 A Career in Bioinformatics http://blackcat.ca/work/bioinform001 http://blackcat.ca/work/bioinform001#comments Fri, 31 May 2002 02:21:05 +0000 Patrick Audley http://blackcat.ca/work/bioinform001 University of Dundee after I moved to the UK to be with Elizabeth. It was, in retrospect, fated to be. I was spending all my time in Elizabeth's lab learning everything I could about molecular biology (thanks Elizabeth!) and invariably ended up bumping into the only other people on campus that had an interest in large scale computing. After a very short and informal interview I started in the Computational Biology Dept. with a larger role overseeing all the high-performance computing in the faculty. This doesn't sound terribly interesting until you consider the research powerhouse that the Life Sciences Faculty contained &emdash; to me, it meant being involved in projects with a huge range of research and some incredibly interesting problems to solve.]]> I started working at the University of Dundee after I moved to the UK to be with Elizabeth. It was, in retrospect, fated to be. I was spending all my time in Elizabeth's lab learning everything I could about molecular biology (thanks Elizabeth!) and invariably ended up bumping into the only other people on campus that had an interest in large scale computing. After a very short and informal interview I started in the Computational Biology Dept. with a larger role overseeing all the high-performance computing in the faculty. This doesn't sound terribly interesting until you consider the research powerhouse that the Life Sciences Faculty contained -- to me, it meant being involved in projects with a huge range of research and some incredibly interesting problems to solve. Cluster running

This job was as large a change as moving to the UK in it's own way -- the pace was terribly different from the corporate world that I'd just left behind. After a brief settling period it was truly a dream job. Looking back, I think I enjoyed Academia most because I got to work with smart people who were always focused on results instead of just passing the time (publish or perish!). I had my own supercomputer (see below) and lots of cool hardware (some of it very strange and wonderful) along with access to all the facilities at the faculty. That last one alone was worth the job alone, which tells you something about me. For the geeks in the crowd, this marked the first time I had access to over 3TB of storage (eventually over 3PB, yes, that's 3,000,000 GB) and a few 100GHz (eventually, much, much more) of computing power. The only thing that was a downgrade from my gear at GT was the network which, at it's peak, reached only around 5 GB/s. I do have the honour of being, as of leaving the job, the person with the fastest ever NFS implementation that IBM's HPC teams have seen in terms of actual wire speed file transfers -- 2GB/s of actual, real file transfer from a single SAN (fronted with 2 paired p-series NFS servers) over NFS to a cluster of computing nodes was a new sustained load record. Err.. ok, that was pretty geeky, but I was in Academia after all, geekiness is king there.

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