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Author
Patrick Audley
Location
56.457478-2.987452University of DundeeDundeeScotlandGB-SCUKhttp://www.dundee.ac.ukSmall Earth Icon
Updated
2003-11-21
Date
My First Paper2003-11-2156.457478-2.987452University of DundeeDundeeScotlandGB-SCUKhttp://www.dundee.ac.ukSmall Earth Icon

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).

Author
Patrick Audley
Location
56.457478-2.987452University of DundeeDundeeScotlandGB-SCUKhttp://www.dundee.ac.ukSmall Earth Icon
Updated
2003-03-31
Date
Pitlochry Symposium 20032003-03-282003-03-3056.457478-2.987452University of DundeeDundeeScotlandGB-SCUKhttp://www.dundee.ac.ukSmall Earth Icon

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*

Cisco Bugs and Network FunNAT Puts Hair on your Chest

Author
Patrick Audley
Location
56.457478-2.987452University of DundeeDundeeScotlandGB-SCUKhttp://www.dundee.ac.ukSmall Earth Icon
Updated
2003-03-21
Date
Cisco Bugs and Network FunNAT Puts Hair on your Chest2003-03-2156.457478-2.987452University of DundeeDundeeScotlandGB-SCUKhttp://www.dundee.ac.ukSmall Earth Icon

I discovered my very own Cisco IOS bug.. Hooray.. After weeks of have network address translation problems on our new Cat6509, Chris and I found a new bug in Cisco’s operating system… Ick. Needless to say this meant much pain until we worked around it by setting up a BSD box to handle the NAT Wink.

In addition to the bug, we also discovered a flaw in how Cisco implements NAT. Essential NAT (or overloaded many-to-one translation) works by hiding several machines behind a router. All conversations go through the router who remembers who on the inside is talking to who on the outside. From the outside (in this instance, the rest of the Internet) it appears as if all the conversations are with the router and from the inside (our local network) it looks normal.

It’s a good trick and normally provides a reasonable level of security because the outside world can’t connect directly to the machines behind NAT. In theory. In the IOS implementation it seems that the last machine to make a connection out gets all traffic to the router’s overloaded address that doesn’t match an active translation. Basically it boils down to a random chance that an attacker can hit any machine behind the NAT. Sure it’s harder to exploit than a non-NAT network; but then Cisco really should be dropping those packets like any sane implementation of NAT.

We found this bug when we firewalled the NAT to protect against this flaw in IOS, we also turned on IP inspection (our in non-Cisco terms: stateful firewalling). This is what caused the fatal bug in IOS and left us with a router that rebooted every half hour. Ick. Apparently the rest of the Cisco users haven’t noticed that NAT is brain dead in IOS and haven’t tried to firewall it. Cisco is working on a fix but it will be a while; hence the BSD box.

Bioinformatics Feb. 2003pretty pictures from DNA

Author
Patrick Audley
Location
56.457478-2.987452University of DundeeDundeeScotlandGB-SCUKhttp://www.dundee.ac.ukSmall Earth Icon
Date
Bioinformatics Feb. 2003pretty pictures from DNA2003-02-1556.457478-2.987452University of DundeeDundeeScotlandGB-SCUKhttp://www.dundee.ac.ukSmall Earth Icon

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.

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Author
Patrick Audley
Location
56.457478-2.987452University of DundeeDundeeScotlandGB-SCUKhttp://www.dundee.ac.ukSmall Earth Icon
Updated
2003-01-01
Date
Careers: Academia2003-01-0156.457478-2.987452University of DundeeDundeeScotlandGB-SCUKhttp://www.dundee.ac.ukSmall Earth Icon

Working in Academia was more satisfying in many ways than working in 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 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.