Ed's Big Plans

Wow, it’s been half the semester already. It’s been a good experience so far. This job has highlighted two key things I should work on though. First, it’s impossible to know everything that can be asked in a given tutorial, so I should figure out what the boundaries for the module are (i.e. what the current module does not approach), and know the most likely places the answers are in the textbook so I can refer to an official explanation when I’ve drawn a blank. Providing answers that go beyond the scope of a course is actually harmful since it affects students’ recall during examinations! Second, I need to reduce the amount of repetition I use to explain something. Specifically, saying the same sentence twice doesn’t help comprehension– clearly, there’s something incompatible about that sentence.

Overall though, I’m happy with how the tutorials are progressing and how our (my and Ariana’s) introductory slide shows go– The quizzes at the end of class have progressed into being a very smooth transaction too.

In about half an hour, I have to head down to watch them all write a midterm along with the other TAs.

Applications for Winter TA positions are due soon.

It might be nice to do a hands-on laboratory course next, but tutorials are certainly pleasant.

I’ve been so out of the loop with iGEM over the last month. I’ll need to figure out how to get back into the swing of things, probably starting with the post mortem meeting on Tuesday. Generally, since no new maths could be put on the table that actually encompassed the problem well– the brute force approach was kicked into high gear with a few more filters to increase the probability of success.

Call these “System Filters” since they aren’t really based on biologically significant concepts, really just sanity checks that are conceptually consistent with the project (i.e. we’d run out of hard disk space otherwise…). Significantly, Matthew implemented “Blank Stare”, which destroys reactants that exceed a given length (thus preventing them from hogging the CPU looking for less parsimonious solutions). Less significant were Andre’s “Lone Gunman” which deletes arbitrary chromosomes with stochastic efficiency and my “Tag” which prevents chromosomes from cross reacting.

(On second thought, “Tag” IS a “Biological Filter” not a “System Filter” because it removes redundancy by implementing the rule that we only admit bacteria that have exactly one chromosome.)

I should mention that “significance” above isn’t about the triviality of the code, it’s about the amount of anticipated efficiency boon we’d gain from an item’s deployment.

Tomorrow’s post mortem will continue the work I’ve started on our iGEM 2009 Wiki Modelling page… We’ll decide what we want to mention, how close we got to our solution and figure out how to precisely characterize the problem space uncovered by our various attempts.

Additionally, we should probably discuss the relevance of John’s attN site cloning and tests to see if the operators show any sign of degeneracy, and which ones in particular.

Finally, I should mention that Brandon has been working on a C++ port of the whole application we wrote in Python to elucidate how much the virtual machine impacted the performance of our solver– the team is quite divided on this idea with a big half (myself included) thinking that the exponential growth due to the algorithm is the greater factor– Brandon may have some answers for us when it’s up and running.

Brief: It changed from being something remarkably daunting to being something remarkably easy– two lines were added to wp-config.php as follows:

/////20091012 - CHANGED for DOMAIN MOVE.
define('WP_SITEURL', 'http://eddiema.ca');
define('WP_HOME', 'http://eddiema.ca');
/////

– After that, the apache ‘.conf’ file got an update so that both tin.blogdns.com and eddiema.ca pointed to the same doc root.

As far as I understand, this means that legacy posts (although branded with the previous subdomain in the mySQL table) can be served up under my new domain name, while new posts will be written to the table using the new branding. This is the behaviour I was hoping for! No need to update legacy entries, and full forward compatibility.

– Great! The wiki and my ticketing system are still working!

Brief: So, I’ve gone out and bought nameserver access from DynDNS so that “eddiema.ca” will actually be the final resolved domain for my site rather than needing to forward it onto “tin.blogdns.com”– the only problem is that moving wordpress from one domain to another is terrible. While it’s still the same physical server, there are a number of icky steps I have to take to edit each URL with the stem “tin.blogdns.com” to “eddiema.ca”– there are a few plug-ins that can assist, but the probability of this breaking the installation is pretty high. I haven’t started on this yet because it’ll take a few hours, so I’ll save it for the weekend after all this work AND the final scholarship application (OGS!) are finished. For the meantime, I should put a link in the test page on “eddiema.ca” that points here. Ironic…

Aside: It took roughly 18 hours for the DNS server and whatever caching mechanisms that exist with GoDaddy (and my client-side ISP, Distributel) to settle down and consistently point “eddiema.ca” to me. For a while, it would jump back and fourth between a parking page from GoDaddy and my test page. This is normal behaviour though– in reality, I got lucky– the estimated time provided by each GoDaddy and DynDNS was 48 hours for the update to finalize, and from some do-it-yourself testimonials up to 72 hours. Note to self: Don’t fiddle with settings when they’re being processed– that restarts the delay!

It occurred to me that I didn’t actually post any images in the past few posts. Here are two TIM Barrels that I’ve arbitrarily picked from DATE. Note– the image files are horribly misnamed, so please use the text description underneath.

From left to right– these figures are 1A53 (Beta Strand C-Face), 1A53 (Beta Strand N-Face), 1BG4 (Beta Strand N-Face), 1BG4 (Beta Strand C-Face). 1A53 is called “indole-3-glycerol phosphate synthase” and 1BG4 is called “xylanase” isolated from Penicillium simplicissimum. I won’t go into the function of each of these enzymes, but they do illustrate what a general beta-alpha TIM barrel looks like. TIM Barrels comprise of eight beta-alpha secondary structure elements. Extra helices and sheets may occur but must flank the TIM Barrel-like portion of the protein domain (1A53 has a very prominent extra alpha helix close to the camera in the far left image). The “barrel” name derives from the twisted cylinder enclosed by the parallel beta sheets in the middle of the object. TIM barrels can be deformed quite a bit too if they’re a subunit part of a larger holoprotein.

The four-character designations (1A53, 1BG4) are RCSB (A Resource for Studying Biological Macromolecules) Protein Data Bank identifiers– I’ve found that SCOP frequently links into PDB while PFAM frequently links to UniProtKB (Knowledge Base) and utilizes UniprotKB identifiers. More on that later…