Ed's Big Plans

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…

Brief: I had this idea a long time ago and didn’t bother to implement it. What if I placed logical volumes of data each on their own USB key? Examples… I would place the htdocs root for an apache installation on a USB stick, so that migration of this logical tree from one host to another would just involve pulling the stick and putting it in another machine. Same could be done for our giant binary SQL databases, SVN repositories, virtual machine disk images etc..

Brief: Parsability is essential for fast machine assisted analysis of vast databases… So, I got lucky with SCOP since the entire protein hierarchy is offered exactly like that… The entries are even linked to ASTRAL pdb-like structure files. Something similar is given CATH, but I don’t comprehend it yet.

Aside: I haven’t really given enough credence to PFAM yet– I should spend a little time figuring out how useful it is. From what I understand, it doesn’t classify proteins by structure so it may be more useful in secondary and later analyses.

Aside: Hey look! A big giant page of alignment tools care of ExPASy. Goody. Reinventing the wheel as least often as possible is certainly a good modus.

Brief: It’s that time of the year again! Yesterday was the department deadline for NSERC applications. Everything’s in order and accounted for more or less. OGS applications are coming up early October. This is truly the first year that I’ve applied where I feel like a worthy candidate for the prize. Let’s hope the judges feel the same way.