Just after I had been through a bit of a posting slump due to some fading tuits, it would seem as if they have magically returned. This week brings the start of the Fall 2009 semester and I have seemingly sprung back to life. With the new semester comes new opportunities to use perl!

First, I wanted to mention the one bit of news that made my summer, maybe even the last 2 years, seem as if I haven’t been running in circles. I noticed that my new department head at the university posted the final new rules regarding the qualification exams. The change is that there is a list of approved courses that will be offering the QE, passing any 3 is sufficient, and there is still no marginal grade. The last exam I took, Data / Text Mining in Bioinformatics, was not listed in the blessed course list. Turns out, the department would still accept the score, so I now only lack 1 remaining pass to be an official “phd candidate“.

This semester I am taking the Design & Analysis of Computer Algorithms course. The down side is this course tends to be theory-centric, so I won’t have many chances to flex my Perl muscles. There are tons of modules on CPAN though that might help understanding the basics. There are plenty of graph, tree, and dynamic programming solutions available.

Interestingly enough, while sifting though those modules, I discovered a module of personal interest. I stumbled across the Algorithm::Viterbi module. I have studied Markov models, Markov chains, and Hidden Markov models a bunch in the last 2 years. One algorithm that keeps showing up is the Viterbi algorithm. I’ll leave it as an exercise to the reader as to how this algorithm is used, but I will point out that the Wikipedia page has Python code. Ironically, “Python’s answer to CPAN” isn’t quite all it’s cracked up to be; it lacks any packages pertaining to “viterbi” and no generic Markov package.

Perl: Automatically tested, student approved.

Since it’s New Year’s Eve, I figured I’d reflect on what I accomplished for 2008 and what I expect out of 2009. If you’re not into these “year-end wrapup” type of posts, just scroll over to Slashdot now.

In 2008, my main goals were to re-evaluate my graduate school plans, finish a half-marathon in 2 hours, run a 5K in 25 minutes, and buy a house. I am pleased to report that I succeeded in most of my goals.

I took the Database Systems qualification exam in the Spring and passed. That was a major hurdle in my willingness to continue taking them and pursuing something beyond a Masters. I also took the Data/Text Mining for Computational Biology this Fall and await the grade (on pins and needles). If I pass that exam, I am 2/3rds of the way to completing that requirement.

I have not run a half-marathon this year. I wanted to do the DRC Half again, but decided against it due to my educational requirements. I have a half marathon on January 25 that I’ve always wanted to do, the 3M Half Marathon. Let’s hope for the best (likely target is 2:05).

During the RunOn! McKinney holiday social run, I finished the 5K course in 25:22. There were about 40 people, nearly twice as many, and I came in with the lead pack. In fact, I was the fourth one to finish. That’s a rather impressive time for me considering I struggled to maintain a 9:00 pace last year. It’s not an official time, but I’m still going to count it until I do another 5K and can beat that time.

In October, we bought a house; well, technically it was in September. We had been wanting to buy a house for nearly 3 years. We aggressively saved, struggled through having to buy a car, unemployement, paying for graduate school, and huge tax payments. We are now the proud owners of a nice home (3/2/1, 2000 square feet). It requires more work and more money, but it beats living in an apartment any day of the week. I will eventually get some pictures up (one thing at a time).

So what do I expect out of 2009? Well, I hope to accomplish just as much. My better half will should be a CPA this time next year and I will be nearly complete of the Masters program. I also hope to be moving towards the PhD program, possibly look into other universities.

I think next year we will get a dog for the empty dog house out back. We might also consider having rugrats of our own, but we don’t want to be neglegent parents (with school’s demand). We’ll have to see how that pans out, her biological clock is ticking loudly.

I want to do a half matarthon in 2:00 and finish a 5K in 23 minutes. I would like to travel to do a race as to keep things fresh. There are still no marathon plans yet because I haven’t grown bored of the half; plus the training for the half allows me ample time for my many pursuits.

Lastly, I intend on committing more effort to my faith. Since I have no problem waking up at 6am to run, I have no excuse to not make early service on Sunday. I won’t make a lofty goal like I did with the Daily Bible. Keep it simple and you’ll surely succeed.

Anyways, I have to finish celebrating the New Year and so should you. Don’t do anything I wouldn’t do.

A few days ago, I started a 13 day vacation for the hoidays. I haven’t had a real vacation since February 2007 when we went to Seattle (pictures will surely follow). Tons of things have happened in the last few months, so I’ll run through them since I have been very negligent of most things. I’ll make a separate post about Christmas and what I expect out of 2009 soon.

We bought a house in October. We moved in and tried unpacking. Until the day before family was slated to visit, we were only half-way unpacked. We now only have the master bedroom to finish.

I finished my Data/Text Mining For Computational Biology course. The workload was lopsided with October and November having the bulk of the work. I also took the qualifier for this class. There were only 2 people taking this exam, myself included with only 1 person having attempted it before. It lasted 3.5 hours and was most definitely written by committee. I don’t know what my final grade is because the website is closed right now (seriously, who “closes” a website?).

I’ve started the Great Music Archive Project. I intend to have every music CD we own ripped to FLAC by the end of the vacation. So far, I am at least half-way done and have a whole box I have not unpacked and checked their status. Afterwards, I’ll start the Great Music Tagging Project.

Speaking of archiving, I’ve started the Great Photography Archive Project as well. This is nearly complete and will begin the Great Photography Publishing Project shortly thereafter.

I signed up for the 3M Half Marathon finally, since I have been training for it for the last 6 months (2 months off can really do damage). The event is on 25 January 2009. I usually loathe reading other peoples’ race reports, so I will gleefully force mine on the few readers that remain.

I also have a plan to start daily perl6 development without altering my schedule. I will post details once I actually start. It involves a laptop and a morning commute. Sounds dangerous, doesn’t it?

Anyways, I must continue my archival projects now since I plan on accomplishing no real work while on vacation.

Image courtesy of duchesssa

So late last week, I logged into WebCT to do my semi-weekly check to see if my qualification exam grade had been posted. It had been 6 weeks at this point, and I was starting to get tired of checking so often. I had basically spent the first month of the semester working overtime, then gradually picked up my studying time until I was basically putting in several hours a night. I sacrificed time with family and loved ones. I skipped running to stay in and study (or found I was too tired from working 10 hours, then going to class for 2 hours, and finally studying for 2 more hours). I neglected everything. I had one goal in mind, and that was to put every ounce of effort I could into getting an A in the class and passing the qualification exam. If I was going to continue flirting with the idea of pursuing a PhD, then I had to do this.

The end result was a Pass!

That’s right. Four months later, countless sleepless nights, and I finally had aquired myself 1/3rd of the requirement to advance candidacy. It may not sound like much to many of the graduate students out there, but let me explain. I am notoriously bad at taking exams; I get nervous, make silly mistakes, rush myself, spend too long on too few points, and ultimately panic when time starts running out. I am much better at putting forth the effort it takes to go from being an ABD than it I am at passing a few tests.

After being disappointed by landing 2 marginals and then being utterly crushed when the department changed policies and forced me to start all over, this was a godsend. In fact, Sunshine and I went out for a celebration and I felt no remorse eating a burger and beer at BJ’s Restuarant.

So this begs the question: what’s next? This summer, I was forced to take off due to a less than convenient schedule. I have only 1 more required course left, Analysis of Algorithms. I covered this material before as an undergraduate, but not as fast or with as high of expectations (>40 on the final probably will not qualify as an A). I’m looking at taking some electives while they are offered since they tend to be very sporadically scheduled. I’m looking at taking this course:

CS 6365 – 501 DATA/TEXT MINING COMPUT BIOLOGY
Hatzivassiloglo
Call Number: 13095

TR 7:00 p.m. – 8:15 p.m., ECSS2.412

CS 6365 Data and Text Mining for Computational Biology (3 semester hours) The course introduces data and text mining as practiced currently in the bioinformatics field. Major topics include: sequence alignment for determining similarity between proteins and genes; properties of similarities and distances; genomic, proteomic, and text databases in the real world; finding patterns (motifs) in genes and proteins; differentiating between valid patterns and noise; classification; clustering and its application to phylogenetic trees; and selected topics from text mining. Prerequisite: CS 6325. (3-0)

I lack the prereq, but that hasn’t stopped me before. I’m also looking at finding a thesis advisor, so I may start that up in the fall as well. As for the QE that I intend to take next, I think I will try the Artificial Intelligence course again in the Spring (2009), depending on what they will change with the program by that time (I’ve heard some rumors of more changes).

The main thing to remember, this test is good for 4 semesters for me, since I am a part-time Masters student (the clock stops when I’m not taking an exam). I will contact the department head soon and start planning my next step. Until then, I can rest easy knowing that a PhD at UT Dallas is still a possibility.

I had originally planned a much more tasteless title for this post, but in light of recent events, I had to change it.

So I spent the last few weeks feverishing working on my Database Systems work. I had a project due, an overly lengthy assignment due the following day, and the final exam the following week. As if that weren’t enough, I had decided this was going to be the exam I was going to give one more shot at, so I signed up for the qualifier. That was yesterday.

Let’s see, after I received an A in the Databases class, I took 7 days off total to study for the qualifier. I spent an average of 8 hours a day studying. I rewrote all of my lecture notes into a huge pile of flash cards, about 200 of them. Then I reread the book (2 and a half times total). Then I worked through all of the problems that had solutions available. Then I worked though other university exams. I found this treasure trove of tests for similar qualifiers over at Stanford. University of California at Berekely had a nice stash of exams as well (few mistakes though). I practiced working under time constraints. I polished my SQL skills though there are MANY ways to answer problems usually.

In the end, the exam was over before I knew it. 90 minutes was barely enough time to come up with answers, not to mention check my work for mistakes, which were bound to be made. Plenty of people were still there with about a minute left. I’m really hoping that other people had a hard time finishing, even though there were only 4 problems. I also found out there were several people (of the large 18 person group taking it) who had not just taken the course. They all had studied material from the reading list the professor said would not be on the exam (decided to exclude it and I asked him about it). I wasn’t too surprised about the questions, but I’m hoping the other students were.

The reason why I had to change the title of this post was because I originally was going to name it “Another One Bites The Dust.” Last week, I finalized my plans to make a surprise visit to see my grandmother, aunts, and mother in Kansas for their Mother’s day get-together. However, in the last few days, my grandmother’s health has taken a serious turn for the worse. She’s dying of many complications, but she is unable to fight off pneumonia right now. My aunts all decided to remove the oxygen supply and let her pass away. They took her off today and she is likely to pass within the next few days. Her birthday is on the 18th.

I might have to fly out a little early tomorrow, depending on my grandmother’s health. Meanwhile, Sunshine has traveled to the last of rising stars (LA) to be with her friend for graduation. I have the house all to myself and all I want to do is watch Detroit crush Dallas, again.