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 ended up discussing the topic with a coworker once. The discussion had ventured to the topic of what happens when a key developer leaves a project. In some teams or projects, the key developer takes with them the potential success of the project. That is, the developer had been employed under the “Superman Syndrome.” This is what happens when a single developer finds themselves in a position to create themselves job security through obscurity. Either they have mastered a complex codebase, memorized certain pieces of information and neglected to share it, or have an extremely high tolerance for bad code. When they leave the project, the remaining members are forced to pick up the pieces (at the peril of their paychecks) or scrap the project. Neither scenario is beneficial.

Under this situation, the developer has created what they believe is job security. The reality of the situation is this is a false sense of security. A lazy company or management may let this slide. It’s a slippery slope and it will only get worse with every day this developer is entrusted with resposibility. The up-tick is that this developer is not likely creating many new technologies, but rather maintaining the seemingly unmaintainable. If you are reading this and think you possess job security, you’re delusional. Your employer has no reason to be tolerant of such behavior; there is always a recent college graduate that can fill your shoes.

The worst kind of Superman is the kind that intentionally does their job in such a bizarre manner that others find it difficult to work with their products. By this I mean they write complex or poor code in the hopes that others will be incapable of maintaining it, thus ensuring the company will always need them. Some do this more indirectly than others by choosing a poor design or omitting the design process entirely. This is more poisonous to the company than anything else and I consider it a form of insider sabotage.

You never know when you or another key developer could be hit by a bus. If you are the key developer, don’t leave a mess for someone else to deal with. If you are not the key developer, it would behoove you to document as many things that can be learned as possible. This will create a knowledge trail that will help you and your co-workers deal with a gaping hole in the team.

I believe that what a single developer adds to a project should not be quantifiable. A high quality developer will add a skill-set to the group to fill a specific role. A developer’s success is measured by their intellectual output, so they must possess the ability to flex, learn, craft, lead, and take direction. For example, I hope that if I left the group or project I am currently assigned to that I will leave the group or project in a better state than I joined it. I also would like to think that the only thing I take with me would be my abilities and experience. I hope that the main thing that will be missed in my absence would be my ability to solve problems and create solutions to complex situations.

Moving on to something in a slightly different direction, I wanted to briefly talk about how to build yourself into key developer that positively impacts every development team you join. Jeff Atwood recently dug up a good article (by Steve Yegge) recently about how to do so. You have to treat software development like a craft. Crafts must be practiced, honed, and enjoyed. Going to work does not merely mean that you are advancing your abilities, so take a peek over at Jeff’s coverage of the article or the original article itself. While you’re at it, be sure to read Norvig’s article about how to develop yourself in the span of 10 years.

I personally believe that I have an ability to perform a craft that must be honed and perfected like any other artisan skill. Even professional football players have to go to practice to maintain and improve their abilities. I practice by playing a little golf, reporting bugs to prominent open source projects, and contributing patches. I eventually gain commitbit access to a full project, then I will likely have to tackle the more social and political aspects to being a developer. I am also a graduate student which requires the most critical and analytical thought process of any task I’ve undergone. If you are a developer, I urge you to practice your craft (or not, it’ll make me look better and get paid more).

So in closing, software engineering is a craft like no other. It’s possible for too many people to get comfortable in their job. It’s possible for some people to poison and ruin everything they touch. It’s also possible for someone to make a hugely positive impact to everything they work on and everyone they work with. As a professional, everyone has to decide what they want their role to be.

Lately, I have been keeping an svn checkout of parrot up to date making sure it compiles properly. The most popular implementation of perl6 appears to currently be Rakudo, which is perl6 on parrot. I was originally following the pugs implementation in haskell but was completely turned off by the language of choice. My attention was forced elsewhere due the primary developer losing focus, abandoning pugs.

Being written in PASM (Parrot Assembly Language), it has received plenty of attention. Also, because it is distributed (temporarity) with parrot in the languages section, there is no short supply of active developers.

Pugs did give the perl6 community one great thing: a starting point for the test suite. As of right now, all of the rakudo tests are pulling the test suite from the pugscode repo. This is a great starting point for any implementation and helps centralize the entire perl6 test suite (the pugscode suite is largely incomplete).

Last night, I was discussing the current state of the perl6 implementations with a few of the developers in the IRC #perl6 channel. I was caught up on what’s going on in the community and found a focus. My urge to write some slick new perl6 code can be satiated by working on the pugscode suite. Eventually, I’d like to start solving those problems in the Rakudo implemtation as well.

We’d like you to join us as a author for Pugs.

My interest and enthusiasm must have impressed someone, because one of the developers gave me commitbit access to the pugscode repo. If I submit enough quality patches to parrot/rakudo, I will get parrot/rakudo commit access as well. While pugs itself may be abandonware, the test suite is still the most advanced yet and is in active development.

Join me in #perl6 and help propel perl6 into history as the most powerful language available, yet again.

The Pee Pants

On Wednesday, during my tempo run, I noticed everyone I passed was giving me a funny look. An elderly couple looked at me as if they were confused. I jokingly thought to myself that they must not be used to seeing a lanky guy like myself expending so much energy to barely move. A mother and daughter walking their dog refused to respond when I greeted them. Then, one woman on a bike initially gave me a welcoming smile but then sort of glanced down and winced. It was then that I realized there was something wrong, so I checked to make sure my baggage was stowed (if you know what I mean) and everything was in order. Everything seemed fine except there was a sweat pattern developing around my crotch. I’m sure it looked like I peed my pants, but I didn’t and it could have looked far worse.

The Ulcer

Jay: I farted on Jason’s pillow, he farted on Jonah’s, thinking it was mine, and eventually pinkeye-d my pillow. I’m not proud of any of this.

Well, I didn’t develop pink-eye, but it sure felt like I did. Friday morning I stuggled to keep my eyes open and found it grew worse throughout the day, leading into light sensitivity and soreness. I assumed it was just something in my eye and a night’s sleep would clear it up. It actually became worse, so I went to the optometrist. Turns out I had developed an ulcer in my upper right eye and it had become emergent. I had to apply drops in my eye hourly and go back the next day to check to see if the prescription was effective. I took the opportunity to live like Batman the next day and avoided spending any time in the sun.

It cleared up by about 80% on Sunday and I was told I could scale back the prescription usage. I should be able to start wearing my contacts again by Friday.

The Stitch

As per our Sunday evening routine, I was finishing a few things on the grill (mushrooms and under-cooked pork) when yet another emergency occurred. Our cheap knives have this bad habit of not staying in the handle, which led to one of the steak-knives doing just that. From about 3 feet off the ground, it feel tip down into my foot. There wasn’t any pain, but gravity took over and blood starting spurting out. I yelled at Sunshine to try and get her to bring me a towel to stop the bleed. Her response: bring a towel and the Britta water pitcher, apply the later before the former. This just caused more blood to pour out, so I took the towel, wrapped the wound, and hurried into the bathroom tub.

I don’t claim to be even remotely medical, so I figured a hospital visit was in order. The hospital may be less than 5 miles away, but we had to wait 2 hours to see a doctor, bleeding wound and all. After a smart-assed male nurse came in to give me a tetanus shot, the PA decided I only needed 1 stitch, which was quickly administered.

She also recommended that I not run (the fact that I was a runner was only logical after she took my blood pressure and found it to be 104/55) until the stitch was removed next Wednesday. I said to hell with that and ran yesterday and today anyways, albeit slower than planned. I figured if there are people that can run without feet at all, then the least I could do was deal with a single stitch without whining.

So here are my pace charts for last week. I burned ~1500 calories and struggled with the heat all week. I took a few walk breaks due to the oppressive heat. Sunday was not a good run, as you can tell from all of the up and down motion in the chart. Hopefully this week will turn out better.

The only thing worth noting is I had an excellent run on Saturday. I did not fatigue until the halfway mark, which is about 2 miles further than it took last week.

I’m posting this late in the week because of the troubles I had with SportTracks again. This software is seriously pushing my patience. I accidentally hit the start button on my Garmin when I was changing on Saturday, so there was a few seconds of no movement until I realized I had done so. The trouble came with importing the data. SportTracks has this nagging bug where it does not successfully delete the last track, so my pace chart was horribly skewed because of that accidental split. I kept trying to remove it and did everything I could think of. The solution I stuck with was splitting the track at the time that I thought I finished, then removed the new activity.

These kinds of bugs are trivial to fix, but take an extrodinary amount of time to get resolved in a closed source environment. Every little nitnoid like this is driving me closer and closer to an open source solution, such as PyTrainer. In fact, I am tempted to get started helping with development.

Anyhoo, here’s the charts:

Tommy went to a farmers market one day. He accidentally kicked over a big basket of eggs and broke every single one of them. Feeling bad, he asked the woman how many there were so he could compensate her appropriately. [author's note: this part gets a little fuzzy to remember] She says that she didn’t count them but had put them in paper bags earlier. When she put 2 in each bag, she had 1 left over (not placed in a bag). So she decided to put 3 in each bag, but still had 1 left over. Then she tried 4, 5, and eventally 6, but they all had 1 remaining egg, but 7 eggs per bag worked without any extra eggs. What is the minimum number of eggs Tommy has to pay for?

So obviously I wrote a perl script in my head while driving to calculate it. I figured I’d test it out when I got to work, but I had 30 minutes until I arrived. I decided to mentally golf my script to come up with the least amount of characters needed to provide the answer. I golfed out 2 more answers and came up with the following:

$_++ until $_%2==1 && $_%3==1 && $_%4==1 && $_%5==1 && $_%6==1 && $_%7==0;
print "Minimum number of eggs: $_\n";

It’s pathetically 2 lines of code, but 1 is a user friendly line to print the answer. I was starting to wonder if I could golf any more of that code down, but after reading some actual perl golf scripts, I came to the conclusion that I clearly a) do not know perl well enough and b) am not clever enough. So I think I am going to embark on trying to golf this down as much as possible. If you remove the unneccessary spaces and print statement, it’s exactly 63 characters.

If anyone has any suggestions, please drop a comment. I would really like to learn to play better golf and develop a much better understanding of perl. Also, if anyone wants to golf this out in another language, feel free to drop a comment (use the code tag).

Update: Refer to the on-going game at perlgolf.

First up, I made a minor change to the site. I am now sifting the main content feed through FeedBurner. This means I will hopefully get a better idea who’s reading the blog. All I know right now is the tiny bit of information from the WordPress Stats plugin and that Google Reader thinks my blog is the most obscure thing I read. You may have also noticed that I updated the plugins and fixed the obsocialbookmarker plugin to provide links to some of the aggregators I’ve heard of. If I’m missing your favorite, do tell.

Also, I hit a milestone with my last post; it marked my 500th blog! That’s right, I’ve written way too many words that way too few people read. I’ve had some ups and downs, a few contintributors who have long stopped contributing, even watched as my wife set up her third Blogger account. Here’s to the next 500 posts!

The reason why I have not posted recently was more out of a superstition. Monday night was an incredibly intense game 5 of the Stanley Cup Finals between the Red Wings and the Penguins. It lasted for well over 100 minutes, into three overtime periods, and ended with a disappointing goal by the Penguins. Fear not, the Red Wings went back to Pittsburg to steal the cup from them on the Pens’ own ice. The celebration afterwards was riddled with boos and hisses, but it was still a sweet victory to see my boys bring The Cup home for the 4th time in 11 years.

Lastly, I never got to posting last week’s pace charts. Monday was tough because I stupidly decided to run in the afternoon and it easily broke the 90’s. The other runs were tough but managable. I’m still struggling with the long run. I felt better than last week, but only slightly. I think I am going to try and focus on maintaining a pace for a long time because I see to have trouble beyond 3 miles. Hopefully, this is just a decreased stamina due to the extended break and not loss of ability. I also need to see about excluding the walk breaks during the intervals as it greatly skews the graphs, so I decided to change to a non-continuous bar graph so it would display something useful.

I’m blathering, so here are the charts:

The problems go on and on, most of which stem from the fact that the organization has greatly strayed from it’s original purpose: source compilable meta-distribution. There has been a large focus on the management and increasingly less focus on Getting Things Done. This is usually what causes the death of a project.

Every so often, I venture into DistroWatch to see what has been popular. Most of the time, I don’t see any promise amongst the distributions to provide the same quality and features that I fell in love with when I found Gentoo. Almost every visit meets with a decrease in Gentoo popularity. Recently I have been watching the rise of a distro called Sabayon. It’s based on Gentoo and seemed to have promise.

Upon further inspection, Sabayon is nothing more than a pre-packaged Gentoo overlay. That’s right, you can check out the overlay from a Gentoo install and quickly change to a Sabayon install. This basically does not impress me. So I continue the search.

Arch looks promising but their application tree is very sparse. I used to use Slackware, and would happily switch back if there was something like an up-to-date repository for packages. The “current” repository is nice but the lack of dependencies with the package maintainer could make things very tricky.

I refuse to use a Debian or RedHat based distribution unless there is something very compelling, like Portage and eutils, to draw my attention away. So if anyone out there has an suggestions, feel free to share.

I decided to start by doing 2 extended interval runs a week before I go to the gym. What I’m referring to as an “extended interval run” is a run where I lump multiple intervals together and run them back-to-back without rest. Of course I can only run a few this way, but I will work my way up to running as far as my body will carry me. I ran 4 continuous quarter mile splits at 800 meter pace, which made for an 8:15 pace. I had struggled to do this last week, but succeeded both times this week.

I did manage to still get to the gym for a 30 minute workout twice. I spent 10 minutes on the stair machine, ten minutes on the rowing machine one day and bike the other, and still did a tough core workout. I have to admit, it was very gratifying to show up already sweaty, as if I am always busting my hump. It garnered interesting looks from the twenty-something girls at the checkin counter.

I also was able to hit my target pace during the intervals on Monday. Started out doing just the 4 800 meter intervals, which grew progressively slower. As you can tell from the pace chart, I walked the rest periods, which seems to greatly scew the chart. I’m not very happy with SportTracks and I’m growing increasingly frustrate with its complete lack of openness. I realize that these are the types of things that will never be fixed and asking for such changes usually results in the overly Windows forum community to write you off unless you’ve donated (read: bought the software). Downloadable shareware that’s closed source? Seriously? Hey Zone Five, 1994 called, they want their business model back.

Saturday was hell though. I made it though about 2 miles without any challenges, but started to find my heartrate had climbed up there and was not relenting. I was struggling to breath and my quads were starting to ache. It didn’t help to realize I had 4 miles left. I stopped about a half dozen times or more, as you can tell from the jumps in pace. However, there were about 3-4 times where I got lost because I decided to explore a neighborhood I had never been in. Getting lost can really take the wind out of my sails. I also made the mistake of thinking I wasn’t hungry when I left the house. I wasn’t, but quickly ran out of gas on the trail. After all of the hills, getting lost, draining my energy, and the complete frustration of not being able to keep pace, I ended the run early as to avoid continuing the horrible experience.

In the end, I think I may scale the Friday easy run back because I don’t think it helped any. It may in fact increase my risk for injury so I think I will scale back by a mile next week. Since I cut back a mile off the 6 miler yesterday, I’ll have to repeat this week next week to make sure I can continue the plan.

Here’s this week’s pace charts. I changed them to graph pace against distance since time doesn’t really help much.

Geez, that took forever to manually add each individual chart to a post like that.