change of plans

So I have been in hibernation mode. Sorry it has been so long since the last post -- my audience deserves better. I promise I have reasons for my lacking of updates. More to come. But speaking of audiences...I just happened to take a look at my blog stats. It feel pretty cool that I have had 446 visitors (well probably 100+ are from me refreshing the page a million times after I make a post), but still it is nice to know people are stopping by. And not just people I know...people from all over the world! Check it out:

So greetings to people from India, Romania, and all those other cool places I wish I have been too (Vietnam--see you in a few weeks). These little stats help remind me that this Google Summer of Code thing is on a global scale and it is nice to know that I am contributing to something like that.

So why the lack of presence? Well, to tell you the truth...there has not been too much to update you on.  We have been in a "transition phase" trying to figure out what to do next. From my last post you may have noted that that we were interested in was to include row-segment metadata to NeXML output. Turns out that this is easier said than done. There is going to have to be some editing of the nexml.jar files (something that Rutger has to do) so we may have to put that on hold until more thought gets put into it. I did add some lines of code that allow for more annotations to be added the row-segments though. You can see that here. But the issue of character state sequence annotations remains an issue.

So what am I doing in the meantime?  Well, I thought it might be nice to take some weight off of TreeBASE's shoulders by suggesting that I fix some of the 64 bugs that are currently open.  This never-ending To Do list is about to get some attention! We settled on bug #3303002: NeXML not working for matrix or tree. For one reason or another, for some studies (not all) can get the tree but not the matrix for nexml.  After doing some investigating, I am working on (and hopefully finishing up tonight) a unit test that is going to nail down the problem. And then I'm going to fix it! :)

Another thing we are considering for me after I get tired of debugging and before row-segment drama gets settled is to add another tree viewer (in addition to PhyloWidget...or maybe in place of?) called jsPhyloSVG ... a bit less catchier of a name but it seems super cool. Hopefully I will have some time to work on that.

Today was the official Midterm Evaluation day and it is nice to say I have made it halfway. I am learning quite a bit about myself -- to name a few:

1. The philosphy of : "1 ) Don't panic; 2 ) Start with what you know" is extremely useful in field of computer science. See previous post for an example. But I pretty much use this when I about to start a new task.
2. I seem to be in my "coding groove" 3PM onward. This is good and bad. 
• It is good because I spend my evenings productively and am able to work diligently with "Seinfeld" episodes on or NPR "Fresh Air" playing in the background, making the mood a little lighter. It gives me time to do morning things like respond to e-mails, read through my Bookmarks bar pages, clean up the apartment, hug my cat excessively etc. Then I finally sit down around noon-ish looking at my code and trying to gather my thoughts. This is much harder than it sounds. I read and reread the latest e-mails and gchats from Rutger and Bill, reminding myself of what I am doing. Then, out of nowhere, things are finally clear and I can often times get obsessed with what I am doing and not want to do anything else.
• It is bad for several reasons:
• I like drinking coffee when I am coding but coffee at 3PM is not the same as coffee at 8AM. Oh well, you can't have it all Laurel...
• On the obsessive note, I can get so involved in what I am doing that I forget to eat dinner and/or socialize. #dweeb
• Most coding jobs are 9-5 and I would be required to readjust my whole circadian rhythm if I were to pursue them. The luxury of Google Summer of Code is that if I want to start working at 3PM and continue throughout the evening, I can :) But it is not exactly normal...
3. Epiphanies are awesome. And they happen to come at very strange hours of the day during very strange times -- such as at 2AM when you are trying to fall asleep but can't because there is no AC and it is 101 degrees outside or mid conversation with someone and you have interrupt them and say "wait! wait! hold that thought I need to write something down..." I haven't really had this sort of experience during my biology research. Maybe one day. But the moment that one dawns on you is truly an experience :)

One last thing worth mentioning...since the last time I posted, Google+ has exploded. And I hope it replaces Facebook because it is so much more awesome (and less creepy).

Okay it's Friday night and I think that is quite enough for one blog post. Bye bye!