infected

Whenever your doctor tells you that the cure to a sickness is just to relax and chill? Believe it. I consider myself a living proof. *grins*

Growing up with a dad who drill me about the importance of being optimistic, I don't get stress out very often. The number of times I get really stressed out can be counted with just my fingers. A major exam, a paper due soon, family events, etc...I get nervous but rarely stressed out. But when I do, I am bound to fall sick soon. Then I'll have to remind myself to cool it and take it one step at a time. Unlike my lil brother, I rarely fall sick too..once or twice a year is all about as much as I get. But if I get stressed out, the once or twice is big deal enough that I am glad that is all I get.

The past week has been really hectic. I had so many plans for experiments but I only got 3 of them done. Why? I had to get some 16S rDNA sequences analyzed and as I started working on it, I realized that some of the solution I need involves multiple programs. Grrrrr...why can't all computer scientist write in the same language? First of all was trying to figure out how to use DOTUR. That was really easy as it runs from command prompt. The same goes for S-Libshuff and TreeClimber...but they were all written by P. Schloss. When I had to take DOTUR's output and input it into EstimateS, I had to use a Java conversion script. It's suppose to be easy right? I mean..hei..it's just Java. Then went into some challenges with the script. Also learned the hard way that I can't copy the path from MS Word into the command prompt. Grrrrr...they are the same!! But apparently the computer must be reading it different. Got that all solved out eventually.

Next I have to built tree. Started out using MEGA. It is a great program and it runs on all MAC, Windows and Linux terminal which is good so I don't have to keep changing the format of my raw data. But guess what...the input for MEGA is totally different from any of the output I get! So what now? Have to do it manually lor. So started writing the script for changing the format of my data into MEGA's format. That was kinda easy...but took me 4 freaking hours straight! Besides playing Diablo or WarCraft, I don't sit in front of the computer for that long!!! And that was just dealing with 250 sequences. Thankfully, MEGA's output can be churned into TreeClimber easily. See..we need more computer scientist who think about other people. They have to learn to accomodata different formats!!

Now, am trying to learn Python. I want to use UniFrac to compare my libraries and this program was writen with the Python interpreter. *pulls hair back in frustration* One day, if I ever have the luxury to stay home and do nothing, I think I will take a class on writing scripts with Perl. Then I'll compile a program that will convert any of these different formats to any format that the user required. There must also be a program that can recognize sequence strings from different library based on their ID and color code them. Wouldn't that be so much easier? Currently we have to import the trees or sequences into Adobe Illustrator and color code them ourselves. Imagine if you have 400 sequences, you have to go through each of them, highlight it and change the color. Too bad the Ctrl button doesn't work for Illustrator. Hmm..now that I'm thinking about this, maybe if we save the Illustrator file with postscript extension then open it in MS Word and use the 'find and replace' function...maybe that might work.

How did I get to talking about all these????? Oh yeah..stressed out. So yeah..that's the spill of my stresses this past week. The challenge I faced last year when constructing a plasmid did not even made me so stressed out. It's only been a week or so since I had to bury myself into programming books and it's already driving me crazy. I think it's because it's not my field and I have no idea what is going on. The worst is when I get erros. Not knowing the codes well enough, it drives me nuts whenever there are 'syntax error' because I don't know where to start correcting. What more when sometimes the error could just be a semi-colon or an extra space (especially Python which is sensitive to spacing AND caps lock).

Due to all these crazy programs, now I am stuck with bacterial infection. Working with bacteria all the time, especially when doing batch growth, it is common to get infection once in a while but when we're healthy physically and mentally, the infection is not obvious. It is only when we get stressed out and the hormones seem to interfere with the immune system that the infection get worse. At this point, it is still at the early stage but I can feel the swell in my lymph nodes already. It gets worst at night when I am tired and my immune system doesn't seem to wanna work with me here. Sleeping is hard because when I lie on one side, the swelling increase due to fluid accumulation. Ice-cream makes me feel better but I don't think I can fit anything in my fridge anymore. Driving to Wendy's to get a freeze right now is too much of a chore too...don't wanna drive. So I've been sucking on ice all day. Am thinking of staying home tomorrow and come in just before my class tomorrow but I have to meet with Tom (the boss) before class. *head hangs down*

At the same time, all these crap is making me miss someone. One of the times that I got infection and it was one of the really bad ones, I didn't have to do anything except sleep and eat ice-cream. He was the sweetest then...

Alright, time to get back to cracking my head trying to use these programs. Praying hard I can get the tree to run on TreeClimber and analyze it with UniFrac. If not, I might have to start using Arb..boo hoo..am trying to avoid that.