Relief?

To open this post, you will understand very little. But I am venting, and vent I will...

Well, I did it. I sent this paper away to a lady in Melbourne who has been very difficult to keep in contact with. I have been working on this paper for over a year now, and I am tired of it. It have slaved countless days, nights, weeks etc trying to analyze the data from two different techniques (surface plasmon resonance (SPR) and circular dichroism (CD), the later of which the picture represents idealized data). We started with a collaboration with a local university around where I live (no train ride, ya for me), but they offered me an honour's student to do the work, and he knew less than I did (of which I didn't know anything about CD.

So he did the work, the pictures looked like shit. For a complete lack of better word, it fits. And the analysis was similar. Sooo, I wrote a program myself entitled PEPFIT Analysis which runs in Excel (Visual Basic) and does the work for you, and is based on another free to use program called PEPFIT which is a pain in the ass to use, and runs in DOS!! What runs in DOS!!! Good program, but runs in DOS!!! I describe this program in a little more detail in my science ref site, greatly named: Another (Not So) Wasted Effort, which bascially puts a few of my bookmarks on the web and acts as a centre for when I analyze gene array data etc.

The picture above is a sample CD spec. This procedure tells you what your protein or peptide's secondary structure may be, with each line representing a different structure. It just shoots polarized light through a sample at different wavelengths (~190nm to ~260nm) and the solution rotates the light left or right, and that's what you see. The more "right" the light is rotated, the more positive the line on the graph goes, and the more "left" the light is rotated, the more negative the line goes. Each strucutre (alpha helix, beta sheet, etc) rotates the light in a particular way at each wavelength, thus the different lines for different structures or conformations. Also, primary structure is simply the amino acid sequence of a protein, and the secondary structure describes what said protein or peptide ... umm.. "looks like", is round like a girl's rignlet (alpha helix) or does it look like corrugated cardboard (beta sheet). That's a great analogy, if I get the opportunity to teach this topic, that's the analogy I will use.. It's perfect!!!

Anyways....

I ended up going and doing all the CD work myself, modified the procedures, and got some beautiful results of which were easily analyzed by my program. Cool, CD bit was done.

Then came the SPR part. I have some beautiful pictures (YES I KNOW I'M A GEEK, I can think of a series of graphs as genuinely beautiful). But I could not analyze them for anything!!!! SOOO many nights till 3 am, trying out other programs like "Clamp"from the University of Utah. And then asking for help from a lady from Melbourne who is probably the best in the world at this, and who has worked with us before, and is a friend of our dept. So I e-mailed her on May 11 (2006). I heard back from her... on July 30 (she has a reputation for e-mailing right back, within 24hrs, except for this time). 2 Months. she asked for a few things, so I sent them to her, the next day or so.

and I am still waiting.

I ended up figuring a way to analyze the graphs myself, by diving into the guts of the analysis. I hate kinetics. It's one of those things where you either "see" it or you don't. I think that I am the later. ALthough, my ego leads me think that if I actually quit resisting it, I would be good at it as I love numbers, and considered it a good exam if I learned something while writing it, Even University Calculus. I don't know, I can always get numbers to make sense. So maybe I will stop resisting and learn some. And maybe not. ANyway though, I did a kinetic analysis, spent the past 2 and a half days finishing the paper and associated figures, and then sent it off to the lovely lady in Melbourne. Hers and one of her student's names are on the paper as they did send me something useful, so maybe I will get a response before I submit...

Disclaimer: I really do like this woman though, she is genuinely nice, and always helpful, and pleasant. I can't honestly say anything bad about her. SHe has had a busy year, office moves, overseas conferences etc.... I'm just frustrated by the time lag. Probably because I am running out...

I swear that I can go on forever, again,
Please let me know that my one bad day will end.
(Blink 182, I'm Lost Without You)