Update

I am writing my thesis proposal, working on my thesis, and yes planning the next set of experiments related to my thesis. I am busy and should be doing some work, but just wanted to let you know that although I am terrible at keeping a daily journal, writing regularly in a blog, and keeping track of all the events of my life, I do have some things I do on a daily basis. I shower, eat, walk to and from school, read, pray, and even have been writing a portion of my thesis or thesis proposal each day. How do I do it you ask? How do I manage to do 6 things on a daily basis? Although, it may not seem easy, it actually is, I am just really good at making it look hard. Take my hair for instance, I am letting it grow, mainly because of a bet with Julie, but also because I can look so much more desheveled now. And everyone knows that those that look deshevled must be important, busy, or crazy...all reasons to leave me alone and let me work on my thesis. It also seems to keep my new found purpose (graduation) on my mind. Let me explain. A few months back I needed a haircut. Julie said that I didn't have to cut it and that I could let it grow until I graduated if I liked. Wasn't that nice of her to give me permission? Anyway, one joke led to another, and then a bet that I would have to cut it before I graduated. So far I haven't. Though, it is starting to annoy me. It falls in my face more often now, and that can be annoying. I find myself blowing it out of the way, which probably looks kind of funny to some people. That is part of the reason it keeps the thesis on my mind, it actually rests on top of my mind. A big hairy mop, collecting my brain waves, thoughts, etc, but always there oozing a reminder that I must keep working to finish, sometimes it even talks to me. "Don't get distracted, get back to work or I might fall in your face...aha I told you I would fall in your face!" I may need a psychiatrist after graduation...I might need one now, aside from that it just goes to show you that there is a reason many grad students having long hair...I just don't think its so that they have an imaginary friend nagging them all the time.

If I do end up getting a haircut maybe I will try not showering next. It seems to keep some of the same distractions at bay.

Tired!

Everyone I talked to today seemed tired, myself included.  I don't know why but it just seemed like the day dragged on and I wasn't on top of my game.  This weekend Julie and I watched a movie called 'Proof' with Gwenyth Paltrow.  I liked it but can't remember why.  I think one of the points it was trying to make was that if you take care of crazy people you love, you might become crazy yourself...and that geniuses are typically crazy as well.  Since I hang out with scientists and engineers a lot, I have to say that in general none of us are crazy.  Perhaps a little over zealous about our work and work habits.  Not as social as some people, yes, and maybe even selfish, but not crazy.  Having had personal experience with some people diagnosed as crazy, I must say that I have asked myself on more than one occasion if I am crazy.  My answer is always no but is biased so I typically poll the people I meet and get to know.  So far 17% say I am on drugs, 23% say I am normal, %33 say I am weird, and only 27% say I should be in a mental institution. Of those polled and replied that I am crazy 29% were relatives or crazy or both. See I am normal.

Me and President Hockfield

Monday we had the grand opening of the basement in Building 5. The basement is where I reside and over the course of the last 9 months there have been some serious renovations across the hall, which luckily have helped improve our side of the hall as well. Thanks to a generous donation from Mr. and Mrs. Pappalardo the labs across the hall will be dedicated to nanotechnology. We will continue to do fluid dynamics on this side of the hall but let me take a second to welcome the really really really ridiculously small people accross the hall. If you don't think that is humorous then this joke will also bore you at the ribbon cutting speach President Susan Hockfield (first woman president of MIT) said "I know you don't like to call this the basement, you prefer to call it the 'ground floor'...pause and laughter... I've been getting a lot of calls from people with offices upstairs that are upset and are requesting offices also on the 'ground floor'." Followed by more laughter. You have to realize that in a place this nerdy, any sort of joke is well rewarded. Anyway, as you may know our lab takes a lot of pictures and such for our experiments and things. Since I had a camera around my neck I was asked by our Department Head Rohan Abeyaratne to take a bunch of pictures of the event, with the stipulation that he would arrange for me to get my picture taken with President Hockfield. So here it is, this picture was taken by Prof. Slocum, and I think it is the best picture of the whole bunch...I am not going to post the other pictures unless I get some requests. Oh, and I got to meet the past president of Northrop Grumman, Joe Gavin. What a great guy, he was hilarious, intriguing, and had some really great stories about MIT and the space industry. He was in charge of the Lunar Lander project! Can you imagine? It was surprisingly fun.

Some answers to a bibliography solution

I was so happy that two people commented on my last entry!  Two people I believe are not members of my immediate family!  Anyway, I am sorry to respond to their responses so slowly, and am happy to report that their advice was fantastic.  I now have a great bibliography system.  I am using bibdesk and have found some hidden features that are making it easier to keep my bibilography organized in one place. 
When entering the different fields I never took advantage of the url or local url feature.  These links allow me to either download the article and then link it to the local url on my hard drive or to link directly to the url on the web.  This is great if I have an old article that I have scanned, I can put it in a folder entitled papers, but link it to the local url link in bibdesk and the next time I look up that article It will appear with just a click of the mouse.  The url link is used to link a file from the internet to bibdesk.  This is a great way to keep track of all my articles that I want to leave online.  For now I am kind of anal and am downloading pdf versions of all the articles I find, and printing them, and filing them. As I use the system more and more I realize that filing them is almost pointless.  The advantage to downloading the article is that I can have it with me at all time. So when I don't have access to the internet or to my schools subscription to a certain journal, I can still keep researching. My system is beginning to feel complete and neat, and that makes me say "sweet". Ok that was lame, but so annoying that I had to leave it in this entry.

Last time I was complaining that there wasn't a great way to comment or put notes in the articles I read because I can't put figures I like or equations I want to input.  It is still true that I cannot do this in the annote section of bibdesk.  Serkan commented that I should use Equation Services, which I downloaded and am very pleased with.  Unfortuneately, bibdesk won't take advantage of this feature, but DevonThink does allow me to use this feature.  The great thing is that I can either take notes in DevonThink (which is the easiest way to take notes) and when I do a full size review I can just go straight to LaTex and make a document there if need be.  When I am done I can link it to the bibiliography file in bibdesk by adding a general category for all files called MyNotes (see picture at top of this entry).  I made the category MyNotes a local url and voila, I put the file I wrote while in DevonThink in the MyNotes section of the bibliography, and the next time I look at the entry the notes are there and they are retrieved ready for me to read and look at! This system also allows me to be lazy with how I file the document. If I use DevonThink it does all the work for me and files it automatically. If I use LaTex I can just put it in a folder near "Papers" entitled "notes" and bibdesk will make the appropriate link for me, making later retrieval easy.

There are two things that I think would make good improvements. One would be for the bibdesk group to add the ability to add pictures, graphics, etc. and equations from equation editors like equation services directly into the annote section or any section for that matter. Bibdesk already utilizes latex editing when the preview is used to look at a specific entry or entries. It would be great to have the annote section work similarly. When you wanted to view it in its final form it could utilize the latex compilers. When you entered the text you could just enter your equations as you would normally do in latex. Bibdesk allows me to do this for all the fields like author, title, etc. but it would be useful to do the same in the annote section and have a way to view the annote section after it is compiled. The second improvement would be a way to automatically backup my bibliography and figure out a slick way to check my bibliography on the other computer I use to see which version of my biliography is the most recent, a sort of syncing function. This would allow me to be lazier about copying my files from one computer to the next and ensure that one article I read on Monday on my laptop, then another article I catalogued on Tuesday on my desktop would all be in the bibliography on Thursday when I start writing.

However, I want to be clear that I am very grateful for bibdesk. It is a great program and working very well for my needs. I have tried Endnote and refworks, and found that bibdesk was much better on all accounts than the other programs. The addition of Equation Services is a small thing and not having this functionality doesn't distract from the usefulness of bibdesk. The anonymous comment helped me to look back at the bibdesk website for hidden functionality, which was very pleasing and fairly straightforward to find. As far as searching goes, it seems bibdesk has a good search tool, but it is important to click on the magnifying glass to ensure that I was searching in the right category or in "all entries".

What do you use?

To start I thought you might like to see the most recent MIT Hack entitled "Caltech Cannon Hack".  I read in the paper today that a while ago Caltech stole this cannon from a prep school near Caltech, and that in response to some prank Caltech played at this time last year, MIT students decided to bring this huge thing out east.  They must have really thought this through.  It must have cost a bit of money too.  Anyway, have a look for yourself here.
I also wanted to know what any of you who read this do once you have read an article you are going to put in your biblography.  Since there are only 2 of you that read this blog that use bibliographies, I guess I may never get a response but I was curious.  I use bibdesk for the mac, but once I have read the article and made my notes I don't know what to use to jot the notes I made into, scan a pdf?  The notes section of bibdesk seems the easiest place to retrieve my notes but I use equations and figures a lot and it won't take those fields.  It also has a poor search tool.  So I was thinking DevonThink but they have poor support for equations as well...ideas are welcome.

Another week of mediocraty

It seems no matter how hard I work, my research takes a back seat.  This week I am going to get up extra early (5 am) and go straight to school.  I want to see if I get more done.  I want to see if my focus can return to my research.  If it can then I might have a chance to graduate before my kids enter college.  

I guess I spend a lot of my time thinking about things that aren't directly related to my research.  The rest of my time is spent helping others actually.  I spend a lot of the week working on the laboratory, homeworks, and answering peoples questions in the lab.  Perhaps if I come in early enough I can avoid getting caught up in all of that and get something done.  Lets see how it goes...I will try to report back in a few days...now I just need to get an alarm clock that will get me up, without excuses.  Steve Pavlina says that I should have a no arguing policy about waking up.  When I hear the alarm I should stretch and wake up and not even allow myself to discuss my options.  Otherwise I will argue myself back into bed.  Honestly I want to go back to bed, even now, but I should be working.  So tomorrow I begin the battle with myself and discipline. I will let you know who wins.

New Mandolin

My mom sent me new mandolin on Friday!  It sounds funny but it is the nicest gift she ever gave me I think...next to life...I don't mean to belittle life, but this thing is awesome!  It has an amplifier so I can bother the kids and neighbors with my playing.  She also sent a tuner, which makes tuning 8 strings a lot easier.  I have been playing the fiddle for a couple of months now and maybe she just thought I sounded crappy... or maybe Julie begged her to change my instrument!hahaha, actully I am pretty sure she just wanted to give me something nice.  I am really please and have already learned a couple of songs.  Nothing to fancy, and I am not really that good (of course), but I am having a lot of fun.  I hope that I can take lessons soon.  I don't really even know if I am playing it right. Anyway it was just the thing I needed.  I have been a little down lately.  Research seems to be taking a backseat these days and I don't like that because it means I am no closer to graduation and no closer to solutions.  Hopefully with the second half of the semester coming up I will gain some momentum and get in a grove...being a TA isn't as easy as I thought it would be, but I am enjoying it.

Posting from a widget

I am posting from a new macintosh widget that posts blog entries to blogspot.com.  Once again the ease of using a free blogging tool is awesome.  I am very excited about this tool.  Perhaps I will be able to blog more often.  For those of you who don't know what a widget is: a widget is a sort of small application that runs on an alternate window.  When I am working under normal conditions on my desktop or whatever I click on f12 and a transparent window appears over my work.  On the window are a couple of very small at a glance applications for instance: a calendar at a glance, a clock, a calculator, a conversion tool, the weather, a dictionary.  I can use them and then return to my work with just one button click.  They look cool and track small pieces of information all day.  I like them and so do many Mac users.  If you use windows you are out of luck, but you probably have some excuse why you are still using a PC and probably don't feel bad.  Let us all strive to be more productive.  I hope this helps me do so.

T-Minus ? To graduation

I don't really know how long it is going to take for me to graduate. I read this article today and some of the comments. It was an interesting article about the need for schools to help doctoral students graduate sooner. The average time it takes to graduate from a BS to PhD is 7.6 years, on the rise over the past 30 years! How can I shorten that time frame? I will definitely have to move faster than I am now!

The study sites a couple of suggestions, but overall I see a problem that isn't mentioned, as it applies to science related PhD's. Many scientific disciplines have become so complex that students must learn much more before they can make a contribution. Students must understand everything about the past before they can look into the future. This requires time and therefore makes PhD completion times rise. Although many students have a head start over students 30 years ago (many high school students can take calculus, whereas 30 years ago it was only taught in college) the distance to make a contribution is increasing rapidly. Scientific discovery has become very competitive and complex. Discovering new and interesting contributions to ones discipline is often more difficult than in the past because so much must be learned and studied before one can attempt to formulate anything new.

I can't be sure that this is the reason why people don't graduate sooner. Perhaps it is the comforts of grad school that keep people here (free pizza, exhaustive dead ends, late nights, and a decline in social life). Aren't those three great reasons to go to graduate school? Perhaps it's an aversion to moving on to something outside of the academy. At some point people tire of it. That is when they either decide to leave or get serious about finishing. And that brings me back to...Well me. Honestly, I am not always this self centered but I have one goal as of late... And that is to get my PhD as quickly as possible. Oh sure I probably have 3 more years... But that doesn't change my goal. I am told that if I write my goals down they will happen a lot sooner. So there you are I wrote them down and maybe I can help move the time to graduate statistic back to 7.599 years!

Once again I think that if you want to graduate sooner it is really up to you. Are you asking the right questions? Are you reading and writing each day? Are you taking courses that will lead you to a solution? Have you found a good mentor? Are you meeting regularly with your advisor? In almost everyway it is up to the graduate student to graduate. So how can we shorten the timeframe? I will be on the look out for solutions. I am getting tired of reading about the problem. I know what the problem is, I have the problem, I am the problem. So lets find some solutions, proactive solutions. Solutions I can actually DO something about.

Nacho Libre

Nacho Libre absolutely intrigues me! I have the feeling that this movie could become my second favorite movie of all time next to Napoleon Dynamite. I mean just look at his picture! Could he be any more serious? Could he look any tougher? Could he have a bigger wedgie? How can he keep a straight face? Two years ago Mindy, Jill, and Jerry took me to Napoleon Dynamite and I laughed/cried through the whole thing. I am absolutely serious. Those who know me or were in the theater that day know I am serious. I was laughing so hard that when Napoleon Dances I had to put my coat over my head and close my ears, because my core muscles hurt so bad and I was starting to get an ear ache from all the smiling. I took some deep breaths so that I could return to the fun. So my expectations are high for this next movie, and I hope that it lives up to them.

Saving a matlab figure on a Mac.

I find that when i have created a figure using matlab on my mac, I sometimes get an image type that I didn't want. Today I wanted a .jpg but got a .eps instead. Furthermore a lot of the images I try to save don't open properly afterwards. So to save myself from the agony I decided to find out the command line for saving figures hoping that it would solve my problems. Sure enough using the command line rocks once again. Here is the command for saving a figure.

saveas(figure(#),'filename','type')

There is a whole list of types at this link, the ones I use most are jpg, tif, ai, and eps.
http://www.mathworks.com/access/helpdesk/help/techdoc/ref/saveas.html

My research has been reduced to the cheshire cat.

I have been messing around with my images to gain a better understanding of how they are analyzed. I analyze them for position of the spheres as they pass through the water. Knowing the position helps me determine the spin rate of the spheres. To get the position data I simply subtract two consecutive images, throw out the points that are gray, and look for the perimeter of the remaining blob. I then match the perimeter to the curve of my ball and I know the center. I got to a certain point and noticed that I had recreated the Cheshire Cat! I couldn't stop laughing. Yes I am a nerd.