Thursday, June 25, 2009

Organizing Proposal Writing

Now that I'm really trying to hunker down on the proposal writing, I have found a few techniques work much better for me than others (although I can't guarantee I'm in the majority here):

  • Lots of hot tea drinking. It's calming, but more exciting than water. I'm an avid tea drinker to begin with, but usually drink less in warm weather. However, it's helped me concentrate very well over the past week, as well as forcing me to need to get out of my chair every few hours.
  • Make a proposal playlist, and listen to it. I'm partially stealing this one from my writer friend Kathleen, as she makes playlists for her different books as she writes. I'm currently using music that is not distracting, but still upbeat to help keep my energy levels up as a write. Lately I've been spending all of my music time on Pandora, as I wrote about before, but sometimes you just need to have too varied of music for that to work. However, if you don't own enough music for your playlist, this could be a nice alternative.
  • Break the file into individual files. Assuming you are writing in LaTeX, this is pretty easy, but is something I never do for writing. Basically, you make a file for each part of your proposal (introduction.tex, chapter1.tex, etc), and then include them in the main file using the command \input{filename}. Fairly straightforward, but makes it easier to find where you are in the file, AND it helps keep you from getting overwhelmed.

However, the most important piece of advice have so far is this: don't work all day on it. Unless you are one of the few people who can work 15 hours/day without ever getting burned out, don't torture yourself from dawn until dusk. Today I really figured this one out, and it's why I decided to post. Today I put all of my proposal and previous writing work on my lab computer (fairly new, so I still use my laptop for a lot of my research). Now, my plan is to only allot time for proposal writing during the day, in the lab, unless I specifically plan to work outside of the lab that day (in which case I'll just have to get the files). This way I feel more pressure to be productive while I'm at school, and can concentrate on other things in the evening (other work, hobbies, wedding planning, moving, etc). Overall, I expect this to lower stress levels significantly, at least for the next few weeks.

I'm lucky in that I have exactly 2 months before I defend my proposal, meaning that if I take a month to finish writing and revising I'll still be done early. But of course that means that motivation on some days can be hard. Therefore I have my last piece of advice for now: if you have enough time between when you start and need to finish your proposal, be sure to have other projects to work on too. Now, all PhD students should have tons of work they should be doing instead of writing their proposals, so that having the work to do shouldn't be an issue. But the point is that if you have enough time to have low motivation, do some work on those other projects! If they are related to your thesis anyway, it's useful even for the proposal. Just don't get too caught up in them; the proposal should be the primary focus, otherwise you'll never get it done.

Wednesday, June 24, 2009

Buffy vs. Edward

Earlier this week my housemate sent me a link to a video created to depict Buffy (from Buffy the Vampire Slayer) beating up Edward (the vampire from book/movie Twilight). The point of the video was basically to show that yes, Edward is a creep, and yes, Buffy could totally take him.

Buffy Summers takes down Edward Cullen

Since I've written before about enjoying Twilight, and vampire stories in general, it seemed appropriate to also share this link. If you know anything about these stories, you will hopefully find great amusement in the video! Also, as you may notice in the credits, something from Harry Potter and the Goblet of Fire was used; see if you can find it, it's only a very short clip, but if you think about it, it becomes very obvious!

First Biology Conference

cropped version of conference poster from

Last week I went to my first biology conference, Systems Biology of Human Diseases, held at Harvard Medical School. It was definitely different from the computer science conferences I have been to thus far. Of course, for me the biggest difference was that I was surrounded by people that were experts in a completely different field from mine, but yet were still working on some similar problems. We just happen to have very different vocabularies. Overall though, I think it was a worthwhile conference to attend. I learned some new keywords, learned more about how biologists describe cancer, and got some new ideas for how to present and do my research. Not bad for a day's worth of time. Unfortunately I couldn't stay through the poster session thanks to a migraine, so hopefully next time I won't have that problem. Luckily this conference will be in Boston again next year before they merge with a European conference, so I will have easy access for at least that year. After that we will have to decide if it is worth traveling to Europe for it.

Tuesday, June 23, 2009

Undergrad Class Again

Earlier in the year I wrote about experiencing undergrad class again. Later in the semester I sat in on two lectures of my own department's intro programming class, as part of an observation for my "teaching undergraduates" class. I was in the same horrible classroom/auditorium I was in for the other class, but it was much emptier and thus quieter.

Overall, I was very impressed with the faculty member giving the lectures. Sure, he wasn't perfect, but he had a great energy to him. This is one of the reasons I had chosen to observe him over some other professors; I knew he brought a lot of energy and excitement to teaching at the graduate level, and I really wanted to see that happen at the undergraduate level.

In the second of the two lectures he brought his research area (Computer Vision) into it. He helped the kids think about how they might go about solving problems in the area with what they had learned in the class: arrays, I/O streams, etc. Really, I think if more professors used this type of lecture throughout their intro courses, we would have a better retention rate in Computer Science. It takes a step back from what can often be boring topics, and shows that there is an interesting use for all of it after all. I hope when I start teaching I am able to bring this sort of thing to my lectures as well.

Monday, June 22, 2009

E-mail becoming unusable?

A few days ago our e-mail system went down overnight. Most people (who I know, at least) didn't notice for awhile. However, I had a big clue: no junk mail. My e-mail account had gone all night without acquiring any spam. Since I tend to get about 45 junk e-mails over the course of 8 hours each night, getting none was quite suspicious.

This leads me to wondering whether or not e-mail is really starting to become unusable. If we don't win against spam, phishing, etc, will we become too frustrated with it? I can get 100 spam messages in a single day. Many of them are moved to the junk e-mail folder; however, when I'm sitting at my computer doing work and the new message icon appears in my system tray, I always end up looking to see what it was, and it is almost always junk. I like to have this indicator, but it's starting to become not worth it.

I think most of my junk e-mail is due to a mailing list I'm on. I'm hoping that once I am off this mailing list in September, i will see a dramatic decrease in unwanted mail.

My Gmail account also recently started having spam issues. I never see spam on that account, and starting earlier this month I started seeing a few e-mails of spam a day. It hasn't happened for a few days, but I am sure it will happen again.

I feel like my e-mail box has become much like my real mail box: mostly just ads for services I don't need or want. How do we fix this? This is not my area at all, so I have no great solutions. I don't like the proposed solution of making e-mail cost money, as right now it's a great medium for staying in touch even just throughout a day (I have entire conversations through e-mail throughout a single day, that sometimes involve 20 messages, which could really add up in cost). I do believe we need to find a way for it to not be profitable for spammers/phishers to bother; or would that just mean even more e-mails, as the likelihood of finding someone who will fall for it is low? I hope that in a decade it will be common knowledge what types of e-mails to ignore, but my brain tells me that is unlikely. Won't spammers just keep evolving with the technology? So how do we get spammers to give up? Maybe we need psychologists to work on this problem.

Sunday, June 14, 2009


Well, now that I've experienced one type of proposal, I need to worry a bit more about the other type: the PhD proposal! I've decided that it's not as scary as it seems. True, you are putting your work and ideas out there to be critiqued and questioned, and you are defining what the remainder of your PhD will contain. But still, it's more of an opportunity for you to get feedback before you try to defend the dissertation, and it's really there to make sure you are on the right track.

I'm rather excited about proposing, which will happen this August. I've had a general view of where I want my thesis to go for a little while now, so it's great to finally get that out there. I wish I had done it earlier, and I wish I understood more about what a proposal is a few years ago. So here is my attempt to make a short list, that at least applies to my own department:

  • Propose as soon as you can! - My advisor was suggested to me that I propose before I was really mentally ready to think about, and it so it was put off for a few years. Looking back, I probably could have done a reasonable proposal LAST summer, which would have been great for making sure I went in the right direction this past year.
  • Think of it as an opportunity - Like most things, it's both a blessing and a curse. The curse is that you will be totally stressed out unless you are never stressed out about anything. The blessing is that it's a great time to take a step back and make sure you're going in the right direction, to get great feedback from successful professors other than your own advisor, and a big step at really defining the core of your thesis.
  • Don't spend forever on the writing - Our department just changed the expectations (de facto requirements) for the proposal: it should be less than 20 pages, and not look anything like a thesis. Those of us who are the first string of people to propose under these guidelines are extra stressed since our proposals may not look like what people are used to, but really it's for the better. A shorter proposal might actually be read, you can spend less time on the writing, and it makes the presentation much easier to put together. This is not a published document, so don't waste lots of time! (I'm still having trouble following this piece of advice)
  • Schedule early - I scheduled my August proposal defense in May. With 4 professors needing to have the same time slot free, don't wait until the last moment. My fiance almost had a fiasco because he waited too long to schedule a time, and everyone's times were conflicting during the month (yes, the entire month!) he wanted to have his proposal during. He fixed his problem by doing the first day of the following month. But the point is still valid: plan early.
  • Propose in the summer - I'm not sure if this is good advice yet, but so far I like it. There is less pressure during the summer, so it is easier to work without feeling stressed out. Hopefully your professors will be easier to schedule for the defense as well, since they won't have teaching and office hours as conflicts.
  • Listen to your advisor - This advice holds for most things. They are faculty already for many reasons, they won't (generally) lead you astray. If they tell you to wait to propose, they probably have a good reason; hopefully your relationship with them is one where you can discuss why you should wait. If they tell you to get a move on, there is probably good reason for that too (probably).

If I come up with any other great suggestions as I work on my proposal, I'll post again. Hopefully I will still be feeling optimistic in a month or two.