Welcome to my summer blog! Use the tabs below to see more.

About Us

Learn more about me and my team.

Project Work Journal

Read more about my work this summer.

Summer Goals

My goals for the summer.

Final Report

My final report for the summer.

Here are some pictures from my summer in Boston:

Week 10: August 2nd August 6th

Our last week at Tufts is almost over! It's been a crazy busy week trying to get the paper finished and all of our loose ends tied up before we leave. My weekend with my family was amazing we went to the Smithsonian to celebrate my little siblings' birthdays and I got to get some quality parent time in. It bums me out that I won't get to see my family again until Christmas, but I'm happy I got the chance to have a relaxing weekend with them. Friday- our last night here- we're having our good friends over for a goodbye Chinese/movie night. I'm going to miss a lot of aspects of Boston and I hope to someday visit it again.

Week 9: July 26th- July 30th

Dani and I spent the past weekend at Charles/MGH, walking around and getting to know the area. Unlike the rest of Boston, I was immediately charmed by Charles street. Though it has a lot more brick than I like, the architecture is like something out of Oliver Twist, which gives the whole area an ambiance. It's hard to explain. Definitely my favorite place in Boston so far. I also ventured down to Mass Ave/Boston Medical Center area to get some necessary vaccinations on Wednesday. That busy area is pretty much the antithesis of sleepy/chill Charles Street. There was a million things going on at once and people everywhere. I will be flying home for the weekend to see my family before I go back to school, so I won't be in Boston for the upcoming weekend. So excited to see my parents again!

Week 8: July 19th July 23rd, 2010

The weeks have been going so fast! We only have two weeks left here and we've just started to become familiar with the area. After an uneventful weekend, we spent more time with Heidy and Lucy during a cheesecake night on the roof of the Tisch library. We plan on going to the science museum this weekend as a late celebration of Dani's 21st birthday. Boston is just starting to grow on me It's too bad time has gone this fast.

Week 7: July 12th July 16th, 2010

We spent all of last weekend in downtown Boston at the molecular biology conference. Dani and I walked down the shopping area during our lunch breaks and window shopped (and occasionally actually shopped). It was fun to be downtown, but exhausting to travel there everyday. The T is really busy in the morning and early afternoon and it can be uncomfortable to squeeze into the packed cars. The lectures we got to see ranged from merely interesting to amazing. A few of my favorites included one on inherently disordered proteins, one on the relation of genotype and phenotype and use of chaperon proteins to reveal hidden traits, and an anthropology lecture on the genetic relationships of humans to Neanderthals. Dani's birthday is today, so we'll get to eat cake and celebrate her turning 21.

Week 6: July 5th July 9th, 2010

It's HOT here! It got up to 98 degrees yesterday, close to the all time record (set in 1911) of 101 degrees. We're trying to make it through the heat wave without air conditioning in the apartment, but it's definitely tough. Shrimp and cheesecake night was great got to swap college stories with the other girls and learned that the size of a CS department makes a huge difference in the dynamic between students. Dani and I ended up going alone to the Charles River to see fireworks for the 4th. It was packed with people, but definitely worth it. The fireworks were insanely amazing especially the 1812 overture with a fireworks finale. We left just before the finale, so we managed to get a spot on the T before the crowds took it over. Considering we passed a huge group of cops getting ready to manage the entry gates to the T, we made a good choice.

Week 5: June 28th July 2nd, 2010

Had an great night on Friday with Chelsea she's the new DREU student. We went to see the Miss Massachusetts pageant. She's actually an engineering major, so it was interesting to compare our experiences in technology fields. Dani and I haven't made firm plans for Fourth of July yet, but I'm guessing a group of DREU students will go see the fireworks over the Charles River. We're also planning a potluck (themed with shrimp dishes and cheesecake) for our group of DREU students for Monday, which we all have off. I had to go get a passport in Harvard Square on Tuesday (long story, but be aware that you need to have a passport that is valid for six months AFTER your departure date if you go on a trip to Honduras). While I was on the T to Harvard Square, I realized that I've become very good at navigating my way around town. It's exciting that I started out the summer scared of the T and am now riding it by myself, no sweat.

Week 4: June 21st June 25th, 2010

Went to the art museum this weekend, which was really fun. It is also free for Tuft's Students, so we got to enjoy the beautiful Egyptian, Greek, and Roman pieces for free! Heidy was telling me that her parents did Egyptian studies in college and that they can read Heiroglyphs. I was struck by a feeling that I really wanted to be able to do something like that. I suppose it's a bit like learning that a friend has mastered a new programming language that lets you build something interesting. I'm terrible with history and dates, so studying the classics is definitely out for me. We met the new DREU students this week Lucy and Chelsea. They are both really nice. I'm amazed at how many cool computer science girls I've met here. It's so different to be surrounded by intelligent, technology-savvy women all the time.

Week 3: June 14th- 18th, 2010

Had a great weekend in Boston, seeing the sights and eating yummy food. Though it's been raining pretty much every other day, we've been trying to get out and look around. Just got my laptop back (yay) from Dell, so I finally have another resource to work from home. Hopefully we'll be able to go to the art museum sometime soon that's our next planned activity. It's been a bit too rainy to navigate the T and everything, so we're hoping it clears up soon.

Week 2: June 7th June 11th, 2010

Check out my project work journal for more information about the project and how everything is going. Dani and I have met two other DREU students working with Carla, a professor here who works with machine learning. The two students, Heidy and Emily, went to lunch with us yesterday and we've all decided to go see downtown Boston and explore this weekend. We're planning on seeing the sights at the Boston Art Museum, maybe visit the Commons, and eating delicious dim sum! It's been really rainy here, so hopefully some time in sunny downtown Boston will clear up the gloom.

Week 1: May 31st June 4th, 2010

I've just started working for the DREU program at Tuft's University in Boston. It's been a crazy week with moving into my apartment and getting everything set up, but hopefully things will start to settle down soon. Dani (my research partner) and I decided to sublease a space together. We've done a very little bit of sightseeing we went into Boston downtown to eat lunch one day. Hopefully we'll get the opportunity to do that again soon. That's all for now. We're still in the process of getting our project started, so hopefully next time I'll have more info about that.

My name is Caitlin Crumm and I am a student at the University of Texas at Austin in the Computer Science department. I'm a rising senior and will graduate in May of 2011. I am majoring in Computer Science. I can be contacted at caitlincrumm (at) gmail (dot) com.

My Mentors:

Dr. Lenore J. Cowen is  a Professor in the Computer Science Department  at Tufts University. Her research interests span three areas: Discrete Mathematics (since high school), Algorithms (since 1991 in graduate school) and Computational Molecular Biology (since 2000). For more information, visit http://www.cs.tufts.edu/~cowen/

Dr. Sara Su is  a visiting Assistant Professor in the Computer Science Department  at Tufts University. Her research lies at the intersection of computer graphics, visualization, and human-computer interaction. For more information, visit http://people.csail.mit.edu/sarasu/

My Team:

Dani Extrum-Fernandez is another DREU student I'll be working with this summer. She hails from Mills College in sunny California and is a double major in Biology and Computer Science. Check out her website http://www.eecs.tufts.edu/~dextru0a/

Connor Gramazio is a Tuft's University student working with us this summer on TuftsViewer. Check out his website http://www.eecs.tufts.edu/~cgrama01/

Week 10: August 2nd August 6th, 2010

August 5th:
This week has been seriously focused on getting our paper ready for DREU. We have pretty much split it down the middle, with Dani handling experimental, results, part of the abstract and conclusion, and all the LaTeX business. I have done part of the abstract and conclusion, the introduction, the discussion, the related works, and the bibliography. I have done a little bit of last minute touches on the website, which is ready to publish after I have someone go through and do all the tutorials. It has been a really reflective week, thinking about what we've done this summer and how we can summarize it and interpret it into meaningful information.

Week 9: July 26th July 30th, 2010

July 30th:
We are up to eighteen users now! Dani and I have been breaking down the results for the paper, comparing average times and finding p-values to determine if the data is actually significant. My tutorial website has been improving each day with new jQuery tools and content. I have been working on the introduction/related works section for the paper also, and it has been pretty successful. It's up to about a page now, with seven cited sources. All of this work has been broken up my on-the-fly video analysis whenever we get new raw source in. Time to get serious on the paper only one week left!

Week 8: July 19th July 23rd, 2010

July 23rd:
It has been a busy workweek. I have mostly been analyzing video I'm up to 7 videos now. I have gotten very efficient at it. My side project is a lot more fun. I'm building a tutorial website for Tuftsviewer. I have been teaching myself how to use CSS/Javascript/HTML/Photoshop to make pretty layouts and I'm impressed with how quickly I managed to pick it up. Check out my website so far: http://bcb.cs.tufts.edu/tuftsviewer/tutorial/
I started an initial draft of the final paper and hopefully we can start filling in the important sections. I have a lot more data analysis to do, but we also have five or six more users signed up for the study. We discovered yesterday that we need to use all of our giftcards, so we've been scrambling a bit to get more users.

Week 7: July 12th July 16th, 2010

July 15th:
The poster presentation at 3DSig went really well we were pleased with the positive response we got from most of the attendees. The general consensus seemed to be that the multiple alignment feature was great, that the new rendering style was very pretty, and that TuftsViewer would make a great educational tool. We have taken feedback from the attendees and made a list of possible new features to add to make TuftsViewer even better. We have been crunching data this week, parsing times and pathways from the user videos. Hopefully once this is done we can begin writing the paper. We have four more user studies over the next two weeks to add to our data. The OpenGL SuperBible is finally in the library, so I'm going to pick it up today and start looking at it.

Week 6: July 5th July 9th, 2010

July 7th:
We are currently prepping for the two big conferences this weekend/next week: 3DSig and ISMB. Dani, Connor, and I will be presenting a poster and demo at the poster session for 3DSig. We've been told that people are going to go crazy for our software, so we've been preparing several demo laptops. The poster goes to the printer today we spent yesterday getting high resolution screenshots for the images. Making the images taught me how to convert desired size and dpi to pixels. I sincerely have been learning a lot about graphics this summer not just through my studying of OpenGL. We'll be downtown every day, starting Friday and ending next Tuesday. Lenore pointed out a visualization lecture track that we're going to follow during our time at ISMB. I'm also hoping to get to see several keynote speakers, including one who is working with sequencing dinosaur genomes and a lecture from Mass Gen Hospital and Harvard Medical that will hopefully be a nice marriage of computational biology and medicine.

Week 5: June 28th July 2nd, 2010

July 1st:
We have done 10 user studies so far and everything has been fairly smooth. We've had a few difficulties with keeping the directions uniform between researchers, but everyone is happy to chime in if the directions need clarification or something is presented in the wrong way. We're planning on maxing out the number of user studies we can do, which is 20 studies. I got my first opportunity to act as the task delegator while Connor was out with strep throat it's definitely a slightly more stressful role. We have blocked out all of next week to crunch data from the video files and start working on compiling everything. We will also be working on getting the poster ready for 3DSig. Connor has had the main role in this, he has Illustrator on his laptop. Matt has added a fun new change to TuftsViewer the images are being rendered in a new way that makes the contrast sharper and gives each structure a sort of "shiny" look.

Week 4: June 21st June 25th, 2010

June 23rd:
Our user pilot studies have been going really well Dani, Connor and I have gotten into a comfortable pattern for each one. I have mostly been working on the follow-up materials. I wrote a quick html form to replace the paper survey and I have been keeping the data neatly organized in a spreadsheet. I have also been organizing our distribution of the giftcards in another spreadsheet. Today we transferred the video files to all of our computers so we can start work soon on quantifying the video data. We took a whiteboard from the other side of the room and wrote down everything we currently think about quantifying the data. Sara was out sick today, but when she gets back we're going to show her our ideas and get approval to being parsing data from the video files. Only 2 weeks until 3Dsig, so we need to get our poster work moving too.

Week 3: June 14th- 18th, 2010

June 17th:
We had our first pilot user study yesterday, on a post-doc student who works in a lab nearby. I got to chat with him a bit before the study and learned about his research in machine learning, which actually turned out to be very interesting. All in all, it was a good learning experience. We ironed out quite a few bugs in our procedure and script and got out feet wet in the procedure. We noticed several interesting phenomenon in the habits of users. We have so far done the study with 4 people, all computer scientists, and they always choose to use the console when using jmol, possibly because of its similarities to a unix console. We are wondering if we will see a different trend when we begin working with hardcore biologists, who have little to no computer knowledge. I've been rooting around in the code a bit and experimenting with making changes here and there and I've only broken the builds a few times. Matt has been really helpful in showing me how to fix the broken code, too. Very interesting stuff.

Week 2: June 7th June 11th, 2010

June 8th:
Yesterday Dani and I worked with Matt to get our wxWidgets and TuftsViewer code running in Visual Studio. Now that everything is up and working great (as long as we don't touch any of the code), we've been running through the code and exploring the functions. There is quite a bit of code to go through. We've updated our June schedule to allow more time to meet with non-biology people. This will delay any biologist studies until June 28th. We approved a draft of an email to send to biologists to recruit users for our studies today. Dani and I have been researching methods of tracking users when they are completing our study. Hopefully we can get a method approved when Sara and Connor are back in town.

Week 1: May 31st June 4th, 2010

June 4th:
Dani and I decided to spend today continuing with installing and compiling the source code for TuftsViewer and wxWidgets. We have looked through the source code sent to us by Matt, the creator, and plan on going through and adding comments to the code that we will be working with frequently. Right now we are mostly looking at the research side of the project, not the coding side, so all of the Visual Studio stuff isn't really urgent. Connor sent us the script for the research study and we sat down with him and Sara to discuss changes we felt were necessary. Dani and I will have to also spend time today going through a schedule for the next month. We will hopefully be working with between 12 and 20 biologists, so we put together a schedule for the next month to make sure everything gets figured out.

June 3rd:
Today I met with everyone working at Tufts this summer. We had a really nice luncheon and got to mingle with the other DREU students. After that, we met with Matt, the graduate student who put together the software we are researching this summer. After a short discussion with him about his implementation of the program, we worked with Connor by acting as mock research subjects for the pilot study he has written. This was really great because we got to "play with" the program and get to know all of its features. His script also taught us how to do some of the tricky things that aren't obvious from the start. After that, we talked with Sara and brought up concerns and changes we'd like to see in the program. Hopefully we'll get the chance to code some of those changes before the end of the summer.

Download my report directly:
Click Here to Download a PDF

My Project:

This summer, I will be working on a piece of software called TuftsViewer. This software was created by a PhD student in an attempt to make modeling of complex protein structures for biologists an easy task. Working with my fellow DREU student Dani Extrum-Fernandez and a Tufts student Connor Gramazio, we will create and run a research study with biologist to see how people use the software and how we can improve it. We will also be doing some coding with creating a tracking program to watch users as they work with TuftsViewer. Near the end of the summer we will get into the actually software itself and make some modifications to viewing options. Check out our project here: http://bcb.cs.tufts.edu/tuftsviewer/tutorial/

My Goals:

1. Learn more about designing an effective research study with human subjects.
2. Improve my skills with Visual Studio and C++.
3. Design a unique feature for TuftsViewer and implement it.
4. Explore the world of a Computer Sciences graduate student by talking to graduate students and professors on campus.