Posted by: jonkujawa | June 13, 2011

Welcome: 2011 Edition!

Welcome to the webpage for the the University of Oklahoma VeRTEx math research group!   The current members are Ore Adekoya, Rhyker Benavidez, Jon Kujawa, Alyssa Leone, Lauren Lajos, and Logan Maingi.

For the summer of 2011 we will be conducting an online reading course of the books “An Introduction to Bioinformatics Algorithms” by Jones and Pevzner and “Computational Molecular Biology: An algorithmic approach” by Pevzner.   The first is a gentle introduction for undergraduates and the second is a gentle introduction for graduate students.

The general area is what I would call “Algebraic Biology”.  These are questions which are important biologically and which use math based in abstract algebra, linear algebra, graph theory, algorithms, etc. (so not using differential equations, etc. like a lot of biology problems).  If you look at the back of P, you will see a couple of hundred open problems (or, at least, problems which were open when the book was written.  This field is moving quickly, so I’m sure some are already solved!), and many of them are straight math problems about the symmetric group, graphs, etc. which you could explain to anyone who’s taken first semester abstract algebra.

The main goal of the summer reading for us to get some background in the relevant math and biology so that we can find some interesting problems to play with in the fall.

What we will do is take turns writing short posts about what we are reading.  You can explain the main points of the sections you were supposed to read, explain things you think other people might find confusing, ask questions about the stuff you got stuck on, explain solutions to interesting problems at the end of each chapter, give extra information if you looked up anything related online, or whatever else you think would be helpful.

Everyone will be doing the reading, so you don’t have to give a full report.  A brief overview + any extra information you want to share should be enough.

I’ll do the first post, and then it’ll be Alyssa, Lauren, Logan, Ore, Rhyker, and then repeat.  You should plan to have a post up no later than 2-3 days after it is your turn.  This will help keep things moving so we can make good progress in the next two months.

Both are written for people who don’t know much biology or math, so I think we shouldn’t have too much trouble.   But you should feel free to ask questions and make comments after each person’s post.  I know I will have lots of questions because I don’t know much about biology and even some of the math topics will be new to me.  (Plus, I just always seem to have lots of questions!)

A few general words of advice:

  • This is a public forum.  The primary participants are the members of the group, but others are welcome to read and make relevant comments.
  • As Einstein said: “A person who never made a mistake never tried anything new” and “If we knew what it was we were doing, it would not be called research, would it?”.  When you’re doing research, all questions, comments, suggestions are welcome.  Often times the simplest question can point out the key idea needed to make progress!  You should never hesitate to contribute.
  • WordPress supports the use of LaTex to type mathematics.  Their page on the topic is here.  The general format is to type“<img title=”[YourLaTeX code]” src=”http://s0.wp.com/latex.php?latex=%3Cem%3E%5BYour+LaTeX+code%5D%3C%2Fem%3E&bg=ffffff&fg=000&s=0&#8243; alt=”[Your LaTeX code]” />” without the quote marks.  For example, replacing the quotes with dollar signs in “latex \int_{a}^{b} f(x) dx = \frac{\pi}{2}” yields \int_{a}^{b} f(x) dx = \frac{\pi}{2}.  There is also a LaTex-to-Wordpress converter here which could be helpful.
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