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An Introduction to Bioinformatics Algorithms

From | From MIT Press
Professors: order an evaluation copy

Table of Contents (by content area)
Sample Chapter (Dynamic Programming Algorithms)
Featuring biosketches (sample)

This introductory text offers a clear exposition of the algorithmic principles driving advances in bioinformatics. Accessible to students in both biology and computer science, it strikes a unique balance between rigorous mathematics and practical techniques, emphasizing the ideas underlying algorithms rather than offering a collection of apparently unrelated problems.

The book introduces biological and algorithmic ideas together, linking issues in computer science to biology and thus capturing the interest of students in both subjects. It demonstrates that relatively few design techniques can be used to solve a large number of practical problems in biology, and presents this material intuitively.


1/8/2008 Extended outtage

The colocated server that hosted this site died, but it has now moved to its new home at UCSD. Hopefully that will be somewhat more stable. During the move, the discussion boards were broken. In my opinion, this is not a bad thing and I probably won't ever revive them in their old format, though I will post the final errata list. Considering that we had over 40,000 users but about 50 posts -- mostly spambots were signing up for accounts so that they could unsuccessfully try to hawk their golf clubs and lingerie -- it seems like more of a haven for abuse than for anything remotely productive. I'll start up a google group for this instead.

2/24/2007 Temporary outtage

The discussion board, class list, and "Who's who" list are currently down. They will be back in a few days; please check back then. In the meantime, all those slides you want to download should still be available.

12/19/2006 WHEW! Site outtage

Let this be a lesson to you, ladies and gentlemen: never let your domain name service expire! And especially don't do it when you forget the account details of how you purchased it. But, we're here for another 6 years, so hopefully that will be the last time that you'll see some random search page instead of this site.

9/1/2005 New code

We have updated the website again. The PowerPoint presentations have changed again. Also, we now have a place to list research projects!

1/26/2006 Site outtage

We apologize for this site's downtime, which started late on January 24th and ended late on the 26th. Hopefully this was not too disruptive.

9/1/2005 New code

We have updated the website again. The PowerPoint presentations have changed again. Also, we now have a place to list research projects!

5/30/2005 New code

I have added implementations to the Longest Common Substring Problem in a few different languages. They are in the Implementation Problems section.

3/21/2005 Website Update

We have updated the website. Most notably, the PowerPoint presentations have changed significantly, and a large number of errors have been found and, hopefully, corrected. We We thank the many students and professors who have given us their critical feedback, helping us identify and fix errors. We strive to improve the site and we plan to have yet another revision in June 2005.

If you want to be informed about the upcoming releases, please enter your email address in the box on the left hand side of the page; we'll only use this address to tell you when the site is updated. This is particularly important for people who use the PowerPoint slides in the classroom, since they tend to get updated frequently.

1/12/2005 Reprinting

The book is about to be reprinted! Thanks to everybody who reported errors or typos in the book---we fixed as many as we could for the second printing. We do appreciate the feedback you've given us, and we don't mind the positive comments either.

1/11/2005 Brief outtage

This site disappeared for about 8 hours yesterday. We've worked around the problem, and hopefully it won't happen again for a while. But, for a free hosting service, reliability ain't so bad.

7/3/2004 Moodle works...

We have installed and tested Moodle, a courseware system. Basically, this means that you can setup, customize, and run a bioinformatics class entirely from this website (you'll need to email us to gain access to create courses). You can look at a sample course for CSE 181. The features that Moodle has that you might not at your own institution:

  • Discussion forums
  • Online quizzes
  • Online assignments
  • Assignment submission
  • File distribution (great for code)
  • Calendar with due dates
  • Online grade information (if you want it)

You might wonder why we're hosting class websites for essentially nothing in return. We feel that the materials that are used in different bioinformatics courses at different institutions are inherently valuable and would be more useful if they were collected on one site. Some student in some other university might benefit from your (students') hard work. However, you may not wish to allow arbitrary outsiders access to your class website---sometimes privacy is important. Either way, Moodle will allow you to set access permissions that fit your needs, and you'll still benefit from the fact that you don't have to do any website maintanence.

6/29/2004 New sample code

Robin Friedman has written a Java class that implements the SpectralAlignment algorithm in section 8.12. For reasonably sized datasets you can use the web version, or for larger datasets you can download the program and run it (requires Java).

About Us | ©2004 Neil Jones