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Our goal for this course (BioSci256) is to introduce you to some of the tools and databases that are widely-used in bioinformatics and give you lots of hands-on practice in using these tools to look at some questions in biology. Since many of you are either studying biotechnology or working in a health-related field, we will focus quite a bit on practical applications.

I posted tonight’s topics here since I’ve been told that some of you might not have access to Blackboard for a couple of days. Feel free to look around the place. ScienceBloggers discuss lots of topics that you might find interesting.

Tonight, we are going to talk about definitions for bioinformatics and what people do with it.

What is bioinformatics?

  • It’s a funny field where just defining it can quite contentious. I’ve had reviewers tell me that “it’s not bioinformatics unless you’re using a database.” This is quite odd, since there are lots of bioinformatics programs that don’t interact with databases at all. I’ve also had reviewers tell me that using PubMed/searching scientific literature is not bioinformatics.

    You can get a flavor of the debate at www.nodalpoint.org and see one person’s opinion of the top ten challenges for the field here.

    I think, by far, the best definition is here at BISTI and in the pdf document, that’s linked to the definition, I found two descriptions that I like very much:

    • Bioinformatics applies principles of information sciences and technologies to make the vast, diverse, and complex life sciences data more understandable and useful.
    • Computational biology uses mathematical and computational approaches to address theoretical and experimental questions in biology.

    Lots of people get these mixed up.

We will also get our hands dirty and start out by having a BLAST!

First assignment
Copy one of the unknown sequences from the BLAST for beginners activity, and use it as query sequence for a blastn search.

Here are your tools:

  • 1. The unknown sequences: BLASTing through the kingdom of life. You’ll be assigned a sequence tonight in class.
  • 2. An animated tutorial showing how to do and interpret some of the results from a blastn search. BLAST for beginners.
  • 3. A PDF document with the questions that you need to answer and an example.
  • 4. Another set of solved examples, with more pictures.
    • Step 1. Digital Biology Friday: Those BLASTed results!
    • Step 2. Digital Biology Friday: What was that gene anyway?
    • Step 3. Digital Biology Friday: It’s still Friday!

Second assignment
Your second assignment – once you get your Blackboard account – is to log in to our Blackboard area and answer our forum question – “What would you like to learn the most about bioinformatics?”

Comments

  1. #1 Janne
    January 9, 2007

    “What would you like to learn the most about bioinformatics?”

    Would “Whatever maximizes my future earnings potential” be an acceptable answer?

  2. #2 Sandra Porter
    January 9, 2007

    Sure it’s acceptable, but it’s a not a question that we can answer it in a four-week class. :-)

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