Gas station without pumps

2011 November 19

Starting a local effort to get bioinformatics into AP bio

Filed under: Uncategorized — gasstationwithoutpumps @ 00:32
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As those who have been reading my blog for a while know, I’m on a task force attempting to get bioinformatics into high school biology (particularly AP bio) classes, and I have a series of posts about Advanced Placement Biology courses and the AP Bio exam.  I recently posted about an attempt in Colorado to introduce bioinformatics into AP bio and invited grad students in my department to do something similar.

I had a couple of students respond right away, and I sent out queries to three local high school biology teachers that I had previously had contact with.  One responded enthusiastically, and so I set up a meeting for him, the two students, and myself to meet Friday afternoon (Nov 18).  In the morning, a third student (who had not subscribed to the mailing list I’d announced effort on) indicated an interest also, but she could not come to the meeting.  I expected the other two students to be there.

I was a little surprised to find not two students, but three at the meeting (the two who had sent me early e-mail had recruited yet another student).  We now have four grad students (Olga, Yulia, Dorothy, and Paola) interested on working on getting bioinformatics into bio classes at one (or more) of the local high schools. (Note: more are still welcome—UCSC grad students should probably talk with Olga, who seems to be recruiting others to join.)

We did a lot of brainstorming today to try to figure out the scope and nature of the project.  We agreed on some general principles:

  • The primary goal is to teach students biology, not computer science or bioinformatics.  The bioinformatics should be good support for the underlying biology lesson.
  • Whatever we produce should be made available on the web (but putting any answer keys behind password protection, should we end up producing anything that needs a key).
  • The students will present the lessons to the class (both to expose the high school students to college student role models and to give the grad students practice teaching), but the lessons should be teachable by non-bioinformaticians.  In particular, the high school teacher should be able to teach it himself next year.
  • If things work out well, it might be worth presenting a paper explaining the project (and advertising the materials) at a high school biology teachers conference (perhaps an NABT conference?).

We discussed various tools and possible topics to teach, but did not settle on any particular topic.  Instead each student will think about what tool or technique they would like to teach and what lesson it will support.  One idea that seemed to have some traction was to go through the process of identifying a gene, getting its sequence (with surrounding DNA) from a genome browser, designing primers for PCR, and verifying that the primers uniquely selected the gene again using the genome browser. We also talked about looking at sequence logos of huge alignments (perhaps of HIV proteins) to identify conserved regions, making phylogenetic trees, and other possible lessons. The use of the genome browser to show introns and exons and the greater conservation in most exons was also discussed.

One cool thing one could do with the PCR lesson is to have the students design primers, order the most promising set, and then do a PCR reaction and gel electrophoresis to confirm amplifying the right length DNA. The problem is that we could design the primers, but not then do the PCR, as the high school does not have a thermocycler, and hand cycling with water baths for PCR is rather tedious. (I did once blog about a very low-cost capillary PCR method I read about, but I don’t know if it actually works.) The reagents for PCR cost about $100 for 200 reactions (for example, for the New England Biolabs kit) and need to be stored at -20ºC.  The primers cost about 30¢ a base (in 10 nmole amounts, which I think is enough for about 200 reactions), so add about $20 to the cost of a PCR experiment for the class.  The most expensive thing is the thermocycler, which costs about $300–500 used—I saw one on for about $220, including shipping.  I wonder if any of our faculty with connections in the biotech industry can get surplus thermocyclers cheaper. In any case, it looks like doing the PCR  wet lab experiment would cost about $500 in startup costs and $40/class in consumables.  This may be too much for the high school, unless we can get donations of reagents or loans of equipment.  The PCR reaction itself takes longer than a 90-minute block, so would have to be an after-school or weekend workshop,which may be too big a project for this year.

Obviously, we have not yet settled on what lesson(s) we want to present, and we’ll be doing brainstorming about it in early December, after the fall quarter winds down.  The hope is to have a lesson or two (probably one or two 50-minute classes followed by a hands-on block of 90 minutes) ready for testing with the high school classes by late January (to reinforce what they will have learned about DNA sequences and replication).

I promised the grad students some links to information about the AP bio curriculum, besides my earlier post about resources for teaching bioinformatics in high school.  Perhaps the most important is the AP bio home page for teachers, which has links to College Board’s resources and to the new AP biology curriculum (which affects AP bio tests starting in May 2013). Another is the BME 110 course at UCSC, which is an intro bioinformatics tools course for biologists.  It may be possible to adapt some of the assignments in that class to AP Bio, though the focus on that class is to teach the use of bioinformatics to students who have already had a few college biology courses, rather than to teach the fundamentals of biology, so most assignments will not be directly usable.

UPDATE (2011 Nov 19)

Ted pointed me to a page where PLoS Computational Biology is gathering resources relevant to bioinformatics in high school bio.  They have 4 things there currently (one the article I blogged about, the other three editorials that provide useful advice).


  1. One of my former students sent me email:

    My group has put together an educational biology video game for high school students, which you may find useful.

    You can find it at

    Comment by gasstationwithoutpumps — 2011 November 19 @ 10:31 | Reply

  2. Since I have been working on a few assignments in bioinformatics for the Biotechnology class I teach and have introduced them partially into AP Bio, I would like to at least keep abreast of what you are doing and at most be a part of the development.

    Just a note on my efforts, the industry is changing at a rapid pace and any lesson plan I have put together in the past needs significant revision each year. Web sites change, technology changes and the science advances at a rapid pace. For biotech i have lessons related to diabetes, sequencing, gene annotation using DNA Subway and others. You mention PCR and I do 5 PCR labs in my Biotech class each year. The giveaways sponsored by Bio Depot and BABEC have been the source of the thermocycler I am now using in my classroom. Low cost reagents is definitely the key and corporate support is the only way to make that happen.

    Comment by Archie Kregear — 2011 November 28 @ 19:12 | Reply

    • I will post on my blog about anything substantive we do, and make sure that any usable products are put in a public place (probably somewhere on my department’s or my professional web pages). I’ll discuss with the group how to maintain the materials over the next few years—particularly how we will maintain and improve the materials once they finish their degrees.

      Comment by gasstationwithoutpumps — 2011 November 28 @ 23:14 | Reply

  3. […] Starting a local effort to get bioinformatics into AP bio  ( […]

    Pingback by PLoS Computational Biology: Bioinformatics: Starting Early « Gas station without pumps — 2012 February 25 @ 17:50 | Reply

  4. […] a previous post about the project, I described our […]

    Pingback by Bioinformatics in AP Bio, lessons released « Gas station without pumps — 2012 June 27 @ 11:03 | Reply

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