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2012 June 27

Bioinformatics in AP Bio, lessons released

Filed under: Uncategorized — gasstationwithoutpumps @ 11:03
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As those who have been reading my blog for a while know, I’ve been working with UCSC grad students to develop materials for bioinformatics lessons for high school biology classes.  I have a series of posts about Advanced Placement Biology courses and the AP Bio exam.

In a previous post about the project, I described our goals:

  • 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 have just released the two lessons we’ve developed so far: one on genetic diseases, the other on phyogenetic trees.

Each was tried at one school, in 3 sections of AP Bio (where AP bio is a required course for all students).  The lessons took one block each (just under 2 hours for a block), with some sections finishing everything with time to spare and others not quite finishing.  (Consistently the first section getting the lesson having trouble finishing and the third one having time to spare—I don’t know if the difference was in the speed of the initial presentation and our quickness in responding to problems or in the competence of the students.  There was more assistance available to the students for the first two sections, which were also the slower two.

The resources can be accessed directly from http://compbio.soe.ucsc.edu/binf-in-AP/  They are released under a Creative Commons attribution/share-alike license.

Other resources people should know about include

2012 February 25

PLoS Computational Biology: Bioinformatics: Starting Early

The Public Library of Science has a a service where they group together open-access articles from their journals to make  PLoS Collections: Article collections published by the Public Library of Science.

One collection that might be particularly interesting to readers of this blog is PLoS Computational Biology: Bioinformatics: Starting Early, which has articles from PLoS Computational Biology about getting bioinformatics into high-school courses.  So far, there are only 4 articles, all from the 27 October 2011 issue of the journal, but I expect that more will come out in the next year.

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 ecrater.com 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).

2011 November 18

Titles for graphs

Filed under: Uncategorized — gasstationwithoutpumps @ 00:25
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An AP Bio teacher on the ap-bio mailing list wrote

I keep finding that the some AP students do not know how to write a proper title for graphs. I tell them that a title basically describes the information that is being presented. They give one- or two-worded titles which I believe is not sufficient enough. 

  1. Does anyone have a suggestion on how to show the AP students how to title their graphs correctly?
  2. Is it okay for them to use “vs.” in a title? An example title: Light intensity vs. depth

The problem is not limited to AP students.  I find that grad students, postdocs, and faculty often have no idea how to label a graph.  The journal literature is full of badly labeled graphs.

I don’t like “light intensity vs. depth” as the title of a graph.

First, the axes should already be labeled (“light intensity (lux)” on the y-axis and “depth (cm)” on the x-axis), so the title adds no information—in fact, it tempts people to omit the more important axis labels.

Second, about 20% of students get the convention reversed for “versus”, doing “x vs. y” instead of the standard “y vs. x”.

Third, what are you measuring light intensity of?  I can’t think of a biology experiment where that is the right thing to plot.  Either you should be plotting luminous flux (in lumens) for something emitting light or absorbance (the more common measurement in bio labs). You might measure lux—that is what a light meter usually measures, but that measurement depends on the distance and size of the sensor, so should be converted to lumens for the  source before plotting, or absorbance of the suspension, depending on what the underlying phenomenon being measured is.

It would be better to give a descriptive title: “Bioluminence is highest at the surface”.  The worst titles are ones that convey no information, like “Results” or “Measurements”.  I hate meaningless section titles also. The style that makes every paper have an identical outline with identical section headers is one I abhor, as it minimizes the information presented to the reader.

If you are doing formal write-ups (rare in AP bio or freshman college classes, but common at the grad level), every figure or table should have a paragraph-long caption, not just a title.  The reasoning is that most readers of a journal article only read the abstract and look at the pictures, and so the figures and captions have to convey the main ideas of the paper. Even those who do read the full paper generally thumb through and look at the pictures first.  The figures and captions should amount to a poster presentation of the whole paper—if the figures are mysterious, the paper never gets read, and the writing of it was wasted.

2011 November 7

A First Attempt to Bring Computational Biology into Advanced High School Biology Classrooms

Filed under: Uncategorized — gasstationwithoutpumps @ 00:32
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As those who have been reading my blog fo awhile 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. Of course, I’m not the only person interested in achieving this, and others have done far more than I have.

There is a nice paper in PLoS Computational Biology: A First Attempt to Bring Computational Biology into Advanced High School Biology Classrooms, that describes one attempt by researchers at University of Colorado, Boulder to get some understanding of BLAST and tree-building algorithms into high-school bio classrooms in a fairly minimal way (3 lessons of 1–2 class periods each).  They provide the curriculum they used and a “post-game” analysis, where they look at what they would do differently next time, based on the successes and failure of this first attempt.

The tools and basic approach they used seem reasonable, though I question the value of teaching what an algorithm is with the “make a peanut butter sandwich” example, classic as that is. Along with the students, I wonder about the relevance to an AP Bio class.  Doing the living computer exercise seems ok, but it might be better to apply it to a curriculum-relevant algorithm, such as creating a Punnett square.

This paper seems like an important resource, and so I have added it to the list I collected at Resources for bioinformatics in AP Bio.  Incidentally, the authors point to this blog, but to the early post Advanced Placement Bio changes announced, rather than to the more relevant Resources for bioinformatics in AP Bio.

Note to UCSC grad students: I have some contacts with local high school bio teachers, if some of you want to try one of these outreach experiments in education, and I would be glad to facilitate meeting and planning.

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