Resources for bioinformatics in AP Bio

I’ve had a series of posts about Advanced Placement Biology courses and the AP Bio exam, though I’m not an AP Bio teacher (nor even a biology teacher—I teach bioinformatics to grad students and seniors at the University).  This series was started because I’m a member of the ISCB Task Force trying to get bioinformatics into high-school biology. The goal of the task force is not to add more content to AP Bio (which is overloaded already), but to use bioinformatics to teach biology more efficiently and effectively.

This post collects pointers to ideas, resources, and lesson plans for using bioinformatics in AP Bio classes, many of which I had informally gathered as comments on the post Adding bioinformatics to AP Bio. The comments there are worth reading, as I have not collected here all the ideas, just those that had pointers to resources.

• The first comment gave a lesson plan (including 37 questions and answers) by mrkregear@charter.net for an exercise in finding human insulin sequences in http://www.ncbi.nlm.nih.gov, then BLASTing to find pig insulin and comparing the pig insulin gene to the human insulin gene. The exercise continues with using PDB to look up the structure of human insulin.  The whole lesson plan is too big to copy into this post, but the pointer to the comment should get you there.  The lesson looks like a good one for introducing the NCBI and PDB databases, but I would have started the students at the Entrez page rather than the NCBI home page, and  BLASTed the protein sequence rather than the nucleotide sequence.  After all, it was the pig protein, not the pig gene that was once given to diabetics. The protein BLAST page has pretty easy navigation to search only the Sus scrofula sequences, and the differences between human and pig insulin are fairly clear in the alignments.  I have other queries about the lesson plan with the original comment.
• Jim Tripp pointed to A. Malcolm Campbell as a resource.  It appears that he is writing a book, and there are several links to bioinformatics resources associated with titles of lectures at http://www.bio.davidson.edu/people/macampbell/111/Bio111reading.html
• One high-school teacher mentioned students extracting their own mitochondrial DNA and getting a hypervariable region that doesn’t code for any proteins sequenced.  PBS has a lesson plan for Race—The Power of an Illusion, that points to both publicly available mitochondrial data and free sequencing through Cold Spring Harbor’s Dolan DNA Learning Center.  But according to http://www.geneticorigins.org/mito/mitoframeset.htm: Effective January 1, 2011 the Dolan DNA Learning Center has discontinued its free Sequencing Service. The DNA Learning Center has arranged deeply discounted rates through the commercial sequencer, GENEWIZ. The $3/sequence price is pretty good for a commercial service, close to what a university sequencing center charges internally, but a bit high for high schools.
• The Genographic Project  has another view of mitochondrial (and Y-chromosome) data for tracing human migrations.  It encourages public participation, at $100 a sample ($200 if you are male and want both the mitochondrial and Y-chromosome data).  They do have some good resources on the ethics of collecting human DNA data.
• The Dolan DNA Learning Center has a lot of lesson plans and services that are worth exploring, not just the mitochondrial sequencing project.
• Robin Groch posted
  

  I have 4 bioinformatics activities that I’ve refined over the years one from a NABT article, one from Kim, and one I made up to augment Bio-Rad’s Fish Lab (Protein Profiler) and one on primates to support Human Evolution. I’ve received a lot of help from Swami’s NGWB at UC San Diego (from Mark Miller who made a tutorial for each activity). Here are the links to the activities and the tutorials.

  Bears and Pandas http://www.grochbiology.org/PandasBearsNewVersion.htm (new version) (comparing nucleotide sequences from http://www.ngbw.org/labs/bears/bears_rev3.pdf : Adapted from Maier, C.A. (2001) “Building Phylogenetic Trees from DNA Sequence Data: Investigating Polar Bear & Giant Panda Ancestry.” The American Biology Teacher. 63:9, Pages 642–646.)

  Here is the information about the extension to the Bio-Rad lab: http://www.grochbiology.org/FishPostLabInformationRevD2010.pdf http://www.grochbiology.org/fish%20lab%20genbank.doc http://www.grochbiology.org/fish_protein_rubric.htm

  Walruses, Whales, Seals http://www.grochbiology.org/WhalesActivity.htm (direct link to online tutorial http://www.ngbw.org/labs/seals/seals.htm) (use of clustal W-P, boxshade, clustal distance, Newick, drawtree) adapted from Kim Foglia

  Primate Activity http://www.grochbiology.org/PrimateActivityNewVersion.htm (new version) http://www.ngbw.org/labs/primates/primate_lesson.htm (help tutorial) (use of clustal W-P, boxshade, clustal distance, Newick data, drawtree).

  Doing the bioinformatics can seem overwhelming but my students run the tutorial animation at the same time as their assignments, a bit at a time. NGWB (new generation workbench) has all the tools for doing bioinformatics in one place no need to download anything just register to be a user. The only issue is that NGWB is a site used by researchers all over the world, check out the map on the front page (http://www.ngwb.org) and if someone does a huge run (an entire bacterial genome) the site can crash … just send an email and they’ll reset the server.

  I have one quibble with Robin’s methods here, and that is the use of Clustal-W for generating trees. Clustal-W is an obsolete method for generating multiple-sequence alignments and has never been a good way to generate trees. There are much better tools available, and have been for several years.

  Disclaimer: I am a minor author on a paper now being submitted about Clustal-Ω, which does much better alignments than Clustal-W, though the trees are still only guide trees for the multiple-sequence alignment, not proper phylogenetic trees.
• Bay Area Biotechnology Education Consortium have done some bioinformatics workshops and modules for high-school biology teachers. I don’t know how eager they are to share their stuff nationwide, though (their mission is focused on the San Francisco Bay Area).
• The HHMI Holiday Lecture for 2010 on viruses by Joe DeRisi emphasizes the important role for bioinformatics in biology, and the HHMI Holiday Lectures in general are an excellent resource for AP Bio teachers, both for their classes and for their own continuing education.
• The bio-itest unit from from the Northwest Association for Biomedical Research includes 8 lesson plans on genetic testing and 10 on genetic research (including a PCR and sequencing wet lab).  They have training workshops for teachers, which at least one participant found very inspiring.
• http://evolution.berkeley.edu has a lot of educational resources, and searching “molecular phylogenetics” is supposed to get some useful bioinformatics labs, though searching for “bioinformatics” finds nothing, and just “phylogenetics” is overwhelming.  One of the problems with large archives is finding the stuff in them that is useful.  If anyone has spent some time in this particular archive, and can point more specifically to bioinformatics labs or exercises that would be suitable for AP bio, more specific pointers would be appreciated.
• ENSI/SENSI has a collection of evolution lessons, some of which may involve bioinformatics, such as Molecular Biology & Phylogeny (Cytochrome C), but the lesson plans seem to be more geared to traditional hand classification of characters rather than molecular phylogenetics. (Note: I may have been looking at the wrong lessons—if someone wants to give me an updated pointer, I’d appreciate it.)
• http://wiki.pingry.org/u/ap-biology/images/a/ac/Phylogeny_Lab_2011.pdf is a lab that uses Clustal-W to generate a tree of Cytochrome C sequences. Personally, I think that this lesson should be reworked, as Clustal-W is not intended for producing phylogenetic trees—the guide trees it makes are just for building the multiple sequence alignment.
• It looks like http://www.phylogeny.fr/ provides a simple interface for phylogenetic analysis of sequence that can be used by novices, but which allows exploration of different tools for alignment, tree-building, and viewing, should someone want to go beyond the default choices. It offers much better default choices than using Clustal-W, which seems to be the default for most biology teachers.
• http://wiki.pingry.org/u/ap-biology/images/b/bb/TMV_bioinformatics.pdf has an exercise on TMV (tobacco mosaic virus) which asks the students to blast an RNA virus and answer a number of questions about interpreting the viral sequence.  It seems like a good intro to some of  the basics of viral biology.
• http://www.genome.gov/glossary/ has a glossary of terms in genomics that some people will find useful. I find the “talking glossary” format, where the real meat is buried in audio clips, very irritating, because I can read 3–5× faster than people speak.  The format might be attractive to students who are slow readers but good listeners, though.
• http://ecsite.cs.colorado.edu/?page_id=353 has an example lesson they taught to high-school bio classes. It actually has 3 lessons: one on algorithms, one on BLAST, and one on phylogenetic trees.
• National Center for Case Study Teaching in Science has a few “cases” for bioinformatics study that are claimed to be at the high-school level: http://sciencecases.lib.buffalo.edu/cs/collection/results.asp?subject_headings=Bioinformatics&educational_level=High+school
• http://caseit.uwrf.edu is the site for the Case It molecular biology simulation, which is described as follows:
  

  CaseItv6.05 is a simulation that performs common laboratory procedures on any DNA or protein sequence. It has all of the capabilities of the earlier version (5.03), but adds new features such as bioinformatics analysis and autoloading of DNA and protein samples to speed loading of gels, blots, ELISA, and 96-well PCR.

  The bioinformatics analysis is actually done by another free package, MEGA4, from http://www.megasoftware.net/mega4/mega.html

  Unfortunately, both tools are Windows-only, so I’ll never use or test them, since all the machines I use are either Linux or Mac OS X.

• Silencing Genomes is about RNAi for knocking-down gene level. “The bioinformatic tools and experiments are described in Experiment 7 (PDF file) on the Silencing Genomes website.”
• The Howard Hughes Medical Institute has funding opportunities for precollege science education, in addition to their better-known funding for research at colleges and universities.  Their database of grants awarded includes 2520 for ones aimed at 12th-grade level, though most of these seem to be museum programs, rather than direct grants to teachers.  I suspect that a teacher who wanted to create a workshop to share with other teachers might stand a good chance, though.  One grant from a few years back introduced minority middle-school students to mycobacteriophages.
• Mycobacteriophage hunting has become a popular college freshman lab in several colleges (again, thanks to a grant from HHMI), and the annotation of the newly isolated phages requires a fair amount of bioinformatics.  The phage hunter labs are within the capabilities of most high school biology labs, I think, aside from the sequencing, which is outsourced even by the colleges that do the labs.  There are several high schools listed on the institution list of phagesdb.org, and there was a teacher workshop in summer 2011.

If you have more pointers to resources directly useful to AP Bio teachers wanting to use bioinformatics in their teaching, please add them as comments here.  If anyone is keeping web pages or wikis or resources for AP Bio teachers, feel free to re-use any of the text on this post (as long as you don’t try to claim copyright)—my goal is to get this information out into people’s hands and used.

UPDATE:

• A First Attempt to Bring Computational Biology into Advanced High School Biology Classrooms, added 2011 Nov 6.  This paper from PLoS Computational Biology describes an attempt to add lessons on BLAST and tree-building algorithms to an AP bio class.
• One of  my former students had her lab group put together an educational biology video game for high school students. (Added 2011 Nov 19)
• From the Netherlands (added 2011 Nov 21):
  

  With regards to bioinformatics in high school education (for pupils and their teachers): NBIC (Netherlands Bioinformatics Centre) has a very active programme called bioinformatics@school. We have > 11000 pupils in the Netherlands that followed our practical in their own classroom and we are organizing teacher training events and performing didactic research on how to train teachers best. The project was presented in the technology track at ISMB2011. You can find more information at http://www.nbic.nl/education/high-school-programmes/bioinformaticsschool/.