Gas station without pumps

2010 July 13

Bioinformatics in high school biology

Filed under: Uncategorized — gasstationwithoutpumps @ 11:38
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One of the main topics in today’s Education Committee meeting of the International Society for Computational Biology was how to get bioinformatics integrated into high-school biology classes.

The tutorial workshop on Saturday was reported as being very successful, with the teachers being enthusiastic about the possibilities of integrating bioinformatics into their courses.  One problem that was pointed out is that AP bio students resist learning anything that won’t be on the test, so we decided to start the process of talking with the College Board about changing the AP curriculum and AP test to include some bioinformatics.  We expect this to be a slow process.

We now have a task force that will be looking at the AP curriculum and trying to find ways to incorporate bioinformatics into teaching that curriculum (so not adding topics, but adding more hands-on learning to the pedagogy). We think that this is a more fruitful approach than trying to add a bioinformatics unit to the courses.

We’ll be relying on the official information about the AP Biology course from the College Board.

I’m hoping that the teachers who attended the workshop will do some blogging on their attempts to include bioinformatics in their own courses.  Having 10 or 20 teachers experimenting with the pedagogy is going to be much more valuable than theoretical thinking about what should be done.

Note: I’m going to add new thoughts to this post as comments, rather than editing the main post, partly because I expect to be dribbling ideas in over the next couple of months. At some point I may start a new post with an actual proposal for discussion.

Note for our international audience: The AP curriculum is a program in the United States for “Advanced Placement” and is an attempt to get first-year college courses taught in high schools.  Many US universities provide college credit for AP courses, if students score sufficiently well on the associated AP test.  The content of the AP Bio courses is fairly standardized (to match the test), but the ways in which it is taught vary considerably. The International Society for Computational Biology is interested in integrating bioinformatics into high-school biology worldwide, but that was too daunting a task to start with.  We decided to start with the region where we had the most volunteers (USA) and see what we could do there.  Hopefully, anything we develop for AP biology will be usable elsewhere, at least in places where instruction is in English.

30 Comments »

  1. We should also look at AP’s future plans, in the draft of the next version of the AP bio course:
    http://apcentral.collegeboard.com/apc/members/courses/208119.html

    Comment by gasstationwithoutpumps — 2010 July 14 @ 17:00 | Reply

  2. I started looking at the DRAFT: Revised AP Biology Curriculum from Sep 2009. It has no mention of bioinformatics, and only 3 of “comput*” words in 63 pages:

    page 2: Quantitative (Computational) Thinking. Students will be encouraged to develop their ability to apply mathematics to wide sectors of biology so that they can better test hypotheses, model biological phenomena, interrogate complex data sets, and represent and interpret visualizations of relationships.

    page 7, 1.A.3: Learning Objective: The student uses data from mathematical computer models based on the HW-equilibrium to analyze genetic drift and artificial selection in the evolution of specific populations.

    page 9, 1.B.2: c. Phylogenetic trees and cladograms can be constructed from fossil records, morphological similarities and from DNA and protein sequence similarities using computer programs that have sophisticated ways of measuring and representing relatedness among organisms.

    d. Phylogenetic trees and cladograms are dynamic (i.e. phylogenetic trees and cladograms are constantly being revised), based on the biological data used, new mathematical and computational ideas, and current and emerging knowledge.

    I’m a bit depressed also about how long the revision process takes. It is a decade (started in 2002, incorporation in the exams in 2012), not 5 years as I had first thought.

    Comment by gasstationwithoutpumps — 2010 July 18 @ 17:54 | Reply

  3. I’ve started looking at the curriculum to figure out where bioinformatics can be naturally added to enhance the learning of basic concepts.

    One obvious place is under “1.A.4 Biological evolution is supported by evidence from many scientific disciplines”. Having students use bioinformatics tools to align DNA sequences from multiple organisms and build a phylogenetic tree of them would be useful enhancement, particularly if different genes were selected that had slightly different trees, so that students could learn some of the limitations of phylogenetic inference. (I think that many assume that the tree is very well known and that there are no questions about what tree is correct.)

    Looking at conserved regions in the UCSC genome browser could also be useful for “1.B.1 Organisms share many conserved core processes and features that evolved and are widely distributed among organisms today.” Building phylogenetic trees from ribosomal RNA also helps support this concept.

    “1.B.2 A phylogenetic tree and/or a cladogram is a graphical representation (model) of evolutionary history that can be tested.” is an obvious place to have students build their own trees. Having some explanations of branch length and bootstrap support would be useful, but may be beyond the scope of an AP class.

    Comment by gasstationwithoutpumps — 2010 July 19 @ 15:29 | Reply

  4. For “1.B.3 Non-eukaryotes can transfer genetic information laterally through the mechanisms of transformation, transduction and conjugation; most eukaryotes do not transfer information laterally”, is there an easy way to demonstrate lateral transfer between Archaea and Eubacteria using the UCSC microbial browser.

    It shouldn’t be too hard to find examples of lateral transfer, but how do we convince the students that they were lateral transfer rather than deletion from a common ancestor? Perhaps the easiest cases are recent bacteria->archaea transfers where the GC content has not equilibrated to the background GC content of the receiving genome. Perhaps we could also look for unusual codon usage (though that is not a built-in track on the browser, so would require an additional tool. Still it would be a fairly easy python script to write, and could be distributed free on a website.

    Comment by gasstationwithoutpumps — 2010 July 19 @ 16:10 | Reply

  5. I would put in a plug for using bioinformatics approaches to work through the biological information system from the level of the whole genome to the structure of a particular protein. It should be pretty easy to take a genome, find and translate a protein, BLAST search for the protein and then investigate the structure in Jmol or some similar tool. You could constrain an activity like this to whatever level of freedom you wanted to give the student.

    As has been mentioned in previous posts, phylogenetic tree creation is another obvious approach.

    Comment by David — 2010 July 19 @ 17:59 | Reply

    • As someone who has spent the past 15 years doing protein structure prediction, I applaud the idea of doing a structure prediction, but need to warn biology teachers that just doing BLAST is a bad idea. There are a number of protein-structure prediction services on the web, but they don’t really have the capacity to do the 1000s of predictions that widespread use in AP classes would entail. Using pre-predicted results, such as in MODBASE, would be feasible, though.

      Comment by gasstationwithoutpumps — 2010 July 19 @ 18:06 | Reply

  6. I teach AP Biology and IB Biology in a school where each student has his/her own laptop computer. One of the required elements for the IB Biology curriculum is that students access a database, so about 3 years ago I reworked a lab I obtained from somewhere (maybe ENSI website) and I use it in both IB and AP Biology classes. The students search for a specific gene in the NCBI database in different animals and then use the Biology Workbench program to produce a phylogenetic tree for the animals to determine relatedness. I have had students do variations and extensions of this activity, and they enjoy it very much. I use this as I am teaching about phylogeny.
    However, I have questions myself about exactly what is used to determine the cladograms or trees (there are a lot of choices) other than just the number of differences in the bases in the genes. So, I think teachers need some background in understanding teh program tool which the students will be using to analyze the base sequences.
    I am sure there is much more to bioinformatics, but this is how I see it most useful in high school.
    Also, I am very interested in knowing more because I have IB students who could use databases to do some research for an extended essay (another IB requirement!)If I had more ideas on what types of things kids could do with data bases, then they could generate their own questions to answer.

    Comment by Brenda Fabian — 2010 July 19 @ 19:23 | Reply

    • There are several different algorithms for generating phylogenetic trees. Explaining them in detail is probably beyond the scope of AP Biology, but a brief introduction to the flavors of different algorithms (neighbor-joining, maximum likelihood, and maximum parsimony, for example) might be reasonable. The distance measures used are based on (usually oversimplified) models of evolution, but explaining them might be tough for kids that haven’t had matrix multiplication yet. Do you know which algorithm you used in your examples?

      It might also be worthwhile to explain when it is appropriate to do trees based on DNA and when to do them on protein sequences (basically, DNA-based trees are more sensitive to small divergences, and protein-based ones more accurate for large divergences). Examples of both could make a nice comparative study.

      Comment by gasstationwithoutpumps — 2010 July 19 @ 19:37 | Reply

  7. Briefly, I teach a high school biotechnology course and have taught AP Bio. I use bioinformatics in my units on phylogeny, protein structure and base sequence comparisons. We wrap bioinformatics around Cold Spring Harbor (beginning with Anastasia and the Romanovs) and thro several Bio-Rad Kits (the protein profiler and pGLO) and as students become more proficient in their own research such as genetic disorders like sickle cell, using STRAP or data mining to assemble their cloned sequences into a config.
    I would like more information training of teachers, keeping up to date with NCBI and new sites that develop, and assisting teachers in updating their lesson plans/labs (because it sounds like the labs submitted to the College Board will be obsolete before they get to the classroom)

    Comment by Linda — 2010 July 19 @ 20:32 | Reply

  8. I have taught AP Biology and Biology I for several years and in the last few years, I have incorporated bioinformatics in my classes. We started first with using BLAST to identify genetic disorder sequences, locations on the gene, size of the gene to create a genetic disorder brochure (this I have done in my Biology I class). From there in AP Biology we did a true case problem solving lab in which we traced the transmission of the HIV virus from a Dentist to his patients using Biology workbench to try to find all the sequences for the dentist and his patients (just do a search in the viral database with “Florida dentist” and you’ll see the all the sequences come up- dentist, local controls and patients). We then utilized their phylogram and sequence alignments to predict what was happening and then accessed the literature accounts of the case. This exercise ties in beautifully with the study of viruses and the immune system. In the evolution unit we used bioinformatics and phylograms again (Biology Workbench)to trace evolutionary trees using protein variations among organisms to show that some proteins are very conserved and others are not but the proteins that we use are ones that the students have knowledge of — hemoglobin b, actin, myosin, enolase, cytochrome c, amylase. We put up everyone’s phylograms and have them explain their findings and then they realize that they are not all the same in their conclusions. We couple this with a lab in which we work with blood sera from livestock and trace lactate dehydrogenase to see where it fits in the evolutionary tree (Modern Biology Lab, Lafayette, IN is source of blood sera and lab instructions). I also have a bear evolution lab in which we trace the origin of the panda bear.

    As you can see, I think there is a place for bioinformatics in the high school curriculum.

    Barb Burkhardt
    recently retired
    Zionsville Community High School
    Zionsville, IN 46077

    Comment by Barb Burkhardt — 2010 July 20 @ 05:46 | Reply

    • What a great assignment. I think I will try this with my Biotech kids next year.

      Comment by Jaime Lee — 2010 July 21 @ 06:47 | Reply

  9. I applaud your interest in expanding the awareness of bioinformatics in AP Bio curriculum. I have been teaching AP Bio for 12 years, after obtaining my Ph. D and doing a post-doc. I try to update my classes continuously and expand on the recommendations of the CB. The posts above are right on, and I agree that there are many places to incorporate bioinformatics into the curriculum. Since we are overwhelmed with a huge curriculum and not enough time, I would love updated, clear approaches available online. For example, the ENSI website is outstanding, and I have used versions of the molecular comparisons contained in http://www.indiana.edu/~ensiweb/lessons/p.tut.db.html several times. It would be helpful to have these activities updated and step-by step, dynamic tutorials included so that students can navigate it more easily with their teacher’s guidance. I also did an outstanding activity comparing allelic variants of superoxide dismutase 1 and exploring ALS. The activity was developed by Sandra Porter at Geospiza, however all the online support has disappeared. This summer, I am working alongside one of my students in a lab at UCSD studying and enzyme and screening for small molecule inhibitors. I was shocked to see how the databases have expanded and how many new, free, modeling programs and databases are available. This is an exciting time in biology and we would like to move forward with you in these explorations!
    Susan Domanico
    La Jolla Country Day School
    La Jolla, CA

    Comment by Susan Domanico — 2010 July 20 @ 10:52 | Reply

  10. I actually took a course at Clemson University this June learning about Bioinformatics and how to introduce it to high school science. I teach AP Biology, and I will be adding how to BLAST a gene, look for similarities, and the evolutionary implications to these similarities.

    Small steps at first, but as I get more used to the the software, I will do more.

    Chuck Conrad
    AP Biology & Physical Science
    Easley High School

    Comment by Chuck Conrad — 2010 July 20 @ 15:28 | Reply

  11. I’ve just been pointed to BEN the BiosciEdNet, a large collection of resources for biology educators. If ISCB builds a collection of resources for bioinformatics, we should make sure that they get included in this larger collection.

    They have supposedly just started a newsletter, which is included in the free registration for the site.

    Comment by gasstationwithoutpumps — 2010 July 26 @ 11:07 | Reply

  12. Chris Ludwig has a post about standards-based grading (SBG) for chemistry and biology. He is supposedly working on applying SBG to AP bio courses also.

    Comment by gasstationwithoutpumps — 2010 July 27 @ 15:26 | Reply

  13. AP-bio teachers are pleased with the “Kim’s site”. So if we are going to do anything, it might be worth providing it in that
    style and level of detail.

    Comment by gasstationwithoutpumps — 2010 August 27 @ 11:28 | Reply

  14. I have just been catching up on these posts. I’m a bioinformatics faculty and a former HS teacher (and former AP Biology student — way back) …..

    I’m reading that there are 3 types of support that ISCB might be able to provide:
    (1) training / updates for teachers: Creating resources that will give teachers background information and knowledge of certain bioinformatic techniques and how they might be used in the classroom? or how to choose among the myriad parameters and options
    (2) Resources which can be tied into commonly used sites (as described above); this will include tools and software which are applicable to HS Teachers and/or students.
    (3) Help developing laboratory modules which don’t add to the curriculum but which enhance a study of an already existing segment of curriculum.

    It also sounds like we should couple individual teachers / projects with specific Bioinformatics helpers from ISCB to create prototype solutions that we can test for effectiveness.

    I’m very interested in helping create tangible solutions or resources.

    Jim

    Comment by Jim Cavalcoli — 2010 September 6 @ 11:33 | Reply

    • I agree that the best approach may be to work with individual AP bio teachers to create new labs or exercises that support the teaching of AP bio. Pull from the teachers may work better than push from the bioinformaticians.

      I would be glad to assist an AP bio teacher also, and I’m sure we can find other bioinformatics faculty interested. I doubt that we’ll get much enthusiasm for creating resources, though, unless there is some evidence that the resources will be used.

      Comment by gasstationwithoutpumps — 2010 September 6 @ 12:34 | Reply

  15. We will looking forward for your AP’s future plans I think new labs or exercises that support the teaching of AP bio should be created. And more experienced should be appointed .

    Comment by scope of bioseoinformatics — 2010 September 16 @ 23:30 | Reply

  16. […] for AP bio teachers (I’m not one, but I had a professional need to communicate with them, see Bioinformatics in high school biology), someone asked We watched “Inner Life of the Cell” a few times during class last […]

    Pingback by Good questions « Gas station without pumps — 2010 October 14 @ 06:09 | Reply

  17. […] (ISCB) Education Committee would like to promote.  We’re particularly interested in any coördination with Advanced Placement or International Baccalaureate biology programs that could be made standard […]

    Pingback by Dolan DNA Learning Center Educator Workshops « Gas station without pumps — 2010 October 22 @ 19:03 | Reply

  18. […] I’m not a teacher of AP Bio, but I’m part of a task force trying to find ways to get bioinformatics into the AP bio curriculum, and I’ve found the discussions of biology education on the blog enlightening.  I regard it […]

    Pingback by 2010 in review « Gas station without pumps — 2011 January 2 @ 12:51 | Reply

  19. […] the International Society for Computational Biology would really like to see: an integration of bioinformatics tools into introductory biology courses. The draft of the proposed changes has no mention of bioinformatics and “comput*” finds […]

    Pingback by Advanced Placement Bio changes announced « Gas station without pumps — 2011 January 8 @ 10:19 | Reply

  20. A site to place materials:
    http://groups.yahoo.com/group/apbioarchive/

    Comment by gasstationwithoutpumps — 2011 January 13 @ 17:52 | Reply

  21. […] a member of the ISCB Task Force trying to get bioinformatics into high-school biology, I would love to be able to point teachers to web sites with lesson plans for bioinformatics […]

    Pingback by Adding bioinformatics to AP Bio « Gas station without pumps — 2011 February 5 @ 09:43 | Reply

  22. In the Netherlands NBIC (Netherlands Bioinformatics Centre) is working on the project bioinformatics@school.
    This project includes:
    1. Bioinformatics practicals that are brought to classes (DNA-labs on the road, read more on: http://www.dnalabs.eu). The lessons include BLAST, ClustalW2 and Yasara.org.
    2. A website containing all sorts of educational material in bioinformatics. We have a English website http://www.bioinformaticsatschool.eu (which needs an update) and a Dutch website http://www.bioinformaticaindeklas.nl (which is getting an update).
    3. Teacher trainings to make your own bioinformatics lessons(read more on http://www.nbic.nl/education/high-school-programmes/bioinformaticsschool/teacher-training/)

    Our idea of getting bioinformatics into high schools is by showing that bioinformatics tools can make abstract concepts, like DNA and proteins, more visible and concrete. I already gave a couple of workshops on this subject and the attending teachers all told that they see the relevance of bioinformatics to improve their lessons and are willing to use bioinformatics in their class.
    When teachers are convinced of the relevance, students will follow.

    I am trying to set up a small international network of people involved in bioinformatics education (e.g. educational research, development of educational material etc.). If you are interested to meet others working in high school education of bioinformatics, please let me know! Send me an email: http://www.nbic.nl/en/about-nbic/who-is-who/pages1/1/details/hienke-sminia

    Comment by Hienke Sminia — 2011 March 30 @ 04:00 | Reply

  23. […] Bioinformatics in high school biology […]

    Pingback by Blogoversary « Gas station without pumps — 2011 June 5 @ 10:51 | Reply

  24. […] 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 […]

    Pingback by Resources for bioinformatics in AP Bio « Gas station without pumps — 2011 July 23 @ 14:16 | Reply

  25. […] Bioinformatics in high school biology […]

    Pingback by Second Blogoversary « Gas station without pumps — 2012 June 2 @ 18:15 | Reply


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