Laura Hoopes Pomona College

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Genomics at Pomona College

Course Overview

 There was already a Bioinformatics class at Pomona College taught by Andre Cavalcanti and a Molecular Evolution class taught by Daniel Martinez when I joined GEP.  Bio 170 is focused on Drosophila with a short general introduction to tools n each section.  When the Finishing is complete, I discuss comparative evolution of various types of proteins such as ATP synthase, ribosomal proteins, and glycolysis enzymes, across broad swaths of taxonomy.  The course doesn't have stringent prerequisites beyond introductory biology of the genetic/biochemical flavor.

In later years, I have used GEP materials for annotation as a unit in the laboratory of Bio 164, Genetic Regulation in Eukaryotes, asking students to annotate a fosmid working individually as one project among several during the laboratory time. 

Implementation

  In spring semester, 2009, I offered the course and three students registered. Ordinarily a course with fewer than five would have been cancelled, but I promised to alternate years with it, it required training and I was afraid I'd forget the training if I couldn't teach the course, and my TA had also been trained. 

I decided to begin with annotation after a conversation with Vidya at ASCB in December about her course, and recalling how much more approachable annotation was for me personally.  The biggest problem with that decision was the timing of the finishing read-calling was too late to be right for Wash U, but Sally graciously allowed us to do it on our original planned schedule and she had the sequencing reactions done in her lab rather than the sequencing center.  The students really got into the annotation and although they originally were stand-offish to each other and just called Jeff or me to help, by the end of that section they were cooperating with each other and sharing new bits they'd sussed out. 

In the installation of Consed, we struggled, but every time it snagged, Wilson was able to help our ITS guys figure out what to do.  I am not a Unix user except for Consed, so I was just a cheerleader.  It's a good think that Jeff and I started trying to get the program up and test it very early, even before the first lab.  By the time we used it, it was mostly OK, although we had problems with it freezing during lab twice.  Finally the Unix ITS man installed it on a few extra computers so if it went down we'd have a backup.  I helped them figure out the new bio mac lab has different operating systems on about half of the computers (hmm, what a help!)

The students have been very positive throughout the processes, and I think they're really excited about producing new data for the world (for GEP then the world).  Cool class!

I took a Bioinformatics Institute run by Joint Genome Institute and Amer Soc for Microbiology and will use material from it in the last few weeks of the class when finishing is over.  I can't move too far into Molecular Evolution, but want to give some perspective for those who will not be taking that class.


In the use of GEP in Genetic Regulation laborartories, I've used just annotation, not finishing, to save time.  Students find it easy to approach this topic since they are famliar with some of the software from introductory courses.  The interactions between students, colloborating to solve problems, seemed to be facilitated by my having chosen fosmids with some overlaps, so they could include parts of the same genes.  I always encouraged students working together during the computer lab sessions and they also told me they worked together on their time "alone" in computer lab. 

Lessons Learned and Future Plans

  I'll offer Bio 170 next in fall, 2010 after I return from sabbatical.  Unless the plans have changed, I can't do finishing in the fall, so I'll combine annotation with more about Drosophila sequences in general, some evolutionary perspectives, more about the proteins in their annotated sequences perhaps or about some particular Drosophila proteins I'll choose. 

I used Gibson and Muse, and liked the discussion of sequence improvement with shots of Consed to encourage the students to think they were doing what 'real' finishers do.  I only used the first two chapters, though, so I might not require the text next time.  I really though parts were unclear, for example the Hidden Markov Model part was just confusing, not enlightening.  I have a much better paper on that from the Bioinformatics Institute I attended. 

I've learned that long lead time for Consed installation and testing is really required.  Also that Wilson is a great resource, but I feel he's probably off to grad school soon so another great resource needs to be discovered. 

I've also learned how very enthusiastic the students are about this type of learning--I predicted that but it's nice to see it confirmed. That has continued in 2010 and 2011 classes using only a single annotation unit in Bio 164.

Syllabus for Bio 170: Drosophila Genomics 

Biology 170: Drosophila Genomics, Spring, 2009
Prof Laura Hoopes, SVBI 021, x77438, lhoopes@pomona.edu
TA: Jeffrey Lin

This is a hands-on computer lab based course in which each pair of students or each student will “own” two sequences from Drosophila. Students will annotate all the genes in the first one and finish the DNA sequencing of the second one. In order to provide a rationale for this project, as well as background materials for the students, this course will include lectures, reading, and discussion on DNA sequencing, finishing of DNA sequences, and annotation, repeated sequences, and chromosome structure.

Both class and lab are held in Seaver South 227, the computer lab for biology. The textbook is A Primer of Genome Science by Gibson and Muse, third edition, and was published in 2009.
The borderline between class and lab is blurred for this course. There will be many times when you’ll work on your project during the ‘class’ hours from 11-11:50 M and W. The lab is 1:15-5 on M, and will almost always be either preparatory exercises towards a project or your own independent work. You need a spacious lab notebook and a thumb or flash drive to store many screen shots in order to properly complete the work in this class. The homework exercises, class participation, lab notebook, submission of data to Wash U, and the two major lab papers will be graded. There are no examinations.

The study carried out by this class is coordinated with the Genomics Education Partnership http://gep.wustl.edu/ through Professor Sarah Elgin, a Pomona alumna, now at Washington University, St Louis. Her laboratory group will collect our information and that of GEP partner schools all over the country, finishing and annotating sequences from Drosophila dot (small) chromosomes in different species. Students are offered co-authorship when published, as long as they participate in the writing, which requires that they keep Prof Laura Hoopes up to date on their email, phone number, and snail mail address so she can let Dr. Elgin know when the paper is being prepared in a year or two. If you are a coauthor, they will send you drafts for your comments. Please carefully review the parts that refer to your fosmid clones to make sure they agree with your findings, and if not, let them know.

A paper already published based on GEP student work is posted on the GEP web site at http://gep.wustl.edu/ . Click on the Slawson et al., 2006 citation along the right side to download a copy. Please print it out and bring it to class and lab with you, as it will be useful in solving your own problems of annotation and sequence.

Materials for this course will be posted on Sakai under Biology 170, so please make sure you can access the course site at https://sakai.claremont.edu:8443/portal. If you have trouble getting to the site, contact the Pomona ITS Help Desk at x18061 or Mary McMahon at x 18774.

Before the first lab, I want you to have taken two items posted on the GEP site under Assessment. The first one is the “Pre Course Survey-Live” and the second is the “Pre Course Quiz.” Please do not be concerned if you don’t know how to answer some of these questions; you’re supposed to show you’ve learned something in the class by your responses on the Post Course Quiz compared to this Pre Course Quiz! By taking these items, you will be entered into a drawing for a prize gift card. If you object to taking them, because we hope to publish the results, we may not require your participation. The results are anonymous and are used to study how well this type of course provides an experience similar to research for students. It’s of interest nationally, as well as positively impacting the GEP’s chances to be funded by grants. The national results in terms of learning outcomes will be published but the names of the students involved will not be included in the publication(s).

Class Schedule:
Weds, January 21, 2009
Class introduction and logistics. Introduction to purpose of experiments part 1.


Mon, January 26
Reading: Gibson and Muse Section 1: Genome Projects. Emphasize pp1-12, 28-39.
Introductory presentation, part 2. After presentation, you can access this Powerpoint on Sakai. Please take the assessment exercises from the GEP site before lab unless you object to them. If no one from Pomona takes them, we probably won’t be invited to participate in GEP in the future.
First lab:
Gene prediction (annotation) begins. Presentation on BLAST based on material by Buhler at WUSTL, introduction to resources on the internet, introduction to Drosophila browser, beginning of first practice exercise.

Weds, Jan 28
Reading: Handout on BLAST from lab; G&M pp 90-91, Slawson et al paper downloaded from GEP site.
First discussion of Slawson paper, continuation of first practice exercise.


Mon, Feb 2
Reading: Gibson and Muse on Annotation, pp 95-130. Emphasize 98-103,113-119, but skim the rest to get familiar with terminology.
Gene prediction: Issues and resources in finding genes.
Second lab: Completion of first practice exercise. Introduction of second practice exercise and beginning to work on it.

Weds, Feb 4
Report on first practice exercise due at start of class.
Work on second practice exercise.


Monday, Feb 9.
Work on second practice exercise in both class and lab; complete exercise 2.
Towards the end of lab, receive your novel fosmid, discussion of strategies and ideas useful in approaching an unknown fosmid from fruit flies. Handout on the report you’ll write on Annotation, along with the other requirements for submitting data to GEP electronically; discussion of what is required for this project.

Weds, Feb 11
Cancel:Report on second exercise due at start of class.
Reading: Gibson and Muse on Repeats in Annotation pp 104-113.
Repeats and how to avoid them at some points and include them at other points in your analysis.
Added: Handout on writing the report for annotation.

Monday, Feb 16
Reading: Handout on Clustal alignment software. G&M 119-130.
Introduction to the use of Clustal to examine phylogenetic trends. In your annotation project, you’ll use Clustal to analyze one feature (gene or regulatory element such as promoter or enhancer) in its evolutionary perspective.
Continue your annotation project.

Weds, Feb 18
Reading: Assigned final reports from Wash U student annotation projects posted on Sakai.
Discussion again of writing the report for the annotation project, and discussion of the reports in terms of how well they accomplish the objectives assigned.


Monday, Feb 23 Continued work on annotation projects.

Weds, Feb 25 Continued work on annotation projects.


Mon, Mar 2 Written annotation report due at 11 AM.
Ten minute Powerpoint oral presentation of annotation reports at the times assigned.
Reading: G&M chapter 2, pp 65-95, especially concentrate on pp 65-83.
Lab: Orientation to finishing project. DNA sequencing chemistries. Video tour of the Wash U sequencing center. Introduction to Guide to Consed. If time, handout Using Consed Graphically and begin Consed practice.

Weds, Mar 4 Presentation of Phred, Phrap. Work on Consed practice.


Mon, Mar 9. Reading: G&M reread 68-79; notice several screenshots from Consed.
Discussion of strategies in finishing sequences. Directions for ordering reads later on your own fosmids. Continue in both sessions to complete the Consed Finishing Homework assignment.
Tues, Mar 10 by 5 PM: Hand in the Consed Finishing Homework assignment.

Wed, Mar 11: no class, LH at bioinformatics institute training back east
Mar 16-20: Spring break, no class

Mon, Mar 23. Discussion of finishing report requirements, the finishing checklist, and submitting data to GEP.
Lab: Receive your file for your finishing fosmid. Begin the examination of it via Consed, Phred, Phrap. Order reads Weds.

Weds, Mar 25. Discussion: Review assigned finishing project reports from Wash U from Sakai; discuss contents of good report.
Student calls vs Autofinish calls: do you need to fix the ends of the contig? Resolving order of contigs, tearing and rejoining.
Order first set of reads.

Mon, Mar 30. Using the restriction digests to check your results. Discussion of data available and possible confounding problems (e.g. vector sequences).
Lab: If results are available (and they may not be until Tues or Weds), using the new reads you’ve ordered, try to get a final assembly of your fosmid.

Weds, Apr 1. Work on finishing fosmid; order final set of new reads.

Mon, Apr 6 Continue in both sessions to work on fosmid analysis.

Weds, Apr 8. Continue to work on fosmid analysis.

Mon, Apr 13. Continue to work on fosmid analysis.

Weds, Apr 15
Mon, Apr 20 Complete fosmid analysis; work on reports.

Weds, Apr 22 Finishing reports and lab notebooks due at start of class.

Mon, Apr 27 Comparative genomics: overview. Papers from the literature will be posted on Sakai.
Lab will be a field trip to a local sequencing center.

Weds, Apr 29 Comparative genomics: primates, humans. Papers from the literature will be posted on Sakai.

Mon, Apr 4 Lecture/discussion. Comparative genomics: regulation in microbes, plants, and animals. Papers from the literature will be posted on Sakai.
No lab today.

Weds, Apr 6 Last day of classes; Required discussion of class structure and function, class evaluation, refreshments.

STUDENT WORK

In 2009, each of the three students in Bio 170 wrote both an Annotation Report on a contig from D. erecta and a

Finishing Report on a contig from D. grimshawi.  Selected reports are posted below.

media:Annotation_of_Contig_14.pdf

Alyssa Ward Annotation

Noah Strait Annotation