News from 2010 Alumni Workshops

Updates and news from the GEP alumni workshops
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Joined: Sun Feb 04, 2007 7:41 pm
Location: Washington University in St. Louis

News from 2010 Alumni Workshops

Post by wleung » Fri Aug 27, 2010 7:40 pm

Dear GEP colleagues,

Good news! Wilson’s paper on the D. virilis comparison is now available as a pdf, which I have attached. We have also mailed everyone two print copies.

Projects: I’m hopeful that with an organized effort this year we can finish up the D. grimshawi and D. mojavensis projects, giving us the data for the four-species analysis. Wilson has all of the needed Drosophila projects up on the GEP website now. Based on the Alumni workshop discussion, we are continuing to generate D. erecta projects as well, as this annotation is more accessible for many students. (Remember that D. erecta is much more closely related to D. melanogaster, so the genes are pretty similar, with most exons conserved.) So the research priority is to work on D grimshawi and D mojavensis projects, but if you need to use D. erecta for pedagogical reasons, we have projects posted. Note that if you would like your students to be able to carry out a reconciliation process after completing their initial annotation, just claim adjacent clones; they will overlap significantly, and students with overlapping clones can compare their results in the region of overlap.

Curriculum: Please be sure to enter material and/or update your entries describing your courses on the public wiki Table of Faculty. We are also getting some nice contributions to the Teaching Materials on the wiki – more would be welcome! Chris has revised the Annotation Instruction Sheet to provide a more specific hierarchy for decision making – for example, which should get more weight, using a high probability splice site, or conserving exon length? See the very end of that document for the one-page summary. And Jeannette has prepared a nice annotation workflow diagram, which is now posted on the Annotation Curriculum page.

At the Alumni workshop, we decided we needed to work on the following:

1. Glossary: a good list is posted on the wiki under the June workshop. Volunteers needed to review so we can post.

2. How do you introduce “genomics” to students – to help them see the interest, power of the approach, relevance? Volunteers needed!

3. How do you introduce the significance of the fourth chromosome? SCRE will annotate and post slides from the four ppt talks that she gives to her students, covering the complexity of genomes (repeat sequences etc), chromatin structure, heterochromatin structure, fourth chromosome.

4. Homework #1: can it be simplified, made more accessible? Volunteers needed.

5. Using Clustal: Susan Parrish will post her introduction; other volunteers?

6. How do you file a report when you find no evidence of a gene in your project? What sorts of evidence that we would like to see in support of such a claim? How do you document a false positive? Wilson has updated the report form to specify the documentation needed.

7. Synteny – what’s the best approach? Chris Shaffer is preparing a one-page guide.

8. Can we prepare short modules – 5 hr, or 10 hr of instruction plus lab – outlining a strategy and what one might be able to accomplish? Jennifer Myka and Joyce Stamm are preparing a framework for this.

If you already have generated curriculum materials that address one of these needs, please share them with us by emailing to Chris Shaffer (; we will review for consistency with the GEP web-posted materials, and put on the wiki under Teaching Materials. If you would be willing to work with a small group on one of these challenges, please let us know by adding a response to this thread on the Forum.

Assessment: The improvements to the survey and new quizzes are ready to go – thanks to all who worked on these this summer! I am awaiting IRB approval (for human subjects research protection) which I must have before we can post these. Note that you must then obtain IRB approval for your students on your campus. Remember we decided to go to an A/B format for the quizzes – students will be randomly given one or the other for their prequiz, and the other for their postquiz. A problem is to connect the prequiz from a student with their postquiz. The Washington University IRB turned down the idea of keeping a record of the student identifier, so instead we have asked for approval of a system where we ask the student to type in their name, but it is immediately encrypted. We shall see if that gets approved. Until the new system is approved, the old system will remain posted – but if you are teaching this fall semester, and have not yet done the survey/quiz, wait a week or so to see if we can get the new one approved quickly.

Remember that our goal is to have all GEP students complete the precourse survey and precourse quiz at the beginning of your course, and the postcourse survey and postcourse quiz at the end of your course. These are posted on the GEP website; use the “live” survey. We do not need any control students for the survey (the SURE students are the control), but please try to recruit a group of control students for the quiz. Control students should be a group of comparable class standing who have completed the prerequisites for your course, but are enrolled in a different course. That course could simply be on another topic, could have a lab or not – Dave Lopatto is interested in a variety of control students, so any such alternative is fine – you will be asked to describe the group on your faculty report at the end of the year. Remember that under the rules of research, you cannot give student grade points or bonus points for participating in the survey and quiz. You can point out that we have a “thank you” raffle for a $25 book certificate (five are awarded for the survey, prequiz, and postquiz, each). You can give them food or other token as a thank you! Bribes are OK, but it can’t be connected to the course grade. I get the greatest participation by taking 20-30 minutes at the end of the class, when the computers are open and on the internet, and asking the students to go to the web site to take the survey and quiz right then. They can do whatever they want – but given this request and immediate time to do it, I usually get around 14/15 participating.

Local clusters/workshops: There was clearly ambivalence about running local GEP workshops staffed solely by local faculty and students. However, there are clearly some geographical areas and some academic clusters where is would be economical to have a GEP workshop at that site, saving travel costs if not housing costs. After considerable discussion, we decided on the following:

1. There will be at least three GEP workshops for new faculty and TA’s in the next year – June 2011, August 2011, and January 2011 – with two of these in St Louis and one elsewhere (off-site). A workshop should have 12-18 participants. The goal of the off-site workshop will be the same as an on-site workshop – to generate participating GEP members. Sally, Chris and Wilson will travel to and lead the off-site workshop. An off-site workshop could be annotation only or annotation and finishing.

2. We will start discussions this fall with GEP members interested in hosting a GEP workshop at their site. We can do an off-site workshop anywhere that a) we have enough GEP members (and their students) to serve as TA’s (need one TA for every 2-3 new participants), and b) we have enough interest to get 12 –18 new participants. Hosts would benefit by being able to nominate colleagues at their or nearby institutions to participate, achieving vertical integration and/or building a local support group. We also have a modest honorarium written into the budget for hosts, to compensate (in part!) for your time.

3. GEP funds will cover travel for GEP staff, lunch and coffee break costs on site, and if needed, overnight hotel costs for participants. However the goal would be to find circumstances where travel costs are minimized, either because the participants can drive in (or take public transportation) or are coming together for another meeting. We will need to find host institutions that are willing to provide a Mac computer lab and coffee/break-out space at little or no cost.

Sound reasonable? Contact me as interested! And of course, if we are able to generate a workflow pipeline that can handle different genomes, there will be the possibility of a workshop on a different organism (for example, we might do something joint with the Chlamy project).

Cheers, Sally

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