June 2010 Alumni workshop

[cshaffer]

This thread is for documents and discussion of topics to be covered in the Alumni workshop scheduled for June 4th -6th.

Please post your thoughts here for all to see – join the dialogue, regardless of whether you will be able to attend, so we have the broadest possible input!

[cshaffer]

Alexis Nagengast sent this in:

Is there any way we could get a primer on deep sequencing or how to access and use the modENCODE data? I haven't had time to figure out how to do it myself but I think a little lesson could go along way and I'd like to incorporate it into my classes.

Thanks,

Alexis

Alexis Nagengast, PhD
Assistant Professor
Departments of Chemistry and Biochemistry
Widener University
One University Place
Chester, PA 19013-5792

[cshaffer]

Sally's response:

Thanks for your note. We have just posted our new “tour” on next-generation sequencing on the website! You can access this from the bottom of the center panel on the home page. This illustrates how the Illumina and 454 sequencing technologies work, and the impact on sequencing costs etc, with some discussions with Elaine Mardis and Rick Wilson on the impact. We will be mailing a DVD with this to all GEP faculty in the next couple of weeks. Libby Slawson and I are starting to work on an assessment piece for this video, and will appreciate your feedback. I hope this serves at least in part as a “primer on deep sequencing.”
And it would be good to have an introduction to the modENCODE data. I’ll make a tentative note on the workshop agenda, and get together with Chris and Wilson to see what we can work out.

[cshaffer]

Dear colleagues,
We need to review and revise our templates for gathering data on how we are using GEP materials (instructors form) and for gathering data on our institutions (intro & inst survey form). These forms were used to gather data for the CBE paper (Shaffer et al 2010), and data of this sort will be needed for our next paper. Take a look and post your critiques and ideas here, or bring with you to the workshops!
Thanks, Sally

P.S. Both forms are in Word ".doc" format. If you cannot open Word documents please send Chris and Wilson an email requesting a compatible format.

[cshaffer]

I have created a wiki page on the faculty only section of the wiki to post those items too large or cumbersome for inclusion here. The page is:

http://gep.wustl.edu/restrictwiki/index ... i_Workshop

Since there have been several requests to add a introductory exercise on using Clustal. I have posted several version we have produced locally (all should be considered "Draft" quality) that could be used as potential starting points – one exercise based on phage proteins, another based on fly proteins, and a third based on yeast. If you have something similar, please post for this dialogue, and we will have a small working group on this at the Workshop.

Additionally, Bob Moss recently attended a workshop to learn more about DNA Subway, the plant genome annotation system developed by the CSHL Dolan DNA Learning Center. His impressions are included there as well.