2015 workshop flyer - Dinsdale Lab



2015 workshop flyer - Dinsdale Lab
Invitation to attend the Faculty working group:
Sequencing Technology Education using Microbial Metagenomes (STEMM)
San Diego State University 7 - 12 of June 2015
Working Group Synopsis
The overall goal of the Sequencing Technology Education using Microbial Metagenomes workshop is to
establish genome sequencing and analysis as a component of undergraduate life sciences education by
providing educators with an opportunity to use next generation sequencing technology at the SDSU
Undergraduate teaching facility and enable the networking of faculty to discuss how best to integrate
genomic technology into the life sciences curricula. The workshop will build on our ecological
metagenomic class, which has become a highly accessed publication in BMC Genomics (2013 14:600).
We seek to facilitate the development of similar courses across other universities by providing 1) training
on various sequencers using DNA from the attendees’ own research, 2) training on bioinformatics tools,
3) potential implementation of similar classes at the attendee’s own university, and 4) discussions on
building assessments for genomic courses. For this project, expected outcomes include establishing a
network of microbial metagenomic undergraduate educators that can introduce genomic sequencing and
analysis into undergraduate classes, collaborate on analysis of the data and assess the effect on student
learning. We will hold the workshop from the 7th to 12th of June, 2015 at the San Diego State University
Sequencing Facility in San Diego, California.
Leaders in the workshop will include:
Elizabeth Dinsdale, an Associate Professor in Biology at SDSU, researcher in microbial and viral
metagenomes from coral reefs, kelp forests, oxygen minimum zones and has sequenced the California sea
lion with the help of undergraduate researchers.
Robert Edwards, an Associate Professor in Computer Sciences at SDSU, researcher in bioinformatics
analysis of microbial and viral metagenomes including the development of online tools such as
MG_RAST, TAG cleaner, Prinseq, Phantome, Scaffold Builder and many others.
Marilee Bresciani Ludvik, Professor in the Department of Administration Rehabilitation and
Postgraduate Education at SDSU and a researcher in evaluating student learning and assessment to
improve higher education outcomes.
We would like to invite Faculty and Postdoctoral Researchers to participate in our workshop. Preference
will be given to attendees from institutions without access to sequencing technology, and those that would
like to use next generations sequencing technology in the classroom.
Please e-mail to Elizabeth Dinsdale ([email protected]) for additional information
and application form.
Tentative timetable
June 7th - Arrive in San Diego – meet and greet 6pm
June 8th - 9 am – 6 pm start DNA extraction, Library preparation
June 9th- 9 am – 12 noon – Assessing student learning objectives
1 pm – 6 pm continue sequencing
June 10th - 9am – 5 pm Sequencing – lectures on metagenomics
5 pm – 7pm question and answer session on Assessment
June 11 - 9- 6pm Sequencing – lectures on bioinformatics
7pm Dinner
June 12th - 9-6pm Bioinformatics – morning session – final discussion afternoon session
Costs – Each application will be sponsored for travel and accommodation up to $1000 and sequencing
costs up to $1000.

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