iPlant Workshop/DNA Subway Day 2

Summary of DNA Subway:

Red Line - construction of gene model using blastx, blastn and other programs.

Yellow Line -  identification of related genes in sequenced genome.
Blue Line - using wet-lab data to draw phylogenic tree for both plants and animals.

Notes from the workshop link

Me w/ Workshop Coordinator, Dr. Ania Wieczorek  and Lecturers/

 Some of the participants of the workshop

My hibiscus plants' DNA in Lane 2 (7A: red) and 3 (7B: white/pink). 

Yes, both of them show up so this means they can be sequenced. 

We had a really short yellow line session so I really need another workshop session to fully understand its function.  Red line although covered extensively on the first day (and part of second day) is not for all students.  It probably will be a good project for students who are planning independent research.  Or I can consider it as a my side research project with students working on it over the years. 

Reflection: Did I reach my goals?

My goals for this workshop:

1. Look for new curriculum ideas for biology class and biotech class.
Yes.  I am going to utilize the blue line for my biology and biotechnology students.  Only problems is money involved in extracting, amplifying, analyzing and sequencing DNA.  I have figure out what I need to run the project then write up a grant.  I also need to be in contact with Jason.  I think they might help me with the initial start up reagents.  I need to start simple and then branch out into NYC project shown in sites like dnabarcoding101.org .

I gained so much not only from the lecture sessions but from talking to others about some possible curriculum ideas.  Sally Irwin from Maui UH maui campus was one of the best sources.   I learned about BBC program Ghost in Genes which discusses epigenetics and that it is inheritable.   I am planning to show the program to my students after they learn about genetics (that they is beyond the code).

I also learned about geospiza.com, a website that teaches bioinformatics.  It will take time for me to learn the site so it will be biotechnology class next school year. 

2. Look for biotechnology independent research idea.
I have couple of idea:  Red line and Blue line.  Red line would be for long term and blue line related projects can be view at http://www.urbanbarcodeproject.org/.  Likely, I will work with blue line in 2013-2014 year biotechnology class.

3. Network with scientists and teachers at high school and college.
Yes.  I had so much fun learning about what all the teachers were doing at different levels of school.   From high school to private 2-year college and 4-year universtity, it was so much fun to talk to them about what they are researching and teaching. 

I've achieved my goals.  To follow up, I need to prep to incorporate blue line lessons and Ghost in Genes video into my curriculum.