Making discoveries in the open: doing digital biology with the class

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Sandra Porter

Would you like to have some fun playing with chromatograms and helping our class identify bacteria in the dirt?

This quarter, my bioinformatics class, at Shoreline Community College, will be working with chromatograms that were obtained by students at Johns Hopkins University, and graciously made available by Dr. Rebecca Pearlman. (See see "Sequencing the campus at the Johns Hopkins University" for more background.)

We are going to do a bit of metagenomics by using FinchTV and blastn to identify the soil bacteria that were sampled from different biomes and then use an SQL query that I wrote and stored in our iFinch to summarize the results.

This image shows where the samples came from.

If you'd like to play along, send an e-mail to me at digitalbio at gmail dot com with your school and contact info and I'll send you information for logging in as a guest. I'll be posting instructions here, throughout the course. I'll leave the guest accounts active until mid November.