Amy Hark, Muhlenberg College

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Amy T. Hark, Ph.D.
Associate Professor of Biology
Co-director of Biochemistry
Muhlenberg College

updated 7.23.17

I have had research/independent study students working on annotation projects for the past eight years.  Students generally spend the first 4 weeks of the fifteen-week semester doing background reading and practice exercises with BLAST and annotation, which seems to prepare them well for working on their own fosmids/contigs.  Specifically I have used the following GEP curriculuar materials:
- An Introduction to NCBI BLAST is given to students initially as a reference/review.
- I use the Powerpoint including Introduction to ab initio and evidence based gene finding to introduce both background on the dot chromosome and methods of gene annotation.
- Students tackle A Simple Annotation Problem before claiming a project of their own.

In Fall 2016, I integrated GEP annotation into a capstone genomics course.  In collaboration with Justin DiAngelo, I adapted GEP and other materials to develop a set of guided inquiry exercises to prepare students for their annotation projects.  These exercises are available on the private wiki for GEP members (July 2017 workshop, Sun 11am talk).  The syllabus for my course is here [1].

We are currently using electronic lab notebooks (Lab Archives platform), which I find works particularly well for this type of research.  I wanted to preserve the integrity of the record (all changes are saved and time-date stamped) but allow students to easily capture their work in a digital form.  This platform has the additional advantage of allowing me and research students to see each other's notebooks (if desired) from anywhere with internet access.

I am happy to share ideas with interested colleagues so feel free to contact me at