Curriculum

Links to resources to annotate P. heparinus and thousands of other bacterial genomes.

Geneva College Pedobacter Genome Annotation Manual

GENI-ACT http://geni-act.org/

GENI-ACT allows collaborative genome annotation on 2,775 bacterial genomes. Researchers or students can collectively suggest changes to an existing genome with supporting evidence. Changes can be ported back to genbank by exporting to a sequin file format.

GENI-ACT also has ported the education components from IMG-ACT. Teachers can assign students work to be completed in a lab notebook that is integrated with the classroom

GENI-ACT annotation resources - http://geni-act.blogspot.ca/p/welcome-to-geni-act-teaching-resources.html

MGAN http://mgan-network.org/

This is the homepage of MGAN (Microbial Genome Annotation Network).  The purpose of MGAN is to promote and provide training in the use of the online bioinformatics platform GENI-ACT.

 

Below are some protocols for Dr. Austin’s research

PCR buffers

Glycerol Stocks

Below are protocols for Dr. Essig’s Research

Recipes for culture medium

Links to other bioinformatic sites which focus on particular genomic features

Microbesonline http://www.microbesonline.org/

Microbesonine is an integrated portal for comparative and functional genomics.  It is an easy way to find predicted operons for bacterial genomes.  There are over 3,700 bacterial genomes in the database.

RegPrecise http://regprecise.lbl.gov/

RegPrecise is a tool to facilitate identification and reconstruction of various transcriptional regulons in bacteria using a comparative approach.  A regulon is composed of transcription factors and a set of operons or genes.

PanDaTox http://exploration.weizmann.ac.il/pandatox/1_0/home.html

PanDaTox is the Pan Genomic Database for Genomic Elements Toxic to Bacteria.  Using PanDaTox, educators or researchers can search for toxic genes and toxic non-coding elements in their bacterial genome of interest.

TADB http://bioinfo-mml.sjtu.edu.cn/TADB/

TADB is Toxin Antitoxin Data Base.  TADB is great resource to search for Toxin-Antitoxin loci in over 900 genomes. TA operons play important roles in bacterial stress physiology and intercellular competition.

BAGEL http://bagel.molgenrug.nl/

BAGEL is an web based bacteriocin mining tool. Bacterocins are peptide antimicrobials secreted by bacteria.  Users can find search hundreds of genomes which contain genes for bacteriocins and associated genes.  Often the bacterocin peptides are novel and provide unique opportunities for discovery based learning.

Resources for inquiry based learning

Evaluation of course based (CURE) and faculty research lab based (URE) research experiences.  Linn, M., Palmer, E., Baranger, A., Garand, E. and Stone, E. Undergraduate research experiencess: impacts and opportunities Science 347, 2015.

A comprehensive overview of the how genomics and bioinformatics can enhance learning in a variety of course settings.  This article features the bioinformatic platform known as IMG-ACT which has been ported and updated to GENI-ACT.  Ditty, J.L., Kvaal, C.A., Goodner, B. Freyermuth, S. K., Bailey, C. et al. Incorporating genomics and bioinformatics across the life sciences curriculum.  PloS Biol 8: e1000448, 2010.