MGAN training workshop - Phoenix College, Phoenix, AZ

January 6-8, 2016

Phoenix College:
Campus address:  1202 W Thomas Rd, Phoenix, AZ 85013, (602) 285-7800


Dr. Anil Kapoor
Biology Faculty, Phoenix College
Dalby Building (602.285.7983), 1202 W Thomas Rd, Phoenix, AZ 85013

Dr. Bronwen Steele
Biology Faculty, Estrella Mountain Community College
3000 North Dysart Road | Avondale, AZ 85392 | 623.935.8000

Image taken from the January, 2015 MGAN workshop in Nashville, TN.  Dr. Brad Goodner (facilitator) and participants.

ADVANCED REGISTRATION IS REQUIRED for the workshop - The deadline to register has passed.


Workshop Facilitators

Dr. Tim Beagley (Website) - Salt Lake Community College, Salt Lake City, UT;

Dr. Jayna Ditty ( Website), University of St. Thomas, Saint Paul, MN;

Dr. Joanna Klein (website),University of Northwestern, St. Paul,

Stephen Koury (website)  University at Buffalo, Buffalo, NY (

Dr. Tara Luke (Website) - Richard Stockton College, Galloway, NY;

Dr. Lori Scott (Website ) - Augustana College, Rock Island, IL; or (309) 794-3440 (emergency contact:  cell phone - 5636760797)




Pre-workshop activities


Annotation video

BLAST activity

TMHMM activity

Answer keys

DAY 1 (9AM-4PM)

 Continental breakfast (8:00am)

 Morning session (begins at 9am)

Meeting the workshop facilitators and participants


Introduction to the workshop (Lori Scott)

·       What is an annotation?

·       Brief introduction to GENI-ACT and the study system

·       Short activity on protein structure


Lori's Powerpoint (entire workshop)

Sample GENI-ACT annotation (SecY)

Module 1 – Using the GENI-ACT lab notebook (Joanna Klein) 

Guest access to computer:  username: pc\pcguest14

Module 2 -  Sequence-based Similarity:  BLAST & CDD (Tim Beagley)


 BLAST powerpoint slides

Module 2 -  Sequence-based Similarity:  T-Coffee & Weblogo (Steve Koury)



Afternoon Session (1:30pm)

Module 3 – Cellular Localization  (Jayna Ditty)


Module 4 - Alternative start codon (Joanna Klein)


 Possible example of alternative start (See T-coffee alignment and Weblogo)

 Module 7 - Paralogs (Tara Luke)



DAY 2 (9AM-4PM)

Continental Breakfast (8am)

Morning Session (9am)


Because we will not get to some of the modules, here are completed lab notebook pages for the three genes used in this workshop.

Module 8 – Horizontal Gene Transfer analysis

·       Phylogenetic tree building (Tara Luke)

·       Operon & %GC 

Examples of how GENI-ACT is integrated into undergraduate courses

·       Tim Beagley Integrating Genome Annotation in a Community College Lab Class

  Tim's project website


Afternoon Session (1:00pm)

Module 5  - Structure-based similarity (Lori Scott) - focus on PFAM (Lori's PowerPoint slide - Click HERE)

Examples of how GENI-ACT is integrated into undergraduate courses

·      Steve Koury 

Instructor resources on GENI-ACT (Tim Beagley)

Steve's instruction manual



Continental Breakfast (8am)

Morning sessions begins at 9am

Module 6 – Enzymes and metabolic pathways (Lori Scott)

Examples of how GENI-ACT is integrated into undergraduate courses

·       Jayna Ditty

·       Joanna Klein

Examples of how GENI-ACT is integrated into undergraduate courses

·       Lori Scott – Studying amino acid biosynthesis in Meiothermus ruber (website CLICK HERE)

·       Tara Luke

Finding a GEBA organism to study  (Lori Scott or watch video sent as homework, or the video on the GENI-ACT blog)

Workshop participants work with workshop facilitators to design a class/research activity

Participants report to the group

Workshop ends (~12pm)



Jayna's project website 

J. Klein:  Cellulophaga lytica Project

Lori's PowerPoint Slides (beginning at Slide 19)

Lori's M. ruber website

IMG/EDU link

NCBI Pubmed link


WORKSHOP SURVEYS:  Links to the pre-workshop and post-workshop surveys

TRAVEL INFORMATION:  See this link (CLICK HERE) or go to the link in the upper left navigation bar

PRE-HOMEWORK ASSIGNMENTS:  CLICK HERE for a webpage, or find a link in the left navigation bar.  


GENI-ACT Workshop RSVP: 

MGAN Travel Award application: