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

WORKSHOP LOCATION:  FANNIN LIBRARY, ENCANTO CLASSROOM 

Hosts:  
Dr. Anil Kapoor
Biology Faculty, Phoenix College
Dalby Building (602.285.7983), 1202 W Thomas Rd, Phoenix, AZ 85013
anil.kapoor@phoenixcollege.edu

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 location:  FANNIN LIBRARY, ENCANTO CLASSROOM

Workshop Facilitators

Dr. Tim Beagley (Website) - Salt Lake Community College, Salt Lake City, UT; tim.beagley@slcc.edu

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

Dr. Joanna Klein (website),University of Northwestern, St. Paul, jrklein@unwsp.edu

Stephen Koury (website)  University at Buffalo, Buffalo, NY (stvkoury@buffalo.edu)

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

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



WORKSHOP SCHEDULE

AGENDA

LINKS TO RESOURCES

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)

Break

 BLAST powerpoint slides

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

 

Lunch

Afternoon Session (1:30pm)

Module 3 – Cellular Localization  (Jayna Ditty)

 

Module 4 - Alternative start codon (Joanna Klein)

Break

 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)

Overview

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

 Lunch

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




 

DAY 3 (MORNING ONLY)

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: http://goo.gl/forms/23c2X7acY6 


MGAN Travel Award application: http://mgan-network.org/awards.html