20150719 Bioinformatics Workshop at AZCTE

Event Organizer	Debra James (AZED)
iPlant Trainers	Uwe Hilgert (BIO5)
TAs	Cheryl Blake (PCC); James De La Rosa (PCC)
Date	July 19, 2015
Time	13:00-17:00 (mas o menos)
Location	Loews Ventana Resort 7000 N Resort Dr, Tucson, AZ 85750 Ventana Canyon-Lab 2 Room

Required Workshop Prep

1. iPlant Account

Get your free account at http://user.iplantcollaborative.org. (Make sure to REMEMBER your username and password.) Please register with an institutional email account (e.g. '.edu' or '.org') only these types of email addresses will be granted access to the iPlant cloud service Atmosphere (see next bullet).

2. Laptop

Please bring your own WiFi enabled laptop to the workshop. Make sure your laptop has the following:

Internet Browser: Please have an up-to-date web browser (We strongly recommend Firefox or Safari - Internet Explorer and Chrome have Java and other compatibility issues.)
Java: Have JAVA installed, enabled and working with Firefox or Safari. (Help)

4. Pre-Workshop Guide and Homework

Download and print this manual to get the most out of the workshop.
Complete this Pre-Workshop Survey

Etherpad/Chatroom

We will use the following Etherpad for instant & shared communications during the workshop: https://etherpad.mozilla.org/eYOfsFktUW

Instructional Materials

Materials are downloadable/accessible from the Resources column in the Workshop Agenda below.

Workshop Agenda

12:30	Doors Open / Sign-in / Set up				This workshop in 20 min. or less	Pre-Survey
Time	Description	Objectives	Tools	Sources	Resources	Links
01:00	Welcome - Self-Introductions				AZ CTE Bioinformatics Standards AZ CTE Bioscience Standards	PLOS Bioinformatics Competency Paper
1:15	Overview	Relatedness By Descent Mobile Genetic Elements (Transposons) Polymorphism Allele			Slides Chromosome 11 Fly-over Transposons (McClintock) Transposons (SINES/LINES) Transposons (How Alu gets copied)	Genetic Origins
01:30	Wet lab isolate DNA start PCR	Identify personal genotype at PV92 locus Isolate and amplify DNA	MolBio lab equipment Pipets Centrifuge Thermocycler MolBio lab supplies Chelex Primers & nucleotides Polymerase	N. Anderson @ UA Carolina Biologicals	PV92 lab manual PCR Reaction 01 PCR Reaction 02 PCR Reaction 03
02:30	eLab Part A Part B	Identify PV92 locus in data bases Identify and isolate PCR primer sequences Conduct PCR electronically Predict size of PCR amplicon	WWW DNALC site Recipes NCBI site BLAST GenBank		PV92 eLab manual Primers	Genetic Origins NCBI
03:00	Break
03:15	eLab Part C	Examine PV92 locus in human genome What chromosome is it on? Is it in a gene?	WWW NCBI site Human Genome Viewer (Mapview) BLAST		PV92 eLab manual Amplicon
04:00	Wet lab Load gel	Identify personal genotype at PV92 locus Analyze amplified DNA	MolBio lab equipment Gel electrophoresis equipment	N. Anderson @ UA Carolina Biologicals Invitrogen E-Gels	Gel Electrophoresis 01 Genetic Origins
04:15	eLab Part D	Identify and analyze all states of PV92 known to man	WWW NCBI BLAST BioServers SequenceServer DNA Subway Blue Line MUSCLE Mega		PV92 eLab manual Amplicon All Amplicons	Human PV92 locus Matera et al., 1990 Batzer et al., 1994 Comas et al., 2001 Bioinformatics NCBI Sequence Server DNA Subway MEGA
04:45	Wet lab Analyze gels	Identify personal genotype at PV92 locus Analyze agarose gel Understand population genetics Hardy-Weinberg equilibrium Genetic Drift versus Selective Pressure Human Migration	MolBio lab equipment Lightbox WWW Allele Server Simulation Server	N. Anderson @ UA Carolina Biologicals IO Rodeo	PV92 lab manual PV92 Hardy Weinberg worksheet PV92 world map	Genetic Origins Allele Server Simulation Server
05:00 m.o.m.	Dismissal				PV92 eLab manual w. answers
	Consultations	Still questions?

Participants

Alonso, Martha Celia	Douglas High School; Douglas, AZ
Chamberlain, Karen A	Central Arizona Valley Institute of Technology (CAVIT); Coolidge, AZ
Cherry, Amanda	Mesa High School; Mesa, AZ
DeJesus, Jo	Tuba City High School; Tuba City, AZ
Dunn, Erynn	Casa Verde High School; Casa Grande, AZ
Ford, Matt	Chino Valley High School; Chino Valley, AZ
Griego, Ken	Miami High School; Miami, AZ
Hoover, Kathy	KOFA High School; Yuma, AZ
Landry, Marni	Paradise Valley High School; Phoenix, AZ
Lettes, Andrew	Pueblo Magnet High School; Tucson, AZ
Livingston, Michele	Marana High School; Tucson, AZ
Lord, Peggy	Stapley Junior High School; Mesa, AZ
Scaife, Rick	Valley Vista High School; Surprise, AZ
Vreyens, John	Chino Valley High School; Chino Valley, AZ
Zeiher, Carolyn	Canyon Del Oro High School; Oro Valley, AZ

Logistics, Accommodations, and other details

Arrival Time

Please arrive at 12:30 PM for registration to avoid delays to the workshop.