Genomics in Education Workshop at Prairie View A&M
Organizers: | Jason Williams |
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Local Point of Contact: | |
Trainers: | Jason Williams, John Fonner |
Date: | Sept 26-27, 2013 |
Location: | Prairie View Texas A&M University |
Section Navigation
Pre-Workshop Homework
Laptop Compatibility
If you are bringing your own laptop:
Most laptops (<5 years old) updated with the latest web browser (we recommend FireFox:http://www.mozilla.org/en-US/firefox/fx/ ) will have no problem.
Here are some things to check:
If possible, make sure you have have administrative privileges on your computer (should it become necessary to install or update software during the workshop).
Ensure that your computer is running a current browser (Mozilla Firefox 13/ Internet Explorer 8 (IE 9 preferred) / Safari 4 or later).
Be aware, Java 7 has known issues that limit some functionality on DNA Subway. Get Java 6 @ this link: http://java.com/en/download/manual_v6.jsp
If you are a Windows user, ensure that your computer is running Java 6 Update 19 or later by going to http://java.com and click ‘Do I Have Java?’ Then click ‘Verify Java version’ and install.
If you are a Mac user, check that your computer has the latest Java installed (probably Java 6) and that it also is enabled. (Check it out at http://java.com or contact williams@cshl.edu for additional advice).
To test your Java installation, go to http://gfx.dnalc.org/files/apollo/test/ and follow the instructions at that site. The test is successful if an image opens up on your computer that looks like this screenshot: Java Screenshot
Make sure you have a valid iPlant account
You should be able to log into the DNA subway at: http://dnasubway.iplantcollaborative.org/.
If you do not have an iPlant account, please get one at: http://user.iplantcollaborative.org/register.
Additional Readings and Assignments
ReviewDNA Subway manual (a printed copy will be presented at the workshop)
Review DNA Barcoding laboratory (a printed copy will be presented at the workshop)
Bring a small sample of plant tissue (a leaf/flower/etc.) or collect one on campus before the experiment.
If you wish to bring sequence data for the DNA barcoding or genome annotation experiments feel free to do so!
Check out the slides and papers mentioned in the agenda.
Workshop Agenda and Resources
Thursday
Time | Topic | Slides | Notes/Links |
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09:00-09:15 | Welcome/Logistics |
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09:15-10:00 | Introductions |
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10:00-10:15 | iPlant Collaborative Overview | | |
10:15-10:30 | Overview, Workshop Objectives, DNA Subway Tour | | |
10:30-10:45 | Break |
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10:45-11:15 | Using DNA Subway to Teach Concepts in Molecular Biology |
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11:15-12:00 | Setting up projects for Annotation - Red Line |
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12:00-01:00 | Lunch |
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01:00-01:15 | DNA Barcoding setup |
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01:15-01:30 | Mini-Seminar: DNA Barcoding | |
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01:30-02:45 | DNA Barcoding wet-lab cont'd |
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02:45-03:00 | Mini-Seminar: Evidence Based Gene Modeling |
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03:15-04:45 | Gene Annotation I |
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04:45-05:00 | Mini-Seminar: Alternative Splicing | |
Friday
Time | Topic | Slides | Notes/Links |
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09:00-09:30 | Mini Seminar: Transposons | | |
09:30-10:15 | Transposon Sleuthing: Yellow Line |
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10:15-10:30 | Break |
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10:30-11:30 | Gene Annotation II |
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11:30-12:00 | DNA Barcoding (PCR) |
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12:00-01:00 | Lunch |
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01:30-02:30 | DNA Barcoding - Blue Line | |
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02:30-02:45 | Break |
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02:45-03:45 | Barcdoing electrophoresis and sequencing prep |
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03:45-04:30 | Implementation and Classroom Planning |
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04:30-05:00 | Summary, Evaluation, and Closure |
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Other Websites and Links and Resources
http://www.learnaboutsma.org/ - SMA website and splicing animation.
http://www.urbanbarcodeproject.org - UBP website
http://www.iBoL.org - International Barcode of Life Project
Attendees (23)
Name | Research Area | Account Status | |
|---|---|---|---|
Mahnaz Kiani-Fariz | Genetics Nucleic Acids | mhkiani@tamu.edu | X |
Jim Hu | Biochem Mol Struc Function | jim.hu.biobio@gmail.com | X |
Idowu Famuyiwa | Training | idnoble_2@yahoo.com | X |
Milton Daley | Biochem Mol Struct Function | mdaley@pvamu.edu |
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Ivonne Ruiz | Biochem Mol Struct Function | ivonne.garcia3@hccs.edu | X |
Marie-therese Simms | Plant Biol | msimms@pvamu.edu |
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Karen Killion | Other | karen.killion@blinn.edu | X |
Yi Lu | Algorithm Dev | yilu@pvamu.edu | X |
Shaye Lewis | Dev Biol | sklewis@pvamu.edu | X |
Damilola Olaleye | Cell Biol | dolaleye@pvamu.edu | X |
Annette James | Agron | aajames@pvamu.edu | X |
Joseph Oleniczak | Biotech/Molec Biol | jolenicz@austincc.edu | X |
Vimlarani Chopra | Cell Biol | vimlarani.chopra@hccs.edu |
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Paul Johnson | Env Biol | pmjohnson@pvamu.edu | X |
Paul Drummond | Mol Biosciences | pbdrummond@pvamu.edu |
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Deirdre Vaden | Genetics Nucleic Acids | dlvaden@pvamu.edu |
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Laura Carson | Chem | lecarson@pvamu.edu |
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Julia Stone | Cell Biol | jmstone@pvamu.edu | X |
Shabnam Eslamfam | Computation Research | shabnam127@hotmail.com | X |
Deforest Peterson | Cell Biol | df0pete@yahoo.com | X |
Charity Woodard | Biochem Mol Struct Function | charity+woodard@yahoo.com | X |
Quincy Moore | Cell Biol | qcmoore@pvamu.edu | X |
Yoonsung Jung | Stats Probability |