2. Student Module 1: Basic Information

Module 1:  Basic Information

There's a great guide regarding Basic Information about your geneIt is in Dropbox (you don't need an account in Dropbox to get these, but it's handy free cloud storage.)  The guide can be downloaded here.

Word Source files for the GENI-ACT Training Manual

In the student tab there are resources to help students use the GENI-ACT resources.

As an instructor, you might choose to alter these to fit your plans.  They are in DropBox, a free cloud storage platform.  If you wish to create your own DropBox account, click here.  This account is not necessary to view these files.

• Background; Getting Started
• Module 1:  Basic Information
• Module 2:  Sequence Based Similarity
• Module 3:  Structure Based Evidence
• Module 4:  Cellular Localization
• Module 5:  Alternative Open Reading Frames
• Module 6:  Enzymatic Function
• Module 7:  Duplications and Degradation
• Module 8:  Horizontal Gene Transfer
• Module 9:  RNA; Final Annotation

Step 3c: Pick a gene from KEGG!

Step 3c:  Pick a gene from KEGG!

 

The URL is http://www.genome.jp/kegg/
 

Step 3b: Pick a gene from IMG/EDU!

Step 3b:  Pick a gene from IMG/EDU! 

The URL is http://img.jgi.doe.gov/cgi-bin/edu/main.cgi

IMG/EDU holds great first-pass annotations of genes with predictions that students can test using the GENI-ACT software.  Dr. Scott ran through how to choose a genome using IMG in the "Interlude" section of this blog.

This movie shows how you can do a "Gene Search" in IMG to find a gene of interest (you could do an exercise with your students in advance to find out what they're interested in).  You paste the Locus_ID into GENI-ACT and create an assignment based on this (Or these!  You can do more than one!)

Step 3a: Pick a gene from a GENI-ACT list!

Step 3a:  Pick a gene from a GENI-ACT list! 

You can pick a gene right from GENI-ACT.  Perhaps you could ask your students to do some research and write down what gene or genes they might like to work with.  You can use your browser's "Find" function to look for similar names.

Interlude: Get inspiration as to what genes to select for assignments

Interlude:  Get inspiration as to what genes to select for assignments 

Creativity is hard.

Do you pick the genes, or should your students get to pick the genes? Once you have a gene name, how do you get it into the assignment?

3. Making an assignment: "TAGM" (excludes details on Gene List)

Step 3:  After students have created accounts, create an assignment! 

Have your students create their own accounts.   Ensure you provide them with your class token so that they appear in your roster. Once they've done so, you can "form a team" to which the assignment will be linked.  Here's the part that can be confusing:  GENI-ACT is designed to allow a single student to annotate a bunch of genes, and annotations can be done individually or through teams.  And the teams can be changed from assignment to assignment.

One way to remember this is TAGM (tag'em).  This stands for the steps:

1. Team creation - assignments are linked to teams; students are put into teams.
2. Assignment creation - Name your assignment and add a description.
3. Gene List (This will be covered in the next three videos to show different ways to pick your genes).
4. Merge - Apply the gene(s) in your assignment to student teams.

Note that separate videos will detail how to create your gene list.