There's a companion Training Manual by Dr. Stephen Koury that you can access here. It will help you and your students complete the GENI-ACT tasks.
Step 1: Make your account!
Step 2: Create a class!After your account is established - you'll get an email letting you know you're approved - you need to create a class. This will create a "virtual space" or "classroom" that is identified by a Course Token (also called a Class ID on some GENI-ACT screens).
Students will use the Token when they create their account. This puts them into that "virtual space" (class). They will then appear in your Roster. You need them in there before you can create assignments for them.
This video shows how you will create your class.
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:
- Team creation - assignments are linked to teams; students are put into teams.
- Assignment creation - Name your assignment and add a description.
- Gene List (This will be covered in the next three videos to show different ways to pick your genes).
- Merge - Apply the gene(s) in your assignment to student teams.
Details on Gene Lists are below!
Interlude: Get inspiration as to what genomes to selectCreativity 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?
Dr. Lori Scott shows how she thinks as she looks through genomes in order to decide what to use as the organism from which her students will take their genes for annotation.
Step 3a: Pick a gene from a GENI-ACT list!The next three videos assume you've decided upon a genome from which you'll draw genes for the assignments.
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.
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 3c: Pick a gene from KEGG!
The URL is http://www.genome.jp/kegg/
Word Source Files for the GENI-ACT Training ManualIn 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