2015 PAG Computer Demo: Difference between revisions

Revision as of 22:11, 5 January 2015

Go to: http://user.iplantcollaborative.org
- CoGe uses iPlant's Authentication and User Identify Management Service
- After clicking on the confirmation link provided in the automated email, your account may take a few minutes to propagate to all of iPlant's Authentication Services.
Sign-in (link is in top-right of any CoGe page)
NOTE: This wiki (CoGePedia) uses a different authentication than CoGe!

Start:
- From your user profile page (must be logged into CoGe): https://genomevolution.org/CoGe/User.pl
  - Click "Create"-> "New Genome"
  - Go directly to LoadGenome: https://genomevolution.org/CoGe/LoadGenome.pl
Search for Organism "Escherichia coli K12 strain K-12 substrain MG1655" (just type in "MG1655")
Set a version (e.g., "1")
Leave "Type:" as "unmasked"
Source: "CoGe" or "NCBI"
Leave as "Restricted"
Press "Add Data"
Select "FTP/HTTP" tab
Paste in the link below:
- E. coli genome: http://de.iplantcollaborative.org/dl/d/555B53F9-E738-4951-85A3-421E23804DFA/genome_7112.faa
Press "Get"
When finished being retrieved, press "Load Genome"
Note: The length of time it takes to load a genome depends on the load on the database and the number of chromosomes/contigs being loaded. For this example, it should take a minute or two.

Go to GenomeInfo by pressing "View Genome"
Press "Load Gene Annotations"
Set a version (e.g., "1")
Source: "CoGe" or "NCBI"
Leave Restricted
Press "Select Data Files"
Select "FTP/HTTP" Tab
Paste in link below:
- E. coli annotations: http://de.iplantcollaborative.org/dl/d/C1ACC5C3-1E0B-409B-8A91-C969943F41F8/7122-structural-annotations.gff
- Press "Get"
- When finished being retrieved, press "Load Annotations"
When the load is finished, pressing "Genome View" will launch the genome viewer (JBrowse).
Note: The length of time it takes to load annotations depends on the load on the database and the number of annotations being loaded. For this example (and no load on the server), it should take ~ 3-5 minutes.

Go to your User Profile page: https://genomevolution.org/CoGe/User.pl
Select a genome by clicking on it.
Information about the genome will appear in the right panel
You can share a genome by clicking on the person icon
You can delete the genome by clicking on the trash can
Double-clicking the genome will open the Detailed View for it (GenomeInfo)
Share it with the person next to you
You can view genomes (and other data) that has been shared with you by clicking on "Shared with me" in the menu on the left.

If you are logged into CoGe, CoGe will record your activities. These are available for review in your User Profile page: https://genomevolution.org/CoGe/User.pl
Click on "Activity" in the menu on the left. This will give you an overview of the number of analyses you've run
Your previously run analyses can be viewed by clicking "Analyses". Clicking on an analysis will re-run it.

@@ Line 51: / Line 51: @@
 * Double-clicking the genome will open the Detailed View for it ([[GenomeInfo]])
 * Share it with the person next to you
+* You can view genomes (and other data) that has been shared with you by clicking on "Shared with me" in the menu on the left.
+===Your History and Activity===
+* If you are logged into CoGe, CoGe will record your activities.  These are available for review in your User Profile page: https://genomevolution.org/CoGe/User.pl
+* Click on "Activity" in the menu on the left.  This will give you an overview of the number of analyses you've run
+* Your previously run analyses can be viewed by clicking "Analyses".  Clicking on an analysis will re-run it.
 ===Comparative Genomics===