Table of Contents

• 1. GIGA Bioinformatics Workshop
  • 1.1. Day 0 (Oct 18)
  • 1.2. Day 1 (Oct 19)
  • 1.3. Day 2 (Oct 20) - Bioinformatics workshop, Blenchi Room
  • 1.4. Day 3 (Oct 21) - Bioinformatics workshop, Blenchi Room
• 2. Workshop Code of Conduct
  • 2.1. Need Help?
  • 2.2. The Quick Version
  • 2.3. The Less Quick Version
• 3. Booting a Jetstream Computer Instance for your use!
  • 3.1. Resources
  • 3.2. Request to log in to the Jetstream Portal
  • 3.3. Use “XSEDE”
  • 3.4. Fill in the username and password and click “Sign in”
  • 3.5. Select Projects and “Create New Project”
  • 3.6. Name the project for yourself, click “create”
  • 3.7. Boot an instance with a pre-built image
  • 3.8. Find the “DIBSI 2018 workshop image” image, click on it
  • 3.9. Name it something simple
  • 3.10. Wait for it to become active
  • 3.11. Click on your new instance to get more information!
  • 3.12. Miscellany
  • 3.13. Suspend your instance
  • 3.14. Shutting down your instance
  • 3.15. Deleting your instance
• 4. Logging in to jetstream from your local terminal with a key file
  • 4.1. Concerning Keys
  • 4.2. Getting the Private Key
  • 4.3. Getting your instance IP address
  • 4.4. On MacOS/Linux
  • 4.5. On Windows
• 5. Instructions for Annotation Tutorial for GIGA III 2018
• 6. Organism and Genes of Interest
• 7. Question One: Are these innate immune recognition genes in my genome?
• 8. Terminal Practice
  • 8.1. Putting data on your remote computer, method 1 - creating a file and copying and pasting information.
  • 8.2. Putting data on your remote computer, method 2 - WinSCP, Cyberduck, Filezilla or other external program.
  • 8.3. Putting data on your remote computer, method 3 - Start Rstudio (which we pre-installed for the class) and transfer files.
  • 8.4. Putting data on your remote computer, method 3 - download a file from an ftp or http location.
  • 8.5. Let’s try a probabilistic approach with HMMER (HMMER: biosequence analysis using profile hidden Markov models)
• 9. Install hmmer
• 10. Install muscle
• 11. Align sequences
• 12. Predict multiple genes simultaneously
• 13. Install databases
• 14. Starting R Studio Server