Quick Introduction to the Workshop and Core

The mission of the Bioinformatics Core facility is to facilitate outstanding omics-scale research through these activities:

Staff

Contacts

• Bioinformatics related questions, include but not limited to bioinformatic methods questions, software use, data questions.
  • Bioinformatics.core@ucdavis.edu
• Computing Issues, include but not limited to user account questions, equipment failure/malfunction, software install, software failures (not related to use)
  • helpdesk@genomecenter.ucdavis.edu
• Training courses information
  • training.bioinformatics@ucdavis.edu

Workshop Goals

• End to End understanding of microbial community analysis (amplicon analysis)
  • Discussions/lectures
  • Technologies
  • Experimental design
  • Cost estimation
  • Workflow
  • Microbial community analysis
• To work through a complete experiment, starting from raw data to completion, including making some figures.
• Goal is 30-40% lecture/discussion 60-70% hands-on

Internet

You will need to access the UCD wireless via your laptop to participate in the hands-on exercises.

Eduroam

Many academic institutions are part of Eduroam. (See “List of Institutions” under “Members” at https://www.eduroam.us/ to find out if your institution is a member.) Please make sure you can log into Eduroam with your device at your home institution, which will make things easier once you come to UCD.

UCD Guest wireless

You will need to access the UCD wireless via your laptop to participate in the hands-on exercises. Please review http://itcatalog.ucdavis.edu/service/wireless-guest-access for access instructions.

Workshop Materials

Workshop materials are all posted on github, and publicly available

http://bioinformatics.ucdavis.edu/training/events/

• Github main page:

  https://github.com/ucdavis-bioinformatics-training

• This Microbial Community Analysis Workshop

  https://ucdavis-bioinformatics-training.github.io/2019_September_UCD_Microbial_Community_Analysis_Workshop/

  https://github.com/ucdavis-bioinformatics-training/2019_September_UCD_Microbial_Community_Analysis_Workshop

Computing Cluster

Course will be conducted using the Bioinformatics Core’s servers and compute cluster tadpole.genomecenter.ucdavis.edu

Everyone should get an account.
https://computing.genomecenter.ucdavis.edu

1. Request an account -> sponsor “Bioinformatics Core Workshop”. If you already have an account on our systems, then please tell us your username.
   • Fill in the remainder of the information, select any username you wish
2. Confirm your email address in your email application
3. I will need to approve your account.
4. You will get an email to set your password
5. Test your account, in terminal ssh yourusername@tadpole.genomecenter.ucdavis.edu
   • Use the username you chose.

Cluster usage will be under the slurm reservation ‘workshop’

Reservation will last 1 full week after the workshop and allow you to practice or run analyze your own data.

workshop ACTIVE 2019-09-02T00:00:00 2019-09-14T00:00:00 13-00:00:00 rafter-[8,14,18]