Quick Introduction to the Workshop and Core
The mission of the Bioinformatics Core facility in the UC Davis Genome Center 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 ESALQ wireless via your laptop to participate in the hands-on exercises.
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://github.com/ucdavis-bioinformatics-training/2019_April_ESALQ_Microbial_Community_Analysis
https://ucdavis-bioinformatics-training.github.io/2019_April_ESALQ_Microbial_Community_Analysis/
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
- Request an account -> sponsor “Bioinformatics Core Workshop”.
- Fill in the remainder of the information, select any username you wish
- If you already have an account on our systems, then please tell us your username.
- Confirm your email address in your email application
- I will need to approve your account.
- You will get an email to set your password
- 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.
**workshop ACTIVE 2019-04-22 2019-04-28