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 and Students
Our team offers custom bioinformatics services to academic and private organizations. We have a strong academic background with a focus on cutting edge, open source software. We replicate standard analysis pipelines (best practices) when appropriate, and/or develop novel applications and pipelines when needed, however we always emphasize biological interpretation of the data.
Contacts
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Request for data analysis services, consultations.
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Bioinformatics training course information
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Computing Issues, include but not limited to user account questions, equipment failure/malfunction, software install, software failures (not related to use).
Workshop Goals
- End to End understanding of the basics of single cell RNAseq experiments
- Lectures/Discussions
- Technologies use
- Experimental design
- Cost estimation
- Workflow
- Data reduction
- Data analysis
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To work through a complete experiment, starting from raw data to completion, including making a few figures.
- Goal is 30-40% lecture/discussion 60-70% hands-on
Workshop Materials
Workshop materials are all posted on github, and publicly available
http://bioinformatics.ucdavis.edu/training
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Workshop registration site:
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Public Github repository listing:
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This Intro to scRNAseq Workshop
https://ucdavis-bioinformatics-training.github.io/2023-June-Single-Cell-RNA-Seq-Analysis/
Computing Cluster
A portion of this course will be conducted on our servers and compute cluster
To get an account.
https://computing.genomecenter.ucdavis.edu
Request an account -> sponsor is “Bioinformatics Core Workshop”
If you already have, or have had in the past, an account on our systems, then please tell us your username, or email, and we will add you to the workshop. Do not create a new account.
Structure of the Workshops
Given the current Covid19 pandemic, we’ve decided to provide a hybrid format to our workshop. Our intent is to offer as much opportunity as possible to everyone who is interested in our workshop. We will hold the same goals and strive for a similar lecture/hand-on ratio. We will be using multiple technologies in order to help facilitate a maximum amount of interaction.
Zoom
Course lecture, discussions, and one-on-one help/troubleshooting will be conducted using a zoom meeting.
- Participants will be provided one-on-one troubleshooting by our staff, screen sharing and even remote control when needed.
- The Chat features of Zoom will not be our primary mode of text communication as its history is not reliable.
- We will stick to a schedule to allow people to plan their day and know when they need to be back at their computers for lecture.
- Video recordings of lectures will be made available to participants.
Because video is involved, we ask everyone to be respectful and we reserve the right to remove someone if they are being disrespectful or disruptive.
Learn more about how we use Zoom in our workshops.
Slack
Text based communication will be conducted via a Slack channel. Staff will be monitoring the Slack channel to answer questions (and schedule a Zoom break out room if needed). If you know the answer to someone else’s question, feel free to answer it.
Learn more about how we use Slack in our workshops.
Patience
We ask for a little more patience as there is a wide background in workshop participants, but we are committed to providing you the best educational experience we can (under the current conditions).