Welcome to the workshop

Data Science for Biology

Goals for this session

1. Get to know your instructors and neighbors

2. Set expectations for the week

3. Get excited!

Workshop materials are at:

https://elsherbini.github.io/durban-data-science-for-biology/

Discussions: discord

Ask questions at #workshop-questions on https://discord.gg/UDAsYTzZE.

Stickies

During an activity, place a yellow sticky on your laptop if you’re good to go and a pink sticky if you want help.

Practicalities

WiFi:

Network: KTB Free Wifi (no password needed)

Network AHRI
Password: @hR1W1F1!17

Network AHRI Internet only
Password: AHRI twenty three!

Network CAPRISA-Corp Password: corp@caprisa17

Bathrooms are out the lobby to your left

Introductions

03:00

Take ~3 minutes to introduce yourself to your neighbors.

Please share …

1. Your name
2. Where you’re from and where you work
3. Your current go-to method for analyzing data

Your Instructors

Who are we?

Let’s make this workshop work for all

1. You belong here. This workshop is intended for a wide-audience with a focus on beginners. If you feel out of place - it’s our problem, not yours!

2. Stay committed. This week-long workshop is intended to build each day and leave you with skills you can really use. Commit to stay engaged for best results, for you and your group!

3. This is a challenging but friendly environment. We are here to learn and grow. In order to make the right environment please follow “the 4 social rules” and code-of-conduct.

Let’s take a poll

Go to the event on wooclap

Pre-workshop survey

10:00

Go to https://forms.gle/GKtsjR8SW9NkhVkh6 to fill out the survey.

The content of this workshop

We’ve created 6 modules as well as an interactive activity for this workshop.

There might be too much material to get through in this week!

As instructors we’re going to be trying to teach at the right pace to keep everyone learning all week.

The materials will stay on the website forever for you to work through at your own pace.

When Might You Not Need Sequencing?

• Known Targets, Limited Scope
  • If your research question only involves confirming a single, well-characterized virus or a small set of variants, qPCR or targeted assays might suffice.
    
• Resource Constraints
  • Sequencing can be expensive and time-consuming. If budgets are tight and your question is narrow, simpler assays may be more practical.
    
• Large Cohort Screening
  • For massive surveillance efforts where you only care about the presence/absence of a known pathogen (e.g., routine screening for a particular strain), targeted testing like qPCR is faster and cheaper.
    
• Quick Turnaround Needed
  • If you need immediate results (hours, not days), rapid antigen or antibody tests can be more appropriate.

Question 1 — Detecting Emerging Variants of Endemic Viruses

Without Sequencing
- Limited Scope: Diagnostic tests (e.g., qPCR) only detect known variants and specific targets.
- Potentially Missed Variants: Novel or unexpected changes may escape traditional assays.
- Inadequate Surveillance: Harder to link genetic variation with clinical or epidemiological outcomes.

With Sequencing
- Identify New Mutations: Discover novel mutations that might impact transmissibility or virulence.
- Track Spread: Pinpoint where and when new variants emerge, supporting epidemiological modeling.
- Predict Drug Resistance: Monitor known resistance-associated mutations

Question 2 — Discovering Viruses in Outbreaks

Without Sequencing
- Knowledge Gaps: You can only use qPCR and ELISA to test for known pathogens and antigens - Speed of Discovery: Cell culture based enrichment of viruses takes time and optimization

With Sequencing
- Unbiased Detection: Metagenomic approaches allow for the identification of entirely new viruses.
- Rapid Characterization: Genome assembly and annotation to quickly compare to known viruses.
- Public Health Preparedness: Early detection can guide containment strategies before widespread transmission.

Let’s take a poll

Go to the event on wooclap