Hackathon Challenges

To help you get the creative juices flowing, we’ve come up with a few challenges that you might decide to tackle. These fall into a the following categories:

Technical

• Identify batch correction methods that allow pseudotime assessment across biological replicates
• Establish best pre-processing practices for pseudotime assessment
• Determine best methods for multiple lineage detection
• Determine how to apply reference-based annotation methods with pseudotime (ie establish a pseudotime for one dataset/sample and predict the pseudotime values for each cell in a separate query sample)

Benchmarking

• Establish a method to determine which pseudotime method works best for a given dataset
• Build methods to ascertain if biological cell states are reproducible across biological replicates

Visualisation

• Develop more intuitive visualisation of temporal dynamics and transitions across states in single-cell datasets

Biological Interpretation

• Construct tools to identify genes that characterise pseudotime
• Build methods to identify biologically-grounded pseudotime that accurately positions cells across dynamic cell states
• Establish platforms to ascertain the biological processes being defined by pseudotime estimations.

If you have a great idea outside of these prompts, that’s great too!