Rework for 2023

[jayhesselberth]

• Move everything into quarto
• Bootcamp only covers shell and R
• No Python anywhere
• Rewrite ChIP / accessbility lectures in R using bioconductor / ComplexHeatmap / valr. No deeptools
• Skip protein block, focus only on DNA sequencing approaches
• Require some kind of pre-requisite (prior experience, prior coursework)
• Course will not be required, offered as an option to BIOS 6606 for more advanced students

[jayhesselberth]

• more bioconductor (maybe include Sean Davis in the planning?)

[jayhesselberth]

What if we only did RNA sequencing, and just fleshed out the different types of analysis?

[nmukherjee]

That could work, though I'm a little on the fence about not getting into CHIP/cut-run. I think we could ditch DNase/MNase/ATAC.

However ditching DNA would allow additional focus on data integration, which is an important way for students to leverage other data sets to gain biological insights from their own experiments. Maybe we could still incorporate DNA level data at least, e.g. using chip-seq peaks to ask if a certain TF is associated with expression changes in their data set.

[jayhesselberth]

Consider introducing student-specific projects earlier (instead of the "final projects", which inevitably lead to a time crunch)

Get them thinking about external data sets they could analyze during the course of the class that would feed into their own projects. Easiest would be gene expression / RNA sequencing but could involve some chromatin analysis.

Related: mabye do the NCBI GEO lecture earlier in the course, in the bootcamp?

[jayhesselberth]

Fall 2023

• August 28 Classes begin
• September 4 Labor Day Holiday No classes. Campus closed.
• November 23-24 Thanksgiving Holiday Campus closed.
• December 15 Last day of semester