ISMB 2026 tutorial feedback

[agitter]

If anyone attended the ISMB 2026 tutorial, please use this issue to leave feedback about the tutorial: questions you still have, errors you encountered, confusing parts, etc.

I will also use it to log my notes:

• At least two participants had problems with Python packages. One was at the python -m pip install . step for the SPRAS package, where there were version conflicts in the dependencies. The other was while running the Snakemake workflow. There were errors related to this part of the Snakefile and others related to NumPy versions.
• Step 1 of the intermediate tutorial takes a lot of time and is passive. Participants do not have anything to execute. Some of the preprocessing is niche and specific to this one proteomics study, like mapping peptides and the Tukey HSD test. A simpler dataset or story may more quickly convey how to go from omics data to SPRAS files.
• There was a question about what a dummy node is in the input file.
• We could provide more direct links or screenshots related to deleting a codespace and checking usage to alleviate concerns about being billed. We can also estimate the CPU and storage usage incurred for running the tutorial if someone has partially used their allocation already.
• One participant's codespace shut down. What is their timeout?
• The tutorial switches between general background, discussion of inputs and outputs, and instructions. We should call out the instruction parts (download this file, upload this file, run this command, open this output, etc.) more distinctly.
• Squeezing both the codespace and the tutorial instructions into a single projected screen is tight. Fonts are small or windows are small.
• Instead of showing the expected outputs from the tutorial, we can show how to open those files in the codespace so participants see where to find them.
• We need to provide a little more context about what the output images show, especially precision-recall figures.
• We can cut parts of the tutorial that discuss SPRAS options that are not used. For example, present only one of the ways to select pathways for evaluation and link to the documentation to describe the alternatives. That will more directly link what participants do to what is written in the tutorial.
• One of the main features of SPRAS is running many algorithms in parallel on the same data. Should we do more with the output files or images to emphasize that?

[tristan-f-r]

With the comment on showing people how to open files, I'm also aware of one other person who also privately requested help on how to see the output for one such file, so it could be worthwhile.