General Notes for the Entire Workshop

Technical Tips

The main directory we will be using during the lesson is /home/user/pan_workshop. Ensure you are familiar with the structure of this directory to navigate easily during the workshop.

Common Issues

This workshop introduces an analysis workflow, where each step is dependent on the previous one. If a participant falls behind or encounters issues at any step, they may struggle to keep up with the rest of the class. To mitigate this, we have prepared solution files that include all output files for each stage of the data processing pipeline, as well as the scripts that participants will develop collaboratively with the instructors during the workshop. These files are available in the hidden .backup_pan_workshop directory.

It is important to inform all helpers about the .backup_pan_workshop directory so they can access these resources to assist participants in catching up if needed.

Time Optimization Tips

In case there is a need to optimize time, the chapters “Introduction to the Command Line for Pangenomics” and “Introduction to Python” could be shared with students beforehand. This allows them to become familiar with the tools needed for “Pangenome Analysis in Prokaryotes” and “Topological Data Analysis for Pangenomics,” which require more dedication and cover more specialized content. However, if sufficient time is available, it is beneficial to provide a complete overview and introduce Bash and Python during the lessons on Pangenomics and TDA to ensure a solid foundation.

Engaging Examples

The lesson features engaging examples tailored for learners interested in pangenomics, providing hands-on experience with real-world scenarios. Additionally, practical examples for enthusiasts in topological data analysis are included, which will help illustrate complex concepts and techniques in an accessible manner. These examples aim to deepen understanding and inspire further exploration in these specialized fields.

Specific Notes for the Workshop

If you are teaching the lesson using the CCM-UNAM server, you can use this spreadsheet to have participants select their user. This will facilitate access management and customize the learning experience during the workshop.