Topological data analysis in Biology

cmo

Jun 29 - Jul 3, 2026

9:00 am - 4:30 pm (UTC-6)

Instructors: Adriana Haydee Contreras Peruyero, Shaday Guerrero Flores, Yesenia Villicaña, Nelly Sélem Mojica

Helpers: Luis Raúl Figueroa, Eugenio Martín Azpeitia


📝 Workshop registration
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General Information

The Carpentries project comprises the Software Carpentry, Data Carpentry, and Library Carpentry communities of Instructors, Trainers, Maintainers, helpers, and supporters who share a mission to teach foundational computational and data science skills to researchers.

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This is a pilot workshop, testing out a lesson that is still under development. The lesson authors would appreciate any feedback you can give them about the lesson content and suggestions for how it could be further improved.

Where: Oaxaca. Get directions with OpenStreetMap or Google Maps.

When: Jun 29 - Jul 3, 2026; 9:00 am - 4:30 pm (UTC-6) Add to your Google Calendar.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below).

Accessibility: We are committed to making this workshop accessible to everybody. The workshop organizers have checked that:

We are dedicated to providing a positive and accessible learning environment for all. We do not require participants to provide documentation of disabilities or disclose any unnecessary personal information. However, we do want to help create an inclusive, accessible experience for all participants. We encourage you to share any information that would be helpful to make your Carpentries experience accessible. To request an accommodation for this workshop, please fill out the accommodation request form. If you have questions or need assistance with the accommodation form please email us.

Glosario is a multilingual glossary for computing and data science terms. The glossary helps learners attend workshops and use our lessons to make sense of computational and programming jargon written in English by offering it in their native language. Translating data science terms also provides a teaching tool for Carpentries Instructors to reduce barriers for their learners.

Workshop Recordings: Carpentries workshops are designed to be interactive rather than lecture-based, with lessons that build upon one another. To foster a positive online learning environment, we strongly recommend that participants join in real time. As a result, workshop recordings are not recommended and may not be available to learners.

Contact: Please email haydeeperuyero@matmor.unam.mx or nselem@matmor.unam.mx for more information.

Roles: To learn more about the roles at the workshop (who will be doing what), refer to our Workshop FAQ.


Code of Conduct

Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.


Collaborative Notes

We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.


Surveys

Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey


Schedule

Day 1 Monday Jun 29

Before starting Pre-workshop survey
09:30 -10:20 am Talk: Topological data analysis captures horizontal gene transfer
10:30 -11:30 am Introduction to the Command Line for Pangenomics 1
11:30 -11:45 am Break
11:45 -12:50 am Introduction to the Command Line for Pangenomics 2
13:00 -14:00 pm Food
14:00 -15:15 pm Introduction to Python
15:15 -15:30 pm Break
15:30 -17:00 pm Introduction to Python 2

Day 2 Tuesday Jun 30

09:00 -10:20 am Pangenome Analysis in Prokaryotes 1
10:30 -11:30 am Pangenome Analysis in Prokaryotes 2
11:30 -11:45 am Break
11:45 -12:50 am Topological Data Analysis for Pangenomics 1
13:00 -14:00 pm Food
14:00 -15:15 pm Topological Data Analysis for Pangenomics 2
15:15 -15:30 pm Break
15:30 -17:00 pm Topological Data Analysis for Pangenomics 3

Day 3 Wednesday, Jul 1

09:30 -10:20 am Talk: Análisis topológico de datos para la caracterización de patrones celulares
10:30 -11:30 am TDA in images practice 1
11:30 -11:45 am Break
11:45 -12:50 am TDA in images practice 2
13:00 -14:00 pm Free atfternoon

Day 4 Thursday Jul 2

09:30 -10:20 am Horizontal Gene Transfer Exercise 1
10:30 -11:30 am Viral evolution
11:30 -11:45 am Break
11:45 -12:50 am Selfwork
13:00 -14:00 pm Food
14:00 -15:15 pm Selfwork 2
15:15 -15:30 pm Break
15:30 -17:00 pm Questions and answers

Day 5 Friday, Jul 3

09:30 -10:20 am Student Talks
10:30 -11:30 am Student Talks
11:30 -11:45 am Break
11:45 -12:50 am Student Talks
13:00 -14:00 pm Lunch
The lesson taught in this workshop is being piloted and a precise schedule is yet to be established. The workshop will include regular breaks. Please contact the workshop organisers if you would like more information about the planned schedule.

Setup

To participate in a workshop, you will need access to software as described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

Please check the "Setup" page of the lesson homepage for instructions to follow to obtain the software and data you will need to follow the lesson.