Gestión y análisis de datos para la investigación metagenómica

Nodo Nacional de Bioinformática UNAM

28-31 de Octubre 2024

9:00 am - 5:00 pm CDMX

Instructors: Nelly Selem-Mojica, César Aguilar, Mirna Vázquez Rosas-Landa, Diana Hernández-Oaxaca

Helpers: Aaron Espinosa-Jaime, Andrea Chávez-Heredia, Andrés Arredondo-Cruz, David Alberto García-Estrada, José Abel Lovaco-Flores, Alicia Milo-Ramírez, Ana Valeria García-Lartigue

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.

Want to learn more and stay engaged with The Carpentries? Carpentries Clippings is The Carpentries' biweekly newsletter, where we share community news, community job postings, and more. Sign up to receive future editions and read our full archive: https://carpentries.org/newsletter/

Data Carpentry develops and teaches workshops on the fundamental data skills needed to conduct research. Its target audience is researchers who have little to no prior computational experience, and its lessons are domain specific, building on learners' existing knowledge to enable them to quickly apply skills learned to their own research. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

For more information on what we teach and why, please see our paper "Good Enough Practices for Scientific Computing".

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.

Who: The course is aimed at graduate students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: . Get directions with OpenStreetMap or Google Maps.

When: 28-31 de Octubre 2024; 9:00 am - 5:00 pm CDMX 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.

Contact: Please email caaguila@purdue.edu or caaguila@tec.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


Lunes

Before starting Pre-workshop survey
9:00 - 11:30 Project Organization and Management Learn how to structure your metadata, organize and document your metagenomics data and bioinformatics workflow, and access data on the NCBI sequence read archive (SRA) database.
11:45-14:00 Introduction to the Command Line Learn to navigate your file system, create, copy, move, and remove files and directories, and automate repetitive tasks using scripts and wildcards.
15:30-17:00 Introduction to the Command Line Learn to navigate your file system, create, copy, move, and remove files and directories, and automate repetitive tasks using scripts and wildcards.

Martes

9:00 - 10:00 Introduction to R Use R studio to manage several data types and structures.
10:00 - 11:30 Data Processing and Visualization for Metagenomics Use command-line tools to perform quality control, metagenomic assembly, metagenomic binning, taxonomic assignment, and diversity exploration.
11:45-14:00 Data Processing and Visualization for Metagenomics Use command-line tools to perform quality control, metagenomic assembly, metagenomic binning, taxonomic assignment, and diversity exploration.
15:30-17:00 Data Processing and Visualization for Metagenomics Use command-line tools to perform quality control, metagenomic assembly, metagenomic binning, taxonomic assignment, and diversity exploration.

Miércoles

9:00-11:30 Phyton Using python to understand changes in communities.
12:00-14:00 Phyton Using python to understand changes in communities.
15:30-17:00 Phyton Using python to understand changes in communities.

Jueves

9:00-11:30 Taxonomic Classification The use of various specialized bioinformatics tools for classifying bacterial taxonomy.
12:00-14:00 Functional annotation Utilization of various specialized bioinformatics tools for annotating bacterial metabolism.
15:30-17:00 Binning The procedure and application of various bioinformatics tools to reconstruct genomes from metagenomic data.
End Post-workshop survey
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 Data Carpentry 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.

The setup instructions for the Data Carpentry Genomics workshops can be found at the workshop overview site

.