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ISCB-LA SoIBio BioNetMX 2020 | Oct 28 – 29, 2020 | Virtual Symposium | Workshops & Tutorials

Workshops and Tutorials

Workshops and tutorials will take place online on October 22nd to 27th

Workshop: Train the Trainer/Entrenamiento de Instructores/Treine o Treinador

María Bernardi, CABANA Project
Patricia Carvajal López, CABANA Project
Piraveen Gopalasingam, EMBL-EBI
Mindy Muñoz,  CABANA Project

9:00AM - 1:00PM Mexican Central Time (CT) on October 22 & 23, 2020
Capacity: 20 (Español), 20 (Português)

This workshop will provide tools, skills, guidance, and tips for developing and providing training from other trainers with the theoretical and practical understanding and adaptation to the new challenges that we are facing. Participants will explore a variety of methods to enable and encourage learning, examine the requirements for a successful course, and obtain appropriate feedback.

Depending on the number and background of participants the workshop will be held in Spanish and/or Portuguese, though all instructors are also fluent in English.

Maximum capacity: Minimum number of participants 6 per language group. Maximum: 20.

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Tutorial: Discovery and phylogenetic characterization of animal viruses from metagenomic samples

Daniel Blanco, Icahn School of Medicine at Mount Sinai
Nicholas Meyerson, University of Colorado Boulder
Miriam Jetzabel Bravo-López, Laboratorio Internacional de Investigación sobre el Genoma Humano
Axel Guzmán-Solís, Cornell University
Qing Yang, University of Colorado Boulder

9:30AM - 1:30PM Mexican Central Time (CT) on October 24 & 25, 2020
Capacity: 30

Bats notoriously harbor a large amount of viruses, many of which have the potential to cross the species barrier and cause disease in humans. In this workshop, we will use high-throughput sequencing datasets from bat specimens to carry out de novo assembly of coronavirus genomes. We will then conduct phylogenetic analyses to classify assembled genomes and carry out evolutionary analyses to identify specific regions within viruses that are rapidly evolving due to positive selection.

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Workshop: Machine Learning in Bioinformatics using Galaxy

Björn Grüning, University of Freiburg  
Alireza Khanteymoori, University of Freiburg
Anup Kumar, University of Freiburg 

9:00AM - 5:00PM Mexican Central Time (CT) on October 26, 2020
Capacity: 30

This workshop will be a one-day event, including six sessions and during which we will train researchers to use Galaxy for machine learning analysis. The first session will provide an introduction to Galaxy. Galaxy is a scientific platform that helps scientists to analyse data without any programming skills. To analyse data, workflows can be created to make the analyses reproducible and shareable. In the second session, basic concepts in machine learning will be introduced. The next three sessions will serve as a hands-one sessions to follow training tutorials with case studies to see how classification algorithms, regression models and unsupervised learning methods in Galaxy can be used to solve real-world problems. In the last session, we will introduce feature selection and hyper parameter optimization methods in Galaxy and the workshop will be summing up at the end.

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Workshop: Identification of disease-associated genetic variants from next-generation sequencing data

Carla Daniela Robels Espinoza, Laboratorio Internacional de Investigación sobre el Genoma Humano and Wellcome Sanger Institute  
Carolina Castañeda-Garcia,  Laboratorio Internacional de Investigación sobre el Genoma Humano
Patricia Basurto-Lozada, Laboratorio Internacional de Investigación sobre el Genoma Humano  
Estefanía Vázquez-Cruz, Laboratorio Internacional de Investigación sobre el Genoma Humano 

10:00AM - 2:00PM Mexican Central Time (CT) on October 26 & 27, 202
Capacity: 25

Learn how to analyze NGS data to identify the genetic variants behind your phenotype of interest! This course will cover the analysis workflow behind variant discovery and association and will include both theoretical and practical sessions, focusing on quality control and variant calling methodologies.

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Workshop: Management and good practices in the assembly of bacterial, archaea and fungal genomes

Karla Ruiz, Winter Genomics
Violeta Larios,  Winter Genomics  
M. en C. Rogelio Reyes, Winter Genomics

9:00AM - 1:00PM Mexican Central Time (CT) on October 27, 2020
Capacity: 15

In this workshop you will gain knowledge and develop basic programming skills for genome assembly using Linux. For the practical part, data analysis will be done using raw files. You will learn which are the main tools used for data assembly like k-mer, ABySS and Spades and will practice how to use some of them. Finally, you will be able to identify the best approaches for data management and its analysis. It is not necessary to have programming skills.

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Workshop: Introduction to structural bioinformatics for evolutionary analysis

Claudia Alvarez Carreno, Georgia Institute of Technology
Alma Carolina Sanchez Rocha, Charles University

1:00PM - 5:00PM Mexican Central Time (CT) on October 27, 2020
Capacity: 50

Three-dimensional structure analysis can provide a biophysical understanding of how proteins work and evolve. Most evolutionary studies are based solely on sequence data. However, point mutations and sequence rearrangements have implications for protein structure. This tutorial will familiarize participants with straightforward bioinformatics protocols for combining evolutionary information and biophysical understanding of proteins. We will provide cutting edge bioinformatics algorithms to analyze both folded protein domains and intrinsically disordered proteins and regions.

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Workshop: How to annotate protein-coding genes in genomic sequences

Thomas Bruna, Georgia Institute of Technology
Alexandre Lomsadze, Georgia Institute of Technology
Mark Borodovsky, Georgia Institute of Technology

1:00PM - 5:00PM Mexican Central Time (CT) on October 27, 2020
Capacity: 20

In the gene finding tutorial, we will present a line of automatic gene finders for all types of genomes (prokaryotic, eukaryotic and metagenomes) with explanation of algorithmic concepts, choice of default parameters, input and output formats - along with demonstrations - and a short review of typical errors.


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