Half day modules

Responsible
Heiko Schmidt and Nidia Trovao

TIME

CONTENT

SPEAKERS

Friday August 25: Morning

Module 1: Large phylogenies - Responsible Heiko Schmidt

8:30
to
9:30

Fast methods for large phylogenies.

H. Schmidt

9:30
to
10:15

Large phylogenies: practice

H. Schmidt

10:15
to
10:45

Coffee break.

10:45
to
11:45

Partition of large phylogenetic trees

H. Schmidt

11:45
to
12:30

Cluster analysis: practice.

H. Schmidt

12:30
to
13:30

Lunch.

Module 2: Molecular adaptation - Responsible Sergei Pond

8:30
to
10:30

Molecular adaptation: theory

A. Lucaci

10:30
to
10:45

Coffee break.

10:45
to
12:30

Molecular adaptation: practice (HYPHY)

A. Lucaci, D. Martin

12:30
to
13:30

Lunch.

Module 3: Biological Fundamentals of Mechanistic and Phylogenetic Modelling - Responsible José Lourenço

8:30
to
9:30

Epidemiological models: back to basics.

J. Lourenço, F. Pinotti

9:30
to
10:30

Epidemiological models: practice.

J. Lourenço, F. Pinotti

10:30
to
10:45

Coffee break.

10:45
to
12:30

Epidemiological dynamics with phylogenetic inference: practice.

J. Lourenço, F. Pinotti

12:30
to
13:30

Lunch.

Module 4: Tracking Pathogens Using Interactive Dashboards - Responsible Joicymara Xavier

08:30
to
09:30

Introduction to Genomic Surveillance and Public Health Informatics.
Preparing a dataset using Python, Jupyter Notebook, and Genome Detective Analysis

M Moir, N Sitharam, C Mavian, J Xavier

09:30
to
10:30

Preparing a dataset using Python, Jupyter Notebook, and Genome Detective

N Sitharam, C Mavian, J Xavier

10:30
to
10:45

Coffee break.

10:45
to
12:30

Introduction to Plotly (15 min) Reproducing a dashboard using the Genomic Dash framework (1:30)

J. Xavier, D. Castro

12:30
to
13:30

Lunch.

Friday August 25: Afternoon

Module 5: Visualization Of Large Phylogenies With Metadata - Responsible Níidia Trovão

13:30
to
14:30

Visualization of large phylogenies with metadata: an introduction

N. Trovão

14:30
to
15:30

Visualization and annotation of phylogenetic trees using ggtree.

T. Lam

15:30
to
16:00

Coffee break.

16:00
to
17:30

Real-time tracking of pathogen evolution using Nextstrain

J. Chang

Module 6: Recombination and networks - Responsible Darren Martin

13:30
to
14:30

Detecting Recombination: theory.

D. Martin

14:30
to
15:30

Detecting Recombination: practical computer session.

D. Martin

15:30
to
16:00

Coffee break.

16:00
to
17:30

Advanced recombination detection and networks: practice.

D. Martin

Module 7: Tools for viral NGS & phylogenetic analysis - Responsible Tulio de Oliveira

13:30
to
15:30

Using pipelines for viral analysis

T. de Oliveira, K. Deforche and V. Fonseca

15:30
to
16:00

Coffee break.

16:00
to
17:30

Panviral typing tools: practice.

T. de Oliveira, K. Deforche and V. Fonseca