Module 4 / Microbial Genomics & Metagenomics Workshop

The workshop is addressed to students and professionals of biology, biomedical research, the health sciences and related fields who are interested in learning and sharing concepts, tools and research results in genomics, metagenomics and the human microbiome. The workshop will train participants in state-of-the-art analytical methods in this area, by means of theoretical lectures and seminars as well as practical hands-on sessions in bioinformatics and biostatistics. Several sessions will be devoted to training in the use of the Integrated Microbial Genomes system (IMG), a database and analysis platform developed at the U.S. DOE Joint Genome Institute (Berkeley, California) for comprehensive studies of genomes and metagenomes. The IMG system will be presented by Dr. Mateus Fiamenghi and Dr. Rheka Seshadri from the JGI's Microbiome Data Science Program, the group responsible for IMG development. In addition, Dr. Vanessa R. Marcelino (Institute of Agrochemistry and Food Technology IATA-CSIC) and Dr. Kshitij Tandon (University of Melbourne) will introduce concepts and methodologies of metabolic reconstruction for single genomes and bacterial communities.

Language: English

Module costs: 350 euros

Location: Library -  Fisabio-Salud Pública. Av. Catalunya, 21. 46020 València

Registration

You can check the program

Instructors

Module program

Monday July 20th

09:00 - 10:00 Welcome and Overview of the Workshop by Dr. M. Pilar Francino, Dr. Rekha Seshadri and Dr. Mateus Fiamenghi. 10:00 - 11:00 Features and Diversity of Microbial Genomes by Dr. M. Pilar Francino.

Break

11:15 - 13:15 Microbial Communities, the Human Microbiome and its Relationship to Health by Dr. M. Pilar Francino

Lunch

15:00 - 16:30 Introduction to the Analysis of Bacterial Communities by Dr. M. Pilar Francino.

16:30 - 18:00 DNA Sequencing: History and Recent Technologies by Dr. Giuseppe D'Auria.

Tuesday July 21th

09:00 - 11:00 Informatic Processing, Quality Control, and Assembly of Sequencing Reads by Dr. Mariana Reyes

Break

11:15 - 12:15 Introduction to the Integrated Microbial Genomics System by Dr. Rekha Seshadri.

12:15 - 13:15 Introduction to Functional Annotation and Comparative Genomics in IMG by Dr. Rekha Seshadri.

Lunch

15:00 - 16:00 Isolate Comparative Genomics Case Study: Live Demo by Dr. Rekha Seshadri

16:00 - 18:00 Hands-on Exercise, Review and Discussion of Solutions (student work and supervision by Dr. Rekha Seshadri and Dr. M. Pilar Francino).

Wednesday July 22th

09:00 - 10:00 Introduction to IMG/M Metagenome Analysis by Dr. Mateus Fiamenghi

10:00 - 11:00 Metagenome Comparisons Case Study: Live Demo by Dr. Mateus Fiamenghi.

Break

11:15 - 13:15 Hands-on Exercise, Review and Discussion of Solutions (student work and supervision by Dr. Mateus Fiamenghi and Dr. M. Pilar Francino).

Lunch

15:00 - 18:00 CRISPR Analyses and Uncovering the Earth's Virome by Dr. David Páez-Espino.

Thursday July 23th

09:00 - 11:00 Preparation of student analysis projects: students form groups, choose their genome or metagenome analysis project and start carrying it out (student work and supervision by Dr. Rekha Seshadri, Dr. Mateus Fiamenghi and Dr. M. Pilar Francino).

Break

11:15 - 13:15 Preparation of student analysis projects: students complete their genome or metagenome analysis project and prepare a presentation (student work and supervision by Dr. Rekha Seshadri, Dr. Mateus Fiamenghi and Dr. M. Pilar Francino).

Lunch

15:00 - 18:00 Presentations of genome or metagenome analysis projects by student groups (student work and supervision by Dr. Rekha Seshadri, Dr. Mateus Fiamenghi and Dr. M. Pilar Francino).

Friday July 24th

09:00 - 11:00 Introduction to metabolic models of microbial communities by Dr. Vanessa R. Marcelino and Dr Kshitij Tandon

1. Introduction.

2. Genome-scale Metabolic Modeling: Live Demo.

Break

11:15 - 12:45

3. Expanding Genome-scale Metabolic Modeling to Bacterial Communities: Hands-on Exercise.

12:45 - 13:15 Workshop Summary and Discussion by Dr. M. Pilar Francino