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. Natalia Ivanova and
Dr. Rekha Seshadri from the JGI's Microbial Genomics & Metagenomics Scientific
Program, the group responsible for IMG development.

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. Natalia Ivanova.
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 - 10:00 Informatic Processing and Quality Control of Sequencing Reads by Dr. Mariana Reyes.
10:00 - 11:00 Microbial Diversity Analyses with 16S rRNA (I) by Dr. Mariana Reyes.

Break

11:15 - 12:15 Introduction to the Integrated Microbial Genomics system by Dr. Natalia Ivanova.

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. Natalia Ivanova

10:00 - 11:00 Metagenome Comparisons Case Study: Live Demo by Dr. Natalia Ivanova.

Break

11:15 - 13:15  Hands-on Exercise, Review and Discussion of Solutions (student work and supervision by Dr. Natalia Ivanova 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

9:00 - 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 - 13:15  3) Expanding Genome-scale Metabolic Modeling to Bacterial Communities: Hands-on Exercise.

Lunch

15:00 - 18:00 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. Natalia Ivanova and Dr. M. Pilar Francino).

Friday July 24th

09:00 - 11:00 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. Natalia Ivanova and Dr. M. Pilar Francino).

Break

11:15 - 12:45 Presentations of genome or metagenome analysis projects by student groups (student work and supervision by Dr. Rekha Seshadri, Dr. Natalia Ivanova and Dr. M. Pilar Francino). 

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