Contact

 
 
Summer School Director: 
M. Pilar Francino
 
Summer School Administrator:
Kevin Cifuentes
Telf.: 961 925 911

 
 
 
 
 
 

 

SUMMER SCHOOL - Module 4

 

 

Module 4 /  Microbial Genomics & Metagenomics Workshop

Dates: June 20th – June24th 2022

Organizer: M. Pilar Francino (francino_pil@gva.es)
         

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 exercises, in a combination of in person and online live sessions in constant interaction with the instructors. 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. Rheka Seshadri from the JGI's Microbial Genomics & Metagenomics Scientific Program, the group responsible for IMG development.

 

REGISTRATION

Module costs: 350 euros

 

 

 

Instructors:

 

M. Pilar Francino, PhD

Scientist, FISABIO-PUBLIC HEALTH Genomics and Health Area and      
CIBERESP

francino_pil@gva.es

 

 

 

Giuseppe D'Auria, PhD

University of Valencia, Bioinformatician at Institutional Chair FISABIO - University of Valencia.

 

dauria_giu@gva.es

 

David Perez-Villarroya, MS

MS in Bioinformatics, FISABIO-PUBLIC HEALTH, Bioinformatics
technicianat FISABIO Sequencing and Bioinformatics Service

pevida@alumni.uv.es

 

M José Gosalbes, PhD

Scientist, FISABIO-PUBLIC HEALTH Genomics and 

Health Area and CIBERESP.

gosables_mjo@gva.es

 

David Páez

PhD. Scientist, JGI, Microbial Genomics & Metagenomics Scientific Program

paezespino@gmail.com

 

 

 

 

Mariana Reyes,

MS. in molecular, cellular biology and genetics, 
FISABIO- PUBLIC HEALTH, Bioinformatician at Sequencing and Bioinformatics Service
 

(reyes_ber@gva.es)

 

 

 

Natalia Ivanova

PhD. Scientist, JGI, Microbial Genomics & Metagenomics Scientific Program

nnivanova@lbl.gov

Rekha Seshadri

PhD. Scientist, JGI, Microbial Genomics & Metagenomics Scientific Program

rseshadri@lbl.gov

 

Module program:

Monday June 20th:

- 14:00 - 14:30 Welcome and Overview of the Workshop by Dr. M. Pilar Francino.
- 14:30 - 15:30 Features and Diversity of Microbial Genomes by Dr. M. Pilar Francino.

Break

- 15:45 - 16:45 Introduction to the Analysis of Bacterial Communities by Dr. María José Gosalbes.

Break

- 17:00 - 18:00 Introduction to Metatranscriptomics by Dr. María José Gosalbes.

Break

- 18:15 - 20:00 Unix commands and moving around the system by David Pérez-Villarroya.

Tuesday June 21st:

- 14:00 - 15:00 Informatic Processing and Quality Control of Sequencing Reads by Dr. Giuseppe D’Auria.

Break

- 15:15 - 16:45 Sequence Assembly by Dr. Giuseppe D’Auria.

Break

- 17:00 - 17:30 IMG UI Intro: Live Demonstration by Dr. Natalia Ivanova
- 17:30 - 18:00 Functional Annotation in IMG by Dr. Rekha Seshadri
- 18:00 - 18:30 Isolate Comparative Genomics Case Study:  Live Demo by Dr. Rekha Seshadri

Break

CLASSWORK or HOMEWORK

- 18:45 - 19:30 Hands-on Exercise (student work)
- 19:30 - 20:00 Review/Discuss solutions

Wednesday June 22nd:

- 14:00 - 15:30 Microbial Diversity Analyses with 16S rRNA by Mariana Reyes

Break

- 15:45 - 16:45 Microbial Diversity Analyses with 16S rRNA by Mariana Reyes.

Break

- 17:00 - 18:00 IMG/M Metagenome Analysis: Live Demonstration by Dr. Natalia Ivanova
- 18:00 - 18:30 Metagenome Comparisons Case Study:  Live Demo by Dr. Natalia Ivanova

Break

CLASSWORK or HOMEWORK

- 18:45 - 19:30 Hands-on Exercise (student work)
- 19:30 - 20:00 Review/Discuss solutions

Thursday June 23rd:

- 14:00 - 15:00 Microbial communities, the human microbiome and its relationship to health by Dr. M. Pilar Francino.

Break

- 15:15 - 16:45 CRISPR analyses by David Páez-Espino.

Break

- 17:00 - 17:30 Preparation of student analysis projects - students form groups and carry out genome or metagenome analysis project
- 17:30 - 20:00 Instructors circulate in Breakout rooms or ON CALL to answer questions or help troubleshoot

Friday June 24th:

- 14:00 - 15:30 Metagenome Analysis Research Talk by Dr. M. Pilar Francino.

Break

- 15:45- 16:45 Uncovering Earth’s virome by David Páez-Espino.

Break

- 17:00 - 19:00 Presentations of projects by student groups
- 19:00 - 20:00 IMG Tutorial Summary, Discussion and Questions

 

Download Document