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 28th – July 2nd 2021

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, all held via 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. Rekha Seshadri from the JGI's Microbiome Data Science Group, the group responsible for IMG development.

 

REGISTRATION

Module costs: 262'5 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

adpaezespino@lbl.gov

 

 

 

 

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 28th:


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.

15:30 - 16:45 Introduction to the Analysis of Bacterial Communities by Dr. María José Gosalbes.

Break

17:00 - 18:00 Uncovering Earth's virome by David Páez-Espino.

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

 

Tuesday June 29th:

14:00 - 15:00 Informatic Processing and Quality Control of Sequencing Reads by Mariana Reyes.

15:00 - 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

CLASSWORK or HOMEWORK

18:30 - 19:30 Hands-on Exercise (student work)

19:30 - 20:00 Review/Discuss solutions

 

Wednesday June 30th:

14:00 - 16:45 Microbial Diversity Analyses with 16S rRNA by Dr. Giuseppe D'Auria.

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

CLASSWORK or HOMEWORK

18:30 - 19:30 Hands-on Exercise (student work)

19:30 - 20:00 Review/Discuss solutions

 

Thursday July 1st:

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

15:00 - 16:45 CRISPR analyses in IMG by Dr. 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 July 2nd:

14:00 - 15:30 Introduction to Metatranscriptomics by Dr. María José Gosalbes.

15:30 - 16:45 Metagenome Analysis Research Talk by Dr. M. Pilar Francino.

Break

17:00 - 19:00 Presentations of projects by student groups

19:00 - 20:00 IMG Tutorial Summary, Discussion and Questions

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