Contacto

 


 

Directora Summer School: 
M. Pilar Francino
 
Administrador Summer School:
Kevin Cifuentes
Telf.: 961 925 911

 


 
 
 

 

SUMMER SCHOOL - Module 4

 

 

Module 4 /  Microbial Genomics & Metagenomics Workshop

Dates: July 16th – July 20th 2018

Organizer: M. Pilar Francino
         

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 (Walnut Creek, California) for comprehensive studies of genomes and metagenomes. The IMG system will be presented by Dr. David Páez from the JGI's Microbial Genomics & Metagenomics Scientific Program, the group responsible for IMG development.

PREREGISTRATION

Module costs: 350 euros

Pre-registration (not open) until 15th of April 2018

Registration deadline 31st of May 2018

 

 

 

Instructors:

 

Alejandro Artacho, MS

Bioinformatician, FISABIO-PUBLIC HEALTH,  Genomics and Health Area.

artacho_ale@gva.es

 

Giuseppe D'Auria, PhD

Scientis, FISABIO-PUBLIC HEALTH,

Genomics and Health Are  and CIBERESP.

Coordinator of FISABIO Sequencing and Bioinformatics Service.

dauria_giu@gva.es

 

 

M. Pilar Francino, PhD

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

francino_pil@gva.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

 

David Perez-Villarroya, MS

MS in Bioinformatics, FISABIO-PUBLIC HEALTH, Bioinformatics technician

at FISABIO Sequencing and Bioinformatics Service

pevida@alumni.uv.es

 

Module program Summer School 2018:

Monday July 16th:


09:00 - 09:15 Welcome and Overview of the Workshop by Dr. M. Pilar Francino.

09:15 - 10:00 Features and Diversity of Microbial Genomes by Dr. M. Pilar Francino.

10:00 - 11:00 Microbial communities, the human microbiome and its relationship to health by Dr. M. Pilar Francino.

Break

11:15 - 13:15 Metagenomic and Metatranscriptomic Analyses of Bacterial Communities by Dr. María José Gosalbes.

Lunch

15:00 - 17:00 Informatic Processing and Quality Control of Sequencing Reads by Alejandro Artacho.

17:00 - 18:00 Unix commands and moving around the system (I) by David Pérez-Villarroya.

Tuesday July 17th:

09:00 - 10:00 Unix commands and moving around the system (II) by David Pérez-Villarroya.

10:00 - 11:00 Microbial Diversity Analyses with 16S rRNA (I) by Dr. Giuseppe D'Auria.

Break

11:15 - 13:15 Microbial Diversity Analyses with 16S rRNA (II) by Dr. Giuseppe D'Auria.

Lunch

15:00 - 18:00 Read Mapping and Variant Calling by Dr. Giuseppe D'Auria.

Wednesday July 18th:

09:00 - 11:00 Sequence Assembly and Annotation (I) by Dr. Giuseppe D'Auria.

Break

11:15 - 12:15 Sequence Assembly and Annotation (II) by Dr. Giuseppe D'Auria.

12:15 - 13:15 Introduction to the Integrated Microbial Genomics system by Dr David Páez.

Lunch

15:00 - 16:00 IMG Genomes: Live Demonstration by Dr. David Páez and Dr. M. Pilar Francino.

16:00 - 17:00 IMG Genes: Live Demonstration by Dr. David Páez and Dr. M. Pilar Francino.

17:00 - 18:00 IMG Functions and Pathways: Live Demonstration by Dr. David Páez and Dr. M. Pilar Francino.

Thursday July 19th:

09:00 - 10:00 Introduction to IMG/M by Dr. David Páez.

10:00 - 11:00 IMG/M Metagenome Analysis: Live Demonstration by Dr. David Páez and Dr. M. Pilar Francino.

Break

11:15 - 12:15 Metagenome Binning Techniques: from a User Perspective by Dr. David Páez.

12:15 - 13:15 Uncovering Earth's virome by Dr. David Páez

Lunch

15:00 - 16:00 Metagenome Analysis Research Talk by Dr. M. Pilar Francino.

16:00 - 18:00 Preparation of student analysis projects: students form groups and design their genome or metagenome analysis project, supervised by Dr. David Páez and Dr. M. Pilar Francino.

Friday July 20th:

09:00 - 11:00 Students complete their projects, supervised by Dr. David Páez and Dr. M. Pilar Francino.

Break

11:15 - 12:15 Presentations of metagenome analysis projects by student groups, supervised by Dr. David Páez and Dr. M. Pilar Francino.

12:15 - 13:15 IMG Tutorial Summary, Discussion and Questions, supervised by Dr. David Páez and Dr. M. Pilar Francino.

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