Contacto
 


Directora Summer:
M. Pilar Francino

 
Administrador Summer School:
Kevin Cifuentes
Telf.: 961 925 911


 

SUMMER SCHOOL - Module 3

 

 

Module 3 / FISABIO Summer School in Biomedical Research and Public Health: Microbial Genomics & Metagenomics Workshop

Dates: June 26th – June 30th 2017

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.

 

Module costs: 350 euros

Pre-registration (now open) until 15th of April 2017

Registration deadline 31st of May 2017

 

 

 

Instructors:

 

Alejandro Artacho

MS in Bioinformatics, FISABIO-SP, Bioinformatician at Genomics and Health Area.

artacho_ale@gva.es

 

Giuseppe D’Auria

PhD., FISABIO-SP, Coordinator of 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

 

Amparo Latorre

PhD. Scientist, FISABIO-PUBLIC HEALTH Genomics and Health Area and
CIBERESP. Professor of Genetics, University of Valencia

amparo.latorre@uv.es

David Páez

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

adpaezespino@lbl.gov

 

David Perez-Villarroya

MS. in Bioinformatics, FISABIO-PUBLIC HEALTH, Bioinformatics technician
at FISABIO Sequencing and Bioinformatics Service

pevida@alumni.uv.es

 

Module program:

Monday June 26th:


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. Amparo Latorre.

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 June 27th:

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 June 28th:

09:00 - 11:00 Sequence Assembly and Annotation by Dr. Giuseppe D’Auria.

Break

11:15 - 12:15 Introduction to the Integrated Microbial Genomics system by Dr David Páez.

12:15 - 13:15 IMG Genomes: Live Demonstration by Dr. David Páez and Dr. M. Pilar Francino.

Lunch

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

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

17:00 - 18:00 Genome Analysis Research Talk by Dr. Amparo Latorre.

Thursday June 29th:

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 June 30th:

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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