Contacto

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

 
 
 

 

SUMMER SCHOOL - Module 1

 

 

Module 1 / FISABIO Summer School in Biomedical Research and Public Health: Basic Computational Skills for Genomic Analysis
 
Dates: June 19th- June 23rd 2023
 
Coordinator: Giuseppe D'Auria (dauria_giu@gva.es)
 
The course is addressed to students and professionals of biology, biomedical research, the health sciences and related fields who are interested in learning the basic computational skills required to pursue their own genomic analyses. The module will be eminently practical and hands-on, and will teach participants skills ranging from the installation and basic use of Linux systems to the building of analysis pipelines and the utilization of Qiime2 as platform for metataxonomy analysis. Theoretical lectures and practical hands-on sessions will be taught by FISABIO researchers and informaticians. 
 
Official language: English. 
 
Central Europe Time.
 
You can check the program  
 
 
Instructors:
 

 

 

 

 

 

 

 

Pascual Asensi. 

Systems Administrator,

University of Valencia (pascual.asensi@uv.es).

Guiseppe D'Auria. 

PhD., FISABIO-SP, Head of Bioinformatics Service (dauria_giu@gva.es).

Rosario GIl. 

Associate professor, University of Valencia (rosario.gil@uv.es).

 

Mariana Reyes.

MS in molecular, cellular biology and genetics, FISABIO-SP, Bioinformatician at Sequencing and Bioinformatics Service (reyes_ber@gva.es).

David Perez-Villaroya.

Bioinformatics technician 

(pevida@alumni.uv.es).

Jorge González Garrido

Bioinformatics technician

jorge.gonzalez@fisabio.es

 

Course program:

 

Monday June 19th:

09:15 – 10:00 Next generation sequencingtechnologies: the birth of the Genomics Era

                        Rosario Gil

10:00 – 10:45 Comparative genomics for genome annotation and functional analysis.

                        Rosario Gil

Break

11:00 – 11:45 NGS in microbial ecology (Taxonomy and metagenomics).

                        Rosario Gil

11:45 – 13:00 Linux system, installing a new distro I.

                        Pascual Asensi

Lunch

14:30 – 16:00 Linux system, installing a new distro II.

                        Pascual Asensi

16:00 – 16:30 From office automation to computation for NGS.

                        Giuseppe D'Auria

16:30 – 17:30 Unix commands, moving around the system, practice I.

                        David Perez-Villarroya

 

Tuesday June 20th:

09:00 – 10:45 Unix commands, moving around the system, practice II.

                        David Perez-Villarroya

Break

11:00 – 12:00  One command line pipelines, practice.

                        David Perez-Villarroya

12.00 – 13.00 NGS Bioinformatics formats, managing data.

                        David Perez-Villarroya

Lunch

14.30 – 15.30 NGS Bioinformatics formats, managing data, practice.

                        Giuseppe D'Auria

15:30 – 16:30 Genome Assembly and mapping.

                        Giuseppe D'Auria

16:30 – 17:30  Genome assembly, practice.

                        Giuseppe D'Auria

 

Wednesday June 21th:

09:00 – 10:45 Genome mapping, practice.

                        Giuseppe D'Auria

Break

11:00 – 12:00 Qiime2: Introduction. How to install the environment, applications.

                        Mariana Reyes

12:00 – 13:00 Qiime2:Data formats and operations.

                        Mariana Reyes

Lunch

14:30 – 15:30 Qiime2: Hands-on section.

                        Mariana Reyes

15:30 – 16:30 Qiime2: Denoising.

                        Mariana Reyes

16:30 – 17:30 Qiime2: Hands-on section.

                        Mariana Reyes

 

Thursday June 22th: 

09:00 – 10:45 Qiime2: Taxonomic annotation and descriptive statistics.

                        Mariana Reyes

Break

11:00 – 12:00 Qiime2: Alignment and phylogenetic reconstruction.

                        Mariana Reyes

12:00 – 13:00 Qiime2: Qiime2: Hands-on section

                        Mariana Reyes

Lunch

14:30 – 16:00 Qiime2: Differential abundance analysis.
                     
                        Jorge González Garrido


16:00 – 17:30 Qiime2: Qiime2: Hands-on section.
                      
                        Mariana Reyes

 

Friday June 23th: 

09:00 – 10:00 Creating scripts and pipelines.

                        Giuseppe D'Auria

10:00 – 10:45 Students projects.

                        Giuseppe D'Auria

Break

11:00 – 11:30 Students projects.

                        Giuseppe D'Auria

11:30 – 12:00 Questionnaires.

                        Giuseppe D'Auria

12:00 – 13:00 NGS sequencing and beyond.

                        Rosario Gil