Contact

 

 

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


SUMMER SCHOOL - Module 3

 

 

 

 



Module 3/ Basic Computational Skills for Genomic Analysis

Dates: July 1st- July 5th 2019

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 the main functions available in the "R" platform for statistical analysis of genomes and metagenomes. Theoretical lectures and practical hands-on sessions will be taught by FISABIO researchers and informaticians.

Official language: English.

Module costs: 350 euros

PREREGISTRATION

Instructors:

Alejandro Artacho. MS in Bioinformatics, FISABIO-SP, Bioinformatician at Genomics and Health Area.
Pascual Asensi. Systems Administrator, University of Valencia, Genomics and Health Area.
Giuseppe D'Auria. PhD., FISABIO-SP, Coordinator of Sequencing and Bioinformatics Service.
Rosario Gil. Associate professor, University of Valencia.
David Perez-Villarroya. MS. in Bioinformatics, FISABIO-SP, Bioinformatics technician at  Sequencing and Bioinformatics Service.

 

Giuseppe D'Auria

PhD., FISABIO-SP, Coordinator of Sequencing and Bioinformatics Service.

dauria_giu@gva.es

 

 

David Perez-Villarroya

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

perez_davvil@gva.es

 

 

Rosario Gil

Associate professor, University of Valencia.

rosario.gil@uv.es

 

 

 

Pascual Asensi

Systems Administrator, University of Valencia, Genomics and Health Area.

Pascual.Asensi@uv.es

 

 

 

 

Mariana Reyes

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

 

 

 

 

 

 

Course program Summer School 2019:

Monday July 1st


09:15 – 10:00 Next generation sequencing technologies: 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 July 2nd:

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.
        Giuseppe D'Auria

12.00 – 13.00 NGS Bioinformatics formats, managing data.
        Giuseppe D'Auria

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 July 3rd:

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 July 4th:

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 – 15:40 Qiime2: Differential abundance analysis.
         Mariana Reyes
 
16:00 – 17:30 Qiime2: Qiime2: Hands-on section.
         Mariana Reyes
 

Friday July 5th:

09:00 – 10:45 Students Projects.
          Giuseppe D'Auria
 
Break
 
11:00 – 12:00 Tests and questionnaires. 
         Giuseppe D'Auria
 
12:00 – 13:00 NGS sequencing and beyond. 
         Rosario Gil
 


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