Bioinformatics 2017

Preliminary programme

 

Monday 26th June

08:00

Pick-up from Hotel Roma

 

08:30

Course Registration

ICGEB Foyer, 'W' Building

09:15

Welcome Address

ICGEB Seminar room, 'W' Building

09:30

Bioinformatics and knowledge representation:
theoretical intro to the course

Sándor Pongor, Pázmány University, Budapest, Hungary

10:45

Coffee break

'C' Building, Area Science Park

11:15

The course computer infrastructure

Leonardo Mariño-Ramirez, Roberto Vera, NCBI, NIH, Bethesda, MD, USA

12:30

Bioinformatics Databases

Sándor Pongor

13:30

LUNCH

Cafeteria, Ground Floor, 'C' Building

14:30

Sequence analysis, database searching (BLAST)

Leonardo Mariño-Ramirez, Roberto Vera

17:00

Get-Together Party

ICGEB Foyer, 'W' Building

18:00

BUS TO HOTEL

 

 

Tuesday 27th June

08:30

Pick-up from Hotel

 

09:00

Intro to Linux (fun with UNIX)

Christoph W. Sensen, Technical University, Graz, Austria

11:00

Coffee break

'C' Building, Area Science Park

11:30

Multiple alignment, tree-building

Christoph W. Sensen

13:30

LUNCH

Cafeteria, Ground Floor, 'C' Building

14:30

Phylogenetics

Christoph W. Sensen

18:00

BUS TO HOTEL

 

 

Wednesday 28th June

08:30

Pick-up from Hotel

 

09:00

Brief introduction to NGS technologies (Illumina, PacBio, Oxford Nanopore).

 

Introduction to QC (FastQC), remapping reads with BWT algorithm (Bowtie, BWA)

Laurent Falquet, University of Fribourg, Switzerland

11:00

Coffee break and Group Photo

'C' Building, Area Science Park

11:30

Exercises: reads QC, remapping, viewing bam files with IGV

Laurent Falquet

13:30

LUNCH

Cafeteria, Ground Floor, 'C' Building

14:30

 Introduction to de novo genome assembly with de Bruijn graph (SPAdes) and OLC for PacBio (HGAP3, Canu)

Exercises: de novo assembly, (optional PROKKA annotation), viewing and comparing draft genomes with MAUVE

Laurent Falquet

18:00

BUS TO HOTEL

 

 

Thursday 29th June

08:30

Pick-up from Hotel

 

09:00

Genome annotation and Metagenomics

Christoph W. Sensen

11:00

Coffee break

'C' Building, Area Science Park

11:30

Genome annotation and Metagenomics

Christoph W. Sensen

13:30

LUNCH

Cafeteria, Ground Floor, 'C' Building

14:30

Genome annotation and Metagenomics

Christoph W. Sensen

18:00

BUS TO HOTEL

 

 

Friday 30th June

08:30

Pick-up from Hotel

 

09:00

Chip-seq, RNA-seq, expression analysis

Leonardo Mariño-Ramirez

11:00

Coffee break

'C' Building, Area Science Park

11:30

Chip-seq, RNA-seq, expression analysis

Leonardo Mariño-Ramirez

13:30

LUNCH

Cafeteria, Ground Floor, 'C' Building

14:30

Chip-seq, RNA-seq, expression analysis

Leonardo Mariño-Ramirez

18:00

Course Ends, BUS TO HOTEL

 

 

Get tutorials

Laurent FALQUET

http://net.icgeb.org/course/2017/materials/05/denovoAssembly_Trieste2017.pdf
http://net.icgeb.org/course/2017/materials/05/Mapping_Trieste2017.pdf
http://net.icgeb.org/course/2017/materials/05/NGS_technologies_Trieste2017.pdf
http://net.icgeb.org/course/2017/materials/05/SNP_Trieste2017.pdf
http://net.icgeb.org/course/2017/materials/05/TPICGEB_asm_script.pdf
http://net.icgeb.org/course/2017/materials/05/TPICGEB_remap-script.pdf
http://net.icgeb.org/course/2017/materials/05/TPICGEB_snpcalling-script.pdf

 

Leonardo MARIÑO-RAMÍREZ

Monday:
http://net.icgeb.org/course/2017/materials/01/course_infrastructure.pptx
http://net.icgeb.org/course/2017/materials/03/Practical_BLAST.pptx

Friday:
http://net.icgeb.org/course/2017/materials/07/1.1-Functional_Genome_Annotation.pptx
http://net.icgeb.org/course/2017/materials/07/1.1-RNA-seq.pptx
http://net.icgeb.org/course/2017/materials/07/1.2-NGS_Analysis_handson.pptx
http://net.icgeb.org/course/2017/materials/07/1.2-RNA-seq-handson.pptx

 

Sándor PONGOR

http://net.icgeb.org/course/2017/materials/00/Pongor_Bioinformatics_intro_2017.pptx
http://net.icgeb.org/course/2017/materials/02/Pongor_Databases.pptx

 

Christoph SENSEN

Tuesday:
http://net.icgeb.org/course/2017/materials/04/Trieste_4D_Bioinformatics.ppt
http://net.icgeb.org/course/2017/materials/04/Trieste_Intro_to_Linux_XFCE.pptx
http://net.icgeb.org/course/2017/materials/04/Trieste_Phylogenetic_Analysis_and_Phylogenetic_Trees.ppt
http://net.icgeb.org/course/2017/materials/04/Trieste_Social_Networking.pptx
http://net.icgeb.org/course/2017/materials/04/Trieste_ThinLinc_Intro.pptx
http://net.icgeb.org/course/2017/materials/04/Trieste_Metagenomics.htm

Thursday:
http://net.icgeb.org/course/2017/materials/06/Trieste_Circulating_Nucleic_Acids.pptx
http://net.icgeb.org/course/2017/materials/06/Trieste_Genome_Annotation.ppt
http://net.icgeb.org/course/2017/materials/06/Trieste_Metagenomic_Analysis.pptx
http://net.icgeb.org/course/2017/materials/06/Trieste_RNA_Seq.ppt
http://net.icgeb.org/course/2017/materials/06/Trieste_Phylogenetics.html
http://net.icgeb.org/course/2017/materials/06/Trieste_Short_Read_Alignment.htm

 

 

Participants will need to have their own laptop with an internet browser installed to access the course Google Cloud infrastructure and remote high speed computing facility for sessions and practical exercises - see technical requirements

 

 

 

 

Meetings&CoursesUnit 27/06/2017