International Centre for Genetic Engineering and Biotechnology
Practical Course
"Bioinformatics: Computer Methods in Molecular and Systems Biology"
AREA Science Park - Trieste, ITALY
26 - 30 June 2017
PRELIMINARY PROGRAMME
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MONDAY, 23 May |
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08:00 |
Pick-up from Hotel Roma |
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08:30 |
Course Registration |
ICGEB Foyer, 'W' Building |
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09:15 |
Welcome Address |
ICGEB Seminar room, 'W' Building |
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09:30 |
Bioinformatics and knowledge representation: theoretical intro to the course |
Sándor Pongor, Pázmány University, Budapest, HU |
10:45 |
Coffee break |
‘C’ Building, Area Science Park |
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11:15 |
The course computer infrastructure |
Leonardo Mariño-Ramirez, |
12:30 |
Bioinformatics Databases |
Sándor Pongor Get Tutorial
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| 13:30 | LUNCH | Cafeteria, Ground Floor, 'C' Building |
14:30 |
Sequence analysis, database searching (BLAST) |
Leonardo Mariño-Ramirez |
17:00 |
Get-Together Party |
ICGEB Foyer, 'W' Building |
| 18:00 | BUS TO HOTEL |
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TUESDAY, 24 May |
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08:30 |
Pick-up from Hotel |
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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 |
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WEDNESDAY, 25 May |
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08:30 |
Pick-up from Hotel |
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09:00 |
Brief introduction to NGS technologies (Illumina, PacBio, Oxford Nanopore) |
Laurent Falquet, University of Fribourg, Switzerland |
10:00 |
Introduction to QC (FastQC), remapping reads with BWT algorithm (Bowtie, BWA) |
Laurent Falquet |
11:00 |
Coffee break |
‘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) |
Laurent Falquet |
15:30 |
Exercises: de novo assembly, (optional PROKKA annotation), viewing and comparing draft genomes with MAUVE |
Laurent Falquet |
| 18:00 | BUS TO HOTEL |
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THURSDAY, 26 May |
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08:30 |
Pick-up from Hotel |
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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 |
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FRIDAY, 27 May |
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08:30 |
Pick-up from Hotel |
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09:00 |
Chip-seq, RNA-seq, expression analysis |
Leonardo Marino-Ramirez |
11:00 |
Coffee break |
‘C’ Building, Area Science Park |
11:30 |
Chip-seq, RNA-seq, expression analysis |
Leonardo Marino-Ramirez |
| 13:30 | LUNCH | Cafeteria, Ground Floor, 'C' Building |
14:30 |
Chip-seq, RNA-seq, expression analysis |
Leonardo Marino-Ramirez |
| 18:00 | Course Ends, BUS TO HOTEL |
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