2nd Bioinformatics Introductory Course
OCTOBER 20th 24th, 2014
Polo d’Innovazione Genomica, Genetica e Biologia S.C. a R.L,
Sant’Andrea delle Fratte, Edificio D 3°piano, Facoltà di Medicina e Chirurgia–Perugia
PROGRAMME:
Mo 20th Oct 2014
9:00-11:00
11:00-11:30
11:30-13:00
13:00-14:30
14:30-18:30
K. Louis - IMBB-FORTH & Dept. Biology, University of Crete, Greece – Centre of
Functional Genomics, University of Perugia, Italy
“Introduction to Bioinformatics and Genomics”
Coffee break
Talk in System Biology
Lunch
P. Palladino – Polo Innovazione GGB, Perugia, Italy
“Linux Fundamentals”
- The Linux Operating System
- Commands and shell
- Filesystem and permissions
- File manipulation and editing
- Advanced file and stream manipulation
- Regular Expressions
- Bash scripting (conditional expr., loops)
- Examples and practice
Tu 21th Oct 2014
9:00-11:00
D. Lawson – European Bioinformatics Institute (EBI), Hinxton, UK
“Mining for biological data: Biological databases and portals”
- Introduction to biological databases
- Sequence databases and portals
- Using Entrez to search Genbank
- Using Biomart to search Ensembl
- FlyBase, WormBase, EuPathDB, VectorBase
- Non sequence specific databases and portals
- Literature databases
- Kyoto Encyclopedia of Genes and Genomes
11:00-11:30
11:30-13:00
13:00-14:30
14:30-18:00
Coffee break
D. Lawson - EBI, Hinxton, UK (cont.)
Lunch
K. Louis – IMBB-FORTH & Dept. Biology, University of Crete, Greece – Centre
of Functional Genomics, University of Perugia, Italy
“Ontologies: a primer”
- Basic characteristic
- Construction of ontologies
- Use of ontologies
- Ontologies in the biomedical domain
- Gene Ontology
- Formats: OBO vs OWL
- Editors: OBO-Edit, Protégé
We 22th Oct 2014
9:00-11:00
11:00-11:30
11:30-13:00
13:00-14:30
14:30-18:00
A. Muzzi - Novartis Vaccines and Diagnostics, Siena, Italy
“Next-Generation Sequencing”
- NGS platforms and technologies
- Whole-genome sequencing
- RNA-sequencing
- Whole-exome sequencing
- Targeted sequencing
- Metagenomics
Coffee break
A. Vitale – Illumina Inc., San Diego, USA
“Illumina NGS-Redifining the trajectory of Sequencing”
Lunch
D. Lawson – European Bioinformatics Institute (EBI), Hinxton, UK
“Genome Assembly and annotation”
Th 23th Oct 2014
9:00-11:00
G. Gasperi - Professor of Zoology - Department of Biology and Biotechnology,
University of Pavia, Italy
“Introduction: Population biology”
11:00-11:30 Coffee break
11:30-13:00 L. M. Gomulski - Assistant Professor of Zoology, Department of Biology and
Biotechnology, University of Pavia, Italy
“Practice: Population biology”
13:00-15:00 Lunch
15:00-17:00 T. Dottorini – Centre of Functional Genomics, University of Perugia, Italy Department of Life Sciences, Imperial College London, London
“Structural bioinformatics”
17:00-18:30 A. Policriti – Professor of Informatics, University of Udine, Italy
Member of Scientific Committe IMOVE/ Polo GGB
Group leader of Bioinformatics -IGA (Istituto di Genomica Applicata), Parco
Scientifico e Tecnologico “L. Danieli”, Udine.
“Sequence Analysis for Epigenomics"
Fr 24th Oct 2014
9:00-11:00 P. Papathanos - Centre of Functional Genomics, University of Perugia, Italy
- Department of Life Sciences, Imperial College London, London
“Gene expression and RNA profiling”
- Expression data Analysis
- Examples and practice
11:00-11:30 Coffee break
11:30-13:00 P. Papathanos (cont.)
13:00-14:30 Lunch
14:30-16:30
Q&As with all Speakers and Seminars
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