Aim of the course is to provide students with the basic knowledge of bioinformatic methodologies, tools and approaches that are essential part of biomedical research. While the students will not be proficient in bioinformatics after this course, the objective is for them to understand that bioinformatics is accessible, the broad range of applications that bioinformatics can have, and how helpful it can be for analysis of any biological dataset.
Prerequisiti
In order to be able to follow the course, the students must have a good grasp of the basic concepts of molecular biology. This should include understanding the concepts of gene, introns and exons, promoters, genome, transcription and translation and so on. Basic knowledge of DNA sequencing techniques is required.
Metodi didattici
All lessons will require the students to have their own laptop. They will be guided in the installation of a virtual machine or a conda environment to allow to perform the subsequent tasks. This will allow to constantly follow a theoretical explanation with a practical execution of the concept. The students will be asked to perform the tasks that the teacher explained, to maximize the connection between theory and practice. The constant presence of tutors will allow to help students that are having issues during the practical parts.
Verifica Apprendimento
The students will be tested through a single examination. The test include both theoretical and pratical, to allow to evaluate the preparation of the students on the different course modules. The practical part will ask the student to solve basic bioinformatic issues using databases, the command line and the softwares covered in the course.
Testi
Due to the quick changing nature of the discipline, the students should mostly lean on the slides and their own notes to study, however some reference textbooks are indicated below. – Lesk A –Introduction to bioinformatics . Oxford Univ. Press, ed.
– Westhead DR, Parish JH, Twyman RM Bioinformatics (Instant notes)- Taylor and Francis, ed.
- NCBI Help Manual (http://www.ncbi.nlm.nih.gov/books/NBK3831/)
Contenuti
The course is divided in modules, each comprising theory explanation and integrated praticals to apply them.
The first module is focused on DNA sequencing technologies
The second module is focused on databases: Databases for Genomics (GenBank, SRA, ENA) Databases for Proteomics and Metabolomics Genome Browsing (UCSC, NCBI-GDV, Ensembl)
The third module is focused on the basic usage of the Unix command line The following modules will be on managing and exploiting sequencing data: Genome assembly Comparative genomics Phylogenetics Mapping Comparative transcriptomics.
