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.
Course Prerequisites
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. The student must possess a laptop computer.
Teaching Methods
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.
Assessment Methods
The exam will be writte, performed on the students computers. The students will be asked to perform basic bioinformatics exercises and answer theoretical questions.
Texts
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/)
Contents
The course is divided in two main modules.
The first module is focused on online Bioinformatics. The students will learn how to navigate databases and retrieve information from them.
The second module is focused on the basic usage of command line for ‘local’ bioinformatics. In this module the students will learn the basics of: Genome assembly Comparative genomics Alignment and Phylogenetics Mapping ranscriptomics
All lessons will start with theorical explanations and will contain pratical exercises to immediately apply the concepts explained.
