Learning objectives
Knowledge and understanding: The course is primarily aimed at the acquisition of practical skills in the use of computers in Biology. Students will be taught the basic theoretical concepts necessary for an understanding of computer applications and bioinformatics.Applying knowledge and understanding: through practical exercises under the guidance of the teacher, the students will have the opportunity to acquire practical skills on how to use open-source personal productivity software, and the most important bioinformatics applications.Communication skills: through examples, students will learn how to report the results of computer analysis in a written report consisting of text and images, and how to organize their results in a multimedia presentation
Prerequisites
Elementary knowledge of Biology at the molecular level. Basics of computer use.
Course unit content
The first part of the course will address basic concepts about the use of computer and file management, as well as practical notions of the use of operating systems with graphical interface. Exercises will be carried out on applications for word processing, spreadsheets, multimedia presentationsThe second part of the course will introduce the areas of bioinformatics and discuss the analysis of the sequences and structures of DNA and proteins. Students will be made familiar with the main databases of biological macromolecules and the most common techniques of bioinformatics analysis
Full programme
Computer SkillsBasic concepts: meaning and scope of computer science.Computer usage and file management: practical notions of using operating systems with a graphical interface.General-purpose applications: practical word processing concepts, spreadsheets use, multimedia presentation preparation.Computer networks: practical uses of the World Wide Web.Bioinformatics skillsIntroduction to bioinformatics: meaning and areas of bioinformatics. Objects of bioinformatics: DNA and protein sequences, DNA and protein structures. Evolution of biological information over time.Biological sequences databases: definition and purpose of the databases; major DNA (GenBank, DDBJ, EMBL) and protein (SwissProt, Pir) databases. Questioning and consulting of the databases. Syntax of sequence FASTA format.Comparison of sequences: meaning and purpose of sequence alignment; Pairs alignment. Local and global algorithms alignment. Penalty for gap insertion and gap extension. Amino acid substitution matrices. Use Needle and Water programs.Search for homology: meaning of homology. Measurements of the significance of the alignment. Database homology research tools. Use of Blast program and interpretation of the homology search result.Multiple sequence alignment and phylogeny: use of multiple alignment using the ClustalX program. Multiple alignment display using the GeneDoc program. Phylogenetic reconstruction with the neighbor-joining algorithm implemented in Clustal. Viewing phylogenetic trees with the Treeview programPrediction of the biochemical characteristics of proteins: protein chemical-physical properties. Using the ProtParam program. Prediction of protein cellular localization. Use PSort and SignalP programs. Protein structure. Consultation of the PDB structure database. Viewing structures with the Rasmol program
Bibliography
Anna Tramontano: Bioinformatics. Zanichelli ed.
Teaching methods
The lessons of computer skills will be carried out mainly through practical exercises involving the use of computers by students. Students will learn the use of software for personal productivity: word processing, spreadsheets, and multimedia presentations.Part of the lectures on bioinformatics skills will focus on theoretical arguments through a discussion of the basic concepts of the subject. The lectures will be interposed with practical exercises directed to the use of the most common bioinformatics applications. During these lessons, students will be trained to search for biological information in the databases and to solve the most common problems of sequence analysis.During the practical exercises students will be able to follow step by step the use of the computer by the teacher and to replicate operations and controls on individual workstations.
Assessment methods and criteria
To check the general skills of the students, each student will present to the teacher a scientific report including text and figures, a spreadsheet table, and a short multimedia presentation.Bioinformatics skills will be tested through an individual test in which the student will provides the solution of some biological problems through bioinformatics applications. An understanding of the basic concepts of bioinformatics will be verified through a short interview.
Other information
The course makes use of a classroom for the practical calculation equipped with 35 workstations connected to the Internet and equipped with general and bioinformatics programs discussed during the course. Only applications and programs in the public domain will be used during the course.
