PRINCIPLES OF COMPUTER MATHEMATICS AND PHYSICS APPLIED TO BIOTECHNOLOGY A - L

Module PRINCIPLES OF COMPUTER MATHEMATICS APPLIED TO BIOTECHNOLOGY

Brief Description.

The course aims to train the knowledge and skills necessary for the application of basic mathematical and computer science concepts for the construction of models helpful in understanding phenomena in Biology. The course also aims to develop the skills necessary to apply the most appropriate mathematical and statistical methodologies in developing such models.

General teaching objectives in terms of expected learning outcomes.

• Knowledge and understanding: The course aims to train the knowledge and skills necessary for the application of basic mathematical and computer science concepts for the construction of models useful in understanding the phenomena of Biology.
  
• Applying knowledge and understanding: the student will acquire the skills necessary for the use of essential mathematical and computer science tools in the field of biotechnology, the use of the main programming languages in bioinformatics, and other fundamental concepts for the development of mathematical or computer science methodology in bioinformatics.
  
• Making judgments: Through concrete examples and case studies, the student can independently develop solutions to specific problems related to computer science and mathematics applied to biotechnology.
  
• Communication skills: the student will acquire the necessary communication skills and expressive appropriateness in using technical language in the general field of computer science and mathematics applied to biotechnology.
  
• Learning skills: the course aims, as an objective, to provide the student with the necessary theoretical and practical methodologies to be able to face and solve independently new problems that may arise during a work activity. To this end, various topics will be covered in class involving the student in the search for possible solutions to real problems.
  

Teaching will be conducted mainly through lectures with a mixture of theory and practical lessons.

Should teaching be carried out in mixed mode or remotely, it may be necessary to introduce changes with respect to previous statements, in line with the programme planned and outlined in the syllabus.

The primary resources made available to the student are face-to-face lectures, whose attendance is MANDATORY.

To better follow the lectures, the slides used for the course are shared with the students. However, the slides do not constitute a means of study: they provide details on the topics covered in class.

The course will be organized into the following modules:

1. Essential computing: computer architecture; operating systems; algorithms and programs; programming languages; servers and web servers; databases.
   
2. Essential statistics: from sampling to parameter estimation (sampling, distributions); statistical inference; multivariate statistics and clustering methods.
   
3. Introduction to programming: basic concepts; the R language.
   
4. Introduction to Linux: the operating system; the shell, and the BASH language.
   
5. Introduction to bioinformatics: alignment between sequences and phylogenetic trees.
   
6. Introduction to biological databases: NCBI; ENSEMBL; Uniprot; biomedical databases.
   
7. Practical applications of informatics to biotechnology: sequencing platforms and computer analysis; genome reconstruction and annotation; transcriptome analysis.
   
8. Perspectives of bioinformatics and challenges of the omics era.
   

We recommend the use of the text "Fondamenti di bioinformatica," Authors: Manuela Helmer Citterich Fabrizio Ferrè Giulio Pavesi Graziano Pesole Chiara Romualdi, Zanichelli Publisher (2018).

Other updated resources will be indicated by the lecturer in the slides used in class.

The final examination consists of a written test and an oral interview.

The written test consists of exercises and theory questions.

Those who fail the written test cannot take the oral one. The written test may be viewed before the oral tests.

Unless otherwise announced, the written examination is held at 9:00 a.m.

Notes:

• Using any hardware tools (calculators, tablets, smartphones, cell phones, BT headsets, etc.), books, or personal papers during the (written) exams is prohibited.
  
• To take the exams, it is mandatory to make a reservation using the appropriate form on the student portal (therefore, in the absence of the prerequisites, it will not be possible to take the exam).
  
• Late bookings via email are not allowed. In the absence of reservation, the exam cannot be verbalized.
  
• Verification of learning may also be conducted electronically, should conditions require it.