B8793 - BIOINFORMATICA APPLICATA ALLE MALATTIE TRASMISSIBILI

Learning outcomes

By the end of the course, the student understands the principles, objectives, and techniques of bioinformatics applied to transmissible diseases; is able to evaluate nucleotide sequencing outputs; knows when and how to use software and algorithms for the analysis of nucleotide and/or amino acid sequences, and can interpret the results to reconstruct the evolution and phylogeny of the agents responsible for transmissible diseases.

Course contents

This course is part of the Integrated Course “B8790 - METODICHE DIAGNOSTICHE E BIOINFORMATICA APPLICATE ALLE MALATTIE TRASMISSIBILI”. Upon completion of the Integrated Course, the student will have acquired knowledge and understanding of the theoretical principles and practical applications of epidemiology, laboratory techniques, and bioinformatics as applied to the diagnosis and study of infectious diseases. The student will be able to apply, perform, and interpret the main diagnostic tests, as well as conduct sequence analyses for the genetic characterization and phylogenetic analysis of pathogens responsible for infectious diseases.

SPECIFIC COURSE CONTENT

The course is structured as follows, integrating theoretical lectures with hands-on practical sessions in a computer laboratory:

• Sanger sequencing and Next-Generation Sequencing (NGS): principles of the methodologies; generation and quality assessment of sequencing data; identification and correction of the main sequencing errors and artefacts (4 hours of lectures and 14 hours of practical sessions).
• Biological databases, sequence alignment algorithms and sequence assembly (2 hours of lectures and 8 hours of practical sessions).
• Sequence analysis for genetic characterization and phylogenetic analysis (2 hours of lectures and 8 hours of practical sessions).
• Practical application of the acquired knowledge and skills in preparation for the final assessment of learning outcomes (2 hours).

Readings/Bibliography

The course is predominantly practice-oriented and includes in-class, face-to-face training aimed at developing the bioinformatics skills required for the examination.

The teaching materials for this course are available on the Virtuale Learning Environment (https://virtuale.unibo.it/?lang=en ).

Supplementary reading:

• The phylogeny Handbook. A practical approach to phylogenetic analyses and hypothesis testing. Second edition. Philippe Lemey, Marco Salemi e Anne-Mieke Vandamme. Cambridge University Press, 2009

Teaching methods

The course consists of face-to-face theoretical lectures integrated with practical sessions conducted in a computer laboratory.

During the practical sessions, students work individually or in pairs at computer workstations using online platforms and open-source bioinformatics software. The hands-on activities are carried out by following the instructor's demonstrations on a shared screen and a tutorial provided at the beginning of the course. Practical sessions also include the analysis of case studies and group work.

Considering the types of activities and teaching methods adopted, attendance for this course requires the successful completion of Modules 1, 2 and 3, via e-learning, on health and safety training in study environments.

Assessment methods

The course B8793 BIOINFORMATICA APPLICATA ALLE MALATTIE TRASMISSIBILI is predominantly practice-oriented and is designed to provide students with the computational skills required to successfully complete the final examination.

The assessment for the Integrated Course unit “METODICHE DIAGNOSTICHE E BIOINFORMATICA APPLICATE ALLE MALATTIE TRASMISSIBILI” consists of two parts:

• First part: a 2-hour multiple-choice written examination comprising 20 questions on the topics covered in B8791 DIAGNOSTICA DELLE MALATTIE PARASSITARIE and 18 questions on the topics covered in B8792 DIAGNOSTICA DELLE MALATTIE INFETTIVE. The examination is designed to assess the acquisition of the expected knowledge. For B8791 DIAGNOSTICA DELLE MALATTIE PARASSITARIE, the examination consists of 20 multiple-choice questions, of which 10 are worth 1 point each and 10 are worth 2 points each. Correct answers are awarded the corresponding number of points, while incorrect or unanswered questions receive 0 points. For B8792 DIAGNOSTICA DELLE MALATTIE INFETTIVE, the examination consists of 18 multiple-choice questions, each worth 1 point. Correct answers are awarded 1 point, while incorrect or unanswered questions receive 0 points. No supplementary materials or electronic devices (e.g., calculators, tablets, smartwatches, computers) may be used during the exam, except for those explicitly allowed by the instructor.
• Second part: a 2-hour practical/written examination covering the topics taught in B8793 BIOINFORMATICA APPLICATA ALLE MALATTIE TRASMISSIBILI. The examination is designed to assess the acquisition of the expected theoretical knowledge and practical skills. The computer-based practical component consists of the qualitative evaluation of a sequencing chromatogram, the interpretation of a scientific paper presenting a phylogenetic tree, and the performance of the bioinformatics analyses covered during the course. Completion of the practical component enables students to answer nine open-ended questions in the written component of the examination. Each correct answer is awarded 2 points, while incorrect or unanswered questions receive 0 points. During the examination, the use of any supporting materials or electronic devices, including calculators, tablets, smartwatches, and computers, is permitted. However, the use of artificial intelligence (AI) tools is strictly prohibited.

The combined assessment components carry a maximum total of 66 points. The final grade is expressed on a 30-point scale. The examination is considered passed with a minimum overall score of 36/66 points, corresponding to 18/30. A score of 61/66 points or higher is awarded the final grade of 30 cum laude.

The final grade will be published on the AlmaEsami platform (https://almaesami.unibo.it/?lang=en ) within 5 working days of the date of the exam. Negative results are not graded numerically but recorded as “withdrawn” or “failed” in the electronic transcript on AlmaEsami, and do not affect the student’s academic record.

Students may reject the final grade, by informing the course examiner via email within 5 working days.

The designated course contact for this course is Prof.ssa Monica Caffara

Students can register for exams through the AlmaEsami platform (http://almaesami.unibo.it/ ). Exams are scheduled during the designated periods in the academic calendar. Additional sessions are available for students beyond the standard program duration.

Students with learning disorders and/or temporary or permanent disabilities: please, contact the office responsible (https://site.unibo.it/studenti-con-disabilita-e-dsa/en/for-students ) as soon as possible so that they can propose acceptable adjustments. The request for adaptation must be submitted in advance (15 days before the exam date) to the lecturer, who will assess the appropriateness of the adjustments, taking into account the teaching objectives.

With regard to the learning assessment, the use of AI is prohibited. Any use of AI constitutes a breach of academic integrity.

Teaching tools

PowerPoint presentations and tutorials for the computer-based practical activities.

In case of difficulty understanding the course content, the instructor is available for clarification meetings, which must be scheduled via email.

Office hours

See the website of Andrea Balboni