Integrated course: Scientific method and linguisticsModule Computer science
Academic Year 2023/2024 - Teacher: ANTONIO DI MARIAExpected Learning Outcomes
Objective of the course is the acquisition of methods for the analysis of biological sequences and structures and the capability of searching in in biological databases (eg. Genes, sequences, functional domains). Starting from primary sequences of nucleic acids or proteins can hypothesize the function, evolutionary history and structure. The tools used to achieve these objectives are the public databases and the tools for the analysis and visualization of such kind of data.
- Knowledge and understanding: Students will gain knowledge on methods for the analysis of biological sequences and for searching in biological databases. In particular students will be able to search on database of sequences and domains. Also, public databases available on NCBI will be presented together with software for the and the analysis and visualization of biological data. Finally, students will acquire the basic tools for the analysis of the transcriptome.
- Applying knowledge and understanding: identify the appropriate tools to manipulate data and extract knowledge underlying; solve problems through the use of appropriate software in bioinformatics.
- Making judgments: Through guided exercises, the students will acquire the basic skills necessary to deal with the analysis of new biological sequences, hypothesizing the function, study the transcriptome.
- Communication skills: the student will acquire the necessary communication skills and expressive appropriateness in the use of technical language within the general framework of the analysis of biological data.
- Learning skills: The course aims, as the goal, to provide students with the necessary basic theoretical methods and practices in order to address and solve problems concerning the analysis of biological data.
Course Structure
Lectures and practical exercises.
Should teaching be carried out in mixed mode or remotely, it may be necessary to introduce changes concerning previous statements, in line with the program planned and outlined in the syllabus.
Required Prerequisites
Attendance of Lessons
Detailed Course Content
The course is organized into lectures that provide a theoretical basis coupled with exercises for learning the use of bioinformatics tools in the field of medicine.
PROGRAM
- Introduction
- Pairwise and Multiple alignment
- Biological Databases: General Databases (NCBI, EMBL), Specialized Databases (OMIM, CIVIC, Drugbank, KEGG Pathway)
- Tools for the analysis of the transcriptome: Microarray, Next Generation Sequencing, Analysis of the transcriptome
- R language and applications to bioinformatics.
Textbook Information
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.
Course Planning
| Subjects | Text References | |
|---|---|---|
| 1 | Introduction to bioinformatics: data types, problems, tools. | Zanichelli Chapters 2 and 16. |
| 2 | Pairwise alignment: basic concepts, alignment theory, formats, BLAST algorithm. | Zanichelli Capitoli 4 e 5 |
| 3 | Multiple alignment: basic concepts, phylogenetic trees, CLUSTALW algorithm and neighbor-joining. | Zanichelli Capitoli 5 e 6. |
| 4 | General biological databases: Gene, Nucleotide, Protein, Pubmed | Materials provided by the lecturer. |
| 5 | Biological databases for medicine: OMIM, CIVIC, Drugbank | Materials provided by the lecturer. |
| 6 | Genome sequencing and analysis: Next Generation Sequencing (NGS) and NGS analysis pipeline | Zanichelli Capitoli 7, 8 e 9. |
| 7 | Transcriptome analysis: microarray and transcriptomic analysis pipeline | Zanichelli Capitolo 10. |
| 8 | Galaxy Platform: General structure of Galaxy and example of genomic analysis in Galaxy | Materials provided by the lecturer. |
| 9 | R language: general constructs, Bioconductor and differential analysis of gene expression in R | Materials provided by the lecturer. |
Learning Assessment
Learning Assessment Procedures
The final exam consists of a written test or an oral interview at the teacher's discretion.
The written test lasts 1 hour.
The grade is expressed in thirtieths up to 30/30 and honors.
Unless otherwise announced, the written exam is held at 11:00 a.m.
The written test consists of multiple-choice questions dealing with the topics of the program of the discipline. The test consists of 20 multiple-choice questions, each of which will be assigned a maximum score of 1.6 points. The minimum grade to pass the test is 18/30.
The test allows to verify: i) the level of knowledge of the discipline; ii) the ability to apply this knowledge to the resolution of specific problems inherent to applications in the clinical field (problem-solving to the autonomy of judgment); iii) clarity of exposition; and iv) property of medical-scientific language.
The following parameters will be taken into account in awarding the final grade:
Grade 29-30 cum laude: the student has a thorough knowledge of the topics covered, readily and correctly succeeds in integrating and critically analyzing the situations presented, independently solving even highly complex problems, has excellent communication skills, and masters the medical-scientific language.
Grade 26-28: The student has a good knowledge of the topics covered, manages to integrate and analyze critically and linearly the situations presented, works to solve complex problems independently enough, and expounds the issues using appropriate medical-scientific language;
Grade 22-25: the student has a fair knowledge of the topics covered, although limited to the main issues; succeeds in integrating and analyzing critically but not always linearly the situations presented, and expounds the problems quite clearly with a fair command of language;
Grade 18-21: the student has minimal knowledge of the topics covered, has a modest ability to integrate and critically analyze the situations presented, and expounds the arguments sufficiently clearly, although language property is poorly developed;
Exam not passed: the student does not possess the required minimum knowledge of the main contents of the teaching. In addition, there is little or no ability to use specific language, and he cannot apply the knowledge acquired independently.
Notes:
- To take the exams, it is mandatory to make reservations using the appropriate form on the student portal.
- Late reservations via email are not allowed. If no reservation is made, the exam cannot be verbalized.