| First cycle degree courses | Second cycle degree courses | Single cycle degree courses |
| School of Science | ||
| COMPUTER SCIENCE | ||
Course unit
STRUCTURAL BIOINFORMATICS
SCP7079278, A.A. 2018/19
Information concerning the students who enrolled in A.Y. 2018/19
STRUCTURAL BIOINFORMATICS
SCP7079278, A.A. 2018/19
Information concerning the students who enrolled in A.Y. 2018/19
Information on the course unit
| Degree course |
Second cycle degree in COMPUTER SCIENCE SC1176, Degree course structure A.Y. 2014/15, A.Y. 2018/19 |
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|---|---|---|
| Number of ECTS credits allocated | 6.0 | |
| Type of assessment | Mark | |
| Course unit English denomination | STRUCTURAL BIOINFORMATICS | |
| Website of the academic structure | http://informatica.scienze.unipd.it/2018/laurea_magistrale | |
| Department of reference | Department of Mathematics | |
| Mandatory attendance | No | |
| Language of instruction | English | |
| Branch | PADOVA | |
| Single Course unit | The Course unit can be attended under the option Single Course unit attendance | |
| Optional Course unit | The Course unit can be chosen as Optional Course unit |
Lecturers
| Teacher in charge | SILVIO TOSATTO | BIO/10 | |
|---|---|---|---|
| Other lecturers | MOISES DI SANTE | BIO/10 |
Mutuated
| Course unit code | Course unit name | Teacher in charge | Degree course code |
|---|---|---|---|
| INP8084204 | STRUCTURAL BIOINFORMATICS | SILVIO TOSATTO | IN2371 |
| SCP7079278 | STRUCTURAL BIOINFORMATICS | SILVIO TOSATTO | SC2377 |
| INP8084204 | STRUCTURAL BIOINFORMATICS | SILVIO TOSATTO | IN2371 |
ECTS: details
| Type | Scientific-Disciplinary Sector | Credits allocated | |
|---|---|---|---|
| Educational activities in elective or integrative disciplines | BIO/10 | Biochemistry | 6.0 |
Course unit organization
| Period | Second semester |
|---|---|
| Year | 1st Year |
| Teaching method | frontal |
| Type of hours | Credits | Teaching hours |
Hours of Individual study |
Shifts |
|---|---|---|---|---|
| Practice | 2.0 | 16 | 34.0 | No turn |
| Lecture | 4.0 | 32 | 68.0 | No turn |
Examination board
| Board | From | To | Members of the board |
|---|---|---|---|
| 2 a.a. 2018/2019 | 01/10/2018 | 28/02/2020 |
TOSATTO
SILVIO
(Presidente)
DI SANTE MOISES (Membro Effettivo) BRINI MARISA (Supplente) SZABO' ILDIKO' (Supplente) ZANOTTI GIUSEPPE (Supplente) |
| 1 a.a. 2017/2018 | 01/10/2017 | 28/02/2019 |
TOSATTO
SILVIO
(Presidente)
BRINI MARISA (Membro Effettivo) CALI' TITO (Membro Effettivo) SZABO' ILDIKO' (Membro Effettivo) ZANOTTI GIUSEPPE (Membro Effettivo) |
| Prerequisites: | Basic knowledge of optimization methods and machine learning. Python programming language. |
| Target skills and knowledge: | The course intends to communicate basic knowledge on structure and function of living material as well as the main computational methods for its study. Moreover, it intends to enable the student to autonomously develop a research project in structural bioinformatics, defining the state of the art for an open problem and providing an attempt to solve it through the extension of existing software libraries and the critical evaluation of obtained results. |
| Examination methods: | The exam covers three separate parts, which have to be all passed: (relative weights in parenthesis)
1) Written test of the biochemistry concepts (ca. 30%) 2) Software project (ca. 40%) 3) Project presentation and critical evaluation (ca. 30%) |
| Assessment criteria: | 1) understanding of concepts and algorithms presented in class
2) the ability to apply the described concepts on real problems 3) the critical capacity of being able to use the methods in the most appropriate ways, choosing between the alternatives 4) the ability to develop reusable software by extending existing libraries 5) the ability for critical presentation and discussion |
| Course unit contents: | The course consists of two parts:
1) Introduction to living matter (2 credits): 1.1) Introduction to organic chemistry, weak interactions and energy 1.2) Structure and function of DNA and proteins 1.3) Lipids, membranes and cellular transport 1.4) Experimental methods for structure determination 2) Computational Biochemistry (4 credits): 2.1) Biological Databases 2.2) Software libraries and concepts for sequence alignments and database searches 2.3) Sequence - structure relationship in proteins and structural classification 2.4) Methods for the prediction of protein structure from sequence, the CASP experiment 2.5) Methods for the prediction of protein function and interactions, the CAFA experiment 2.6) Non-globular proteins, disorder and structural repeats |
| Planned learning activities and teaching methods: | The course consists of lectures, practical computer exercises, lecture note contribution and the development of a project and presentation of the same with critical discussion. The exercises are intended to familiarize the student with software libraries to use for a bioinformatics project on a current problem differentiated for each group. The project presentation will require a discussion in which to bring out the strengths and weakness of the implemented software. |
| Additional notes about suggested reading: | Many materials for the course are made available on the E-learning site. These include the transparencies of the course (as soon as available), lecture notes and literature used for the projects. The lecture notes can be downloaded in PDF format containing over 300 pages to facilitate the study. |
| Textbooks (and optional supplementary readings) |
|
- Lecturing
- Laboratory
- Problem solving
- Loading of files and pages (web pages, Moodle, ...)
