Wydział Biotechnologii i Hodowli Zwierząt - Biotechnology (S2)
Sylabus przedmiotu Bioinformatics:
Informacje podstawowe
| Kierunek studiów | Biotechnology | ||
|---|---|---|---|
| Forma studiów | studia stacjonarne | Poziom | drugiego stopnia |
| Tytuł zawodowy absolwenta | magister inżynier | ||
| Obszary studiów | charakterystyki PRK, kompetencje inżynierskie PRK | ||
| Profil | ogólnoakademicki | ||
| Moduł | — | ||
| Przedmiot | Bioinformatics | ||
| Specjalność | przedmiot wspólny | ||
| Jednostka prowadząca | Katedra Nauk o Zwierzętach Przeżuwających | ||
| Nauczyciel odpowiedzialny | Daniel Zaborski <Daniel.Zaborski@zut.edu.pl> | ||
| Inni nauczyciele | |||
| ECTS (planowane) | 4,0 | ECTS (formy) | 4,0 |
| Forma zaliczenia | egzamin | Język | angielski |
| Blok obieralny | — | Grupa obieralna | — |
Formy dydaktyczne
Wymagania wstępne
| KOD | Wymaganie wstępne |
|---|---|
| W-1 | The knowledge of mathematics, biophysics and biochemistry |
Cele przedmiotu
| KOD | Cel modułu/przedmiotu |
|---|---|
| C-1 | Learning about selected biological databases, sequence alignment algorithms, the issues of structural and functional genomics, phylogenetics and structural bioinformatics |
| C-2 | Acquiring the skills at retrieving necessary information from biological databases and using available programs for bioinformatics analyses |
Treści programowe z podziałem na formy zajęć
| KOD | Treść programowa | Godziny |
|---|---|---|
| laboratoria | ||
| T-L-1 | Biological literature databases. PubMed | 2 |
| T-L-2 | Nucleotide and protein sequence databases. GenBank, GenPept | 3 |
| T-L-3 | Data retrieval from biological databases. The NCBI databases. The Entrez system | 4 |
| T-L-4 | PCR primer design. Restriction site analysis. The Primer3 and NebCutter programs | 2 |
| T-L-5 | Python programming basics | 2 |
| T-L-6 | Searching nucleotide and protein sequence databases. BLAST | 2 |
| T-L-7 | Biological sequence analysis using Biopython | 2 |
| T-L-8 | An introduction to R | 2 |
| T-L-9 | Microarray data analysis using R and other programs | 4 |
| T-L-10 | Multiple sequence alignment. Phylogenetic tree construction. The Mega program | 4 |
| T-L-11 | Protein structural alignment | 2 |
| T-L-12 | Macromolecule visualization | 1 |
| 30 | ||
| wykłady | ||
| T-W-1 | An introduction to bioinformatics. Nucleotide and protein sequence databases. Data formats | 2 |
| T-W-2 | Databases of protein families and structures | 2 |
| T-W-3 | Pairwise sequence alignment and sequence database searching | 2 |
| T-W-4 | Genome sequence analysis. Genome comparisons | 2 |
| T-W-5 | Phylogenetics and phylogenetic trees | 3 |
| T-W-6 | Gene expression analysis. Microarray data analysis | 2 |
| T-W-7 | Selected issues of structural bioinformatics | 2 |
| 15 | ||
Obciążenie pracą studenta - formy aktywności
| KOD | Forma aktywności | Godziny |
|---|---|---|
| laboratoria | ||
| A-L-1 | Taking classes | 30 |
| A-L-2 | Preparation for classes | 18 |
| A-L-3 | Preparation for tests | 18 |
| A-L-4 | Consultation with the teacher | 2 |
| 68 | ||
| wykłady | ||
| A-W-1 | Participation in lectures | 15 |
| A-W-2 | Consultation with the teacher | 2 |
| A-W-3 | Preparation for the examination | 13 |
| A-W-4 | Examination | 2 |
| 32 | ||
Metody nauczania / narzędzia dydaktyczne
| KOD | Metoda nauczania / narzędzie dydaktyczne |
|---|---|
| M-1 | Lectures presenting theoretical issues |
| M-2 | Multimedia presentations |
| M-3 | Practical classes using computers |
Sposoby oceny
| KOD | Sposób oceny |
|---|---|
| S-1 | Ocena podsumowująca: Examination |
| S-2 | Ocena formująca: Practical test including classes 1-7 |
| S-3 | Ocena podsumowująca: Practical test including classes 8-15 |
Zamierzone efekty uczenia się - wiedza
| Zamierzone efekty uczenia się | Odniesienie do efektów kształcenia dla kierunku studiów | Odniesienie do efektów zdefiniowanych dla obszaru kształcenia | Odniesienie do efektów uczenia się prowadzących do uzyskania tytułu zawodowego inżyniera | Cel przedmiotu | Treści programowe | Metody nauczania | Sposób oceny |
|---|---|---|---|---|---|---|---|
| BTap_2A_BTA-S2-B02_W01 A student describes selected biological databases and basic data formats, explains the principles of sequence alignment, characterizes the types of genomic maps and the methods of genome sequencing, assembling, annotating and comparing, names the most important computer programs supporting the above-mentioned processes | BTap_2A_W14 | — | — | C-1 | T-W-1, T-W-2, T-W-3, T-W-4 | M-1, M-2 | S-1 |
| BTap_2A_BTA-S2-B02_W02 A student characterizes basic microarray types, their applications and the stages of DNA microarray data analysis, defines the concept of molecular phylogenetics, characterizes the methods of phylogenetic tree building and evaluation, describes the principles of protein secondary structure prediction, names the most important computer programs used in the above-mentioned analyses | BTap_2A_W14 | — | — | C-1 | T-W-6, T-W-7, T-W-5 | M-1, M-2 | S-1 |
Zamierzone efekty uczenia się - umiejętności
| Zamierzone efekty uczenia się | Odniesienie do efektów kształcenia dla kierunku studiów | Odniesienie do efektów zdefiniowanych dla obszaru kształcenia | Odniesienie do efektów uczenia się prowadzących do uzyskania tytułu zawodowego inżyniera | Cel przedmiotu | Treści programowe | Metody nauczania | Sposób oceny |
|---|---|---|---|---|---|---|---|
| BTap_2A_BTA-S2-B02_U01 A student can retrieve necessary information from an appropriate biological database, correctly interprets information contained in database records, efficiently uses basic computer programs for biological sequence analysis and basic Python commands | BTap_2A_U02 | — | — | C-2 | T-L-1, T-L-5, T-L-2, T-L-3 | M-3 | S-2 |
| BTap_2A_BTA-S2-B02_U02 A student can retrieve data from biological databases, create simple computer programs for nucleic acid sequence analysis, search for similar sequences in databases and align multiple sequences, construct phylogenetic trees based on appropriately selected sequences and interpret such trees | BTap_2A_U02 | — | — | C-2 | T-L-10, T-L-7, T-L-6 | M-3 | S-2, S-3 |
| BTap_2A_BTA-S2-B02_U03 A student uses basic R commands and the Bioconductor package for microarray data analysis, identifies differently expressed genes, creates and interprets heatmaps, uses computer programs for macromolecule visualization and protein structural alignments | BTap_2A_U02 | — | — | C-2 | T-L-11, T-L-12, T-L-8, T-L-9 | M-3 | S-3 |
Zamierzone efekty uczenia się - inne kompetencje społeczne i personalne
| Zamierzone efekty uczenia się | Odniesienie do efektów kształcenia dla kierunku studiów | Odniesienie do efektów zdefiniowanych dla obszaru kształcenia | Odniesienie do efektów uczenia się prowadzących do uzyskania tytułu zawodowego inżyniera | Cel przedmiotu | Treści programowe | Metody nauczania | Sposób oceny |
|---|---|---|---|---|---|---|---|
| BTap_2A_BTA-S2-B02_K01 A student uses bioinformatics tools for the interpretation of biological phenomena and processes, thus being convinced of their cognizability | BTap_2A_K02 | — | — | C-2 | T-L-10, T-L-11, T-L-12, T-L-1, T-L-7, T-L-8, T-L-5, T-L-6, T-L-2, T-L-3, T-L-9 | M-1, M-2, M-3 | S-2, S-3 |
| BTap_2A_BTA-S2-B02_K02 A student is aware of the abundance of biological information available in the Internet databases and the increasing importance of bioinformatics tools in the future | BTap_2A_K01 | — | — | C-2 | T-W-1, T-W-3, T-L-1, T-L-2 | M-1, M-2, M-3 | S-2 |
| BTap_2A_BTA-S2-B02_K03 A student is able to effective individual work based on provided teaching materials and information sources available on the Internet | BTap_2A_K05 | — | — | C-2 | T-L-10, T-L-11, T-L-12, T-L-1, T-L-7, T-L-8, T-L-5, T-L-6, T-L-2, T-L-3, T-L-9 | M-3 | S-2, S-3 |
Kryterium oceny - wiedza
| Efekt uczenia się | Ocena | Kryterium oceny |
|---|---|---|
| BTap_2A_BTA-S2-B02_W01 A student describes selected biological databases and basic data formats, explains the principles of sequence alignment, characterizes the types of genomic maps and the methods of genome sequencing, assembling, annotating and comparing, names the most important computer programs supporting the above-mentioned processes | 2,0 | |
| 3,0 | A student names selected biological databases, describes the concept of sequence alignment, names the basic programs for sequence database searching, describes the types of genomic maps, genome sequencing methods, genome assembly stages, and genome annotation, briefly characterizes the goals of comparative genomics | |
| 3,5 | ||
| 4,0 | ||
| 4,5 | ||
| 5,0 | ||
| BTap_2A_BTA-S2-B02_W02 A student characterizes basic microarray types, their applications and the stages of DNA microarray data analysis, defines the concept of molecular phylogenetics, characterizes the methods of phylogenetic tree building and evaluation, describes the principles of protein secondary structure prediction, names the most important computer programs used in the above-mentioned analyses | 2,0 | |
| 3,0 | A student names basic microarray types, the stages of DNA microarray data analysis, defines the concept of molecular phylogenetics, briefly characterizes the structure of a phylogenetic tree, the most important methods of phylogenetic tree construction and validation, names and briefly describes the algorithms for protein secondary structure prediction | |
| 3,5 | ||
| 4,0 | ||
| 4,5 | ||
| 5,0 |
Kryterium oceny - umiejętności
| Efekt uczenia się | Ocena | Kryterium oceny |
|---|---|---|
| BTap_2A_BTA-S2-B02_U01 A student can retrieve necessary information from an appropriate biological database, correctly interprets information contained in database records, efficiently uses basic computer programs for biological sequence analysis and basic Python commands | 2,0 | |
| 3,0 | A student uses basic tools for searching selected biological databases, interprets information contained in GenBank records, uses basic options of computer programs for biological sequence analysis and basic Python commands | |
| 3,5 | ||
| 4,0 | ||
| 4,5 | ||
| 5,0 | ||
| BTap_2A_BTA-S2-B02_U02 A student can retrieve data from biological databases, create simple computer programs for nucleic acid sequence analysis, search for similar sequences in databases and align multiple sequences, construct phylogenetic trees based on appropriately selected sequences and interpret such trees | 2,0 | |
| 3,0 | A student uses basic Biopython commands for creating simple scripts for nucleic acid sequence analysis, uses basic options of the BLAST and Clustal programs for database searching and multiple sequence alignment, can construct phylogenetic trees and interpret them | |
| 3,5 | ||
| 4,0 | ||
| 4,5 | ||
| 5,0 | ||
| BTap_2A_BTA-S2-B02_U03 A student uses basic R commands and the Bioconductor package for microarray data analysis, identifies differently expressed genes, creates and interprets heatmaps, uses computer programs for macromolecule visualization and protein structural alignments | 2,0 | |
| 3,0 | A student uses basic R commands, can import and export data in R, create R scripts, preprocess microarray data, identify differently expressed genes using appropriate statistical methods, create heatmaps and interpret them | |
| 3,5 | ||
| 4,0 | ||
| 4,5 | ||
| 5,0 |
Kryterium oceny - inne kompetencje społeczne i personalne
| Efekt uczenia się | Ocena | Kryterium oceny |
|---|---|---|
| BTap_2A_BTA-S2-B02_K01 A student uses bioinformatics tools for the interpretation of biological phenomena and processes, thus being convinced of their cognizability | 2,0 | |
| 3,0 | A student uses bioinformatics tools for the interpretation of biological phenomena and processes, thus being convinced of their cognizability | |
| 3,5 | ||
| 4,0 | ||
| 4,5 | ||
| 5,0 | ||
| BTap_2A_BTA-S2-B02_K02 A student is aware of the abundance of biological information available in the Internet databases and the increasing importance of bioinformatics tools in the future | 2,0 | |
| 3,0 | A student is aware of the abundance of biological information available in the Internet databases and the increasing importance of bioinformatics tools in the future | |
| 3,5 | ||
| 4,0 | ||
| 4,5 | ||
| 5,0 | ||
| BTap_2A_BTA-S2-B02_K03 A student is able to effective individual work based on provided teaching materials and information sources available on the Internet | 2,0 | |
| 3,0 | A student is able to effective individual work based on provided teaching materials and information sources available on the Internet | |
| 3,5 | ||
| 4,0 | ||
| 4,5 | ||
| 5,0 |
Literatura podstawowa
- Xiong J., Essential Bioinformatics, Cambridge University Press., Cambridge, 2006
- Higgs P. G., Attwood T. K., Bioinformatics and Molecular Evolution, Blackwell Science Ltd., Oxford., 2005
- Baxervanis A. D., Ouellette B. F. F. (red.), Bioinformatics. A Practical Guide to the Analysis of Genes and Proteins, John Wiley & Sons, Inc., New York, 2001
Literatura dodatkowa
- Hall B. G., Phylogenetic Trees Made Easy. A How-to-Manual, Sinauer Associates, Inc., Sunderland, MA, 2008
- Westhead D. R., Parish J. H., Twyman R. M., Bioinformatics. Instant Notes, Taylor & Francis, London & New York, 2002