Zachodniopomorski Uniwersytet Technologiczny w Szczecinie

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

Forma dydaktycznaKODSemestrGodzinyECTSWagaZaliczenie
laboratoriaL1 30 2,70,41zaliczenie
wykładyW1 15 1,30,59egzamin

Wymagania wstępne

KODWymaganie wstępne
W-1The knowledge of mathematics, biophysics and biochemistry

Cele przedmiotu

KODCel modułu/przedmiotu
C-1Learning about selected biological databases, sequence alignment algorithms, the issues of structural and functional genomics, phylogenetics and structural bioinformatics
C-2Acquiring the skills at retrieving necessary information from biological databases and using available programs for bioinformatics analyses

Treści programowe z podziałem na formy zajęć

KODTreść programowaGodziny
laboratoria
T-L-1Biological literature databases. PubMed2
T-L-2Nucleotide and protein sequence databases. GenBank, GenPept3
T-L-3Data retrieval from biological databases. The NCBI databases. The Entrez system4
T-L-4PCR primer design. Restriction site analysis. The Primer3 and NebCutter programs2
T-L-5Python programming basics2
T-L-6Searching nucleotide and protein sequence databases. BLAST2
T-L-7Biological sequence analysis using Biopython2
T-L-8An introduction to R2
T-L-9Microarray data analysis using R and other programs4
T-L-10Multiple sequence alignment. Phylogenetic tree construction. The Mega program4
T-L-11Protein structural alignment2
T-L-12Macromolecule visualization1
30
wykłady
T-W-1An introduction to bioinformatics. Nucleotide and protein sequence databases. Data formats2
T-W-2Databases of protein families and structures2
T-W-3Pairwise sequence alignment and sequence database searching2
T-W-4Genome sequence analysis. Genome comparisons2
T-W-5Phylogenetics and phylogenetic trees3
T-W-6Gene expression analysis. Microarray data analysis2
T-W-7Selected issues of structural bioinformatics2
15

Obciążenie pracą studenta - formy aktywności

KODForma aktywnościGodziny
laboratoria
A-L-1Taking classes30
A-L-2Preparation for classes18
A-L-3Preparation for tests18
A-L-4Consultation with the teacher2
68
wykłady
A-W-1Participation in lectures15
A-W-2Consultation with the teacher2
A-W-3Preparation for the examination13
A-W-4Examination2
32

Metody nauczania / narzędzia dydaktyczne

KODMetoda nauczania / narzędzie dydaktyczne
M-1Lectures presenting theoretical issues
M-2Multimedia presentations
M-3Practical classes using computers

Sposoby oceny

KODSposób oceny
S-1Ocena podsumowująca: Examination
S-2Ocena formująca: Practical test including classes 1-7
S-3Ocena podsumowująca: Practical test including classes 8-15

Zamierzone efekty uczenia się - wiedza

Zamierzone efekty uczenia sięOdniesienie do efektów kształcenia dla kierunku studiówOdniesienie do efektów zdefiniowanych dla obszaru kształceniaOdniesienie do efektów uczenia się prowadzących do uzyskania tytułu zawodowego inżynieraCel przedmiotuTreści programoweMetody nauczaniaSposób 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_W14C-1T-W-1, T-W-2, T-W-3, T-W-4M-1, M-2S-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_W14C-1T-W-6, T-W-7, T-W-5M-1, M-2S-1

Zamierzone efekty uczenia się - umiejętności

Zamierzone efekty uczenia sięOdniesienie do efektów kształcenia dla kierunku studiówOdniesienie do efektów zdefiniowanych dla obszaru kształceniaOdniesienie do efektów uczenia się prowadzących do uzyskania tytułu zawodowego inżynieraCel przedmiotuTreści programoweMetody nauczaniaSposób 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_U02C-2T-L-1, T-L-5, T-L-2, T-L-3M-3S-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_U02C-2T-L-10, T-L-7, T-L-6M-3S-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_U02C-2T-L-11, T-L-12, T-L-8, T-L-9M-3S-3

Zamierzone efekty uczenia się - inne kompetencje społeczne i personalne

Zamierzone efekty uczenia sięOdniesienie do efektów kształcenia dla kierunku studiówOdniesienie do efektów zdefiniowanych dla obszaru kształceniaOdniesienie do efektów uczenia się prowadzących do uzyskania tytułu zawodowego inżynieraCel przedmiotuTreści programoweMetody nauczaniaSposób 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_K02C-2T-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-9M-1, M-2, M-3S-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_K01C-2T-W-1, T-W-3, T-L-1, T-L-2M-1, M-2, M-3S-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_K05C-2T-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-9M-3S-2, S-3

Kryterium oceny - wiedza

Efekt uczenia sięOcenaKryterium 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
3,0A 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
3,0A 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 sięOcenaKryterium 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
3,0A 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
3,0A 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
3,0A 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 sięOcenaKryterium 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
3,0A 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
3,0A 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
3,0A 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

  1. Xiong J., Essential Bioinformatics, Cambridge University Press., Cambridge, 2006
  2. Higgs P. G., Attwood T. K., Bioinformatics and Molecular Evolution, Blackwell Science Ltd., Oxford., 2005
  3. 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

  1. Hall B. G., Phylogenetic Trees Made Easy. A How-to-Manual, Sinauer Associates, Inc., Sunderland, MA, 2008
  2. Westhead D. R., Parish J. H., Twyman R. M., Bioinformatics. Instant Notes, Taylor & Francis, London & New York, 2002

Treści programowe - laboratoria

KODTreść programowaGodziny
T-L-1Biological literature databases. PubMed2
T-L-2Nucleotide and protein sequence databases. GenBank, GenPept3
T-L-3Data retrieval from biological databases. The NCBI databases. The Entrez system4
T-L-4PCR primer design. Restriction site analysis. The Primer3 and NebCutter programs2
T-L-5Python programming basics2
T-L-6Searching nucleotide and protein sequence databases. BLAST2
T-L-7Biological sequence analysis using Biopython2
T-L-8An introduction to R2
T-L-9Microarray data analysis using R and other programs4
T-L-10Multiple sequence alignment. Phylogenetic tree construction. The Mega program4
T-L-11Protein structural alignment2
T-L-12Macromolecule visualization1
30

Treści programowe - wykłady

KODTreść programowaGodziny
T-W-1An introduction to bioinformatics. Nucleotide and protein sequence databases. Data formats2
T-W-2Databases of protein families and structures2
T-W-3Pairwise sequence alignment and sequence database searching2
T-W-4Genome sequence analysis. Genome comparisons2
T-W-5Phylogenetics and phylogenetic trees3
T-W-6Gene expression analysis. Microarray data analysis2
T-W-7Selected issues of structural bioinformatics2
15

Formy aktywności - laboratoria

KODForma aktywnościGodziny
A-L-1Taking classes30
A-L-2Preparation for classes18
A-L-3Preparation for tests18
A-L-4Consultation with the teacher2
68
(*) 1 punkt ECTS, odpowiada około 30 godzinom aktywności studenta

Formy aktywności - wykłady

KODForma aktywnościGodziny
A-W-1Participation in lectures15
A-W-2Consultation with the teacher2
A-W-3Preparation for the examination13
A-W-4Examination2
32
(*) 1 punkt ECTS, odpowiada około 30 godzinom aktywności studenta
PoleKODZnaczenie kodu
Zamierzone efekty uczenia sięBTap_2A_BTA-S2-B02_W01A 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
Odniesienie do efektów kształcenia dla kierunku studiówBTap_2A_W14knows advanced bioinformatics techniques and the possibilities of their use in the field of biotechnology
Cel przedmiotuC-1Learning about selected biological databases, sequence alignment algorithms, the issues of structural and functional genomics, phylogenetics and structural bioinformatics
Treści programoweT-W-1An introduction to bioinformatics. Nucleotide and protein sequence databases. Data formats
T-W-2Databases of protein families and structures
T-W-3Pairwise sequence alignment and sequence database searching
T-W-4Genome sequence analysis. Genome comparisons
Metody nauczaniaM-1Lectures presenting theoretical issues
M-2Multimedia presentations
Sposób ocenyS-1Ocena podsumowująca: Examination
Kryteria ocenyOcenaKryterium oceny
2,0
3,0A 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
PoleKODZnaczenie kodu
Zamierzone efekty uczenia sięBTap_2A_BTA-S2-B02_W02A 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
Odniesienie do efektów kształcenia dla kierunku studiówBTap_2A_W14knows advanced bioinformatics techniques and the possibilities of their use in the field of biotechnology
Cel przedmiotuC-1Learning about selected biological databases, sequence alignment algorithms, the issues of structural and functional genomics, phylogenetics and structural bioinformatics
Treści programoweT-W-6Gene expression analysis. Microarray data analysis
T-W-7Selected issues of structural bioinformatics
T-W-5Phylogenetics and phylogenetic trees
Metody nauczaniaM-1Lectures presenting theoretical issues
M-2Multimedia presentations
Sposób ocenyS-1Ocena podsumowująca: Examination
Kryteria ocenyOcenaKryterium oceny
2,0
3,0A 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
PoleKODZnaczenie kodu
Zamierzone efekty uczenia sięBTap_2A_BTA-S2-B02_U01A 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
Odniesienie do efektów kształcenia dla kierunku studiówBTap_2A_U02knows how to plan and analyze biotechnology research using bioinformatics tools
Cel przedmiotuC-2Acquiring the skills at retrieving necessary information from biological databases and using available programs for bioinformatics analyses
Treści programoweT-L-1Biological literature databases. PubMed
T-L-5Python programming basics
T-L-2Nucleotide and protein sequence databases. GenBank, GenPept
T-L-3Data retrieval from biological databases. The NCBI databases. The Entrez system
Metody nauczaniaM-3Practical classes using computers
Sposób ocenyS-2Ocena formująca: Practical test including classes 1-7
Kryteria ocenyOcenaKryterium oceny
2,0
3,0A 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
PoleKODZnaczenie kodu
Zamierzone efekty uczenia sięBTap_2A_BTA-S2-B02_U02A 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
Odniesienie do efektów kształcenia dla kierunku studiówBTap_2A_U02knows how to plan and analyze biotechnology research using bioinformatics tools
Cel przedmiotuC-2Acquiring the skills at retrieving necessary information from biological databases and using available programs for bioinformatics analyses
Treści programoweT-L-10Multiple sequence alignment. Phylogenetic tree construction. The Mega program
T-L-7Biological sequence analysis using Biopython
T-L-6Searching nucleotide and protein sequence databases. BLAST
Metody nauczaniaM-3Practical classes using computers
Sposób ocenyS-2Ocena formująca: Practical test including classes 1-7
S-3Ocena podsumowująca: Practical test including classes 8-15
Kryteria ocenyOcenaKryterium oceny
2,0
3,0A 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
PoleKODZnaczenie kodu
Zamierzone efekty uczenia sięBTap_2A_BTA-S2-B02_U03A 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
Odniesienie do efektów kształcenia dla kierunku studiówBTap_2A_U02knows how to plan and analyze biotechnology research using bioinformatics tools
Cel przedmiotuC-2Acquiring the skills at retrieving necessary information from biological databases and using available programs for bioinformatics analyses
Treści programoweT-L-11Protein structural alignment
T-L-12Macromolecule visualization
T-L-8An introduction to R
T-L-9Microarray data analysis using R and other programs
Metody nauczaniaM-3Practical classes using computers
Sposób ocenyS-3Ocena podsumowująca: Practical test including classes 8-15
Kryteria ocenyOcenaKryterium oceny
2,0
3,0A 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
PoleKODZnaczenie kodu
Zamierzone efekty uczenia sięBTap_2A_BTA-S2-B02_K01A student uses bioinformatics tools for the interpretation of biological phenomena and processes, thus being convinced of their cognizability
Odniesienie do efektów kształcenia dla kierunku studiówBTap_2A_K02demonstrates understanding of biotechnological processes used in various areas of human activity; interprets and describes these processes using a scientific approach
Cel przedmiotuC-2Acquiring the skills at retrieving necessary information from biological databases and using available programs for bioinformatics analyses
Treści programoweT-L-10Multiple sequence alignment. Phylogenetic tree construction. The Mega program
T-L-11Protein structural alignment
T-L-12Macromolecule visualization
T-L-1Biological literature databases. PubMed
T-L-7Biological sequence analysis using Biopython
T-L-8An introduction to R
T-L-5Python programming basics
T-L-6Searching nucleotide and protein sequence databases. BLAST
T-L-2Nucleotide and protein sequence databases. GenBank, GenPept
T-L-3Data retrieval from biological databases. The NCBI databases. The Entrez system
T-L-9Microarray data analysis using R and other programs
Metody nauczaniaM-1Lectures presenting theoretical issues
M-2Multimedia presentations
M-3Practical classes using computers
Sposób ocenyS-2Ocena formująca: Practical test including classes 1-7
S-3Ocena podsumowująca: Practical test including classes 8-15
Kryteria ocenyOcenaKryterium oceny
2,0
3,0A 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
PoleKODZnaczenie kodu
Zamierzone efekty uczenia sięBTap_2A_BTA-S2-B02_K02A student is aware of the abundance of biological information available in the Internet databases and the increasing importance of bioinformatics tools in the future
Odniesienie do efektów kształcenia dla kierunku studiówBTap_2A_K01demonstrates the need to constantly improve general and directional knowledge; is aware of the purposefulness of raising the acquired knowledge both in professional activities and personal development
Cel przedmiotuC-2Acquiring the skills at retrieving necessary information from biological databases and using available programs for bioinformatics analyses
Treści programoweT-W-1An introduction to bioinformatics. Nucleotide and protein sequence databases. Data formats
T-W-3Pairwise sequence alignment and sequence database searching
T-L-1Biological literature databases. PubMed
T-L-2Nucleotide and protein sequence databases. GenBank, GenPept
Metody nauczaniaM-1Lectures presenting theoretical issues
M-2Multimedia presentations
M-3Practical classes using computers
Sposób ocenyS-2Ocena formująca: Practical test including classes 1-7
Kryteria ocenyOcenaKryterium oceny
2,0
3,0A 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
PoleKODZnaczenie kodu
Zamierzone efekty uczenia sięBTap_2A_BTA-S2-B02_K03A student is able to effective individual work based on provided teaching materials and information sources available on the Internet
Odniesienie do efektów kształcenia dla kierunku studiówBTap_2A_K05shows discipline in individual work; willing to participate in group work; can creatively plan and implement own and team activities
Cel przedmiotuC-2Acquiring the skills at retrieving necessary information from biological databases and using available programs for bioinformatics analyses
Treści programoweT-L-10Multiple sequence alignment. Phylogenetic tree construction. The Mega program
T-L-11Protein structural alignment
T-L-12Macromolecule visualization
T-L-1Biological literature databases. PubMed
T-L-7Biological sequence analysis using Biopython
T-L-8An introduction to R
T-L-5Python programming basics
T-L-6Searching nucleotide and protein sequence databases. BLAST
T-L-2Nucleotide and protein sequence databases. GenBank, GenPept
T-L-3Data retrieval from biological databases. The NCBI databases. The Entrez system
T-L-9Microarray data analysis using R and other programs
Metody nauczaniaM-3Practical classes using computers
Sposób ocenyS-2Ocena formująca: Practical test including classes 1-7
S-3Ocena podsumowująca: Practical test including classes 8-15
Kryteria ocenyOcenaKryterium oceny
2,0
3,0A 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