Course modules

Course Information

Course Information Course Information

Page

Contact information 3MK013 Contact information 3MK013 1

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Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark completed Must mark this module item done in order to complete Marked completed Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Page

Information for first year students: courses, applications and reexams 2025-03-31 Information for first year students: courses, applications and reexams 2025-03-31 2

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Page

Previous Course evaluations Previous Course evaluations 4

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Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark completed Must mark this module item done in order to complete Marked completed Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Page

Welcome to the course Welcome to the course 5

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Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark completed Must mark this module item done in order to complete Marked completed Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Page

Registration to Uppmax Registration to Uppmax 6

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Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark completed Must mark this module item done in order to complete Marked completed Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Page

Software installation Software installation 7

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Part 0 Introduction to Linux

Part 0 Introduction to Linux Part 0 Introduction to Linux

Context Module Subheader

Lectures 1

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Page

25-03-31 Introduction to bioinformatics [Rubin] 25-03-31 Introduction to bioinformatics [Rubin] 2

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Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark completed Must mark this module item done in order to complete Marked completed Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Page

25-04-01 Introduction to Linux [Rubin] 25-04-01 Introduction to Linux [Rubin] 3

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Page

25-04-02 Servers and computer clusters [Rubin] 25-04-02 Servers and computer clusters [Rubin] 4

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Page

25-04-02 Introduction to Bash scripting [Rubin] 25-04-02 Introduction to Bash scripting [Rubin] 5

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Context Module Subheader

Computer labs 7

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Assignment

25-04-01 Linux 1: Introduction to LINUX [Rubin] 25-04-01 Linux 1: Introduction to LINUX [Rubin] 1 8

assignment 1347009 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark completed Must mark this module item done in order to complete Marked completed Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Assignment

25-04-03 Linux 2: Servers and clusters [Rubin] 25-04-03 Linux 2: Servers and clusters [Rubin] 1 9

assignment 1347010 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark completed Must mark this module item done in order to complete Marked completed Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Assignment

25-04-03 Linux 3: Bash scripting [Rubin] 25-04-03 Linux 3: Bash scripting [Rubin] 1 10

assignment 1347011 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark completed Must mark this module item done in order to complete Marked completed Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete

Part 1 Microbial Evolution and Epidemiology

Part 1 Microbial Evolution and Epidemiology Part 1 Microbial Evolution and Epidemiology

Page

Microbial Evolution and Epidemiology - General information Microbial Evolution and Epidemiology - General information 1

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Context Module Subheader

Lectures 2

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Page

MEE Lecture 1: Introduction to genomics and evolution MEE Lecture 1: Introduction to genomics and evolution 3

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Page

25-04-04 NGS 1: Analysis of modern sequencing data [Webster] 25-04-04 NGS 1: Analysis of modern sequencing data [Webster] 4

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Page

MEE Lecture 2: Online resources MEE Lecture 2: Online resources 5

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Page

MEE Lecture 3: Bacterial genomics and horizontal gene transfers MEE Lecture 3: Bacterial genomics and horizontal gene transfers 6

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Page

MEE Lecture 4: Phylogenetic approaches to study evolution MEE Lecture 4: Phylogenetic approaches to study evolution 7

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Page

MEE Lecture 5: Selective forces driving evolution MEE Lecture 5: Selective forces driving evolution 8

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Page

MEE Lecture 6: Introduction to Epidemiology MEE Lecture 6: Introduction to Epidemiology 9

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Attachment

MEE Lecture 7 Descriptive Epidemiology.pdf MEE Lecture 7 Descriptive Epidemiology.pdf 10

attachment 1345116 0

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Attachment

MEE Lecture 8: Analytical epidemiology.pdf MEE Lecture 8: Analytical epidemiology.pdf 11

attachment 1358127 0

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Page

MEE Lecture 9: Observational and interventional studies MEE Lecture 9: Observational and interventional studies 12

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MEE Lecture 10: Sampling MEE Lecture 10: Sampling 13

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Page

MEE Lecture 11: Molecular epidemiology MEE Lecture 11: Molecular epidemiology 14

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Page

MEE Lecture 12: Bias MEE Lecture 12: Bias 15

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Page

MEE Lecture 13: Association, causality and attributable fraction MEE Lecture 13: Association, causality and attributable fraction 16

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Page

MEE Lecture 15: Applied epidemiology lecture MEE Lecture 15: Applied epidemiology lecture 18

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Attachment

QnA_epidemiology.pdf QnA_epidemiology.pdf 20

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Mini-project - instructions Mini-project - instructions 22

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Mini-project: list Mini-project: list 23

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Assignment

Mini-project - presentation, hand-in Mini-project - presentation, hand-in 0 24

assignment 1175257 1

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Page

Applied epidemiology exercise Applied epidemiology exercise 25

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Assignment

Applied epidemiology exercise Applied epidemiology exercise 0 26

assignment 1175259 1

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Page

Previous exams Previous exams 27

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Part 2 Antimicrobial drugs, development and resistance

Part 2 Antimicrobial drugs, development and resistance Part 2 Antimicrobial drugs, development and resistance

Page

Antimicrobial drugs, development and resistance - General information Antimicrobial drugs, development and resistance - General information 1

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Page

Examples of previous exam questions Examples of previous exam questions 2

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Context Module Subheader

LECTURES 3

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Discussion topic

Online discussions related to all lectures Online discussions related to all lectures 4

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Page

Zoom links for the Question times (Q&A) related to the lectures Zoom links for the Question times (Q&A) related to the lectures 5

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Page

Additional material related to lectures 05 to 08 Additional material related to lectures 05 to 08 6

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Context Module Subheader

Handouts of lectures 7

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Page

Lecture: Introduction to the module 2025/05/05 Lecture: Introduction to the module 2025/05/05 8

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Page

Lecture 1: Mechanisms of antibiotic action - 1 - 2025/05/05 Lecture 1: Mechanisms of antibiotic action - 1 - 2025/05/05 9

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Lecture 2: Mechanisms of antibiotic action - 2 - 2025/05/05 Lecture 2: Mechanisms of antibiotic action - 2 - 2025/05/05 10

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Lecture 3: Surveillance and resistance testing - 2025/05/06 Lecture 3: Surveillance and resistance testing - 2025/05/06 11

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Lecture 4: Anti-fungal and anti-TB drugs - 2025/05/06 Lecture 4: Anti-fungal and anti-TB drugs - 2025/05/06 12

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Lecture 5: Mechanisms of antibiotic resistance - 2025/05/07 Lecture 5: Mechanisms of antibiotic resistance - 2025/05/07 13

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Lecture 6: Ecology & evolution of antibiotic resistance 2025/05/07 Lecture 6: Ecology & evolution of antibiotic resistance 2025/05/07 14

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Lecture 7: Dynamics of antibiotic resistance - 2025/05/08 Lecture 7: Dynamics of antibiotic resistance - 2025/05/08 15

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Lecture 8: Alternatives to antibiotics - 2025/05/08 Lecture 8: Alternatives to antibiotics - 2025/05/08 16

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Lecture 9: Mobile genetic elements- 2025/05/12 Lecture 9: Mobile genetic elements- 2025/05/12 17

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Lecture 10: Resistance in the hospital - 2025/05/12 Lecture 10: Resistance in the hospital - 2025/05/12 18

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Attachment

Lecture 11. Finding Antibiotic Targets 2025 05 14.pdf Lecture 11. Finding Antibiotic Targets 2025 05 14.pdf 19

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Page

Odilorhabdin antibiotic film (for lecture 11) Odilorhabdin antibiotic film (for lecture 11) 20

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Attachment

Lecture 12. Chemical Starting Points_2025 05 14.pdf Lecture 12. Chemical Starting Points_2025 05 14.pdf 21

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Lecture 13: ADME - 2025/05/15 Lecture 13: ADME - 2025/05/15 22

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Attachment

SELECTED EQUATIONS Master Programme in Infection Biology.pdf SELECTED EQUATIONS Master Programme in Infection Biology.pdf 23

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Lecture 14: PKPD- 2025/05/19 Lecture 14: PKPD- 2025/05/19 24

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Lecture 15: Antiviral drugs - 1 - 2025/05/20 Lecture 15: Antiviral drugs - 1 - 2025/05/20 25

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Lecture 16: Antiviral drugs - 2 - 2025/05/20 Lecture 16: Antiviral drugs - 2 - 2025/05/20 26

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Attachment

Lecture 17. H2L and L2CD 2025.pdf Lecture 17. H2L and L2CD 2025.pdf 27

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Attachment

Lecture 18. TPP, Clinical trials and Economics_2025.pdf Lecture 18. TPP, Clinical trials and Economics_2025.pdf 28

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Attachment

Lecture 19. Current Antibiotic Pipeline_2025.pdf Lecture 19. Current Antibiotic Pipeline_2025.pdf 30

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Lecture 20: Phage therapy - 2025/05/23 Lecture 20: Phage therapy - 2025/05/23 31

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Context Module Subheader

SEMINARS 32

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Seminar 1 - AMR genes in the environment - 2025/05/09 Seminar 1 - AMR genes in the environment - 2025/05/09 33

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Discussion topic

Questions and discussion about Seminar 1 Questions and discussion about Seminar 1 34

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Seminar 2 - AMR fitness and compensation - 2025/05/13 Seminar 2 - AMR fitness and compensation - 2025/05/13 35

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Discussion topic

Questions and discussion about Seminar 2 Questions and discussion about Seminar 2 36

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Seminar 3 - Teixobactin, a new antibiotic - 2025/05/16 Seminar 3 - Teixobactin, a new antibiotic - 2025/05/16 37

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Discussion topic

Questions and discussion about Seminar 3 Questions and discussion about Seminar 3 38

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Seminar 4. Antiviral drugs - 2025/05/26 Seminar 4. Antiviral drugs - 2025/05/26 39

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Discussion topic

Questions and discussion about Seminar 4 Questions and discussion about Seminar 4 40

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Context Module Subheader

EXERCISE PKPD 41

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Problem solving exercise: PK & PKPD - 2025/05/22 Problem solving exercise: PK & PKPD - 2025/05/22 42

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Discussion topic

Questions and discussion about Exercise PK & PKPD Questions and discussion about Exercise PK & PKPD 43

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Context Module Subheader

MINI SYMPOSIUM 44

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Information and guidelines for mini symposium assignments Information and guidelines for mini symposium assignments 45

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Examples of written assignments and oral presentations from previous years Examples of written assignments and oral presentations from previous years 46

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Schedule for meetings with teachers 2025/05/09 Schedule for meetings with teachers 2025/05/09 47

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Schedule for Symposium days 2025/06/04 and 2025/06/05 Schedule for Symposium days 2025/06/04 and 2025/06/05 48

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Discussion topic

General discussion about the mini symposium General discussion about the mini symposium 49

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Context Module Subheader

Discusison groups for upload of research proposals and feedback 50

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Discussion topic

Discussion group 1 & group 2 Discussion group 1 & group 2 51

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Discussion topic

Discussion group 3 & group 4 Discussion group 3 & group 4 52

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Discussion topic

Discussion group 5 & group 6 Discussion group 5 & group 6 53

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Discussion topic

Discussion group 7 & group 8 Discussion group 7 & group 8 54

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Discussion topic

Discussion group 9 & group 10 Discussion group 9 & group 10 55

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Discussion topic

Discussion group 11 & group 12 Discussion group 11 & group 12 56

discussion_topic 1175317 0

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark completed Must mark this module item done in order to complete Marked completed Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark completed Must mark this module item done in order to complete Marked completed Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete

Course modules

Course Information

Part 0 Introduction to Linux

Lectures 1

Computer labs 7

Part 1 Microbial Evolution and Epidemiology

Lectures 2

Part 2 Antimicrobial drugs, development and resistance

LECTURES 3

Handouts of lectures 7

SEMINARS 32

EXERCISE PKPD 41

MINI SYMPOSIUM 44

Discusison groups for upload of research proposals and feedback 50