Umeå universitet - 5MO115, Bioinformatics and Genome Analys..., +1 Course event (2)


	Time	Course name	Course code	Module	Activity	Room, Location	Map link	Staff	Public comment
w17	Fri 2023-04-28 w17
	09:00 - 09:30	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Information			Uwe Sauer	Schedule may be subject to change Course starts. NOTE: Study free day Course leader: Uwe Sauer uwe.sauer@umu.se
	09:00 - 09:15	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Information				Text book: "Introduction to Bioinformatics 5th ed." By Arthur M. Lesk. Oxford University Press 2019, ISBN: 978-0-19-879414-1. (pp 408) ca. 538 Kr
w18	Mon 2023-05-01 w18
	09:00 - 09:15	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Information				Swedish holiday
	Tue 2023-05-02
	09:00 - 09:45	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Mandatory Roll-call/Introduction	6K Thymine 6L Uracil	Map Map	Uwe Sauer	Roll-call Welcome to the course Information and goals Lecture: Background to the "Neanderthal K-Ras” Case study Lesk5 Ch-1: 1-43 Lesk5 Ch-2: 48-70 Lesk5 Ch-3: 88-121
	10:00 - 10:45	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Lecture	6K Thymine 6L Uracil	Map Map		Lecture: Introduction to Bioinformatics Serial Cloner & Sequence alignment I: Pairwise Sequence alignments, PSA Lesk5 Ch-4 123-135 (ex. 172)
	11:00 - 12:00	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Lecture	6K Thymine 6L Uracil	Map Map		Lecture: cont. Sequence alignment I: Pairwise Sequence alignments, PSA Lesk5 Ch-4 123-135 (ex. 172)
	Wed 2023-05-03
	09:00 - 09:45	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Lecture	6K Thymine 6L Uracil	Map Map		Lecture: Sequence alignment I: Pair-wise seq. alignments & "Dot plots" Lesk5 Ch-4 123-135 (ex. 172) Introduction PC1: Gene finding and sequence searches
	10:00 - 10:45	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Lecture	6K Thymine 6L Uracil	Map Map		Lecture: Sequence alignment II: Substitution matrices Lesk5 Ch-4 123-135 (ex. 172)
	11:00 - 12:00	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Lecture	6K Thymine 6L Uracil	Map Map		Lecture: Sequence alignment II: Substitution matrices, E-values and scores Lesk5 Ch-4 123-135 (ex. 172)
	13:00 - 16:00	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Mandatory Laboratory session	6K Thymine 6L Uracil	Map Map		PC1: Sequence searches, gene finding and ORFs
	16:00 - 17:00	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Laboratory session	6K Thymine 6L Uracil	Map Map		Unsupervised PC1: Sequence searches, gene finding and ORFs
	Thu 2023-05-04
	09:00 - 09:45	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Lecture	6K Thymine 6L Uracil	Map Map		Summary PC1 Lecture: Sequence alignment II: Substitution matrices, E-values and scores Lesk5 Ch-4 123-135 (ex. 172)
	10:00 - 10:45	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Lecture	6K Thymine 6L Uracil	Map Map		Lecture: Sequence alignment II: Dynamic programming Lesk5 Ch-4 137-141 (ex. 172)
	11:00 - 12:00	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Lecture	6K Thymine 6L Uracil	Map Map		Lecture: Sequence alignment II: Multiple sequence alignments, MSA, visualizing alignments Lesk5 Ch-4 143-151 (ex. 172) Intro PC2: PSA, MSA, Patterns
	13:00 - 16:00	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Mandatory Laboratory session	6K Thymine 6L Uracil	Map Map		PC2: PSA, MSA
	16:00 - 17:00	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Laboratory session	6K Thymine 6L Uracil	Map Map		Unsupervised PC2: PSA, MSA
	Fri 2023-05-05
	09:00 - 09:45	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Lecture	6K Thymine 6L Uracil	Map Map		Summary PC2 Lecture: Hidden Markov Models I - theory Lesk5 Ch-4 152-153, 171 (ex. 172)
	10:00 - 10:45	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Lecture	6K Thymine 6L Uracil	Map Map		Lecture: Hidden Markov Models II - applications Lesk5 Ch-4 152-153, 171 (ex. 172)
	11:00 - 12:00	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Lecture	6K Thymine 6L Uracil	Map Map		Lecture: Domains in proteins Lesk5 Ch-5 190, 197-200 (ex 228) Intro PC3 Ras structure
	13:00 - 16:00	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Mandatory Laboratory session	6K Thymine 6L Uracil	Map Map		PC3: Ras structure
	16:00 - 17:00	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Laboratory session	6K Thymine 6L Uracil	Map Map		Unsupervised PC3: Ras structure
w19	Mon 2023-05-08 w19
	10:00 - 10:45	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Lecture	6K Thymine 6L Uracil	Map Map		Summary PC3 Lecture: Structure superimposition Lesk5 Ch-5 192-197 (ex 228)
	11:00 - 12:00	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Lecture	6K Thymine 6L Uracil	Map Map		Lecture: Protein folding and stability: Levinthal & Anfinson Lesk5 Ch-5 180-190 (ex. 228) Intro PC4: Domains
	13:00 - 16:00	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Mandatory Laboratory session	6K Thymine 6L Uracil	Map Map		PC4: Protein domains
	16:00 - 17:00	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Laboratory session	6K Thymine 6L Uracil	Map Map		Unsupervised PC4: Protein domains
	Tue 2023-05-09
	09:00 - 09:45	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Lecture	6K Thymine 6L Uracil	Map Map		Summary PC4: Domains Lecture: Fold recognition & Threading Lesk5 Ch-5 205-207 (ex 228)
	10:00 - 10:45	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Lecture	6K Thymine 6L Uracil	Map Map		Lecture: Introduction to Comparative modelling Lesk5 Ch-5 201-214 (ex 228) Lesk5 Ch-5 215-219 (ex 228)
	11:00 - 12:00	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Lecture	6K Thymine 6L Uracil	Map Map		Lecture: Comparative modelling with AI – AlphaFold 2 Intro PC5: Comparative Modeling
	13:00 - 16:00	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Mandatory Laboratory session	6K Thymine 6L Uracil	Map Map		PC5: Comparative Modeling
	16:00 - 17:00	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Laboratory session	6K Thymine 6L Uracil	Map Map		Unsupervised PC5: Comparative Modeling
	Wed 2023-05-10
	09:00 - 09:45	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Lecture	6K Thymine 6L Uracil	Map Map		Lecture: Protein design; Paracelsus challenge. Lesk5 Ch-5 197 & 213 (ex 228)
	10:00 - 10:45	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Lecture	6K Thymine 6L Uracil	Map Map		Lecture: Disordered Proteins
	11:00 - 12:00	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Lecture	6K Thymine 6L Uracil	Map Map		Lecture: Python Reviewed part 1 Lesk5 Ch-6 233-268 (ex 269) Summary PC5 and Tutorial: Concluding the "Neanderthal KRas ” Case study
	13:00 - 16:00	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Mandatory Laboratory session	6K Thymine 6L Uracil	Map Map		PC6: Python-1
	16:00 - 17:00	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Laboratory session	6K Thymine 6L Uracil	Map Map		Unsupervised PC6: Python-1
	Thu 2023-05-11
	08:45 - 09:00	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Information				NOTE: You will need to use Umeå universities VPN (virtual private network) You also need to install “PuTTy" https://www.chiark.greenend.org.uk/~sgtatham/putty/latest.html
	09:00 - 09:45	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Lecture	6K Thymine 6L Uracil	Map Map		Lecture: Phylogenetic analysis Lesk5 Ch-4 154-171 (ex. 172)
	10:00 - 10:45	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Lecture	6K Thymine 6L Uracil	Map Map		Lecture: Python Reviewed part 2 Lesk5 Ch-6 233-268 (ex 269)
	11:00 - 12:00	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Lecture	6K Thymine 6L Uracil	Map Map		Lecture: Introduction to the Linux/Unix operating systems
	13:00 - 16:00	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Mandatory Laboratory session	6K Thymine 6L Uracil	Map Map		PC8 Linux practical (you will need VPN* to UmU and install “PuTTy”**)
	16:00 - 17:00	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Laboratory session	6K Thymine 6L Uracil	Map Map		PC8: Linux OS practical Unsupervised
	Fri 2023-05-12
	10:00 - 10:45	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Lecture	6K Thymine 6L Uracil	Map Map		Lecture: “Introduction to statistics” Patrik Ryden, PR
	11:00 - 12:00	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Lecture	6K Thymine 6L Uracil	Map Map		Lecture: “Introduction to statistics”, PR
	13:00 - 16:00	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Mandatory Laboratory session	6K Thymine 6L Uracil	Map Map		PC7: Python -2
	16:00 - 17:00	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Laboratory session	6K Thymine 6L Uracil	Map Map		Unsupervised PC7: Python -2
w20	Mon 2023-05-15 w20
	10:00 - 10:45	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Lecture	6K Thymine 6L Uracil	Map Map		Lecture: “Omics data analysis and systems biology” Nathaniel Street Lesk5, Ch-8, 296-314 (ex. 314)
	11:00 - 12:00	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Lecture	6K Thymine 6L Uracil	Map Map		11:30-12:00: “Omics data analysis and systems biology” Nathaniel Street Lesk5, Ch8, 296-314 (ex. 314)
	13:00 - 16:00	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Mandatory Laboratory session	6K Thymine 6L Uracil	Map Map		PC7: Python -2
	16:00 - 17:00	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Laboratory session	6K Thymine 6L Uracil	Map Map		PC7: Time to finish the Python labs (unsupervised)
	Tue 2023-05-16
	10:00 - 10:45	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Lecture	6K Thymine 6L Uracil	Map Map		Lecture: Artificial Intelligence (AI) – Deep Learning. Tommy Löfstedt Lesk5 Ch-7 271-931 (ex. 293)
	11:00 - 12:00	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Lecture	6K Thymine 6L Uracil	Map Map		Lecture: Artificial Intelligence (AI) – Deep Learning. Tommy Löfstedt Lesk5 Ch-7 271-931 (ex. 293)
	13:00 - 13:45	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Lecture	6K Thymine 6L Uracil	Map Map		Lecture on Ethics and Bioinformatics Lesk5, Ch-2, 80-82
	14:00 - 14:45	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Lecture	6K Thymine 6L Uracil	Map Map		Film: GATTACA or “Bioinformatics in the not so far future?”
	15:00 - 15:45	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Lecture	6K Thymine 6L Uracil	Map Map		Film: GATTACA
	Wed 2023-05-17
	09:00 - 12:00	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Lecture	6K Thymine 6L Uracil	Map Map		Lecture: Next Generation Sequencing (NGS) and sequence analysis Per Stenberg, PS Lesk5, Ch-2, 48-79 (ex. 84) Lesk5, Ch-3, 88-120 (ex. 121)
	13:00 - 17:00	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Mandatory Laboratory session	6K Thymine 6L Uracil	Map Map		PC9: NGS fragment assembly and analysis. PS You need to install student VPN on your PCs!*
	Thu 2023-05-18
	09:00 - 09:15	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Information				Swedish holiday
	Fri 2023-05-19
	13:00 - 16:00	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Mandatory Take-home examination				13.00 start On-Line Take Home Exam, THE, is on-line
w21	Mon 2023-05-22 w21
	09:00 - 16:00	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Mandatory Take-home examination				Take Home Exam (THE)
	Tue 2023-05-23
	09:00 - 16:00	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Mandatory Take-home examination				Take Home Exam (THE)
	Wed 2023-05-24
	09:00 - 16:00	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Mandatory Take-home examination				Take Home Exam (THE)
	Thu 2023-05-25
	09:00 - 16:00	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Mandatory Take-home examination				Take Home Exam (THE)
	Fri 2023-05-26
	09:00 - 15:45	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Mandatory Take-home examination				Take Home Exam (THE)
	15:45 - 16:00	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Mandatory Deadline Take-home examination				NOTE! 17.00 sharp DEADLINE for returning the THE!!
w22	Mon 2023-05-29 w22
	09:00 - 16:00	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Independent study				Prepare for Written Exam (WEx)
	Tue 2023-05-30
	09:00 - 10:00	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Independent study				Prepare for Written Exam (WEx)
	10:00 - 12:00	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Question time	6K Thymine 6L Uracil	Map Map		Question session: Last chance to ask questions before the written Exam (WEx)
	13:00 - 16:00	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Independent study				Prepare for Written Exam (WEx)
	Wed 2023-05-31
	09:00 - 16:00	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115		Independent study				Prepare for Written Exam (WEx)
	Thu 2023-06-01
	08:00 - 11:00	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115	Examination	Papperstentamen	ÖP Skrivsal 5	Map	Raiyan Ibrahim
w34	Fri 2023-08-25 w34
	08:00 - 11:00	Bioinformatics and Genome Analysis Bioinformatics and Genome Analysis	5MO115 5MO115	Examination	Papperstentamen Omtentamen	ÖP Skrivsal 1	Map	Raiyan Ibrahim

09:00 - 09:30

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Information

Uwe Sauer

Schedule may be subject to change

Course starts. NOTE: Study free day

Course leader: Uwe Sauer
uwe.sauer@umu.se

09:00 - 09:15

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Information

Text book: "Introduction to Bioinformatics 5th ed." By Arthur M. Lesk. Oxford University Press 2019, ISBN: 978-0-19-879414-1. (pp 408) ca. 538 Kr

09:00 - 09:15

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Information

Swedish holiday

09:00 - 09:45

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Mandatory
Roll-call/Introduction

6K Thymine
6L Uracil

Map
Map

Uwe Sauer

Roll-call
Welcome to the course
Information and goals
Lecture: Background to the "Neanderthal K-Ras” Case study
Lesk5 Ch-1: 1-43
Lesk5 Ch-2: 48-70
Lesk5 Ch-3: 88-121

10:00 - 10:45

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Lecture

6K Thymine
6L Uracil

Map
Map

Lecture: Introduction to Bioinformatics
Serial Cloner &
Sequence alignment I: Pairwise Sequence alignments, PSA
Lesk5 Ch-4 123-135 (ex. 172)

11:00 - 12:00

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Lecture

6K Thymine
6L Uracil

Map
Map

Lecture: cont.
Sequence alignment I: Pairwise Sequence alignments, PSA
Lesk5 Ch-4 123-135 (ex. 172)

09:00 - 09:45

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Lecture

6K Thymine
6L Uracil

Map
Map

Lecture: Sequence alignment I: Pair-wise seq. alignments & "Dot plots"
Lesk5 Ch-4 123-135 (ex. 172)

Introduction PC1:
Gene finding and sequence searches

10:00 - 10:45

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Lecture

6K Thymine
6L Uracil

Map
Map

Lecture: Sequence alignment II: Substitution matrices
Lesk5 Ch-4 123-135 (ex. 172)

11:00 - 12:00

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Lecture

6K Thymine
6L Uracil

Map
Map

Lecture: Sequence alignment II: Substitution matrices, E-values and scores
Lesk5 Ch-4 123-135 (ex. 172)

13:00 - 16:00

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Mandatory
Laboratory session

6K Thymine
6L Uracil

Map
Map

PC1: Sequence searches, gene finding and ORFs

16:00 - 17:00

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Laboratory session

6K Thymine
6L Uracil

Map
Map

Unsupervised
PC1: Sequence searches, gene finding and ORFs

09:00 - 09:45

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Lecture

6K Thymine
6L Uracil

Map
Map

Summary PC1

Lecture: Sequence alignment II: Substitution matrices, E-values and scores
Lesk5 Ch-4 123-135 (ex. 172)

10:00 - 10:45

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Lecture

6K Thymine
6L Uracil

Map
Map

Lecture: Sequence alignment II: Dynamic programming
Lesk5 Ch-4 137-141 (ex. 172)

11:00 - 12:00

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Lecture

6K Thymine
6L Uracil

Map
Map

Lecture: Sequence alignment II: Multiple sequence alignments, MSA, visualizing alignments
Lesk5 Ch-4 143-151 (ex. 172)

Intro PC2: PSA, MSA, Patterns

13:00 - 16:00

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Mandatory
Laboratory session

6K Thymine
6L Uracil

Map
Map

PC2: PSA, MSA

16:00 - 17:00

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Laboratory session

6K Thymine
6L Uracil

Map
Map

Unsupervised
PC2: PSA, MSA

09:00 - 09:45

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Lecture

6K Thymine
6L Uracil

Map
Map

Summary PC2

Lecture: Hidden Markov Models I - theory
Lesk5 Ch-4 152-153, 171 (ex. 172)

10:00 - 10:45

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Lecture

6K Thymine
6L Uracil

Map
Map

Lecture: Hidden Markov Models II - applications
Lesk5 Ch-4 152-153, 171 (ex. 172)

11:00 - 12:00

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Lecture

6K Thymine
6L Uracil

Map
Map

Lecture: Domains in proteins
Lesk5 Ch-5 190, 197-200 (ex 228)

Intro PC3 Ras structure

13:00 - 16:00

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Mandatory
Laboratory session

6K Thymine
6L Uracil

Map
Map

PC3: Ras structure

16:00 - 17:00

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Laboratory session

6K Thymine
6L Uracil

Map
Map

Unsupervised
PC3: Ras structure

10:00 - 10:45

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Lecture

6K Thymine
6L Uracil

Map
Map

Summary PC3

Lecture: Structure superimposition
Lesk5 Ch-5 192-197 (ex 228)

11:00 - 12:00

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Lecture

6K Thymine
6L Uracil

Map
Map

Lecture: Protein folding and stability: Levinthal & Anfinson
Lesk5 Ch-5 180-190 (ex. 228)

Intro PC4: Domains

13:00 - 16:00

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Mandatory
Laboratory session

6K Thymine
6L Uracil

Map
Map

PC4: Protein domains

16:00 - 17:00

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Laboratory session

6K Thymine
6L Uracil

Map
Map

Unsupervised
PC4: Protein domains

09:00 - 09:45

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Lecture

6K Thymine
6L Uracil

Map
Map

Summary PC4: Domains

Lecture: Fold recognition & Threading
Lesk5 Ch-5 205-207 (ex 228)

10:00 - 10:45

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Lecture

6K Thymine
6L Uracil

Map
Map

Lecture: Introduction to Comparative modelling
Lesk5 Ch-5 201-214 (ex 228)
Lesk5 Ch-5 215-219 (ex 228)

11:00 - 12:00

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Lecture

6K Thymine
6L Uracil

Map
Map

Lecture: Comparative modelling with AI – AlphaFold 2

Intro PC5: Comparative Modeling

13:00 - 16:00

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Mandatory
Laboratory session

6K Thymine
6L Uracil

Map
Map

PC5: Comparative
Modeling

16:00 - 17:00

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Laboratory session

6K Thymine
6L Uracil

Map
Map

Unsupervised
PC5: Comparative
Modeling

09:00 - 09:45

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Lecture

6K Thymine
6L Uracil

Map
Map

Lecture: Protein design; Paracelsus challenge.
Lesk5 Ch-5 197 & 213 (ex 228)

10:00 - 10:45

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Lecture

6K Thymine
6L Uracil

Map
Map

Lecture: Disordered Proteins

11:00 - 12:00

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Lecture

6K Thymine
6L Uracil

Map
Map

Lecture: Python Reviewed part 1
Lesk5 Ch-6 233-268 (ex 269)

Summary PC5 and
Tutorial: Concluding the
"Neanderthal KRas ” Case study

13:00 - 16:00

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Mandatory
Laboratory session

6K Thymine
6L Uracil

Map
Map

PC6: Python-1

16:00 - 17:00

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Laboratory session

6K Thymine
6L Uracil

Map
Map

Unsupervised
PC6: Python-1

08:45 - 09:00

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Information

NOTE: You will need to use Umeå universities VPN (virtual private network)

You also need to install “PuTTy" https://www.chiark.greenend.org.uk/~sgtatham/putty/latest.html

09:00 - 09:45

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Lecture

6K Thymine
6L Uracil

Map
Map

Lecture: Phylogenetic analysis
Lesk5 Ch-4 154-171 (ex. 172)

10:00 - 10:45

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Lecture

6K Thymine
6L Uracil

Map
Map

Lecture: Python Reviewed part 2
Lesk5 Ch-6 233-268 (ex 269)

11:00 - 12:00

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Lecture

6K Thymine
6L Uracil

Map
Map

Lecture: Introduction to the Linux/Unix operating systems

13:00 - 16:00

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Mandatory
Laboratory session

6K Thymine
6L Uracil

Map
Map

PC8 Linux practical
(you will need VPN* to UmU and install “PuTTy”**)

16:00 - 17:00

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Laboratory session

6K Thymine
6L Uracil

Map
Map

PC8: Linux OS practical
Unsupervised

10:00 - 10:45

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Lecture

6K Thymine
6L Uracil

Map
Map

Lecture: “Introduction to statistics” Patrik Ryden, PR

11:00 - 12:00

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Lecture

6K Thymine
6L Uracil

Map
Map

Lecture: “Introduction to statistics”, PR

13:00 - 16:00

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Mandatory
Laboratory session

6K Thymine
6L Uracil

Map
Map

PC7: Python -2

16:00 - 17:00

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Laboratory session

6K Thymine
6L Uracil

Map
Map

Unsupervised
PC7: Python -2

10:00 - 10:45

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Lecture

6K Thymine
6L Uracil

Map
Map

Lecture: “Omics data analysis and systems biology” Nathaniel Street
Lesk5, Ch-8, 296-314 (ex. 314)

11:00 - 12:00

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Lecture

6K Thymine
6L Uracil

Map
Map

11:30-12:00: “Omics data analysis and systems biology” Nathaniel Street
Lesk5, Ch8, 296-314 (ex. 314)

13:00 - 16:00

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Mandatory
Laboratory session

6K Thymine
6L Uracil

Map
Map

PC7: Python -2

16:00 - 17:00

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Laboratory session

6K Thymine
6L Uracil

Map
Map

PC7: Time to finish the Python labs (unsupervised)

10:00 - 10:45

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Lecture

6K Thymine
6L Uracil

Map
Map

Lecture: Artificial Intelligence (AI) – Deep Learning. Tommy Löfstedt
Lesk5 Ch-7 271-931 (ex. 293)

11:00 - 12:00

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Lecture

6K Thymine
6L Uracil

Map
Map

Lecture: Artificial Intelligence (AI) – Deep Learning. Tommy Löfstedt
Lesk5 Ch-7 271-931 (ex. 293)

13:00 - 13:45

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Lecture

6K Thymine
6L Uracil

Map
Map

Lecture on Ethics
and Bioinformatics
Lesk5, Ch-2, 80-82

14:00 - 14:45

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Lecture

6K Thymine
6L Uracil

Map
Map

Film: GATTACA or
“Bioinformatics in the not so far future?”

15:00 - 15:45

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Lecture

6K Thymine
6L Uracil

Map
Map

Film: GATTACA

09:00 - 12:00

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Lecture

6K Thymine
6L Uracil

Map
Map

Lecture: Next Generation Sequencing (NGS) and sequence analysis
Per Stenberg, PS
Lesk5, Ch-2, 48-79 (ex. 84)
Lesk5, Ch-3, 88-120 (ex. 121)

13:00 - 17:00

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Mandatory
Laboratory session

6K Thymine
6L Uracil

Map
Map

PC9: NGS fragment assembly and analysis. PS
You need to install student VPN on your PCs!*

09:00 - 09:15

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Information

Swedish holiday

13:00 - 16:00

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Mandatory
Take-home examination

13.00 start On-Line
Take Home Exam, THE, is on-line

09:00 - 16:00

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Mandatory
Take-home examination

Take Home Exam (THE)

09:00 - 16:00

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Mandatory
Take-home examination

Take Home Exam (THE)

09:00 - 16:00

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Mandatory
Take-home examination

Take Home Exam (THE)

09:00 - 16:00

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Mandatory
Take-home examination

Take Home Exam (THE)

09:00 - 15:45

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Mandatory
Take-home examination

Take Home Exam (THE)

15:45 - 16:00

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Mandatory
Deadline
Take-home examination

NOTE! 17.00 sharp DEADLINE for returning the THE!!

09:00 - 16:00

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Independent study

Prepare for Written Exam (WEx)

09:00 - 10:00

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Independent study

Prepare for Written Exam (WEx)

10:00 - 12:00

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Question time

6K Thymine
6L Uracil

Map
Map

Question session: Last chance to ask questions before the written Exam (WEx)

13:00 - 16:00

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Independent study

Prepare for Written Exam (WEx)

09:00 - 16:00

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Independent study

Prepare for Written Exam (WEx)

08:00 - 11:00

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Examination

Papperstentamen

ÖP Skrivsal 5

Map

Raiyan Ibrahim

08:00 - 11:00

Bioinformatics and Genome Analysis
Bioinformatics and Genome Analysis

5MO115
5MO115

Examination

Papperstentamen
Omtentamen

ÖP Skrivsal 1

Map

Raiyan Ibrahim

+0	+1	+2	+3	+4	+5
+6	+7	+8	+9	+10	+11
+12

End date:Full

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Course code	Course name, Event code
5MO115	Bioinformatics and Genome Analysis, 51539vt23
5MO115	Bioinformatics and Genome Analysis, A5159vt23