Course Home Page: http://babel.ucmp.umu.se/bioinf/

Course Schedule (ver.0.1 170327)

5MO115 BioInformatics and Genome Analysis, 7.5hp (2017-04-28 – 2017-06-02) Course leader: Uwe Sauer, Dept. of Chemistry, Computational Life Science Cluster, CLiC and KBC,

tel.: 090 786-5930, e-mail: uwe.sauer@chem.umu.se

Course time: Start Friday, April 28, End Friday June 2, 2017

Lecture locations: Building 6L: XXXXX

PC-Lab location: YYYYY

Take Home Examination, THE: Starting on Monday 22 May 13:00 and ending on Monday 29 May 16:00 sharp!

Written Examination, WEx: Date: Friday June 2, 2016 from 09:00-12:00

Place: Östra Paviljongen (ÖP)

Re-Exam scheduled for Friday August 25, 2017, 09:00-12:00 (ÖP)

Text book: "Introduction to Bioinformatics 4th ed." By Arthur M. Lesk.

Oxford University Press 2014, ISBN: 978-0-19-965156-6. (pp 371)

Additional literature: "Trends guide to BIOINFORMATCS", Trends Supplement 1998, Elsevier Trends Journals (available via CAMBRO).

The reviews cover all aspects of BioInformatics. I strongly recommend to read it from cover to cover! (only 33 pages!)

Course lecturers & PC-lab tutors: Uwe Sauer (US) Dept. of Chemistry & Computational Life Science Cluster, CLiC

Anna Linusson (AL) Dept. of Chemistry, Computational Life Science Cluster, CLiC

David Andersson (DA) Dept. of Chemistry, Computational Life Science Cluster, CLiC

Jeanette Tångrot Dept. of Mol. Biol. & Computational Life Science Cluster, CLiC, Bioinformatics Infrastructure for Life Sciences, BILS

Patrik Rydén (PR) Dept. of Statistical Mathematics, Computational Life Science Cluster, CLiC

Nathaniel Street (NS) Dept. of Plant Physiology, Umeå Plant Science Centre, UPSC

Erik Johansson (EJ) Umetrics AB

Week 18

Monday 01/05

Holiday

Tuesday 02/05

Wednesday 03/05

Thursday 04/05

Friday 05/05

9:00 – 09:50

Welcome to the course

Information and goals

Lecture: Background to the

"Neanderthal K-Ras” Case

study

Lecture: Sequence

alignment I: Pair-wise seq.

alignments & "Dot plots" Lesk4 Ch-5

Summary PC1

Lecture: Sequence

alignment II: Substitution

matrices, E-values and

scores Lesk4 Ch-5

Summary PC2

Lecture: Hidden Markov

Models Lesk4 Ch-5, 201-203

10:00 – 10:50

Lecture: Introduction to

Bioinformatics

Serial Cloner &

Sequence alignment I:

Pairwise Sequence

alignments, PSA Lesk4 Ch-5

Lecture: Sequence

alignment II: Substitution

matrices Lesk4 Ch-5

Lecture: Pair-wise seq. ali.

III: Dynamic programming Lesk4 Ch-5

Lecture: Disordered

Proteins

11:00 – 11:50

Lecture: cont.

Sequence alignment I:

Pairwise Sequence

alignments, PSA

Lesk3 Ch-1, 1-61,

Lecture: Sequence

alignment II: Substitution

matrices Lesk4 Ch-5

Introduction PC1: Gene finding and sequence

searches

Lecture: Multiple sequence

alignments, MSA,

visualizing alignments Lesk4 Ch-5

Intro PC2: PSA, MSA,

Patterns

Lecture: Structure

superimposition

Lesk4 Ch-6, 235-241

Intro PC3 Ras structure

12:00 – 13:00

Lunch

Lunch

Lunch

13:00 – 16:00

PC1: Sequence searches,

gene finding and ORFs

PC2: PSA, MSA PC3: Ras structure

16:00 – 17:00

unsupervised

PC1: unsupervised lab time PC2: unsupervised lab time PC3: unsupervised lab time

Week 19

Monday 08/05

Minor Groove

Tuesday 09/05

Minor Groove

Wednesday 10/05

Minor Groove

Thursday 11/05

Minor Groove

Friday 12/05

AFH-A103

9:00 – 09:50

Lecture: How to identify

domains in proteins Lesk4 Ch-2, 101-102, Ch-8,

310-312

Summary PC4 Domains

Lecture: Introduction to

Comparative modelling Lesk4 Ch-6, 238-250

Summary PC5 Lecture: Concluding the

"Neanderthal KRas ” Case

study

Lecture: Python Reviewed

Lecture: Protein folding

and stability: 2ry structure

revisited, US Levinthal &

Anfinson Lesk4, Ch-6, 223-230

10:00 – 10:50

Lecture: Fold recognition

& Threading

Lesk4 Ch-6, 250-255

Lecture: Critical

Assessment of Structure

Prediction, CASP, US Lesk3 Ch-6, 337-343

Lecture: Phylogenetic

analysis

Lecture: Python Reviewed

Lecture: Protein stability Lesk3, Ch-6, 314-322

11:00 – 11:50

Intro PC4: Domains

Intro PC5:

Lecture: Introduction to

Linux

Lecture: Python Reviewed

Lecture: Ab initio structure

predictions

12:00 – 13:00

Lunch

Lunch

Lunch

Lunch

Lunch

13:00 – 16:00

PC4: Protein domains

PC5: Comparative

Modeling

PC6 Linux practical PC7-Python-1 PC7 unsupervised lab time

16:00 – 17:00

unsupervised

PC4: unsupervised lab time PC5: unsupervised lab time PC6: unsupervised lab time PC7: unsupervised lab time PC7 unsupervised lab time

Week 20

Monday 15/05

Tuesday 16/05

Wednesday 17/05

Thursday 18/05

Friday 19/05

9:00 – 09:50

Lecture: Next Generation

Sequencing (NGS) and

sequence analysis

Jeanett Tångrot

Lecture: “Omics data

analysis and systems

biology” Nathaniel Street Lesk3, Ch-3, 148-165

Lecture: Kemometri

Anna Linusson, AL

PC-lab Kemometri DA

Quick Exam (Dugga)

Ethical aspects of

Bioinformatics

10:00 – 10:50

Lecture: NGS

Jeanett Tångrot

Lecture: “Omics data

analysis and systems

biology” Nathaniel Street

Lecture: Kemometri

Anna Linusson, AL

PC-lab Kemometri DA

Film: GATTACA Bioinformatics in the not so

distant future.

11:00 – 11:50

Lecture: NGS

Jeanett Tångrot Lecture: “Omics data

analysis and systems

biology” Nathaniel Street

Lecture: Kemometri AL

PC-lab Kemometri DA

Discussion: Ethics of

Bioinformatics

12:00 – 13:00

Lunch

Lunch

Lunch

Lunch

Lunch

13:00 – 16:00

PC-lab: NGS fragment

assembly and analysis

(SN)

PC8- Python -2 PC- Python - finish PC-lab Kemometri DA

16:00 – 17:00

unsupervised

PC-lab: NGS fragment

assembly and analysis

(SN)

PC8 unsupervised lab time PC Python – finish

unsupervised lab time

PC-lab Kemometri

unsupervised lab time

19:00 – 21:00

voluntarily

19:00 – 21:00

“Wet-lab” Sampling of

the liquid Database at

Bishop Arms

Week 21

Monday 22/05

Tuesday 23/05

Wednesday 24/05

Thursday 25/05

Holiday

Friday 26/05

9:00 – 09:50

Lecture: “Introduction to

statistics” Patrik Rydén, PR

Take Home Exam (THE) Take Home Exam (THE) Take Home Exam (THE)

10:00 – 10:50

Lecture: “Introduction to

statistics” PR

Take Home Exam (THE) Take Home Exam (THE) Take Home Exam (THE)

11:00 – 11:50

Lecture: “Introduction to

statistics” PR

Take Home Exam (THE) Take Home Exam (THE) Take Home Exam (THE)

12:00 – 13:00

Lunch

Lunch

Lunch

Lunch

13:00 – 17:00

13.00

Take Home Exam,

THE, is on-line

Take Home Exam (THE) Take Home Exam (THE) Take Home Exam (THE)

Week 22

Monday 30/05

Tuesday 31/05

Wednesday 01/06

Thursday 02/06

Friday 03/06

9:00 – 09:50

Take Home Exam (THE) Prepare for WEx Prepare for WEx Written Exam (WEx)

09.00 – 12.00

N420

Natural Science Buildg.

10:00 – 10:50

Take Home Exam (THE) Question session: Last

chance to ask questions

before the written Exam

(WEx)

Prepare for WEx

Prepare for WEx

Written Exam (WEx)

N420

11:00 – 11:50

Take Home Exam (THE) Question session: Last

chance to ask questions

before the WEx

Prepare for WEx

Prepare for WEx

Written Exam (WEx)

N420 Ends 12.00

12:00 – 13:00

Lunch

Lunch

Lunch

Lunch

END of the

5MO083 Course

13:00 – 16:00

Thymine Take Home Exam (THE)

Prepare for WEx Prepare for WEx

Prepare for WEx

Room: XXX

Optional Seminars:

Advanced

Bioinformatics Project

Presentations

16:00

16.00 sharp

DEADLINE for

submitting the THE!!

Prepare for WEx Prepare for WEx

Prepare for WEx

Advanced

Bioinformatics Project

Presentations