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

Course Schedule (v150508) 5MO083

BioInformatics and Genome Analysis, 7.5hp

Course leader:

Uwe Sauer, Dept. of Chemistry, Computational Life Science Cluster, CLiC and KBC, tel.: 090 786-5930, e-mail: [email protected]

Course time:

Start Monday, May 4, End Friday June 5, 2015

Lecture locations:

Building 6L: Gamla biblioteket (GB), (1 floor up) / Thymine (TH) (2 floors up), Minor Groove (MG)/ see schedule for details

PC-Lab location:

Room GB / TH / MG

Take Home Examination, THE:

Starting on Wednesday 27 May 10:00 and ending on Monday 01 June 16:00 sharp!

Written Examination, WEx:

Date: Friday June 5, 2015 from 09:00-12:00 Place: Sal 1, Östra Paviljongen

Text book:

"Introduction to Bioinformatics 3rd ed." By Arthur M. Lesk. Oxford University Press 2008, ISBN: 978-0-19-920804-3. (pp 474)

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 Patrick Rydén (PR) Dept. of Statistical Mathematics, Computational Life Science Cluster, CLiC Nathaniel Street (NS) Dept. of Plant Physiology, Umeå Plant Science Centre, UPSC Sergiu Netotea (SN) Dept. of Chemistry & Computational Life Science Cluster, CLiC, Bioinformatics Infrastructure for Life Sciences, BILS David Andersson (DA) Dept. of Chemistry, Computational Life Science Cluster, CLiC Erik Johansson (EJ) Umetrics AB

Week 19

Monday 04/05 Gamla Biblioteket

9:00 – 09:50

Lecture: Welcome to the course Information and goals

10:00 – 10:50

Lecture: Background to the "Neanderthal K-Ras” Case study

Tuesday 05/05 Gamla Biblioteket

Wednesday 06/05 Gamla Biblioteket

Thursday 07/05 Gamla Biblioteket

Summary PC1 Lecture: Sequence alignment I: Pair-wise seq. alignments & "Dot plots"

Summary PC2 Lecture: Sequence alignment II: Substitution matrices

Lecture: Hidden Markov Models

Summary PC4 Domains

Lesk3 Ch-5, 278-281 (-296)

Lesk3 Ch-5, 242-254

Lesk3 Ch-5, 254-258

Lecture: Sequence alignment II: Substitution matrices

Lecture: Pair-wise seq. ali. III: Dynamic programming

Lecture: How to identify domains in proteins

Lesk3 Ch-5, 258-271

Lesk3 Ch-6, 322-324, 331-332

Lecture: Fold recognition & Threading Lesk3 Ch-6, 345-350 Lecture: Introduction to Comparative/Homology modelling

Lesk3 Ch-5, 242-254

11:00 – 11:50

Lecture: Introduction to Bioinformatics Serial Cloner & Sequence alignment I: Pairwise Sequence alignments, PSA Lesk3 Ch-1, 1-61,

Lecture: Sequence alignment II: Substitution matrices

Friday 08/05 Gamla Biblioteket

Lesk3 Ch-6, 333-358

Lecture: Multiple sequence alignments, MSA, visualizing alignments

Lecture: Structure superimposition Lesk3 Ch-6, 324-332

Lecture: Disordered Proteins

Lesk3 Ch-5, 271-278

Intro PC4: Domains Intro PC2: PSA, MSA, Patterns

Intro PC3 Ras structure

Introduction PC1: Sequence searches

12:00 – 13:00 13:00 – 17:00

Lunch

Lunch

Lunch

Lunch

Lunch

Gamla Biblioteket

Gamla Biblioteket

Gamla Biblioteket

Gamla Biblioteket

Gamla Biblioteket

PC1: Sequence searches, gene finding and ORFs

PC2: PSA, MSA, Dotplot

PC3: Ras structure

PC4: Protein domains

PC5: Comparative Modeling

Week 20

9:00 – 09:50

Monday 11/05 Thymine Lecture: Protein folding and stability: 2ry structure revisited, US Levinthal & Anfinson

Tuesday 12/05 Thymine Lecture: Critical Assessment of Structure Prediction, CASP, US

Wednesday 13/05 Thymine Lecture: Python Reviewed

Lesk3 Ch-6, 337-343

Lesk3, Ch-6, 307-324

Lecture: Protein stability

10:00 – 10:50

11:00 – 11:50

Lesk3, Ch-6, 314-322

Introduction: PC-Struct-1 Lecture: Ab initio structure predictions

12:00 – 13:00

13:00 – 13:50

Lecture: Concluding the "Neanderthal KRas ” Case study

Lecture: Python Reviewed

Lecture: Introduction to Linux

Lecture: Python Reviewed

Lunch

Lunch Thymine

Thymine

PC6 cont. Comp. Modeling

PC7 Linux practical

PC6

PC7

PC6

PC7

PC6

PC7

14:00 – 14:50

15:00 – 15:50 16:00 – 16:50

Free Lunch! Sponsor: Umetrics AB Restaurang Örnen Tviste vägen 48 Lecture: Umetrics I Tviste vägen 48, 2nd floor, seminar room: “Biotech production and multivariate analysis with examples from Amgen, Lonza, Biogen, Merck” Lecture: Umetrics I Continue. Lecture: Umetrics II “Where does Umetrics see the well-paid jobs in biotech”

Thursday 14/05 Kristi himmelfärds dag

Friday 15/05

Week 21

Monday 18/05 Thymine

13:00 – 13:50

Thursday 21/05 Gamla Biblioteket

PC-lab Kemometri DA

Lecture: Python Reviewed

Lecture: Kemometri Anna Linusson, AL

PC-lab Kemometri DA

Quick Exam (Dugga)

Lecture: Phylogenetic analysis

Lecture: Kemometri AL

PC-lab Kemometri DA

PC9- Python -2

10:00 – 10:50

12:00 – 13:00

Wednesday 20/05 Thymine

Lecture: Kemometri Anna Linusson, AL

9:00 – 09:50

11:00 – 11:50

Tuesday 19/05 Gamla Biblioteket

Lunch

Lunch

Lunch

Lunch

Lecture: NGS Sergiu Netoteat

Lunch

Minor Groove

Minor Groove

Minor Groove

Minor Groove

PC8-Python-1

Lecture: Kemometri Anna Linusson, AL

PC-lab Kemometri DA

PC9- Python -2

PC8- Python -1

Lecture: Kemometri Anna Linusson, AL

PC-lab Kemometri DA

PC9- Python -2

PC-lab: NGS fragment assembly and analysis (SN) PC-lab: NGS fragment assembly and analysis (SN)

PC8- Python -1

Lecture: Kemometri AL

PC-lab Kemometri DA

PC9- Python -2

PC-lab: NGS fragment assembly and analysis (SN)

PC-lab Kemometri DA

PC9- Python -2

PC-lab: NGS fragment assembly and analysis (SN)

15:00 – 15:50

19:00 – 21:00

Lecture: Next Generation Sequencing (NGS) and sequence analysis Sergiu Netotea Lecture: NGS Sergiu Netotea

Thymine

14:00 – 14:50

16:00 – 16:50

Friday 22/05 Gamla Biblioteket

PC8- Python -1

19:00 – 21:00 “Wet-lab” Sampling of the liquid Database at Bishop Arms

Week 22

9:00 – 09:50

Monday 25/05 Thymine Lecture: “Omics data analysis and systems biology” Nathaniel Street

Tuesday 26/05 Gamla Biblioteket

Wednesday 27/05 Gamla Biblioteket

Lecture: “Introduction to statistics” Patrik Rydén, PR

Thursday 28/05 Gamla Biblioteket

Friday 29/05 Gamla Biblioteket

Take Home Exam (THE)

Take Home Exam (THE)

Lesk3, Ch-3, 148-165

Lecture: “Introduction to statistics” PR

10.00 Take Home Exam, THE, is on-line

Take Home Exam (THE)

Take Home Exam (THE)

10:00 – 10:50

Lecture: “Omics data analysis and systems biology” Nathaniel Street

Lecture: “Introduction to statistics” PR

Take Home Exam (THE)

Take Home Exam (THE)

Take Home Exam (THE)

11:00 – 11:50

Lecture: “Omics data analysis and systems biology” Nathaniel Street

12:00 – 13:00

Lunch

Lunch

Lunch

Lunch

Lunch

Thymine

Gamla Biblioteket

Gamla Biblioteket

Gamla Biblioteket

13:00 – 13:50

Ethics of Bioinformatics Film: GATTACA

Take Home Exam (THE)

Take Home Exam (THE)

Take Home Exam (THE)

Take Home Exam (THE)

Take Home Exam (THE)

Take Home Exam (THE)

14:00 – 14:50

Ethics of Bioinformatics Film: GATTACA Discussion: Ethics of Bioinformatics

Take Home Exam (THE)

Take Home Exam (THE)

Take Home Exam (THE)

15:00 – 15:50

Take Home Exam (THE)

Take Home Exam (THE)

Take Home Exam (THE)

Bioinformatics in the not so far future?

16:00 – 16:50

Week 23

Monday 01/06 Thymine

Tuesday 02/06 Thymine

Take Home Exam (THE)

Wednesday 03/06 Prepare for WEx

Thursday 04/06 Prepare for WEx

9:00 – 09:50

10:00 – 10:50 Take Home Exam (THE)

11:00 – 11:50

Lunch

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

Lunch

Prepare for WEx (Adv. Bioinfo presentations)

Prepare for WEx (Adv. Bioinfo presentations)

Written Exam (WEx)

Prepare for WEx (Adv. Bioinfo presentations)

Prepare for WEx (Adv. Bioinfo presentations)

Written Exam (WEx)

Lunch

Lunch

Prepare for WEx

Prepare for WEx

Prepare for WEx

Take Home Exam (THE)

Prepare for WEx

Prepare for WEx

Prepare for WEx

Take Home Exam (THE)

Prepare for WEx

Prepare for WEx

Prepare for WEx

16.00 sharp DEADLINE for returning the THE!!

Prepare for WEx

Prepare for WEx

Prepare for WEx

Thymine 13.00-14.00 13:00 – 13:50

Take Home Exam (THE)

14:00 – 14:50

15:00 – 15:50

16:00 – 17:00

Written Exam (WEx) 09.00 – 12.00

Sal 1, Östra Paviljongen Take Home Exam (THE)

12:00 – 13:00

Friday 05/06

Sal 1, ÖP

Sal 1, ÖP Ends 12.00

END of the 5MO083 Course