MVE130 Large Scale Genomics, Techniques and
Analysis
Gothenburg, Spring
2011
May 10: Master projects meeting: May 12@15.15 Euler
May 4:
Schedule changes for Friday May 6:
12.00-13.45 MVF21 Metagenomics,
Eric Kristiansson
14.00-15.00 KC
(Chemistry Building) Towards a knowledge-based Human Protein Atlas,
Mathias Uhlén – Honorary Doctor Seminar
Teachers and topics
Main responsible teacher and
examiner:
OlleNerman (nerman(at)chalmers.se), work phone: 031-7723565, home
phone: 031-880877
Metabolomics:
GouthamVemui (goutham(at)chalmers.se), Biotechnology,
Chalmers
Proteomics:
JoakimNorbeck (norbeck(at)chalmers.se),
Biotechnology, Chalmers
Gene Expression with
microarrays:
OlleNerman
Gene
Expresssion with Real time PCR:
Anna Johnning (anna.johnning(at)gmail.com),
Medical Physiology, GU
Clustering, principal
components and discriminant analysis, expression
profiling:
OlleNerman
Next Generation Sequencing and
Metagenomics:
Erik Kristiansson (erik.kristiansson(at)chalmers.se), MV, Chalmers
Cancer Genomics and Systems
Biology:
Sven Nelander (sven.nelander(at)wlab.gu.se), Wallenberg Lab, GU
Statistical Genetics:
Staffan Nilsson (staffan(at)chalmers.se),
MV, Chalmers
Home page and lab
assistance:
Marija Cvijovic (marija.cvijovic(at)chalmers.se), MV,
Chalmers
Examination
1. Obligatory
hand in of two lab reports (done in group of max 3 students together) to be
sent to Marija (marija.cvijovic(at)chalmers.se). Deadline May 25
2. Hand
in of three individually written essays with max 2 pages on each:
a) Metabolomics task: decided by Goutham Vemuri and OlleNerman (hand out 25 March, hand in 22 May)
b) Proteomics task: decided by Joachim Norbeck
and OlleNerman
(hand out 1 April, hand in 5 May)
c) Microarray task: decided by OlleNerman
(hand out 15 April, hand in 16 May)
These
essays will be marked together with the written exam, and will result in max 12
points (4 points each) out of a total of 30.
3. The
remaining 18 points will result from a conventionally set exam on all parts of
the course besides the metabolomics and proteomics parts.
The
limits for the marks 3, 4 and 5 will be 15, 20 and 25 respectively, and minimum
7 points on essays are required for passing.
Place and date for the regular
examination:30/05-2011 am in V-house
Preliminary Schedule MVE130
Week
12
Tuesday 22 March, 10.00-11.45 in MVF21
Introduction
and course overview (OlleNerman)
Thursday
24 March, 10.00-11.45 in MVF21
Metabolomics 1 (GouthamVemuri)
Friday 25 March, 13.15-15.00 in MVF21
Metabolomics 2 (GouthamVemuri)
Week 13
Tuesday 29 March, 10.00-11.45 in MVF 21
Proteomics I (Joachim Norbeck)
Thursday
31 March, 10.00-11.45 in MV21
Introduction to microarrays 1 (OlleNerman)
Friday 1 April 9.15-11.45 in MVF25
Microarrays
lab 1 Introduction to preprocessing of microarrays and to LIMMA (OlleNerman+MarijaCvijovic)
Friday 1
April 13.15-15.00 in MVF21
Proteomics
II (Joachim Norbeck)
Week 14
Tuesday
5 April 10.00-11.45 in MVF21
Introduction
to Microarrays 2 (OlleNerman)
Thursday
7 April 10.00-11.45 in MVF21
Clustering
and Discriminant Analysis 1 (OlleNerman)
Friday 8
April 9.00-11.45
in MVF25
Microarrays
lab 2: LIMMA and Profiling of Expression data (OlleNerman+MarijaCvijovic)
Friday 8
April 13.15-15.00 in MVF21
Real
time PCR expression analysis (Anna Johnning)
Week 15
Tuesday
12 April 10.00-11.45 in MVF21
Clustering
and Discriminant Analysis 2 (OlleNerman)
Thursday
14 April 9.00-11.45 in MVF21
Principal
Component Lab (OlleNerman+Marija Cvijovic)
Friday
15 April 9.00-10.45 in MVF25
Clustering
and Discriminant Analysis 3(OlleNerman)
Friday
15 April 13.15-15.00 in Pascal
MSc
thesis presentation
Week 18
Tuesday 3 May 10.00-11.45 in MVF21
Next generation sequencing andmetagenomics
1(Erik Kristiansson)
Thursday 5 May 10.00-11.45 in MVF21
Next generation sequencing and Metagenomics2
(Erik Kristiansson)
Friday 6 May 9.00-11.45 in MVF25
Metagenomics
lab (Erik Kristiansson)
Friday 6 May 13.15-15.00 in MVF21
Clustering and Discriminant
Analysis 4 (OlleNerman)
Week 19
Tuesday 10 May 10.00-11.45 in MVF21
Cancer genomics and systems biology 1 (Sven Nelander)
Thursday 12 May 10.00-11.45 in MVF21
Cancer genomics and systems biology 2 (Sven Nelander)
Friday 13 May 9.00-11.45 in MVF25
Cancer genomics Lab (Sven Nelander+MarijaCvijovic)
Friday 13 May 13.15-15.00 in MVF21
Clustering and discriminant
analysis 5 (OlleNerman)
Week 20
Tuesday 17 May 10.00-11.45 in MVF21
Statistical Genetics 1 (Staffan
Nilsson)
Thursday 19 May 10.00-11.45 in MVF21
Statistical Genetics 2 (Staffan
Nilsson)
Friday 20 May 9.00-11.45 in MVF25
Statistical Genetics Lab (Staffan
Nilsson)
Friday 20 May 13.15-15.00 in MVF21
Reserve time (OlleNerman)
All course material will be either handed out
or linked to. If you use course homepage link for academic year 2009/2010 you
will find much of the material that will be used in the course, but:
§ Essay questions will be new for this year.
§ You are not allowed to “copy and paste” in the essays. We will use a
system that detects texts that are copies of websites, published papers, other student´s
texts etc. to check your submitted texts. Main purpose of the essays is to
train your general writing and English writing capacity, and of course also
your capacity to read and understand scientific texts as they appear in
journals.
Finally I wish to mention that we plan to have
a couple of seminars in mid- May with suggestions for applied master thesis
projects in various bioscience and medical environments.
I look forward to the course with great
expectations.
Olle