Computational Life Science 2012, 15.0 hp

 
   
  • Course coordinator: Torgeir R. Hvidsten
  • Teachers
    • Henrik Antti
    • Torgeir R. Hvidsten
    • Patrik Ryden
  • Module 1: Statistics for life sciences
    • Teacher: Patrik Ryden
    • Book: Biomeasurement - understanding, analysing, and communicating data in the biosciences, Dawn Hawkins, Oxford University Press. ISBN: 9780199265152.
  • Module 2: Elements of bioinformatics
    • Teacher: Torgeir R. Hvidsten
    • Computer labs: David Sundell
    • Book: Introduction to Bioinformatics. Arthur M. Lesk, Oxford University Press. ISBN 978-0-19-920804-3.
  • Module 3: Chemometrics
    • Teacher: Henrik Antti
    • Books: "Design of Experiments" and "Introduction to Multi- and Megavariate Data Analysis using Projection Methods"
  • Module 4: Project

 

upsc

Umeå Plant Science Centre

Department of Plant Physiology, Umeå University

Department of Forest Genetics and Plant Physiology, SLU Umeå

 

Upon completing the course, the student should be able to:
    • perform hypothesis testing and basic statistical analysis, and correctly interpret the results.
    • perform classification, regression and  model evaluation.
    • plan a biological experiment where many variables influence the outcome.
    • describe different algorithm design techniques and analyze their time/space complexity.
    • apply classic bioinformatics tools in appropriate situations, understand how they work and correctly interpret their output.
    • use a combination of appropriate computational techniques discussed in the course to analysis a real life science dataset, and discuss the pros and cons of choosing different methods.
 
 
   
           
 

Type of activity (Time/place)

Topics

Material

 
         
Module 1: Statistics for life sciences
 
2012.09.03
2012.09.19
  Course plan available here.  

Module 2: Elements of bioinformatics
Student evaluations: 2009, 2010, 2011, 2012

2012.09.20
Thursday
Lecture 1: 9-11
KBF30
Introduction to bioinformatics Slides 1 WEEK 38
Self-Study Introduction, Scientific publication and archives, Archives and information retrieval Chapter 1, 3 and 4
2012.09.21
Friday
Lecture 2: 9-11
KB4C10
Programming in Perl: Introduction 1 Slides 2
Self-study Introduction, Scientific publication and archives, Archives and information retrieval Chapter 1, 3 and 4
2012.09.24
Monday
Computer LAB 1: 9-11
MA316
Basic expressions, scalars, arrays, loops, conditions, file handling

Lab 1 (solutions)
numbers.txt
Perl tutorials

WEEK 39
Lecture 3: 13-15
KBF30
Programming in Perl: Introduction 2 Slides 3
2012.09.25
Tuesday
Computer LAB 2: 9-11
MA316
Hashes, data structures, references, subroutines, modules Lab 2 (solutions)
microarray.txt
network.txt
Self-study LAB 2 cont.  
2012.09.26
Wednesday
Lecture 4: 9-11
KBF30
Programming in Perl: Introduction 3 Slides 4
Computer LAB 3: 13-15
MC333
Bioperl Lab 3 (solutions)
hvidsten.com.html
genpept.txt
2012.09.27
Thursday
Computer LAB 3: 8-10
MA316
LAB 3 cont.  

Lecture 5: 13-15
KBF30

Algorithm design and time/space complexity analysis

Slides 5
2012.09.28
Friday
Computer LAB 4: 13-15
MA141
Pseudo-code, algorithm design and time/space complexity analysis Lab 4 (solutions)
promoters.txt
MEME
MEME shuffled
Self-study LAB 3/Lab 4  
2012.10.01
Monday
Lecture 6: 9-11
KBF30
Sequence alignment Slides 6
Chapter 5
WEEK 40
Computer LAB 5: 13-15
MA316
Sequence alignment Lab 5 (solutions)
2012.10.02
Tuesday
Lecture 7: 9-11
KBF30
Evolutionary analysis, phylogenetic analysis Slides 7
Chapter 2 and 5
Computer LAB 6: 13-15
MA141
Phylogenetic analysis Lab 6
get_sequences.pl
change_names.pl
hiv_ids.txt
2012.10.03
Wednesday
Lecture 8: 9-11
KBF30
Protein structure analysis Slides 8
Chapter 6
Self-study Read the book Chapter 2, 5 and 6
2012.10.04
Thursday
Lecture 9: 9-11
KBF30
Machine learning Slides 9
Computer LAB 7: 13-15
MA316
Machine learning Lab 7
adenoca_markers.xls
Dennis-ClinCancerRes2005.pdf
2012.10.05
Friday
Lecture 10: 9-11
KB4C10
Systems biology Slides 10
Course evaluation: eval
If not present at the last lecture, mail the evaluation to me. Thanks!
Chapter 7
Self-study Read the book Chapter 2, 5, 6 and 7
Module 3: Chemometrics
2012.10.9
Tuesday
Lecture 1: 9-11
KB7B12
Intro MVA + PCA Slides
2012.10.11
Thursday
Lecture 2: 9-11
KB7B12
PLS, OPLS Slides
2012.10.12
Friday
Lecture 3: 9-11
KB7B12
Classification and Calibration Slides1, Slides2
Module 4: Project
2012.10.22-
2012.11.02
  Project  
2012.10.22
Monday
Lecture: 13-15
KBF30
Description of the project  
2012.11.06

Exam: 09-15

Skrivsal 3, Östra paviljongen Old exams: 2009, 2010, 2011