Computational Life Science 2010, 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 l abs: Jenny Önskog
    • 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.
 
 
Student evaluations: 2009, 2010  
           
 

Type of activity (Time/place)

Topics

Material

  
         
Module 1: Statistics for life sciences
  
2010.08.30
2010.09.15
  Course plan available here.  
Module 2: Elements of bioinformatics
2010.09.16
Thursday		 Lecture 1: 9-11
KBF30		 Introduction to bioinformatics, computational biology and systems biology Slides 1 WEEK 37
Self-Study Introduction, Scientific publication and archives, Archives and information retrieval Chapter 1, 3 and 4
2010.09.17
Friday		 Lecture 2: 9-11
KBF30		 Programming in Perl: Introduction 1 Slides 2
Self-study Introduction, Scientific publication and archives, Archives and information retrieval Chapter 1, 3 and 4
2010.09.20
Monday
Computer LAB 1: 9-11
MA336		 Basic expressions, scalars, arrays, loops, conditions, file handling Lab 1 (solutions)
numbers.txt
 WEEK 38
Lecture 3: 13-15
KBF30		 Programming in Perl: Introduction 2 Slides 3
2010.09.21
Tuesday
Computer LAB 2: 9-11
MA336		 Hashes, data structures, references, subroutines, modules Lab 2 (solutions)
microarray.txt
network.txt
Self-study LAB 2 cont.  
2010.09.22
Wednesday
Lecture 4: 9-11
KBF30		 Programming in Perl: Introduction 3 Slides 4
Computer LAB 3: 13-15
MA336		 Bioperl Lab 3 (solutions)
hvidsten.com.html
genpept.txt
2010.09.23
Thursday		 Computer LAB 3: 10-12
MA336 		LAB 3 cont.  

Lecture 5: 13-15
KBF30

Algorithm design and time/space complexity analysis

 Slides 5
2010.09.24
Friday		 Self-study LAB 3 cont./Lab 4
Computer LAB 4: 13-15
MA336		 Pseudo-code, algorithm design and time/space complexity analysis Lab 4 (solutions)
promoters.txt
MEME results (pdf)
MEME results shuffled (pdf)
2010.09.27
Monday
Lecture 6: 9-11
KBF30		 Sequence alignment Slides 6
Chapter 5		 WEEK 39
Computer LAB 5: 13-15
MA336		 Sequence alignment Lab 5 (solutions)
2010.09.28
Tuesday
 Lecture 7: 9-11
KBF30		 Evolutionary analysis, phylogenetic analysis Slides 7
Chapter 2 and 5
Computer LAB 6: 13-15
MA336		 Phylogenetic analysis Lab 6
get_sequences.pl
change_names.pl
hiv_ids.txt
2010.09.29
Wednesday
Lecture 8: 9-11
KBF30		 Protein structure analysis Slides 8
Chapter 6
Self-study Read the book Chapter 2, 5 and 6
2010.09.30
Thursday		 Lecture 9: 9-11
KBF30		 Machine learning Slides 9
Computer LAB 7: 13-15
MA336		 Machine learning Lab 7
adenoca_markers.xls
Dennis-ClinCancerRes2005.pdf
2010.10.01
Friday		 Lecture 10: 9-11
KBF30		 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

2010.10.04-
2010.10.18

  Course plan available here. OBS: Only the two first weeks + the lecture "MVA, Classification and calibration".

 
Module 4: Project
2010.10.19-
2010.11.01
   Project.  
2010.11.05
Friday

Exam: 09-15
Skrivsal 3, Östra paviljongen