Computational Life Science 2011, 15.0 hp

  
   
  • Course coordinator: Torgeir R. Hvidsten
  • Teachers
    • Anna Linusson
    • 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: Anna Linusson
    • 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, 2011  
           
 

Type of activity (Time/place)

Topics

Material

  
         
Module 1: Statistics for life sciences
  
2011.09.12
2011.09.21
  Course plan available here.  
Module 2: Elements of bioinformatics
2011.09.22
Thursday		 Lecture 1: 9-11
KBF30		 Introduction to bioinformatics, computational biology and systems biology Slides 1 WEEK 38
Self-Study Introduction, Scientific publication and archives, Archives and information retrieval Chapter 1, 3 and 4
2011.09.23
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
2011.09.26
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
2011.09.27
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.  
2011.09.28
Wednesday
Lecture 4: 9-11
KBF30		 Programming in Perl: Introduction 3 Slides 4
Computer LAB 3: 13-15
MA316		 Bioperl Lab 3 (solutions)
hvidsten.com.html
genpept.txt
2011.09.29
Thursday		 Computer LAB 3: 9-11
MA316 		LAB 3 cont.  

Lecture 5: 13-15
KBF30

Algorithm design and time/space complexity analysis

 Slides 5
2011.09.30
Friday		 Computer LAB 4: 13-15
MA316 		Pseudo-code, algorithm design and time/space complexity analysis Lab 4 (solutions)
promoters.txt
MEME results (pdf)
MEME results shuffled (pdf)
Self-study LAB 3/Lab 4  
2011.10.03
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)
2011.10.04
Tuesday
 Lecture 7: 9-11
KBF30		 Evolutionary analysis, phylogenetic analysis Slides 7
Chapter 2 and 5
Computer LAB 6: 13-15
MA316		 Phylogenetic analysis Lab 6
get_sequences.pl
change_names.pl
hiv_ids.txt
2011.10.05
Wednesday
Lecture 8: 9-11
KBF30		 Protein structure analysis Slides 8
Chapter 6
Self-study Read the book Chapter 2, 5 and 6
2011.10.06
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
2011.10.07
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

2011.10.10-
2011.10.24

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

 
Module 4: Project
2011.10.24-
2011.11.04
   Project  
2011.10.24
Monday		 Lecture: 14-15
KBF30		 Description of the project  
2011.11.08
Tuesday
Exam: 09-15
Rotundan, Universum
   Old exams: 2009, 2010, 2011