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Algorithms in Bioinformatics - #27623
Information for participants
GENERAL SCHEDULE
Lectures will be Tuesdays from 13.00 - 17.00, and Fridays from 9.00 - 12.00.
Tuesdays will consist of lectures and small
practical exercises introducing the different algorithms, and Fridays will consist of programming exercises where
the algorithms will be implemented.
The main programming language will be C, and all program templates provided in the course will be written in C.
Prior knowlegde of C programming is NOT required. However, basic programming skills are required to follow the course.
LITERATURE:
The course curriculum consists of review paper and selected chapters from Immunological Bioinformatics,
Lund et al., MIT Press, 2005. All course material will be made available online during the course. All course
material is available here Course material.
PROGRAMS AND TOOLS
- Flash 6 or better
For following the lectures you need a browser with Flash 6 or better. Flash is freeware and can be downloaded by clicking on the link above
- UNIX - Beginner's Guide to UNIX is available on-line.
- For doing the exercises on our server you must be able to connect to
the server using Secure Shell (SSH) and tunnel X through the connection.
See informations on prerequisites on:
Tools for SSH and X11
- If you have problems login to the CBS server, try using the following link Login problems.
Course Programme
Please note that the programme is updated on a regular basis - click the 'refresh' button once in a while to make sure that you have the most updated information
LITERATURE:
-
The course curriculum consists of review paper and selected chapters from Immunological Bioinformatics,
Lund et al., MIT Press, 2005. All course material will be made available online during the course.
All course material is available here Course material
Tuesday, 30. August 13-17
Introduction to course, UNIX crash course 101
Morten Nielsen
- 13.00 - 13.25
- Introduction to course
- Introduction to course. [PDF] .
- 13.25 - 13.50
- Introduction to the immune system
- Introduction to the immune system. [PDF] .
- 13.50 - 14.00
- A few notes on sequence alignment for Fridays exercise
- Some notes on sequence alignment [PDF] .
- 14.15 - 17.00
- Unix crash course
- A UNIX/Linux crash course
Friday, 2. September 9.00-12.00
C-programming crash course 101
Morten Nielsen
BACKGROUND TEXTS
- 9.00 - 12.00
- C-programming crash course 101
- Details on C routines, linked lists and C programming
- Some notes on command line parsing.
[PDF].
- Doing it on your local machine
- C-programming crash course
- Answers to C-programming exercise
Tuesday, 6. September 13.00 - 17.00
Weight matrix (PSSM) construction, Gibbs sampling, and Psi-Blast
Morten Nielsen
BACKGROUND TEXTS
- 13.00 - 13.15
- Questions to previous lectures
- 13.15 - 13.35
- Blosum scoring matrices [PDF] .
- 13.35 - 15.00
- Weight matrix construction. [PDF].
- Handout. Estimation of pseudo counts
- Answer
- 15.00 - 15.20
- Break
- 15.20 - 15.40
- Sequence profiles. [PDF] .
- 15.40 - 16.00
- Gibbs sampling. [PDF] .
Friday, 9. September 9.00 - 12.00
Implementation of PSSM construction from pre-aligned sequences including pseudo count
correction for low counts and sequence clustering
Morten Nielsen
- 9.00 - 12.00
- Implementation of PSSM construction from pre-aligned sequences including pseudo count
correction for low counts and sequence clustering
- PSSM construction and evaluation
- PSSM answers
Tuesday, 13. September 13.00 - 17.00. NOTE, we wil be in room 208/060
Sequence alignment and Dynamic programming
Morten Nielsen
BACKGROUND TEXTS
- 13.00 - 13.30
- Summary of Fridays exercise
- 13.30 - 15.30
- Sequence alignment [PDF] .
- Handout (O3)
- Handout (O2)
- Handout answers
- 15.30 - 16.00
- Break
- 16.00 - 17.00
- Blast alignment heuristics, Psi-Blast, and sequence profiles [PDF] .
- Handout, Psi-Blast sequence alignment
Friday, 16. September 9.00 - 12.00
Implementation of Smith-Waterman Dynamic programming algorithm
Morten Nielsen
BACKGROUND TEXTS
- 9.00 - 12.00
- Some details on the O2 alignment algorithm . [PDF] .
- Note, a small inconsistency in the slides for the O2 algorithm from Tuesday.
- Implementation of the Smith-Waterman Dynamic
programming algorithm
- Matrix dumps from alignment programs (to be used for debugging)
- Answers to sequence alignment exercise
Tuesday, 20. September 13.00 - 17.00
Support Vector Machines (SVM)
Olivier Thierry Taboureau
Morten Nielsen
BACKGROUND TEXTS
- 13.00 - 13.15
- Summary of Fridays exercise
- 13.15 - 13.45
- Overview in cheminformatics
- 13.45 - 13.55
- Break
- 13.55 - 14.40
- SVM
- 14.40 - 15.00
- Break
- 15.00 - 15.30
-
Cross validation and sequence encoding
[PDF]
- 15.30 - 16.30
- Hands on SVM using WEKA
Friday, 23. September 9.00 - 12.00
Use of SVMs for prediction of peptide MHC binding
Olivier Thierry Taboureau
Morten Nielsen
- 9.00 - 9.15
- Recap SVM
- 9.20 - 12.00
- Using WEKA to train SVM for MHC peptide binding prediction
- Answers
Tuesday, 27. September 13.00 - 17.00
Hidden Markov Models
Morten Nielsen
BACKGROUND TEXTS
- 13.00 - 14.00
- Hidden Markov models introduction
- HMM slides [ PDF].
- 14.00 - 14.45
- Viterbi decoding
- Viterbi Handout
- Answers
- 14.45 - 15.00
- Break
- 15.00 - 16.15
- Forward/Backward algorithm, Posterior decoding, Baum-Welsh learning
- Forward Handout
- Answers
- Some slides on the backwards algorithm
- 16.15 - 17.00
- Profile Hidden Markov Models.
Friday, 30. September 9.00 - 12.00
Hidden Markov Models
Morten Nielsen
BACKGROUND TEXTS
- 9.00 - 12.00
- Implementation of Viterbi and posterior decoding
- Training of a profile Hidden Markov model using HMMer
- Hidden Markov exercises
- Answer to Hidden Markov exercises
Tuesday, 4. October 13.00 -17.00. NOTE, we wil be in room 208/060
Data selection and homology
Stabilization Matrix Method (SMM)
Introduction to Mini-project
Morten Nielsen
BACKGROUND TEXTS
- 13.00 - 14.00
- Data redundancy reduction algorithms (Hobohm1 and Hobohm2). [ PDF].
- 14.00 - 14.30
- Optimization procedures - Gradient decent, Monte Carlo
- Optimization procedures, Cross-validation and SMM introduction [PDF]
- handout
- 14.30 - 15.15
- Cross validation and training of data driven prediction methods
- 15.15 - 15.45
- SMM background
- 15.45 - 16.15
- Introduction to mini project
- SMM algorithms and MINI-project
- 15.15 - 17.00
- Mini project work
Friday, 7. October 9.00 - 12.00
Data selection and homology. SMM mini-project work
Morten Nielsen
BACKGROUND TEXTS
- 9.00 - 10.30
- Hobohm redundancy reduction algorithms
- Answers to Hobohm programming exercise
- 10.30 - 12.00
- Work in groups on SMM mini-project
Tuesday, 11. October 13.00 - 17.00
- No lectures. Project work.
Friday, 14. October 9.00 - 12.00
- No lectures. Project work.
Tuesday, 18. October and Friday 21. October
AUTUMN BREAK
- Project is to be handed in via campusnet Friday 21nd at 23.59 at the latest.
Tuesday, 25. October
Stabilization Matrix Method (SMM). Project evaluation
Morten Nielsen
BACKGROUND TEXTS
- 13.00 - 17.00
- Stabilization Matrix Method (SMM). Project evaluation
- 13.00 - 13.20. Group 1
- Janni Brochner Nielsen
- Dan Borge Jensen
- 13.20 - 13.40. Group 2
- Grzegorz Slodkowicz
- Piotre Dworzynski
- Gabriel Durac
- 13.40 - 14.05. Group 3
- Marlene Hansen
- Juliet Wairimu Frederiksen
- Josef Korbinian Vogt
- 14.05 - 14.30. Group 4
- Corinna Theis
- Sabarinathan Radhakrishnan
- Sachin Pundbur
- 14.30 - 14.55. Group 5
- Ulrich Johan Kudahl
- Karin Marie Brandt Wolffhechel
- Christoffer Norn
- 14.55 - 15.10
- Break
- 15.10 - 15.30. Group 6
- Damian Rafal Plichta
- Helle Krogh Pedersen
- 15.30 - 15.45. Group 8
- Soeren Brander
- 15.45 - 16.00. Group 9
- Claes Gustav Oliver Ahlberg
Friday, 28. October
Gibbs sampling and Gibbs clustering
Morten Nielsen
Massimo Andreatta
BACKGROUND TEXTS
- 9.00 - 10.15
- Gibbs sampling and Gibbs clustering
- PDF
- 10.15 - 12.00
- Implementating of a Gibbs sampling algorithm for prediction of MHC class II binding
- Answers
Tuesday, 1. November 13.00 - 17.00
Artificial neural networks - I. Sequence encoding and feedforward algorithm
Morten Nielsen
BACKGROUND TEXTS
- Immunological Bioinformatics. MIT Press. Chapter 4.
- Background
- Feed forward algorithm
- Sequence encoding
- Prediction of protein secondary structure using NN
- 13.00 - 14.30
- Artificial neural networks. [PDF] .
- Handout
- 14.30 - 14.45
- Break
- 14.45 - 16.30
- Web exercise in construction of neural network prediction methods
- Web exercise answers
Friday, 4. November 9.00 - 12.00
Artificial neural networks - I. Sequence encoding and feedforward algorithm
Morten Nielsen
BACKGROUND TEXTS
- Immunological Bioinformatics. MIT Press. Chapter 4.
- 9.00 - 12.00
- Implementation of sequence encoding and feed forward algorithm
- Network part I answers
Tuesday 8. November 13.00 - 17.00
Back-propagation and neural network training
Morten Nielsen
BACKGROUND TEXTS
- Immunological Bioinformatics. MIT Press. Chapter 4.
- 13.00 - 13.30
- Description of potential projects
- Project suggestions, and descriptions. [PDF] .
- 13.30 - 16.00
- Network training - backpropagation, cross-validation, and and over-fitting
Training of artificial neural networks.. [PDF] .
- Handout
- Handout answers
Friday, 11. November 9.00 - 12.00
Back-propagation and neural network training
Morten Nielsen
BACKGROUND TEXTS
- Immunological Bioinformatics. MIT Press. Chapter 4.
- 9.00 - 9.30
- Formation of project groups, and selection of project
- Project suggestions, and descriptions. [PDF] .
- 9.30 - 12.00
- Implementation of Implementation of back-propagation and neural network training
- Network part 2 answers
Tuesday, 15. November. Project work
Start of project work
Morten Nielsen
- 13.00 - 17.00
- No lectures. Project work
Tuesday, 15. November - Friday 2. December. Project work
- No lectures. Project work
- Projects must be submitted (in PDF format) via campusnet Friday 2. of December 23.59 at the latest.
19. December. 9.00-17.00
Exam
- 9.30 - 10.05
- Isa Kristina Kirk
- Per Kantsø Nielsen
- 10.05 - 10.25
- Janni Brøchner Nielsen
- 10.25 - 10.45
- Dan Børge Jensen
- 10.45 - 11.30
- Juliet Wairimu Frederiksen
- Piotr Dworzynski
- Grzegorz Slodkowicz
- 11.30 - 12.30
- Lunch
- 12.30 - 13.40
- Karin Marie Brandt Wolffhechel
- Ulrich Johan Kudahl
- Christoffer Norn
- Damian Rafal Plichta
- Helle Krogh Pedersen
- 13.40 - 14.25
- Marlene Hansen
- Gabriel Durac
- Josef Korbinian Vogt
- 14.25 - 14.45
- Søren Brander
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