Lecture Notes on Bioinformatic Processes/Computational Biology

On this wikispace lecture notes are collected, which were made by the assistents of the Bioinformatic Porcesses/Computational Biology course. The wikispace was started in 2006-2007 and contains notes from multiple course years.

The structure so far:
- trying to make a readable framework originally based on the lectures of the 2006-2007 course Bioinformatic Process which is nicely linked to Wikipedia (or other external links) with references. The pages have been updated in 2014-2015 to reflect the structure of the course (now called "Computational Biology") at that point.
- below the references there are direct notes as recorded in the lectures: we could transform these into a clearer note form which can be more easily referenced.
- any thoughts welcome ...

Please be aware that this wiki does not claim to cover the full contents of the course, nor that these notes are necessarily a fully correct representation of it. They were made by assistents of the course and provided
to you
as a complementary source of information. You can use them in combination with your own lecture notes to check your comprehension of the concepts.

Getting Started

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TODO List: Some pages have a list added at the top of the page where one can add bullet points of what needs to be done on that page. This helps people to be aware of what is missing on a page, as well as allowing people to add comments or discussion at the top of each page.

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The following topics are covered in this wiki (see also the menu in the sidebar):
  1. Introduction
  2. Modeling formalisms and concepts
    • here we lay the ground work: an overview of various kinds of modeling formalisms
    • we develop concepts, in particular that of mesoscale patterns.
  3. TODO: Opportunity vs optimality
    • here we look at the role of opportunities in the environment relative to adaptation and the evolution of behaviour
  4. Prebiotic evolution and more
    • here we look at the origin of life and evolution in light of various model formalisms
  5. Constructive evolution
    • here we look at how the evolutionary process can be a constructive process (rather than merely optimizing)
  6. Coping with variable environments
    • here we look at evolutionary adaptations to variable environments
  7. Multi-level modeling
    • here we look at various multi-level modeling approaches (incomplete!)
  8. Conclusion
    • here we draw up conclusions about modeling complex (and evolving) biological systems
  9. Links to old pages
    • Topics that have been discussed in earlier years but are no longer part of the course.
      NOTE: topics are removed from the course for various reasons. Information on these pages might be outdated.
      (last updated in 2014-2015)