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2 Modeling formalisms and concepts
3 TODO: Opportunity vs optimality
4 Prebiotic evolution and more
5 Constructive evolution
6 Coping with variable environments
7 Multi-level modeling
9 Links to old pages
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
as a complementary source of information. You can use them in combination with your own lecture notes to check your comprehension of the concepts.
You can browse the contents with the navigation menu on the left. If you are an authorized member of this group you can edit the contents of the documents. Anyone can add comments with the 'discussion' link at the top of every page. If something is unclear, you can add questions/comments with this discussion link. If you don't have anything to add, but you would like something added please add a comment in brackets in capital letters. This will help others realize that something could be changed / added / clarified.
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.
For more information on how to use Wikispaces, see the
The following topics are covered in this wiki (see also the menu in the sidebar):
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
TODO: Opportunity vs optimality
here we look at the role of opportunities in the environment relative to adaptation and the evolution of behaviour
Prebiotic evolution and more
here we look at the origin of life and evolution in light of various model formalisms
here we look at how the evolutionary process can be a constructive process (rather than merely optimizing)
Coping with variable environments
here we look at evolutionary adaptations to variable environments
here we look at various multi-level modeling approaches (incomplete!)
here we draw up conclusions about modeling complex (and evolving) biological systems
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)
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