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The following is a general set of links to find various animaions but there are specific animation links in the various topic pages.

McGraw-Hill
Contains a lot of very good biology animations. Not all are relevant for the IB syllabus though.

Biological Animations
A good collection of animations.

John Kirk - Cell Biology Animation
A VERY colourful web site (difficult to read in places) but it has some good animations and pictures to explain some complicated concepts.

LearnersTV
Some animations are better than others but a good collection of animations overall, well worth searching through the five pages of animations (not in alphabetical order though).

McGraw-Hill - Virtual Labs
Trawl through the various chapters to view animations and virtual labs.

Animated Tutorials
Some good animations and explanations.

Interactive Animations
Very concise animations and explanations but it may go into too much detail in places.

Google
Google is one of the most powerful tools at your disposal and I use it to find animations all the time. To find animations using Google just type the name of the process you want an animation for and follow it by "animation", "flash" or "swf". Chances are you will have to go through a lot of bad animations before you find one you like.

YouTube
Another very useful place for finding animations. To find animations using YouTube, just type the name of the process you want an animation for but you you will have to go through a lot of bad animations before you find one you like.