Cell Craft Flash game
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This engaging strategy game leads players through the parts of the cell and their functions. Reading is required, and the topics covered are on a middle school and high school level. There is nothing about the game that is inappropriate for younger kids, except that it's probably too hard. Here's the description from the developer's website:
CellCraft, is a thought-provoking strategy game set in the microscopic world of single-celled organisms. Players take on the role of a simple amoeba who must survive and thrive in various hostile environments.
Players must make, use, and transform resources like ATP, glucose, and amino acids, as well as the cell's various organelles, including mitochondria, lysosomes, and the endoplasmic reticulum. The player must hunt down and digest organic material, survive waves of infectious viruses, and more. Players can earn "extra lives" by splitting their cell through mitosis. In-between levels, the player has the opportunity to "splice" their cell's DNA in order to change its capabilities, and adapt to differing circumstances.
CellCraft was commissioned by Anthony Pecorella of Wake Forest University, through a generous grant from the McArthur foundation.
This is a long, challenging game-- I spent about an hour playing, and gave up on level 5 (it's fun but I just can't spend anymore time on it right now). I can't promise that there isn't something inappropriate beyond that, but it doesn't seem likely to me.
Please be aware that the site hosting the game has links to the other games on their site, and not all the games are appropriate.