Some comments:
* Add an "undo" button. I'm not sure if it is possible to choose a bad reaction, but I’d like to undo some of the tries. (And perhaps a "restart+areyousure" button.)
* Add a lithe graphic to each molecule, so they look more real.
* Some reactions are too fast, for example [Glucose 6-phosphate] -> [Fructose 6-phosphate] is almost instantaneous, so it took me like a minute to realize that something had happened. You should add some delay and more highlighting.
* The page is very tall, so it is not possible to see at the same time the reactives and the enzymes at the bottom, like [Pyruvate kinase] or [ATP synthase].
* Add an "easy" mode, so that when you pick a molecule, all the possible enzyme targets are highlighted.
* If you put a [ATP] in the [Pyruvate transport] and you don’t got any [Pyruvate] then the [ATP] is splited, but no [Pyruvate] is transported. So you lost a [ATP] :( !! I don’t know if it is biology correct, but I would like that the [Pyruvate transport] is dissable / does nothing when there is no [Pyruvate]. (Same problem with the [NAHD transport].)
* If you put a [ADP] in the [ATP/ADP Translocase] in the Mitochondrial matrix side the [ADP] get stuck until you put a [ATP] in its place. First, it is not possible to remove the [ADP] from the enzyme. Second, I’m not sure, but it looks like that the enzyme is translocating the third phosphate from the [ATP] to the [ADP] on the same side of the membrane.
Nice work.
* Added delay for every reaction
* Made the page less tall, everything is smaller now (I'd underestimated the size, working on a 27" iMac)
* The easy mode was already there, enzymes lit up when you picked up a substrate. I've added an extra help now: when you hover over an enzyme, the available substrates light up.
* The transporters are only visible (and usable) if enough ATP/substrate is available
Please don’t make the transporters invisible, only disable them.
(I don’t like starting with a Pyruvate, it is like cheating.)
