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Here are a few quick, random things I noticed after looking through the PDF.

The emphasis on documentation is great. We need more of this.

You say that the "hint text" in the various form fields should disappear when the field has focus. I actually find it much easier to use when the text gets lighter but doesn't disappear until the user has started to type. I usually navigate forms by tabbing through the fields, and I hit tab as soon as I'm done with one field, which means that by the time my eyes get down to the next field the hit text would be gone. The jQuery In-Field Labels plugin is a great way to make it a little bit more usable: http://fuelyourcoding.com/scripts/infield/

I'm assuming that users create groups. When two users inevitably create similar groups, is there any way to merge them?

Do you really need a separate "add link" button for each reagent? Why not just show the link field and clearly mark it as optional, so someone doesn't have to click many times if they have a bunch of reagents with links?

You mentioned videos for steps. Are you thinking people will upload them? If so, that's tricky. What formats do you accept, do you have the space/bandwidth to host them, etc? Or are you thinking that people will upload them to YouTube/Vimeo/etc and paste the link? If so, are they embedded or do users need to go to the video page to view it?

The requirements for the step editor seem awfully specific. I'd suggest taking a look at the available editors around like CKEditor or WMD and choosing one of them as a baseline.

http://ckeditor.com/ http://wmd-editor.com/

The page describing the fonts, buttons, etc seems extremely specific. If the PDF is a collection of wireframes and not a design (maybe I misunderstood it) then there are probably things more important to nail down than the border-radius (border-radii?) of input fields.

For the log in lightbox, have you considered using email verification (user signs up, gets emailed an activation link, clicks link, logs in) instead of a captcha?

Do you really need the "Ban User" functionality for group admins? Does banning a user make them not able to see that group at all? What if they log out, or create a new account? It seems like the troll rate on a site like this would be extremely low, so is this necessary or just adding extra complexity?

What is that "Language" link in the header? Will the site support multiple languages? Can users translate protocols? If so, which user "owns" the translated protocol? This could potentially add quite a bit of work, so it should probably be nailed down.

Is the "Blog" in the header just a link to a Tumblr/WordPress/whatever blog or is it part of the site?

Something that seems to be missing is a rough overview of the data. A page describing the data would be very helpful, even something as simple as "protocols are divided into groups, groups are created by users, and users can add new group admins" would go a long way.

I'm a bit confused about the "DIYBio Protocols" page. Is this a group? It seems like it has a bunch of groups inside it. Maybe I'm misunderstanding what a group is. A rough data model would help with this a lot.

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2. There's no explicit way to merge groups, because it sounded like more of a hassle than it was worth. What do you think of avoiding the problem in the first place by suggesting existing groups as the user types in a group name to be created?

4. Video: lets forget it. I've never done anything involving video uploading, and once I had a look at what a hassle it is to do, I don't think it's worth it for the amount of our users that will actually use it.

9. early on, many of the people who've expressed interest in the site wanted to use it in non-english speaking settings. since there is no "settings" page yet (not enough settings to make it worth having one) the languages selector goes on the top menu rather than inside a settings section. Changing it at the very least changes the language of the UI (assuming this isn't too difficult) but could also change which protocols are shown (this sounds much harder.) Not an essential launch feature, on reflection.