Here's my proposal: Every function documentation must have these entries:

Short Description: (appears in the search page)
Detailed Description: 
[Algorithm Description: in some cases]
Usage: 
Simple Example:
I agree 100% with this suggestion by Riccardo. Also, that was a great example that he used about how the existing documentation doesn't help in many cases.

Here is the thing: as it stands now, it is fine for the lab and close friends to use IMP, because we can walk over to Daniel or Ben when we have a problem and quickly get it answered (thanks guys!). But the goal for IMP is to get it distributed globally. If a lab that doesn't have any connection to ours wants to use it, currently nothing but the most simple functionality will be usable due to the lack of documentation. So really the overall impact of the software is reduced.

A point of comparison is Modeller. Modeller is used by many labs without having to email us for tech support. That's because if you go to the Modeller website, it not only has a great tutorial, but also massive class and method documentation. Most questions can be answered by using that documentation as a reference, and I would argue that the documentation more than almost anything else is responsible for Modeller's widespread use.

The problem is that people don't want to document their code because once you get something working, you either feel great about it and want to apply it to something right away instead of writing how it works, or you're so sick of it that you don't want to go through each method and document it, or you say you'll do it later (but of course, later never comes). I am as guilty as anyone about this for lab stuff. Some insight from my brief time working in industry: I have to document everything I write here for IP reasons and there is a lot going on every day so I don't really have time to revisit old code.  Therefore I have to document right away or it's never going to happen.

I thought Barak's attempt at organizing this was noble and was sad to see that people didn't have time to do it, even if it was just a day or two. I think another attempt should be made. Remember that your legacy as a scientist will be defined in large part by who uses your code after you have moved on from the lab. Therefore a day or two of your life to document as much as possible will have a high impact on your output. We have many lab alumni who spent five years on a project that no one else can use because it wasn't properly documented (I myself am still trying to make sure this doesn't happen). Honestly, I think Andrej should crack down a little more on this, i.e not signing off on paper submission until all the code that was used to do it is documented, or something like that, but I imagine he would prefer a more organic solution.

Another suggestion which might be extreme is to hire a summer college intern whose sole job would be documentation. That would actually get them to be the IMP expert and if they wanted to go into our field it would be a great way to start, and we would get the benefit of documented code.

(tl;dr ?)

thanks,
dave










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