I’m not a biologist but I develop OpenWetWare for them. Many of the lab notebooks we host are used by teams. MediaWiki is our platform and, among other things, is first and foremost a document manager.

The software ideally focuses on individual pages and not upon sets of pages. At OpenWetWare, we have constructed tools and tempates to facilitate managing document hierarchies to support our researchers: they see their lab notebooks as a more-or-less unified set of pages.

This is 180 degrees from Git’s notion of managing revisions of a project and not to focus on individual files. In our world, that would be a ‘lab notebook’ for a project that a set of our members were participating in. I like the idea of knowing what’s going on with the project a lot. But we can never lose sight of any single contribution; data is data and we really need to preserve it

Part of the reason for using a lab notebook based upon MediaWiki is that not only the current state of a document is accessible but all of the revisions to it are as well.

This may present concerns for some folks: we hear that people don’t want to put things into our lab notebooks that they do not know to be 100% accurate since their contributions will become part of the collective record of the project. The notebook can be, and is often a record.

But if creating an official record does not directly lead to an individual researcher being a better researcher, it won’t be seen as a useful tool. It reminds me of companies who keep “2 sets of books”: one formal for tax purposes and the other that accurately but privately represents the real value of the company.

We’re thinking that a structure similar to the way WordPress handles writing blog posts may be worth considering. Create a document, save the changes until you’re happy with it, then publish it. The act of publishing is the ‘commit’ that would become part of the record. In the interim, the researcher has a safe and secure way to enter data that will not go away. They could save their drafts and have access to multiple checkpoints on their way to completing a protocol or doing data analysis.

By doing this, it would perhaps help alleviate another problem we see. People keep a document open for a long time knowing that when they save, their changes become accessible to all. This can also be a path to pickledom: connections can come and go. And so can sessions.

If we were to support this ‘private until published’ revision model, I’m curios as to how it would be received.

Thanks.

Garrett’s site looks like a great way to share a notebook. From what I can tell, TiddlyWiki isn’t a distributed system per se, although there’s some experimental work in that direction. It can pickle itself into a single file which can be used in a DVCS of course.

I suspect the pull/marshall/push discipline of distributed version control systems is too much for this sort of notebook. It’s best for building on top of someone else’s work, for example doing new or revised analysis on a dataset, or a updating a living review article. But for sharing thoughts and ideas, something like a feed reader inside TiddlyWiki would be better, so you could read, and easily import, updates from other notebooks.