I've been thinking of ways to keep and share lab notebooks online, both for myself and for fellow DIY bio/science enthusiasts. After some thought, I find I value the following criteria:
- Notebooks are stored in open, royalty-free, standard file formats.
- Easily share any notebook page with anyone in the world just by sending them a URL. No need for them to log in or install any software or app to view any page of my notebooks. All they need is a web browser.
- Mobile friendly, for both reading and editing.
- Easily handle hundreds of users, easy for collaborators to set up their own notebooks.
- Writing, editing pages, or commenting requires log in, to try to prevent spam.
- WYSIWYG editor. Intuitive for newcomers. No need to learn MediaWiki markup or LaTeX codes. Should be very easy for any logged-in user to make entries combining text, photos, sketches, and file attachments.
- Hosted on free open-source software running on commodity hardware.
- Easy to migrate to another server/platform.
- The previous two criteria are because we shouldn't chance being locked in to any company's platform. Our notebooks' lifespans should be as independent of any external entity as possible. Yes, some folks think Google and AWS are gods and will be here 1000 years from now and trust their cloud. I don't -- I started using the Internet when Altavista, Geocities, and MySpace were the dominant platforms. I've outlived those companies. You may outlive Benchling, Protocols.io, Google, Facebook, Amazon, etc. For the sake of science, our work should outlive our employers and ourselves, especially our records of what did not work -- stuff that journals won't publish and hence isn't archived anywhere, yet should be a searchable part of human knowledge.
- Easy to backup, make snapshots, and mirror notebooks to other servers for safekeeping.
- Version control of edits. Saves edit history.
- Easy for other DIYers to set up their own notebook servers if they wish.
- Easy to move/copy a notebook from one server to another (e.g. keep a copy of your work when moving to another lab).
- The last two criteria: ease of setting up your own notebook server and copying or moving your notebooks around means you never have to rely on any particular company, service, or provider to keep your data published and safe. You are always in control and can keep your notebook published using the hardware/platform of your choice.
I'm exploring different approaches to this problem. This site is one of those approaches: adapting off-the-shelf wiki software.
First, I'm using the software as a notebook for my own projects to learn what features are useful in an online collaborative scientific notebook. Second, once it seems the notebook is useful to other community members (i.e. once “it has legs”), the priority becomes making reproducing this notebook system onto other servers really easy to do. A dream would be a single shell archive that you could upload to the new server, run, and with no further human intervention have a fully functioning replica of the original notebook server. Such a thing would need to be tested on at least three different cloud service providers or hardware setups to ensure portability. I think it's safe to restrict our choice of servers to those that run Linux since there are so many providers of Linux cloud services as well as a strong worldwide DIY Linux enthusiast community.