This is the third in a series of posts by Anthony Salvagno about open notebook science.
An open notebook is ideally an online representation of your standard lab notebook. Everyone has a different style and volume of notes though, and an open notebook is no different. Software engineers need to take notes in their code, biologists need to take pictures, and mathematicians need any medium that can contain pages of equations.
There are consequently an array of open notebook platforms to choose from, and some better suited for certain applications than others. Five such platforms are discussed below, all capable of supporting scientific disciplines in varying aspects.
Originally developed as a blogging platform, WordPress has become much more than that. It is the go to Content Management System (CMS) in web design, and is used for online shopping, blogs, artistic portfolios, personal websites, and even open notebooks. Personally speaking, WordPress is the most versatile platform for open notebooks and should be the model that open notebook designers look toward.
WordPress has a very intuitive interface both on the front and backend. The tagging/categorization system keep your notebook organized and allows for easy navigation. Posts are automatically organized reverse chronologically (like a blog). And editing posts is very easy with several options for bulk editing, saving drafts, revision histories, scheduled publishing, and much more.
As a CMS, WordPress allows you to upload images and videos quite easily. There is a lot of support from Automattic though (the makers of WordPress), and the community is huge with an impressive array of free plug-ins and themes that enable you to tailor the platform to meet your needs. And the comment system allows you to create a community centered around your research, ideal for collaboration and project planning.
Unfortunately most of the features and plug-ins are limited to those who self host (have their own website), but even using a WordPress.com site has a decent amount of features and is ideal for those who want to try ONS and play around with the WordPress interface.
We all have seen Media Wiki in one shape or another, as it is the backbone of Wikipedia. What you may not know is that it is freely available for download for installation on your own website. There are even some websites that allow users to register and begin using their version for use. The most prevalent site I know of is OpenWetWare.org which actually has an open notebook setup tool (for free).
With Media Wiki, the possibilities are endless. You can do nearly anything you want: create pages, categories, upload files, keep track of changes, and access an openly accessible revision history. The only issue is that you will need to learn some basic HTML, CSS, and wiki markup language. There are plenty of sites that have tutorials on Mediawiki, and getting started won’t take very long, but it does require some time. The other drawback is there are no automatic organization or navigation features, which makes finding notes from the past very difficult. So if you go this route, make sure you plan accordingly.
If you are into software, you need to be using Github. There is no better tool (in my mind) for sharing and distributing code than Github. You can upload any file to the repository either online or directly from the command prompt of your PC/Mac. Collaborators and strangers can copy your code/files and edit them as they see fit without affecting your version. If you allow it, those same collaborators can contribute back to your work directly by combining their work with yours. And it does this all seamlessly.
And there is a lesser known feature in Github that makes it especially powerful for notebooking. It has a wiki. Even if you aren’t a software developer, the use of a wiki combined with the ability to upload any file to your repository allows for a very powerful and dynamic notebook. It could be a little unorganized, and with less features than Media Wiki, but that doesn’t make it any less amazing.
And the feather in the cap, is the social media type structure. You can follow other repositories, comment, contribute, and share. It should also be mentioned that open repositories are free, but if you want your work to be private (which isn’t very ONS) you’ll need to pay.
Evernote was designed as a private notebook type of service. It has just about everything you’d want in a notebook except that the upload features are limited to just pictures and videos. You can organize work in notebooks, and updating a notebook creates a new note. There are tools for smartphones and computers that allow you to work without needing to be on a web browser, and using the system is pretty straight forward since it was developed for the general public.
By default your notes are private, so if you don’t like the idea of being open this may be the tool for you. There is the option to make your notes public, but the mechanism isn’t all that intuitive, and public notes may not be search indexed (which makes it hard for others to find your useful protocols).
Google Docs are the best and easiest way to collaborate on the web. This Open Notebook Blog series were created with Google Docs themselves, and because of the service I haven’t used Microsoft Office in 5 years. If your note taking requires basic text/html and some image files, then Google Docs is your platform. You also have access to spreadsheet creation (useful for inventories and protocols/recipes), a powerpoint clone, and a drawing tool all of which have the same creation, sharing, and collaboration abilities as the documents feature.
The shining feature of Google Docs is collaboration. You can have fully documented chats, users can simultaneously edit any of the document tools, and comments can be made inline. The collaboration is so good that everyone should use Google Docs to develop their next scientific publication. It also is excellent for peer review and critique.
Like Evernote, your notes are private by default, but making them public is very easy and straightforward. If you want to speed up the process, you can create a public folder with some collaborators and add newly created notes to the folder. Any settings the folder has gets automatically adopted by all subfolders and documents.
Overall though, the key with open notebook science is to find what works for you, so be creative, bridge platforms, and share your science.
About the author
Anthony Salvagno (Twitter: thescienceofant) is a grad student in the KochLab in the Physics and Astronomy department at the University of New Mexico. He is an open notebook scientist and publishes all of his experimental results in real-time on his IheartAnthony open notebook / blog. Anthony is also a member of the Science Advocate program.