Open Notebook Platforms

The open notebook should ideally be the online representation of a standard lab notebook. Everyone has a different style, need, storage requirement and ultimately the open notebook should reflect this. To make all scientists adapt to one tool makes very little sense and would be a major discouragement to open notebook science. Software engineers take notes in their code, biologists need to take pictures, and mathematicians need any medium that can contain pages of equations.

There are a wide variety of electronic note taking applications available for consumer use both paid and free to use. In particular, I’ve discovered many applications that weren’t designed as electronic notebook platforms, but serve that purpose well. These platforms also have the distinction of being freely available tools and, in some cases, are products of the open source community. The platforms described here have the capability of being the most widely accepted and useful applications. As technology changes, I expect many new and useful tools to emerge and eventually supplant these platforms.

WordPress

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 scientists look toward.

WordPress has a very intuitive interface both on the front- and backend. Creating new content requires a couple mouse clicks and the ability to type. The tagging/categorization system keeps 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. There is even the capability of creating static pages, where content is sparsely altered (think “About” pages on websites).

As a CMS you can upload images and videos quite easily, but unfortunately you won’t be able to upload all file types (.pdf, .doc, etc) without messing with the website architecture. There is a lot of support from Automattic (makers of WordPress), and the community of third-party developers 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, project planning, and even real-time peer review.

Unfortunately many 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 get started in open notebook science, have limited technological prowess, or want something that works immediately.

This site and all the notebooks contained on the network are self-hosted WordPress sites.

Media Wiki

Almost everyone is familiar with MediaWiki because it is the backbone of Wikipedia. It is an open sourced application that is free to download and install on any public/private server. There are even some websites that allow users to register and begin using their customized version for use. OpenWetWare.org is one such site that is built around sharing scientific research and even has an open notebook setup tool.

With MediaWiki, the possibilities are endless. You can do nearly anything you want: create pages, categories, upload just about any file you want, and so much more. One of the largest advantages of MediaWiki over other platforms is that versioning is very intuitive. The revision history of pages is specially marked on every created page by default and allows visitors to see changes to any page.

However, most of these capabilities require at least a basic knowledge of HTML/CSS and some basic web scripting/coding may be necessary. There are plenty of sites that have tutorials and getting started won’t take very long, but the initial learning curve is a bit more than WordPress, for instance. Other drawbacks include lack of automated organization or navigation features, which makes finding old notes very difficult. There are several capabilities within MediaWiki that can make this a little easier.

Github

Open sourced software developers primarily use GitHub. It is a code repository that makes parallel code editing simple and is probably the most comprehensive tool for sharing and distributing code. It even has social media capabilities built into the site, which makes collaboration incredibly simple.

While not intended to be an open notebook platform, it has several features that make it perfect for the practice. It is possible to upload any file to the repository either online or directly from the command prompt of your PC/Mac. Collaborators and even 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. These features are built into the site structure, so GitHub does this all seamlessly.

GitHub even has a wiki associated with each individual repository, which makes it especially useful for open notebook science. Even if you aren’t a software developer, the use of the wiki combined with the ability to upload any file to your repository allows for a very powerful and dynamic notebook. It doesn’t have many of the features available in MediaWiki, but that doesn’t make it any less useful.

The social media-like capabilities allow you to follow other repositories, comment, contribute, share, etc. Other site architecture adds the support of a blog-like platform within GitHub. This capability isn’t all that user-friendly, but has the potential to make GitHub even more robust and attractive as an ONS platform. While GitHub is a very powerful technology, many of its drawbacks are of the user-friendly sort. Since it was developed with software developers in mind, less tech savvy users may become frustrated with the site interface.

Physics Junior Lab 308-L (University of New Mexico, Spring 2012) open notebooks, software, and labs are hosted on GitHub.

Google Drive

Google Drive is a cloud-based office package similar to the Microsoft Office suite of tools. It provides word processing, spreadsheet creation, presentation development, online form hosting, and even a drawing tool. In fact, this document was created in Google Drive. Drive “documents” support basic text formatting, some html, and can host images in-line in documents. Recently, Drive has added the functionality of full file hosting capabilities, similar to Dropbox. It can even convert .pdf and MS Office files into Drive documents for editing.

Google Drive is one of the best and easiest ways to collaborate on the web. Drive allows users to share documents with collaborators for viewing and editing. The most impressive feature is simultaneous editing. Users can interact through inline commenting, or through a chat window within the document. The collaboration features are perfect for joint publication creation, review, and editing. Potentially, it has the power to provide real-time in-document peer review capabilities.

Documents are private by default, but making them public is a simple process. Documents can even be embedded in other websites, for enhanced functionality. The organizational features of Drive work much like the file system in PC or Mac environments. Folders within Drive can even have public sharing or collaborator specific sharing. Any documents placed within shared folders are automatically given the same attributes as the parent folder.

Drive office tools are limited in fuctionality beyond collaboration, publication, and basic editing capabilities. Many features available in other notebook platforms are unavailable in Drive, but it does serve a useful purpose. It even provides a revision history that tracks changes and can revert documents to past states.

Evernote

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. It also has optical character recognition capabilities so images of handwritten words or pdf documents are scoured for text allowing all documents to be searchable within the platform.

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 the intuitive and public notes may not be search indexed (which makes it hard for others to find your useful protocols).

Miscellaneous

There are too many tools on the internet to for any one person to keep track of, but if another mechanism is desired, here are some useful and still freely available tools:

  • Flickr/Picasa – Hosting images may be a great workaround. Take images of handwritten notes and upload them to a photo repository.
  • Social Media – The real-time capabilities of social media gives you the outlet to post what you want when you want it. I’ve used FriendFeed to take notes in real-time before facebook had the feature, and essentially you can do this from any social media platform available. Twitter is a bit limiting in this regard, and data is lost quickly without various workarounds. Many tools are available that aggregate social information in one place (think Storify and HootSuite). So working with multiple outlets is not as burdening.
  • Tablets/SmartPhones – There are plenty of apps that let you take notes, share images/videos, bridge platforms and publish to the web right from your phone/tablet. Capabilities are expanded with desktop application access as well.
  • Blogs – I’ve already talked about WordPress, which is more than a blog. But blogging services like Blogger and Tumblr offer comparable features, intuitive interface, and social promotion capabilities.
  • Wikispaces – Quick and easy wiki setup in the cloud. No need to self install like Media Wiki, but also not as customizable.
  • Dropbox – While not specifically a notebook platform, you could maintain electronic notes and then upload the files to a public folder. The desktop client makes uploading easy.

The most important aspect of open notebook science is to find a tool quickly that suits most of your needs. Many of the platforms can be supplemented using other tools that have embed capabilities. IheartAnthony’s Research is a notebook that incorporates Google Drive, SlideShare, Scribd, Google Maps, Youtube, BenchFly, figshare, Mindmeister, and others into the WordPress structure.

The most approachable platform may be WordPress since it is very intuitive, has a low learning curve, is very robust, incorporates plug-ins and a variety of themes for customization, features a strong and large user and developer base, and is easy to organize and search. For any scientist wishing to get started in ONS, WordPress is the place to begin.

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