ONS Dual Blogging: Open Notebook Platforms – Supplemental Information and Comments

Up on Science Exchange, I’ve written a post that describes the most ideal open notebook platforms and how they can be used for scientific documentation. Their design is certainly not intended for those purposes, but they are effective tools nonetheless. Here is a sample of the post:

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.

I also go on to discuss Media Wiki, Google Docs, Evernote, and Github. And you can check out the whole post here:

Open Notebook Series: Open Notebook Platforms

I think each service has a lot to offer to open notebook scientists, and with services like Evernote and Google Docs, you could certainly get away with using multiple services. Think combining Google Docs with WordPress/Media Wiki.

The most intriguing service to me is Github. If the wiki was more powerful, Github would be the ultimate notebook in my opinion. The reason is because you can upload any file type to your repository, and there is a social network, and you have access to a wiki to supplement your notebook. I haven’t played too much with the social network component, but if it is even 10% as effective as facebook it could prove very useful.

Github also makes sharing repositories easy and collaboration very easy. Anyone can fork your repository (make a copy to their repository) and if you are collaborating, pushing updates is at the discretion of the original repository’s owner. And it is all versioned in case some files get deleted.

And I’m not sure how true this is, but I’ve heard that Github is open sourced in some capacity so you may even be able to self host your own guthub repository. This would be amazing for ONS and scientists could setup their own lab site to enable collaboration amongst only the members of the lab.

And to further supplement my ONS Platform post, I offer some alternative platforms/tools to aid your open notebooking skills:

Creative Solutions to ONS

There are too many tools on the internet to keep track of, but if you don’t like the options that I mention in my post, here are a few creative alternatives that you may appreciate.

  • Flickr/Picasa – Do you want to keep writing with paper and pen? Try taking pictures of your handwritten notes and upload them to one of the many photo sharing websites. I’ve done this from time to time and upload the image files here to supplement my notebook, when I don’t want to rescribe all the work I’ve already done.
  • Social Media – The real-time capabilities of social media gives you the outlet to post what you want when you want it. Steve and I have 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. If you use a platform like WordPress/Media Wiki, you can even embed your FriendFeed posts into your notebook and people could see your notes in real time in your native platform.
  • 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. Who says you need to be tethered to your lab pc?
  • Blogs – I’ve already talked about WordPress, which is more than a blog. But blogging services like Blogger and Tumblr offer comparable features. Blogger is trying to be more like a CMS, but still doesn’t have all the functionality of WordPress, but the Google Suite of Apps helps ease the burden quite a bit. Tumblr however is more limited in its capacity, but if you are going with just text and images for your notebook then it will suit you just fine.
  • Wikispaces – Quick and easy wiki setup in the cloud. No need to self install like Media Wiki, but also not as customizable.

And if you use a tool that I haven’t mentioned I’d love to hear about it and how you make it work for you. ONS doesn’t work if it is tedious and you don’t want to update. The goal of technology is to enhance your workflow and make life a little easier. And I’ve found that the tools and platforms I mention above and in my post at Science Exchange aid my quest for scientific domination.

  • http://www.carlboettiger.info Carl Boettiger

    Great post. I agree that wordpress is the platform I’d first recommend to anyone interested in trying out an open notebook, since it’s both very powerful and very intuitive, and has a very active scientific community around it (e.g. see wordpress-for-scientists googlegroup, & plugins like kcite, mendeley, etc)

    I also agree that of all the options, Github is the most intriguing.  There are at least three ways to keep a notebook on github: Github wiki (under repository), Github-hosted blog in Jekyll, or just a Github repo with folders & entries as markdown files. The Jekyll blog idea is the most powerful but least user-friendly.  Github Issues Tracker is so thorough it could be a notebook itself, organized as a series of tasks, grouped, tracking the progress of each task.  Being able to use markdown to write posts with images & code blocks anywhere on github, and having stable links to everything & a built-in social network is all quite nice.  Other users can edit the wiki pages, comment on the issues tracker, & approved users can edit & commit files on the repo.  Wikis & repos are version managed and can be forked.  

    One could use all of these in concert: Issues tracker to handle all tasks/goals, repository for all working content: manuscripts, code, figures, wiki for protocols and how-to tricks one wants to remember, and github Jekyll blog to provide a professional website + blog/official lab notebook.  There’s a powerful API to enable all kinds of programmatic access to the content, from displaying the latest issues or commits on the notebook page to graphing your commit dates or version trees.  Most of this is easily portable, in case Github disappeared or you wanted to migrate content to a different platform.  

    The disadvantages: significant learning curve, particularly for the Jekyll blog.  The Jekyll blog (& wiki) can display mathjax equations, but the markdown files in the repository & the issues trackers cannot.  There’s no automatic citation tool, like kcite.  Image files can be dumped in the repo, but better to host them elsewhere, like figshare, and link to embed the image into a post.  There’s the question of having one repo for everything, or a different repo for each project or paper.  Overall I worry that this is too complicated with content spread out over too many different places, rather than all in some chronological, version-managed notebook. 

    I’m trying the Jekyll-based notebook out for the moment, having (as you know) been on the media-wiki based OWW for a year and WordPress for another year and half.  Never-ending fun, we’ll see how it goes!

    • http://www.iheartanthony.com Anthony Salvagno

      Thanks for letting me know about Jekyll. I’ll have to check that out. Just for reference, are you referring to this: http://pages.github.com/ or this: https://github.com/mojombo/jekyll/ or something else? And let me know how it goes, if we end up getting funded for the IGERT we will most likely look to incorporate something like this as the central hub for the open research effort here at UNM.

      • http://www.carlboettiger.info Carl Boettiger

        Github’s pages and jekyll are kinda the same thing.  Github will automatically host any html file you put in a branch named “gh-pages” of a repository, using the url: http://username.github.com/repositoryname.  Jekyll is a static-site generator, which lets you create a blog from static pages written in markdown.  Jekyll will automatically run on any “gh-pages” branch if you stick in markdown files instead of html, which is why I call them the same thing.  A user can create their own website at http://username.github.com by creating a repo called “username.github.com”.  (Jekyll was created by github founder ‘mojombo’, that repo you linked is its source-code, but also has lots of useful info on its wiki pages.)

        http://jekyllbootstrap.com is probably the best place to start to get a Jekyll blog up and running.  The static blog concept takes a bit of getting used to, and is most powerful if you’re happy working with html & css (or even better, with ruby scripts), though you don’t need to know any of that to use it.  err, like I said, a bit of a learning curve unfortunately…

        • http://www.iheartanthony.com Anthony Salvagno

          Sounds like some experience with a wiki is useful (since you learn basic html/css with that platform). I don’t know why, but whenever I read any tutorial that is github related I’m always overwhelmed and the tutorials sound really complicated, but once I start using the system it turns out to be relatively straight forward. From what I’ve read so far about Jekyll and Pages, I have the same feelings, but I keep telling myself it probably isn’t as annoying and confusing in practice as the help makes it. When I have time I’ll play with it some. Thanks for pointing out this interesting addition to github, which now makes it even more intriguing. Keep me posted on your thoughts.