When it comes to site organization, there is no better platform than those used for blogging. This is precisely the reason why we’re using WordPress for our open notebooks. Every platform has advantages and disadvantages, but no other platform really handles site organization as well and makes it as easy. And for an open notebook, site organization should be priority number one. Additionally, WordPress has many other features that can be exploited for open notebooks  and today I’m going to tell you all about them.

When it comes to organization, the first thing you’ll notice is that all posts are organized reverse chronologically, meaning new stuff displays first. To expand on the power of the site, you have the ability to add categories and tags to your posts. On sites hosted via WordPress.com tags and categories serve similar but slightly varying functions. Tags were designed to give public blogs some exposure across the WordPress network, but both options served to organize posts. Here on self-hosted WordPress sites (like the ONS Network), tags and categories are nearly identical with one main difference: hierarchy. Tags have no hierarchy, but categories can be nested.

My notebook (research.iheartanthony.com)  is a good example of how to effectively use both. In my notebook, I use categories to list subject matter and experiments and list specific experiments as categories nested under project names. I use tags to organize specific types of posts that could appear in multiple categories (for instance “data” or “methods”). Remember, there is no one-way to do this, so feel free to experiment for organizational techniques that suit your mood, personality, and need.

WordPress also has the very powerful ability to create static pages. The main blog page of your site is constantly changing (a dynamic page), but static pages contain the same content for the duration of your site unless you manually edit them. Creating and editing pages works just like creating and editing posts in the backend, only they are listed under the “Pages” tab of the dashboard. The other difference is that pages have no category/tag options, since they aren’t intended to be a huge backlog of information. You can, however, create nested pages like those found on the main ONSNetwork.org main page. A great use of pages would be to create an archive for navigating your site, or to host introductions to your projects. A great use of pages would be to create a contents page for your most frequently needed information, this will speed up navigation for your site.

Bonus Feature: As an add-on to ONSNetwork.org the Open Science Federation gave us the ability to create forms. Usually forms have the ability to add feedback forms to websites, but simply they are just input boxes for users. If you enter tabular data frequently it may be handy for you to take advantage of this feature. From your notebook dashboard, navigate to the “Forms” tab and try to create a new one. I’ve created an example form on a test site here. All the data you enter gets saved to a database that is kept private that you can access via the dashboard. If you want to make it public, you can download the information as a .csv file and upload it in a notebook entry.

One of the biggest benefits of using WordPress is the power of adding themes and plug-ins to expand the capability of your notebook. I’ll get into those more in the last module of the course, but I wanted to mention the power of one particular plug-in: Jetpack. Jetpack has a ton of features built into the plug-in. One of my favorite features is the ability to access site analytics. You’ll be able to see the amount of daily visitors you receive, which posts are most popular, and how users are visiting and accessing your site. This will help you understand how your research is being digested and impacting the world. The statistics you get from here could help you convince others in your field to the merits of doing open notebook science. Most scientists care about impact factor and standard metrics regarding publications, and the metrics offered by Jetpack provide a much more robust measure of impact and use.

In addition to site stats, Jetpack gives your posts the ability to digest Latex code and display them on your site. You can also greatly expand the usability of each post page. There are options that allow you to expand the functionality of comments, you can directly share to social media from posts, you can share comments to social media, and a whole lot more. There are a lot of options within Jetpack, which is so powerful it gets its own tab in your notebook dashboard, so feel free to learn about and play with each function.

There is one last feature that I want to mention that makes WordPress an extremely powerful tool for open notebook science. That feature is commenting. While most web platforms now come with a comment feature, the ones that are more used for personal content (think Evernote, Google Drive, Wikis) don’t have public commenting built into the system. Commenting allows your notebook to be much more than a tool used solely for yourself. By allowing comments, you are bridging your research with the world. For one, comments allow easy communication between yourself and your lab mates especially during those times when you are unavailable. Comments also can enhance collaborations and increase communication between yourself and your peers. But personally speaking, the most powerful use of comments is that it allows real-time peer review. Mistakes made in the notebook could be caught and corrected much faster than they would be had an experiment gone to publication. If a result is unclear, more insight could be added. If a protocol is unrepeatable, gaps could be filled. The real-time peer review aspect of the open notebook could make the publication process go a bit smoother, will add some extra validity (to fight those people who scream “but is it peer-reviewed”), and most definitely will make you a better scientist!

This weeks assignments:

1. If you haven’t already done so, come up with an organizational structure for your notebook. Incorporate tags/categories as you see fit. Make sure that categories and tags are visible on the side bar of your site. To do this go into Appearance >> Widgets on your notebook dashboard. From here you should see a side bar menu. Just click and drag buttons for categories and tags into the side bar menu. Press save and away you go.
2. Create a static page. Best uses are as introductions to experiments/projects, or as a navigation supplement to your site. To create a static page, go to Pages >> Add New on your notebook dashboard. If you would like to create nested pages, make sure to select a parent page before you click “Publish.”
3. Activate Jetpack. To do this, click “Jetpack” on your notebook dashboard. You should see a big blue bar near the top of the page with a button that says “Connect to WordPress.com.” The jetpack features are hosted there so you’ll need to create a wordpress.com account if you don’t have one (or just sign-in if you do). Once Jetpack is activated, activate the features you want. At the very least read a little about each feature and get a feel for what Jetpack offers your site.
4. If you have a smartphone (either Android or iPhone) download the WordPress app and connect it to your notebook. All you will need is the exact url of your notebook (for instance http://http://onsnetwork.org/testing) your username and your password. Once you have that input, the app takes care of the rest. From here you have full editing capabilities of your notebook.
5. Continue posting experimental details. Getting in the habit of documenting your research takes time, and the sooner you develop this habit the better.
6. Read entries from your classmates and comment.