ONS Course – Module 4: Expanding the open notebook.

No single web platform has every capability that you could want/need in your notebook. This is why your choice in notebook software needs to be a versatile system, and is the reason why we chose to work with WordPress. WordPress has a ton of features and if there isn’t a feature that you need, there is probably a plug-in that has that capability. In some cases however, you may need to combine the functionality of another platform with WordPress. Lucky for us, we can do that.

The easiest way to combine software functionality is through embeds. Most web services will provide you an embed code that you can then stick into a new post. The service I use most frequently with this feature is Google Docs, because of the spreadsheets function. Saving is automatic, and creating new documents is very simple. Once you add content you can make the document public and then you can “publish to the web”. I specifically mention that because “publish to the web” and “public” are two different functions in a document. Once you publish your document, you can grab the embed code and paste it in WordPress.

Another useful site for research/notebook purposes is figshare. A few weeks ago I would upload data, documents, presentations, posters, etc and then copy the link into my notebook with a slight description. Now the developers have expanded the functionality so you can embed a figshare set wherever you want. The benefit of using figshare over anything else is that you get a DOI for everything you upload to the site, and your work is citable. There are some nice stat counters as well, and at some point they will add the ability to track citations. The only reason why I wouldn’t use figshare for everything is the lengthy form you need to fill out every time you post something. While it is essentially the same information you would post in a notebook entry, if you opted to post everything in your notebook to figshare you would end up doing everything twice, which is exactly what we are trying to eliminate.

Another great service is BenchFly. It is a video repository for scientific protocols, so essentially it is like the youtube for science. They even have a smartphone app so you can record from your phone without having to worry about a lot of post processing. While the site was originally intended for scientific protocols, I’ve spoken with the CEO of BenchFly, Alan Marnett, about uploading data or other non-protocol videos and it was well received, so don’t feel required to upload only protocols.

There are a lot of tools to use online that can expand the capability of your notebook so don’t be afraid to try a service and see if it can enhance your workflow. Here are a few more of my favorites:

  • Slideshare is a slideshow/document sharing software. I’ve been using this since before figshare had the capability and it still does it better than they do so I will continue to use it. It’s also very handy to have the slideshow embedded in your notebook in case something happens to your presentations. Now I give talks straight from the web and right from my notebook. Do that and you’re bound to get the ultimate ooh’s and aah’s.
  • Evernote is a very popular note taking app with optical character recognition for uploaded images. They don’t technically have an embed feature but there is a very simple workaround.
  • Mindmeister is an online mind mapping program. I use it frequently when trying to get my thoughts together and trying to plan out documents/experiments. It is a pay service, but there is a free version that is pretty limited. I only mention it because when I first got started with open notebooks this was the only web mind mapping program. I’m sure there are many more options now with better free capabilities. But mind mapping is a very useful tool and would be a great addition to any notebook.

Additionally, some themes may expand the capabilities of your notebook as well. Themes are basically the wrapper for your WordPress site and is what users see when looking at the public side of the site. There are a lot of themes available and some free themes are very good, but generally speaking the ones you pay for are better. The Open Science Federation has provided us with a couple of really useful themes if you’d like to mix it up.

The theme that is equipped by default is a twist on the Twenty Twelve theme. It has a minimal design and puts content front and center. But you have the capability of making it look like whatever you need, so poke around the backend and add an image to the header or some widgets to the sidebar. There are 3 other themes that you can enable and play with as well. Twenty Eleven is similar to Twenty Twelve but with a much bolder look. You’ll also notice P2 and PulsePress. Both themes allow you to post directly from the front-end of the site in a microblogging fashion (think twitter). You’ll still have the same backend capabilities, but if you need you can post quickly directly from your public site (just make sure you are logged in). On this side posts are limited to 140 characters. Note: PulsePress is based on P2 and has some extra features, but I’m not sure what those are since I can’t find much documentation on the theme. You’ll just have to play around 🙂

There is one last way that I want you to consider when expanding your notebook: science outreach. #Scifund Challenge believes that science outreach is an important cog in the scientific process. It becomes especially important in the quest to fund scientific research. It turns out that the open notebook platform that we’ve been working with is a blogging platform at its heart and was designed to send a message to the world. Take advantage of that every once in a while and make your research more accessible. Combine your notebook with some outreach, build readership, engage your community, and encourage future scientists. Outreach is easier than you think too! First you will need a message. Next, make your message as simple as possible so that as many people can understand it as possible. Finally share your message.

Services like Hootsuite can post to your social media outlets automatically so make use of that function to deliver your message. It can also serve the purpose of sharing your research. Over time you’ll notice more traffic to your notebook, and you may even have a positive influence on others which will make them want to know more about your research, your notebook, or science in general. Outreach does require more time than your standard notebook entries, but you won’t be posting every day. If you decide to incorporate outreach, aim to post once a week, or once every other week. And if you need help, we have a ton of references available to you.

Final assignment (yay!):

  1. Sign up for figshare.
  2. Share something and embed it in your notebook. If you can’t think of anything, consider an old presentation or poster. If you have some new data share that. Once you complete the submission form, go to the public link and get the embed code and copy that into a new notebook entry.
  3. Play with the other themes to figure out what works best for you. Themes are accessible from the WordPress dashboard under Appearance >> Themes. You can preview each theme by clicking “Live Preview” and install it by clicking “Activate.”
  4. Write a short post about a particular aspect of your research that is meant for a broad audience. Avoid the use of too many technical terms. Try to keep the post short and don’t spend too much time doing it. The goal is to make science outreach an encouraging experience. Focus on a small part of your research to make the task less daunting.
  5. Continue posting notebook entries and share the love. If you want to have more of an impact, sign up for a service that will automate the posting process. Hootsuite does a great job.