Slightly over a month ago, I came across the Winnower and began a project in open notebook science. The concept was to upload notes from my notebook to the Winnower, archive the notes, and get DOI’s for each post. Then I would write 2 papers: one to summarize the experiment and the other to theorize a complete publication system that would incentive open documentation of real-time research (open notebook science). I chose the Repeating Crumley experiment for this experiment in ONS, and you can read about the reasoning here.
Well I’m happy to say that I’ve completed Steps 1, 2, and 3! I’ve posted every notebook entry in the RC series (there’s a physics pun there somewhere) to the Winnower and received DOI’s for almost every post. A few posts didn’t translate, at all, on the platform. They are uploaded, but I didn’t bother with the DOI. Regardless, you can go on any of my Winnower posts and get a DOI (or click through to my notebook), or look through the RC entries and click the DOI to get to the Winnower archive of that post.
One cool side effect of this project was that a Twitter friend noticed a post that had embedded .gifs and I think I am now credited with being the first to publish a scientific paper with embedded .gif’s.
Now it’s time to write the paper based on all this research. I got the process started a couple years ago with a Google Doc about the project. I think I never followed through, because I didn’t value the traditional publication process. I think open science and peer review publication are on a course to merge and the incentives for ONS will shift, but this is a topic for another time.
Anyway, here is the previous write-up which I’ll work on, merge with some info from my dissertation, and to which add some new thoughts.
This part may take some time…
This post is open to read and review on The Winnower.
It took me a while, but I finally got my data from the Repeating Crumley set of experiments up on FigShare. Of course, I didn’t call it Repeating Crumley there since that experiment has no context. You can download the data sets and figures here:
Repeating Crumley FigShare Data and Figures
The interesting thing about this site is that your data remains your data but is openly accesible. Each upload is given a citation. Mine is:
Salvagno, Anthony; Koch, Steven J; Salvagno, Anthony (2012): Repeating Crumley: Tobacco Seed Growth in D2O. figshare.
Retrieved 22:15, Mar 02, 2015 (GMT)
Also there is a little section for social media promotion and it tracks the page analytics for you as well. That is pretty neat!
It did take me a while to get this up on FigShare unfortunately. For a while I couldn’t log in with Twitter, Facebook, or Google. I was asked repeatedly to sign in while trying to upload stuff. Eventually I just gave up and created a new account. Then when I tried to upload my first images, the site was unresponsive. I did spend a considerable amount of time organizing my resources so it would be presentable on FigShare, so that added to the mess a bit. And I also spent some time collecting links from my notebook to incorporate with the data so all experimental information can be collected. I also monified my active experiments page a little so some of the links are easier to navigate.
Despite how time consuming this first run was, it was definitely worth it.
Here are all the time lapse slideshows in one easy to load post. Juct click the links and away you go. It is worth mentioning that the arabidopsis images are much more dramatic because they grew so fast, but the growth rates are more obvious in the tobacco seed (VG) samples. Enjoy!
DOI: 10.15200/winn.142722.25149 provided by The Winnower, a DIY scholarly publishing platform
DOI: 10.15200/winn.142722.25145 provided by The Winnower, a DIY scholarly publishing platform
DOI: 10.15200/winn.142722.25141 provided by The Winnower, a DIY scholarly publishing platform