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.
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:
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.
Since the lab is a blistering 95F, I’m officially ending this experiment. I will still take pictures for about 7 more days because I want to watch the evaporation rate, but none of this data will be counted towards anything. Most tellingly is that the seeds in DI water barely sprouted and there hasn’t been much change in the past couple of days. Compare that to the DDW seeds and that spells problem…
Since this past Friday (Sept 23, 2011) the cooling system at CHTM has been down. I’m not sure if it is turned off for the impending winter or temporarily broken. This means that right now the lab is a toasty 92F and has been that way all weekend long. Unfortunately this can potentially mean a lot with regards to my seed growth experiments. Now I’m not sure if this is actually the case, but I think with regards to the experiments it may be in the best interest to scrap Try 2 for both the Repeating Crumley and the DDW Effects on Seed Growth until the temperature becomes a bit more stabilized. Now I will still record data and keep track of the experiments, but I will not include these results in any final markups. But that doesn’t mean I can’t learn something from these experiment!