All posts by Anthony

Advanced ape that understands logic, creativity, emotion, and expression. Displays great cognitive skills with somewhat limited communication skills. I'm some kind of new smart ape, artist extraordinaire, lover and fighter, and damned fine scientist.

Repeating Crumley Publication Prep

  1. I need a title for the paper. I’ve always called it Repeating Crumley, and maybe it makes sense to continue that trend, but is there a more fitting/descriptive name? Does it even matter?
  2. I think it makes sense to create .gifs from all the plant germination images for each sample of each experiment.
    1. From RC1-4 I had slideshows, which allowed you to click through each sample at your own pace. Then after I had started making .gifs (especially since that was around the time of memes on the web).
    2. I still think it makes sense to have all the data as pictures as well. If they aren’t already there, I will upload all the images to figshare, and have a separate dataset as gifs.
  3. Should the gifs be stored via my notebook (and thus the Winnower), or figshare?
    1. Both?
    2. Since the Winnower can actively display the .gifs, this has my preference, but I’m not sure. Maybe both… just because.
  4. Making a citation list for every notebook entry may be tiring, but it must be done.
  5. I’ll have to go through my figshare profile to see what data is currently up there.
  6. I worry that I don’t remember some of the data analysis methods. I think the only one I have absolutely no recollection of is the root length vs time graph. I remember it happening but I don’t remember going from Point A to B. I think of this like getting in the car and driving to work. You remember getting in the car, but you have no recollection of the in-between time because you were lost in thought. This is what happens when your brain is in Dissertation/Defense mode.
  7. The primary focus on this paper is going to be about the replication of the Crumley experiment through my methods and the difference in our results. I will include some of the cooler data, but won’t be able to write a follow-up (yet) since there is insufficient data on some of the cooler experiments. But I can show preliminary stuff!

I think that’s all I got now. I’ll keep adding notes like this when I get more ideas, come across roadblocks, or something else.

The Repeating Crumley-ONS Project: Next Steps

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…

Small-ish issue with digital object identifiers

I’m no expert in this space, but I came across an issue with digital object identifiers because of my annoyingly persistent use (overuse? hahaha) of figshare. What happens if the archive tool you use for your data switches from one permanent link system to another?

Back in the early days of figshare, they used the handle system to provide a permanent link for data stored in their system. At some point they switched to using the DOI system. I have no idea when it happened and I don’t even think I noticed the change. The only thing I know now is that my older figshare datasets are full of dead links.

The point of using a permanent link, ie a handle or a DOI, is to maintain a connection to the source if the URL or data at that source changes. Any changes will result in a change to the metadata which will allow the permanent link to point to the correct location. This allows you to change the URL for a dataset on figshare, for instance, and the DOI link will point you to the updated location.

In my case old projects that were linked via the handle system are all updated with DOIs. Since the two systems are different, I have the unique situation of having broken permanent links! Obviously, this defeats the purpose of a permanent link. So it seems I have some work to do to find all the outdated figshare sets and update them, which presents a very tedious set of challenges.

Has anyone ever experienced anything like this? I’m not familiar with the internal workings of permanent link systems, but is there a way to easily move from one system to another? Does this present an issue for the future of web science where DOIs or handles are obsolete? I imagine in that world there would need to be a system wide effort to ensure everything is upgraded properly (like switching from paper to electronic records).

100% Real-time publication: an experiment in #opennotebookscience

I’ve long been an advocate of open notebook science. In my advocacy, I am always looking for new ways to encourage fellow researchers to pursue this methodology for their own research. The latest of which pertains to archival and citability.

The ability to receive credit for your research, has been a requirement of science culture for quite some time, and is presently essential to an academic career. The altmetrics movement has been a valuable way to track and receive academic credit for new and nontraditional publication methods. Online tools like Impactstory help to track these activities, while tools like Figshare help propagate data and track your online impact as well.

This has always been missing from open notebooks.

I’ve always advocated against the need for a singular open notebook platform for the reason that ONS needs to have the flexibility to meet the needs of the scientists who use it. I’ve also never actively pursued a tool that can provide that formal citation credit since there are APA, MLA, etc rules for citing websites and other online resources. But the success of Figshare and other software has made me rethink this approach.

If open notebooks could have an automatic way to apply either a handle or a DOI, and could be archived, I think people would pay attention. If there was a publishing platform that could freely contain all the information of an open notebook, give the notebook a DOI (for instance) for each entry, and then host the final publication for peer review, there would be an even bigger incentive for ONS. And obviously there would be more transparency in the research process.

Where am I going with this?

Well a few days ago, I did a search for “DOI for WordPress” and came up with this, a plugin for a website called The Winnower. I had never heard of this organization so I went to the website and found a world of opportunity.

The Winnower, in case you are unfamiliar, is self-labeled as a DIY science publication platform that features a post-publication peer-review process to expedite and lower the entry barrier for publication. Once you submit your manuscript you can request a DOI for your article, which will undergo changes as you receive feedback for the publication.

The aforementioned plugin allows you to post blog entries (self-hosted WordPress blogs only for now) to the Winnower and receive DOIs, and with it the easy ability to be cited, for those entries. Integration between an open notebook and the Winnower (or a platform like it) could be a huge step forward for the ONS movement.

Imagine being able to see the entire scientific record for a study contained in the same system. Even better, imagine being able to witness the development of the study in real-time, providing feedback to the experiment, and being active in its development. When it comes time for peer-review, the process should theoretically be quick, because the work should have been vetted. If it hasn’t already, then it is relatively easy to review the prior work summarized in the publication, because it is all self-contained on the publishing platform (or the open notebook where the publication is).

In the interest of open science, I will perform an experiment. I will re-publish a series of notebook entries pertaining to one experiment and will write a paper based on that experiment. All of that will be published on the Winnower, since the mechanism is in place to cross-post from this notebook to that site.

The experiment I have in mind is the Repeating Crumley experiment that was the basis for my work on deuterium depleted water. It is the perfect experiment for this trial in ONS publication because the work turned out to reveal a mistake in the original study from the 1960’s, and I also propose a correction to the methods.

The key to this ONS experiment would be to understand what would be required of an open notebook or publication system to be able to provide a complete, organized, and user-friendly documentation system, or at least what is required for proper interaction between an open notebook and a publication platform. Additionally I hope to demonstrate another benefit to open notebook science in an effort to encourage others to participate in ONS.

In the spirit of open notebook science, I will document my interactions here and possibly also on the Winnower, and then write another publication on the Winnower about ONS and the peer-review system.

You can follow the documentation process through my Winnower profile.

UNM’s panel discussion about the use of Open Data #oaweek2014

I’m a bit slow to catch up on these things, but UNM has been holding a series of conversations about open access. For instance, today Mark Hanel discussed the growth of figshare and how much has changed since the organization began. Here are the collected tweets from a panel discussion regarding open access data sharing. Definitely worth the read.

Storify and tweets by Steve Koch

#Scifund Challenge Round 4 with David Shiffman

Each day we are going to highlight one of the amazing research projects seeking funding in Round 4 of the #Scifund Challenge. Today we chat with David Shiffman, who you may know as @WhySharksMatter on Twitter. His project goes to fund (surprise!) crucial shark research, more specifically the feeding habits of sharks.

Tell us about yourself, where you are from, and where you see yourself going.
I’m originally from Pittsburgh, PA (go Steelers!), and I majored in Biology at Duke University (go Blue Devils!) I got my Masters in Marine Biology at the College of Charleston (go Cougars!) After I finish my Ph.D, I hope to do university-level teaching and research somewhere warm.
How did you get involved in your research project?
I’ve always loved sharks, and as I advanced in my education, I learned what kind of data fisheries managers need in order to better conserve and protect them. Stable isotope analysis is a non-lethal, minimally invasive technique that helps get the kind of diet and food web interactions that managers need.
Why is your research important to you? Why should others fund it?

Sharks are ecologically and economically important animals, but many species are in danger of extinction. The kind of data that I’ll be generating in my project can help.

Why did you decide to participate in the SciFund Challenge?

As an active online science communicator (@WhySharksMatter,, I’ve seen the previous round of the SciFund challenge and how successful they were.

Tell us something random. Something funny. Something borrowed. Something blue.

There is a hot dog named after me at Pauly Dogs, a hot dog stand at Duke. It’s called a Shiffman, and it is a hot dog served on a twinkie.
Check out his project here.


#Scifund Round 4 with David Pappano

Each day we are going to highlight one of the amazing research projects seeking funding in Round 4 of the #Scifund Challenge. Today we introduce David Pappano, who studies Geladas (a very social primate) social organization and behavior. He also is an open notebook scientist (author note: <3)!

Tell us about yourself, where you are from, and where you see yourself going.

My name is David Pappano and I recently finished my Ph.D. from the University of Michigan-Ann Arbor. I am currently a postdoctoral research fellow in the Department of Ecology and Evolutionary Biology at Princeton University. I actually grew up in New Jersey not far from where I currently work. I am a primatologist by training—meaning I specialize in understanding the behavior, ecology, and evolution of monkeys and apes. My particular study species is the gelada (Theropithecus gelada), a species that is only found in the mountains of Ethiopia. One day I hope to blend research with teaching as a university professor, but for now I am focused on research full-time.


How did you get involved in your research project?

Geladas live in a modular society where small “core groups” (containing females and a single breeding male) join up and split apart from each other to create herds of over 1000 monkeys. This is really strange, because most primates live in stable groups of about 50 individuals. During my dissertation research, I noticed that “all-male groups” (containing only adult bachelor males) influenced the spacing and grouping of core groups. Basically, as bachelors approached core groups, females within core groups would clump together. This is the exact same response you would expect if the bachelors were a predator, like a hyena or leopard. I reasoned that the unit males and females responded like this because bachelors are observed to kill offspring if they enter a unit. Although this was only a small part of my dissertation research, it spurred my interest in animal movement. As a result, my current project focuses on how relationships among females within and between units influences collective movement of the entire gelada herd.

Why is your research important to you? Why should others fund it?

For me, doing science is my lifestyle as much as it is my profession. I love collecting data, analyzing (and re-analyzing) data, and solving problems. My current project is very interdisciplinary and draws from biology, ecology, and computer science to understand complex patterns of movement and herding in geladas. You should fund this project if you love primates and innovate methods to understand complex behavior.

Do you have a favorite story that came from working on your research project?

This isn’t a “favorite” story, but it is a memorable one. In April 2011 I was wrapping up my field work on my dissertation research in Ethiopia. I travelled to the capital (Addis Ababa) to speak at a Youth Conference organized by the U.S. Embassy. A few days before the conference, I broke a molar in half (ouch!) while eating doro wat (a delicious chicken stew and national dish of Ethiopia). I had to get half my tooth pulled and capped in Ethiopia. Regrettably this fix didn’t hold and I had to go back to the U.S. a few weeks earlier than I expected. I never got to say goodbye to my field assistants and park rangers in the Simien Mountains National Park. I have yet to go back to Ethiopia, but if I get funded then I will be able to return.

Why did you decide to particpate in the SciFund Challenge?

Two months ago, I unsuccessfully tried to fund this project through a crowdfunding campaign. Although I was disheartened, I reasoned that I needed a bit more time to refine my project. After speaking with the organizers of SciFund, I decided to give it a second chance.

What was the most difficult aspect of building your SciFund Proposal? What was your favorite?

Making the video was pretty tough. I’m not exactly Steven Spielberg.
My favorite part of the process so far has been reading through everyone else’s projects. Everyone is doing such great work. It is really exciting to see such amazing work from concept to completion.

Tell us something random. Something funny. Something borrowed. Something blue.

I have an identical twin brother. He works in the financial industry in New York City. A few years ago, he wanted to try out for the Amazing Race. We made a video, but we (obviously) didn’t get selected. Maybe if the whole academic thing doesn’t work out we’ll try again.
His project is available here.