Introducing the Open Derby (guest post)

Ensuring openness and reproducibility in ecology is an ongoing challenge, although open tools (e.g., R Studio, Github) are free to use, and user support is everywhere. To illustrate how ecology collaborations can fit within an open science framework, we had the idea of running an ‘Open Derby’. Similar to a research derby, where grad students and post-docs from different academic departments and universities collaborate together to solve a conservation problem, our idea extends the derby concept to working fully openly: learning version control in GitHub, writing and analysing data in RMarkdown, and publishing all project development in an open notebook. Our end goal is to examine a conservation issue using open access (OA) data, and publish our findings and code in an OA journal. Ultimately, we hope to share Open Derby with other graduate students and academics across the life sciences, with the hope that we can provide a model for switching entire lab groups into open and reproducible research machines.

If you are not familiar with open science tools, RMarkdown is a wonderful method of writing code into a manuscript that can be formatted into manuscripts, reports, and presentations. We use RMarkdown in tandem with GitHub, a service that allows version control of your data, analyses, and manuscripts, and is incredibly useful for managing input between collaborators. Learning these tools can be daunting but learning with friends makes it easier and more fun to build these skills. We are six PhD students from 4 institutions based in 3 countries, who are present or past members of Dr. Julia Baum’s marine ecology lab at the University of Victoria and have come together to demo the Open Derby concept:

James Robinson: PhD student in the Baum lab, studying macroecology of tropical Pacific coral reefs (defending April 2017) and leader of the Open Derby project

Danielle Claar: PhD student in the Baum Lab, studying the dynamics of coral symbioses in response to environmental stressors

Easton White: PhD student at the University of California, Davis. He uses mathematical and statistical techniques to address various ecological and conservation questions.

Jillian Dunic: PhD student at Simon Fraser University, studying the effect of multiple stressors on tipping points in eelgrass. (Recently graduated from Jarrett Byrnes’ lab)

Jamie McDevitt-Irwin: MSc student in the Baum lab evaluating how stressors, specifically human disturbance and bleaching stress from an El Niño event, influence the community structure of the coral microbiome (defending April 2017).

Geoffrey Osgood: PhD student in the Baum lab, using data and models to study shark populations in South Africa and on Pacific reefs

In January 2017, we met (virtually) to decide on a research question for Open Derby. Our aim was to address a question that would be accessible under an open science platform (e.g. open source data). And **SPOILER**, we failed in our first attempt. In the interests of openness, and publishing null results, here is what we did:

Our workflow

Tools used: Rmarkdown, Github, Slack, etherpad, Skype

As mentioned earlier, we used Rmarkdown and Github to manage our workflow. We met once every one or two weeks on Skype to discuss project goals and delegated tasks, taking notes on Skype calls in a publicly accessible etherpad. These meetings, combined with Github, allowed us to divide and conquer without duplicating each other’s work. The goal was to have everyone only spend 1-3 hours on the project per week (after all, we each have dissertations to write). Everyone contributed to coding in R—whether it was data cleaning, analysis, or visualizations—and writing the initial manuscript. We also used Slack to regularly chat about the project in between Skype meetings. Slack eliminates the need for endless email chains and also integrates with Github, allowing participants to be notified when a repository change has occurred. In the future, we might take notes on a markdown file that can be easily version controlled, and may make use of Github’s wiki and project planning features.

Open datasets – oil spills and fisheries catch

We extracted oil spill data from the Emergency Response Division of the National Oceanic and Atmospheric Administration (NOAA; https://incidentnews.noaa.gov/raw/index) which recorded all major spills that occurred between 1967-2016 in marine environments on the west coasts of U.S.A. and Canada (Figure 1). However, we were unable to find oil spill data from British Columbia (BC). After extensive web searches, emails and even a freedom of information request, we were told there is no existing electronic record of BC coastal oil spills.

oil_map_spillsize

Figure 1 Oil spill location and size across west coast of North America from 1967-2016 included in NOAA’s incident news dataset.

We extracted fisheries catch data from the Sea Around Us Project (SaU), which collates global, spatially-explicit estimates of annual fisheries catch at the national level (Pauly & Zeller 2015; Zeller et al. 2016). The SaU dataset uses international and national catch statistics to generate taxon-level catch estimates at a 0.5 degree resolution, spanning 1950-2013, and provided us with California, Oregon, Washington, BC, and Alaska fisheries catch. Yet, as promising as this data appeared at first, we were advised not use this data at spatial scales below the exclusive economic zone (EEZ) level, as data are aggregated. We also contacted Canadian and US fisheries departments to request port-level catch data.

Sadly, data resolution issues sunk our project. With fishing catch data, smaller spatial aggregations of the SaU dataset were simply EEZ level trends with catch estimates scaled downwards (Figure 2), and we did not reasonably expect to detect oil spill impacts at the EEZ level. We were also unable to locate consistent port-level data that spanned either BC, California, or Alaska. Similarly, the oil spill incidents were not consistently reported, and it was unclear how spill estimates were generated – a contact from NOAA warned us that there was no established methodology for estimating the size of an oil spill, and many reported incident volumes involve some amount of guesswork.

EEZ_vs_05degree_catch_trends_USWC_only
Figure 2 Catch estimates for USA west coast EEZ (top panel) and 3 randomly selected 0.5 degree resolution grid cells (bottom 3 panels, labelled with lat-lon centroid of grid cell) from 1970-2010.

Beyond data issues, the ecological impact of an oil spill is highly context-dependent, and will be affected by the environmental conditions, clean-up response, and type of oil contaminant. As a result, our understanding of oil spill impacts on marine ecosystems is, sadly, limited to large, catastrophic events. We urge more openness and data collection of spill characteristics, so that researchers may begin to quantify the cumulative impacts of smaller, more frequent spills on marine ecosystems.

Future Work

You can find our ideas, data, and progress in our public Github repository. We welcome any suggestions that might help us to resurrect this project, and hope to inspire others to write up their failed projects. Our project lead – James Robinson – is currently developing Open Derby for general consumption as a member of Mozilla’s Open Science Leadership training programme.

But, we are now brainstorming conservation questions for our next attempt. Ecologists, please, send us your unanswered conservation problems, unanalyzed datasets, and suggestions for advancing open ecology! This time we will each bring a dataset and question to the brainstorming session. We will let you know how we progress!

Seeking a Postdoc for the Byrnes Lab!

All right, folks! The time has come – I’m looking for a Postdoc for the Byrnes lab! The text of the advert is below, but, to be brief – I’m looking for someone who is interested in asking questions relating to marine subtidal community ecology. These next two years I’m getting a program up and running looking at kelp forests, climate change, and food web structure around New England. But I want someone who comes in with some interesting ideas and plans. The goal is to do hot science and further the postdoc’s career.

So drop me a line with ideas or questions after you read this and the ad below. Application instructions are at the bottom.

The Department of Biology seeks applicants for a Post-Doctoral Research Assistant interested in obtaining postdoctoral research experience in marine subtidal community ecology, climate change, and food web ecology. The appointment will start in September 2013. The candidate will assist the lab PI, Dr. Jarrett Byrnes, in new and ongoing research projects in the lab and field. The researcher will develop a two-year project that complements ongoing work in in the lab. The researcher will also be asked to help organize and participate in field research. Other duties will depend on interest and prior experience and may include programming in R or other languages; conducting and supervising basic lab and field work; organizing and leading field expeditions to remote locales and field stations. A detailed list of Dr. Byrnes’s research is available on his web page http://jarrettbyrnes.info.

Applicants must hold a PhD degree or must expect to earn one on or before June 2013. One to three years of experience, training, and/or education in sub-tidal research techniques and the ability to handle supplies and items of up to 40 pounds required. Strong quantitative and programming skills, as well as boating experience are recommended. AAUS certification or equivalent is required.

Interested individuals should send cover letter, current resume and a statement of research experience and interest online:

http://umb.interviewexchange.com/candapply.jsp?JOBID=38104

A maximum of three recommendation letters should be sent electronically to jarrett.byrnes@umb.edu

UMass Boston is an Affirmative Action, Equal Opportunity, Title IX employer.

PeerJ launches open access into a new realm

A service that is travelling along similar lines of what I’m interested in for open publishing has launched today. PeerJ is being pitched as a cross between PLoS ONE and arXiv and indeed the company was founded by former PLoS ONE and Mendeley folk. It’s an interesting model where authors signup with a pre-paid plan. $99 gets you unlimited public preprints and 1 peer reviewed paper per year. $169 adds unlimited private preprints and another paper per year. $259 ups you to unlimited publications. And its nice as you can chose to pay once your paper is accepted (see how it works) so an author isn’t just being fleeced. There also appear to be reasonable plans for large numbers of co-authors etc. They also require members to review once per year. Nice.

I’m still reading through all of the materials about it myself, and there’s a lot here to digest and meditate on. It still appears that review is not open – both before and after ‘publication’ – although you can publish the review-trail and previous versions along with the finished product if you’d like. But in general, this is pretty fantastic

Here are some links about the launch and useful additional reading. I’d love to know what folk out there think. Will you be using it? Time to put our money where our #openaccess mouths are? I’m thinking yes!

  • PeerJ Blog
  • PeerJ formally announced: Innovative new business model for open access at Confessions of a Science Librarian
  • An interview with the founders of PeerJ, an innovative new academic publishing startup at the Mendeley Blog
  • Scholarly Publishing 2012: Meet PeerJ at Publishers Weekly
  • Interview with Peter Binfield and Jason Hoyt of PeerJ at Confessions of a Science Librarian
  • PeerJ – a brave new world? at Reciprocal Space
  • Pay (less) to publish: ambitious journal aims to disrupt scholarly publishing at Ars Technica
  • Scientific Journal Offers Flat Fee to Authors for ‘All You Can Publish’ at SciAm
  • New OA Journal, Backed by O’Reilly, May Disrupt Academic Publishing
  • The Publishing Buffet

    My question to you all – does this new entry to the publishing market solve everything? Is it a panacea? Are there things you wish it did better, or is it just the right balance?

  • Ecology in 2020?

    Today’s issue of Nature rings in the New Decade with an interesting article on where Science needs to be in 2020. With respect to Ecology, Robert Holt makes the following observation:

    A key task will be to predict and mitigate this loss of biodiversity and the degradation of ecosystem function. One step is to gauge the resilience of ecological networks such as food webs — in particular, their capacity to withstand disturbance and species loss. This will require insights from many disciplines. Stable isotope analysis and genetic bar-coding should provide a clearer picture of who eats whom in a community.

    Um. I think that describes my research program. Except the whole isotope/bar-coding thing. Damn. Add that to the list of things I need to learn, as right now, figuring out who-eats-who can be a real show-stopper! But overall, I guess I’m on the right track. Ha!

    Lytechinus: Pack Wolf of the Sea

    ResearchBlogging.orgSo, you know, I’m cruising along, trying to determine the diet of the white urchin, Lytechinus anamesus, from the literature. There’s your usual “It eats kelp” papers, a few red algae papers, and nothing else special and then – A PAPER ON LYTICHINUS EATING OTHER SPECIES OF URCHINS.

    That’s right, baby, urchin on urchin predation. Could the ocean get much weirder?

    A red urchin mobbed by the ravening horde.

    A red urchin mobbed by the ravening horde.


    Turns out, on urchin barrens (i.e., areas with such ridonculous numbers of urchins – purples, reds, and even whites – that all of the surrounding edible algae has been grazed away) when white urchins get hungry enough, they turn into little pack animals. They mob red and purple urchins (but not each other) and gnaw away at their spines and test until they reach their gooey center.

    Or, as gooey as the center of an echinoderm can be.

    I cannot resist giving lolcaptions to figures from scientific papers.  I clearly have a problem.

    I cannot resist giving lolcaptions to figures from scientific papers. I clearly have a problem.

    How intense is this predation? In lab trials, purples were mobbed within 20 minutes. 1/3 were dead by the end of the day. 90% of big fat red urchins tested were severely damaged.

    These guys are not kidding around.

    Perhaps more strangely, injured whites were left alone. Cannibalism for white urchins, apparently, is not on the menu.

    So, dear reader, if you should find yourself hanging out in an urchin barren one day, just remember, don’t turn your back or the urchins will eat you!

    MUAHAHAHAHAHAHAHA!

    (Also of note, the first author of this paper was the man who turned me into a scientific diver. Huh!)

    COYER, J., ENGLE, J., AMBROSE, R., & NELSON, B. (1987). Utilization of purple and red sea urchins (Strongylocentrotus purpuratus Stimpson and S. franciscanus Agassiz) as food by the white sea urchin (Lytechinus anamesus Clark) in the field and laboratory Journal of Experimental Marine Biology and Ecology, 105 (1), 21-38 DOI: 10.1016/S0022-0981(87)80027-8