Publish or Perish, UC Davis February 2014

Data Publication Etcetera at the CDL

Carly Strasser & John Kratz California Digital Library

@carlystrasser

From Wikimedia Commons

Back in the day…

From ahswhg.wikispaces.com

Back in the day…

Da Vinci

Curie Newton

classicalschool.blogspot.com

Darwin

Research has changed

Better Worse

From wikimedia

Such Internet!

So many tools!

From Flickr by John Jobby

So much data!

Research has changed Worse

Digital data Fr

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Ideas, data, analysis

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Most marine benthic invertebrate life cycles include a plank-tonic larval phase that facilitates dispersal among adult popula-tions (Thorson 1950). Connectivity, or the degree to which geo-graphically separated populations exchange individuals, is animportant factor in the spatial population dynamics of manymarine organisms (Moilanen and Nieminen 2002). An under-standing of connectivity in marine benthic populations isimportant because of the role spatial dynamics play in fisheriesmanagement and the design and implementation of marineprotected areas. However, studying larval dispersal is challeng-ing due to small larval sizes, high dilution rates, and high larvalmortality rates (Thorson 1950, 1966).

In recent years, the use of artificial and natural tags to trackmarine larvae has been explored (e.g., Levin 1990; Thorrold etal. 2002). One type of natural tag that may be useful for identi-fying natal origins is elemental signatures recorded in biogenic

carbonate. This technique relies on the observation that someelements are incorporated into the calcium carbonate matrixin amounts that are related to the dissolved concentrationsand physical properties of the ambient water (e.g., Bath et al.2000; Elsdon and Gillanders 2003; Fowler et al. 1995; Thorroldet al. 1997; Vander Putten et al. 2000). Provided water chem-istry or temperature is significantly different among natalhabitats, such variation can serve as a natural tag, or signature,of the geographic origin of organisms. The use of geochemicalsignatures in fish otoliths as natural tags for population stud-ies is well established (Campana and Thorrold 2001). Recentefforts have expanded the use of elemental tags to inverte-brates including decapods (DiBacco and Levin 2000), gas-tropods (Zacherl et al. 2003), bivalves (Becker et al. 2005), andcephalopods (Arkhipkin et al. 2004).

Most studies attempting to obtain time-resolved elementalsignatures from calcified tissues have used laser ablation induc-tively coupled plasma mass spectrometry (ICP-MS). Conven-tional solution-based ICP-MS analyses are generally more pre-cise than laser ablation assays but lack the ability to resolveelemental signatures from individual life stages (Campana et al.1997). Laser ablation ICP-MS is particularly useful for larvalstudies because it allows the core of an otolith or the larval shellof a juvenile bivalve to be targeted. Yet, surprisingly few studieshave empirically tested the effective spatial resolution of laser

Laser ablation ICP-MS analysis of larval shell in softshell clams(Mya arenaria) poses challenges for natural tag studiesC.A. Strasser, S.R. Thorrold, V.R. Starczak, and L.S. MullineauxWoods Hole Oceanographic Institution, Woods Hole, MA 02543

AbstractWe investigated whether laser ablation inductively coupled plasma mass spectrometry (ICP-MS) could be used

to quantify larval shell compositions of softshell clams, Mya arenaria. The composition of aragonitic otoliths hasbeen used as a natural tag to identify natal habitat in connectivity studies of fish. If it is possible to measure lar-val shell reliably, this technique could also be applied to marine bivalves. To determine whether the first larvalshell (prodissoconch I) could be measured independent of underlying material, we conducted laboratory exper-iments in which larval M. arenaria were exposed to enrichments of the stable isotope 138Ba during different stagesin shell development. We were unable to isolate the chemical signature of the prodissoconch I from subsequentlife stages in all combinations of shell preparation and instrument settings. Typical instrument settings burnedthrough the prodissoconch I on a post-settlement juvenile and at least 9 d of second larval shell (prodissoconch II)growth. Our results suggest instrumental and technical improvements are needed before laser ablation ICP-MScan be useful for connectivity studies that require analysis of larval shell on a post-settlement M. arenaria juve-nile. Laser burn-through is potentially a problem in any connectivity study where it is necessary to assay thesmall amounts of shell material that are deposited before a larva disperses away from its natal location.

AcknowledgmentsThis work was supported by NSF project numbers OCE-0241855 andOCE-0215905. Special thanks to Henry Lind of the Eastham Departmentof Natural Resources for supplying clams and culturing expertise, and toDiane Adams, Benjamin Walther, Travis Elsdon, Anne Cohen, Dale Leavitt,Phil Alatalo, and Susan Mills for helpful discussions. We also thank D.Zacherl and an anonymous reviewer for their helpful comments.

Limnol. Oceanogr.: Methods 5, 2007, 241–249© 2007, by the American Society of Limnology and Oceanography, Inc.

LIMNOLOGYand

OCEANOGRAPHY: METHODS

Provenance

“Reproducibility Crisis”

“Digital Dark Age”

“Erosion of Trust”

Can we fix science? the way we

communicate our

v Change nothing

Change everything

Change nothing

Change everything

work within publishing paradigm

take advantage of new tools

incentivize sharing, reproducibility

From Flickr by Leo Reynolds

We are in the midst of a culture shift.

What will scholarly communication look like in 10 years?

notebook science source content access data government repository knowledge Fr

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Enable data sharing Encourage

new incentives

Think about code sharing

Work with libraries, publishers and

researchers

Explore new tools to help

change system

Build tools

Create and manage persistent identifiers ARKs, DOIs, etc.

Platform for publishing + repository for OA publications

“Data Publication”

John Kratz, CLIR Postdoc

What does “data publication” mean? 1. Available 2. Citable 3. Trustworthy*

Data are

*peer reviewed? certified?

Available | Citable | Trustworthy

Publish means to “make public”. You should not have to email the author. The data doesn’t have to be open access. Where to publish?

“Email me!” CC-0 on web

Repository choices…

Repositories for data

General content

Non-institutional

Institutional

Discipline-specific

Repository choices…

Simple case…

Data citations should be in reference list. Five-element citation: author, year, title, publisher, identifier

Available | Citable | Trustworthy

Boettiger C, Dushoff J, Weitz JS (2009). Data from: Fluctuation domains in adaptive evolution. Theoretical Population Biology. Published in Dryad. doi:10.5061/dryad.j8n0p7vc

More complicated…

Deep data citation: what if you want to cite a subset? Dynamic data: how to create a reliable citation when a dataset is changing?

Available | Citable | Trustworthy

Technical VS. Scientific

Package review: data + paper

Sometimes consider impact and/or novelty

Guidelines provided

Available | Citable | Trustworthy

From Flickr by Percival Lowell

1.  Traditional article: Data published

alongside a traditional journal article.

Example: Supplemental material hosted by the journal publisher. Available + citable. Review is up to the journal

What does a data publication look like?

From Flickr by subsetsum

2.  Data paper: Data published alongside a

descriptive “data paper”.

Most require data be in a trusted repository. All have a component of peer review. What they are NOT: results, analysis, conclusions. Examples: •  Standalone journals: Nature Scientific Data, Geoscience Data

Journal, Ecological Archives •  Journals that publish data papers: GigaScience, F1000 Research,

Internet Archaeology

What does a data publication look like?

From Flickr by subsetsum

3.  Standalone data: Data published without a

related journal article.

Rich metadata (structured or unstructured) Examples: •  Open Context •  NASA PDS Peer Review Data •  figshare (but no validation)

What does a data publication look like?

From Flickr by subsetsum

Change nothing

Change everything

?

Beyond Data… Code! Workflows!

…?

From Flickr by Klearchos Kapoutsis

From  Flickr  by  dotpolka  

Scholarly communication is changing – for the better.

Website Email Tweet Slides

carlystrasser.net carlystrasser@gmail.com @carlystrasser slideshare.net/carlystrasser

Big thanks to John Kratz, CLIR Postdoc