User:Daniel Mietchen/Talks/Science 2.0 Conference 2014

File:Open research.ogv

• ''A figure from a recent paper:{{Cite journal | last1 = Lescroël | first1 = A. L. | last2 = Ballard | first2 = G. | last3 = Grémillet | first3 = D. | last4 = Authier | first4 = M. | last5 = Ainley | first5 = D. G. | editor1-last = Descamps | editor1-first = Sébastien | title = Antarctic Climate Change: Extreme Events Disrupt Plastic Phenotypic Response in Adélie Penguins | doi = 10.1371/journal.pone.0085291 | journal = PLoS ONE | volume = 9 | issue = 1 | pages = e85291 | year = 2014 | pmid =

24489657| pmc =

3906005}}''

File:Automated weighbridge for Adélie penguins - journal.pone.0085291.g002.pngs are identified and weighed each time they cross the automated weighbridge on their way to and from the sea. The data are recorded but not made public, not even in or alongside the "publication".]]

• Two videos providing the basis for an article{{Cite journal | last1 = Yanashima | first1 = R. | last2 = García | first2 = A. A. | last3 = Aldridge | first3 = J. | last4 = Weiss | first4 = N. | last5 = Hayes | first5 = M. A. | last6 = Andrews | first6 = J. H. | editor1-last = Docoslis | editor1-first = Aristides | title = Cutting a Drop of Water Pinned by Wire Loops Using a Superhydrophobic Surface and Knife | doi = 10.1371/journal.pone.0045893 | journal = PLoS ONE | volume = 7 | issue = 9 | pages = e45893 | year = 2012 | pmid = 23029297| pmc =3454355 }} but not published along with it.

• Inconsistent XML as a Barrier to Reuse of Open Access ContentMietchen, D.; Maloney, C.; and Moskopp, N. D. (2013) [http://www.ncbi.nlm.nih.gov/books/NBK159964/ Inconsistent XML as a Barrier to Reuse of Open Access Content]. Journal Article Tag Suite Conference (JATS-Con) Proceedings 2013.

A specification anyone can edit:

1. Dynamics: Research is a process. The scientific journal of the future provides a platform for continuous and rapid publishing of workflows and other information pertaining to a research project, and for updating any such content by its original authors or collaboratively by relevant communities. Eventually, all scientific records should have a public version history or a public justification for not having one.
2. :File:Research cycle.png
3. :*[http://juretriglav.si/how-scientific-figures-should-work-in-2014/ example]
4. :**Version of record
5. :**Updates automatically
6. :**Editable format (SVG)
7. :**Data and code on GitHub under open licenses
8. :*PLOS Computational Biology [http://topicpages.ploscompbiol.org/wiki/Topic_Pages Topic Pages] ([http://topicpages.ploscompbiol.org/wiki/Category:PLoS_Computational_Biology_articles list])
9. :*The workflows include writing of research documents, as piloted by the Biodiversity Data Journal.{{Cite journal | last1 = Smith | first1 = V. | last2 = Georgiev | first2 = T. | last3 = Stoev | first3 = P. | last4 = Biserkov | first4 = J. | last5 = Miller | first5 = J. | last6 = Livermore | first6 = L. | last7 = Baker | first7 = E. | last8 = Mietchen | first8 = D. | last9 = Couvreur | first9 = T. L. P. | last10 = Mueller | first10 = G. | last11 = Dikow | first11 = T. | last12 = Helgen | first12 = K. M. | last13 = Frank | first13 = J. I. | last14 = Agosti | first14 = D. | last15 = Roberts | first15 = D. | last16 = Penev | first16 = L. | title = Beyond dead trees: integrating the scientific process in the Biodiversity Data Journal | doi = 10.3897/BDJ.1.e995 | journal = Biodiversity Data Journal | volume = 1 | pages = e995 | year = 2013 | pmid = | pmc = }}
10. Scope: Data come in many different formats. The scientific journal of the future interoperates with databases and ontologies by way of open standards and concentrates on the contextualization of knowledge newly acquired through research, without limiting its scope in terms of topic or methodology.
11. :File:Eupolybothrus cavernicolus male paratype.jpg of the centipede Eupolybothrus cavernicolus, a species described{{Cite journal | last1 = Stoev | first1 = P. | last2 = Komerički | first2 = A. | last3 = Akkari | first3 = N. | last4 = Liu | first4 = S. | last5 = Zhou | first5 = X. | last6 = Weigand | first6 = A. M. | last7 = Hostens | first7 = J. | last8 = Hunter | first8 = C. I. | last9 = Edmunds | first9 = S. C. | last10 = Porco | first10 = D. | last11 = Zapparoli | first11 = M. | last12 = Georgiev | first12 = T. | last13 = Mietchen | first13 = D. | last14 = Roberts | first14 = D. | last15 = Faulwetter | first15 = S. | last16 = Smith | first16 = V. | last17 = Penev | first17 = L. | title = Eupolybothrus cavernicolus Komerički & Stoev sp. N. (Chilopoda: Lithobiomorpha: Lithobiidae): The first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data | doi = 10.3897/BDJ.1.e1013 | journal = Biodiversity Data Journal | volume = 1 | pages = e1013 | year = 2013 | pmid = | pmc = }} with its full transcriptome, micro CT and DNA barcoding, in addition to a morphological description.]]
12. :*[http://www.theguardian.com/technology/2014/jan/25/online-gamers-solving-sciences-biggest-problems another example: citizen science]
13. Access: Free access to scientific knowledge, and permissions to re-use and re-purpose it, are an invaluable source for research, innovation and education. The scientific journal of the future provides legally and technically barrier-free access to its contents, along with options for re-use and re-purposing that are stated clearly for both humans and machines.
14. :*[https://twitter.com/Jessifer/status/427154942751555584 "Academic publishing is no guarantee of anything, except possibly the paywalled obsolescence of your work."] ([http://www.webcitation.org/6N0rn8lZS WebCite copy])
15. :File:Xanthichthys ringens - pone.0010676.g191.png is sourced from an open-access scholarly article{{Cite journal

| last1 = Williams | first1 = J. T.

| last2 = Carpenter | first2 = K. E.

| last3 = Van Tassell | first3 = J. L.

| last4 = Hoetjes | first4 = P.

| last5 = Toller | first5 = W.

| last6 = Etnoyer | first6 = P.

| last7 = Smith | first7 = M.

| editor1-last = Gratwicke

| editor1-first = Brian

| title = Biodiversity Assessment of the Fishes of Saba Bank Atoll, Netherlands Antilles

| doi = 10.1371/journal.pone.0010676

| journal = PLoS ONE

| volume = 5

| issue = 5

| pages = e10676

| year = 2010

| pmid = 20505760

| pmc = 2873961

}}

File:Cc-zero.svg [http://creativecommons.org/publicdomain/zero/1.0/ CC0]

{{sister-inline

|project=wikisource

|short=yes

|links=full text

}}

{{sister-inline

|project=commons

|short=yes

|links=media

}}

{{sister-inline

|project=wikidata

|short=yes

|links=metadata

}}

licensed for re-use (details).]]

1. :*Open Access Media Importer Bot ([http://blogs.plos.org/mindthebrain/2013/10/21/asap-awards-winners-announced/ ASAP award winner])
2. :*[http://tools.wmflabs.org/glamtools/baglama.php?group=Leibniz-Gemeinschaft&date=201310 Leibniz @Wikimedia]
3. :*[http://tools.wmflabs.org/glamtools/baglama.php?group=Open+access+%28publishing%29&date=201310 Open Access @Wikimedia]
4. Replicability: Open access to all relevant core elements of a publication facilitates the verification and subsequent re-use of published content. The scientific journal of the future requires the publication of detailed methodologies — including all data and code — that form the basis of any research project.
5. :NIH plans to enhance reproducibility{{Cite journal | last1 = Collins | first1 = F. S. | last2 = Tabak | first2 = L. A. | doi = 10.1038/505612a | title = Policy: NIH plans to enhance reproducibility | journal = Nature | volume = 505 | issue = 7485 | pages = 612 | year = 2014 | pmid = 24482835| pmc = 4058759}}
6. Review: The critical, transparent and impartial examination of information submitted by the professional community enhances the quality of publications. The scientific journal of the future supports post-publication peer review, and qualified reviews of submitted content shall always be made public.
7. :*example{{Cite journal | doi = 10.1901/jaba.1974.7-497b | title = Reviewer's Comments | journal = Journal of Applied Behavior Analysis | volume = 7 | issue = 3 | pages = 497–1453 | year = 1974 | pmid = | pmc = }}
8. :*public peer review{{Cite journal | last1 = Mietchen | first1 = D. | last2 = Keupp | first2 = H. | last3 = Manz | first3 = B. | last4 = Volke | first4 = F. | title = Non-invasive diagnostics in fossils - Magnetic Resonance Imaging of pathological belemnites | doi = 10.5194/bg-2-133-2005 | journal = Biogeosciences | volume = 2 | issue = 2 | pages = 133 | year = 2005 | pmid = | pmc = }}
9. :*public review of grant proposals
10. Presentation: Digitization opens up new opportunities to provide content, such as through semantic and multimedia enrichment. The scientific journal of the future adheres to open Web standards and creates a framework in which the technological possibilities of digital media can be exploited by authors, readers and machines alike, and content remains continuously linkable.
11. :File:Demo of interactive taxonomic paper from ZooKeys.ogv. Courtesy of Rod Page.]].
12. :*[http://www.pubchase.com/lens/six-new-deep-water-sternaspid-species-annelida-s-by-salazar-vallejo-si-b-zookeys-24294071 Interactive presentation] using [https://github.com/elifesciences/lens Lens]
13. :*Composition of plates on the fly (as opposed to static composite figures)
14. Transparency: Disclosure of conflicts of interest creates transparency. The scientific journal of the future promotes transparency by requiring its editorial board, the editors and the authors to disclose both existing and potential conflicts of interest with respect to a publication and to make explicit their contributions to any publication.
15. Sustainability: Resources are limited. Ecological considerations are reflected in the design and production of the scientific journal of the future.
16. Flexibility: Innovation is stifled by inflexible rules. Exceptions to the above rules are possible if justified in public.
17. :[http://www.realclearscience.com/blog/2014/01/shortest_science_papers.html examples]

• [https://github.com/swcarpentry/bc/issues/199 GitHub thread: What should we teach about writing/publishing papers in a webby world?]

• Talk Transforming the way we publish research at Academic Publishing in Europe 2012:
• :File:Transforming the way we publish research - APE 2012 talk.ogv

• Talk at User:Daniel Mietchen/Talks/ISMTE 2012/Transforming the way we publish research

{{Wikimedia Foundation}}

• WP:SCIENCE
• WP:BIOLOGY
• WP:COMPBIO
• WP:OPENACCESS

• Five pillars
• Notability
• No original research
• Conflicts of interest

• Definition of free cultural works
• [http://opendefinition.org/ Open Definition]
• Open license
• Open knowledge

• DBpedia
• Semantic MediaWiki
• [http://iphylo.org/linkout/Main_Page Rod's Linkout wiki]
• [http://iphylo.org/linkout/Ncbi:188590 Example]
• Wikidata
• [http://korrekt.org/page/Wikidata:_A_Free_Collaborative_Knowledge_Base Denny Vrandečić, Markus Krötzsch. Wikidata: A Free Collaborative Knowledge Base. In Communications of the ACM (to appear). ACM 2014.]
• Showcases
• Cactaceae

• :mw:API:Main page

• WP:DUMPS

• [http://listen.hatnote.com/ Listen to Wikipedia]
• [http://wikipulse.herokuapp.com/ Wikipulse]
• [http://www.lkozma.net/wpv/index.html Map of recent edits]
• [http://wikistream.inkdroid.org/ Wikistream]
• [http://stats.wikimedia.org/wikimedia/animations/growth/AnimationProjectsGrowthWp.html Wikimedia project growth animation]
• [https://wikipedia-irc.herokuapp.com/ Wikipedia live monitor]
• [http://toolserver.org/~emijrp/wikimediacounter/ Wikimedia counter]

See also :wikidata:Wikidata:Tools/External tools.

• [http://tools.wmflabs.org/wikidata-todo/cloudy_concept.php?q=Q4541810 Concept cloud]
• [http://tools.wmflabs.org/reasonator/?lang=oc&q=Q52 Reasonator]
• [http://simia.net/treeoflife/ Tree of Life]
• [http://tools.wmflabs.org/glamtools/baglama.php?group=Type+specimens&date=201311 BaGLAMa]
• [http://tools.wmflabs.org/glamtools/glamorous.php?doit=1&category=Open+access+(publishing)&use_globalusage=1&ns0=1&depth=5&show_details=1&show_details_limited=1 GLAMorous]

• WP:BOTS
• [http://nl.wikipedia.org/w/index.php?title=Telemetrie&action=history Telemetrie]
• :commons:User:Open Access Media Importer Bot

• :outreach:GLAM

• :m:Wikimedia Labs
• [http://stats.wikimedia.org/ Wikimedia stats]
• Signalling OA-ness
• :m:List of Wikipedias
• GLAM Newsletter
• WP:GLAM/Ship
• QRpedia
• Wikidata Toolkit
• Eupolybothrus
• Chenopodium
• [http://www.wikidata.org/wiki/Wikidata:WikiProject_Taxonomy WikiProject Taxonomy (i)]
• WikiProject Taxonomy (ii)
• WikiProject Taxonomy (iii)

• Wikipedia:School of Open course
• Wikipedia:The Wikipedia Adventure
• User:Rockpocket/Training
• MPI workshop

{{reflist}}

This page and its subpages belong to a Wikimedia workshop organized on March 25, 2014, as a satellite event to the [http://www.science20-conference.de/ Science 2.0 Conference 2014], in Hamburg.

• See subpage.

• See subpage.

• [http://www.naturkundemuseum-berlin.de/en/institution/mitarbeiter/mietchen-daniel/ Institutional]
• @[https://twitter.com/EvoMRI EvoMRI] on Twitter
• Wikipedia talk page
• Wikipedia email

The subpages help organize the presentation and its preparation.