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Science-2-0-at-Eurodoc-2010

Version 3318
Saved March 11, 2010
This pad serves as a notepad for the Science 2.0 session at the Eurodoc 2010 conference:
http://docs.google.com/present/edit?id=0ASQvcnWHnwgmZGR3aHFkNmtfMjY0c210Y202aHM&hl=en . 
Some of the planning takes place at http://ff.im/gaWDe .
 
The text in this document is synchronized as you type, so that everyone viewing this page sees the same text.  You do not have to log in to type here, though providing your name in the top right box would be nice.
 
Please do not edit above the line of "=" but feel free to take notes below it. To pose questions, please use the chat on the right or a Twitter message tagged with #eurodoc2010 . Comments on the individual items in the pad should be placed directly below them, preceded by "Comment:".
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Warm-up:
- A blog post: http://onebiglab.blogspot.com/2008/04/envisioning-scientific-community-as-one.html
- An image: http://www.flickr.com/photos/dullhunk/3389581452/
- Some questions: How many of you (answers in %)
  • have not done a Google search within the past 24h before leaving for this conference? 
  • have been to a library within the past month? 
  • read blogs on a regular basis? 
  • read research-related blogs on a regular basis? 
  • use Twitter, Friendfeed or identi.ca? 
  • do not use any social network online? 
  • know what the (Journal) Impact Factor is? 
  • know how it is calculated? 
  • have heard of Open Science? (see FAQ section) 
  • know someone who does it? 
  • do it themselves?
  • would be willing to help write the protocol of this session, directly in this document? 
 
FAQ on Open Science:
- 1st Open Science Round-up: http://shirleywho.wordpress.com/2008/09/19/corpus-callosum-1st-edition-of-open-science-round-up/
- Breakthroughs of the year in Open Science 2009 - http://ways.org/en/blogs/2009/dec/16/breakthroughs_of_the_year_2009_in_open_science_the_polymath_project_and_articlelevel_metrics
- http://cspannagel.wordpress.com/2008/05/18/der-offentliche-wissenschaftler/
- http://cspannagel.wordpress.com/2008/07/06/pioniere-offentlicher-wissenschaft/
-  http://scienceblogs.com/clock/2010/03/why_it_is_important_for_media.php states "As a rule, the very best coverage of every paper in the past month was done by a blogger or two or three. "
 
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Clickstream
For those who prefer slides: http://docs.google.com/present/edit?id=0ASQvcnWHnwgmZGR3aHFkNmtfMjY0c210Y202aHM&hl=en . A related presentation is at http://www.slideshare.net/Daniel.Mietchen/timing-young-researchers-decisions . Other presentations are embedded in several of the posts we will come across.
Start with http://scienceblogs.com/geneticfuture/2009/07/conference_blogging_icons_for.php , structure as in research cycle ( http://docs.google.com/present/edit?id=0ASQvcnWHnwgmZGR3aHFkNmtfMjEyZHo5YjNyZzI&hl=en# ) and then mention some of the currently most pressing challenges to (and opportunities for) open science, as summarized at http://ways.org/en/node/17356 .
 
 
READ/IDEA
Overview of recent papers
http://friendfeed.com/brain-morphometry via feeds from http://www.hubmed.org/
 
Overview of relevant papers
http://openwetware.org/wiki/User:Daniel_Mietchen/Notebook/Evolutionary_MRI/List_of_non-human_brain_MRI_studies
 
Show example of "Questions for further research"
http://frontiersin.org/neuroscience/neuroinformatics/paper/10.3389/neuro.11/025.2009/html/#h5
 
"...if you want to have great creativity and innovation, you must give complete freedom, but if you want to reap the bene fits, you must provide a framework."
Fernando Nottebohm (via http://shirleywho.wordpress.com/2008/09/19/corpus-callosum-1st-edition-of-open-science-round-up/ )
 
Commenting on papers - the classical approach
http://scienceblogs.com/ethicsandscience/2009/08/the_saga_of_the_journal_commen.php
 
Commenting on papers - blog about them
http://researchblogging.org/
 
Commenting on papers - in the lab notebook
http://openwetware.org/wiki/User:Anthony_Salvagno/Notebook/Research/2010/03/01/Catching_up_on_class_work
 
Commenting on papers - annotations in Mendeley
http://www.mendeley.com/research-papers/collections/1374711/EarlyWarningSigns/ - download sample plos paper, annotate it
 
Socially filtered papers
http://friendfeed.com/search?q=http+%2F%2Fwww.citeulike.org%2Fuser%2F+likes%3A2+friends%3Adanielmietchen
http://ways.org/en/blogs/2010/jan/07/social_filtering_of_scientific_information_a_view_beyond_twitter
 
 
DEVELOP/FUND
Classical:
http://friendfeed.com/science-2-0/9835e8c4/possible-way-to-go-global-7-countries-with-some
 
Open: Request for collaborators
http://plindenbaum.blogspot.com/2009/09/from-friendfeed-to-nucleic-acids.html
 
Open: Collaboratively written grant proposal
http://ff.im/1IRF2
 
Open: Funding decisions made in public:
http://fundscience.org/blog/2010/03/fundscience-announces-its-acceptance-of-applications-for-round-one-of-funding/#
 
There currently is no public evidence that the dominant system of reviewing grant proposals and manuscripts (i.e. via non-public peer review) is efficient (see also similar discussion in PUBLISH section below).
http://friendfeed.com/cameronneylon/effdfe5b/peer-review-what-is-it-good-for
http://friendfeed.com/danielmietchen/d7d0ab3f/hypios-50k-problem-to-love-challenge
 
"We suggest that developing countries could leapfrog ahead by adopting from the start science grant systems that encourage innovation."
http://ways.org/en/blogs/2009/apr/09/research_grant_systems_that_encourage_innovation
 
How to spend a budget of X on science?
http://ways.org/en/blogs/2009/may/24/implementing_fantasy_science_funding
http://ff.im/9SvED
 
 
PLAN/RECORD
Protocols
http://openwetware.org/wiki/Protocols
 
Theory:
http://polymathprojects.org/
http://ways.org/en/blogs/2009/feb/03/open_mathematics_the_view_of_a_fields_medalist
http://gowers.wordpress.com/2009/03/10/problem-solved-probably/
http://arxiv.org/find/all/1/all:+polymath/0/1/0/all/0/1
 
Engaging with the public is possible at any stage:
http://communicatescience.com/corpse/exquisite_corpse_of_science.html
http://seedmagazine.com/slideshow/exquisite_corpse/#1
 
Research/ teaching games:
http://fold.it/portal/
http://www.freerice.com/index.php?&t=354421149034&s=Famous%20Paintings
 
Citizen science
http://friendfeed.com/coturnix/bfd04a36/citizen-science-online
 
Conference reporting: http://opensciencefoundation.com/scs/author/brianglanz/ / http://opensciencefoundation.com/scs/2010/02/20/science-creative-commons/ / http://science-2-0.piratenpad.de/Science-Commons-Symposium-Cameron-Neylon
 
Seminars at Second Life
http://ff.im/9Lckw
 
RECORD/PROCESS
Protocols and measurements
http://onschallenge.wikispaces.com/list+of+experiments
 
Lab notebooks
http://openwetware.org/wiki/Special:RecentChanges
 
Visualizations
http://manyeyes.alphaworks.ibm.com/manyeyes/visualizations/plos-article-citations-per-day-col
 
Databases:
http://sumsdb.wustl.edu/sums/index.jsp
 
Robot scientists:
http://nextbio.wordpress.com/2009/04/07/is-the-human-ego-good-for-science/#comment-161
 
Problems: How to mashup CC-BY & CC-NC-SA data?
http://pantonprinciples.org/
 
Archiving
http://usefulchem.blogspot.com/2010/03/nature-precedings-as-archiving-tool-for.html
 
 
PROCESS/PUBLISH
Conferences:
Abstract drafting:
http://etherpad.com/ep/pad/view/A-charter-for-the-structuring-of-knowledge/rev.1496
 
Drafting of full conference paper:
http://ways.org/en/blogs/2010/mar/02/conference_abstract_accepted_what_if_science_were_sustainable
 
Online poster session
http://apecs.is/virtual-poster-session
 
Journals:
The pleasure and importance of printed journals
http://ff.im/4GWlM
 
Journal Impact Factor:
http://bjoern.brembs.net/news.php?item.499.11
 
PLoS ONE on track to become world's largest journal this year:
http://friendfeed.com/mattodd/0fd81ef3/am-mentioning-plos-one-in-current-grant
 
Article-level metrics
http://en.citizendium.org/wiki/Article-level_metrics
 
Licensing
http://www.doaj.org/doaj?func=licensedJournals
 
Open Access "is not the same as non-peer-reviewed"!
http://friendfeed.com/future-of-education/eecb71a5/david-weinberger-on-remnant-notions-and
 
Public peer review (see also similar section in FUND above)
http://www.biogeosciences.net/5/25/2008/bg-5-25-2008.html
http://friendfeed.com/the-life-scientists/8255a527/who-owns-copyright-of-reviews-are-we-allowed-to
 
Manuscript revision - just send the link
http://en.citizendium.org/wiki?title=User%3ADaniel_Mietchen%2FSandbox%2FBrain_changes&diff=100503328&oldid=100502035
 
Fast lane: PLoS Currents
http://fundscience.org/blog/2009/08/science-publishing-on-the-fast-lane-plus-optionally-in-journals/
 
Current way is ineffective, since new information is not published in the context of the old:
http://ways.org/en/blogs/2010/feb/10/the_illustrated_anatomy_of_a_paper_and_how_it_may_look_like_on_a_wiki
 
Efficiency:
http://dmm.biologists.org/content/2/5-6/201 (getting back to the One Big Lab idea)
See also slides 51-54 in
http://www.slideshare.net/CameronNeylon/science-in-the-open-science-commons-pacific-northwest
http://ways.org/en/blogs/2010/mar/02/conference_abstract_accepted_what_if_science_were_sustainable
 
 
PUBLISH/READ
Context:
http://www.flickr.com/photos/tonomura/2712913340/
Wikis grow context organically:
"Science is already a wiki if you look at it a certain way. It’s just a highly inefficient one -- the incremental edits are made in papers instead of wikispace, and significant effort is expended to recapitulate existing knowledge in a paper in order to support the one to three new assertions made in any one paper." (John Wilbanks, http://scienceblogs.com/commonknowledge/2009/07/publishing_science_on_the_web.php )
 
Wikis grow in number and volume, also for scientific uses: http://en.wikiversity.org/wiki/Wikis_in_scholarly_communication
 
Problems with wikis:
Vandalism: http://en.wikipedia.org/wiki/Special:RecentChanges / http://en.wikipedia.org/w/index.php?title=Arguing_with_Idiots&curid=24482357&diff=348070022&oldid=348061113
Licenses: http://www.scholarpedia.org/wiki/index.php?title=Special:Copyright&id=1
Gaps: http://en.citizendium.org/wiki/Special:WantedPages
Chances:
Context again: http://en.citizendium.org/wiki/Life/Related_Articles
Teaching: http://en.citizendium.org/wiki/CZ:Eduzendium
 
Integration with databases:
http://en.wikipedia.org/wiki/Portal:Gene_Wiki
 
Duplicate publications ( http://etblast.org/ ) are easily noted in a wiki, due to unique page names:
http://en.wikipedia.org/wiki/Thesis_%28disambiguation%29
 
Alternatives to wikis:
- Etherpad http://code.google.com/p/etherpad/wiki/Instructions
- Google Wave http://www.slideshare.net/CameronNeylon/google-wave-ripple-or-tsunami-for-research-2800410 / https://wave.google.com/
 
If authors had a unique ID, their contributions to human knowledge could all be aggregated, and not just paper counts:
http://dx.doi.org/10.1038/embor.2008.217
http://www.orcid.org/
http://www.google.com/profiles/daniel.mietchen
 
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SOCIAL NETWORKS:
- Can in principle be used for any of these steps, possibly different platforms for different purposes. Key issue: Interoperability, which requires open standards in data and communication formats, plus overcoming significant cultural barriers ( http://ff.im/f6VWP ).
- Are "Breeding like rabbits"
http://blog.openwetware.org/scienceintheopen/2008/08/01/facebooks-for-scientists-theyre-breeding-like-rabbits/
http://friendfeed.com/search?q=%22Facebook+for+scientists%22
http://friendfeed.com/fb4sci
http://bjoern.brembs.net/news.php?item.492.5
 
- Start getting attention from funders: http://www.nih.gov/news/health/nov2009/ncrr-02.htm
- Are beginning to be surveyed more systematically:
http://ff.im/fkh5m (related threads are at http://ff.im/fMiCa and http://ff.im/eHTjI )
    With image:
    http://friendfeed-media.com/3d85c60be264040660503dea85248e722ff53424
    
 Discipline-specific ones:
 http://openanthcoop.ning.com/
 http://www.radrounds.com/   
 
WAYS
http://ways.org/en/tagexplorer
http://ways.org/en/map/user
http://ways.org/en/about_ways/sister_networks_and_subnetworks
http://www.biovision.org/
 
 
See also: Euroscience is launching a "Young researchers network" at Eurodoc 2010
http://www.esof2010.org/news/nwsltr_4
http://ways.org/en/blogs/2009/nov/11/open_science_session_accepted_for_esof_2010
 
 
http://onebiglab.blogspot.com/2008/04/envisioning-scientific-community-as-one.html
 
Link to politics, e.g. gender equality:
http://en.citizendium.org/wiki/Female_scientist/Related_Articles
 
Possible side effects of attending online:
http://pyre.third-bit.com/blog/archives/3547.html (via http://ff.im/gvr1n )
 
 
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Tentative recommendations for the final communiqué of the Eurodoc 2010 conference (all workshop participants - on-site and remote - are invited to participate in rephrasing this draft text; the official format is roughly "Recognizing that A, we recommend B and C". ):
 
The World Wide Web started out as a project to facilitate scientific research and communication, and in the nearly two decades since its inception, it has revolutionized many aspects of our society, from the local to the global level, with a broad range of web-based tools and services now allowing for multiple forms of direct interactions between providers and users of information. Yet although scientific research is, at its core, a collaborative endeavour which would greatly benefit from such direct interactions between participants and from opening them up to the wider community, few researchers have started to explore these new possibilities. Young researchers will have to play a special role in this transition from the paper-based era to web-based research and would profit from educating themselves and their peers about the chances and pitfalls of doing research in the open via the Web. Science policy with regard to young researchers should pay attention to supporting open collaborative environments for all elements of the scientific process, to recognizing the role of such web-based collaboration in the design of research awards and competition, and to promoting a diversification of the measures used to assess the impact of a single researcher.