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This site provides information and resources regarding open science for vision scientists. From past and future events, to open source software options, to open access publishers, to data and code sharing solutions and the politics and policy that shapes the type of science that we do, this site is intended to provide a broad resource to those interested in making vision science a more open science.  


[[Holcombe:OpenVisionScienceVSS|OpenVisionScienceVSS]]
=Background=


Physical location: Royal Ballroom 1-3
These videos provide a useful introduction to some of the issues surronding the need and potential for open science; you might also find them useful resources to introduce your students to these issues and problems.


Twitter hashtag: #OpenVisionSci (who will commit to tweeting or taking some notes for a report we'll post on the web?)
* Amusing video [http://www.youtube.com/watch?v=GMIY_4t-DR0 Scientist Meets Publisher] satirizes the current situation with closed journal publishing
 
* Inspiring video [http://www.youtube.com/watch?v=DnWocYKqvhw Michael Nielsen - Open Science] setting out a very different vision for how to do science.
 
=Open source software options=
 
Statistics [http://www.r-project.org/ R] - for an open source integrated development environment see [http://rstudio.org/ R studio].
 
Experiment construction options include [http://www.psychopy.org/ PsychoPy] and [http://osdoc.cogsci.nl/#downloadandinstallation OpenSesame].
 
Reference Management with [http://www.zotero.org/ Zotero]; you can find a guide to using it [http://gestaltrevision.be/wiki/zotero here]
 
For a more in-depth discussion of open science software options for the whole process of running an experiment, see the blog by Jonas Kubilius [http://klab.lt/2011/10/04/doing-science-in-the-open/ doing-science-in-the-open]
 
=Publishing Options=


We all hope for an open system of science in which:  
We all hope for an open system of science in which:  
Line 12: Line 26:
* Experiments can be fully replicated by anyone.  
* Experiments can be fully replicated by anyone.  


Achieving these goals is more feasible than ever, but most publishers, journals, and researchers have made few changes to the way they do business. This workshop will include discussion of possible solutions. We want constructive suggestions, possibly leading to an action plan.
Achieving these goals is more feasible than ever, but most publishers, journals, and researchers have made few changes to the way they do business.
==Background==
 
* Amusing video [http://www.youtube.com/watch?v=GMIY_4t-DR0 Scientist Meets Publisher] satirizes the current situation with closed journal publishing
Fully open access journals in Vision Science:
<html>
[http://www.journalofvision.org/ Journal of Vision] (though this does not allow one to retain one's own copyright) and [http://i-perception.perceptionweb.com/ i-Perception].
<object width="400" height="233"><param name="movie" value="http://www.youtube.com/v/GMIY_4t-DR0?version=3&amp;hl=en_US&amp;rel=0"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/GMIY_4t-DR0?version=3&amp;hl=en_US&amp;rel=0" type="application/x-shockwave-flash" width="400" height="233" allowscriptaccess="always" allowfullscreen="true"></embed></object>
 
</html>
For a full list in neuroscience/psychology [http://www.cogsci.nl/open-access-journals go here].
 
=Peer review Options=
 
Blog from Nikolaus Kriegeskorte: [http://futureofscipub.wordpress.com/ Open post-publication peer review]
 
Publication from Dwight Kravitz and Chris Baker: [http://www.frontiersin.org/Journal/Abstract.aspx?ART_DOI=10.3389/fncom.2011.00055&name=computational_neuroscience "Toward a new model of scientific publishing: discussion and a proposal"]
 
A selection of Frontiers in Computational Neuroscience papers exploring [http://www.frontiersin.org/computational_neuroscience/researchtopics/Beyond_open_access_visions_for/137 visions for open evaluation]
 
=Policy and politics for open science=
 
Chris Chambers and Petroc Sumner [http://www.guardian.co.uk/commentisfree/2012/sep/14/solution-scientific-fraud-replication Replication is the only solution to scientific fraud]
"If academia is to be cleaned up, the Research Excellence Framework must prize replication over politics"
 
Brian A. Nosek, Jeffrey R. Spies, Matt Motyl, [http://arxiv.org/abs/1205.4251 Restructuring incentives and practices to promote truth over publishability]
 
Dorothee Bishop, [http://deevybee.blogspot.co.uk/2010/08/how-our-current-reward-structures-have.html How our current reward structures have distorted and damaged science]


Inspiring video [http://www.youtube.com/watch?v=DnWocYKqvhw Michael Nielsen - Open Science] setting out a very different vision for how to do science.
Reuters, [http://in.reuters.com/article/2012/07/17/science-publishing-idINL6E8IHFQJ20120717 EU Commission backs open-access science publishing]


[http://thecostofknowledge.com/ Over 12000 researchers] are refusing to review, edit, and/or publish with Elsevier. Vision researchers spotted on the list include George Lovell, Jon Pierce, Edward Adelson, Alex Holcombe (who is only partially boycotting, and also made a  pledge at [http://www.openaccesspledge.com OpenAccessPledge]), Deborah Aphtorp, Joan Lopez-Moliner, Rainer Mausfeld, Nick Scott-Samuel, Michel Treisman,
=Future Events=


Recent related talk by Alex
[https://sites.google.com/site/nzauopenresearch/home Open Research], 6-8, Feb2013, Auckland, Nealand
<html>
<div style="width:340px" id="__ss_12072433"> <strong style="display:block;margin:12px 0 4px"><a href="http://www.slideshare.net/holcombea/woolcock-institute-20-mar-2012" title="Woolcock Institute 20 Mar 2012" target="_blank">Woolcock Institute 20 Mar 2012</a></strong> <object id="__sse12072433" width="340" height="284"> <param name="movie" value="http://static.slidesharecdn.com/swf/ssplayer2.swf?doc=woolcocktalk-key-120319185214-phpapp02&rel=0&stripped_title=woolcock-institute-20-mar-2012&userName=holcombea" /> <param name="allowFullScreen" value="true"/> <param name="allowScriptAccess" value="always"/> <param name="wmode" value="transparent"/> <embed name="__sse12072433" src="http://static.slidesharecdn.com/swf/ssplayer2.swf?doc=woolcocktalk-key-120319185214-phpapp02&rel=0&stripped_title=woolcock-institute-20-mar-2012&userName=holcombea" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" wmode="transparent" width="340" height="284"></embed> </object> <div style="padding:5px 0 12px"> </div> </div>
</html>


==Publishing Solutions- subscription model==
=Past Events=
==ECVP 2012==


===Subscription but non-profit===
Slides from Symposium, a vision for open science:


* Oxford Journals of OUP?
1. Lee de-Wit, [http://www.slideshare.net/leedewit/does-rewarding-that-which-is-easy-to-measure-lead-to-better-science  Does rewarding that which is easy to measure lead to better science?]
**Annals of Botany editor [https://plus.google.com/113040210411045341720/posts/PS7oieki7qP says they're great]
* Would ARVO take VR on board?
* Duke University Press?
* MIT Press?
* [http://journals.cambridge.org/action/stream?pageId=3820&level=2&menu=Societies&pageId=3644 Cambridge University Press]? [http://journals.cambridge.org/action/stream?pageId=3648&type=ju looks like] the Australian Academic Press journals recently moved to it
* Highwire Press (Stanford)?
* If she doesn't answer soon, then ask Raym Crow, a Senior Consultant at SPARC who helps journals with their business models.
* Society for Neuroscience
* Brill - publishes Seeing & Perceiving, is green
* Ubiquity
* Bloomsbury Qatar
* Wiley- green, opposed RWA


===Subscription, for-profit but at least not-ridiculously-profitable publishers===
2. Nick Scott-Samuel, [http://www.slideshare.net/scottsne  Why have so many academics decided to boycott Elsevier?]


Danger with these is that eventually they'll be bought up by the mega-profitable mega-publishers. Quite likely actually.
3. Amye Kenall,[http://www.slideshare.net/leedewit/open-access-and-author-owned-copyright16-aug  Open access and author-owned copyright]


So why hasn't Pion (publisher of Perception) been swallowed up by one of the megapublishers? Is there something about Pion that suggests it won't ever be?
4. Deborah Anthorp, [http://www.slideshare.net/dapthorp/file-drawer-talk  Publication bias, the File Drawer Problem, and how innovative publication models can help]


==Open Access (a dream, but not an impossible one)==
5. Jonathan Peirce, [http://www.slideshare.net/peircej/opensource-your-science  Opensource your science]


* Open Journal Systems
6. Ian Thornton, [http://www.slideshare.net/imthornton/academic-apps  Exploiting modern technology in making experiments: the academic app store]
* Annotum
* Ubiquity uses customised versions of OJS for research journals and @Annotum for meta journals.
* PLoS Currents has been re-launched using Annotum With [http://www.plos.org/publications/currents/ PLoS Currents], submission to publication can take place in a matter of days and there are no publication fees. Authors use Annotum to write their submission and are in complete control of the appearance of their article.


* [http://www.arl.org/sparc/publisher/journal_management.shtml list of similar resources]
==Woolcock Institute 2012==
1. Alex Holcombe [http://www.slideshare.net/holcombea/woolcock-institute-20-mar-2012 The broadest problem in science: Our publishing system]


With these options, if some universities/libraries/societies banded together, staff could presumably be hired to do administration of the above software etc.
==VSS 2012==
1. Alex Holcombe [http://www.slideshare.net/holcombea/vss-satellite-talk3 Moving towards inexpensive and open publishing]


The savings by eliminating the subscription fees for university libraries might well allow them to fund this ([http://pages.cmns.sfu.ca/heather-morrison/chapter-4-economics-of-scholarly-communication-in-transition/ Heather Morrison's thesis] includes calculations).
For more information on the VSS event, go to:
[[Holcombe:OpenVisionScienceVSS|OpenVisionScienceVSS]]  


==Agenda==
Chaired by [http://www.psychology.nottingham.ac.uk/research/vision/jwp/ Jon Pierce] and  [http://www.psych.usyd.edu.au/staff/alexh/lab/ Alex Holcombe]<br>
11:00 Dwight J. Kravitz, coauthor of [http://www.frontiersin.org/Journal/Abstract.aspx?ART_DOI=10.3389/fncom.2011.00055&name=computational_neuroscience "Toward a new model of scientific publishing: discussion and a proposal"] <br>
11:20 Questions for Dwight <BR>
11:25 Alex Holcombe: Moving towards inexpensive and open publishing <br>
11:45-12pm General Discussion <BR>


VSS Slides
=Ways to take action=
[http://www.slideshare.net/holcombea/vss-satellite-talk3 slides of Alex's talk]


ECVP Slides
Join the [http://openscienceframework.org/ Open Science Framework]


[http://www.slideshare.net/leedewit/does-rewarding-that-which-is-easy-to-measure-lead-to-better-science 1. Does rewarding that which is easy to measure lead to better science?]
Sign [http://thecostofknowledge.com/ the cost of knowledge petition] where over 12000 researchers are refusing to review, edit, and/or publish with Elsevier. Vision researchers spotted on the list include George Lovell, Jon Pierce, Edward Adelson, Alex Holcombe (who is only partially boycotting, and also made a  pledge at [http://www.openaccesspledge.com OpenAccessPledge]), Deborah Aphtorp, Joan Lopez-Moliner, Rainer Mausfeld, Nick Scott-Samuel, Michel Treisman,


[http://www.slideshare.net/scottsne Why have so many academics decided to boycott Elsevier?]
==Continue the discussion==


Continue the discussion at the [http://groups.google.com/group/publishPerceptionAttention Google Group], and on CVnet.
At the [http://groups.google.com/group/publishPerceptionAttention Google Group], and on CVnet.


==Attendance==
Or on Twitter: #OpenVisionSci, @openscience, @costofknowledge, @ceptional, @i_Perception,
All welcome. Members of the Vision Research, JoV, and i-Perception/Perception editorial boards have said they plan to attend, as has Beau Watson (founder of JoV) and Amye Kenall, publishing editor of i-Perception and Perception.
@michael_nielson

Latest revision as of 02:47, 4 January 2013

This site provides information and resources regarding open science for vision scientists. From past and future events, to open source software options, to open access publishers, to data and code sharing solutions and the politics and policy that shapes the type of science that we do, this site is intended to provide a broad resource to those interested in making vision science a more open science.

Background

These videos provide a useful introduction to some of the issues surronding the need and potential for open science; you might also find them useful resources to introduce your students to these issues and problems.

Open source software options

Statistics R - for an open source integrated development environment see R studio.

Experiment construction options include PsychoPy and OpenSesame.

Reference Management with Zotero; you can find a guide to using it here

For a more in-depth discussion of open science software options for the whole process of running an experiment, see the blog by Jonas Kubilius doing-science-in-the-open

Publishing Options

We all hope for an open system of science in which:

  • Journal articles are inexpensive or free.
  • Peer review is fair and efficient.
  • Experiments can be fully replicated by anyone.

Achieving these goals is more feasible than ever, but most publishers, journals, and researchers have made few changes to the way they do business.

Fully open access journals in Vision Science: Journal of Vision (though this does not allow one to retain one's own copyright) and i-Perception.

For a full list in neuroscience/psychology go here.

Peer review Options

Blog from Nikolaus Kriegeskorte: Open post-publication peer review

Publication from Dwight Kravitz and Chris Baker: "Toward a new model of scientific publishing: discussion and a proposal"

A selection of Frontiers in Computational Neuroscience papers exploring visions for open evaluation

Policy and politics for open science

Chris Chambers and Petroc Sumner Replication is the only solution to scientific fraud "If academia is to be cleaned up, the Research Excellence Framework must prize replication over politics"

Brian A. Nosek, Jeffrey R. Spies, Matt Motyl, Restructuring incentives and practices to promote truth over publishability

Dorothee Bishop, How our current reward structures have distorted and damaged science

Reuters, EU Commission backs open-access science publishing

Future Events

Open Research, 6-8, Feb2013, Auckland, Nealand

Past Events

ECVP 2012

Slides from Symposium, a vision for open science:

1. Lee de-Wit, Does rewarding that which is easy to measure lead to better science?

2. Nick Scott-Samuel, Why have so many academics decided to boycott Elsevier?

3. Amye Kenall,Open access and author-owned copyright

4. Deborah Anthorp, Publication bias, the File Drawer Problem, and how innovative publication models can help

5. Jonathan Peirce, Opensource your science

6. Ian Thornton, Exploiting modern technology in making experiments: the academic app store

Woolcock Institute 2012

1. Alex Holcombe The broadest problem in science: Our publishing system

VSS 2012

1. Alex Holcombe Moving towards inexpensive and open publishing

For more information on the VSS event, go to: OpenVisionScienceVSS


Ways to take action

Join the Open Science Framework

Sign the cost of knowledge petition where over 12000 researchers are refusing to review, edit, and/or publish with Elsevier. Vision researchers spotted on the list include George Lovell, Jon Pierce, Edward Adelson, Alex Holcombe (who is only partially boycotting, and also made a pledge at OpenAccessPledge), Deborah Aphtorp, Joan Lopez-Moliner, Rainer Mausfeld, Nick Scott-Samuel, Michel Treisman,

Continue the discussion

At the Google Group, and on CVnet.

Or on Twitter: #OpenVisionSci, @openscience, @costofknowledge, @ceptional, @i_Perception, @michael_nielson

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