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This site provides information and resources regarding open science for vision scientists. From information regarding 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.
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==
=Background=


This 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.  
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.  


* Amusing video [http://www.youtube.com/watch?v=GMIY_4t-DR0 Scientist Meets Publisher] satirizes the current situation with closed journal publishing
* Amusing video [http://www.youtube.com/watch?v=GMIY_4t-DR0 Scientist Meets Publisher] satirizes the current situation with closed journal publishing
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* Inspiring video [http://www.youtube.com/watch?v=DnWocYKqvhw Michael Nielsen - Open Science] setting out a very different vision for how to do 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.


==Open source software options==
=Open source software options=


Statistics [http://www.r-project.org/ R], for an open source integrated development environment see [http://rstudio.org/ R studio].
Statistics [http://www.r-project.org/ R] - for an open source integrated development environment see [http://rstudio.org/ R studio].


Experiment construction [http://www.psychopy.org/ PsychoPy]
Experiment construction options include [http://www.psychopy.org/ PsychoPy] and [http://osdoc.cogsci.nl/#downloadandinstallation OpenSesame].


==Policy and politics for open science==
Reference Management with [http://www.zotero.org/ Zotero]; you can find a guide to using it [http://gestaltrevision.be/wiki/zotero here]


Chris Cahmbers and Petroc Sumner [http://www.guardian.co.uk/commentisfree/2012/sep/14/solution-scientific-fraud-replication Replication is the only solution to scientific fraud]
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]
"If academia is to be cleaned up, the Research Excellence Framework must prize replication over politics"
 
=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:
[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].
 
For a full list in neuroscience/psychology [http://www.cogsci.nl/open-access-journals go here].
 
=Peer review Options=


===Ways to take action===
Blog from Nikolaus Kriegeskorte: [http://futureofscipub.wordpress.com/ Open post-publication peer review]


Sign [http://thecostofknowledge.com/ the cost of knowledge petition] were 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,
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=


==EVENTS FUTURE==
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"


===EVENTS PAST===
Brian A. Nosek, Jeffrey R. Spies, Matt Motyl, [http://arxiv.org/abs/1205.4251 Restructuring incentives and practices to promote truth over publishability]


==Woolcock Institute 2012==
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]
1. Alex Holcome [http://www.slideshare.net/holcombea/woolcock-institute-20-mar-2012 The broaest problem in science: Our publishing system]


==VSS 2012==
Reuters, [http://in.reuters.com/article/2012/07/17/science-publishing-idINL6E8IHFQJ20120717 EU Commission backs open-access science publishing]
1. Alex Holcome [http://www.slideshare.net/holcombea/vss-satellite-talk3 Moving towards inexpensive and open publishing]


2. Dwight Kravitz [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"]
=Future Events=


For more information on the VSS event, go to:
[https://sites.google.com/site/nzauopenresearch/home Open Research], 6-8, Feb2013, Auckland, Nealand
[[Holcombe:OpenVisionScienceVSS|OpenVisionScienceVSS]]  


=Past Events=
==ECVP 2012==
==ECVP 2012==
Slides from Symposium, a vision for open science:


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?]
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?]
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4. Deborah Anthorp, [http://www.slideshare.net/dapthorp/file-drawer-talk  Publication bias, the File Drawer Problem, and how innovative publication models can help]
4. Deborah Anthorp, [http://www.slideshare.net/dapthorp/file-drawer-talk  Publication bias, the File Drawer Problem, and how innovative publication models can help]


5. Jonathan Peirce, [http://www.slideshare.net/peircej/opensource-your-science  http://www.slideshare.net/peircej/opensource-your-science]
5. Jonathan Peirce, [http://www.slideshare.net/peircej/opensource-your-science  Opensource your science]


6. Ian Thornton, [http://www.slideshare.net/imthornton/academic-apps  Exploiting modern technology in making experiments: the academic app store]
6. Ian Thornton, [http://www.slideshare.net/imthornton/academic-apps  Exploiting modern technology in making experiments: the academic app store]


==Publishing Solutions- subscription model==
==Woolcock Institute 2012==
1. Alex Holcombe [http://www.slideshare.net/holcombea/woolcock-institute-20-mar-2012 The broadest problem in science: Our publishing system]


We all hope for an open system of science in which:
==VSS 2012==
* Journal articles are inexpensive or free.
1. Alex Holcombe [http://www.slideshare.net/holcombea/vss-satellite-talk3 Moving towards inexpensive and open publishing]
* 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. This workshop will include discussion of possible solutions. We want constructive suggestions, possibly leading to an action plan.
For more information on the VSS event, go to:
 
[[Holcombe:OpenVisionScienceVSS|OpenVisionScienceVSS]]
===Subscription but non-profit===


Oxford Journals of OUP, Annals of Botany editor [https://plus.google.com/113040210411045341720/posts/PS7oieki7qP says they're great], ARVO (Would ARVO take Vision Research on board?), Duke University Press, MIT Press, Highwire Press (Stanford), Society for Neuroscience.


==Open Access (a dream, but not an impossible one)==
=Ways to take action=


* Open Journal Systems
Join the [http://openscienceframework.org/ Open Science Framework]
* 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]
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,


With these options, if some universities/libraries/societies banded together, staff could presumably be hired to do administration of the above software etc.
==Continue the discussion==


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


Continue the discussion at the [http://groups.google.com/group/publishPerceptionAttention Google Group], and on CVnet.
Or on Twitter: #OpenVisionSci, @openscience, @costofknowledge, @ceptional, @i_Perception,
Twitter hashtag: #OpenVisionSci (who will commit to tweeting or taking some notes for a report we'll post on the web?)
@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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