Discuss what we will consider a GPF - Revision history

Yolanda: Added PropertyValue: Participants = Jon Goodall

2015-04-26T18:39:25Z

Added PropertyValue: Participants = Jon Goodall

Yolanda: Set PropertyValue: Progress = 100

2015-04-17T05:07:37Z

Set PropertyValue: Progress = 100

Yolanda: /* Discussion */

2015-04-11T16:02:24Z

‎Discussion

Yolanda: /* Discussion */

2015-04-11T16:02:12Z

‎Discussion

Yolanda: /* Discussion */

2015-04-11T16:01:46Z

‎Discussion

Yolanda: /* More References */

2015-04-11T15:55:18Z

‎More References

Yolanda: /* Opening Science */

2015-04-11T15:54:32Z

‎Opening Science

Yolanda: /* What is a Geoscience Paper of the Future? */

2015-04-11T15:46:39Z

‎What is a Geoscience Paper of the Future?

Yolanda: /* Opening Science */

2015-04-09T22:54:53Z

‎Opening Science

Yolanda: /* Science is Changing */

2015-04-09T22:47:37Z

‎Science is Changing

@@ Line 84: / Line 84: @@
 	Expertise=Geosciences|
 	Owner=Yolanda_Gil|
 	Participants=Chris_Duffy|
 	Participants=Scott_Peckham|

@@ Line 84: / Line 84: @@
 	Expertise=Geosciences|
 	Owner=Yolanda_Gil|
 	Participants=Chris_Duffy|
 	Participants=Scott_Peckham|
@@ Line 102: / Line 101: @@
 	Participants=Ji-Hyun_Oh|
 	Participants=Allen_Pope|
-	Progress=50|
+	Participants=Kyo_Lee|
 	StartDate=2015-02-06|
 	TargetDate=2015-05-29|

← Older revision		Revision as of 16:02, 11 April 2015
Line 63:		Line 63:

	Perhaps, the concept of a 'paper' can be better reflected in the concept of a 'wrapper' or a collection of materials and resources. The purpose is to assure that publications are representative of the work, effort, and results achieved in the research process.		Perhaps, the concept of a 'paper' can be better reflected in the concept of a 'wrapper' or a collection of materials and resources. The purpose is to assure that publications are representative of the work, effort, and results achieved in the research process.
−

	=== Figures ===		=== Figures ===

← Older revision		Revision as of 16:02, 11 April 2015
Line 65:		Line 65:


−	'=== Figures ===	+	=== Figures ===

	Do we want to do exactly the same figure automatically? Figures in the paper may be a clean versions of an image generated by software. To the extent possible, authors have included clear delineations of provenance. The goal is to assure that readers may regenerate the figures using documented workflows, data, and codes. An important note (Allen, Sandra) is that frequently figures are generated by code, scripts, etc. yet the actual figure is finalized with user..... Is it really worth belaboring the point about how the prettified version of the figure is made? If it is: both of the visualization software I've used (Matlab and SigmaPlot) have actual code in the background that specifies how to set up the prettification, and this code can be found, copied out, and rerun to generate the exact same figure with all of the prettification in the same place. SigmaPlot uses Visual Basic (I think) in its macros. If it is an important point about explicit code, this should be doable. But I'm not sure it's strictly necessary to specify exactly where all the prettifications are to get the gist across.		Do we want to do exactly the same figure automatically? Figures in the paper may be a clean versions of an image generated by software. To the extent possible, authors have included clear delineations of provenance. The goal is to assure that readers may regenerate the figures using documented workflows, data, and codes. An important note (Allen, Sandra) is that frequently figures are generated by code, scripts, etc. yet the actual figure is finalized with user..... Is it really worth belaboring the point about how the prettified version of the figure is made? If it is: both of the visualization software I've used (Matlab and SigmaPlot) have actual code in the background that specifies how to set up the prettification, and this code can be found, copied out, and rerun to generate the exact same figure with all of the prettification in the same place. SigmaPlot uses Visual Basic (I think) in its macros. If it is an important point about explicit code, this should be doable. But I'm not sure it's strictly necessary to specify exactly where all the prettifications are to get the gist across.

← Older revision		Revision as of 16:01, 11 April 2015
Line 64:		Line 64:
	Perhaps, the concept of a 'paper' can be better reflected in the concept of a 'wrapper' or a collection of materials and resources. The purpose is to assure that publications are representative of the work, effort, and results achieved in the research process.		Perhaps, the concept of a 'paper' can be better reflected in the concept of a 'wrapper' or a collection of materials and resources. The purpose is to assure that publications are representative of the work, effort, and results achieved in the research process.

		+
		+	'=== Figures ===
		+
		+	Do we want to do exactly the same figure automatically? Figures in the paper may be a clean versions of an image generated by software. To the extent possible, authors have included clear delineations of provenance. The goal is to assure that readers may regenerate the figures using documented workflows, data, and codes. An important note (Allen, Sandra) is that frequently figures are generated by code, scripts, etc. yet the actual figure is finalized with user..... Is it really worth belaboring the point about how the prettified version of the figure is made? If it is: both of the visualization software I've used (Matlab and SigmaPlot) have actual code in the background that specifies how to set up the prettification, and this code can be found, copied out, and rerun to generate the exact same figure with all of the prettification in the same place. SigmaPlot uses Visual Basic (I think) in its macros. If it is an important point about explicit code, this should be doable. But I'm not sure it's strictly necessary to specify exactly where all the prettifications are to get the gist across.
		+
		+	=== What to Document: Timing and Intermediate Proceses, Failed Experiments ===
		+
		+	When should we document and what are the bounds on what we document?
		+
		+	For example, should data and workflows for 'failed' experiments be included? Should dataset DOIs be assigned before there are results from using them?
		+
		+	How much of your experimental history does one include? The experimental process often ends up nowhere. Should all the failed experiments be documented? Should there be a DOI for the results of the successful experiment, and another for failed trials?
		+
		+	Good ideas/practices may include documenting and sharing data when you have a clear understanding of the outcomes worth reporting. For example successful experiments should have clear, clean data documented and shared. Whereas one strategy with 'failed' experiments could include bundling the intermediate datasets with one DOI and a more general discussion of the process/methods.

	<!-- Add any wiki Text above this Line -->		<!-- Add any wiki Text above this Line -->

@@ Line 177: / Line 177: @@
 [Baggerly and Coombes 2009] "Deriving chemosensitivity from cell lines: Forensic bioinformatics and reproducible research in high-throughput biology." Keith A. Baggerly and Kevin R. Coombes. Annals of Applied Statistics, Volume 3, Number 4, pp. 1309-1334, 2009.
-[Holdren 2013] "Increasing Public Access to the Results of Scientific Research." John Holdren, Memorandum of the US Office of Science and Technology, 22 February 2013. Available from https://petitions.whitehouse.gov/response/increasing-public-access-results-scientific-research
+[Holdren 2013] "Increasing Public Access to the Results of Scientific Research." John Holdren, Memorandum of the US Office of Science and Technology, 22 February 2013. Available from https://petitions.whitehouse.gov/response/increasing-public-access-results-scientific-research.
 [Piwowar et al 2007] "Sharing Detailed Research Data Is Associated with Increased Citation Rate." Heather A. Piwowar, Roger S. Day, Douglas B. Fridsma. PLoS ONE 2(3): e308. doi:10.1371/journal.pone.0000308

@@ Line 5: / Line 5: @@
 == Opening Science ==
-Scientific data has tremendous value, so much so that new government policies declare data "an asset for progress" [Holdren 2013].
+The US Office of Science and Technology Policy released a memorandum requiring all agencies to develop plans for releasing data and other results from federally funded scientific research [Holdren 2013].  The memo emphasizes that scientific data has tremendous value, so much so that it is declared "an asset for progress" [Holdren 2013].  Other governments are pursuing similar initiatives.  As a result, federal funding agencies are developing new initiatives and programs to make research results widely available [NSF 2013].
-−
-Discuss also: “National Science Foundation Collaborates with Federal Partners to Plan for Comprehensive Public Access to Research Results”, NSF Press Release 13-030.
 Although scientists state many reasons that make sharing data difficult [Tenopir et al 2011], there are many good reasons to share data. Sharing data keeps us honest and improves peer review and mutual validation [Corbyn 2012; Krugman 2013; Baggerly and Coombes 2009]. Another reason is the increased reputation and citation of research when datasets become available [Piwowar et al 2007].  Similar arguments can be made for making software available [CITE].

← Older revision		Revision as of 15:46, 11 April 2015
Line 55:		Line 55:

	Not all the GPF papers will be able to satisfy all of these things. For example, some collaborators may not want to release data, or some of the software. In those cases, the papers will explain the issues in trying to do these releases, and the challenges that they pose to the future of open reproducible publications.		Not all the GPF papers will be able to satisfy all of these things. For example, some collaborators may not want to release data, or some of the software. In those cases, the papers will explain the issues in trying to do these releases, and the challenges that they pose to the future of open reproducible publications.
		+
		+	== Discussion ==
		+
		+	It's possible that small or very large contributions are not well captured in the current publishing paradigms.
		+
		+	For example, nanopublications are a possible way to reflect advances in a research process that may not merit a full pubication but they are useful advances to share with the community. A challenge here is that there is a stigma in publishing for publishing units that are too small or very small.
		+
		+	Alternatively, a very large piece of research or work with many parts may be better suited to a GPF style publication.
		+
		+	Perhaps, the concept of a 'paper' can be better reflected in the concept of a 'wrapper' or a collection of materials and resources. The purpose is to assure that publications are representative of the work, effort, and results achieved in the research process.
		+

	<!-- Add any wiki Text above this Line -->		<!-- Add any wiki Text above this Line -->

← Older revision		Revision as of 22:54, 9 April 2015
Line 6:		Line 6:

	Scientific data has tremendous value, so much so that new government policies declare data "an asset for progress" [Holdren 2013].		Scientific data has tremendous value, so much so that new government policies declare data "an asset for progress" [Holdren 2013].
		+
		+	Discuss also: “National Science Foundation Collaborates with Federal Partners to Plan for Comprehensive Public Access to Research Results”, NSF Press Release 13-030.

	Although scientists state many reasons that make sharing data difficult [Tenopir et al 2011], there are many good reasons to share data. Sharing data keeps us honest and improves peer review and mutual validation [Corbyn 2012; Krugman 2013; Baggerly and Coombes 2009]. Another reason is the increased reputation and citation of research when datasets become available [Piwowar et al 2007]. Similar arguments can be made for making software available [CITE].		Although scientists state many reasons that make sharing data difficult [Tenopir et al 2011], there are many good reasons to share data. Sharing data keeps us honest and improves peer review and mutual validation [Corbyn 2012; Krugman 2013; Baggerly and Coombes 2009]. Another reason is the increased reputation and citation of research when datasets become available [Piwowar et al 2007]. Similar arguments can be made for making software available [CITE].

@@ Line 1: / Line 1: @@
 [[Category:Task]]
-= Science is Changing =
+= Science is Changing: Making Research Accessible =
 == Opening Science ==
@@ Line 7: / Line 7: @@
 Scientific data has tremendous value, so much so that new government policies declare data "an asset for progress" [Holdren 2013].
-Although scientists state many reasons that make sharing data difficult [Tenopir et al 2011], there are many good reasons to share data. Sharing data keeps us honest and improves peer review and mutual validation [Corbyn 2012; Krugman 2013; Baggerly and Coombes 2009].
+Although scientists state many reasons that make sharing data difficult [Tenopir et al 2011], there are many good reasons to share data. Sharing data keeps us honest and improves peer review and mutual validation [Corbyn 2012; Krugman 2013; Baggerly and Coombes 2009]. Another reason is the increased reputation and citation of research when datasets become available [Piwowar et al 2007].  Similar arguments can be made for making software available [CITE].
-−
 Another reason is the increased reputation and citation of research when datasets become available [Piwowar et al 2007].
-−
-Keeping it to yourself is questionable practice when it is funded by taxpayers that much prefer to see those assets fuel innovation than rot (quite literally) in a lab.
 == Reproducibility ==