16. You know the drill
Write some background.
copy-paste the intro from your last paper
17. You know the drill
Write some background.
copy-paste the intro from your last paper
Explain what you did.
18. You know the drill
Write some background.
copy-paste the intro from your last paper
Explain what you did.
not including the 3 days you spent debugging that one plotting error
19. You know the drill
Write some background.
copy-paste the intro from your last paper
Explain what you did.
not including the 3 days you spent debugging that one plotting error
Report what you got from that work.
20. You know the drill
Write some background.
copy-paste the intro from your last paper
Explain what you did.
not including the 3 days you spent debugging that one plotting error
Report what you got from that work.
and triple check the units
21. You know the drill
Write some background.
copy-paste the intro from your last paper
Explain what you did.
not including the 3 days you spent debugging that one plotting error
Report what you got from that work.
and triple check the units
Pontificate on said results.
22. You know the drill
Write some background.
copy-paste the intro from your last paper
Explain what you did.
not including the 3 days you spent debugging that one plotting error
Report what you got from that work.
and triple check the units
Pontificate on said results.
maybe name something after yourself or significant other
29. Keepin’ it Real
Writing a paper is fraking hard
I can’t find anything about this TeX error
30. Keepin’ it Real
Writing a paper is fraking hard
I can’t find anything about this TeX error
Why won’t the table stay in the same place?
31. Keepin’ it Real
Writing a paper is fraking hard
I can’t find anything about this TeX error
The science is hard
Why won’t the table stay in the same place?
32. Keepin’ it Real
Writing a paper is fraking hard
I can’t find anything about this TeX error
Emailing versions and comments back and forth
The science is hard
Why won’t the table stay in the same place?
33. Keepin’ it Real
Writing a paper is fraking hard
I can’t find anything about this TeX error
Emailing versions and comments back and forth
The science is hard
Why won’t the table stay in the same place?
How the hell do I get my plotting library to do that?
34. Keepin’ it Real
Writing a paper is fraking hard
I can’t find anything about this TeX error
Emailing versions and comments back and forth
The science is hard
Why won’t the table stay in the same place?
How the hell do I get my plotting library to do that?
35. You are a scientist
http://www.corbisimages.com/Enlargement/HU001769.html
36. You are a scientist
http://www.corbisimages.com/Enlargement/HU001769.html
37. You are a scientist
Not a typesetter
http://www.corbisimages.com/Enlargement/HU001769.html
38. The Editor Landscape
http://tutorialfreakz.com/wp-content/uploads/2009/08/Grassland-Landscape-Wallpaper.jpg
47. Spectrum
WYSIWYG Document Source
Monolithic file “Repository”
Has that shiny Microsoft look
http://nlu.nl.edu/careerservices/search/images/WordIcon.jpg
48. Spectrum
WYSIWYG Document Source
Monolithic file “Repository”
Has that shiny Microsoft look Source looks insane, output is gorgeous
http://nlu.nl.edu/careerservices/search/images/WordIcon.jpg
65. Things you can do
The power of the internets
Planning for interactive plots (pan and zoom) with inline link to plotted data
66. Things you can do
Syntax highlighting wizardry
The power of the internets
Planning for interactive plots (pan and zoom) with inline link to plotted data
67. Things you can do
Syntax highlighting wizardry
eventually interactive?
The power of the internets
Planning for interactive plots (pan and zoom) with inline link to plotted data
68. Version Control
In the works, but it will be completely transparent to the user.
Example Diff...
69. Modern Information
http://www.tacc.utexas.edu/feature_stories/2008/powering_discoveries.php
70. Modern Information
http://www.tacc.utexas.edu/feature_stories/2008/powering_discoveries.php
71. Modern Information
Should have been like 5 years ago
http://www.tacc.utexas.edu/feature_stories/2008/powering_discoveries.php
75. Pages?
Limitation of print.
Presents problems:
Breaks flow by introducing unnecessary gaps in content
Items must be sized down to fit page (large tables, hi-res images)
76. Pages?
Limitation of print.
Presents problems:
Breaks flow by introducing unnecessary gaps in content
Items must be sized down to fit page (large tables, hi-res images)
... many things I could rant about for too long ...
77. Pages?
Limitation of print.
Presents problems:
Breaks flow by introducing unnecessary gaps in content
Items must be sized down to fit page (large tables, hi-res images)
... many things I could rant about for too long ...
journals being able to charge a page cost
82. β
I really need feedback to make this useful.
You can influence big design decisions.
83. β
I really need feedback to make this useful.
You can influence big design decisions.
You can (maybe) give up LaTeX.
84. β
I really need feedback to make this useful.
You can influence big design decisions.
You can (maybe) give up LaTeX.
http://paperhustler.com/
@paperhustler
86. Web Full Text
http://www.cell.com/fulltext/S0092-8674(11)00107-3
87. Web Full Text
http://www.cell.com/fulltext/S0092-8674(11)00107-3
88. Web Full Text
http://www.cell.com/fulltext/S0092-8674(11)00107-3
89. Web Full Text
Richer content, much
better reading
experience, ...
but needs work before
it beats the PDF.
http://www.cell.com/fulltext/S0092-8674(11)00107-3
93. Beyond The PDF
Workshop at UCSD, January 19 - 21
All the open science usual suspects
Big product was “Research Objects of the Future”
94. Beyond The PDF
Workshop at UCSD, January 19 - 21
All the open science usual suspects
Big product was “Research Objects of the Future”
The La Jolla Manifesto (https://sites.google.com/site/beyondthepdf/home/program-
draft/notes-from-the-breakout)
98. Research Objects
Replayable – go back and see what happened
Repeatable – run the experiment again
Reproducible – run new experiment to reproduce the results
99. Research Objects
Replayable – go back and see what happened
Repeatable – run the experiment again
Reproducible – run new experiment to reproduce the results
Reusable – use as part of new experiments
100. Research Objects
Replayable – go back and see what happened
Repeatable – run the experiment again
Reproducible – run new experiment to reproduce the results
Reusable – use as part of new experiments
Repurposeable – reuse the pieces in a new experiment
101. Research Objects
Replayable – go back and see what happened
Repeatable – run the experiment again
Reproducible – run new experiment to reproduce the results
Reusable – use as part of new experiments
Repurposeable – reuse the pieces in a new experiment
Reliable – robust under automation
103. Modern Information
Papers are the preservation of science.
Science must be reproducible.
⇒ The paper should include everything.
104. Modern Information
Papers are the preservation of science.
Science must be reproducible.
⇒ The paper should include everything.
Procedure
105. Modern Information
Papers are the preservation of science.
Science must be reproducible.
⇒ The paper should include everything.
Procedure
Raw Data
106. Modern Information
Papers are the preservation of science.
Science must be reproducible.
⇒ The paper should include everything.
Procedure
Analysis
Raw Data
107. Modern Information
Papers are the preservation of science.
Science must be reproducible.
⇒ The paper should include everything.
Procedure Processed Data
Analysis
Raw Data
108. Modern Information
Papers are the preservation of science.
Science must be reproducible.
⇒ The paper should include everything.
Procedure Processed Data
Analysis
Derivations
Raw Data
110. Totality
The paper isn’t an overview - it’s the record of the entire project.
http://www.openresearchcomputation.com/
111. Totality
The paper isn’t an overview - it’s the record of the entire project.
“publishes peer reviewed articles that describe the
development, capacities, and uses of software designed
for use by researchers in any field.”
http://www.openresearchcomputation.com/
112. Totality
The paper isn’t an overview - it’s the record of the entire project.
“publishes peer reviewed articles that describe the
development, capacities, and uses of software designed
for use by researchers in any field.”
Submission requirements:
http://www.openresearchcomputation.com/
113. Totality
The paper isn’t an overview - it’s the record of the entire project.
“publishes peer reviewed articles that describe the
development, capacities, and uses of software designed
for use by researchers in any field.”
Submission requirements:
•Code and license
http://www.openresearchcomputation.com/
114. Totality
The paper isn’t an overview - it’s the record of the entire project.
“publishes peer reviewed articles that describe the
development, capacities, and uses of software designed
for use by researchers in any field.”
Submission requirements:
•Code and license
•Fully documented
http://www.openresearchcomputation.com/
115. Totality
The paper isn’t an overview - it’s the record of the entire project.
“publishes peer reviewed articles that describe the
development, capacities, and uses of software designed
for use by researchers in any field.”
Submission requirements:
•Code and license
•Fully documented
•100% test coverage of public functions
http://www.openresearchcomputation.com/
116. Totality
The paper isn’t an overview - it’s the record of the entire project.
“publishes peer reviewed articles that describe the
development, capacities, and uses of software designed
for use by researchers in any field.”
Submission requirements:
•Code and license
•Fully documented
•100% test coverage of public functions
•Example data and code
http://www.openresearchcomputation.com/
117. The Future
http://www.flixist.com/the-future-is-here-maybe-3d-without-3d-glasses-update--197839.phtml
118. Blogs?
Great model for
instant publication,
but journals are
centralized for a
reason.
http://terrytao.wordpress.com/
119. Open Notebook Science
Keep extremely
detailed records as
you do research.
“real-time research”
Becoming serious
business in chem
http://usefulchem.wikispaces.com/dopal
122. “Paper 2.0”
http://michaelnielsen.org/blog/scientific-communication/
Versions
Different content for different readers
http://www.geekologie.com/2010/04/26/magic-major.jpg
123. “Paper 2.0”
http://michaelnielsen.org/blog/scientific-communication/
Versions
Different content for different readers
“Levels”
http://www.geekologie.com/2010/04/26/magic-major.jpg
124. “Paper 2.0”
http://michaelnielsen.org/blog/scientific-communication/
Versions
Different content for different readers
“Levels”
Choose how detailed you want your information
http://www.geekologie.com/2010/04/26/magic-major.jpg
125. “Paper 2.0”
http://michaelnielsen.org/blog/scientific-communication/
Versions
Different content for different readers
“Levels”
Choose how detailed you want your information
Distributed editing
http://www.geekologie.com/2010/04/26/magic-major.jpg
126. “Paper 2.0”
http://michaelnielsen.org/blog/scientific-communication/
Versions
Different content for different readers
“Levels”
Choose how detailed you want your information
Distributed editing
Open, public annotation
http://www.geekologie.com/2010/04/26/magic-major.jpg
127. “Paper 2.0”
http://michaelnielsen.org/blog/scientific-communication/
This would be amazing, but scientists already have
Versions no time writing the brief version of the paper
Different content for different readers
“Levels”
Choose how detailed you want your information
Distributed editing
Open, public annotation
http://www.geekologie.com/2010/04/26/magic-major.jpg
128. “Paper 2.0”
http://michaelnielsen.org/blog/scientific-communication/
This would be amazing, but scientists already have
Versions no time writing the brief version of the paper
Different content for different readers
“Levels”
Choose how detailed you want your information
Distributed editing
Open, public annotation
http://www.geekologie.com/2010/04/26/magic-major.jpg
129. “Paper 2.0”
http://michaelnielsen.org/blog/scientific-communication/
This would be amazing, but scientists already have
Versions no time writing the brief version of the paper
Different content for different readers
“Levels”
Choose how detailed you want your information
Distributed editing
Open, public annotation
Still, it is what we should aim for.
http://www.geekologie.com/2010/04/26/magic-major.jpg
130. Summary
Scientists should never do an editor’s job.
We are in need of a new model of the paper.
At least an update on the technology behind them.
Check out Paper Hustler for suping up your papers.
http://thestarkeffect.com/
@caseywstark
131. Summary
Scientists should never do an editor’s job.
We are in need of a new model of the paper.
At least an update on the technology behind them.
Check out Paper Hustler for suping up your papers.
http://thestarkeffect.com/ http://paperhustler.com/
@caseywstark @paperhustler