Difference between revisions of "ExecutablePapers"

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Our focus is on papers whose ''computational experiments'' can be reproduced and validated. We note that our approach is orthogonal to others which focus on semantics and authoring, and can be combined with these.
Our focus is on papers whose ''computational experiments'' can be reproduced and validated. We note that our approach is orthogonal to others which focus on semantics and authoring, and can be combined with these.


Here's a position paper that details the challenges of computational repeatability and the solutions we have developed:
Here's a '''position paper''' that details the challenges of computational repeatability and the solutions we have developed:
http://www.cs.utah.edu/~juliana/pub/vistrails-executable-paper.pdf
http://www.cs.utah.edu/~juliana/pub/vistrails-executable-paper.pdf


To see our infrastructure in action, check out the following videos:
To see our infrastructure in action, check out the following '''videos''':
* Editing an executable paper written using LaTeX: {{qt|link=http://www.vistrails.org/download/download.php?type=MEDIA&id=executable_paper_latex.mov|text=View}}
* Editing an executable paper written using LaTeX: {{qt|link=http://www.vistrails.org/download/download.php?type=MEDIA&id=executable_paper_latex.mov|text=View}}
* Editing a Web-hosted paper using MediaWiki and server-based computation: {{qt|link=http://www.vistrails.org/download/download.php?type=MEDIA&id=executable_paper_wiki.mov|text=View}}
* Editing a Web-hosted paper using MediaWiki and server-based computation: {{qt|link=http://www.vistrails.org/download/download.php?type=MEDIA&id=executable_paper_wiki.mov|text=View}}
== Examples of Executable Publications ==
=== ALPS2.0===


For a real example of an executable paper, whose results can be reproduced and validated, check out the PDF for ALPS2.0 paper at http://arxiv.org/pdf/1101.2646
For a real example of an executable paper, whose results can be reproduced and validated, check out the PDF for ALPS2.0 paper at http://arxiv.org/pdf/1101.2646
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The ALPS2.0 package is included in VisTrails 1.6.
The ALPS2.0 package is included in VisTrails 1.6.


=== CFD Flow Analysis ===
Another example of an executable publication, can be found at: http://www.vistrails.org/index.php/User:Tohline/CPM/Levels2and3
Another example of an executable publication, can be found at: http://www.vistrails.org/index.php/User:Tohline/CPM/Levels2and3
Because this paper is published on a Wiki, it is possible to interact with the results using a Web browser. Try it out!
Because this paper is published on a Wiki, it is possible to interact with the results using a Web browser. Try it out!

Revision as of 21:43, 16 January 2011

While computational experiments have become an integral part of the scientific method, it is still a challenge to repeat such experiments, because often, computational experiments require specific hardware, non-trivial software installation, and complex manipulations to obtain results. We posit that integrating data acquisition, derivation, analysis, and visualization as executable components throughout the publication process will make it easier to generate and share repeatable results. We have built an extensible infrastructure to support the life-cycle of executable publications---their creation, review and re-use. Our focus is on papers whose computational experiments can be reproduced and validated. We note that our approach is orthogonal to others which focus on semantics and authoring, and can be combined with these.

Here's a position paper that details the challenges of computational repeatability and the solutions we have developed: http://www.cs.utah.edu/~juliana/pub/vistrails-executable-paper.pdf

To see our infrastructure in action, check out the following videos:

  • Editing an executable paper written using LaTeX: Quicktime.png View
  • Editing a Web-hosted paper using MediaWiki and server-based computation: Quicktime.png View


Examples of Executable Publications

ALPS2.0

For a real example of an executable paper, whose results can be reproduced and validated, check out the PDF for ALPS2.0 paper at http://arxiv.org/pdf/1101.2646

To repeat the experiments shown in the paper, you will need to download VisTrails from: You can download VisTrails from: http://www.vistrails.org/index.php/Downloads The ALPS2.0 package is included in VisTrails 1.6.

CFD Flow Analysis

Another example of an executable publication, can be found at: http://www.vistrails.org/index.php/User:Tohline/CPM/Levels2and3 Because this paper is published on a Wiki, it is possible to interact with the results using a Web browser. Try it out!