ExecutablePapers - Revision history

Juliana at 12:23, 7 August 2011

2011-08-07T12:23:06Z

← Older revision		Revision as of 12:23, 7 August 2011
Line 42:		Line 42:
	We have been investigating better methods to modify embedded computational results more directly. As part of this work, we have extended the current embedding assistant to parse LaTeX source files so that users can examine and modify the results more directly. A screenshot of this updated assistant is shown below. We plan to release this functionality in a future version of VisTrails.		We have been investigating better methods to modify embedded computational results more directly. As part of this work, we have extended the current embedding assistant to parse LaTeX source files so that users can examine and modify the results more directly. A screenshot of this updated assistant is shown below. We plan to release this functionality in a future version of VisTrails.
	[[File:Editing_latex.png\|center\|400px\|thumb\|Editing existing papers directly]]		[[File:Editing_latex.png\|center\|400px\|thumb\|Editing existing papers directly]]

			== Funding ==

			This project is sponsored by the National Science Foundation awards [http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1139832 IIS#1139832], [http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1050422 IIS#1050422], [http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1050388 IIS#1050388], [http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0905385 IIS#0905385], and [http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0751152 CNS#0751152].
			For more information about our research project, see [[RepeatabilityCentral]]

Dakoop at 23:44, 20 May 2011

2011-05-20T23:44:47Z

← Older revision		Revision as of 23:44, 20 May 2011
Line 37:		Line 37:

	* [[ExecutableLatexTutorial \| Editing an executable paper using VisTrails and its LaTeX extensions]]		* [[ExecutableLatexTutorial \| Editing an executable paper using VisTrails and its LaTeX extensions]]

			== Ongoing Work ==

			We have been investigating better methods to modify embedded computational results more directly. As part of this work, we have extended the current embedding assistant to parse LaTeX source files so that users can examine and modify the results more directly. A screenshot of this updated assistant is shown below. We plan to release this functionality in a future version of VisTrails.
			[[File:Editing_latex.png\|center\|400px\|thumb\|Editing existing papers directly]]

Dakoop at 21:51, 20 May 2011

2011-05-20T21:51:34Z

← Older revision		Revision as of 21:51, 20 May 2011
Line 33:		Line 33:
	=== WikiQuery ===		=== WikiQuery ===
	We performed a [http://www.cs.utah.edu/~juliana/WikiQuery/WikiQuery_casestudy.pdf case study] for the [http://www.sigmod2011.org/calls_papers_sigmod_research_repeatability.shtml SIGMOD Repeatability effort]. For more details on how to run the WikiQuery experiments, and to obtain the experiments (data, code, workflows) please see the [[WikiQuery]] page.		We performed a [http://www.cs.utah.edu/~juliana/WikiQuery/WikiQuery_casestudy.pdf case study] for the [http://www.sigmod2011.org/calls_papers_sigmod_research_repeatability.shtml SIGMOD Repeatability effort]. For more details on how to run the WikiQuery experiments, and to obtain the experiments (data, code, workflows) please see the [[WikiQuery]] page.

			== Tutorials ==

			* [[ExecutableLatexTutorial \| Editing an executable paper using VisTrails and its LaTeX extensions]]

Dakoop: /* Infrastructure */

2011-05-20T17:46:07Z

Infrastructure

← Older revision		Revision as of 17:46, 20 May 2011
Line 10:		Line 10:
	== Infrastructure ==		== Infrastructure ==

	We have developed a set of techniques to help authors, reviewers, and readers construct and interact with executable papers. Many of these techniques have been integrated with the [http://www.vistrails.org/ VisTrails] system and the [http://crowdlabs.org crowdLabs] site. VisTrails is an open-source scientific workflow and provenance management system, and our extensions for executable papers allow users to create papers and Web publications whose figures and results are directly tied to the computations that generated them. Both the [http://www.latex-project.org LaTeX] and [http://www.mediawiki.org MediaWiki] extensions call VisTrails (either a server or local executable) to embed results into their documents. In addition, authors can embed images of the workflows that generated a particular result or the history of their explorations. These capabilities are included in the [[Downloads \| VisTrails 1.6.2 release]] available for Windows, Mac, and Linux.		We have developed a set of techniques to help authors, reviewers, and readers construct and interact with executable papers. Many of these techniques have been integrated with the [http://www.vistrails.org/ VisTrails] system and the [http://www.crowdlabs.org crowdLabs] site. VisTrails is an open-source scientific workflow and provenance management system, and our extensions for executable papers allow users to create papers and Web publications whose figures and results are directly tied to the computations that generated them. Both the [http://www.latex-project.org LaTeX] and [http://www.mediawiki.org MediaWiki] extensions call VisTrails (either a server or local executable) to embed results into their documents. In addition, authors can embed images of the workflows that generated a particular result or the history of their explorations. These capabilities are included in the [[Downloads \| VisTrails 1.6.2 release]] available for Windows, Mac, and Linux.

	Authors can also choose to couple a publication with the actual computations by embedding links to the workflows in the paper. The embedding assistant in VisTrails can generate these links automatically when computations are hosted on an accessible database. Using a compatible PDF reader (e.g. [http://get.adobe.com/reader/ Adobe Acrobat]), readers can click on a result, and the embedded link will access a <code>vtl</code> file that contains the workflow or the necessary information to access a remotely-hosted workflow. VisTrails can open <code>vtl</code> files, and from that file will open the corresponding workflow. Note that you may have to alert your operating system of the file extension association. A reader can then explore the result by changing the input data or original parameters. That reader might choose to publish the modified result to a Web page or another publication.		Authors can also choose to couple a publication with the actual computations by embedding links to the workflows in the paper. The embedding assistant in VisTrails can generate these links automatically when computations are hosted on an accessible database. Using a compatible PDF reader (e.g. [http://get.adobe.com/reader/ Adobe Acrobat]), readers can click on a result, and the embedded link will access a <code>vtl</code> file that contains the workflow or the necessary information to access a remotely-hosted workflow. VisTrails can open <code>vtl</code> files, and from that file will open the corresponding workflow. Note that you may have to alert your operating system of the file extension association. A reader can then explore the result by changing the input data or original parameters. That reader might choose to publish the modified result to a Web page or another publication.

	Our [http://www.mediawiki.org MediaWiki] extensions allow authors to embed computational results into wiki pages. The wiki extension allows authors to reference results by tag which allows a user to update results without updating the wiki text. Again, the embedding assistant in VisTrails can generate the markup automatically, and a user simply copies that markup into the wiki page. The [http://crowdlabs.org crowdLabs] site allows authors to host computations and interactive results; VisTrails supports synchronizing workflows with this site. Besides hosting computations, crowdLabs can host input and output data, allows users to search for results, and provides social networking features so other readers can add comments, rate workflows, or form groups. In addition, users can embed results from crowdLabs directly using links on the computation pages. Both the MediaWiki extensions and crowdLabs site support ''server-based'' executions of workflows so users can interact with and modify results from a Web browser. [[VisMashup]] support allows authors to generate Flash applications that allow users to interactively explore an author-defined subset of parameters and input data.		Our [http://www.mediawiki.org MediaWiki] extensions allow authors to embed computational results into wiki pages. The wiki extension allows authors to reference results by tag which allows a user to update results without updating the wiki text. Again, the embedding assistant in VisTrails can generate the markup automatically, and a user simply copies that markup into the wiki page. The [http://www.crowdlabs.org crowdLabs] site allows authors to host computations and interactive results; VisTrails supports synchronizing workflows with this site. Besides hosting computations, crowdLabs can host input and output data, allows users to search for results, and provides social networking features so other readers can add comments, rate workflows, or form groups. In addition, users can embed results from crowdLabs directly using links on the computation pages. Both the MediaWiki extensions and crowdLabs site support ''server-based'' executions of workflows so users can interact with and modify results from a Web browser. [[VisMashup]] support allows authors to generate Flash applications that allow users to interactively explore an author-defined subset of parameters and input data.

	== Demonstrations ==		== Demonstrations ==

Dakoop: /* WikiQuery */

2011-05-20T17:44:47Z

WikiQuery

← Older revision		Revision as of 17:44, 20 May 2011
Line 32:		Line 32:

	=== WikiQuery ===		=== WikiQuery ===
	~~Here's~~ a case study ~~we did~~ for the [http://www.sigmod2011.org/calls_papers_sigmod_research_repeatability.shtml SIGMOD Repeatability effort]~~: http://www~~.~~cs.utah.edu/~juliana/WikiQuery/WikiQuery_casestudy.pdf~~		We performed a [http://www.cs.utah.edu/~juliana/WikiQuery/WikiQuery_casestudy.pdf case study] for the [http://www.sigmod2011.org/calls_papers_sigmod_research_repeatability.shtml SIGMOD Repeatability effort]. For more details on how to run the WikiQuery experiments, and to obtain the experiments (data, code, workflows) please see the [[WikiQuery]] page.

	For more details on how to run the WikiQuery experiments, and to obtain the experiments (data, code, workflows) see [[WikiQuery]].

Dakoop: /* CFD Flow Analysis */

2011-05-20T17:43:57Z

CFD Flow Analysis

← Older revision		Revision as of 17:43, 20 May 2011
Line 29:		Line 29:

	=== CFD Flow Analysis ===		=== CFD Flow Analysis ===
	This [http://www.vistrails.org/index.php/User:Tohline/CPM/Levels2and3 example] is published on the Web via the MediaWiki extensions we have developed. Because this paper is published on a Wiki, it is possible to interact with the results using a Web browser. Try it out!		This [http://www.vistrails.org/index.php/User:Tohline/CPM/Levels2and3 CFD analysis example] is published on the Web via the MediaWiki extensions we have developed. Because this paper is published on a Wiki, it is possible to interact with the results using a Web browser. Try it out!

	=== WikiQuery ===		=== WikiQuery ===

Dakoop: /* CFD Flow Analysis */

2011-05-20T17:43:02Z

CFD Flow Analysis

← Older revision		Revision as of 17:43, 20 May 2011
Line 29:		Line 29:

	=== CFD Flow Analysis ===		=== CFD Flow Analysis ===
	~~Another example of an executable publication, can be found at:~~ http://www.vistrails.org/index.php/User:Tohline/CPM/Levels2and3		This [http://www.vistrails.org/index.php/User:Tohline/CPM/Levels2and3 example] is published on the Web via the MediaWiki extensions we have developed. 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!

	=== WikiQuery ===		=== WikiQuery ===

Dakoop: /* ALPS 2.0 */

2011-05-20T17:41:20Z

ALPS 2.0

← Older revision		Revision as of 17:41, 20 May 2011
Line 26:		Line 26:
	=== ALPS 2.0===		=== ALPS 2.0===

	For a real example of an executable paper, whose results can be reproduced and validated, please see the ALPS 2.0 paper published in the [http://www.iop.org/EJ/abstract/1742-5468/2011/05/P05001 Journal of Statistical Mechanics]. To repeat the experiments shown in the paper, you will need to [[Downloads download]] VisTrails 1.6.2. The ALPS 2.0 package is included in VisTrails 1.6.		For a real example of an executable paper, whose results can be reproduced and validated, please see the ALPS 2.0 paper published in the [http://www.iop.org/EJ/abstract/1742-5468/2011/05/P05001 Journal of Statistical Mechanics]. To repeat the experiments shown in the paper, you will need to [[Downloads \| download]] VisTrails 1.6.2. The ALPS 2.0 package is included in VisTrails 1.6.

	=== CFD Flow Analysis ===		=== CFD Flow Analysis ===

Dakoop: /* ALPS 2.0 */

2011-05-20T17:40:42Z

ALPS 2.0

← Older revision		Revision as of 17:40, 20 May 2011
Line 26:		Line 26:
	=== ALPS 2.0===		=== ALPS 2.0===

	For a real example of an executable paper, whose results can be reproduced and validated, please see the ALPS 2.0 paper published in the [http://www.iop.org/EJ/abstract/1742-5468/2011/05/P05001 Journal of Statistical Mechanics]		For a real example of an executable paper, whose results can be reproduced and validated, please see the ALPS 2.0 paper published in the [http://www.iop.org/EJ/abstract/1742-5468/2011/05/P05001 Journal of Statistical Mechanics]. To repeat the experiments shown in the paper, you will need to [[Downloads download]] VisTrails 1.6.2. The ALPS 2.0 package is included in VisTrails 1.6.

	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 ALPS 2.0 package is included in VisTrails 1.6.

	=== CFD Flow Analysis ===		=== CFD Flow Analysis ===

Dakoop: /* Infrastructure */

2011-05-20T17:39:12Z

Infrastructure

← Older revision		Revision as of 17:39, 20 May 2011
Line 12:		Line 12:
	We have developed a set of techniques to help authors, reviewers, and readers construct and interact with executable papers. Many of these techniques have been integrated with the [http://www.vistrails.org/ VisTrails] system and the [http://crowdlabs.org crowdLabs] site. VisTrails is an open-source scientific workflow and provenance management system, and our extensions for executable papers allow users to create papers and Web publications whose figures and results are directly tied to the computations that generated them. Both the [http://www.latex-project.org LaTeX] and [http://www.mediawiki.org MediaWiki] extensions call VisTrails (either a server or local executable) to embed results into their documents. In addition, authors can embed images of the workflows that generated a particular result or the history of their explorations. These capabilities are included in the [[Downloads \| VisTrails 1.6.2 release]] available for Windows, Mac, and Linux.		We have developed a set of techniques to help authors, reviewers, and readers construct and interact with executable papers. Many of these techniques have been integrated with the [http://www.vistrails.org/ VisTrails] system and the [http://crowdlabs.org crowdLabs] site. VisTrails is an open-source scientific workflow and provenance management system, and our extensions for executable papers allow users to create papers and Web publications whose figures and results are directly tied to the computations that generated them. Both the [http://www.latex-project.org LaTeX] and [http://www.mediawiki.org MediaWiki] extensions call VisTrails (either a server or local executable) to embed results into their documents. In addition, authors can embed images of the workflows that generated a particular result or the history of their explorations. These capabilities are included in the [[Downloads \| VisTrails 1.6.2 release]] available for Windows, Mac, and Linux.

	Authors can also choose to couple a publication with the actual computations by embedding links to the workflows in the paper. The embedding ~~wizard~~ in VisTrails can generate these links automatically when computations are hosted on an accessible database. Using a compatible PDF reader (e.g. [http://get.adobe.com/reader/ Adobe Acrobat]), readers can click on a result, and the embedded link will access a <code>vtl</code> file that contains the workflow or the necessary information to access a remotely-hosted workflow. VisTrails can open <code>vtl</code> files, and from that file will open the corresponding workflow. Note that you may have to alert your operating system of the file extension association. A reader can then explore the result by changing the input data or original parameters. That reader might choose to publish the modified result to a Web page or another publication.		Authors can also choose to couple a publication with the actual computations by embedding links to the workflows in the paper. The embedding assistant in VisTrails can generate these links automatically when computations are hosted on an accessible database. Using a compatible PDF reader (e.g. [http://get.adobe.com/reader/ Adobe Acrobat]), readers can click on a result, and the embedded link will access a <code>vtl</code> file that contains the workflow or the necessary information to access a remotely-hosted workflow. VisTrails can open <code>vtl</code> files, and from that file will open the corresponding workflow. Note that you may have to alert your operating system of the file extension association. A reader can then explore the result by changing the input data or original parameters. That reader might choose to publish the modified result to a Web page or another publication.

	Our [http://www.mediawiki.org MediaWiki] extensions allow authors to embed computational results into wiki pages. The wiki extension allows authors to reference results by tag which allows a user to update results without updating the wiki text. Again, the ~~embededding wizard~~ in VisTrails can generate the markup automatically, and a user simply copies that markup into the wiki page. The [http://crowdlabs.org crowdLabs] site allows authors to host computations and interactive results; VisTrails supports synchronizing workflows with this site. Besides hosting computations, crowdLabs can host input and output data, allows users to search for results, and provides social networking features so other readers can add comments, rate workflows, or form groups. Both the MediaWiki extensions and crowdLabs site support ''server-based'' executions of workflows so users can interact with and modify results from a Web browser. [[VisMashup]] support allows authors to generate Flash applications that allow users to interactively explore an author-defined subset of parameters and input data.		Our [http://www.mediawiki.org MediaWiki] extensions allow authors to embed computational results into wiki pages. The wiki extension allows authors to reference results by tag which allows a user to update results without updating the wiki text. Again, the embedding assistant in VisTrails can generate the markup automatically, and a user simply copies that markup into the wiki page. The [http://crowdlabs.org crowdLabs] site allows authors to host computations and interactive results; VisTrails supports synchronizing workflows with this site. Besides hosting computations, crowdLabs can host input and output data, allows users to search for results, and provides social networking features so other readers can add comments, rate workflows, or form groups. In addition, users can embed results from crowdLabs directly using links on the computation pages. Both the MediaWiki extensions and crowdLabs site support ''server-based'' executions of workflows so users can interact with and modify results from a Web browser. [[VisMashup]] support allows authors to generate Flash applications that allow users to interactively explore an author-defined subset of parameters and input data.

	== Demonstrations ==		== Demonstrations ==