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Lee Worden

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I've just done a minimal test of the new WorkingMarkdown tool, based on #WorkingWiki and currently in alpha. It works! Very exciting new stuff. Many thanks to +Lee Worden  for building awesome reproducible science tools!
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. . . This will provide a way to publish blog posts and web pages including research data, source code, figures, tables, citations and manuscripts in a transparent and reproducible way. Instead of creating some figures and uploading the image files into a blog post, you'll be able to write the blog posts using special directives telling it to update and include the figures directly from the code and data that make it. . . .

#workingwiki #openaccess #openscience #reproducibility  
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Evidence that #WorkingWiki  is not just an online tool, it's a new kind of programming environment
I want something #WorkingWiki -like using Markdown. Just like RMarkdown, but with the ability to run anything that can run in the shell, like WorkingWiki. I want it to run locally, detect the language from the ```{x} tag, and put the output into a Markdown file that I can then convert to HTML if I want.

So, you know, +Lee Worden +Jonathan Dushoff +David Leaman , if you have nothing else to do...
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Progress in WorkingWiki development since April 2013:

* Presented WorkingWiki at WikiSym and Wikimania meetings, Hong Kong, August 2013

* Created a tutorial on using WorkingWiki for beginners, based on programming in R:

* Led a 1-day WorkingWiki tutorial at the annual Clinic on Dynamical Approaches to Infectious Disease Data (DAIDD), Gainesville, FL, Dec. 2013

* Created a jQuery-enabled WorkingWiki epidemic disease exercise based on one in use at the DAIDD workshop:

* Update of WorkingWiki internal code, achieving full compatibility with current releases of MediaWiki (versions 1.19 and greater).  This is very important to maintain WorkingWiki's future viability, and to make it available to a wide audience of potential users.

* Created an entirely new file-importing interface, using state-of-the-art jQuery framework to provide a smooth, responsive experience in the browser.

* Created MultiUpload extension as a side-effect of the file-importing development.  This has been released as a general-purpose multiple-file upload tool ( for MediaWiki installations, independent of WorkingWiki.

* Created a WorkingWiki demo video:

* Created a MultiUpload demo video:

* Major interface redesign, phase 1: most of the WorkingWiki actions offered in the wiki page are now performed inline without leaving the page, using state-of-the-art jQuery framework that makes AJAX calls to do lightweight operations on the server.

* Preliminary development for phase 2 of major interface design: lazy loading of WorkingWiki output files using COMET framework with jQuery, to reduce the wait time for wiki pages to load and allow fine-grained feedback on the computation processes during their execution.

* Improvements to the WorkingWiki/Grid Engine interface, which allows wiki users to submit jobs to the local compute cluster, track their progress, and retrieve the results.

* Made improvements to automatic processing of .tex files.

* Enabled and tested integration with iTex, an alternative to LaTeXML and MathJax that is popular in mathematical communities for formatting math content for the web.

* Created WorkingWiki demo pages illustrating the ease of creating diagrams in WorkingWiki using latex's tikz and xy packages, with fully scalable SVG output in the wiki page (,

* Created an informational page,, explaining what WorkingWiki has to offer math researchers.

* Created a project demonstrating use of the Sage mathematical computing system in WorkingWiki (

* Creation of a WorkingWiki API framework allowing operations on WW projects to be requested flexibly by outside programs.  This paves the way for integration of WorkingWiki features into other tools.

* Worked with Dushoff's group to upgrade the lalashan WorkingWiki installation (more than 100 wikis) to current versions of MediaWiki.

* Many bugs fixed

* Have had exploratory discussions with Daniel Mietchen  ( about WorkingWiki's potential as a platform for his "Beethoven's Repository of Science" (

* Created a report on "forking" projects in WorkingWiki:

* Improved the documentation ( and added new documentation about using LaTeX and Makefiles in WorkingWiki (,

#mediawiki #jquery #workingwiki  
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A completely new implementation of Extension:MultiUpload.
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