paper

My Paper Writing Dream Machine 1.0

Martin Fenner
June 14, 2008 1 min read

I’ve written a similar post before (https://web.archive.org/web/20081014105337/http://network.nature.com/blogs/user/mfenner/2008/03/31/pubmed-and-other-annoyances-in-the-paper-writing-process?), put I would like to talk about some of the features that I would like to see in an ideal paper writing application.

Intelligent Formatting
Content and formatting should be separated from each other. A manuscript should require as little formatting as possible, and that formatting (including the format of references) should be defined in a Journal style that is automatically applied to the manuscript. Publicon (https://web.archive.org/web/20081014105337/http://www.wolfram.com/products/publicon/index.html?) by Wolfram Research tried to achieve this, but unfortunately appears to be a dead product.

References
A reference database should be integrated into the paper writing application. Ideally this would be a web-based database such as Connotea (https://web.archive.org/web/20081014105337/http://www.connotea.org/?), CiteULike (https://web.archive.org/web/20081014105337/http://www.citeulike.org/?). Both Refworks (https://web.archive.org/web/20081014105337/http://www.refworks.com/?) and EndNote Web (https://web.archive.org/web/20081014105337/http://www.endnoteweb.com/enwebinfo.asp?) already offer some level of integration.

Versioning
Storing all versions of a manuscript is very important for obvious reasons: backup, keeping track of revisions and coordinating the input from more than one author. Version control is standard practice in software development, using tools like Subversion (https://web.archive.org/web/20081014105337/http://subversion.tigris.org/?) or the newer Git (https://web.archive.org/web/20081014105337/http://git.or.cz/index.html?).

Integration with Online Submission Systems
Submitting a manuscript to an online manuscript submission system such as EditorialManager (https://web.archive.org/web/20081014105337/http://www.editorialmanager.com/homepage/home.htm?) or Topaz (https://web.archive.org/web/20081014105337/http://www.topazproject.org/trac/?) is too complicated. This process could and should be automated.

Summary
My Paper Writing Dream Machine will in all likelihood turn out to be a web-based application, using on one of the more advanced platforms Google Gears (https://web.archive.org/web/20081014105337/http://gears.google.com/?), Microsoft Silverlight (https://web.archive.org/web/20081014105337/http://silverlight.net/?) or Adobe Flex (https://web.archive.org/web/20081014105337/http://www.adobe.com/de/products/flex/?). And the data will be in XML using a standard DTD (https://web.archive.org/web/20081014105337/http://en.wikipedia.org/wiki/Document_Type_Definition?). Some of the pieces of the puzzle already exist, but nobody has yet put them together in a way that it creates a compelling alternative to the currently used systems.

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The Nobel Prize in Physiology or Medicine 2005. (2015). In web.archive.org. https://web.archive.org/web/20150814032045/http://www.nobelprize.org/nobel_prizes/medicine/laureates/2005/index.html
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