Scientific Editor

This article is originally published at https://logfc.wordpress.com

I have a dream: a scientific editor that would be suitable for editing scientific papers. Currently, Word is king. There is no way around it: everybody has it, everybody uses it, sooner or later you will have a co-author who knows how to edit text only when writing an e-mail or when writing in Word. Chances are, that collaborator will be one of the big fishes on your authors list, maybe even your boss. Word has some basic collaborative options (like tracking changes and comments), bibliography (via Endnote or similar tools), and is accepted by most journals.

However, Word sucks. Big time. I know you know it.

I envision an open source solution that is based on an updated markdown syntax and the pandoc system. Here is, point by point, an informal specification of the system.

1. Markdown as the primary text format. A user should be able to edit markdown directly without compromising any information contained in the document or write the document in rmarkdown and directly pass it down to the system.
2. Zip file as the primary format: documents would be exchanged using a zip file containing
   • manuscript file in markdown
   • bibliography file (I would recommend BibTeX)
   • figure files
3. Bibliography as in pandoc — bibliography in a format that is acceptable by pandoc, with CLS for reference formatting.
4. Figures: figures are a major pain in the neck. Publishers require usually a vector graphic format or a high resolution image, but you want low-res previews in your print files or documents. The manuscript zip file should therefore either contain both, or only previews, with original files to be contained later.
5. Markdown extensions:
   • extensions that would allow a “rich” export to Word’s docx: marking reviews, comments etc.
   • (better) figure and label captioning and cross-referencing
   • special bibliography sections (currently, you can only place the references at the end of the file)
6. A visual UI with editor:
   • Java or similar that allows a painless installation process for even the least computer-savvy users, and allows them to edit the manuscript in a way that they are used to
   • GUI operations for an easy update of bibliography (I mean like really easy, just paste+copy of whatever: pubmed ids, google scholar links etc)
   • Equation editor, table editor etc. suitable for saving in markdown format
   • Version tracking
7. Version tracking and managing revisions. Still pondering how to do this best, but this should be one of the major points for the system.
8. Misc operations. The system should be able to quickly and painlessly accomplish following tasks:
   • split the manuscript into submission files by using logical definitions in the markdown (e.g. in the main manuscript file, separate figure files, separate supplementary data files)
   • provide detailed statistics on the document (word count)
   • possibly the visual UI could provide a plug-in to facilitate submission specifically in some of the most common manuscript submission systems (e.g. manuscript central).

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