How to Organise writing and research using Overleaf, Evernote, and Zotero

In combination, Overleaf, Zotero and Evernote make for a nice research and writing environment. You can research and write within a web browser without switching between desktop apps. This not only saves time but also saves one from stopping and starting while writing and researching ideas and less distracting. Overleaf is a complete writing app that merges the best of LaTeX and rich text editing. Which means that even if you do not know LaTeX or find it hard to use, you my as well write in plain text and use Overleaf’s features in their web based rich text editor. In this article, I am going to write about a workflow I have used with Overleaf, Zotero and Evernote to to write once, and push everywhere.

You will need:

  • An account with Overleaf
  • Installation of git and pandoc
  • An Evernote standalone app and browser plug-in
  • A Zotero installation
  • A PDF reader where you can take notes and export annotation
  • Git and Pandoc installed for your system

Notes: 
 Overleaf is free and there is nothing to install. You can use any web browser to write. You can install Git for your system from the following source. You can install pandoc for your system from the following source. Zotero is a firefox web based browser plug in and for this tutorial I suggest you use Firefox browser and Zotero plug in. You can however, install Zotero as a stand alone app and a browser plug in as well (but that’s just two apps and it will involving switching your apps). For more information, check Zotero website. You can use any PDF for annotation if you use something like Sumnotes, another web app that lets you export your annotations and images from the PDF and you can either push them to Evernote or to another app. You can copy the annotations and then paste them directly to your zotero reference or citation information. See sumnotes for more information.

Overleaf is more than just a LaTeX writing web app

On the face of it, Overleaf looks like a simple web app that allows you to just write LaTeX documents. You can certainly use it that way. Yet under the hood, Overleaf is a very powerful and versatile tool. Overleaf as a web app with a rich text writing controls to write LaTeX documents; that makes it easy for you to write complex documents in LaTeX in a web browser. Really, as a tool, Overleaf is much more than just that. Overleaf has several advantages and features that make it a great web based tool for academic (and other forms of) writing that other writing tools do not quite match.

  • First, it is a great text processor that lives entirely on the web, and makes writing LaTeX on the web as easy as possible.
  • Second, as a LaTeX writing tool, it has most of the packages loaded so that if you wanted to use something like tikz to work with, you can use Overleaf for that purpose. The benefit of this for regular users who are suited to use word processing tools is that, you do not have to configure the complex task of installing a LaTeX installation to work.
  • Third, this brings the power of LaTeX within a web browser so much so that you can use Overleaf not just to write papers, but also to create infographics, and developing slide decks and posters (something like Powerpoint) using packages such as tikz.
  • Fourth, Overleaf has built in connections with many other web apps (such as Zotero and Mendeley for free reference management systems)
  • Fifth, Overleaf integrates very well with git so that you can not only maintain a nice version control system, but you can also use git to clone your article on your own desktop computer, use the other tools that you want to work with and then push everything back to Overleaf for final processing if you like. These are just a few features I could write about here (as these are relevant for the workflow I am about to write here), and there are other features in that app. As this app is free to use and nothing to download, you may want to work along.

As I want to write once and share everywhere, I’d like to write in Overleaf and submit an article not just to Overleaf and through Overleaf to other channels as well. Overleaf has several connections; for instance, Figshare, TheWinnower, PeerJ, and others. At the time of writing this, you cannot style your writing to push to your blog or say something like Medium directly from Overleaf but using simple tools you can bring your content to your desktop based browser and write to push it elsewhere. Also, while Overleaf is great for writing and using bibtex to store references, by itself it does not offer any tool to manipulate references or stored pdfs. By manipulating references I mean more than simple search and retrieval of citation from stored reference files. This means annotation of references, and integrating the pdfs and html documents, or using epubs and mobi formatted documents. This is why we will need to combine other tools. We use two other tools to complement this: the first is a web based reference management system named Zotero, and the other is Evernote. Zotero, like, Overleaf is more than just a reference management system,and Evernote is just more than a store and archive of information. Both systems also allow you to store notes, and write on them, and both of them have free tiers (and paid alternative tiers as well).

Zotero and Evernote

Like Overleaf, Zotero is more than just a web-based reference manager. 
 It is a free, open-source app, maintained by a very active developer community; you can use for not just bibliographic manager and reference management, but also archiving other kinds of information. You can 
 extend Zotero by writing your own translators and web scrapers, and plugins. A rich plug in repository will let you use it in many different ways.

Zotero stands out on several counts against other desktop based traditional reference 
 managers such as Endnote and Papers or Bibdesk.

  • First of all, Zotero is extensible and as an Open source app, you can script it to use it for more than just archiving and retrieving your information.
  • Second, Zotero like Overleaf lives on the web, and is essentially a web app. For this workflow, I recommend that you use Zotero as the Firefox browser add on rather than its stand alone version. While it does not have an integrated PDF reader, it has a very nice annotation feature that can be used quite well.
  • Third, it is great for archiving and reading web pages that you can work on. As you can configure documents to be read on their own apps rather than within itself, Zotero actually frees you from being locked into their services
  • Fourth, Zotero supports exporting to Evernote and we will see that this is a great feature we shall make use of.

Evernote is useful for research. You can install a stand-alone version of Evernote and you can have browser plug in for all browsers. The advantage of Evernote is that it is like an electronic brain. You can store hundreds of facts and quotes and snippets in it and recall using tags. Then work on the notebooks to write your paper. These texts can then be imported back into a text file and you can process these files.

Pandoc and git are needed in this workflow because they are tools that let you keep versions of your work and allow you to connect the webpage with the command line interface on your computers and work on the files. Git is a version control system and Pandoc is a document converter. As you will be working and interfacing between html and plain text formats such as markdown and LaTeX, this is a great tool to have.

How to use Overleaf with Zotero, Evernote, Pandoc and Git?

Here are the steps:

  1. Start creating a new project in Overleaf and start your research in Zotero.
  2. In Overleaf, add Zotero as a source of bibtex file and connect the two.
  3. Create a git repository from the Overleaf article
  4. Clone the repository in a folder in your computer
  5. Search and work on data from webpages and PDFs Annotate webpages in browser and push to Evernote.
  6. Save webpages in Zotero and write your own notes in Zotero in the notes panel. This is important as this helps you to organise your papers later. Save PDFs to Zotero.
  7. Open PDFs in external application (a PDF reader that will allow annotation), not in the browser.
  8. Export the annotations from Zotero as an Evernote enex file
  9. Import the enex file in Evernote
  10. Export the Evernote finished research with figures and tables as an html folder to the same git folder you created with Overleaf on your computer
  11. Use Pandoc to convert the html files to latex files
  12. Upload using git to Overleaf and distribute from there.

Notes: 
 It may seem like a lot of steps. But essentially there are three steps. In the first step, you start with creating a document in Overleaf and start keeping a reference list in Zotero. Then in the second step, connect your Zotero repository to Overleaf and clone your overleaf to your desktop. In the third step, pull from your git repository and control the contents etc in your desktop and browser as you may want. Here, Evernote becomes central to your organising the research. Evernote and Zotero become your main tools for research and Overleaf the main tool for your writing. If you want, you can use a Jupyter notebook and a Ghost installation to write everything in browser and push to your blogs and places such as Medium.


Originally published at webnotes-arin.rhcloud.com on October 1, 2016.

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