Writing an academic paper in Classeur, and Overleaf — part II of the series

Part I here

In this series, I am exploring the tools to write scholarly, academic papers collaboratively and presenting them in a range of outlets. Specifically, what tools will let us write our papers collaboratively and let us share our thoughts on academic and scholarly topics, rather than as opinion pieces?

More specifically, this is what I am looking for:

1. The tool will let me write in plain text
2. I should be able to write using markdown in that tool as Markdown is an easy, and flexible tool to write virtually anything including embedded code and is very lightweight. For more information on Markdown, see this
3. So, the tool should let me write in Markdown and or convert Markdown codes from an input (that is, I can write Markdown as plain text but can read that in directly, more on this aspect in the next part)
4. But Markdown is not going to be my primary output mode, I should be able to output the paper in LaTeX and PDF as this is the de facto mode of academic speak
5. So, I input in markdown (either through plain text or natively) and be flexible in putting out the stuff, but one of the outputs have to be in LaTeX and html so that I can put them out in my blogs or in Medium and in a format that will let me communicate
6. It should allow for three key elements: tables that I can correctly format, equations, formulae, and codes, images, and most importantly citations

In the first installment of this series, I wrote about using a combination of Ulysses writing app and Overleaf for writing and sharing scholarly and academic documents.
In this part, I am going to write about another tool, classeur.io. Also, we found:

1. Markdown is a great tool to write but markdown needs to be beefed up for writing academic staff. On the other hand, LaTeX is great for writing academic scholarly papers and publishes very well to PDF but not necessarily very easy and intuitive to write. Word and their friends (whether open or closed source) are quite complex and not necessarily helpful for writing
2. So, a combination of Markdown and Pandoc makes for a great combined tool. In our previous post, we used Ulysses and Pandoc to work.
3. Then again, Pandoc is not necessarily the friendliest of tools and require overheads.
4. What if the same app where we wrote the initial concept paper were to enable us stitch together the plain text and export to LaTeX? Then we could process it using Overleaf, the online, collaborative, freemium modelled LaTeX editor?

Enter, Classeur and Overleaf

Classeur and Overleaf are two complementary tools to write academic papers. Further, Overleaf has this feature of submitting to everywhere (virtually everywhere), and hundreds of templates, and built in collaborative features, including sharing on social networks. You can also style Overleaf to write really complex documents.

Here is the workflow we were discussed in part one:

1. Write. — Write the paper in Classeur
2. Process. — Export the paper to LaTeX and add a bibtex file for citations
3. Share. — Use Overleaf to share the article as widely as possible

Write and Collaborate with Classeur

Classeur.io addresses an interesting problem of letting writing free flow text a breeze. It has a nice interface that is lean, fast, free, and does not look like geeky at all. Using hyperlinks is easy, so for instance, if I want to add a link to Overleaf, I can use a standard hyperlink structure or formatOverleaf Linking and it will do the rest. It is also very visual with a good UI, you can hit control and L, or cmd and L in Mac and insert hyperlinks.

Tables and figures

Adding tables and figures too is easy. Tables are particular strong points, but for writing for something like Medium, it is best we avoid using tables and instead use Figures instead. Here is a figure to add (but best to add the figure to something like imgur and then use the hyperlink).

This is an image of a Model of Behavioural Genetics

In the live window next to the desktop version, you won’t get to see the image, but the code gets inserted. You may see it when it goes live on the web, or when you convert the file to LaTex with some modification. You need to import the file from a web address to directly to your space in Overleaf (that is easy and saves you time).

Insertion of tables is easy as well. In Ulysses, we saw it does not allow table creation natively; in Classeur, you can use the pipe symbols | to separate table columns and craft your tables. Or you can use online tables generator to format and style your tables and directly insert here in the app.

Codes and equations

Codes are really easy to write. The short cut is to use control K or command K in Mac, and the codes get inserted. Or use tabs or four spaces to indent codes.

addone <- function(x){
y <- x + 1
return(y)
}

Inserting Citations

For insertion of citations, you can make it straightforward. Use a bibtex processor (virtually any bibliography software will let you work with bibtex files), and there are excellent web based citation organisers. Use for instance, CiteULike to create an author group and share all your references and full texts etc. Then, all you need to do is to insert the {citation ID} from the citeulike page to your manuscript and you are all set

In built Collaboration tools in Classeur

Classeur lets you share your work. See the screenshot below:

Thus, you can share an editable version of the work. Plus, you can generate messages with each chunk of the text you write and comment on them. There is a commenting box. This is a plus feature.
In addition, classeur.io allows sharing an editable version of the paper with Markdown formats to your collaborators.

Process with Overleaf

Once you are done with the Classeur, export Classeur document to LaTeX and make the following changes:

1. Classeur puts .latex to every filename, change that to .tex
2. If you have used citeulike, then note the citeulike username (you will need this in the overleaf stage)
3. If you have used imgur or another web based image hosting service, be prepared to import the images to your Overleaf
4. Have your Overleaf username and password ready
5. Visit overleaf and log in, create a new project, select “blank”, and upload your classeur formatted latex paper

Do Medium and Blogs play well?

It’s possible to just copy and paste the html (not the code but output) from the classeur.io app to post to Medium. As long as there are no tables, symbols, and citation markup, Medium will take it in. For showing those elements, either use images, or use plain texts. There is a read and write share button but that does not work with Medium. Also note that Medium does not play well with tables and citations natively. One other way might be to first post to a wordpress or blogger blog and then read it back to Medium. Blogs certainly work well seamlessly.

Next?

In the next part (Part III) of the series, I am going to write aboutManuscripts.app and how this can be used for synchronising between Markdown format and LaTeX without using Pandoc.