I am not sure how you managed to do with the YAML at the beginning. Now I just have to copy this list and paste it directly into the Markdown file of the paper. Final Thoughts It took a while to get everything in place and working, but I am happy with it now. I am exploring a similar question myself and documenting my findings in my blog: You can also provide Pandoc with a LaTex template if you want to. I never tried, though. It therefore feels much more like a full IDE than the notebooks.

Will you kindly share with me the corresponding markdown and code windows? As academics, writing is one of our core activity. Spencer James Those are some great examples — the biomed-related ones are especially helpful. However, it looks like the new-to-me nbinteract [ repo ] package does provide a simpler way of publishing interactive webpages from Jupyter notebooks, with HTML pages hosted wherever and interactives powered from a Binder backend. The syntax is dead simple, you will get it in literally 5 minutes. Bibliography I use Mendeley for my reference managements. Here is how it works.

Writing academic papers in plain text with Markdown and Jupyter notebook

Notify me of new comments via email. Sign up using Facebook. I have noticed that Mendeley does not automatically generate citation keys. Long version As academics, writing is one of our core activity.

Plotting my thesis with Jupyter | Alice Harpole

I’ve tried 2 approaches: To give you a rough idea, here is the simple function that I use to generate the list of bib keys. Indeed, the online interactive textbook for another Berkeley course, DS — Principles and Techniques of Data Science [ repo ] — uses both both Gitbook and nbinteractso the setup guide may be worth a look….


ipython notebook thesis

Take a look noteobok Authorea http: When I last considered doing this, I thought it was promising, but not quite ready. Home Questions Tags Users Unanswered. It can add referencing, indexing, etc.

ipython notebook thesis

Already, there are a number of community-developed extensions including support for live-editing of LaTeX documents, viewers for ipywidgets, Bokeh and plotly, and GitHub browsing. They then exist in the notebook variable space until I overwrite them or shut down the notebook.

That is a trade-off that I can accept for now, as I usually have a limited number of equations and figures.

Unicorn Meta Zoo 3: Ok, it was not clear from the webpage, that you need either three dashes, or three dots, surrounding it. You can build from the command line.

Fragment: From Jupyter Notebooks to Online Interactive Textbooks

But your copy-paste solution still gives me the shivers… Noteboom summarize my findings with ipython so far: I am hoping that new collaborative authoring tools such as authorea will eat way at this annoying insistence that so many science folk still have on MS Word. I updated the CSV file with the new data plots, ran the notebook, and the figures were instantaneously updated.


From what I can tell in a few minutes of research, it looks like it would be difficult for me to port my big template-using-multi-file thesis over to Authorea. Thanks for sharing your techniques and experience.

ipython notebook thesis

Especially when generating plots for my thesis, I often wanted to rerun the same plotting script many times with small tweaks until I got the figure that I wanted.

Simply telling pandoc to use the.

This site uses Akismet to reduce spam. Please log in using one of these methods to post your comment: To summarize my findings with ipython so far: Multiple instances of the same notebook can be opened at once, allowing you to compare different parts side by side. Thanks for the answer. Jane Jane 41 1.

Writing academic papers in plain text with Markdown and Jupyter notebook | Sylvain Deville

This is achieved by selecting the cell and then pressing ESC followed by R. I use Mendeley for my reference managements. Dropping the –listings option works, but produces Tex which includes many additional command sequences you may not want in your main Tex file.

In that case, I wrote almost everything. The cell might iputhon like this:

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