It is always a pleasure to hear from you, and it sounds like you are doing a ton of interesting stuff! Ice templating, also known as freeze casting, is a popular shaping route for macroporous materials. The newly released JupyterLab provides an updated environment for Jupyter Notebooks, generally improving their usability. 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. This was particularly useful when writing that particular paper.

A particular challenge is working with colleagues who like to write collaboratively in MSWord using Track Changes. I am exploring a similar question myself and documenting my findings in my blog: Simply telling pandoc to use the. Leave a Reply Cancel reply Enter your comment here Of particular interest in this case: It therefore feels much more like a full IDE than the notebooks. I’m working on my thesis using LaTeX via overleaf.

As I run the notebook, the figures are generated and saved in a folder.

They then exist in the notebook variable space until I overwrite them or shut down the notebook. They may be useful as a reference. Dashi is a wrapper around the matplotlib histogram object that makes it easy to use; if you prefer to use matplotlib histograms without Dashi, that should work very similarly but with more coding.

I am currently using pandoc-crossref for a manuscript combined with the approach here, and it is quite good for cross-reference. Putting everything together So I have everything I need now. Another possible approach would be thedis use a gitbook workflow.

Dropping the –listings option works, but produces Tex which includes many additional command sequences you may not want in your main Tex file. The text is structured, and include figures, lots of maths usuallyand many citations. You are commenting using your WordPress. I do not want to depend on a file format that might become obsolete.


JupyterLab is built on top of an extension system, which means that it is incredibly customisable. Using the notebook for plotting. Bibliography I use Mendeley for my reference managements. Pandoc does not do cross-references. You can also do everything from Sublime Text.

ipython notebook thesis

Spencer On Mon, Apr 20, at 1: Any suggestion is welcome. Use Pandoc to convert the markdown into LaTeX, as in pandoc –listings -f markdown -t latex test.

ipython notebook thesis

Hi Abie, Hope things are well back in Seattle! Jupyter WebBook [ repo ]. 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. I’m still going to have a few issues with the formating of the pdfs exported from the Jupyter Notebook but that’s down to Jupyter, not LaTeX.

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

Option 2 is difficult because I can’t figure out how to get the included pdf pages to be numbered correctly or to show up in the table of contents. 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. Similarly, I love being able to have a terminal open in the same window so that I can run my code to generate the data I then plot in the notebook without having to continuously switch and resize windows.


Essentially, I’m just wondering if anyone out there has figured out a good way or even a not-so-good way that at least works to include Jupyter notebooks as pages in large LaTeX documents. For Option 2, does it do what you want if you use something like this? If I am in charge of the paper, I choose the tools. Devillewhich turned out to be super convenient later.

Writing academic papers in plain text with Markdown and Jupyter notebook

The main selling points for me were the following: Markdown use relative references to folder and files, take note how I point to the figure thesia. I updated the CSV file with the new data plots, ran the notebook, and the figures were instantaneously updated.

Background Jupyter Thexis is a “a web application that allows you to create and share documents that contain live code, equations, visualizations and explanatory text. The main selling points for me were the following:.

ipython notebook thesis

I am a big fan of LaTex for long documents PhD manuscript, etc. Ideally, the list would be automatically generated within the Markdown file, so that there is even less friction in the whole process.