6. Slides#

Content format

This page is written in the Markdown Notebook format. While it is intended to be rendered through RISE as reveal.js slides, it can also be viewed as a Jupyter Book section or a Jupyter Notebook. The code blocks embedded in this page can be executed through Jupyter Notebook via MyBinder – this option is available from the Launch Menu that appears after hovering the mouse cursor over the icon shown in the top bar. Alternatively, the code boxes can be executed directly on this page with Thebe by activating  Live Code from the  Launch Menu.

In addition to this article page and the corresponding Jupyter Notebook, static and interactive reveal.js slides are built from the page source. The static slides can be accessed with this button View Slides. To launch the interactive version of the slides (with executable code boxes), first open this page as a Jupyter Notebook through Binder – either via the  Launch Menu or using this button Open in Binder; next execute all of the code cells (using the Kernel → Restart & Run All Jupyter Notebook menu); then open RISE by clicking the button located in the top bar of the Jupyter Notebook interface.

Tip

This page includes a number of Python cells holding setup code. You can reveal the content of these cells by clicking the buttons, which appear towards the right edge of this page.

You Only Write Thrice

Creating Documents, Computational Notebooks and Presentations From a Single Source




Kacper Sokol
and Peter Flach

%matplotlib widget
import ipywidgets as widgets
import numpy as np
import matplotlib.pyplot as plt

from IPython.display import IFrame

plt.style.use('seaborn')

DISTILL = 'https://distill.pub/2019/activation-atlas/'
OPEN_REVIEW = 'https://openreview.net/forum?id=i4zpuNRiU4G'
YOU_ONLY_WRITE_THRICE = 'https://so-cool.github.io/you-only-write-thrice/'
SIMPLY_LOGICAL = 'https://too.simply-logical.space/src/text/2_part_ii/4.2.html'

def preview_url(url, height=600):
    return IFrame(url, width=800, height=height)  # 1200

def interactive_plot():
    fig, ax = plt.subplots(figsize=(10, 4))
    fig.patch.set_alpha(0)
    ax.set_ylim([-4, 4])
    ax.grid(True)
    x = np.linspace(0, 2 * np.pi, 100)

    def my_sine(x, w, amp, phi):
        """Returns a sine for x with angular frequeny w and amplitude amp."""
        return amp * np.sin(w * (x - phi))

    @widgets.interact(w=(0, 10, 1),
                      amp=(0, 4, .1),
                      phi=(0, 2 * np.pi + 0.01, 0.01))
    def update(w=1.0, amp=1, phi=0):
        """Removes old lines from plot and plots new one."""
        [l.remove() for l in ax.lines]
        ax.plot(x, my_sine(x, w, amp, phi), color='C0')

Publishing Process

Stagnation

Ideas: distill.pub

preview_url(DISTILL, height=500)

Ideas: OpenReview

surrogate

Ideas: The Open Journals (The Journal of Open Source Software)

surrogate

Issues

  • Standalone tools

    • Not integrated

    • Lack of a dedicated process

  • Not covering the entire publishing process

    • Compose (write / revise)

    • Review (comment / rebut)

    • Publish (format / version)

Format Multiplicity

(Conference) Publishing


  • Manuscripts
  • Presentations
  • Posters
  • Promotional videos
  • Press releases
  • Blog posts
  • Source code
  • Computational examples
  • ...
  • Reviews
  • Revisions
  • Versions

Source Formats

  • \(\LaTeX\) documents and Beamer slides

  • Microsoft Word / OpenOffice Writer / Google Docs

  • Microsoft PowerPoint / OpenOffice Impress / Google Slides

  • Markdown / HTML (and other web technologies such as JavaScript)

  • Code hosted on Dropbox / GitHub / BitBucket

  • Jupyter Notebooks / CodaLab documents

Multiple (out-of-sync) copies of the same content in different formats

Lowest Common Denominator: Static Outputs and Artefacts

Artefacts reusability:

  • visualisations / figures

  • tables

  • code snippets

  • mathematical typesetting

enforces their simplest – often static – type

Towards Online and Interactive Research Outputs

Authoring

Multiple Entry Points – Single Source

MyST Markdown →

  • Jupyter Notebook – computational narrative
    • Google Colab
    • MyBinder
  • Reveal.JS – interactive slides
  • Jupyter Book – interactive report/document/book

Version-controlled Environment

  • Source versioning and history tracking
  • E.g., git or mercurial

Reviewing

  • Akin to source code review, e.g., through Issues and Pull Requests infrastructure
  • Permanently attached to the document source
    • Provenance record
    • Resubmission history
  • Conversational review with inline comments and discussions
surrogate

Publishing

  • Tag a version

  • Release to an archiving platform

Bibliometrics

  • DOI minting (e.g., Zenodo) to support citations

  • Google Analytics-like dissemination tracking

Presenting

  • Three formats: documents, slides and computational notebooks

  • Native interactivity support

  • Improved accessibility

    • Execute directly in the browser – no need to install stuff

    • Support for web-enabled assistive technologies

  • Web technologies are the limit

interactive_plot()

The Way Forward

  • Extend the Jupyter Book / Sphinx plugin ecosystem

    • Support non-mainstream programming languages (SWI Prolog, ProbLog and cplint)

    • Linked exercise and solution blocks

    • Custom code syntax highlighting

  • Bespoke publishing lifecycle platform (instead of GitHub or BitBucket)

  • Compute resources suitable for hosting and executing the (interactive) content

Horizon 2020 ICT-48 European AI excellence centre exploring new ways of working and AI-powered research and collaboration tools.

Exhibit

Source

surrogate

Preview

preview_url(YOU_ONLY_WRITE_THRICE, height=500)

Thank You!




K.Sokol@bristol.ac.uk