Markdown Files#
Whether you write your book’s content in Jupyter Notebooks (.ipynb) or
in regular markdown files (.md), you’ll write in the same flavor of markdown
called MyST Markdown.
This is a simple file to help you get started and show off some syntax.
What is MyST?#
MyST stands for “Markedly Structured Text”. It is a slight variation on a flavor of markdown called “CommonMark” markdown, with small syntax extensions to allow you to write roles and directives in the Sphinx ecosystem.
For more about MyST, see the MyST Markdown Overview.
Sample Roles and Directives#
Roles and directives are two of the most powerful tools in Jupyter Book. They are kind of like functions, but written in a markup language. They both serve a similar purpose, but roles are written in one line, whereas directives span many lines. They both accept different kinds of inputs, and what they do with those inputs depends on the specific role or directive that is being called.
Here is a “note” directive:
Note
Here is a note
It will be rendered in a special box when you build your book.
Here is an inline directive to refer to a document: Notebooks with MyST Markdown.
Citations#
You can also cite references that are stored in a bibtex file. For example,
the following syntax: {cite}`holdgraf_evidence_2014` will render like
this: [].
Moreover, you can insert a bibliography into your page with this syntax:
The {bibliography} directive must be used for all the {cite} roles to
render properly.
For example, if the references for your book are stored in references.bib,
then the bibliography is inserted with:
Maël Balluet, Florian Sizaire, Youssef El Habouz, Thomas Walter, Jérémy Pont, Baptiste Giroux, Otmane Bouchareb, Marc Tramier, and Jacques Pecreaux. Neural network fast‐classifies biological images through features selecting to power automated microscopy. Journal of Microscopy, 285(1):3–19, November 2021. URL: http://dx.doi.org/10.1111/jmi.13062, doi:10.1111/jmi.13062.
Giulia Bertolin, Florian Sizaire, Claire Déméautis, Catherine Chapuis, Fabienne Mérola, Marie Erard, and Marc Tramier. Optimized fret pairs and quantification approaches to detect the activation of aurora kinase a at mitosis. ACS Sensors, 4(8):2018–2027, July 2019. URL: http://dx.doi.org/10.1021/acssensors.9b00486, doi:10.1021/acssensors.9b00486.
Julia Bonnet, Youssef El-Habouz, Célia Martin, Maelle Guillout, Louis Ruel, Baptiste Giroux, Claire Demeautis, Benjamin Mercat, Otmane Bouchareb, Jacques Pécreaux, and Marc Tramier. The roboscope: smart and fast microscopy for generic event-driven acquisition. bioRxiv, September 2024. URL: http://dx.doi.org/10.1101/2024.09.24.614735, doi:10.1101/2024.09.24.614735.
Claire Demeautis, François Sipieter, Julien Roul, Catherine Chapuis, Sergi Padilla-Parra, Franck B. Riquet, and Marc Tramier. Multiplexing pka and erk1&2 kinases fret biosensors in living cells using single excitation wavelength dual colour flim. Scientific Reports, January 2017. URL: http://dx.doi.org/10.1038/srep41026, doi:10.1038/srep41026.
Orestis Faklaris, Leslie Bancel-Vallée, Aurélien Dauphin, Baptiste Monterroso, Perrine Frère, David Geny, Tudor Manoliu, Sylvain de Rossi, Fabrice P. Cordelières, Damien Schapman, Roland Nitschke, Julien Cau, and Thomas Guilbert. Quality assessment in light microscopy for routine use through simple tools and robust metrics. Journal of Cell Biology, September 2022. URL: http://dx.doi.org/10.1083/jcb.202107093, doi:10.1083/jcb.202107093.
Max Heydasch, Lucien Hinderling, Jakobus van Unen, Maciej Dobrzynski, and Olivier Pertz. Gtpase activating protein dlc1 spatio-temporally regulates rho signaling. eLife, December 2023. URL: http://dx.doi.org/10.7554/eLife.90305.1, doi:10.7554/elife.90305.1.
Lucien Hinderling, Remo Hadorn, Moritz Kwasny, Joël Frei, Benjamin Grädel, Sacha Psalmon, Yannick Blum, Rémi Berthoz, Alex Landolt, Benjamin D. Towbin, Daniel Riveline, and Olivier Pertz. Teach your microscope how to print: low-cost and rapid-iteration microfabrication for biology. bioRxiv, February 2025. URL: http://dx.doi.org/10.1101/2025.02.20.639256, doi:10.1101/2025.02.20.639256.
Lucien Hinderling, Guillaume Witz, Roman Schwob, Ana Stojiljkovic, Maciej Dobrzynski, Mykhailo Vladymyrov, Joel Frei, Benjamin Graedel, Agne Frismantiene, and Olivier Pertz. Convpaint - universal framework for interactive pixel classification using pretrained neural networks. bioRxiv, September 2024. URL: http://dx.doi.org/10.1101/2024.09.12.610926, doi:10.1101/2024.09.12.610926.
Alexander Kirillov, Eric Mintun, Nikhila Ravi, Hanzi Mao, Chloe Rolland, Laura Gustafson, Tete Xiao, Spencer Whitehead, Alexander C. Berg, Wan-Yen Lo, Piotr Dollár, and Ross Girshick. Segment anything. 2023. URL: https://arxiv.org/abs/2304.02643, doi:10.48550/ARXIV.2304.02643.
David McFadden, Laszlo Barna, Luis-Francisco Acevedo-Hueso, Sergiy V Avilov, Gert-Jan Bakker, Sebastian Beer, Ivan Belyaev, Valeria Berno, Mariana T Carvalho, Yann Cesbron, Catalin Chiritescu, Orestis Faklaris, Nathalie Gaudreault, David Grunwald, Thomas Guilbert, Mathias Hammer, Rainer Heintzmann, Gerhard Holst, Ayse Aslihan Koksoy, Gabriel G Martins, Glyn Nelson, Roland Nitschke, Alex L Payne-Dwyer, Santosh Podder, Sathya Srinivasan, Kees van der Oord, Andre Zeug, and Britta Schroth-Diez. Characterization of the photon conversion factor, noise, and dynamic range of light microscope detection systems v1. protocols.io, September 2024. URL: http://dx.doi.org/10.17504/protocols.io.14egn61pyl5d/v1, doi:10.17504/protocols.io.14egn61pyl5d/v1.
Glyn Nelson, Ulrike Boehm, Steve Bagley, Peter Bajcsy, Johanna Bischof, Claire M. Brown, Aurélien Dauphin, Ian M. Dobbie, John E. Eriksson, Orestis Faklaris, Julia Fernandez‐Rodriguez, Alexia Ferrand, Laurent Gelman, Ali Gheisari, Hella Hartmann, Christian Kukat, Alex Laude, Miso Mitkovski, Sebastian Munck, Alison J. North, Tobias M. Rasse, Ute Resch‐Genger, Lucas C. Schuetz, Arne Seitz, Caterina Strambio‐De‐Castillia, Jason R. Swedlow, Ioannis Alexopoulos, Karin Aumayr, Sergiy Avilov, Gert‐Jan Bakker, Rodrigo R. Bammann, Andrea Bassi, Hannes Beckert, Sebastian Beer, Yury Belyaev, Jakob Bierwagen, Konstantin A. Birngruber, Manel Bosch, Juergen Breitlow, Lisa A. Cameron, Joe Chalfoun, James J. Chambers, Chieh‐Li Chen, Eduardo Conde‐Sousa, Alexander D. Corbett, Fabrice P. Cordelieres, Elaine Del Nery, Ralf Dietzel, Frank Eismann, Elnaz Fazeli, Andreas Felscher, Hans Fried, Nathalie Gaudreault, Wah Ing Goh, Thomas Guilbert, Roland Hadleigh, Peter Hemmerich, Gerhard A. Holst, Michelle S. Itano, Claudia B. Jaffe, Helena K. Jambor, Stuart C. Jarvis, Antje Keppler, David Kirchenbuechler, Marcel Kirchner, Norio Kobayashi, Gabriel Krens, Susanne Kunis, Judith Lacoste, Marco Marcello, Gabriel G. Martins, Daniel J. Metcalf, Claire A. Mitchell, Joshua Moore, Tobias Mueller, Michael S. Nelson, Stephen Ogg, Shuichi Onami, Alexandra L. Palmer, Perrine Paul‐Gilloteaux, Jaime A. Pimentel, Laure Plantard, Santosh Podder, Elton Rexhepaj, Arnaud Royon, Markku A. Saari, Damien Schapman, Vincent Schoonderwoert, Britta Schroth‐Diez, Stanley Schwartz, Michael Shaw, Martin Spitaler, Martin T. Stoeckl, Damir Sudar, Jeremie Teillon, Stefan Terjung, Roland Thuenauer, Christian D. Wilms, Graham D. Wright, and Roland Nitschke. Quarep‐limi: a community‐driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. Journal of Microscopy, 284(1):56–73, August 2021. URL: http://dx.doi.org/10.1111/jmi.13041, doi:10.1111/jmi.13041.
Dominik Niopek, Pierre Wehler, Julia Roensch, Roland Eils, and Barbara Di Ventura. Optogenetic control of nuclear protein export. Nature Communications, February 2016. URL: http://dx.doi.org/10.1038/ncomms10624, doi:10.1038/ncomms10624.
Katsuhiko Ogata. Modern control engineering. Pearson, Upper Saddle River, NJ, 4 edition, November 2001.
Josiah B. Passmore, Alfredo Rates, Jakob Schröder, Menno T. P. van Laarhoven, Vincent J. W. Hellebrekers, Henrik G. van Hoef, Antonius J. M. Geurts, Wendy van Straaten, Wilco Nijenhuis, Florian Berger, Carlas S. Smith, Ihor Smal, and Lukas C. Kapitein. Outcome-driven microscopy: closed-loop optogenetic control of cell biology. bioRxiv, December 2024. URL: http://dx.doi.org/10.1101/2024.12.12.628240, doi:10.1101/2024.12.12.628240.
Florian Sizaire, Gilles Le Marchand, Jacques Pécréaux, Otmane Bouchareb, and Marc Tramier. Automated screening of aurka activity based on a genetically encoded fret biosensor using fluorescence lifetime imaging microscopy. Methods and Applications in Fluorescence, 8(2):024006, February 2020. URL: http://dx.doi.org/10.1088/2050-6120/ab73f5, doi:10.1088/2050-6120/ab73f5.
Nicholas Sofroniew, Talley Lambert, Grzegorz Bokota, Juan Nunez-Iglesias, Peter Sobolewski, Andrew Sweet, Lorenzo Gaifas, Kira Evans, Alister Burt, Draga Doncila Pop, Kevin Yamauchi, Melissa Weber Mendonça, Genevieve Buckley, Wouter-Michiel Vierdag, Loic Royer, Ahmet Can Solak, Kyle I. S. Harrington, Jannis Ahlers, Daniel Althviz Moré, Oren Amsalem, Ashley Anderson, Andrew Annex, Peter Boone, Jordão Bragantini, Matthias Bussonnier, Clément Caporal, Jan Eglinger, Andreas Eisenbarth, Jeremy Freeman, Christoph Gohlke, Kabilar Gunalan, Hagai Har-Gil, Mark Harfouche, Volker Hilsenstein, Katherine Hutchings, Jessy Lauer, Gregor Lichtner, Ziyang Liu, Lucy Liu, Alan Lowe, Luca Marconato, Sean Martin, Abigail McGovern, Lukasz Migas, Nadalyn Miller, Hector Muñoz, Jan-Hendrik Müller, Christopher Nauroth-Kreß, David Palecek, Constantin Pape, Eric Perlman, Kim Pevey, Gonzalo Peña-Castellanos, Andrea Pierré, David Pinto, Jaime Rodríguez-Guerra, David Ross, Craig T. Russell, James Ryan, Gabriel Selzer, MB Smith, Paul Smith, Konstantin Sofiiuk, Johannes Soltwedel, David Stansby, Jules Vanaret, Pam Wadhwa, Martin Weigert, Jonas Windhager, Philip Winston, and Rubin Zhao. Napari: a multi-dimensional image viewer for python. 2025. URL: https://zenodo.org/doi/10.5281/zenodo.3555620, doi:10.5281/ZENODO.3555620.
Rémy Torro, Beatriz Díaz-Bello, Dalia El Arawi, Ksenija Dervanova, Lorna Ammer, Florian Dupuy, Patrick Chames, Kheya Sengupta, and Laurent Limozin. Celldetective: an ai-enhanced image analysis tool for unraveling dynamic cell interactions. eLife, March 2025. URL: http://dx.doi.org/10.7554/eLife.105302.1, doi:10.7554/elife.105302.1.
Learn more#
This is just a simple starter to get you started. You can learn a lot more at jupyterbook.org.