index.html

---
layout: default
title: Manubot - Manuscripts, open and automated
description: A tool set and workflow for scholarly publishing that is open, collaborative, continuous, automated, reproducible, and free.
keywords: scholarly, publishing, publisher, manuscript, document, academic, education, open, collaborative, reproducible, free, edit, collaborate, ideas, version control, code, writing, automatic, digital, interactive, print, fair, hackable
logo: logo.svg
header: Manubot
subheader: Manuscripts, open and automated.
---

<section>
  <div class="row">
    <p>
      <span class="semibold"
        >Manubot is a workflow and set of tools for the next generation of
        scholarly publishing.</span
      >
      Write your manuscript in
      <a href="https://www.markdownguide.org/">markdown</a>, track it with
      <a href="https://git-scm.com/">git</a>, automatically convert it to
      <code>.html</code>, <code>.pdf</code>, or <code>.docx</code>, and deploy
      it to your <a href="https://pages.github.com/">destination</a> of choice.
    </p>
  </div>
  <div class="row">
    <a href="/docs/getting-started.html" class="button_link">
      <i class="fas fa-graduation-cap"></i>
      Get Started
    </a>
    <a href="https://github.com/manubot" class="button_link">
      <i class="fab fa-lg fa-github"></i>
      On GitHub
    </a>
  </div>
</section>
<section id="how-it-works">
  <h3>How It Works</h3>
  <div class="row workflow_row">
    <figure class="workflow_figure">
      <img src="images/step1.png" class="workflow_image" />
      <figcaption>input <code>markdown</code></figcaption>
    </figure>
    <div class="workflow_arrow">
      <i class="fas fa-long-arrow-alt-right fa-lg"></i>
    </div>
    <figure class="workflow_figure">
      <img src="images/step2.png" class="workflow_image" />
      <figcaption>
        process w/ Manubot tools and
        <a href="https://pandoc.org/">Pandoc</a>
      </figcaption>
    </figure>
    <div class="workflow_arrow">
      <i class="fas fa-long-arrow-alt-right fa-lg"></i>
    </div>
    <figure class="workflow_figure">
      <img src="images/step3.png" class="workflow_image" />
      <figcaption>
        output <code>.html</code>, <code>.pdf</code>, <code>.docx</code>
      </figcaption>
    </figure>
    <div class="workflow_arrow">
      <i class="fas fa-long-arrow-alt-right fa-lg"></i>
    </div>
    <figure class="workflow_figure">
      <img src="images/step4.png" class="workflow_image" />
      <figcaption>test and deploy</figcaption>
    </figure>
  </div>
</section>
<section id="the-best-parts">
  <h3>The Best Parts</h3>
  <div class="row">
    <div class="col_text">
      <h4><i class="fas fa-atlas fa-lg"></i> Open, collaborative, versioned</h4>
      <p>
        Author your manuscript the open-source way. Let anyone propose changes.
        <a href="https://greenelab.github.io/meta-review/#fig:workflow"
          >Iteratively</a
        >
        review, discuss, and refine with collaborators. Coordinate teams of
        <a href="https://greenelab.github.io/meta-review/#fig:contrib"
          >any size</a
        >
        with ease. Keep track of versions, to-dos, revisions, and who wrote what
        and when. All in a
        <a href="https://github.com/">central location</a>.
      </p>
    </div>
    <div class="col_image">
      <div class="feature_tile slideshow">
        <img src="images/open-1.png" />
        <img src="images/open-2.png" />
        <img src="images/open-3.png" />
      </div>
    </div>
  </div>
  <div class="row">
    <div class="col_image">
      <div class="feature_tile slideshow">
        <img src="images/automated-1.png" />
        <img src="images/automated-2.png" />
        <img src="images/automated-3.png" />
      </div>
    </div>
    <div class="col_text">
      <h4><i class="fas fa-magic fa-lg"></i> Automated and continuous</h4>
      <p>
        Never use a reference manager again. Provide a DOI, ISBN, PubMed ID,
        URL, etc., and let Manubot generate and number citations for you. Choose
        from <a href="https://www.zotero.org/styles">thousands</a> of existing
        <a title="Citation Style Language" href="https://citationstyles.org/"
          >citation styles</a
        >. See your manuscript update right away as you make changes. Test and
        deploy automatically with
        <a href="https://travis-ci.org/">continuous integration</a>.
      </p>
    </div>
  </div>
  <div class="row">
    <div class="col_text">
      <h4>
        <i class="fas fa-hand-point-up fa-lg"></i> Beautiful and interactive
      </h4>
      <p>
        Static is out, dynamic is in. The contemporary look and interactive
        features people have come to love and expect from modern webpages, now
        applied to scholarly articles: tooltips, public annotations, table of
        contents, figure viewer, and more.
      </p>
    </div>
    <div class="col_image">
      <div class="feature_tile slideshow">
        <img src="images/interactive-1.png" />
        <img src="images/interactive-2.png" />
        <img src="images/interactive-3.png" />
      </div>
    </div>
  </div>
  <div class="row">
    <div class="col_image">
      <div class="feature_tile slideshow">
        <img src="images/free-1.png" />
        <img src="images/free-2.png" />
        <img src="images/free-3.png" />
      </div>
    </div>
    <div class="col_text">
      <h4><i class="fas fa-lock-open fa-lg"></i> Free and open-source</h4>
      <p>
        There's no need to pay to produce brilliant manuscripts. Manubot is free
        and open-source (aside from optional workflow integration with
        <a href="http://github.com/">GitHub</a> and
        <a href="https://travis-ci.org/">Travis CI</a>). Its tools are developed
        and supported by a community of responsive and passionate software
        developers and researchers.
      </p>
    </div>
  </div>
</section>
<section id="made-with-manubot">
  <h3>
    Made With Manubot
  </h3>
  <div class="row">
    {% assign papers = site.data.catalog | sort: "manubot.date_iso" | reverse %}
    <div class="catalog_tile slideshow">
      {% for paper in papers %} {% assign index = forloop.index | modulo: 4 %}
      {% if index == 0 and paper.manubot.thumbnail_url %}
      <div class="catalog_tile_item">
        <img
          class="catalog_tile_image"
          data-src="{{ paper.manubot.thumbnail_url }}"
        />
        <div class="catalog_tile_caption">
          <a href="{{ paper.manubot.url }}">
            <i class="fas fa-scroll fa-sm"></i
            >{{ paper.manubot.title }}
          </a>
        </div>
      </div>
      {% endif %}{% endfor %}
    </div>
    <div class="catalog_tile slideshow">
      {% for paper in papers %}{% assign index = forloop.index | modulo: 4 %} {%
      if index == 1 and paper.manubot.thumbnail_url %}
      <div class="catalog_tile_item">
        <img
          class="catalog_tile_image"
          data-src="{{ paper.manubot.thumbnail_url }}"
        />
        <div class="catalog_tile_caption">
          <a href="{{ paper.manubot.url }}">
            <i class="fas fa-scroll fa-sm"></i
            >{{ paper.manubot.title }}
          </a>
        </div>
      </div>
      {% endif %}{% endfor %}
    </div>
    <div class="catalog_tile slideshow">
      {% for paper in papers %} {% assign index = forloop.index | modulo: 4 %}
      {% if index == 2 and paper.manubot.thumbnail_url %}
      <div class="catalog_tile_item">
        <img
          class="catalog_tile_image"
          data-src="{{ paper.manubot.thumbnail_url }}"
        />
        <div class="catalog_tile_caption">
          <a href="{{ paper.manubot.url }}">
            <i class="fas fa-scroll fa-sm"></i
            >{{ paper.manubot.title }}
          </a>
        </div>
      </div>
      {% endif %}{% endfor %}
    </div>
    <div class="catalog_tile slideshow">
      {% for paper in papers %} {% assign index = forloop.index | modulo: 4 %}
      {% if index == 3 and paper.manubot.thumbnail_url %}
      <div class="catalog_tile_item">
        <img
          class="catalog_tile_image"
          data-src="{{ paper.manubot.thumbnail_url }}"
        />
        <div class="catalog_tile_caption">
          <a href="{{ paper.manubot.url }}">
            <i class="fas fa-scroll fa-sm"></i
            >{{ paper.manubot.title }}
          </a>
        </div>
      </div>
      {% endif %}{% endfor %}
    </div>
  </div>
  <div class="row">
    <a href="/catalog" class="button_link">
      <i class="fas fa-book-open fa-lg"></i> Catalog
    </a>
  </div>
</section>
<section id="our-philosophy">
  <h3>
    Our Philosophy
  </h3>
  <div class="row">
    <p>
      Manuscripts are the primary basis of scholarly communication, yet the
      process of creating them has not kept in step with the advancement of
      technology or the evolving best-practices of science.
    </p>
    <p>
      Traditionally, authoring of manuscripts takes place in a closed manner.
      While most scientific material is eventually distributed to some kind of
      public medium, the process of developing and reviewing the material is
      usually done in private, contained to a handful of individuals. The tools
      used are often outmoded, restrictive, and overall poorly-suited for the
      task of collaborative, scientific writing. The time it takes to review and
      publish can be
      <a
        href="https://www.nature.com/news/does-it-take-too-long-to-publish-research-1.19320"
        >unreasonably long</a
      >.
    </p>
    <p>
      We believe that this process is antiquated and must be reformed. Good
      science depends upon many things that the conventional approach doesn't
      provide: A diversity of input and perspectives. Spontaneous and
      cross-discipline contributions. Organic and wide-spread discovery and
      dissemination of knowledge. The fostering of a free, global information
      commons. A method of real-time, continuous science, performed entirely in
      the open.
    </p>
    <p>
      Current technology easily affords huge advantages over the old way of
      doing things, both in convenience and in the quality of the result.
      Manubot is a solution to the past and a push towards a future ideal, where
      scientific writing is transparent, reproducible, immediate,
      permissionless, versioned, automated, collaborative, open, linked,
      provenanced, decentralized, hackable, interactive, annotated, and free of
      charge.
    </p>
  </div>
</section>
<section id="cite-manubot">
  <h3>
    Cite Manubot
  </h3>
  <div class="row">
    <p>
      To reference the Manubot project, you can cite the following software
      paper (AKA the "Meta Review") describing the functionality and benefits of
      Manubot:
    </p>
  </div>
  <div class="row">
    <div class="banner_box">
      <b>Open collaborative writing with Manubot</b><br />
      Daniel S. Himmelstein, Vincent Rubinetti, David R. Slochower, Dongbo Hu,
      Venkat S. Malladi, Casey S. Greene, Anthony Gitter<br />
      <i>PLOS Computational Biology</i> (2019-06-24)
      <a href="https://doi.org/c7np">https://doi.org/c7np</a><br />
      DOI:
      <a href="https://doi.org/10.1371/journal.pcbi.1007128"
        >10.1371/journal.pcbi.1007128</a
      >
      · PMID:
      <a href="https://www.ncbi.nlm.nih.gov/pubmed/31233491">31233491</a>
    </div>
    <p>
      Take a look at the
      <a href="https://greenelab.github.io/meta-review/"
        >Manubot version of the paper</a
      >
      and its
      <a href="https://github.com/greenelab/meta-review">source code</a>.
    </p>
  </div>
</section>
<section id="acknowledgements">
  <h3>
    Acknowledgements
  </h3>
  <div class="row">
    <figure>
      <a href="https://sloan.org/"
        ><img src="images/alfred-p-sloan-foundation.png" height="60px"
      /></a>
      <figcaption>
        <a href="https://sloan.org/grant-detail/8501">Grant G-2018-11163</a>
      </figcaption>
    </figure>
    <figure>
      <a href="https://www.moore.org/"
        ><img src="images/gordon-betty-moore-foundation.png" height="60px"
      /></a>
      <figcaption>
        <a href="https://www.moore.org/grant-detail?grantId=GBMF4552"
          >Grant GBMF4552</a
        >
      </figcaption>
    </figure>
  </div>
  <div class="row">
    <figure>
      <a href="https://github.com/dhimmel"
        ><img
          src="images/daniel-himmelstein.png"
          class="acknowledgement_image"
          height="170px"
      /></a>
      <figcaption>
        <span class="semibold">Daniel Himmelstein</span><br />
        <a href="http://www.greenelab.com/">Greene Lab</a><br />
        <a href="https://www.upenn.edu/">Univ. of Pennsylvania</a>
      </figcaption>
    </figure>
    <figure>
      <a href="https://github.com/agitter"
        ><img
          src="images/anthony-gitter.png"
          class="acknowledgement_image"
          height="170px"
      /></a>
      <figcaption>
        <span class="semibold">Anthony Gitter</span><br />
        <a href="https://morgridge.org/research/virology/gitter-lab/"
          >Morgridge Institute</a
        ><br />
        <a href="https://www.biostat.wisc.edu/~gitter/"
          >Univ. of Wisconsin-Madison</a
        >
      </figcaption>
    </figure>
  </div>
  <div class="row">
    <p>
      As an open source project, Manubot relies on a community of maintainers,
      contributors, and users. For a list of all the individuals who have made
      Manubot possible, see
      <a href="https://github.com/manubot/rootstock/graphs/contributors"
        >the contributors on GitHub</a
      >
      and
      <a href="https://greenelab.github.io/meta-review/"
        >the authors and acknowledgements here</a
      >.
    </p>
  </div>
</section>
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