Reinventing the scholarly writing stack with the Manubot

[dhimmel]

Confused? New to Github? Visit the GitHub help page on our site for more information!

At a glance

• Submission Name: Continuous Publishing with the Manubot
• Contact Lead: @dhimmel ( Daniel Himmelstein <[email protected]>)
• External Site Link: https://github.com/greenelab/manubot-rootstock
• Region: Global
• Issue Area: OpenAccess, OpenResearch
• Issue Type: Project
• Types of Support Needed: Coding, GraphicDesign, Users

Description

The Manubot let's you write and continuously publish a manuscript on GitHub. Write in markdown and cite using just DOIs or other identifiers. Free yourself from antiquated or proprietary software such as Microsoft Word, LaTeX, EndNote, Mendeley, BibTeX, or MathType. While still young, the Manubot already powers the Deep Review (a massively collaborative review paper), the Sci-Hub Coverage Study, and has even reproduced the Bitcoin Whitepaper.

The Manubot aims to make scholarly publishing transparent, reproducible, and collaborative. It's an open source project and gratis to use. In a world of ever-increasing scholarly publishing costs, take a stand to show how publishing can be entirely free of charge, while also offering a superior user experience to existing journals. More details in these slides.

What are we working on during the do-a-thon? What kinds of support do we need?

At the do-a-thon, we will first help users setup new Manubot instance for their manuscripts. The setup process can be a bit technical, so this tutorial may be helpful for many users.

Next, attendees are encouraged to help improve the Manubot and contribute features they'd like to see. While the Manubot already supports tables, figures, equations, citation by identifiers, custom bibliographic styles, templating, timestamping, and more, there's still work needed to perfect the system and make it more user friendly as well as interoperable with the existing scholarly infrastructure.

Specifically expertise that's relevant for contributions is frontend or Python development, creating bots / automation, documentation writing, continuous integration, git / GitHub, Pandoc, publishing experience, and copyediting. If you have other skills, we can likely use them as well!

How can others contribute?

Try setting up your own manuscripts!

Specific issues for anyone looking for tasks are:

• diffing manuscripts: Creating a diff between two manuscript versions manubot/rootstock#54
• perfecting the bibliographic style: Creating a Manubot CSL that perfects the format of bibliographic entries manubot/rootstock#53
• archiving manuscripts and comments on GitHub: Archiving metadata (issues, pull request, etc.) manubot/rootstock#45
• measuring manuscript contribution: see Create Deep Review contribution visualization greenelab/meta-review#16
• automating the setup process and further automation in general
• improving the viewer or integrating with JATS-based viewers: Preliminary JATS XML output manubot/rootstock#82
• retrieve ISBN citation metadata: ISBN citation of books manubot/manubot#14
• retrieve legal citation metadata: Automatically generating JSON CSL (citation metadata) for legal cases manubot/manubot#1
• improving citation parsing: Do not extract or replace citation strings inside code or code_blocks manubot/manubot#13
• accept multiple paths/URLs with templating variables Specifying --template-variables-path multiple times manubot/manubot#18

This post is part of the OpenCon 2017 Do-A-Thon. Not sure what's going on? Head here.

[chartgerink]

Way to get the OpenCon feeling started early @dhimmel! :-)

[npscience]

Sign me up as a tester to get started with ManuBot @dhimmel!

[dhimmel]

Excited for the do-a-thon tomorrow. Attendees are encouraged to bring a laptop, so you can get involved and setup your own manuscripts. However, even if you don't have a laptop, your feedback will be appreciated!

[dhimmel]

One more note: You don't need to know Python or any other programming language to attend. If you write manuscripts / scholarly documents, then you are the target audience! You will likely get the most out of Manubot if you're computer-savvy, but we're looking for diverse feedback, so don't be shy.

[RaoOfPhysics]

@dhimmel: Do you know where you might be camping? I'll come find you.

[dhimmel]

Location

11:30: We will initially meet in Goethe (the main auditorium) at a table in the rear. Look for the Manubot table tent.

[RaoOfPhysics]

Added issues:

• Generic URL ––> archive.org persistent ID/URL ––> Manubot manubot/rootstock#85
• gh-publisher: lessons to learn? manubot/rootstock#86
• Autogenerate DOIs (with Zenodo?) based on releases/tags manubot/rootstock#87
• Setting up manubot-rootstock for GitLab with GitLab-CI manubot/rootstock#88
• Bake hypothesis into the HTML versions of the manuscripts manubot/rootstock#90

[dhimmel]

For new mansucript setup, see https://github.com/greenelab/manubot-rootstock/blob/master/SETUP.md.

Windows users, try Git Bash to enter to commands.

[broadwym]

https://broadwym.github.io/manu1/ (editing manuscript in-progress)

[schliebs]

Here is a link to the instances: https://github.com/schliebs/open_manuscript

[npscience]

Sorry I didn't get to this today! Genuinely want to know how this works / try it out, for obvious reasons. Is it possible to do this remotely another time please?

Thanks!!

[dhimmel]

Is it possible to do this remotely another time please?

Certainly! It's always possible, and we're trying to document the setup process, so most users won't need any in-person help. At the moment, things are a bit more complicated for Windows users... but macOS and Linux users should have an easier time. @npscience also happy to help you out or discuss the project more generally. Just drop me an email anytime.

[dhimmel]

2018 OpenCon Update

I won't be at OpenCon 2018 sadly, but attendees should feel free to contribute or experiment with Manubot as part of the Do-A-Thon.

For some more up-to-date information on the project, see

• the project manuscript titled Open collaborative writing with Manubot
• slides from FORCE2018

Some things Do-A-Thon attendees could do in 2018 (or future years):

• Set up a Manubot manuscript for their next paper (or migrate an existing paper to Manubot). We are especially interested in suggestions or pain points users experience.
• Look through open GitHub Issues and implement a solution or contribute a discussion. It may be a good idea to comment here if you're interested with your skillset and I can point you in the right direction.

Happy DO-ing!