Analysis of ISCB honorees and keynotes reveals disparities

Citation

This manuscript is now published at:

Analysis of scientific society honors reveals disparities Trang T Le, Daniel S Himmelstein, Ariel A Hippen, Matthew R Gazzara, Casey S Greene Cell Systems (2021-08) https://doi.org/gmhq49 DOI: 10.1016/j.cels.2021.07.007

Manuscript description

Professional societies and the conferences that they manage provide an important venue for the dissemination of scientific knowledge. Being invited to deliver a keynote at an international society meeting or named a fellow of such a society is a major recognition. We sought to understand the extent to which such recognitions reflected the composition of their corresponding field. We collected keynote speaker invitations for the international meetings held by the International Society for Computational Biology as well as the names of Fellows. We compared these individuals with last and corresponding author contributions in the society’s partner journals. We used multiple methods to estimate the gender and nationality of authors and the recipients of these honors. Individuals from certain ancestries and countries appear to be under-recognized among honorees.

Manubot

Manubot is a system for writing scholarly manuscripts via GitHub. Manubot automates citations and references, versions manuscripts using git, and enables collaborative writing via GitHub. An overview manuscript presents the benefits of collaborative writing with Manubot and its unique features. The rootstock repository is a general purpose template for creating new Manubot instances, as detailed in SETUP.md. See USAGE.md for documentation how to write a manuscript.

Please open an issue for questions related to Manubot usage, bug reports, or general inquiries.

Repository directories & files

The directories are as follows:

• content contains the manuscript source, which includes markdown files as well as inputs for citations and references. See USAGE.md for more information.
• output contains the outputs (generated files) from Manubot including the resulting manuscripts. You should not edit these files manually, because they will get overwritten.
• webpage is a directory meant to be rendered as a static webpage for viewing the HTML manuscript.
• build contains commands and tools for building the manuscript.
• ci contains files necessary for deployment via continuous integration.

Local execution

The easiest way to run Manubot is to use continuous integration to rebuild the manuscript when the content changes. If you want to build a Manubot manuscript locally, install the conda environment as described in build. Then, you can build the manuscript on POSIX systems by running the following commands from this root directory.

# Activate the manubot conda environment (assumes conda version >= 4.4)
conda activate manubot

# Build the manuscript, saving outputs to the output directory
bash build/build.sh

# At this point, the HTML & PDF outputs will have been created. The remaining
# commands are for serving the webpage to view the HTML manuscript locally.
# This is required to view local images in the HTML output.

# Configure the webpage directory
manubot webpage

# You can now open the manuscript webpage/index.html in a web browser.
# Alternatively, open a local webserver at http://localhost:8000/ with the
# following commands.
cd webpage
python -m http.server

Sometimes it's helpful to monitor the content directory and automatically rebuild the manuscript when a change is detected. The following command, while running, will trigger both the build.sh script and manubot webpage command upon content changes:

bash build/autobuild.sh

Continuous Integration

Whenever a pull request is opened, CI (continuous integration) will test whether the changes break the build process to generate a formatted manuscript. The build process aims to detect common errors, such as invalid citations. If your pull request build fails, see the CI logs for the cause of failure and revise your pull request accordingly.

When a commit to the master branch occurs (for example, when a pull request is merged), CI builds the manuscript and writes the results to the gh-pages and output branches.

The gh-pages branch uses GitHub Pages to host the following URLs:

• HTML manuscript at https://greenelab.github.io/iscb-diversity-manuscript/
• PDF manuscript at https://greenelab.github.io/iscb-diversity-manuscript/manuscript.pdf

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License

Except when noted otherwise, the entirety of this repository is licensed under a CC BY 4.0 License (LICENSE.md), which allows reuse with attribution. Please attribute by linking to https://github.com/greenelab/iscb-diversity-manuscript.

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• *.sh
• *.py
• *.yml / *.yaml
• *.json
• *.bib
• *.tsv
• .gitignore

All other files are only available under CC BY 4.0, including:

• *.md
• *.html
• *.pdf
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