Search and transformation for human cells via latent space representations

Manuscript description

This repository holds an application in response to the Seed Networks for the Human Cell Atlas RFA from the Chan-Zuckerberg Initiative. Our team proposes to develop and disseminate methods and software that enable fast search over and transformation of cell profiles via latent space representations.

The RFA requests a set of documents. We note which ones are included here:

• Project Details:

  • Project Title (Included)
  • Full paper or preprint citations (with PubMed or bioRxiv links), GitHub repository links, data repositories, protocols.io submissions and/or similar documentation for up to five of the most significant contributions members of the Seed Network have made that are relevant to the proposal. (Included)
  • Abstract/Project Summary (250 words maximum). (Included)
  • List of Co-Principal Investigators and individual statements from each co-PI describing their specific contributions (up to 750 words total). (Co-PI's Discretion)

• Project Proposal including:

  • Abstract: Succinct description of the Seed Network research project (250 words maximum; can be the same as above in project details). (Included)
  • Proposal Body: (2000 words maximum) Should include two parts:
    • Scientific goals of the project: Define the scientific goals of your research, as well as the contribution to the wider HCA community and how the project will benefit from being a part of the Seed Networks. (Included)
    • Tools and resources : We are particularly interested in the tools, resources, and/or specific expertise that your group would like to develop or bring to the collaborative Seed Network projects, and the tools/resources that could be generated by other Seed Networks or CZI that would benefit your work. (Included)
  • Figures (optional): limited to one page, inclusive of legends. (Included)
  • References Cited in your proposal (no word/page limit). (Included)

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. The Manubot 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 the 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. For the CI configuration, see .travis.yml.

Local execution

To run the Manubot locally, install the conda environment as described in build. Then, you can build the manuscript on POSIX systems by running the following commands.

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

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

# Configure the webpage directory
python build/webpage.py

# View the manuscript locally at http://localhost:8000/
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 and webpage.py scripts upon content changes:

sh build/autobuild.sh

Continuous Integration

Whenever a pull request is opened, Travis CI 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 Travis 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), Travis 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/czi-seed-rfa/
• PDF manuscript at https://greenelab.github.io/czi-seed-rfa/manuscript.pdf

For continuous integration configuration details, see .travis.yml.

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/czi-seed-rfa.

Since CC BY is not ideal for code and data, certain repository components are also released under the CC0 1.0 public domain dedication (LICENSE-CC0.md). All files matched by the following glob patterns are dual licensed under CC BY 4.0 and CC0 1.0:

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

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

• *.md
• *.html
• *.pdf
• *.docx

Except for the following files with different licenses:

• build/assets/anchors.js which is released under an MIT License

Please open an issue for any question related to licensing.