CompBioTeam Website

Testing the website

With Nix (recommended)

The repository ships a flake that pins the whole toolchain. Run

nix run .#serve

to install all dependencies and serve the site at http://localhost:8080 with live reload.

Maintainers: after changing dependencies (package.json / package-lock.json), refresh the dependency hash in flake.nix:

nix run nixpkgs#prefetch-npm-deps -- package-lock.json

and paste the printed hash into npmDepsHash. To pick up newer package versions from nixpkgs, run nix flake update.

Without Nix

You will need Node.js 22 and to install the 11ty package from here. Ensure that installation is a local install and not a global install. Once the packages have been installed, you can deploy the website locally on your machine using:

npm ci
npx @11ty/eleventy --serve

Please refer the documentation for more information.

Instructions to students/alumni/collaborators

All students are required to only add information to the _data directory and to not edit files in any other files in the repository. Everything there is hand-edited: team and project data as JSON, publications as BibTeX (see below). You should fill in the students_ms.json or the students_phd.json files with your information as in individual entry in the members array. For collaborators, the relevant file is colab.json. You are required to add the link to your isu profile. Each entry to the json file looks like:

{
  "name": "",
  "photo": "",
  "info": "",
  "website": "",
  "email": "",
  "interests": "[""]",
  "about": "",
  "github": "#"
}

You are required to upload a profile pic to the assets/images/team/ directory as well and mention only the file name in the json entry.

Home Page

The homepage template is in index.md. In order to change the homepage, you can simply edit the text in the homepage at the index.md file. Be careful to not alter any import section on any of the template files

Home Page Carousel

To change the hompage carousel, please replace the image you want in place of one of the existing images. The new image must use the same name as the one it is replacing. Only four images will display in the carousel.

Projects

If you would like to list your projects on the ASL website, you can add the link to the codebase on github in the projects.json in the _data. Each entry to the json file looks like:

{
  "name": "",
  "photo": "",
  "github": "",
  "website": "",
  "about": ""
}

You are required to upload a profile pic to the assets/images/projects/ directory as well and mention only the file name in the json entry.

photo and website are both optional. If the project has a deployed page (like but not necessarily GitHub Pages, usually https://<owner>.github.io/<repo>/) put its URL in website and a Website button appears at the bottom right of the card, beside the GitHub button. Leave the field out and no button renders.

Publications

Lab publications are listed in _data/pubs.bib.

@article{markin2022rf,
  title = {RF-Net 2: fast inference of virus reassortment and hybridization networks},
  author = {Markin, Alexey and Wagle, Sanket and Anderson, Tavis K and Eulenstein, Oliver},
  year = {2022},
  journal = {Bioinformatics},
  volume = {38},
  number = {8},
  pages = {2144--2152},
  url = {https://doi.org/10.1093/bioinformatics/btac075}
}

Preprints are detected automatically and shown in their own section above the year-by-year list. An entry counts as a preprint if it is on bioRxiv/medRxiv/arXiv. Alternatively, add keywords = {preprint} to the .bib entry to force it.

@article{smith2026something,
  title = {A Preprint About Supertrees},
  author = {Smith, Jane and Eulenstein, Oliver},
  year = {2026},
  journal = {bioRxiv},
  doi = {10.1101/2026.01.15.123456}
}

To check your work before committing, run

nix run .#bib -- check

to identify missing titles/years/authors, duplicate cite keys, and author fields that look like several names crammed together. nix run .#bib -- to-json prints the data exactly as the site will render it.