docs: add AngieHinrichs as a contributor for code

.all-contributorsrc

@@ -26,7 +26,8 @@
       "profile": "http://genome.ucsc.edu/",
       "contributions": [
         "ideas",
-        "data"
+        "data",
+        "code"
       ]
     }
   ],
@@ -35,5 +36,7 @@
   "projectOwner": "theosanderson",
   "repoType": "github",
   "repoHost": "https://github.com",
-  "skipCi": true
+  "skipCi": true,
+  "commitType": "docs",
+  "commitConvention": "angular"
 }

README.md

@@ -1,17 +1,16 @@
 # Taxonium
-<!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->
-[![All Contributors](https://img.shields.io/badge/all_contributors-2-orange.svg?style=flat-square)](#contributors-)
-<!-- ALL-CONTRIBUTORS-BADGE:END -->
 
-Taxonium is a tool for exploring trees.
+[![Published in eLife](https://img.shields.io/badge/Published%20in-eLife-blue.svg)](https://elifesciences.org/articles/82392) <!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->[![All Contributors](https://img.shields.io/badge/All_contributors-7-orange.svg?style=flat-square)](#contributors-)<!-- ALL-CONTRIBUTORS-BADGE:END -->
 
-<p align="center"><a href="https://taxonium.org"><img src="https://user-images.githubusercontent.com/19732295/169698808-48204d73-c468-4e80-aff5-876e5df7eab4.png" width=250 /></a></p>
+Taxonium is a tool for exploring trees, including those with millions of nodes.
+
+<!--<p align="center"><a href="https://taxonium.org"><img src="https://user-images.githubusercontent.com/19732295/169698808-48204d73-c468-4e80-aff5-876e5df7eab4.png" width=250 /></a></p>-->
 
 ### [➡️ Launch Taxonium](https://taxonium.org)
 
 ### [📚 Consult the documentation](https://taxonium.readthedocs.io/en/latest/)
 
-### [📝 Read the preprint](https://www.biorxiv.org/content/10.1101/2022.06.03.494608v1)
+### [📝 Read the paper](https://elifesciences.org/articles/82392)
 
 ## How do I..
 
@@ -21,59 +20,87 @@ Upload a Newick file to [Taxonium.org](http://taxonium.org), and optionally a me
 
 ### explore the global SARS-CoV-2 phylogeny?
 
-Visit [Cov2Tree.org](http://Cov2Tree.org) which uses Taxonium to allow you to explore a tree built by researchers at UCSC using public data contributed by researchers across the world to the INSDC databases.
+Visit [Cov2Tree.org](http://Cov2Tree.org) which uses Taxonium to allow you to explore a tree built by [researchers at UCSC](http://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/UShER_SARS-CoV-2/) using public data contributed by researchers across the world to the INSDC databases.
 
 ### build my own mutation-annotated tree to explore in Taxonium, or add my own metadata to an existing phylogeny?
 
 Use [UShER](https://github.com/yatisht/usher/) to build a mutation-annotated tree. Then use [taxoniumtools](./taxoniumtools/) to convert it to a Taxonium format you can upload to the interface at [Taxonium.org](Taxonium.org)
 
-You can also use taxoniumtools to add your own metadata to the existing public phylogeny.
+You can also use taxoniumtools to add your own metadata to [the existing public phylogeny](https://hgwdev.gi.ucsc.edu/~angie/UShER_SARS-CoV-2/).
 
 Find out more in [📚 the documentation](https://taxonium.readthedocs.io/en/latest/).
 
-## Structure
+### load really huge trees?
 
-Taxonium now consists of a number of components:
+For trees larger than about 6M tips, loading local trees in the browser at Taxonium.org can be unreliable on some systems due to browser memory limitations. To avoid these issues, use the [Taxonium desktop app](https://docs.taxonium.org/en/latest/app.html).
 
-- [taxoniumtools](./taxoniumtools/) - a Python package that lets you easily generate Taxonium files from Usher protobuf files
-- [taxonium_web_client](./taxonium_web_client/) - the web client that is available at e.g. taxonium.org and let's you explore Taxonium files in your browser
-- [taxonium_backend](./taxonium_backend/) - a server-based backend that allows Taxonium trees to be explored without the user downloading the full tree (N.B. Taxonium can also be used without this backend, with static files acccessed in taxonium_web_client)
-- [taxonium_data_handling](./taxonium_data_handling/) - this is a node package upon which both the web client and the backend depend (it handles core logic common to both)
+### use Taxonium in my own web application?
+
+Use the [Taxonium component](./taxonium_component).
 
 ## See Taxonium in action
 
-- [Cov2Tree](https://cov2tree.org/)
+- [Cov2Tree](https://cov2tree.org/) - (the repo that runs this is [here](https://github.com/theosanderson/cov2tree))
 - [Exploring the NCBI Taxonomy](https://taxonium.org/?treeUrl=https%3A%2F%2Fcov2tree.nyc3.digitaloceanspaces.com%2Fncbi%2Ftree.nwk.gz&ladderizeTree=true&metaUrl=https%3A%2F%2Fcov2tree.nyc3.digitaloceanspaces.com%2Fncbi%2Fmetadata.tsv.gz&configUrl=https%3A%2F%2Fcov2tree.nyc3.digitaloceanspaces.com%2Fncbi%2Fconfig.json)
 - [Serratus](https://serratus.io/trees) (click Tree Viewer on any tree)
-- [mpxTree](http://mpxtree.taxonium.org/)
 
-## Contributors
+## Citing Taxonium
+
+```
+Sanderson, T (2022). Taxonium, a web-based tool for exploring large phylogenetic trees. eLife, 11:e82392
+https://doi.org/10.7554/eLife.82392
+```
 
-Taxonium is built and maintained by Theo Sanderson at the Francis Crick Institute.
+N.B. If you are citing the _tree_ displayed at Cov2Tree.org, please cite [the UCSC tree](https://pubmed.ncbi.nlm.nih.gov/34469548/) (.. and ideally Taxonium too if you relied on it for exploration)
+
+There is a separate [paper](https://academic.oup.com/bioinformatics/article/39/1/btac772/6858450) for the Treenome Browser feature (Kramer et al., Bioinformatics, 2022).
+
+## Structure
+
+Taxonium is structured as a 'monorepo' containing a number of components:
+
+- [taxoniumtools](./taxoniumtools/) - a Python package that lets you easily generate Taxonium files from Usher protobuf files
+- [taxonium_component](./taxonium_component/) - a React component that implements the Taxonium tree explorer
+- [taxonium_website](./taxonium_website/) - The Taxonium website found at [Taxonium.org](https://taxonium.org), a wrapper around taxonium_component
+- [taxonium_backend](./taxonium_backend/) - a server-based backend that allows Taxonium trees to be explored without the user downloading the full tree (N.B. Taxonium can also be used without this backend, with static files acccessed in taxonium_website)
+- [taxonium_data_handling](./taxonium_data_handling/) - this is a node package upon which both the web client and the backend depend (it handles core logic common to both)
+
+## Contributing
+
+We welcome [contributions](CONTRIBUTING.md). We require that that all contributors follow [the Contributor Covenant Code of Conduct](https://github.com/theosanderson/genomium/blob/main/CODE_OF_CONDUCT.md).
+
+### Contributors
+
+Taxonium development was initiated and is led by Theo Sanderson at the Francis Crick Institute.
 
 <table>
   <tr>
     <td align="center"><a href="http://theo.io"><img src="https://avatars.githubusercontent.com/u/19732295?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Theo Sanderson</b></sub></a><br /><a href="https://github.com/theosanderson/taxonium/commits?author=theosanderson" title="Code">💻</a> <a href="https://github.com/theosanderson/taxonium/commits?author=theosanderson" title="Documentation">📖</a> <a href="#design-theosanderson" title="Design">🎨</a> <a href="#ideas-theosanderson" title="Ideas, Planning, & Feedback">🤔</a> <a href="#infra-theosanderson" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="#maintenance-theosanderson" title="Maintenance">🚧</a></td>
   </tr>
 </table>
 
-
 We are very grateful to our contributors:
 
 <!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section -->
 <!-- prettier-ignore-start -->
 <!-- markdownlint-disable -->
 <table>
-  <tr>
-    <td align="center"><a href="http://theo.io"><img src="https://avatars.githubusercontent.com/u/19732295?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Theo Sanderson</b></sub></a><br /><a href="https://github.com/theosanderson/taxonium/commits?author=theosanderson" title="Code">💻</a> <a href="https://github.com/theosanderson/taxonium/commits?author=theosanderson" title="Documentation">📖</a> <a href="#design-theosanderson" title="Design">🎨</a> <a href="#ideas-theosanderson" title="Ideas, Planning, & Feedback">🤔</a> <a href="#infra-theosanderson" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="#maintenance-theosanderson" title="Maintenance">🚧</a></td>
-    <td align="center"><a href="http://genome.ucsc.edu/"><img src="https://avatars.githubusercontent.com/u/186983?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Angie Hinrichs</b></sub></a><br /><a href="#ideas-AngieHinrichs" title="Ideas, Planning, & Feedback">🤔</a> <a href="#data-AngieHinrichs" title="Data">🔣</a></td>
-  </tr>
+  <tbody>
+    <tr>
+      <td align="center"><a href="https://github.com/amkram"><img src="https://avatars.githubusercontent.com/u/6502785?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Alex Kramer</b></sub></a><br /><a href="https://github.com/theosanderson/taxonium/commits?author=amkram" title="Code">💻</a> <a href="#design-amkram" title="Design">🎨</a> <a href="#ideas-amkram" title="Ideas, Planning, & Feedback">🤔</a></td>
+      <td align="center"><a href="http://genome.ucsc.edu/"><img src="https://avatars.githubusercontent.com/u/186983?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Angie Hinrichs</b></sub></a><br /><a href="#ideas-AngieHinrichs" title="Ideas, Planning, & Feedback">🤔</a> <a href="#data-AngieHinrichs" title="Data">🔣</a> <a href="https://github.com/theosanderson/taxonium/commits?author=angiehinrichs" title="Code">💻</a></td>
+      <td align="center"><a href="https://github.com/richardgoater"><img src="https://avatars.githubusercontent.com/u/1429721?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Richard Goater</b></sub></a><br /><a href="#design-richardgoater" title="Design">🎨</a> <a href="https://github.com/theosanderson/taxonium/commits?author=richardgoater" title="Code">💻</a></td>
+      <td align="center"><a href="https://github.com/chaoran-chen"><img src="https://avatars.githubusercontent.com/u/18666552?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Chaoran Chen</b></sub></a><br /><a href="#ideas-chaoran-chen" title="Ideas, Planning, & Feedback">🤔</a></td>
+      <td align="center"><a href="https://github.com/corneliusroemer"><img src="https://avatars.githubusercontent.com/u/25161793?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Cornelius Roemer</b></sub></a><br /><a href="#ideas-corneliusroemer" title="Ideas, Planning, & Feedback">🤔</a></td>
+      <td align="center"><a href="https://github.com/sungyeonkwon"><img src="https://avatars.githubusercontent.com/u/25865179?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Sung Kwon</b></sub></a><br /><a href="#infra-sungyeonkwon" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a></td>
+      <td align="center"><a href="https://kvargha.com/"><img src="https://avatars.githubusercontent.com/u/35252220?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Koorous Vargha</b></sub></a><br /><a href="https://github.com/theosanderson/taxonium/commits?author=kvargha" title="Code">💻</a></td>
+    </tr>
+  </tbody>
 </table>
 
 <!-- markdownlint-restore -->
 <!-- prettier-ignore-end -->
 
 <!-- ALL-CONTRIBUTORS-LIST:END -->
 
-
-
+[Alex Kramer](https://corbett-lab.github.io/People/Current/alex/) at UCSC built the _Treenome Browser_ component within Taxonium, described [here](https://www.biorxiv.org/content/10.1101/2022.09.28.509985v1).