# How this site is made

> Static pages, a little JavaScript where it earns its place, open data, and illustrations drawn from scratch.

Source: https://khushisingh.in/colophon/
Author: Khushi Singh (khushisingh.in). Licence: CC BY 4.0 for text and original illustrations, unless a credit says otherwise.
Evidence labels used on this site: established, strong evidence, emerging, hypothesis, debated. Where a page has Simple, Curious and Expert versions, all three follow.

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Colophon

## Principles

- **Truth before glow.** Scientific claims carry evidence labels and references. Hypotheses are labelled as hypotheses.
- **No lab data.** This site shows research *context* only. It never shows unpublished results, lab images or anyone’s private data.
- **Open data.** Visuals are built from open sources (e.g. Protein Data Bank structures, FlyBase, PubMed) or drawn from scratch, with credits.
- **Fast and light.** Pages are plain HTML. Heavy 3D models load only when you ask for them.
- **Private by design.** No cookies, no trackers, no third-party fonts or embeds. The one exception is the [AlphaFold explorer](https://khushisingh.in/tools/alphafold/), which fetches live data from AlphaFold DB and UniProt (plus PDBe and the EBI Proteins API on request) only when you use it ([details](https://khushisingh.in/privacy/#alphafold-explorer)).
- **Readable by people and machines.** Every page has structured data (schema.org) and a plain markdown copy (add `.md` to its address), and AI assistants get a map of the site at [/llms.txt](https://khushisingh.in/llms.txt). Search engines and AI crawlers are welcome; the text is CC BY 4.0.

## Built with

- [Astro](https://astro.build/) (static site), [Svelte](https://svelte.dev/) (interactive islands) and [Tailwind CSS](https://tailwindcss.com/)
- [<model-viewer>](https://modelviewer.dev/) and [three.js](https://threejs.org/) for 3D and augmented reality
- [D3](https://d3js.org/) for charts, drawn at build time so they need no JavaScript
- [Pagefind](https://pagefind.app/) for private, static search
- Live protein data from [AlphaFold DB](https://alphafold.ebi.ac.uk/) (including AlphaMissense) and [UniProt](https://www.uniprot.org/), with experimental structures from [PDBe](https://www.ebi.ac.uk/pdbe/) and reported variants from the [EBI Proteins API](https://www.ebi.ac.uk/proteins/api/doc/), analysed and drawn in your browser
- The [ESM-2](https://github.com/facebookresearch/esm) protein language model (Meta AI, MIT licence), run on your device with [ONNX Runtime Web](https://onnxruntime.ai/) (MIT)
- [UTIF.js](https://github.com/photopea/UTIF.js) (MIT) for reading microscope TIFF images in the browser
- The [tools](https://khushisingh.in/tools/) are written for this site and run on your device: the Image lab follows ImageJ’s definitions and exports ImageJ macros, the statistics are checked against R, and the primer Tm against Biopython
- Typefaces: [Fraunces](https://fonts.google.com/specimen/Fraunces), Atkinson Hyperlegible Next & Mono (Braille Institute), Mukta and Tiro Devanagari Hindi, all self-hosted

## Data and image credits

Every visual credits its own sources on its page. The Image lab demo images come from the [Broad Bioimage Benchmark Collection](https://bbbc.broadinstitute.org/) (BBBC022 and BBBC039, CC0), and the sequence demo is the GFP mRNA (ENA M62653). Molecular structures come from the [RCSB Protein Data Bank](https://www.rcsb.org/) (data CC0). Gene-expression data come from [FlyBase](https://flybase.org/) (CC BY 4.0). Publication counts come from [PubMed](https://pubmed.ncbi.nlm.nih.gov/) via NCBI E-utilities.

## Use of AI

Parts of this site were drafted with AI assistance and reviewed by me; all scientific claims are checked against cited sources. No AI-generated images or data are used. Illustrations are drawn by hand in code or generated from real, cited data.

## Colour and accessibility

Text colours meet WCAG 2.2 AA contrast in both themes. Charts use colour-blind-safe palettes (Okabe–Ito, viridis), and fluorescence-style art can be re-coloured for colour-blind readers. See the [accessibility statement](https://khushisingh.in/accessibility/).