Lecture notes for Computational Biology Course

Built with Typst using the Touying presentation framework (Metropolis theme, 16:9).

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Installing Typst

You only need the typst CLI. Pick the line for your platform.

Platform	Command
Windows	winget install --id Typst.Typst
macOS	brew install typst
Linux	distro package where available — e.g. pacman -S typst on Arch, nix-shell -p typst on Nix
Any (via Rust)	cargo install --locked typst-cli

If none of those fit, grab a prebuilt binary from the releases page and put it on your PATH.

Confirm it worked:

typst --version     # this deck was last built with typst 0.14.2

Fonts

The deck sets Aptos as its body font (line 6 of src/BLAST.typ). Aptos ships with Microsoft 365, so it is usually already present on Windows and on machines with Office installed. On a bare system Typst will warn about an unknown font family and silently substitute another — the slides still build, they just look different.

To check what your system has:

typst fonts | grep -i aptos

If it is missing, either install Aptos or change line 6 to a font you do have, for example #set text(font: "Fira Sans").

Editing

For live preview, use VS Code with the Tinymist Typst extension. Open this folder as the workspace — Tinymist then treats it as the project root, which is what the asset paths expect (see below).

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Building the deck

From the repository root:

typst compile --root . src/BLAST.typ pdfs/BLAST.pdf

Or, to rebuild automatically on every save while you work:

typst watch --root . src/BLAST.typ pdfs/BLAST.pdf

Why --root . is required

Typst refuses to read files outside the project root, and by default the root is the input file's own folder — here that would be src/, which contains no images. Because the assets live one level up, the deck refers to them with root-relative paths (/pictures/…, /references.bib), and --root . tells Typst that "root" means the repository root.

Omitting the flag produces:

error: failed to load file (access denied)
  = hint: cannot read file outside of project root

The fix is always to add --root ., not to change the paths.

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Repository contents

.
├── src/
│   └── BLAST.typ        the entire deck — one Typst source file
├── pictures/
│   ├── Blosum62.png     BLOSUM62 substitution matrix (source: LabXchange.com)
│   ├── WSAI Logo.png    title-slide branding
│   └── iitm.png         title-slide branding
├── pdfs/
│   └── BLAST.pdf        compiled pdf
├── references.bib       BibTeX bibliography, exported from Zotero
└── README.md            this file

A few notes on the pieces:

src/BLAST.typ — everything lives here: theme configuration, a small set of custom helpers, and all slide content. The helpers worth knowing about are #question / #answer / #definition (coloured callout boxes built on gentle-clues), #match / #mismatch (green/red residue colouring), and alignment_grid (the two-row grids used to draw sequence alignments).

references.bib — Zotero generated bibliography

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