A Comprehensive Guide to MyST Markdown with Elsevier CAS Templates

Introduction¶

This document demonstrates the full integration of MyST Markdown Cockett et al., 2024 with Elsevier’s CAS templates. MyST provides a powerful authoring experience while maintaining compatibility with traditional LaTeX journal requirements Lamport, 1994.

Background¶

Scientific publishing has traditionally relied on LaTeX for high-quality typesetting Krewinkel & Winkler, 2017. However, the learning curve and complexity of LaTeX can be a barrier for many researchers. MyST Markdown bridges this gap by providing:

1. A familiar Markdown syntax based on CommonMark Gruber, 2004

2. Rich scientific features (equations, citations, cross-references)

3. Export to multiple formats including PDF via LaTeX

Reproducible research workflows have become increasingly important, with tools like Jupyter Notebooks Kluyver et al., 2016 enabling literate programming approaches.

Typography Features¶

This section demonstrates MyST Markdown typography features and how they render in the PDF output.

Inline Formatting¶

Standard inline formatting includes bold text, italic text, and inline code. You can also use strikethrough text and underlined text for special emphasis.

For chemical formulas, use subscripts: H₂O, CO₂, C₆H₁₂O₆. For ordinals and exponents, use superscripts: the 4^th of July, 1^st place, x² + y² = r².

Line Breaks¶

The world’s shortest poem demonstrates line breaks:
Fleas
Adam
Had 'em.

—Strickland Gillilan

Quotations¶

Block quotes are useful for highlighting important passages:

Definition Lists¶

MyST supports definition lists for glossaries or term explanations:

MyST

Markedly Structured Text, a markdown flavor for scientific writing

LaTeX

A document preparation system for high-quality typesetting

jtex

A Jinja-based templating system for LaTeX documents

CAS

Content Acquisition System, Elsevier’s journal template system

Footnotes¶

MyST supports footnotes^[1] which are automatically numbered and placed at the end of the document. You can have multiple footnotes^[2] throughout your text.

Task Lists¶

Task lists can track progress (rendered as bullet points in LaTeX):

• Create template structure

• Add typography examples

• Add math demonstrations

• Add proof environments

• Submit to journal

• Celebrate publication!

Mathematical Content¶

The templates support full LaTeX math with custom macros defined in frontmatter.

Inline Mathematics¶

Inline math like $E = mc^2$ or $\E[X] = \mu$ works seamlessly. Using our custom macros: for $x \in \R$, we have $\Var(X) = \E[X^2] - (\E[X])^2$.

Display Equations¶

The quadratic formula:

Maxwell’s equations in differential form:

The Bellman equation for dynamic programming:

Equations can be cross-referenced: see (1) for the quadratic formula and (2) for Maxwell’s equations.

Proofs and Theorems¶

MyST supports formal mathematical environments using proof directives. These are essential for mathematical and theoretical papers.

Definitions¶

Theorems¶

Proofs¶

Lemmas and Corollaries¶

Remarks and Examples¶

Admonitions¶

Admonitions (callouts) are useful for highlighting important information. MyST supports many types:

Code Blocks¶

Code blocks with syntax highlighting are supported:

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import numpy as np
from typing import Tuple

def quadratic_formula(a: float, b: float, c: float) -> Tuple[float, float]:
    """Solve ax^2 + bx + c = 0 using the quadratic formula."""
    discriminant = b**2 - 4*a*c
    if discriminant < 0:
        raise ValueError("No real solutions")
    x1 = (-b + np.sqrt(discriminant)) / (2*a)
    x2 = (-b - np.sqrt(discriminant)) / (2*a)
    return x1, x2

# Example usage
roots = quadratic_formula(1, -5, 6)
print(f"Roots: {roots}")  # Output: (3.0, 2.0)

As shown in Program 1, code can be captioned, numbered, and cross-referenced.

Multiple languages are supported:

function quadratic_formula(a, b, c)
    discriminant = b^2 - 4*a*c
    x1 = (-b + sqrt(discriminant)) / (2*a)
    x2 = (-b - sqrt(discriminant)) / (2*a)
    return x1, x2
end

Algorithms¶

For algorithm pseudocode, use raw LaTeX blocks with the algorithm and algorithmic environments:

The algorithm environment provides a float with caption and label for cross-referencing.

Tables¶

Markdown Tables¶

MyST tables convert cleanly to LaTeX:

Results are summarized in Table 1.

List Tables¶

List tables provide an alternative syntax useful for complex content:

CSV Tables¶

Raw LaTeX Tables¶

For complex tables requiring advanced features, use raw LaTeX blocks. The CAS templates include booktabs, multirow, makecell, array, and dcolumn packages:

Figures and Images¶

As shown in Figure 1, the template properly handles figure placement and captions.

Cross-References Summary¶

This document demonstrates various cross-reference capabilities:

• Equations: (1), (2), (3)

• Figures: Figure 1

• Tables: Table 1, Table 2, Table 3

• Code: Program 1, Program 2

• Algorithms: Algorithm 1 (via raw LaTeX \ref{alg:binary-search})

• Theorems: Theorem 1, Theorem 2

• Definitions: Definition 1, Definition 2

• Lemmas: Lemma 1

• Corollaries: Corollary 1

• Examples: Example 1

• Sections: Introduction, Typography

Discussion¶

This approach enables researchers to write in MyST Markdown while producing publication-ready documents that meet Elsevier’s submission requirements.

Advantages¶

1. Reproducibility: Source files are plain text and version-controllable

2. Flexibility: Single source exports to HTML, PDF, and other formats

3. Modern tooling: Integration with Jupyter, VS Code, and other tools

4. Rich features: Full LaTeX math, cross-references, and citations

Limitations¶

Conclusion¶

The Elsevier CAS MyST template provides a modern workflow for scientific writing while maintaining compatibility with traditional journal submission systems. This document has demonstrated:

• Typography: formatting, footnotes, definition lists

• Mathematics: inline, display, custom macros

• Formal environments: definitions, theorems, proofs, examples

• All admonition types

• Multiple table formats

• Code blocks with syntax highlighting

• Figures with cross-referencing

• Citations and bibliography

For questions or contributions, please visit the template repository.