### Conventional Commits Example

Source: https://github.com/tucca-cellag/caail/blob/main/CONTRIBUTING.md

Example of a commit message following the Conventional Commits specification (Angular flavor), used for tracking changes.

```text
feat(papers): add Cosenza 2024 multi-fidelity BO paper
```

--------------------------------

### APA Citation Style Example

Source: https://github.com/tucca-cellag/caail/blob/main/CONTRIBUTING.md

An example demonstrating the expected APA citation format for entries in Papers.md. Ensure journal names are italicized and DOIs are full URLs.

```text
Author, A. B., Coauthor, C. D., & Third, E. F. (2024). Title of the paper. *Journal Name, 12*(3), 456–478. https://doi.org/10.xxxx/yyyy
```

--------------------------------

### Adding Other Resources (e.g., YouTube Videos)

Source: https://github.com/tucca-cellag/caail/blob/main/CONTRIBUTING.md

Other resources like YouTube videos are added as a flat bulleted list under category headings. Create new '##' sections for different resource types.

```markdown
* [<Title>](<URL>)
```

--------------------------------

### Structuring Software, Datasets, or Databases Entries

Source: https://github.com/tucca-cellag/caail/blob/main/CONTRIBUTING.md

Entries for software, datasets, or databases should follow a hierarchical structure with an H3 link and a summary paragraph. Link to the canonical URL for the resource.

```markdown
## <Application area>
Short framing paragraph (optional if the section already exists).

### [<Tool or dataset or database name>](<canonical URL>)

Summary: One to three sentences describing what it is and, importantly, *how it applies to cellular agriculture* — not just what it does in general.
```

--------------------------------

### Markdown for Software, Datasets, and Databases

Source: https://github.com/tucca-cellag/caail/blob/main/CLAUDE.md

Outlines the common hierarchical pattern used for Software.md, Datasets.md, and Databases.md files.

```markdown
### `Software.md`, `Datasets.md`, and `Databases.md`

All three use the same hierarchical pattern:

```markdown
## <Application area>
Short paragraph framing the area (optional).
```
```

--------------------------------

### Code Repository for Multi-objective Bayesian Algorithm

Source: https://github.com/tucca-cellag/caail/blob/main/Papers.md

This repository contains code related to multi-objective Bayesian optimization for cellular agriculture applications, as described in the referenced paper.

```link
https://github.com/ZacharyCosenza/GradStuff_Cosenza
```

--------------------------------

### Code Repository for Principal Odor Map

Source: https://github.com/tucca-cellag/caail/blob/main/Papers.md

This repository contains code related to the principal odor map, which unifies diverse tasks in olfactory perception.

```link
https://github.com/osmoai/publications/tree/main/lee_et_al_2023
```

--------------------------------

### Code Repository for ZIFA

Source: https://github.com/tucca-cellag/caail/blob/main/Papers.md

This repository contains the implementation of ZIFA, a deep adversarial variational autoencoder for dimensionality reduction in single-cell RNA sequencing.

```link
https://github.com/epierson9/ZIFA
```

--------------------------------

### Link Associated Code for a Paper

Source: https://github.com/tucca-cellag/caail/blob/main/CONTRIBUTING.md

Add this blockquote to link to the GitHub repository associated with a paper. Replace `<owner>/<repo>` with the actual repository path.

```markdown
> **Code**: https://github.com/<owner>/<repo>
```

--------------------------------

### Add Primary Research Paper Reference

Source: https://github.com/tucca-cellag/caail/blob/main/CONTRIBUTING.md

Format for adding a new primary research paper to the `Papers.md` file. Ensure the ID is unique and the DOI is a full URL.

```markdown
<a id="42">42</a> Author, A. B., & Coauthor, C. D. (2024). Title of the paper. *Journal Name, 12*(3), 456–478. https://doi.org/10.xxxx/yyyy
```

--------------------------------

### Add New AI Method Row to Matrix

Source: https://github.com/tucca-cellag/caail/blob/main/CONTRIBUTING.md

Format for adding a new row to the research matrix when a paper uses an AI method not yet listed. The method name should link to its Wikipedia article.

```markdown
| [Reinforcement Learning](https://en.wikipedia.org/wiki/Reinforcement_learning) | | | [42](#42) | | |
```

--------------------------------

### Adding a Review or Perspective Paper

Source: https://github.com/tucca-cellag/caail/blob/main/CONTRIBUTING.md

Reviews and perspective papers are added to the 'Reviews & Perspectives' section. Ensure to pick the next available ID and format the reference in APA style.

```markdown
<a id="43">43</a> Author, A. B. (2024). Title of the review. *Journal, vol*(issue), pp. https://doi.org/...
```

--------------------------------

### Cite CAAIL Repository (BibTeX)

Source: https://github.com/tucca-cellag/caail/blob/main/README.md

BibTeX citation format for the CAAIL repository. Use this when referencing the library in academic work.

```bibtex
@misc{caail2026,
  author       = {Plotts, Jim and Bromberg, Benjamin and Kaplan, David L. and {The Tufts University Center for Cellular Agriculture (TUCCA)}} and {The CAAIL Contributors}},
  title        = {{CAAIL}: Cellular Agriculture {AI} Library},
  year         = {2026},
  version      = {1.0.0},
  doi          = {10.5281/zenodo.20295590},
  publisher    = {Zenodo},
  url          = {https://doi.org/10.5281/zenodo.20295590},
  note         = {Resource library, MIT licensed}
}
```

--------------------------------

### Code Repository for scGNN

Source: https://github.com/tucca-cellag/caail/blob/main/Papers.md

This repository contains the scGNN framework, a novel graph neural network for single-cell RNA-Seq analyses.

```link
https://github.com/juexinwang/scGNN
```