📚 Statement of Credits

This website was developed as part of the "Introduction to Website and Database Design (BILG11016)" course at the University of Edinburgh.

Below is a breakdown of all the external resources and tools that were used throughout the development of this site, along with what I used them for.

Code Resources & References

PHP to PDO migration: SitePoint
Session & PHP logic references: StackOverflow
HTML & CSS help: W3Schools — used for layout structure, form styling, navigation inspiration, and general front-end design
Shell scripting guide: AWK quickref
Favicon: Teleport icon by Mihimihi on Flaticon
Font: Poppins via Google Fonts
Hero Banner Image: Generated using ChatGPT's image generation with some version of the prompt: "Create a hero banner with a protein spiral to the left, padding and a clean color background."

Clustal Omega: used to perform multiple sequence alignment, guide tree generation, and identity matrix plots.
- Official README documentation
- Sievers et al. (2018) paper
EMBOSS patmatmotifs: used to detect motifs in protein sequences
- Official EMBOSS patmatmotifs help
- Supported sequence file formats
jsPhyloSVG: Used to visualise guide trees interactively in-browser.
- Library by Samuel Smits, distributed under the GPL License
- As per the license, appropriate credit has been given and the original citation is included below:
- Smits SA, Ouverney CC, 2010. jsPhyloSVG: A Javascript Library for Visualizing Interactive and Vector-Based Phylogenetic Trees on the Web. PLoS ONE 5(8): e12267. https://doi.org/10.1371/journal.pone.0012267
- Original license and source available on GitHub
Raphael.js: Visualisation dependency for jsPhyloSVG, loaded via CDN.
File Format References:

ChatGPT was used extensively as a learning and debugging assistant. It was especially helpful when:

Translating code from pymysql to PHP's PDO, after realising that Python-based SQL interaction was not within the accepted scope of the assessment.
Writing bash scripts to loop over sequences and run patmatmotifs individually
Cleaning up form validation, PHP display logic, and layout edge cases
Understanding and integrating jsPhyloSVG for tree rendering
Creating Python scripts to generate image plots (motif bar chart, identity matrix, etc.)
Writing regular expressions and parsing outputs from EMBOSS and Biopython
Suggesting content and layout improvements (e.g. how to use `ob_start()`, sticky footer, loading states — although didn't end up using that feature)
Explaining unfamiliar parts of PHP or bash when I got stuck

All suggestions were tested, reviewed, and mostly rewritten to match the structure of my project.

Database structure (tables and relationships), designed based on course material
SQL logic for inserting and retrieving data
Layout and interface structure: forms, results pages, error handling, user views
Styling written using custom CSS
Also wrote the logic for saving results into a database, showing previous queries, and handling demo vs user searches

You can view the full codebase here: GitHub Repository

Thanks for reading! This site was built with lots of learning, assisted with the tools listed above and help from ChatGPT 💡