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Research Notebooks

Curated computational investigations in molecular genetics and bioinformatics.

Purpose

This repository contains public Jupyter notebooks developed from explicit biological questions. It is separate from my private learning journal, which contains informal reflections, incomplete thoughts, and personal notes.

The notebooks published here are curated so another learner or researcher can understand:

  • the biological question being investigated;
  • where the data came from;
  • how the analysis was performed;
  • what the results do and do not support;
  • which limitations and failed attempts shaped the final interpretation.

Notebook Standard

Question → Hypothesis → Data provenance → Quality control → Analysis
         → Results → Interpretation → Limitations → Next steps

Repository Structure

research-notebooks/
│
├── notebooks/
│   ├── 00_research_notebook_template.ipynb
│   ├── 01_gc_content_analysis.ipynb
│   ├── 02_kcnq_ortholog_comparison.ipynb
│   └── ...
│
├── data/
│   ├── raw/
│   ├── processed/
│   └── README.md
│
├── figures/
│   └── README.md
│
├── requirements.txt
└── README.md

Dataset files that are too large, restricted, or easily retrievable are not committed. Their accession numbers, retrieval dates, and download instructions are documented instead.

Investigations

# Biological Question Methods Status
01 How does GC content vary across a bacterial genome, and does the pattern align with known genomic features? Python, Biopython, sliding-window analysis, Matplotlib Planned
02 Which sequence regions are most conserved among vertebrate KCNQ orthologs? NCBI, MAFFT, Jalview, Biopython Planned

Reproducibility

Every completed notebook should include:

  1. Dataset accession or stable source URL
  2. Retrieval date and inclusion criteria
  3. Software and library versions
  4. Parameters and random seeds where relevant
  5. Saved figures with informative filenames
  6. A requirements file or environment specification
  7. A clear distinction between observation, interpretation, and speculation

Publication Checklist

  • The question and hypothesis are explicit
  • All copied code is attributed
  • Secrets, tokens, personal paths, and private data are removed
  • The notebook runs from top to bottom without hidden state
  • Data sources and accession numbers are documented
  • Figures have labels, units, legends, and descriptive captions
  • Biological claims are supported by results or citations
  • Limitations and failed approaches are documented honestly
  • Large generated files are excluded from version control
  • The conclusion does not overstate what the analysis can establish

Personal Journal vs. Public Notebook

Private Learning Journal Public Research Notebook
Personal reflection and emotion Biological question and scientific rationale
Unfiltered failed code Selected failed attempts with technical lessons
Informal notes and reminders Reproducible methods and documented parameters
Written for me Written so another person can inspect and reproduce it

Both are valuable. Only the curated research notebook belongs in a public portfolio.

Attribution

This repository is part of the public learning portfolio of Osungade Elijah Temiloluwa.