An open research notebook for genomic and transcriptomic work on the bubble-tip anemone, Entacmaea quadricolor, its microbial and dinoflagellate partners, and associated anemonefishes including Amphiprion frenatus and A. clarkii.
 |
 |
| Natural-habitat specimen · Leon Perrie · CC BY 4.0 | Aquarium specimen · Haplochromis · public domain |
Image credits and reusable source links are recorded in assets/ATTRIBUTION.md.
- construct and assess E. quadricolor reference transcriptomes;
- distinguish host transcripts from symbiont-derived sequences;
- improve genome annotation with RNA-seq evidence and gene-prediction workflows;
- examine expression patterns and candidate fluorescent-protein genes; and
- preserve dated computational notes for transparent, reproducible follow-up.
| Location | Contents |
|---|---|
docs/ |
Research plan and project-level documentation |
notes/daily/ |
Dated research logs |
notes/legacy/ |
Converted notebooks and their original text sources |
data/primers/ |
Small, shareable primer-design tables |
results/figures/ |
Versioned summary figures and PDF plots |
scripts/ |
Lightweight helpers for logs and note conversion |
project-management/ |
Planning templates and archived organizational notes |
assets/ |
Open-access images and attribution records |
The figures below compare GC-content patterns before host/symbiont filtering, after filtering, and in the putative symbiont fraction. They are exploratory quality-control views, not final biological conclusions.
Before filtering |
Host-enriched set |
Symbiont fraction |
Create a dated entry with:
./scripts/newlog.shConvert archived text notes to Markdown without committing automatically:
./scripts/txt2md_git.shSome historical logs contain machine-specific paths and exploratory commands. Review them before reuse. Raw sequencing data and large intermediate files are intentionally kept outside this repository.
Active research notebook. Methods, annotations, and conclusions may change as analyses are checked and extended.