GIGANTIC is a modular framework for AI-assisted comparative genomics and phylogenomics. It is designed to be cloned from GitHub, copied into a renamed project directory, and then operated through AI assistant sessions rooted at that renamed project directory.
The mantra: you (the user) guide an AI; the AI does the work. GIGANTIC's structure, conventions, and documentation are built around that model.
GIGANTIC use is built around a given project implemented through human-AI chat. It provides a framework of subprojects containing automated bioinformatic and phylogenetic workflows under the hood. It includes extensive documentation at every turn - READMEs for humans and AI_GUIDEs for AIs. For the non-expert user, it is intended as a wandering yet guided - often surprising & hopefully more fun than frustrating - research conversation to explore species, genomes, ideas, and data with an AI in chat. One where the human is guided and guides - and the AI acts. GIGANTIC floats you along in conversation - but with an exosuit grounded in sequence exploration - built to provide rigorous tools and methods in phylogenomics - and less excitingly but perhaps most critically - on-demand and behind the scenes documentation of chat as a record of research development and implementation, providing provenance in support of attribution, transparency, reproducibility, and publication. In this sense, a GIGANTIC project serves as a digital research notebook for comparative genomic and phylogenetic work - intended in the end to be archived and maintained no differently than a lab notebook at the bench.
Species for the demo are below - species set is species42. It is built for discovery of gene and genome evolution within a comparative framework of deuterostomes. It leverages deep functional knowledge in human, mouse and to a lesser extent zebrafish - and in the worm and fly models as outgroups. Hippo & splattering of cetaceans - plus octopus - fill things out. Entry requirements into species42 included a public high-quality annotated genome.
Demo species set (species42, 42 species, deuterostome-focused):
| Phylum | Species | Common name | Genome |
|---|---|---|---|
| Chordata | Homo sapiens | human | GCF_000001405.40 |
| Chordata | Mus musculus | house mouse | GCF_000001635.27 |
| Chordata | Danio rerio | zebrafish | GCF_049306965.1 |
| Chordata | Balaenoptera musculus | blue whale | GCF_009873245.2 |
| Chordata | Megaptera novaeangliae | humpback whale | GCA_041834305.1 |
| Chordata | Balaenoptera borealis | sei whale | GCF_965194805.1 |
| Chordata | Orcinus orca | killer whale | GCF_937001465.1 |
| Chordata | Tursiops truncatus | common bottlenose dolphin | GCF_011762595.2 |
| Chordata | Phocoena phocoena | harbor porpoise | GCF_963924675.1 |
| Chordata | Hippopotamus amphibius kiboko | hippo | GCF_030028045.1 |
| Chordata (Cephalochordata) | Branchiostoma floridae | Floridian lancelet | GCF_000003815.2 |
| Chordata (Cephalochordata) | Branchiostoma lanceolatum | Mediterranean amphioxus | GCF_035083965.1 |
| Chordata (Urochordata) | Ascidia mentula | sea squirt | GCF_947561715.1 |
| Chordata (Urochordata) | Botryllus schlosseri | star tunicate | GCF_051294905.1 |
| Chordata (Urochordata) | Corella eumyota | orange-tipped sea squirt | GCF_963082875.1 |
| Chordata (Urochordata) | Phallusia mammillata | white sea squirt | GCF_965637545.1 |
| Chordata (Urochordata) | Styela clava | rough sea squirt | GCF_964204865.1 |
| Chordata (Urochordata) | Aplidium turbinatum | colonial sea squirt | GCF_918807975.1 |
| Chordata (Urochordata) | Ciona intestinalis | vase tunicate | GCF_018327825.1 |
| Chordata (Urochordata) | Clavelina lepadiformis | light-bulb sea squirt | GCF_947623445.1 |
| Chordata (Urochordata) | Oikopleura dioica | larvacean | GCF_907165135.1 |
| Chordata (Urochordata) | Thalia democratica | salp | GCF_965202585.1 |
| Echinodermata | Antedon bifida | rosy feather star | GCF_963402885.1 |
| Echinodermata | Asterias rubens | European sea star | GCF_902459465.1 |
| Echinodermata | Lytechinus pictus | Cyclins Nobel Prize painted sea urchin | GCF_037042905.1 |
| Echinodermata | Amphiura filiformis | brittlestar | GCF_039555335.1 |
| Echinodermata | Antedon mediterranea | Mediterranean feather star | GCF_964355755.1 |
| Echinodermata | Apostichopus japonicus | Japanese sea cucumber | GCF_037975245.1 |
| Echinodermata | Asterias amurensis | Northern Pacific sea star | GCF_032118995.1 |
| Echinodermata | Diadema setosum | long-spined sea urchin | GCF_964275005.2 |
| Echinodermata | Eupentacta fraudatrix | sea cucumber | GCA_056552365.1 |
| Echinodermata | Holothuria leucospilota | black sea cucumber | GCA_029531755.1 |
| Echinodermata | Lytechinus variegatus | green sea urchin | GCF_018143015.1 |
| Echinodermata | Mesocentrotus franciscanus | red sea urchin | GCA_037976565.1 |
| Echinodermata | Patiria miniata | bat sea star | GCF_015706575.1 |
| Echinodermata | Strongylocentrotus purpuratus | purple sea urchin | GCF_000002235.5 |
| Hemichordata | Glandiceps talaboti | enteropneust acorn worm | GCF_964340395.1 |
| Hemichordata | Ptychodera flava | enteropneust acorn worm | GCF_041260155.1 |
| Hemichordata | Schizocardium californicum | enteropneust acorn worm | figshare:25816303 |
| Nematoda | Caenorhabditis elegans | roundworm | GCF_000002985.6 |
| Arthropoda | Drosophila melanogaster | fruit fly | GCF_000001215.4 |
| Mollusca | Octopus bimaculoides | California two-spot octopus | GCF_001194135.2 |
git clone https://github.com/000generic/GIGANTIC.git
gigantic_project-COPYME/ (inside the cloned GIGANTIC/) is the project
template. Copy it to a working location outside the GIGANTIC/ clone, and
rename it to something specific to your research project:
cp -r GIGANTIC/gigantic_project-COPYME /path/to/work/gigantic_project-cephalopod_evolution
Project naming convention: gigantic_project-<your_project_name>.
Examples:
gigantic_project-cephalopod_evolutiongigantic_project-early_animal_phylogenomicsgigantic_project-mollusc_neural_genes
The renamed directory is now your project. It is self-contained: every input, workflow, output, and documentation file lives inside it. You can archive the whole directory as the complete record of your project.
Open a new AI assistant session (Claude Code, Cursor, ChatGPT, Gemini, or
any other codebase-aware AI assistant) and root it at the renamed project
directory, not at the cloned GIGANTIC/ directory.
For example, if you renamed your project to
gigantic_project-cephalopod_evolution, your AI session should treat that
directory as its working root.
All subsequent project work happens through AI sessions rooted at your
renamed project directory. The GIGANTIC/ clone is the framework; your
renamed project directory is where you actually do science.
GIGANTIC/is the framework that gets versioned on GitHub. It ships; it doesn't run.- Your renamed project is what runs. It is the canonical record of your research project — fully reproducible, fully archivable, fully separable from any other project that uses GIGANTIC.
- AI sessions rooted at the renamed project stay focused on your project scope and don't have to mentally subtract framework-development context from every response.
- Project template setup, conventions, and AI guidance: inside
gigantic_project-COPYME/— specificallyREADME.md,AI_GUIDE.md, andCLAUDE.mdin that directory. Their content travels with your renamed copy. - AI-assistant-facing guidance for the framework itself:
AI_GUIDE.mdin this directory. - Behavior and posture for research-grade work (full documentation,
transparency, archival, replication): see
CLAUDE.mdandAI_BEHAVIOR.mdinsidegigantic_project-COPYME/(these travel with each renamed project copy — research-grade posture belongs at the project level, not at the framework level). - Standard repository files:
LICENSE,CITATION.cff,CONTRIBUTING.md,CODE_OF_CONDUCT.md.
Detailed documentation of subprojects, workflows, conventions, and
AI-assistant behavior lives inside gigantic_project-COPYME/ and travels
with each renamed project copy. This top-level README is intentionally a
minimal landing page.