Atlas
Atlas
The Atlas maps TJID3 Research as connected artifacts, methods, lineages, and recurring ideas. Start here if you want the shape of the whole corpus before opening individual files.
How this index works
Collections Artifacts are the objects: one file, one job, one destination. Prototypes stay visible without swallowing the main shelf. Older foundations stay folded, not buried.
Botanical primitivesIdentification keys, character matrices, pest and disease tools, and biodiversity informatics roots.
Historical physics restorationsSource reconstructions and companions for difficult foundational texts.
Methods, language, and timeThe publishing architecture, Tabula, geologic scale, and browser-based scholarship.
Pathogen and pest prototypesMedical references, lifecycle plates, mortality visualizations, agricultural keys, and state-linked pest tools.
Selected artifacts
Start with these
Objects that explain the range: atlas, botany, physics, method, language, and source restoration.
Botany
Florilegium Caricis · North America
Zero-dependency character matrix for 466 North American Carex taxa, derived from FNA Volume 23.
CarexFNA Vol. 23
Physics
Companion to Boltzmann (1872)
Interactive companion to Boltzmann's H-theorem and kinetic theory, with glossaries and multilingual layers.
RestorationH-theorem
Physics
Companion to Einstein 1905
Interactive companion to Einstein's Brownian motion paper, separated from the primary-source reconstruction.
Brownian motionCompanion
Method
Hummingbird V14
A whole genome tree builder for small things: virus, bacteria, viroids, and plastids.
MethodologyExecutable scholarship
Language
Tabula: A Constructed Global Pidgin
Phonemically stable auxiliary language synthesized from 50 source languages, with compression tests on canonical texts.
LanguageExperiment
Collection map
Shelves, not a junk drawer
This is the orienting layer. The full rosters sit below it.
Botanical primitives
Interactive taxonomic and applied identification work.
Physics restorations
Companions and source restorations for historically important papers.
Methods and time
Pages that explain or stress-test the architecture.
Foundations
Earlier papers, dissertation work, Lucid keys, and visual tools.
Main shelf
Botanical primitives and identification tools
The taxonomic and applied plant work, kept as direct destinations.
Florilegium Caricis · North America
466 North American Carex taxa in a field-ready character matrix.
Regulated Pest ExplorerZero-dependency key for North American regulated pests.
Glossary of Botanical TermsPrimitive glossary to botanical jargon.
U.S. Noxious Weeds · All Taxa IndexAPHIS and state-listing index: 458 taxa, 1,064 state listings, live search, habitat ontology.
Main shelf
Historical physics restorations
Primary-source reconstructions and companions, separated so readers know whether they are entering a text, a guide, or both.
Companion to Boltzmann (1872)
H-theorem companion with reader guidance and glossary layers.
Boltzmann (1872) · Thermal Equilibrium of Gas MoleculesRestored source layer for the original kinetic theory text.
Companion to Einstein 1905Reader-facing explanation of the 1905 Brownian motion paper.
Einstein (1905) · Hybrid Primary Source ReconstructionPrimary source reconstruction with multilingual and mathematical support.
Main shelf
Methods, linguistics, economics, and time
The architecture explains itself here: primitives, compression, market analysis, and scale.
Digital Paratypes
Durable HTML publishing argument, offline and rot-resistant.
Tabula: A Constructed Global PidginPhonemic compression experiment across 50 source languages.
Seeing Geologic TimeA geologic-scale page built to make time legible in-browser.
Michigan Cannabis Market AnalysisLongitudinal market study and applied data artifact.
Prototype shelf
Human pathogens
Medical references and companion plates, grouped as a suite so the reader sees the pattern before the individual doors.
Malaria burden, lifecycle, genomics, treatment, resistance, and eradication logic.
DENV 1-4, vector biology, ADE shock mechanism, and epidemic surge context.
Trypanosoma cruzi, Triatominae vectors, latency, DTUs, and oral transmission outbreaks.
YFV structure, 17D vaccine, toxic phase, sylvatic reservoir, and preventable mortality.
WNV, Culex vectors, neuroinvasive disease, H249P virulence, and One Health surveillance.
Chagas, dengue, malaria, West Nile, yellow fever, TB, measles, pertussis, typhus, and cholera.
Prototype shelf
Plant pathogens and pests
Agricultural keys and state-linked pest tools, kept compact so the page does not turn into a warehouse aisle.
Mobile identification system for pests, weeds, and applied pathways.
V1 artifact for Poaceae pest and disease taxa.
Fabaceae Pests and DiseasesV1 artifact for Fabaceae pest and disease taxa.
Solanaceae Pests and DiseasesV1 artifact for Solanaceae pest and disease taxa.
Vitaceae Pests and DiseasesV1 artifact for Vitaceae pest and disease taxa.
Rutaceae Pests and DiseasesV1 artifact for Rutaceae pest and disease taxa.
Prunus Pests and DiseasesV1 artifact for Prunus pest and disease taxa.
Interactive Pests derived from APHIS / USDASelectable by U.S. state.
First MapsV1 distribution maps for pest taxa.
Data sport
Baseball
The game is a data system. It belongs in the corpus. One artifact, one destination, more to follow.
Live artifact
Baseball Reference Tool
Zero-dependency baseball data artifact. The game is fundamentally a data system: discrete events, deep historical records, and verifiable outcomes. It fits here exactly.
Earlier work
Foundations
Earlier biodiversity informatics and teaching tools, retained because the later primitives did not fall from the sky.
Open earlier papers, dissertation, Lucid keys, and visual teaching tools
A visual identification key utilizing both gestalt and analytic approaches to identification of Carices present in North America
Why is the lawn buzzing?
Trends in access of plant biodiversity data revealed by Google Analytics
Web-based Computational Tools for Studying Plant Biodiversity
Carex of North America
Carex of Europe
Skill level Carex
Eleocharis of Canada and USA
Scleria of North America
Generic Grasses of Canada and USA
Bromus of Canada and USA
Panicum / Dichanthelium of Canada and USA
Paspalum of Canada and USA
Visual Kingdom Plantae
Visual Carex of North America
Visual Grasses of Louisiana