TDA Bioinformatics Foundry

The Foundry itself

Design records

Everywhere else on this site the subject is topological data analysis. Here it is the Foundry holding it: why the machinery is shaped this way, and what is actually built. Records are notes like any other — typed, tagged, and checked — so what this page lists is the corpus rather than a hand-kept index of it.

Foundry design records 4 records

Why the Foundry is shaped this way: the design pressure behind each choice, and what the choice costs.

  1. Positioning 01 A knowledge base connecting TDA research and software to reproducible bioinformatics environments, Galaxy tools, workflows, and training. revised · revision 2 · revised
  2. Guiding Principles 02 The design pressure behind runnability, licensing as a fact, replication before extension, fixing upstream, and corpus-first restraint. draft · revision 1 · revised
  3. Architecture Map 03 A short map of the Foundry's domain spine, what it inherits from the pattern, and the focused records that own each part. draft · revision 1 · revised
  4. Replication Experiments 04 Why a replication recreates a paper's reported numbers rather than merely running its code, and which half of that work lives outside this Foundry. revised · revision 2 · revised

Project infrastructure 4 records

How it is built: the code, the content contract, what runs, and where files belong.

  1. Code Architecture 01 The Astro and TypeScript implementation as it stands — components, dependency seams, entry points, and deliberate absences. revised · revision 4 · revised
  2. Content Model 02 How TDA knowledge is represented here as kinds, collections, frontmatter, tags, links, references, and companions. revised · revision 5 · revised
  3. Repository Layout 03 Where authored knowledge, implementation code, generated metadata, and build recipes belong, and what each location implies. revised · revision 4 · revised
  4. Build and Validation 04 The commands, generators, and gates that turn authored source into a checked, rendered site — and what is deliberately not checked yet. revised · revision 3 · revised

Rendered evidence

See the visual system under load.

The component gallery renders every case the shared site kit declares in this Foundry's theme, then places the filtration, barcode, point-cloud, and topology-navigation motifs beside them. It is both a design record and a regression surface.

Open the component gallery →