TDA Bioinformatics Foundry

Frontier → hardening → delivery

Topological methods, made runnable.

A knowledge base connecting TDA research and software to reproducible bioinformatics environments, Galaxy tools, workflows, and training.

Browse 101 typed notes → Install a cast skill

Vietoris–Rips filtration

Structure appears across scale.

03 · stable loop
Interactive filtration of a point cloud Increasing the scale joins nearby points into edges and filled triangles. A central loop remains unfilled at the final scale, illustrating a persistent topological feature.

Move the scale to watch local observations become a stable global shape.

The Foundry follows the same idea: connect evidence across scales until a runnable method holds its shape.

Current typed content slice

Packages Profiles of upstream TDA software and the facts needed to harden it. 24 profiles Environments Runnable biopixi fixtures, graded L0 to L4 for how portable their packaging is. 34 fixtures Recipes In-repo builds for the packages no conda channel carries, and the route out. 17 builds Molds Abstract actions with typed dependencies, ready to become castable artifacts. 1 action Papers Reviews of external TDA papers and surveys, linked rather than copied. 6 reviews Replication experiments What happened when we ran the papers ourselves, pinned to the evidence. 3 studies Methods The techniques themselves — what each computes, and what implements it here. 7 techniques Applications The biological problems — how they are scored, what leads, and where topology sits. 1 problem Glossary The terms that keep the Foundry's content and machinery precise. Tags Browse typed notes through the controlled vocabulary they carry. 17 terms

The Foundry itself

Design records

Why this Foundry is shaped the way it is, and how it is built. Records are typed notes like any other, split across two shelves: foundation records argue, infrastructure records describe.