Extending Topological Data Analysis in Biological Systems

Advances in experimental techniques and data collection have fueled the rise of the complex systems perspective throughout biology. The complex systems approach appreciates the entirety of the system; focusing not on individual units but on how the collection of pieces together, in context, give rise to function. This perspective informs analysis directions, but in and of itself does not naturally invoke a specific methodological mate. In this work we argue that algebraic topology is an ideological match as a framework for the complex systems perspective, because topology by nature represents, operates on, and involves the system totality. We demonstrate the ability of topology to provide insight into biological and linguistic system structures, and offer suggestions for further method development. Finally we close with a discussion of the frontiers of topological data analysis, which we believe will indeed shape the future of research in complex biological systems

VEuPathDB/web-monorepo: v1.0.86

<h2>What's Changed</h2> <ul> <li>Genomics: Finalize menu code for maps by @dmfalke in https://github.com/VEuPathDB/web-monorepo/pull/477</li> <li>Interim non-handling of date variables for bubble markers (but allows EdaDataService#309 to be merged) by @bobular in https://github.com/VEuPathDB/web-monorepo/pull/453</li> <li>Add new analysis button to all analyses component in map by @chowington in https://github.com/VEuPathDB/web-monorepo/pull/459</li> <li>Genes phyletic tree search box by @dmfalke in https://github.com/VEuPathDB/web-monorepo/pull/561</li> <li>Collection map type by @dmfalke in https://github.com/VEuPathDB/web-monorepo/pull/399</li> <li>Incorporate p value floor from backend by @asizemore in https://github.com/VEuPathDB/web-monorepo/pull/565</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/VEuPathDB/web-monorepo/compare/v1.0.85...v1.0.86</p&gt

VEuPathDB/web-monorepo: v1.0.93

<h2>What's Changed</h2> <ul> <li>Display useful message to user when analysis fails to load by @dmfalke in https://github.com/VEuPathDB/web-monorepo/pull/645</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/VEuPathDB/web-monorepo/compare/v1.0.92...v1.0.93</p&gt

VEuPathDB/web-monorepo: v1.0.90

A monorepo that contains all frontend code for VEuPathDB website

VEuPathDB/web-monorepo: v1.0.88

<h2>What's Changed</h2> <ul> <li>Add more reference org filters by @jernestmyers in https://github.com/VEuPathDB/web-monorepo/pull/577</li> <li>Eda study type error by @dmfalke in https://github.com/VEuPathDB/web-monorepo/pull/590</li> <li>Eda categorical collection type by @dmfalke in https://github.com/VEuPathDB/web-monorepo/pull/592</li> <li>Increase row count font size in beta Downloads table by @jernestmyers in https://github.com/VEuPathDB/web-monorepo/pull/593</li> <li>Reposition reference filter by @jernestmyers in https://github.com/VEuPathDB/web-monorepo/pull/591</li> <li>Add min-width to prevent confusing overflow UX by @jernestmyers in https://github.com/VEuPathDB/web-monorepo/pull/599</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/VEuPathDB/web-monorepo/compare/v1.0.87...v1.0.88</p&gt

VEuPathDB/web-monorepo: v1.0.95

<h2>What's Changed</h2> <ul> <li>Feature 556 connect correlation backend by @asizemore in https://github.com/VEuPathDB/web-monorepo/pull/560</li> <li>Fix breakage from variableId -> collectionId changes by @jernestmyers in https://github.com/VEuPathDB/web-monorepo/pull/655</li> <li>Studies menu filter bug by @jernestmyers in https://github.com/VEuPathDB/web-monorepo/pull/656</li> <li>update default effect size and var names by @asizemore in https://github.com/VEuPathDB/web-monorepo/pull/664</li> <li>add maaslin citation and link by @asizemore in https://github.com/VEuPathDB/web-monorepo/pull/653</li> <li>Allow for displayOrder values < 1 by @dmfalke in https://github.com/VEuPathDB/web-monorepo/pull/660</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/VEuPathDB/web-monorepo/compare/v1.0.94...v1.0.95</p&gt

VEuPathDB/web-monorepo: v1.0.96

<h2>What's Changed</h2> <ul> <li>temporarily turn off correlation by @asizemore in https://github.com/VEuPathDB/web-monorepo/pull/662</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/VEuPathDB/web-monorepo/compare/v1.0.95...v1.0.96</p&gt