From 0d1ad994e92911686998a94be68904867507cc72 Mon Sep 17 00:00:00 2001 From: Shai Pilosof Date: Thu, 3 Sep 2026 13:16:15 -0400 Subject: [PATCH] refactor: rename whymira.html -> about.html "About" reads better than "Why MiRA" for the page's role in the nav. - Rename the page and update every reference (nav, breadcrumb, toolbar pill, canonical, og:url, BreadcrumbList JSON-LD, sitemap.xml, llms.txt, manual, tutorials, faqSchema test). - Relabel the visible nav/pill/breadcrumb from "Why MiRA" to "About"; the meta descriptions keep their "Why MiRA is..." phrasing, which still reads as prose. - Keep redirect stubs at compare.html and whymira.html (both were published, and GitHub Pages cannot issue a 301): each carries rel=canonical to about.html and is noindex,follow so signals consolidate on the new URL. - Update scripts/make_anonymous.py (in the dev worktree) to match. Co-Authored-By: Claude Opus 4.8 --- about.html | 956 ++++++++++++++++++++++++++++++++ compare.html | 13 +- data-format.html | 4 +- docs/manual.html | 2 +- index.html | 4 +- llms.txt | 4 +- sitemap.xml | 2 +- tests/faqSchema.test.js | 6 +- tutorial-brain-network.html | 4 +- tutorial-plant-pollinator.html | 4 +- tutorial-spatial-map.html | 4 +- tutorial-temporal.html | 4 +- whymira.html | 957 +-------------------------------- 13 files changed, 989 insertions(+), 975 deletions(-) create mode 100644 about.html diff --git a/about.html b/about.html new file mode 100644 index 0000000..615a1b0 --- /dev/null +++ b/about.html @@ -0,0 +1,956 @@ + + + + + + + The right tool for multilayer network visualization | MiRA (muxViz, Arena3Dweb, Gephi, Cytoscape) + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ MiRA — Multilayer Interactive Rendering Application + +
+
+ + +
+
+

Multilayer network visualization — every view, in one browser tab

+

+ MiRA (Multilayer Interactive Rendering Application) is a free, browser-based, installation-free + tool for interactive visualization of multilayer networks in ecology and biology — multiplex, + temporal, spatial, and bipartite. Other tools each cover a piece; MiRA brings the whole picture + together. +

+
+ Open MiRA → + Read the manual +
+

No sign-up — runs in your browser.

+
+ + + No installation + + + No coding + + + Bipartite & geographic + + + Free & open source +
+
+
+ + + +
+
+
At a glance
+

Interact with your multilayer network and format it for publications

+

+ Load a multilayer network, explore it through seven linked modes, and save the result — + all in the browser, without installing anything or writing code. +

+ MiRA at a glance: (1) load multilayer data from the example datasets, the emln R package, a JSON file, or CSV files; (2) explore it in seven interactive modes — Network, Map, Layer, Grid, Meta-Network, Dashboard, and Data; (3) save the result as a PNG, JPG, or PDF image, or as a session file that reloads the full state including the data. MiRA is browser-based with no install, free and open source, requires no coding, offers coordinated mode transitions, and supports bipartite networks. +
+
+ + +
+
+
One tool, seven views
+

Seven linked visualization modes

+

+ Each mode provides a different perspective about the same network. MiRA is the only tool that + offers all of them — and switches between them in a single click, keeping your selection, + color, and filtering choices intact across every view. +

+
+
+
+ + + +
+

Network

+

All layers in one 3D space — rotate, pan, and drag to explore structure.

+
+
+
+ +
+

Map

+

Layers pinned to their real geographic coordinates on an interactive world map.

+
+
+
+ + + + + + +
+

Layer

+

Each layer as a force-directed bubble, with side-by-side comparison panels.

+
+
+
+ + + + +
+

Grid

+

Small multiples — one panel per layer, side by side for direct comparison.

+
+
+
+ +
+

Meta-Network

+

Aggregate cross-layer structure into a single monolayer graph.

+
+
+
+ + + +
+

Dashboard

+

Charts, presence matrices, similarity heatmaps, and degree distributions.

+
+
+
+ + + + +
+

Data

+

Inspect, filter, and subset the underlying node, link, and layer tables.

+
+
+
+
+ + +
+
+
The whole picture
+

Others cover part of it. MiRA covers all of it.

+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Multilayer-nativeRuns in browserNo codingInteractiveBipartiteGeographic7 linked modes
MiRA
muxViz
Arena3Dweb
pymnet
BiMultiNetPlot
Gephi
Cytoscape
+
+
+ Full support + Partial / limited + Not available +
+

+ Several tools for multilayer visualization exist, but none combines the full set of features + ecological research needs. muxViz is an established analysis tool, but it runs in R, offers no + interactive browser interface, and does not support bipartite networks. BiMultiNetPlot fills the + bipartite gap yet produces only static figures with no built-in analysis. Arena3Dweb + offers polished interactive 3D, but was designed for biomedical networks — without bipartite or + geographic layouts, or multiple linked views. General-purpose tools such as Gephi and Cytoscape + are not multilayer-native. Each covers only a fragment of what ecological multilayer + visualization requires, which is the gap MiRA fills. See each tool's docs for current features. +

+
+
+ + +
+
+
See it in action
+

Designed with biological and ecological networks in mind

+

Follow a short walkthrough with a bundled empirical dataset — no setup required.

+
+ +

Plant–pollinator →

+

Visualize a bipartite plant–pollinator multilayer network.

+ + +

Spatial map →

+

Place network layers on a geographic map with Map Mode.

+ + +

Temporal →

+

Track how interactions change across seasons in a temporal network.

+ + +

Brain network →

+

Explore a multilayer human brain connectome — beyond ecology.

+ +
+
+ MiRA showing a five-layer bipartite multilayer network in Network Mode, with interlayer links connecting shared species across layers +
+
+
+ + +
+
+
FAQ
+

Frequently asked questions

+
+
+ What is a multilayer network? +

A multilayer network is composed of a set of layers (each is a network), which represent + different states of the entire system, such as different kinds of interactions, spatial + locations or temporal time points. The layers are a single linked structure via interlayer + links, rather than collapsed into a single graph. MiRA visualizes all of these — see the + visualization modes in the manual.

+
+
+ Is MiRA free? +

Yes. MiRA is free and open source under the CC BY-NC-SA 4.0 license, runs in any modern + web browser, and requires no account or sign-up. See License & + Attribution in the manual.

+
+
+ Do I need to know how to code to use MiRA? +

No. MiRA is entirely point-and-click in the browser. If you work in R, you can also plot + directly from the emln + package — see emln integration in the manual — but coding is optional. +

+
+
+ Can MiRA visualize bipartite networks such as plant–pollinator or host–parasite webs? +

Yes. MiRA has a dedicated bipartite layout that draws the two node sets — for example + pollinators and plants — in separate rows. Mark a layer as bipartite in your data and MiRA + lays it out automatically; see bipartite layers in the + manual, or the plant–pollinator walkthrough.

+
+
+ What data formats does MiRA read? +

MiRA reads JSON or CSV (an extended edge list plus optional layer, node, and state-node + attribute files), or a network passed directly from the emln R package. See the + data format guide or the manual's + import section. +

+
+
+ How is MiRA different from other software? +

Each of the existing tools covers part of what multilayer visualization needs. For example, + muxViz and pymnet are focused on analysis, Arena3Dweb for biomedical 3D scenes, and + Gephi and Cytoscape for general single-layer graphs. MiRA is the only browser-based, no-code + tool that combines bipartite and geographic support with seven linked visualization modes.

+
+
+ How do I cite MiRA? +

Cite the preprint: Nehoray, Bloch & Pilosof (2026), Interactively visualizing + biological multilayer networks using MiRA, + arXiv:2605.09597. To cite the software itself, use the + Zenodo DOI 10.5281/zenodo.22096810. +

+
+
+
+
+ + +
+
+

See your own network in MiRA

+

Load a built-in example in seconds, or bring your own data as JSON or CSV — or plot straight from + the emln R package.

+
+ Open MiRA → +
+
+
+ +
+
+

How to cite MiRA

+

If MiRA helped you explore your networks or produce figures for your research, please cite the preprint:

+

Nehoray, S. M., Bloch, Y., & Pilosof, S. (2026). Interactively visualizing biological + multilayer networks using MiRA. arXiv:2605.09597. https://arxiv.org/abs/2605.09597

+

To cite the software itself (archived release), use the Zenodo DOI:

+

Nehoray, S. M., Bloch, Y., & Pilosof, S. (2026). MiRA — Multilayer Interactive Rendering + Application (v1.1). Zenodo. https://doi.org/10.5281/zenodo.22096810

+

MiRA is developed by the Ecological Complexity Lab at Ben-Gurion University + of the Negev.

+
+ +
+ + + \ No newline at end of file diff --git a/compare.html b/compare.html index 5e15f56..c326034 100644 --- a/compare.html +++ b/compare.html @@ -2,15 +2,14 @@ - Why MiRA — page moved - - - + MiRA — page moved + + + -

This page has moved to Why MiRA.

+

This page has moved to About MiRA.

diff --git a/data-format.html b/data-format.html index ab20524..96b3317 100644 --- a/data-format.html +++ b/data-format.html @@ -28,7 +28,7 @@ App Manual Data format - Why MiRA + About GitHub Preprint @@ -149,7 +149,7 @@

Worked example — edge list

MiRA (Multilayer Interactive Rendering Application) — app · manual · - tool comparison · + tool comparison · preprint diff --git a/docs/manual.html b/docs/manual.html index b9340f0..0d7a7a8 100644 --- a/docs/manual.html +++ b/docs/manual.html @@ -407,7 +407,7 @@

MiRA — Multilayer Interactive Rendering Applica Spatial map · Temporal · Brain network · - Why MiRA + About
diff --git a/index.html b/index.html index 577e787..cf85984 100644 --- a/index.html +++ b/index.html @@ -722,11 +722,11 @@ Docs - + - Why MiRA + About diff --git a/llms.txt b/llms.txt index f4cc69c..77106d3 100644 --- a/llms.txt +++ b/llms.txt @@ -26,8 +26,8 @@ layer placement, temporal and multiplex networks, and directed links. - [Temporal network visualization](https://mira.ecomplab.com/tutorial-temporal.html): visualizing change across time in a temporal multilayer network. - [Multilayer brain network visualization](https://mira.ecomplab.com/tutorial-brain-network.html): visualizing a multilayer human brain connectome. -## Why MiRA -- [Why MiRA](https://mira.ecomplab.com/whymira.html): why MiRA is the browser-based, no-code tool for interactive multilayer network visualization, and how it relates to muxViz, Arena3Dweb, Gephi, and Cytoscape. +## About +- [About MiRA](https://mira.ecomplab.com/about.html): why MiRA is the browser-based, no-code tool for interactive multilayer network visualization, and how it relates to muxViz, Arena3Dweb, Gephi, and Cytoscape. ## Source and citation - [GitHub repository](https://github.com/Ecological-Complexity-Lab/MiRA): source code, issue tracker, CC BY-NC-SA 4.0. diff --git a/sitemap.xml b/sitemap.xml index 444bf96..500276d 100644 --- a/sitemap.xml +++ b/sitemap.xml @@ -13,7 +13,7 @@ 0.9 - https://mira.ecomplab.com/whymira.html + https://mira.ecomplab.com/about.html 2026-08-04 monthly 0.8 diff --git a/tests/faqSchema.test.js b/tests/faqSchema.test.js index 538d6bd..fc1909c 100644 --- a/tests/faqSchema.test.js +++ b/tests/faqSchema.test.js @@ -1,7 +1,7 @@ /** * tests/faqSchema.test.js — FAQ structured-data sync. * - * whymira.html carries the FAQ twice: once as visible
markup and once + * about.html carries the FAQ twice: once as visible
markup and once * as a FAQPage JSON-LD block for search and answer engines. Google requires the * schema to reflect the visible page, so the two must not drift apart. These * tests fail if they do. @@ -11,7 +11,7 @@ import { readFileSync } from 'fs' import { resolve, dirname } from 'path' import { fileURLToPath } from 'url' -const PAGE_PATH = resolve(dirname(fileURLToPath(import.meta.url)), '../whymira.html') +const PAGE_PATH = resolve(dirname(fileURLToPath(import.meta.url)), '../about.html') const JSON_LD_RE = / - - - - - - + MiRA — page moved + + + + - -
-
- MiRA — Multilayer Interactive Rendering Application - -
-
- - -
-
-

Multilayer network visualization — every view, in one browser tab

-

- MiRA (Multilayer Interactive Rendering Application) is a free, browser-based, installation-free - tool for interactive visualization of multilayer networks in ecology and biology — multiplex, - temporal, spatial, and bipartite. Other tools each cover a piece; MiRA brings the whole picture - together. -

-
- Open MiRA → - Read the manual -
-

No sign-up — runs in your browser.

-
- - - No installation - - - No coding - - - Bipartite & geographic - - - Free & open source -
-
-
- - - -
-
-
At a glance
-

Interact with your multilayer network and format it for publications

-

- Load a multilayer network, explore it through seven linked modes, and save the result — - all in the browser, without installing anything or writing code. -

- MiRA at a glance: (1) load multilayer data from the example datasets, the emln R package, a JSON file, or CSV files; (2) explore it in seven interactive modes — Network, Map, Layer, Grid, Meta-Network, Dashboard, and Data; (3) save the result as a PNG, JPG, or PDF image, or as a session file that reloads the full state including the data. MiRA is browser-based with no install, free and open source, requires no coding, offers coordinated mode transitions, and supports bipartite networks. -
-
- - -
-
-
One tool, seven views
-

Seven linked visualization modes

-

- Each mode provides a different perspective about the same network. MiRA is the only tool that - offers all of them — and switches between them in a single click, keeping your selection, - color, and filtering choices intact across every view. -

-
-
-
- - - -
-

Network

-

All layers in one 3D space — rotate, pan, and drag to explore structure.

-
-
-
- -
-

Map

-

Layers pinned to their real geographic coordinates on an interactive world map.

-
-
-
- - - - - - -
-

Layer

-

Each layer as a force-directed bubble, with side-by-side comparison panels.

-
-
-
- - - - -
-

Grid

-

Small multiples — one panel per layer, side by side for direct comparison.

-
-
-
- -
-

Meta-Network

-

Aggregate cross-layer structure into a single monolayer graph.

-
-
-
- - - -
-

Dashboard

-

Charts, presence matrices, similarity heatmaps, and degree distributions.

-
-
-
- - - - -
-

Data

-

Inspect, filter, and subset the underlying node, link, and layer tables.

-
-
-
-
- - -
-
-
The whole picture
-

Others cover part of it. MiRA covers all of it.

-
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Multilayer-nativeRuns in browserNo codingInteractiveBipartiteGeographic7 linked modes
MiRA
muxViz
Arena3Dweb
pymnet
BiMultiNetPlot
Gephi
Cytoscape
-
-
- Full support - Partial / limited - Not available -
-

- Several tools for multilayer visualization exist, but none combines the full set of features - ecological research needs. muxViz is an established analysis tool, but it runs in R, offers no - interactive browser interface, and does not support bipartite networks. BiMultiNetPlot fills the - bipartite gap yet produces only static figures with no built-in analysis. Arena3Dweb - offers polished interactive 3D, but was designed for biomedical networks — without bipartite or - geographic layouts, or multiple linked views. General-purpose tools such as Gephi and Cytoscape - are not multilayer-native. Each covers only a fragment of what ecological multilayer - visualization requires, which is the gap MiRA fills. See each tool's docs for current features. -

-
-
- - -
-
-
See it in action
-

Designed with biological and ecological networks in mind

-

Follow a short walkthrough with a bundled empirical dataset — no setup required.

-
- -

Plant–pollinator →

-

Visualize a bipartite plant–pollinator multilayer network.

- - -

Spatial map →

-

Place network layers on a geographic map with Map Mode.

- - -

Temporal →

-

Track how interactions change across seasons in a temporal network.

- - -

Brain network →

-

Explore a multilayer human brain connectome — beyond ecology.

- -
-
- MiRA showing a five-layer bipartite multilayer network in Network Mode, with interlayer links connecting shared species across layers -
-
-
- - -
-
-
FAQ
-

Frequently asked questions

-
-
- What is a multilayer network? -

A multilayer network is composed of a set of layers (each is a network), which represent - different states of the entire system, such as different kinds of interactions, spatial - locations or temporal time points. The layers are a single linked structure via interlayer - links, rather than collapsed into a single graph. MiRA visualizes all of these — see the - visualization modes in the manual.

-
-
- Is MiRA free? -

Yes. MiRA is free and open source under the CC BY-NC-SA 4.0 license, runs in any modern - web browser, and requires no account or sign-up. See License & - Attribution in the manual.

-
-
- Do I need to know how to code to use MiRA? -

No. MiRA is entirely point-and-click in the browser. If you work in R, you can also plot - directly from the emln - package — see emln integration in the manual — but coding is optional. -

-
-
- Can MiRA visualize bipartite networks such as plant–pollinator or host–parasite webs? -

Yes. MiRA has a dedicated bipartite layout that draws the two node sets — for example - pollinators and plants — in separate rows. Mark a layer as bipartite in your data and MiRA - lays it out automatically; see bipartite layers in the - manual, or the plant–pollinator walkthrough.

-
-
- What data formats does MiRA read? -

MiRA reads JSON or CSV (an extended edge list plus optional layer, node, and state-node - attribute files), or a network passed directly from the emln R package. See the - data format guide or the manual's - import section. -

-
-
- How is MiRA different from other software? -

Each of the existing tools covers part of what multilayer visualization needs. For example, - muxViz and pymnet are focused on analysis, Arena3Dweb for biomedical 3D scenes, and - Gephi and Cytoscape for general single-layer graphs. MiRA is the only browser-based, no-code - tool that combines bipartite and geographic support with seven linked visualization modes.

-
-
- How do I cite MiRA? -

Cite the preprint: Nehoray, Bloch & Pilosof (2026), Interactively visualizing - biological multilayer networks using MiRA, - arXiv:2605.09597. To cite the software itself, use the - Zenodo DOI 10.5281/zenodo.22096810. -

-
-
-
-
- - -
-
-

See your own network in MiRA

-

Load a built-in example in seconds, or bring your own data as JSON or CSV — or plot straight from - the emln R package.

-
- Open MiRA → -
-
-
- -
-
-

How to cite MiRA

-

If MiRA helped you explore your networks or produce figures for your research, please cite the preprint:

-

Nehoray, S. M., Bloch, Y., & Pilosof, S. (2026). Interactively visualizing biological - multilayer networks using MiRA. arXiv:2605.09597. https://arxiv.org/abs/2605.09597

-

To cite the software itself (archived release), use the Zenodo DOI:

-

Nehoray, S. M., Bloch, Y., & Pilosof, S. (2026). MiRA — Multilayer Interactive Rendering - Application (v1.1). Zenodo. https://doi.org/10.5281/zenodo.22096810

-

MiRA is developed by the Ecological Complexity Lab at Ben-Gurion University - of the Negev.

-
- -
+

This page has moved to About MiRA.

- - \ No newline at end of file +