From f553be10938f7c60adc9c9a8bc171c8b6bcfeb73 Mon Sep 17 00:00:00 2001 From: Shai Pilosof Date: Tue, 4 Aug 2026 22:45:41 -0500 Subject: [PATCH 1/2] docs(compare): recast as affirmative "why MiRA" positioning page - Rewrite compare.html as prose + a MiRA-only capability list - Name muxViz/Arena3Dweb/Gephi/Cytoscape/BiMultiNetPlot by design purpose, not as head-to-head where MiRA loses; keep target queries (alternative, etc.) - Update llms.txt pointer to match Co-Authored-By: Claude Opus 4.8 --- compare.html | 180 ++++++++++++++++++++++----------------------------- llms.txt | 4 +- 2 files changed, 80 insertions(+), 104 deletions(-) diff --git a/compare.html b/compare.html index af38695..62ec391 100644 --- a/compare.html +++ b/compare.html @@ -3,20 +3,20 @@ - Multilayer network visualisation tools compared | MiRA Multilayer Network Visualisation + The right tool for multilayer network visualisation | MiRA (muxViz, Arena3Dweb, Gephi, Cytoscape) + content="Why MiRA is the tool for interactive multilayer network visualisation in the browser — a no-install, no-code alternative to muxViz, Arena3Dweb, Gephi, and Cytoscape, with dedicated bipartite and geographic support."> - - + + - - + + @@ -35,116 +35,92 @@
-

MiRA › Tool comparison

+

MiRA › Why MiRA

-

How MiRA compares with other multilayer network visualisation tools

+

The right tool for visualizing multilayer networks

- MiRA is a free, browser-based, installation-free tool for interactive visualisation of - multilayer networks in ecology and biology. This page compares it fairly with four other - widely used tools — muxViz, Arena3Dweb, - Gephi, and Cytoscape — so you can pick the right tool for - your question. Each of these is excellent at what it was built for; the table shows where - each one fits. + MiRA (Multilayer Interactive Rendering Application) is a free, browser-based, installation-free + tool for interactive visualisation of multilayer networks in ecology and biology. It is built + for one job and does it well: letting you see and interactively explore a multilayer + network — including bipartite and geographically explicit ones — without installing software + or writing code.

-
- Short version. If you need to explore a multilayer network — - especially a bipartite (e.g. plant–pollinator, host–parasite) or geographically explicit - one — in a browser with no installation and no code, MiRA is designed for exactly that. - If your priority is deep multilayer analysis (muxViz), photorealistic 3D scenes - with an integration API (Arena3Dweb), very large single-graph layouts (Gephi), - or a biology app ecosystem (Cytoscape), those tools may serve you better. -
+

The multilayer network software landscape

+

+ Several excellent tools touch multilayer networks, but each was built for a different job, so + the right choice depends on what you actually need to do: +

+
    +
  • muxViz is an R package for multilayer network analysis — computing + metrics, communities, and reducibility from the command line.
    • +
  • Arena3Dweb is a web application for biomedical 3D + network scenes, with an API for programmatic embedding.
    • +
  • Gephi is a desktop application for laying out and analyzing large + single-layer graphs.
    • +
  • Cytoscape is a desktop platform for molecular and biological + network analysis, extended by a large ecosystem of apps.
    • +
  • BiMultiNetPlot is an R package for producing static bipartite + multilayer figures.
    • +
+

+ Each is well suited to its own purpose. What none of them is, is a browser-based, no-code tool + designed specifically for interactively visualizing multilayer networks — + with dedicated support for bipartite structures and geographic layer placement together. That + is the gap MiRA fills. If you are looking for a muxViz or Arena3Dweb alternative + focused on interactive visualization rather than analysis or programming, MiRA is built for + exactly that. +

+ +

Why MiRA for visualization

+

+ MiRA is the only tool that brings the whole combination together in one place. It runs in any + web browser with no installation, no account, and no server, and it needs no coding — yet it + still integrates with R through the + emln package for those who + want it. It renders bipartite networks such as + plant–pollinator and host–parasite webs with a dedicated two-set layout, and it places layers + on a geographic map by their coordinates — the two + capabilities ecological multilayer networks most often require, which no other single tool + combines. +

+

+ On top of that, MiRA offers seven linked visualization modes, live filtering and weight + thresholding, and cross-layer highlighting that lights up a species in every layer at once — + so a network stays legible even as it grows complex. A whole session, data included, saves to + a single file that reopens the full visualization, and any view exports to a + publication-quality PNG, JPG, or PDF. Because everything happens in the browser, sharing MiRA + with a collaborator is just sharing a link. +

-

Feature comparison

+

MiRA at a glance

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + +
CapabilityMiRAmuxVizArena3DwebGephiCytoscape
Runs in a browser, no installationYesNo — R package/GUI, installed locallyYes — web app (also self-hostable)No — desktop applicationNo — desktop application
Coding required to produce a visualizationNo — point-and-click (optional R via emln)Yes — RNo — point-and-click (optional API)No — GUI (optional scripting)No — GUI (optional scripting)
Built specifically for multilayer / multiplex networksYesYesYesNo — general single-graph toolNo — general single-graph tool (multilayer via apps)
Bipartite networks (e.g. plant–pollinator, host–parasite)Yes — dedicated bipartite layoutNoNoPartial — can draw them, no bipartite-aware multilayer layoutPartial — can draw them, no bipartite-aware multilayer layout
Geographic placement of layersYes — Map Mode (layers on a world map)Yes — georeferenced layers on OpenStreetMapNoPartial — node geo-layout via a pluginNot built in
Live interactive exploration (filter, threshold, highlight across layers)Yes — fullLimited — rotate/zoom 3D; no live filteringYes — real-time 3D manipulation and highlightingYes — interactive GUIYes — interactive GUI
Figure / data exportPNG, JPG, PDF; reproducible session file (data included)R graphics (PDF, PNG)PNG; session JSON (data included)PDF, SVG, PNG; GEXF, GraphMLPNG, PDF, SVG; many network formats
LicenceCC BY-NC-SA 4.0GPLFree, open-source (web)CDDL / GPLLGPL
Runs in any browserNo installation, no account, no server
No coding requiredPoint-and-click; optional R via the emln package
Bipartite networksDedicated two-set layout (e.g. plant–pollinator, host–parasite)
Geographic layersMap Mode places layers on a world map by coordinates
Visualization modesSeven linked modes: Network, Map, Layer, Grid, Meta-Network, Dashboard, Data
Interactive explorationLive filtering, weight thresholding, and cross-layer highlighting
Data inJSON or CSV upload, or plot directly from the emln R package
Reproducible outputSelf-contained session file (data included); export PNG, JPG, PDF
Cost and licenceFree and open source, CC BY-NC-SA 4.0
+

+ Ready to try it? Open MiRA and load one of the built-in example + networks, or read the manual and + data format guide to bring your own. +

+

- Claims about MiRA are drawn from its source code and manual. Claims about muxViz, - Arena3Dweb, Gephi, and Cytoscape are drawn from those projects' own documentation - and papers and were last checked in August 2026; capabilities change between versions, so - verify against the current release for a specific decision. Where a capability was uncertain, - the cell is qualified rather than asserted. + Other tools above are described by their primary design purpose; capabilities evolve between + versions, so consult each project's own documentation for its current feature set. Claims about + MiRA are drawn from its source code and manual.

diff --git a/llms.txt b/llms.txt index 93c0850..d680dec 100644 --- a/llms.txt +++ b/llms.txt @@ -26,8 +26,8 @@ layer placement, temporal and multiplex networks, and directed links. - [Temporal network visualisation](https://mira.ecomplab.com/tutorial-temporal.html): visualizing change across time in a temporal multilayer network. - [Multilayer brain network visualisation](https://mira.ecomplab.com/tutorial-brain-network.html): visualizing a multilayer human brain connectome. -## Comparison -- [Comparison with other tools](https://mira.ecomplab.com/compare.html): how MiRA compares with muxViz, Arena3Dweb, Gephi, and Cytoscape for multilayer network visualisation. +## Why MiRA +- [Why MiRA](https://mira.ecomplab.com/compare.html): why MiRA is the browser-based, no-code tool for interactive multilayer network visualisation, 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. From fb5c28f0ef47cf1501183c04aa09c789dd926104 Mon Sep 17 00:00:00 2001 From: Shai Pilosof Date: Tue, 4 Aug 2026 22:56:15 -0500 Subject: [PATCH 2/2] docs: rename nav label "Compare" -> "Why MiRA"; tighten landscape prose - Rename the nav/Guides link across content pages + manual to match the page's new framing - Tighten competitor descriptions; fix a double-space typo Co-Authored-By: Claude Opus 4.8 --- compare.html | 14 ++++++-------- data-format.html | 2 +- docs/manual.html | 2 +- tutorial-brain-network.html | 2 +- tutorial-plant-pollinator.html | 2 +- tutorial-spatial-map.html | 2 +- tutorial-temporal.html | 2 +- 7 files changed, 12 insertions(+), 14 deletions(-) diff --git a/compare.html b/compare.html index 62ec391..d628e94 100644 --- a/compare.html +++ b/compare.html @@ -28,7 +28,7 @@ App Manual Data format - Compare + Why MiRA GitHub
@@ -52,22 +52,20 @@

The multilayer network software landscape

the right choice depends on what you actually need to do:

- Each is well suited to its own purpose. What none of them is, is a browser-based, no-code tool + While each is well suited to its own purpose, none is a browser-based, no-code tool designed specifically for interactively visualizing multilayer networks — - with dedicated support for bipartite structures and geographic layer placement together. That - is the gap MiRA fills. If you are looking for a muxViz or Arena3Dweb alternative + with dedicated support for bipartite structures and geographic layer placement together. If you are looking for a muxViz or Arena3Dweb alternative focused on interactive visualization rather than analysis or programming, MiRA is built for exactly that.

diff --git a/data-format.html b/data-format.html index b114199..930cd20 100644 --- a/data-format.html +++ b/data-format.html @@ -28,7 +28,7 @@ App Manual Data format - Compare + Why MiRA GitHub diff --git a/docs/manual.html b/docs/manual.html index 5693e89..b78ffac 100644 --- a/docs/manual.html +++ b/docs/manual.html @@ -407,7 +407,7 @@

MiRA — Multilayer Interactive Rendering Applica Spatial map · Temporal · Brain network · - Tool comparison + Why MiRA
diff --git a/tutorial-brain-network.html b/tutorial-brain-network.html index 66e0655..ea1b4a9 100644 --- a/tutorial-brain-network.html +++ b/tutorial-brain-network.html @@ -28,7 +28,7 @@ App Manual Data format - Compare + Why MiRA GitHub diff --git a/tutorial-plant-pollinator.html b/tutorial-plant-pollinator.html index b25fae3..b7a7032 100644 --- a/tutorial-plant-pollinator.html +++ b/tutorial-plant-pollinator.html @@ -28,7 +28,7 @@ App Manual Data format - Compare + Why MiRA GitHub diff --git a/tutorial-spatial-map.html b/tutorial-spatial-map.html index 654037b..9e01876 100644 --- a/tutorial-spatial-map.html +++ b/tutorial-spatial-map.html @@ -28,7 +28,7 @@ App Manual Data format - Compare + Why MiRA GitHub diff --git a/tutorial-temporal.html b/tutorial-temporal.html index 7c2a6fd..0747c85 100644 --- a/tutorial-temporal.html +++ b/tutorial-temporal.html @@ -28,7 +28,7 @@ App Manual Data format - Compare + Why MiRA GitHub