Skip to content

docs(compare): affirmative "why MiRA" positioning page #86

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
shainova merged 2 commits into from
Aug 5, 2026
Merged

docs(compare): affirmative "why MiRA" positioning page #86

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
f553be1
docs(compare): recast as affirmative "why MiRA" positioning page
shainova Aug 5, 2026
fb5c28f
docs: rename nav label "Compare" -> "Why MiRA"; tighten landscape prose
shainova Aug 5, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
180 changes: 77 additions & 103 deletions compare.html
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,20 +3,20 @@
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Multilayer network visualisation tools compared | MiRA Multilayer Network Visualisation</title>
<title>The right tool for multilayer network visualisation | MiRA (muxViz, Arena3Dweb, Gephi, Cytoscape)</title>
<meta name="description"
content="A factual comparison of MiRA, muxViz, Arena3Dweb, Gephi, and Cytoscape for visualizing multilayer networks: browser-based use, programming, bipartite and geographic support, interactivity, analysis, export, and licence.">
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.">
<link rel="canonical" href="https://mira.ecomplab.com/compare.html">
<link rel="icon" type="image/svg+xml" href="assets/favicon.svg">
<meta property="og:type" content="article">
<meta property="og:site_name" content="MiRA — Multilayer Network Visualisation">
<meta property="og:title" content="Multilayer network visualisation tools compared">
<meta property="og:description" content="How MiRA compares with muxViz, Arena3Dweb, Gephi, and Cytoscape for multilayer network visualisation.">
<meta property="og:title" content="The right tool for multilayer network visualisation">
<meta property="og:description" content="Why MiRA is the browser-based, no-code tool for interactive multilayer network visualisation — an alternative to muxViz, Arena3Dweb, Gephi, and Cytoscape.">
<meta property="og:url" content="https://mira.ecomplab.com/compare.html">
<meta property="og:image" content="https://mira.ecomplab.com/assets/social-card.png">
<meta name="twitter:card" content="summary_large_image">
<meta name="twitter:title" content="Multilayer network visualisation tools compared">
<meta name="twitter:description" content="MiRA vs muxViz, Arena3Dweb, Gephi, and Cytoscape.">
<meta name="twitter:title" content="The right tool for multilayer network visualisation">
<meta name="twitter:description" content="Why MiRA is the browser-based tool for interactive multilayer network visualisation.">
<meta name="twitter:image" content="https://mira.ecomplab.com/assets/social-card.png">
<link rel="stylesheet" href="css/content.css">
</head>
Expand All @@ -28,123 +28,97 @@
<a href="index.html">App</a>
<a href="docs/manual.html">Manual</a>
<a href="data-format.html">Data format</a>
<a href="compare.html">Compare</a>
<a href="compare.html">Why MiRA</a>
<a href="https://github.com/Ecological-Complexity-Lab/MiRA">GitHub</a>
</nav>
</div>
</header>

<div class="wrap">
<p class="crumbs"><a href="index.html">MiRA</a> › Tool comparison</p>
<p class="crumbs"><a href="index.html">MiRA</a> › Why MiRA</p>

<h1>How MiRA compares with other multilayer network visualisation tools</h1>
<h1>The right tool for visualizing multilayer networks</h1>
<p class="lead">
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 — <strong>muxViz</strong>, <strong>Arena3D<sup>web</sup></strong>,
<strong>Gephi</strong>, and <strong>Cytoscape</strong> — 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 <em>see</em> and interactively explore a multilayer
network — including bipartite and geographically explicit ones — without installing software
or writing code.
</p>

<div class="callout">
<strong>Short version.</strong> If you need to <em>explore</em> 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 <em>analysis</em> (muxViz), photorealistic 3D scenes
with an integration API (Arena3D<sup>web</sup>), very large single-graph layouts (Gephi),
or a biology app ecosystem (Cytoscape), those tools may serve you better.
</div>
<h2>The multilayer network software landscape</h2>
<p>
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:
</p>
<ul>
<li><strong>muxViz</strong> is an R package focused on multilayer network <em>analysis</em>.</li>
<li><strong>Arena3D<sup>web</sup></strong> is a web application for <em>biomedical</em> 3D
network scenes.</li>
<li><strong>Gephi</strong> is a desktop application for laying out and analyzing large
<em>single-layer</em> graphs.</li>
<li><strong>Cytoscape</strong> is a desktop platform for <em>molecular and biological</em>
network analysis.</li>
<li><strong>BiMultiNetPlot</strong> is an R package for producing <em>static</em> bipartite
multilayer figures.</li>
</ul>
<p>
While each is well suited to its own purpose, none is a browser-based, no-code tool
designed specifically for <strong>interactively visualizing multilayer networks</strong> —
with dedicated support for bipartite structures and geographic layer placement together. If you are looking for a muxViz or Arena3D<sup>web</sup> alternative
focused on interactive visualization rather than analysis or programming, MiRA is built for
exactly that.
</p>

<h2>Why MiRA for visualization</h2>
<p>
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
<a href="https://github.com/Ecological-Complexity-Lab/emln">emln</a> package for those who
want it. It renders <a href="tutorial-plant-pollinator.html">bipartite networks</a> such as
plant–pollinator and host–parasite webs with a dedicated two-set layout, and it places layers
on a <a href="tutorial-spatial-map.html">geographic map</a> by their coordinates — the two
capabilities ecological multilayer networks most often require, which no other single tool
combines.
</p>
<p>
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.
</p>

<h2>Feature comparison</h2>
<h2>MiRA at a glance</h2>
<div class="tablewrap">
<table>
<thead>
<tr>
<th>Capability</th>
<th>MiRA</th>
<th>muxViz</th>
<th>Arena3D<sup>web</sup></th>
<th>Gephi</th>
<th>Cytoscape</th>
</tr>
</thead>
<tbody>
<tr>
<td>Runs in a browser, no installation</td>
<td class="tool"><span class="yes">Yes</span></td>
<td class="tool"><span class="no">No</span> — R package/GUI, installed locally</td>
<td class="tool"><span class="yes">Yes</span> — web app (also self-hostable)</td>
<td class="tool"><span class="no">No</span> — desktop application</td>
<td class="tool"><span class="no">No</span> — desktop application</td>
</tr>
<tr>
<td>Coding required to produce a visualization</td>
<td class="tool"><span class="yes">No</span> — point-and-click (optional R via emln)</td>
<td class="tool"><span class="warn">Yes</span> — R</td>
<td class="tool"><span class="yes">No</span> — point-and-click (optional API)</td>
<td class="tool"><span class="yes">No</span> — GUI (optional scripting)</td>
<td class="tool"><span class="yes">No</span> — GUI (optional scripting)</td>
</tr>
<tr>
<td>Built specifically for multilayer / multiplex networks</td>
<td class="tool"><span class="yes">Yes</span></td>
<td class="tool"><span class="yes">Yes</span></td>
<td class="tool"><span class="yes">Yes</span></td>
<td class="tool"><span class="warn">No</span> — general single-graph tool</td>
<td class="tool"><span class="warn">No</span> — general single-graph tool (multilayer via apps)</td>
</tr>
<tr>
<td>Bipartite networks (e.g. plant–pollinator, host–parasite)</td>
<td class="tool"><span class="yes">Yes</span> — dedicated bipartite layout</td>
<td class="tool"><span class="no">No</span></td>
<td class="tool"><span class="no">No</span></td>
<td class="tool"><span class="warn">Partial</span> — can draw them, no bipartite-aware multilayer layout</td>
<td class="tool"><span class="warn">Partial</span> — can draw them, no bipartite-aware multilayer layout</td>
</tr>
<tr>
<td>Geographic placement of layers</td>
<td class="tool"><span class="yes">Yes</span> — Map Mode (layers on a world map)</td>
<td class="tool"><span class="yes">Yes</span> — georeferenced layers on OpenStreetMap</td>
<td class="tool"><span class="no">No</span></td>
<td class="tool"><span class="warn">Partial</span> — node geo-layout via a plugin</td>
<td class="tool"><span class="no">Not built in</span></td>
</tr>
<tr>
<td>Live interactive exploration (filter, threshold, highlight across layers)</td>
<td class="tool"><span class="yes">Yes</span> — full</td>
<td class="tool"><span class="warn">Limited</span> — rotate/zoom 3D; no live filtering</td>
<td class="tool"><span class="yes">Yes</span> — real-time 3D manipulation and highlighting</td>
<td class="tool"><span class="yes">Yes</span> — interactive GUI</td>
<td class="tool"><span class="yes">Yes</span> — interactive GUI</td>
</tr>
<tr>
<td>Figure / data export</td>
<td class="tool">PNG, JPG, PDF; reproducible session file (data included)</td>
<td class="tool">R graphics (PDF, PNG)</td>
<td class="tool">PNG; session JSON (data included)</td>
<td class="tool">PDF, SVG, PNG; GEXF, GraphML</td>
<td class="tool">PNG, PDF, SVG; many network formats</td>
</tr>
<tr>
<td>Licence</td>
<td class="tool">CC BY-NC-SA 4.0</td>
<td class="tool">GPL</td>
<td class="tool">Free, open-source (web)</td>
<td class="tool">CDDL / GPL</td>
<td class="tool">LGPL</td>
</tr>
<tr><td>Runs in any browser</td><td class="tool">No installation, no account, no server</td></tr>
<tr><td>No coding required</td><td class="tool">Point-and-click; optional R via the emln package</td></tr>
<tr><td>Bipartite networks</td><td class="tool">Dedicated two-set layout (e.g. plant–pollinator, host–parasite)</td></tr>
<tr><td>Geographic layers</td><td class="tool">Map Mode places layers on a world map by coordinates</td></tr>
<tr><td>Visualization modes</td><td class="tool">Seven linked modes: Network, Map, Layer, Grid, Meta-Network, Dashboard, Data</td></tr>
<tr><td>Interactive exploration</td><td class="tool">Live filtering, weight thresholding, and cross-layer highlighting</td></tr>
<tr><td>Data in</td><td class="tool">JSON or CSV upload, or plot directly from the emln R package</td></tr>
<tr><td>Reproducible output</td><td class="tool">Self-contained session file (data included); export PNG, JPG, PDF</td></tr>
<tr><td>Cost and licence</td><td class="tool">Free and open source, CC BY-NC-SA 4.0</td></tr>
</tbody>
</table>
</div>

<p>
Ready to try it? <a href="index.html">Open MiRA</a> and load one of the built-in example
networks, or read the <a href="docs/manual.html">manual</a> and
<a href="data-format.html">data format</a> guide to bring your own.
</p>

<hr>
<p class="note">
Claims about MiRA are drawn from its source code and manual. Claims about muxViz,
Arena3D<sup>web</sup>, 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.
</p>

<footer class="site">
Expand Down
2 changes: 1 addition & 1 deletion data-format.html
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@
<a href="index.html">App</a>
<a href="docs/manual.html">Manual</a>
<a href="data-format.html">Data format</a>
<a href="compare.html">Compare</a>
<a href="compare.html">Why MiRA</a>
<a href="https://github.com/Ecological-Complexity-Lab/MiRA">GitHub</a>
</nav>
</div>
Expand Down
2 changes: 1 addition & 1 deletion docs/manual.html
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -407,7 +407,7 @@ <h1 style="margin-bottom:4px;">MiRA — Multilayer Interactive Rendering Applica
<a href="../tutorial-spatial-map.html">Spatial map</a> ·
<a href="../tutorial-temporal.html">Temporal</a> ·
<a href="../tutorial-brain-network.html">Brain network</a> ·
<a href="../compare.html">Tool comparison</a>
<a href="../compare.html">Why MiRA</a>
</div>

<hr>
Expand Down
4 changes: 2 additions & 2 deletions llms.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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.
Expand Down
2 changes: 1 addition & 1 deletion tutorial-brain-network.html
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@
<a href="index.html">App</a>
<a href="docs/manual.html">Manual</a>
<a href="data-format.html">Data format</a>
<a href="compare.html">Compare</a>
<a href="compare.html">Why MiRA</a>
<a href="https://github.com/Ecological-Complexity-Lab/MiRA">GitHub</a>
</nav>
</div>
Expand Down
2 changes: 1 addition & 1 deletion tutorial-plant-pollinator.html
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@
<a href="index.html">App</a>
<a href="docs/manual.html">Manual</a>
<a href="data-format.html">Data format</a>
<a href="compare.html">Compare</a>
<a href="compare.html">Why MiRA</a>
<a href="https://github.com/Ecological-Complexity-Lab/MiRA">GitHub</a>
</nav>
</div>
Expand Down
2 changes: 1 addition & 1 deletion tutorial-spatial-map.html
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@
<a href="index.html">App</a>
<a href="docs/manual.html">Manual</a>
<a href="data-format.html">Data format</a>
<a href="compare.html">Compare</a>
<a href="compare.html">Why MiRA</a>
<a href="https://github.com/Ecological-Complexity-Lab/MiRA">GitHub</a>
</nav>
</div>
Expand Down
2 changes: 1 addition & 1 deletion tutorial-temporal.html
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@
<a href="index.html">App</a>
<a href="docs/manual.html">Manual</a>
<a href="data-format.html">Data format</a>
<a href="compare.html">Compare</a>
<a href="compare.html">Why MiRA</a>
<a href="https://github.com/Ecological-Complexity-Lab/MiRA">GitHub</a>
</nav>
</div>
Expand Down
Loading