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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<link rel="icon" type="image/svg+xml" href="favicon.svg">
<title>LIVIA — Tutorials</title>
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</head>
<body>
<div class="header">
<div class="container" role="main">
<h1><span style="color:#2471A3;">LIVIA</span> — Tutorials</h1>
<p>Step-by-step visual walkthroughs for each LIVIA tool</p>
<div class="header-links">
<a href="index.html">Home</a>
<a href="universal.html">Prediction Analysis</a>
<a href="flypredictome.html">FlyPredictome</a>
<a href="ortholog_predictome.html">Ortholog Interactome</a>
<a href="dimer.html">AFDB Dimer</a>
<a href="monomer.html">AFDB Monomer Subdomain</a>
<a href="clip.html">cLIP</a>
<a href="network.html">PPI Network</a>
<a href="https://flyark.github.io/livia-atlas/" target="_blank" rel="noopener">LIVIA Atlas<span class="new-tag">new</span></a>
<a href="tutorials.html" class="active">Tutorials</a>
<a href="about.html">About</a>
<a href="https://github.com/flyark/LIVIA" target="_blank">GitHub</a>
</div>
</div>
</div>
<div class="container">
<div class="page-intro">
<h2>Learn LIVIA by Example</h2>
<p>Each tutorial below walks through a real workflow with auto-advancing screenshots. Click any step to jump to it, or let it play through automatically. Ready to try it yourself? Click the <strong>Try it</strong> button.</p>
</div>
<!-- The full tour: the 69-second film (files on flyark.github.io/livia-media; nothing downloads until play) -->
<div class="tour-full" id="tour">
<h2>The full tour</h2>
<p>69 seconds, no sound: one prediction, from loading it to every map, 3D view and ChimeraX/PyMOL export, then cLIP on a whole screen.</p>
<video controls playsinline loop preload="none" poster="https://flyark.github.io/livia-media/livia-full.webp" aria-label="LIVIA full tour, 69 seconds (no sound)">
<source src="https://flyark.github.io/livia-media/livia-full.mp4" type="video/mp4">
</video>
</div>
<!-- ============================================================ -->
<!-- TUTORIAL 1: Prediction Analysis (6 steps) -->
<!-- ============================================================ -->
<div class="tutorial-card" id="tut-universal">
<div class="tutorial-header">
<div>
<h3>Prediction Analysis</h3>
<p>Load prediction files from any platform and analyze interface confidence</p>
</div>
<a class="try-btn" href="universal.html">Try it →</a>
</div>
<!-- The customization film (files on flyark.github.io/livia-media; nothing downloads until play) -->
<div class="tut-film">
<p>46 seconds, no sound: chain colors, map colors and labels, cartoon gaps, and SVG or PNG export, set on the Prediction Analysis page.</p>
<video controls playsinline loop preload="none" poster="https://flyark.github.io/livia-media/livia-custom.webp" aria-label="Making LIVIA figures your own, 46 seconds (no sound)">
<source src="https://flyark.github.io/livia-media/livia-custom.mp4" type="video/mp4">
</video>
</div>
<div class="tutorial-body">
<div class="steps-sidebar" data-tutorial="universal">
<div class="step-item active" data-step="0" onclick="goToStep('universal', 0)">
<div class="step-badge">1</div>
<div class="step-text">Load your prediction files or select example files</div>
</div>
<div class="step-item" data-step="1" onclick="goToStep('universal', 1)">
<div class="step-badge">2</div>
<div class="step-text">Review per-model metrics — iLIS, iLIA, iLISA, ipSAE, actifpTM, ipTM</div>
</div>
<div class="step-item" data-step="2" onclick="goToStep('universal', 2)">
<div class="step-badge">3</div>
<div class="step-text">Identify chains via UniProt, then check Reported Interactions (MIST)</div>
</div>
<div class="step-item" data-step="3" onclick="goToStep('universal', 3)">
<div class="step-badge">4</div>
<div class="step-text">Score Matrix and PAE/LIS/cLIS heatmaps across all models</div>
</div>
<div class="step-item" data-step="4" onclick="goToStep('universal', 4)">
<div class="step-badge">5</div>
<div class="step-text">Label Settings — custom axis names and per-chain labels</div>
</div>
<div class="step-item" data-step="5" onclick="goToStep('universal', 5)">
<div class="step-badge">6</div>
<div class="step-text">Sequence Viewer — interaction residues highlighted</div>
</div>
<div class="step-item" data-step="6" onclick="goToStep('universal', 6)">
<div class="step-badge">7</div>
<div class="step-text">Linear Contact Map — cLIR pairs, domains, and MIST evidence</div>
</div>
<div class="step-item" data-step="7" onclick="goToStep('universal', 7)">
<div class="step-badge">8</div>
<div class="step-text">Circular Contact Map — chord diagram with domain and pLDDT rings</div>
</div>
<div class="step-item" data-step="8" onclick="goToStep('universal', 8)">
<div class="step-badge">9</div>
<div class="step-text">View the 3D structure in Mol* viewer</div>
</div>
<div class="step-item" data-step="9" onclick="goToStep('universal', 9)">
<div class="step-badge">10</div>
<div class="step-text">Visualization Script — color presets and custom chain colors</div>
</div>
<div class="step-item" data-step="10" onclick="goToStep('universal', 10)">
<div class="step-badge">11</div>
<div class="step-text">Per-Residue intra-chain LIS & pLDDT charts</div>
</div>
</div>
<div class="screenshot-area" data-tutorial="universal">
<img id="img-universal" src="screenshots/tut_universal_1.png" alt="Tutorial step">
<div class="screenshot-caption" id="cap-universal">Load prediction files or pick a p53–MDM2 example</div>
<div class="progress-dots" id="dots-universal"></div>
<div class="playback-controls">
<button class="playback-btn" onclick="togglePlayback('universal')" id="play-btn-universal" title="Pause/Resume">▮▮ Pause</button>
</div>
</div>
</div>
</div>
<!-- ============================================================ -->
<!-- TUTORIAL 2: Bookmarklet for AFDB and FlyPredictome -->
<!-- ============================================================ -->
<div class="tutorial-card" id="tut-dimer">
<div class="tutorial-header">
<div>
<h3>Bookmarklet for AFDB and FlyPredictome</h3>
<p>One-click jump from AlphaFold DB or FlyPredictome straight into LIVIA</p>
</div>
<a class="try-btn" href="#bm-install">Get it →</a>
</div>
<!-- The bookmarklet film (files on flyark.github.io/livia-media; nothing downloads until play) -->
<div class="tut-film">
<p>53 seconds, no sound: drag it to your bookmarks bar once, then one click from AlphaFold DB (MYC–MAX) or FlyPredictome (Yki–Sd) shows which residues of each protein bind.</p>
<video controls playsinline loop preload="none" poster="https://flyark.github.io/livia-media/livia-bookmarklet.webp" aria-label="LIVIA bookmarklet, 53 seconds (no sound)">
<source src="https://flyark.github.io/livia-media/livia-bookmarklet.mp4" type="video/mp4">
</video>
</div>
<div class="tutorial-body">
<div class="steps-sidebar" data-tutorial="dimer">
<div class="step-item active" data-step="0" onclick="goToStep('dimer', 0)">
<div class="step-badge">1</div>
<div class="step-text">Drag the <em>Open in LIVIA</em> button to your browser's bookmarks bar (one-time)</div>
</div>
<div class="step-item" data-step="1" onclick="goToStep('dimer', 1)">
<div class="step-badge">2</div>
<div class="step-text">Open any AlphaFold DB dimer entry page</div>
</div>
<div class="step-item" data-step="2" onclick="goToStep('dimer', 2)">
<div class="step-badge">3</div>
<div class="step-text">Click the bookmark — LIVIA dimer opens in a new tab with metrics auto-loaded</div>
</div>
<div class="step-item" data-step="3" onclick="goToStep('dimer', 3)">
<div class="step-badge">4</div>
<div class="step-text">Interactive 3D structure of the dimer in Mol* viewer</div>
</div>
<div class="step-item" data-step="4" onclick="goToStep('dimer', 4)">
<div class="step-badge">5</div>
<div class="step-text">Same workflow on FlyPredictome — visit a famdb_details page and click the bookmark</div>
</div>
<div class="step-item" data-step="5" onclick="goToStep('dimer', 5)">
<div class="step-badge">6</div>
<div class="step-text">LIVIA FlyPredictome opens with the same analysis pipeline</div>
</div>
<div class="step-item" data-step="6" onclick="goToStep('dimer', 6)">
<div class="step-badge">7</div>
<div class="step-text">FlyPredictome's ortholog detail pages also route to LIVIA Ortholog</div>
</div>
</div>
<div class="screenshot-area" data-tutorial="dimer">
<img id="img-dimer" src="screenshots/tut_dimer_1.png" alt="Tutorial step">
<div class="screenshot-caption" id="cap-dimer">Drag the blue button to your bookmarks bar to add the bookmarklet</div>
<div class="progress-dots" id="dots-dimer"></div>
<div class="playback-controls">
<button class="playback-btn" onclick="togglePlayback('dimer')" id="play-btn-dimer" title="Pause/Resume">▮▮ Pause</button>
</div>
</div>
</div>
<div id="bm-install" style="border-top:1px solid #eef1f5; margin:0 1.5rem 1.5rem; padding-top:1.2rem;">
<h3 style="color:#1a5276; font-size:1.05rem; margin-bottom:.4rem;">Add the bookmarklet</h3>
<p style="font-size:.9rem; color:#555; line-height:1.55;">Drag the blue button to your browser's bookmarks bar. On an AlphaFold DB entry or a FlyPredictome details page, click the bookmark and LIVIA opens the matching analysis page automatically.</p>
<div style="display:flex; align-items:center; gap:1rem; margin:1rem 0 .5rem; flex-wrap:wrap;">
<a title="Drag me to your bookmarks bar" style="display:inline-block; padding:.6rem 1.2rem; background:#2471A3; color:#fff; border-radius:10px; font-weight:600; font-size:.95rem; text-decoration:none; cursor:grab; user-select:none;"
href="javascript:(function(){var u=location.href,p=location.origin+location.pathname,t=null,m;if(m=u.match(/alphafold\.ebi\.ac\.uk\/entry\/(AF-\d+)/))t='https://flyark.github.io/LIVIA/dimer.html?id='+m[1];else if(m=u.match(/alphafold\.ebi\.ac\.uk\/entry\/(?:AF-)?([A-Z][0-9][A-Z0-9]{3}[0-9](?:[A-Z][A-Z0-9]{2}[0-9])?)/i))t='https://flyark.github.io/LIVIA/monomer.html?id='+m[1].toUpperCase();else if(/flyrnai\.org\/tools\/fly_predictome\/web\/famdb_details[a-z_]*\//.test(u)){var mt=u.match(/\/(\d+)\/(\d+)\/?(?:[?#]|$)/);t='https://flyark.github.io/LIVIA/'+((/_ortho/.test(u)||(mt&&mt[1]!=='7227'))?'ortholog_predictome':'flypredictome')+'.html?url='+encodeURIComponent(p);}if(t)window.open(t,'_blank','noopener');else alert('LIVIA bookmarklet is up to date. This page is not an AlphaFold DB entry or a FlyPredictome details page, so there is nothing to open here.');})();">Open in LIVIA</a>
<span style="font-size:.82rem; color:#6B6B6B;">← drag to your bookmarks bar</span>
</div>
<div style="background:#eaf2f8; border:1px solid #d4e3f0; border-radius:8px; padding:.7rem 1rem; margin-top:.5rem; font-size:.85rem; color:#1a5276;">If the bookmarks bar isn't visible, enable it with <strong>View → Show Bookmarks Bar</strong> or <strong>Ctrl/Cmd+Shift+B</strong>.</div>
<h4 style="color:#1a5276; font-size:.92rem; margin:1.1rem 0 .4rem;">Where it works</h4>
<div style="background:#f8f9fa; border-radius:8px; padding:.6rem 1rem; font-size:.84rem; color:#555; line-height:1.6;">
AlphaFold DB dimer/complex → <b style="color:#1a5276">AFDB Dimer</b> · AFDB monomer → <b style="color:#1a5276">AFDB Monomer Subdomain</b> · FlyPredictome → <b style="color:#1a5276">FlyPredictome</b> · FlyPredictome ortholog → <b style="color:#1a5276">Ortholog Interactome</b>. On any other page it shows a short message and does nothing.
</div>
<h4 style="color:#1a5276; font-size:.92rem; margin:1.1rem 0 .4rem;">If drag doesn't work</h4>
<p style="font-size:.9rem; color:#555; line-height:1.55;">Right-click the bookmarks bar → <em>Add page</em>, name it <code>LIVIA</code>, and paste this as the URL:</p>
<div style="background:#f4f6f8; border:1px solid #e0e6ec; border-radius:8px; padding:.7rem .9rem; margin-top:.5rem; font-family:ui-monospace,Menlo,monospace; font-size:.76rem; color:#555; line-height:1.45; white-space:pre-wrap; word-break:break-all;">javascript:(function(){var u=location.href,p=location.origin+location.pathname,t=null,m;if(m=u.match(/alphafold\.ebi\.ac\.uk\/entry\/(AF-\d+)/))t='https://flyark.github.io/LIVIA/dimer.html?id='+m[1];else if(m=u.match(/alphafold\.ebi\.ac\.uk\/entry\/(?:AF-)?([A-Z][0-9][A-Z0-9]{3}[0-9](?:[A-Z][A-Z0-9]{2}[0-9])?)/i))t='https://flyark.github.io/LIVIA/monomer.html?id='+m[1].toUpperCase();else if(/flyrnai\.org\/tools\/fly_predictome\/web\/famdb_details[a-z_]*\//.test(u)){var mt=u.match(/\/(\d+)\/(\d+)\/?(?:[?#]|$)/);t='https://flyark.github.io/LIVIA/'+((/_ortho/.test(u)||(mt&&mt[1]!=='7227'))?'ortholog_predictome':'flypredictome')+'.html?url='+encodeURIComponent(p);}if(t)window.open(t,'_blank','noopener');else alert('LIVIA bookmarklet is up to date. This page is not an AlphaFold DB entry or a FlyPredictome details page, so there is nothing to open here.');})();</div>
</div>
</div>
<!-- ============================================================ -->
<!-- TUTORIAL 3: FlyPredictome -->
<!-- ============================================================ -->
</div>
<div class="footer">
<a href="https://github.com/flyark/LIVIA" target="_blank">LIVIA GitHub</a> · <a href="https://github.com/flyark/AFM-LIS" target="_blank">AFM-LIS GitHub</a>
<br>
<a href="https://doi.org/10.64898/2026.05.01.721633" target="_blank">Kim & Perrimon (2026)</a>
<br>
Ah-Ram Kim · Harvard Medical School
</div>
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{ src: 'screenshots/tut_universal_1.png', caption: 'Load prediction files or pick a p53\u2013MDM2 example (AlphaFold-Multimer via ColabFold, AlphaFold3, Boltz-2, Chai-1, OpenFold3, Protenix-v2, ESMFold2), or a 3\u20134 chain AlphaFold3 complex (PRC2, BBSome, MIS12C)' },
{ src: 'screenshots/tut_universal_2.png', caption: 'Per-model metrics \u2014 iLIS, iLIA, iLISA, ipSAE, actifpTM, ipTM, LIS, cLIS, and LIR/cLIR counts, with iLIS FPR thresholds below' },
{ src: 'screenshots/tut_universal_identity.png', caption: 'Chain identity resolves each chain in UniProt (gene, organism, domains), then Reported Interactions (MIST) checks whether the pair is already on record \u2014 physical (PPI) and genetic (GI) interaction paper counts' },
{ src: 'screenshots/tut_universal_3.png', caption: 'Score Matrix \u2014 each triangle picks from iLIS, iLIA, iLISA, ipTM, ipSAE, actifpTM, LIS, cLIS, LIR, cLIR, pDockQ, LIpDockQ, pDockQ2 or LIpDockQ2 \u2014 alongside PAE, LIS, and cLIS heatmaps across all models' },
{ src: 'screenshots/tut_universal_labels.png', caption: 'Label Settings \u2014 axis name mode, style, and a custom "chain,label" editor that renames chains everywhere they appear' },
{ src: 'screenshots/tut_universal_seq.png', caption: 'LIR (light): PAE \u2264 12 \u00C5 residues. cLIR (dark bold): also within C\u03B2 8 \u00C5' },
{ src: 'screenshots/tut_universal_linear.png', caption: 'Linear Contact Map \u2014 cLIR contact lines with UniProt/Pfam domain tracks, pLDDT coloring, and MIST-reported interaction counts' },
{ src: 'screenshots/tut_universal_chord.png', caption: 'Circular Contact Map \u2014 chord diagram with cLIR contact lines and optional pLDDT/domain rings, per model or all models combined' },
{ src: 'screenshots/tut_universal_4.png', caption: 'View the 3D structure in Mol* viewer (with LIR/cLIR coloring)' },
{ src: 'screenshots/tut_universal_5.png', caption: 'Visualization Script \u2014 color presets, custom per-chain colors, and ChimeraX/PyMOL script preview with full/partial structure downloads' },
{ src: 'screenshots/tut_universal_6.png', caption: 'Per-Residue intra-chain LIS & pLDDT for both chains' }
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dimer: {
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{ src: 'screenshots/tut_dimer_1.png', caption: 'Drag the blue Open in LIVIA button to your browser\u2019s bookmarks bar \u2014 a one-time step' },
{ src: 'screenshots/tut_dimer_2.png', caption: 'Open any AlphaFold DB dimer entry page (alphafold.ebi.ac.uk/entry/AF-\u2026)' },
{ src: 'screenshots/tut_dimer_3.png', caption: 'Click the bookmark \u2014 LIVIA dimer opens in a new tab with interface metrics auto-loaded' },
{ src: 'screenshots/tut_dimer_3d.png', caption: 'Interactive 3D structure of the dimer in Mol* viewer (LIR cartoons, cLIR residues highlighted)' },
{ src: 'screenshots/tut_fly_bm.png', caption: 'Same flow on FlyPredictome \u2014 visit a famdb_details page and click the bookmark' },
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{ src: 'screenshots/tut_ortho_bm.png', caption: 'FlyPredictome’s ortholog detail pages also route to LIVIA Ortholog Interactome' }
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