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<!doctype html>
<html class="welcome" lang="{{ str_replace('_', '-', app()->getLocale()) }}">
@include('layouts.head')
@php
use App\Http\Controllers\StatisticsController;
@endphp
<body>
<div id="page-top"></div>
<!-- Navigation-->
<nav class="navbar navbar-expand-lg navbar-light fixed-top py-3" id="mainNav">
<div class="container px-4 px-lg-5">
<ul class="navbar-nav ms-auto my-2 my-lg-0">
<li class="nav-item">
<a class="nav-link" href="#page-top"> <span class="nav-icon" style="">⌂</span> FAIRMD Lipids</a>
</li>
</ul>
<button class="navbar-toggler navbar-toggler-right" type="button" data-bs-toggle="collapse"
data-nav-target="#navbarResponsive" aria-controls="navbarResponsive" aria-expanded="false"
aria-label="Toggle navigation">
<span class="navbar-toggler-icon"></span>
</button>
<div class="collapse navbar-collapse" id="navbarResponsive">
<ul class="navbar-nav ms-auto my-2 my-lg-0">
<!-- li class="nav-item">
<form action="{{ route('search.results') }}" method="get" class="d-flex align-items-center">
<input type="text" name="text" class="form-control form-control-sm" placeholder="Search..." aria-label="Search" style="width: 150px;">
<button class="btn btn-sm btn-outline-light ms-1" type="submit">Go</button>
</form>
</li --- IGNORE --->
<li class="nav-item"><a class="nav-link" href="{{ route('new_advanced_search.form') }}" title="Search simulations by membrane composition, force field, temperature and more"><span class="nav-icon" aria-hidden="true" style="font-size: 1.2rem;">⌕ </span>Advanced Search</a></li>
<li class="nav-item"><a class="nav-link" href="{{ route('lipids.list') }}" title="Browse all lipid molecules in the databank"><span class="nav-icon" aria-hidden="true">◌</span>Lipids</a></li>
<li class="nav-item"><a class="nav-link" href="{{ route('experiments.list') }}" title="Browse experimental NMR and X-ray measurements"><span class="nav-icon" aria-hidden="true">⚗</span>Experiments</a></li>
<li class="nav-item"><a class="nav-link" href="{{ route('simulations.list') }}" title="Browse and compare MD simulation trajectories"><span class="nav-icon" aria-hidden="true">◈</span>Simulations</a></li>
<li class="nav-item"><a class="nav-link" href="{{ config('app.github_contribute_url') }}" title="Learn how to contribute your simulation data to the databank"><span class="nav-icon" aria-hidden="true">✦</span>Contribute</a></li>
<li class="nav-item"><a class="nav-link" href="#about" title="About FAIRMD Lipids Databank"><span class="nav-icon" aria-hidden="true">ⓘ</span>About</a></li>
<li class="nav-item d-flex align-items-center ms-2">
<button class="contrast-toggle" id="contrastToggle" type="button" title="Toggle high-contrast mode" aria-label="Toggle high-contrast mode">◔</button>
</li>
</ul>
</div>
</div>
</nav>
<div class="container-fluid p-0" style="display: flex; flex-direction: column; min-height: 50vh;">
<!-- Masthead-->
<header class="masthead">
<div class="container px-4 px-lg-5">
{{-- Hero area --}}
<div class="row justify-content-center text-center pt-2 pt-lg-4">
<div class="col-lg-8">
<img class="img-fluid d-block mx-auto fairmd-logo" alt="FAIRMD Lipids Databank Logo"
src="{{ asset('images/fairmd_w_letras.png') }}"
style="max-width: 420px; width: 100%; padding: 0.5rem 0 1rem;">
<p class="text-white-75" style="font-size: 0.85rem; margin-bottom: 0.25rem;">version {{ config('app.version') }}</p>
<p class="text-white-80 mb-4" style="max-width: 600px; margin: 0 auto; line-height: 1.6;">
Browse, search and compare atomistic MD simulations and experimental data of lipid membranes from the
<a href="https://github.com/NMRLipids/Databank">FAIRMD Lipids Databank</a>.
</p>
</div>
</div>
{{-- Search card --}}
<div class="row justify-content-center">
<div class="col-lg-7 col-xl-6">
<div class="hero-card">
{{-- Main search --}}
<form action="{{ route('search.results') }}" method="get" class="mb-3">
<div class="input-group input-group-lg">
<input id="BasicSearch" type="text" name="text" class="form-control"
placeholder="Search by name, InChI, SMILES, DOI…"
aria-label="Search field">
<button class="btn btn-accent" type="submit">Search</button>
</div>
</form>
{{-- Quick links --}}
<div class="d-flex flex-wrap gap-2 justify-content-center mb-3">
<a href="{{ route('search.results') }}" class="btn btn-outline-light btn-sm">Browse All</a>
<a href="{{ route('new_advanced_search.form') }}" class="btn btn-outline-light btn-sm">Advanced Search</a>
<a href="{{ route('lipids.list') }}" class="btn btn-outline-light btn-sm">Lipids</a>
<a href="{{ route('experiments.list') }}" class="btn btn-outline-light btn-sm">Experiments</a>
<a href="{{ route('simulations.list') }}" class="btn btn-outline-light btn-sm">Simulations</a>
</div>
<hr style="border-color: rgba(255,255,255,0.2); margin: 0.75rem 0;">
{{-- Best simulation finder --}}
<form action="{{ route('simulations.list') }}" method="get" class="d-flex justify-content-center">
<input type="hidden" name="sort" value="best">
<input type="hidden" name="direction" value="desc">
<div class="input-group" style="max-width: 400px;">
<select name="lipid" class="form-select" aria-label="Select lipid">
<option value="" selected disabled>Best simulations for lipid…</option>
@foreach ($lipids as $lipid)
<option value="{{ $lipid->molecule }}">{{ $lipid->molecule }}</option>
@endforeach
</select>
<button class="btn btn-warning" type="submit"
data-bs-toggle="tooltip" data-bs-placement="top"
title="Rank product of order-parameter (NMR) and form-factor (X-ray) agreement — a non-parametric statistic that combines two independent quality dimensions without scale assumptions.">★ Find Best</button>
</div>
</form>
<p class="text-white-75 mb-0 mt-2" style="font-size: 0.78rem; line-height: 1.35;">
Simulations are scored by the <strong>rank product</strong> ({!! renderDOI('10.1016/j.febslet.2004.07.055') !!}) of their agreement with NMR order parameters and X-ray form factors — two independent experimental observables. Lower rank product = better overall quality.
</p>
</div>
</div>
</div>
{{-- Examples & stats --}}
<div class="row justify-content-center text-center mt-3 mb-2 mb-lg-3">
<div class="col-lg-7">
<p class="text-white-75 mb-2" style="font-size: 0.85rem;">
Try:
<a href="#" id="expopc" class="hero-example">POPC</a>,
<a href="#" id="expopcpope" class="hero-example">POPC:POPE</a>, or
<a href="#" id="lipid_name_example" class="hero-example">full lipid names</a>.
Search by trajectory ID (<code style="color: #ffe0b2;">ID123</code>) or
DOI (<code style="color: #ffe0b2;">DOI:10.1021/…</code>).
</p>
<div class="hero-stats-card" role="status" aria-label="Databank totals">
<p class="hero-stats-label mb-1">Databank at a glance</p>
<p class="hero-stats mb-0">
{{ StatisticsController::totals() }}
</p>
</div>
</div>
</div>
</div>
</header>
<!--div class="container" style=" height: 10em; display: flex; background-color: #00000000;">
</div-->
<!-- About-->
<section class="page-section" id="about" style="padding: 2.25rem 0 4rem;">
<div class="container px-4 px-lg-5">
<div class="row justify-content-center">
<div class="col-lg-9">
<h2 class="text-center mb-4" style="color: #0e4a56; font-weight: 700;">About FAIRMD Lipids Databank</h2>
<hr class="divider mb-4">
<div class="about-card mb-4">
<h4>What is FAIRMD Lipids Databank?</h4>
<p>FAIRMD Lipids Databank is a community-driven catalogue containing
atomistic molecular dynamics (MD) simulations of biologically relevant
lipid membranes emerging from the <a href="http://nmrlipids.blogspot.com/">NMRlipids open collaboration</a>.
It improves the <a href="https://www.go-fair.org/fair-principles/">Findability, Accessibility, Interoperability, and Reuse (FAIR)</a>
of MD simulation data using an overlay databank structure described in the
<a href="https://www.nature.com/articles/s41467-024-45189-z">databank publication</a>.
See the <a href="https://databank.readthedocs.io/">online documentation</a> for full details.</p>
</div>
<div class="about-card mb-4" style="border-left: 4px solid #e8a735; background: linear-gradient(135deg, #fffbe6 0%, #fff 100%);">
<h4 style="color: #7a5e00;">✦ Contribute to the Databank</h4>
<p>FAIRMD Lipids Databank grows through community contributions. You can add your
simulation and experimental data, report issues, or help improve the codebase.</p>
<div class="d-flex flex-wrap gap-2">
<a href="{{ config('app.submission_portal_url') }}" class="btn btn-warning btn-sm" target="_blank" rel="noopener noreferrer">Submission Portal</a>
<a href="{{ config('app.github_contribute_url') }}" class="btn btn-outline-secondary btn-sm" target="_blank" rel="noopener noreferrer">How to Contribute Data</a>
<a href="https://github.com/NMRLipids/Databank/issues" class="btn btn-outline-secondary btn-sm" target="_blank" rel="noopener noreferrer">Report an Issue</a>
<a href="https://github.com/NMRLipids/databank-template/blob/main/scripts/" class="btn btn-outline-secondary btn-sm" target="_blank" rel="noopener noreferrer">Jupyter Notebooks & API Examples</a>
</div>
</div>
<div class="about-card mb-4">
<h4>Components</h4>
<div class="row g-3">
<div class="col-md-4">
<div class="component-pill">
<strong>Databank-UI</strong>
<span>This website — browse, search and compare simulations.
<a href="https://github.com/NMRLipids/BilayerUI_laravel">GitHub</a></span>
</div>
</div>
<div class="col-md-4">
<div class="component-pill">
<strong>Databank-API</strong>
<span>Programmatic access for data-driven applications.
<a href="http://github.com/NMRlipids/Databank/">GitHub</a></span>
</div>
</div>
<div class="col-md-4">
<div class="component-pill">
<strong>BilayerData</strong>
<span>Metadata repository with trajectories on <a href="https://zenodo.org/">Zenodo</a>.
<a href="https://github.com/NMRLipids/BilayerData">GitHub</a></span>
</div>
</div>
</div>
</div>
<div class="row g-3 mb-4">
<div class="col-md-6">
<div class="about-card h-100">
<h4>Citing & Licensing</h4>
<p>Please cite the <a href="https://www.nature.com/articles/s41467-024-45189-z">Databank publication</a>
and relevant trajectory entries.</p>
<ul class="small mb-0">
<li>Data: <a href="https://github.com/NMRLipids/BilayerData/blob/main/LICENSE">CC-BY-4.0</a></li>
<li>API code: <a href="https://github.com/NMRLipids/Databank/blob/main/LICENSE">GPLv3</a></li>
<li>GUI code: <a href="https://github.com/NMRLipids/BilayerGUI_laravel/blob/main/LICENSE">MIT</a></li>
</ul>
</div>
</div>
<div class="col-md-6">
<div class="about-card h-100">
<h4>Resources</h4>
<ul class="small mb-2">
<li><a href="https://databank.readthedocs.io/">Full documentation</a></li>
<li><a href="http://nmrlipids.blogspot.com/">NMRlipids blog</a></li>
<li><strong>AI assistants:</strong> connect via our
<a href="https://modelcontextprotocol.io/">MCP</a> server at
<code style="color: #0e4a56;">{{ url('/mcp/fairmd-lipids') }}</code>
(see <a href="{{ url('/llms.txt') }}">llms.txt</a>).</li>
</ul>
<p class="small text-dark mb-0">All data and code are provided AS-IS with no warranty. Report issues via each component's GitHub tracker.</p>
</div>
</div>
</div>
</div>
</div>
</div>
</section>
</div>
<script>
$(function() {
$("#BasicSearch").autocomplete({
source: function(request, response) {
$.ajax({
url: "{{ route('search.basic') }}",
dataType: "json",
data: {
term: request.term
},
success: function(data) {
response(data);
}
});
}
});
$('#expopc').click(function(e) {
e.preventDefault();
$('#BasicSearch').val('POPC').focus();
});
$('#expopcpope').click(function(e) {
e.preventDefault();
$('#BasicSearch').val('POPC:POPE').focus();
});
$('#lipid_name_example').click(function(e) {
e.preventDefault();
$('#BasicSearch').val('1-octadecanoyl-2-(9Z)-octadecenoyl-sn-glycero-3-phosphocholine').focus();
});
});
</script>
@include('layouts.foot')