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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<meta http-equiv="x-ua-compatible" content="ie=edge">
<meta name="author" content="Nejc Zupan">
<link rel="icon" type="image/png" href="/static/img/favicon.png">
<title>Kipoi</title>
<!-- Font Awesome -->
<link rel="stylesheet" type="text/css" href="/static/css/font-awesome.min.css">
<!-- Bootstrap core CSS -->
<link rel="stylesheet" type="text/css" href="/static/css/bootstrap.min.css">
<!-- Material Design Bootstrap -->
<link rel="stylesheet" type="text/css" href="/static/css/mdb.min.css">
<!-- Material Design Lite -->
<link rel="stylesheet" type="text/css" href="/static/css/material.min.css">
<!-- DataTables Material Design -->
<link rel="stylesheet" type="text/css" href="/static/css/dataTables.material.css"/>
<!-- Highlight -->
<link rel="stylesheet" type="text/css" href="/static/css/custom_highlight_github.css"/>
<!-- Custom styles -->
<link rel="stylesheet" type="text/css" href="/static/css/style.css?v=150318">
</head>
<body>
<section class="mb-3">
<!--Navbar-->
<nav class="navbar fixed-top navbar-expand-sm navbar-dark unique-color-kipoi">
<!-- Navbar brand -->
<span>
<a class="nav-title-link navbar-brand-nopad text-hide left-margin" href="/"
><img src="/static/img/nav_bar_logo_v3.png" height="50px" alt="Kipoi"/></a>
</span>
<!-- Collapse button -->
<button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbarNav1" aria-controls="navbarNav1" aria-expanded="false" aria-label="Toggle navigation"><span class="navbar-toggler-icon"></span></button>
<!-- Collapsible content -->
<div class="collapse navbar-collapse text-center" id="navbarNav1">
<!-- Links -->
<ul class="navbar-nav mr-auto text-center">
<!-- Group list -->
<li class="nav-item">
<a id="components-related-1" class="nav-button btn btn-outline-primary navbar-dark nabar-button " href="/groups/">Models</a>
</li>
<!-- About -->
<li class="nav-item">
<a id="components-related-2" class="nav-button btn btn-outline-primary navbar-dark nabar-button " href="/about/">About</a>
</li>
<!-- Docs -->
<li class="nav-item">
<a id="components-related-3" class="nav-button btn btn-outline-primary navbar-dark nabar-button" href="/docs/">Docs</a>
</li>
<!-- Seminar -->
<li class="nav-item">
<a id="components-related-4" class="nav-button btn btn-outline-primary navbar-dark nabar-button " href="/seminar/">Seminar</a>
</li>
<!-- Summit -->
<li class="nav-item">
<a style="border: 1px solid #ff4081 !important" id="components-related-5" class="nav-button btn btn-outline-primary navbar-dark nabar-button " href="/summit/">Kipoi Summit</a>
</li>
</ul>
<!-- Search form -->
<ul class="navbar-nav ml-auto text-center d-sm-none d-md-flex">
<li class="nav-item">
<a id="components-related-6" class="text-nowrap nav-link waves-effect waves-light" href="https://www.biorxiv.org/content/early/2018/07/24/375345.full.pdf">White paper<i class="fa fa-file-text-o" aria-hidden="true"></i></a>
</li>
<li class="nav-item">
<a id="components-related-7" class="text-nowrap nav-link waves-effect waves-light" href="https://github.com/kipoi/models">Model repository<i class="fa fa-github" aria-hidden="true"></i></a>
</li>
<li class="nav-item">
<a id="components-related-8" class="text-nowrap nav-link waves-effect waves-light" href="https://github.com/kipoi/kipoi">API repository<i class="fa fa-github" aria-hidden="true"></i></a>
</li>
</ul>
</div>
</nav>
</section>
<section class="main-content">
<div class="row" style="margin-right: 0; margin-left: 0;">
<div class="col-lg-9 mx-auto">
<div class="row mb-4">
<div class="col media kipoi-title-box d-none d-sm-flex">
<div class="media-left">
<img src="/static/img/kipoi_small.png" class="media-object" alt="Kipoi logo" height="80px">
</div>
<div class="media-body ">
<h3 class="media-heading">: Model zoo for genomics</h3>
</div>
</div>
<div class="col media kipoi-title-box d-flex d-sm-none">
<div class="media-body ">
<h3 class="media-heading">Model zoo for genomics</h3>
</div>
</div>
</div>
<div class="row mb-5">
<div class="col-md-6 col-sm-12">
<img src="/static/img/fig1_v8_hires.png" class="img-fluid p-3" alt="Kipoi overview figure">
</div>
<div class="col-md-6 col-sm-12">
<p class="p-3">
Kipoi (pronounce: kípi; from the Greek κήποι: gardens) is an <a href='https://github.com/kipoi/kipoi'>API</a> and a <a href='https://github.com/kipoi/models'>repository</a> of ready-to-use
trained models for genomics. It currently contains 2206
different models, covering canonical predictive tasks in transcriptional and post-transcriptional gene regulation.
Kipoi's API is implemented as a python package (<a href='https://github.com/kipoi/kipoi'>github.com/kipoi/kipoi</a>) and it is also accessible from the command line or R.
<!-- API to use, re-use and combine these models efficiently
and a flexible toolbox for downstream analysis like variant effect prediction. -->
<!-- The model is an abstraction over the model from major machine-learning frameworks in python
(Keras, TensorFlow, PyTorch, Scikit-learn) with the option to write a custom model.
The dataloader loads data from raw files and returns processed data, ready to be consumed by the
model together with the metadata.
This allows the models to be used directly with typical bioinformatics file formats like fasta or
bed and to, out-of-the-box, predict the effects of genetic variants.
The source is a remote storage for models and dataloaders. Users can access models from private or public sources.
The main public Kipoi source is hosted on github.com/kipoi/models with model parameters being stored with Git Large File Storage (LFS).
Model and dataloader are defined with YAML description files.
These provide general information about the model, authors, supported downstream analysis and required dependencies managed by pip or conda.
Models and dataloaders are contributed and reviewed through pull-requests on github. -->
<!-- - Unified and easy way to run models on new data
- Model dependencies managed by Conda
- Variant effect prediction for x models
- Transparency and overview
- Enriched functionality for the contributed models (less boilerplate code)
- Flexibility and ease of contribution
-->
</p>
</div>
</div>
<hr class="w-100 clearfix">
<div class="row mb-5">
<div class="col-lg-4 col-md-6 col-sm-6 col-12">
<h4>Numbers</h4>
<p><strong># of models:</strong> 2206</p>
<p><strong># of model groups:</strong> 38</p>
<p><strong># of contributors:</strong> 12</p>
<p><strong># of model groups supporting postprocessing:</strong></p>
<ul>
<li><strong>Variant effect prediction:</strong> 7/38</li>
</ul>
</div>
<!--Show some plots about Kipoi-->
<div class="col-lg-4 col-md-5 col-sm-6 col-9">
<h4>Model groups by framework</h4>
<div style="max-width:85%; max-height:85%;" class="px-3">
<canvas id="models-by-framework"></canvas>
</div>
</div>
<!-- <div class="col-md-4">
<h4>Model groups by <br />license</h4>
<canvas id="models-by-license"></canvas>
</div>
-->
<div class="col-lg-4 col-md-4 col-sm-4 col-9">
<h4>Model groups by tag</h4>
<div style="height: 280px">
<canvas id="models-by-genomics-tag"></canvas>
</div>
</div>
</div>
<hr class="w-100 clearfix">
<div class="row">
<div class="col">
<h3>Getting Started</h3>
</div>
</div>
<div class="row mb-5">
<div class="col-lg-4">
<h4>Use models</h4>
<ul>
<!-- <li>Install git-lfs: <code>$ conda install -c conda-forge git-lfs && git lfs install</code></li> -->
<li>Install Kipoi: <code>$ pip install kipoi</code></li>
<li>Choose the model from <a href="/groups/">http://kipoi.org/models</a></li>
<li>Use the model from CLI/python/bash by copying code snippets from <a href="../models/Basenji">http://kipoi.org/models/my_model</a></li>
</ul>
<a class="btn btn-outline-info waves-effect" href="../docs/using/01_Getting_started/">Learn more</a>
</div>
<div class="col-lg-4">
<h4>Contribute models</h4>
<ul>
<!-- <li>Install git-lfs: <code>$ conda install -c conda-forge git-lfs && git lfs install</code></li> -->
<li>Install Kipoi: <code>$ pip install kipoi</code></li>
<li>Run <code>$ kipoi ls</code></li>
<li>Explore the models locally at <code>~/.kipoi/models</code></li>
<li>Upload model weights to <a href='https://zenodo.org'>zenodo</a> or <a href='https://figshare.com/'>figshare</a>.</li>
<li>Add the model to <code>~/.kipoi/models/</code> (copy&edit the existing model or run <code>kipoi init</code>)</li>
<li>Test the model: <code>kipoi test ~/.kipoi/models/my_model</code></li>
<li>Submit the pull-request to <a href="https://github.com/kipoi/models">github.com/kipoi/models</a></li>
</ul>
<a class="btn btn-outline-info waves-effect" href="../docs/contributing/01_Getting_started/">Learn more</a>
</div>
<div class="col-lg-4">
<h4>Contribute code</h4>
<ul>
<li>Setup the development environment: <code>$ pip install kipoi[develop]</code></li>
<li>Read <a href="https://github.com/kipoi/kipoi/blob/master/CONTRIBUTING.md">CONTRIBUTING.md</a></li>
<li>Submit an issue/pull-request to <a href="https://github.com/kipoi/kipoi">github.com/kipoi/kipoi</a></li>
</ul>
</div>
</div>
<hr class="w-100 clearfix">
<div class="row mb-4">
<div class="col-lg-4 col-md-12">
<div style="padding:10px"></div>
<a class="twitter-timeline" data-width="auto" data-tweet-limit="10" data-dnt="true" data-show-replies="true" href="https://twitter.com/KipoiZoo?ref_src=twsrc%5Etfw">Tweets KipoiZoo</a> <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
</div>
<div class="col-lg-8 col-md-12">
<!-- Some news -->
<!--<h4>News</h4>
<ul>
<li></li>
<li></li>
<li></li>
</ul>-->
</div>
</div>
</div>
</div>
</section>
<footer class="page-footer center-on-small-only unique-color">
<!--Footer links-->
<div class="container-fluid">
<div class="row">
<!--First column-->
<div class="col-lg-3 col-md-6 ml-auto">
<h5 class="title mb-3"><strong>About KIPOI project</strong></h5>
<p>Kipoi is an API and a repository of ready-to-use trained models for genomics.</p>
</div>
<!--/.First column-->
<hr class="w-100 clearfix d-md-none">
<!--Second column-->
<div class="col-lg-2 col-md-6 ml-auto">
<h5 class="title mb-3"><strong>Useful links</strong></h5>
<ul>
<li>
<a href="https://github.com/kipoi/kipoi">API repository <i class="fa fa-github" aria-hidden="true"></i></a>
</li>
<li>
<a href="https://github.com/kipoi/models">Model repository <i class="fa fa-github" aria-hidden="true"></i></a>
</li>
<li>
<a href="https://github.com/kipoi/website">Website repository <i class="fa fa-github" aria-hidden="true"></i></a>
</li>
</ul>
</div>
<!--/.Second column-->
<hr class="w-100 clearfix d-lg-none">
<!--Third column-->
<div class="col-lg-4 col-md-12 ml-auto text-center">
<ul>
<li>
<h5>Like the project?</h5>
</li>
<li>
<a target="_blank" href="https://twitter.com/KipoiZoo" class="btn btn-primary waves-effect waves-light" rel="nofollow">Tweet us!</a>
</li>
</ul>
</div>
<!--/.Third column-->
</div>
</div>
<!--/.Footer links-->
<!--Copyright-->
<div class="footer-copyright">
<div class="containter-fluid">
© 2025 The Kipoi team, website developed by
<a href="https://github.com/zupan" class="Nejc Zupan github">
Nejc Zupan
<i class="fa fa-github" aria-hidden="true"></i>
</a>
</div>
</div>
<!--/.Copyright-->
</footer>
<!-- SCRIPTS -->
<!-- JQuery -->
<script type="text/javascript" src="/static/js/jquery-3.2.1.min.js"></script>
<!-- Bootstrap tooltips -->
<script type="text/javascript" src="/static/js/popper.min.js"></script>
<!-- Bootstrap core JavaScript -->
<script type="text/javascript" src="/static/js/bootstrap.min.js"></script>
<!-- MDB core JavaScript -->
<script type="text/javascript" src="/static/js/mdb.min.js"></script>
<!-- DataTables -->
<script type="text/javascript" src="/static/js/jquery.dataTables.min.js"></script>
<script type="text/javascript" src="/static/js/dataTables.material.min.js"></script>
<!-- Highlight -->
<script type="text/javascript" src="/static/js/highlight.pack.js"></script>
<!-- Global site tag (gtag.js) - Google Analytics -->
<script async src="https://www.googletagmanager.com/gtag/js?id=UA-115025493-1"></script>
<script>
window.dataLayer = window.dataLayer || [];
function gtag(){dataLayer.push(arguments);}
gtag('js', new Date());
gtag('config', 'UA-115025493-1');
</script>
<script src="https://cdn.jsdelivr.net/npm/[email protected]/palette.js"></script>
<script language="JavaScript">
$(document).ready(function() {
var color_pallete = 'cb-Set2';
// models-by-framework
var colors = palette(color_pallete, 5).map(function(hex) {
return '#' + hex;
});
var ctxP = document.getElementById("models-by-framework").getContext('2d');
var myPieChart = new Chart(ctxP, {
type: 'doughnut',
data: {
labels: ['keras', 'pytorch', 'custom', 'tensorflow', 'sklearn'],
datasets: [
{
data: [9, 2, 2, 1, 1],
backgroundColor: ['#ff8f5a', '#8da0cb', '#66c2a5', '#ffd92f', '#e78ac3'],
hoverBackgroundColor: ['#ff8f5a', '#8da0cb', '#66c2a5', '#ffd92f', '#e78ac3'],
/* backgroundcolor: ["#F7464A", "#46BFBD", "#FDB45C", "#949FB1", "#4D5360"],
hoverBackgroundColor: ["#FF5A5E", "#5AD3D1", "#FFC870", "#A8B3C5", "#616774"]*/
}
]
},
options: {
responsive: true
}
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// models-by-license
/* var ctxP = document.getElementById("models-by-license").getContext('2d');
* var myPieChart = new Chart(ctxP, {
* type: 'doughnut',
* data: {
* labels: ['MIT', 'Apache License v2', 'BSD 3-Clause', 'Other / Non-commercial (see LICENSE.txt)', 'Non-comercial', 'GPL-3', 'CC-BY-ND', 'GPL-v3', 'CC BY-NC 4.0', 'Apache License 2.0'],
* datasets: [
* {
* data: [27, 3, 1, 1, 1, 1, 1, 1, 1, 1],
* backgroundColor: ["#F7464A", "#46BFBD", "#FDB45C", "#949FB1", "#4D5360"],
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* }
* ]
* },
* options: {
* responsive: false
* }
* });*/
//bar
var ctxB = document.getElementById("models-by-genomics-tag").getContext('2d');
var myBarChart = new Chart(ctxB, {
type: 'horizontalBar',
data: {
labels: ['RNA splicing', 'DNA binding', 'DNA accessibility', 'RNA expression', 'Histone modification', 'DNA methylation', 'RNA binding'],
datasets: [{
label: null,
data: [7, 6, 5, 3, 3, 3, 2],
/* backgroundColor: ["#F7464A80", "#46BFBD80", "#FDB45C80", "#949FB180", "#F3E06980", "#4D536080", "#AAABAA80"],*/
backgroundColor: palette(color_pallete, 7).map(function(hex) {
return '#' + hex;
}),
/* borderColor: [
'rgba(255,99,132,1)',
'rgba(54, 162, 235, 1)',
'rgba(255, 206, 86, 1)',
'rgba(75, 192, 192, 1)',
'rgba(153, 102, 255, 1)',
'rgba(255, 159, 64, 1)',
'rgba(255, 159, 64, 1)'
],*/
/* borderWidth: 1*/
}]
},
options: {
maintainAspectRatio: false,
responsive: true,
legend: {
display: false,
},
scales: {
ticks: {
autoSkip: false
},
xAxes: [{
beginAtZero: true,
ticks: {
beginAtZero: true,
autoSkip: false
/* maxRotation: 90*/
},
}],
yAxes: [{
beginAtZero:true,
ticks: {
beginAtZero:true
}
}]
}
}
});
});
</script>
</body>
</html>