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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">
<title>Monash Genomics & Bioinformatics Platform - GitHub Projects</title>
<!-- Tailwind CSS from CDN -->
<script src="https://cdn.tailwindcss.com"></script>
<!-- Vue.js from CDN -->
<script src="https://unpkg.com/vue@3/dist/vue.global.js"></script>
<script>
tailwind.config = {
theme: {
extend: {
colors: {
monash: '#005F9A',
}
}
}
}
</script>
<style type="text/tailwindcss">
@layer components {
.repo-card {
@apply bg-white rounded-lg shadow-md overflow-hidden transition-transform hover:shadow-lg hover:scale-105;
}
.repo-card-header {
@apply bg-monash text-white px-4 py-3 font-bold text-xl;
}
.repo-card-body {
@apply p-4;
}
.repo-name {
@apply text-gray-700 mb-3 font-mono text-sm;
}
.repo-image {
@apply bg-gray-100 h-40 w-full flex items-center justify-center mb-3 rounded;
}
.section-header {
@apply text-2xl font-bold text-monash mb-6 mt-12 border-b-2 border-monash pb-2;
}
}
</style>
</head>
<body class="bg-gray-50 min-h-screen">
<div id="app">
<header class="bg-monash text-white py-10">
<div class="container mx-auto px-4">
<h1 class="text-4xl font-bold">Monash Genomics & Bioinformatics Platform</h1>
<p class="text-xl mt-2">Open Source GitHub Projects</p>
</div>
</header>
<main class="container mx-auto px-4 py-8">
<!-- Web apps and dashboards -->
<section>
<h2 class="section-header">Web Apps and Dashboards</h2>
<div class="grid grid-cols-1 md:grid-cols-3 gap-6">
<repo-tile
v-for="repo in webApps"
:key="repo.name"
:title="repo.title"
:repo-name="repo.repoName"
:description="repo.description"
:url="repo.url"
:source='repo.source'
:repo-image="repo.repoImage">
</repo-tile>
</div>
</section>
<!-- Commandline tools -->
<section>
<h2 class="section-header">Commandline Tools</h2>
<div class="grid grid-cols-1 md:grid-cols-3 gap-6">
<repo-tile
v-for="repo in commandlineTools"
:key="repo.name"
:title="repo.title"
:repo-name="repo.repoName"
:description="repo.description"
:url="repo.url"
:repo-image="repo.repoImage">
</repo-tile>
</div>
</section>
<!-- Data Analysis -->
<section>
<h2 class="section-header">Data Analysis Tools</h2>
<div class="grid grid-cols-1 md:grid-cols-3 gap-6">
<repo-tile
v-for="repo in dataAnalysisTools"
:key="repo.name"
:title="repo.title"
:repo-name="repo.repoName"
:description="repo.description"
:url="repo.url"
:repo-image="repo.repoImage">
</repo-tile>
</div>
</section>
<!-- Empty sections for future additions -->
<section>
<h2 class="section-header">Pipelines</h2>
<div class="grid grid-cols-1 md:grid-cols-3 gap-6">
<div class="flex items-center justify-center p-8 bg-gray-100 rounded-lg">
<p class="text-gray-500 italic">Future pipelines will be listed here</p>
</div>
</div>
</section>
<section>
<h2 class="section-header">Training & Workshops</h2>
<div class="grid grid-cols-1 md:grid-cols-3 gap-6">
<repo-tile
v-for="repo in trainingWorkshops"
:key="repo.name"
:title="repo.title"
:repo-name="repo.repoName"
:description="repo.description"
:url="repo.url"
:repo-image="repo.repoImage">
</repo-tile>
</div>
</section>
<section>
<h2 class="section-header">Open Analysis Projects</h2>
<div class="grid grid-cols-1 md:grid-cols-3 gap-6">
<div class="flex items-center justify-center p-8 bg-gray-100 rounded-lg">
<p class="text-gray-500 italic">Future analysis projects will be listed here</p>
</div>
</div>
</section>
</main>
<footer class="bg-gray-800 text-white py-8">
<div class="container mx-auto px-4">
<div class="flex flex-col md:flex-row justify-between items-center">
<div class="mb-4 md:mb-0">
<h3 class="text-xl font-bold">Monash Bioinformatics Platform</h3>
<p class="mt-2">Providing bioinformatics support and solutions</p>
</div>
<div>
<a href="https://github.com/MonashBioinformaticsPlatform" target="_blank" class="inline-flex items-center text-white hover:text-gray-300">
<svg class="h-6 w-6 mr-2" fill="currentColor" viewBox="0 0 24 24" aria-hidden="true">
<path fill-rule="evenodd" d="M12 2C6.477 2 2 6.484 2 12.017c0 4.425 2.865 8.18 6.839 9.504.5.092.682-.217.682-.483 0-.237-.008-.868-.013-1.703-2.782.605-3.369-1.343-3.369-1.343-.454-1.158-1.11-1.466-1.11-1.466-.908-.62.069-.608.069-.608 1.003.07 1.531 1.032 1.531 1.032.892 1.53 2.341 1.088 2.91.832.092-.647.35-1.088.636-1.338-2.22-.253-4.555-1.113-4.555-4.951 0-1.093.39-1.988 1.029-2.688-.103-.253-.446-1.272.098-2.65 0 0 .84-.27 2.75 1.026A9.564 9.564 0 0112 6.844c.85.004 1.705.115 2.504.337 1.909-1.296 2.747-1.027 2.747-1.027.546 1.379.202 2.398.1 2.651.64.7 1.028 1.595 1.028 2.688 0 3.848-2.339 4.695-4.566 4.943.359.309.678.92.678 1.855 0 1.338-.012 2.419-.012 2.747 0 .268.18.58.688.482A10.019 10.019 0 0022 12.017C22 6.484 17.522 2 12 2z" clip-rule="evenodd"></path>
</svg>
GitHub Organization
</a>
</div>
</div>
<div class="mt-8 pt-8 border-t border-gray-700 text-center text-sm text-gray-400">
© 2025 Monash Genomics and Bioinformatics Platform. All rights reserved.
</div>
</div>
</footer>
</div>
<!-- Vue Component Templates -->
<script type="text/x-template" id="repo-tile-template">
<a :href="url" target="_blank" class="repo-card">
<div class="repo-card-header">{{ title }}</div>
<div class="repo-card-body">
<div class="repo-name">{{ repoName }}</div>
<div class="repo-image">
<img v-if="repoImage" :src="repoImage" :alt="title" class="h-full w-full object-contain">
<svg v-else xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke="currentColor" class="h-12 w-12 text-gray-400">
<path stroke-linecap="round" stroke-linejoin="round" stroke-width="1" d="M4 16l4.586-4.586a2 2 0 012.828 0L16 16m-2-2l1.586-1.586a2 2 0 012.828 0L20 14m-6-6h.01M6 20h12a2 2 0 002-2V6a2 2 0 00-2-2H6a2 2 0 00-2 2v12a2 2 0 002 2z" />
</svg>
</div>
<p class="text-gray-600">{{ description }}</p>
</div>
</a>
</script>
<!-- Vue.js Application Code -->
<script>
// Define the repo-tile component
const { createApp } = Vue;
const app = createApp({
data() {
return {
webApps: [
{
title: 'Laxy',
repoName: 'MonashBioinformaticsPlatform/laxy',
description: 'A web platform for running RNAseq QC and counts table',
source: 'https://github.com/MonashBioinformaticsPlatform/laxy',
url: 'https://laxy.io/#/',
repoImage: 'https://github.com/MonashBioinformaticsPlatform/laxy/raw/master/docs/screenshots/job_page.png'
},
{
title: 'Degust',
repoName: 'drpowell/degust',
description: 'A web platform for running RNAseq Differential Expression Analysis',
url: 'https://degust.erc.monash.edu/',
source: 'https://github.com/drpowell/degust',
repoImage: 'https://raw.githubusercontent.com/drpowell/degust/master/docs/images/screenshot-mds.png'
},
{
title: 'Analyst Suites',
repoName: 'MonashBioinformaticsPlatform/LFQ-Analyst, ',
description: 'A web application for analyzing proteomics data and functional enrichment',
source: 'https://github.com/MonashBioinformaticsPlatform/LFQ-Analyst',
url : 'https://analyst-suites.org/',
repoImage: 'https://github.com/MonashBioinformaticsPlatform/LFQ-Analyst/raw/master/www/LFQ_analyst.svg'
}
],
commandlineTools: [
{
title: 'Bio-Ansible',
repoName: 'MonashBioinformaticsPlatform/bio-ansible',
description: 'Ansible playbooks for setting up bioinformatics environments',
url: 'https://github.com/MonashBioinformaticsPlatform/bio-ansible',
repoImage: null
},
{
title: 'Rocker-Ultra',
repoName: 'MonashBioinformaticsPlatform/rocker-ultra',
description: 'Extended Docker containers for R-based bioinformatics',
url: 'https://github.com/MonashBioinformaticsPlatform/rocker-ultra',
repoImage: null
}
],
dataAnalysisTools: [
{
title: 'Varistran',
repoName: 'MonashBioinformaticsPlatform/varistran',
description: 'Variance-stabilizing transformation for RNA-seq data visualization',
url: 'https://github.com/MonashBioinformaticsPlatform/varistran',
repoImage: 'https://github.com/MonashBioinformaticsPlatform/varistran/blob/master/doc/heatmap-example.png?raw=true'
}
],
trainingWorkshops: [
{
title: 'Recommended Learning Resources',
repoName: 'MonashBioinformaticsPlatform/learning-resource-links',
description: 'A list of learning resources for bioinformatics, genomics and computational biology',
url: 'https://github.com/MonashBioinformaticsPlatform/learning-resource-links',
repoImage: null
},
{
title: 'Introduction to R',
repoName: 'MonashDataFluency/r-intro-2',
description: 'An Introduction to the basics of using R. Ideal for beginners',
url: 'https://monashdatafluency.github.io/r-intro-2/',
repoImage: 'https://monashdatafluency.github.io/r-intro-2/plotting_files/figure-html/unnamed-chunk-7-1.png'
},
{
title: 'Best Practices in Using R',
repoName: 'MonashBioinformaticsPlatform/r-more',
description: 'Advanced R workshop - builds on the Introduction to R workshop',
url: 'https://monashbioinformaticsplatform.github.io/r-more/',
repoImage: null
},
{
title: 'Linear Models in R',
repoName: 'MonashDataFluency/r-linear',
description: 'Workshop on using linear models in R. Includes an example for RNAseq differential analysis',
url: 'https://monashdatafluency.github.io/r-linear/',
repoImage: null
},
{
title: 'Introduction to single cell analysis with Seurat',
repoName: 'MonashBioinformaticsPlatform/scRNAseq_Workshop',
description: 'An introduction to analysing single cell data using Seurat. Includes cell type annotation with singleR, dataset integration with harmony',
url: 'https://monashbioinformaticsplatform.github.io/scRNAseq_Workshop/',
repoImage: 'https://monashbioinformaticsplatform.github.io/scRNAseq_Workshop/scRNAseqInR_ABACBS_2024_Doco_files/figure-html/harmony4-1.png'
},
{
title: 'Functional Enrichment Workshop',
repoName: 'MonashBioinformaticsPlatform/Functional_Enrichment_BioCommons_2024',
description: 'This workshop is designed to guide you through the process of performing functional enrichment analysis using a variety of tools and methodologies, both online and via command-line interfaces.',
url: 'https://monashbioinformaticsplatform.github.io/Functional_Enrichment_BioCommons_2024/',
repoImage: 'https://monashbioinformaticsplatform.github.io/Functional_Enrichment_BioCommons_2024/images/fea_types.jpg'
},
{
title: 'Mastering Bulk RNA-seq: Plan, Analyse and Interpret',
repoName: 'MonashBioinformaticsPlatform/RNAseq_workshop',
description: 'An introduction to analysing bulk RNAseq data using web based tools - no coding required',
url: 'https://monashbioinformaticsplatform.github.io/RNAseq_workshop/',
repoImage: 'https://monashbioinformaticsplatform.github.io/RNAseq_workshop/images/degust/degust.png'
}
]
}
}
});
// Register the repo-tile component
app.component('repo-tile', {
template: '#repo-tile-template',
props: {
title: String,
repoName: String,
description: String,
url: String,
repoImage: String
}
});
// Mount the app
app.mount('#app');
</script>
</body>
</html>