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<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8">
<title>Division of Computational Systems Medicine</title>
<meta name="viewport" content="width=device-width, initial-scale=1.0, minimum-scale=1.0, maximum-scale=1.0">
<link href="static/css.css" media="screen" rel="stylesheet" type="text/css" />
<script src="static/modernizr.js" type="text/javascript"></script>
</head>
<body>
<div class="wrapper">
<div class="profile">
<section class="profile-masthead" id="masthead">
<header class="profile-logo">
<div class="profile-logo-image">
<img alt="CSM" src="static/images/csm-logo-pdf-80x133.png" />
</div>
</header>
<aside class="profile-summary">
<div class="summary-location summary-module">
<a href="http://github.com/csmsoftware">github.com/csmsoftware</a>
</div>
</aside>
</section>
<section class="profile-content" id="content">
<div class="profile-description">
<p>Welcome to the Github website for the Division of Computational and Systems Medicine at Imperial College London.
Here you can find the source code and documentation for publically available software developed by CSM.</p>
</div>
<article class="profile-menu" id="menu">
<nav class="menu-navigation">
<ul class="menu-navigation-list">
<li class="menu-navigation-list-item"><a href="#python">Python</a></li>
<li class="menu-navigation-list-item"><a href="#r">R</a></li>
<li class="menu-navigation-list-item"><a href="#matlab">Matlab</a></li>
</ul>
</nav>
<div id="python" class="menu-category">
<h3 class="menu-category-name">Python</h3>
<ol class="menu-category-list has-images">
<li class="menu-item">
<div class="menu-item-info">
<h4 class="menu-item-name">nPYc Toolbox</h4>
<span class="menu-item-price">
<a href="https://github.com/phenomecentre/nPYc-Toolbox" target="_blank">GitHub source</a> |
<a href="http://npyc-toolbox.readthedocs.io/en/latest/index.html" target="_blank">Documentation</a> |
<a href="https://opensource.org/licenses/MIT" target="_blank">Licence</a>
</span>
<p class="menu-item-description">
<br />
A Python implementation of the NPC toolchain for the import, quality-control, and preprocessing of metabolic profiling datasets.
<br /><br />
Requirements:
<br />
<br /> - Python3.6
</p>
</div>
<div class="menu-item-image has-meta-content">
<img src="static/images/npyc_logo_276.png" />
</div>
</li>
<li class="menu-item">
<div class="menu-item-info">
<h4 class="menu-item-name">SampleDB</h4>
<span class="menu-item-price">
<a href="https://github.com/csmsoftware/SampleDB" target="_blank">GitHub source</a> |
<a href="https://github.com/csmsoftware/SampleDB/blob/master/licence.txt" target="_blank">Licence</a>
</span>
<p class="menu-item-description">
<br />
Web app for storing sample location data for HTA and GDPR compliance.
<br /><br />
Requirements:
<br />
<br /> - Linux
<br /> - Python3.6
<br /> - SQLite3/PostgreSQL/MySQL,
<br /> - Nginx/Apache
<br /> - uWSGI/Gunicorn
<br /> - Redis
</p>
</div>
<div class="menu-item-image has-meta-content">
<img src="static/images/sampledb_logo_276.png" />
</div>
</li>
</ol>
</div>
<div id="r" class="menu-category">
<h3 class="menu-category-name">R</h3>
<ol class="menu-category-list has-images">
<li class="menu-item">
<div class="menu-item-info">
<h4 class="menu-item-name">PeakPantheR</h4>
<span class="menu-item-price">
<a href="https://github.com/phenomecentre/peakPantheR" target="_blank">GitHub source</a> |
<a href="http://htmlpreview.github.io/?https://github.com/phenomecentre/peakPantheR/blob/master/inst/doc/getting-started.html" target="_blank">Documentation</a> |
<a href="http://choosealicense.com/licenses/gpl-3.0/" target="_blank">Licence</a>
</span>
<p class="menu-item-description">
<br />
peakPantheR (_Peak Picking and ANnoTation of High resolution Experiments in R_) is a R and Shiny package for the parallel detection, integration and reporting of pre-defined features in high number of MS files
<br /><br />
Requirements:
<br /> - R (>= 3.4.0)
</p>
</div>
<div class="menu-item-image has-meta-content">
<img src="static/images/peakPantheR_276-276.png" />
</div>
</li>
<li class="menu-item">
<div class="menu-item-info">
<h4 class="menu-item-name">SPUTNIK</h4>
<span class="menu-item-price">
<a href="https://github.com/paoloinglese/SPUTNIK" target="_blank">GitHub source</a> |
<a href="https://paoloinglese.github.io/SPUTNIK" target="_blank">Documentation</a> |
<a href="http://choosealicense.com/licenses/gpl-3.0/" target="_blank">Licence</a>
</span>
<p class="menu-item-description">
<br />
SPUTNIK (_SPatially aUTomatic deNoising for Ims toolKit_) A set of tools for the peak filtering of mass spectrometry imaging data (MSI or IMS) based on spatial distribution of signal.
<br /><br />
Requirements:
<br /> - R (>= 3.4.0)
</p>
</div>
<div class="menu-item-image has-meta-content">
<img src="static/images/SPUTNIK_276-276.png" />
</div>
</li>
</ol>
</div>
<div id="matlab" class="menu-category">
<h3 class="menu-category-name">Matlab</h3>
<ol class="menu-category-list has-images">
<li class="menu-item">
<div class="menu-item-info">
<h4 class="menu-item-name">IMPaCTS toolbox</h4>
<span class="menu-item-price">
<a href="https://github.com/csmsoftware/impacts" target="_blank">GitHub source</a> |
<a href="https://csmsoftware.github.io/docs/impacts/index.html" target="_blank">Documentation</a> |
<a href="https://csmsoftware.github.io/docs/impacts/licence.txt" target="_blank">Licence</a>
</span>
<p class="menu-item-description">
<br />
The Imperial Metabolic Profiling and Chemometrics Toolbox for Spectroscopy.
<br /><br />
A general purpose toolbox for NMR and peak-picked MS spectra that covers data import, export, preprocessing and basic metabolomic analysis.
<br /><br />
Requirements:
<br />
- Matlab >2016a, Stats Toolbox.
</p>
</div>
<div class="menu-item-image has-meta-content">
<img src="static/images/impacts_logo_276-whitebg.jpg" />
</div>
</li>
</ol>
</div>
<a id="btn-view-full-menu" class="btn-view-full-menu" href="https://github.com/csmsoftware/">View full list of repositories</a>
</article>
</section>
</div>
</div>
</script>
</body>
</html>