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mapping.html
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<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width,initial-scale=1.0,user-scalable=no">
<meta property='og:type' content='website'>
<meta property='og:title' content='Isotope Calculation Gadgets'>
<meta property='og:url' content='https://nobuyukiokahashi.github.io/github.io-Isotope_calc_gadgets_tutorial/'>
<meta property='og:description' content='Isotope Calculation Gadgets'>
<meta property="og:image" content="img/ogp.png">
<meta name="description" content="Isotope Calculation Gadgets" />
<title>Isotope Calculation Gadgets</title>
<link rel="preconnect" href="https://fonts.gstatic.com">
<link href="https://fonts.googleapis.com/css2?family=Montserrat:wght@400;700&display=swap" rel="stylesheet">
<link href="https://fonts.googleapis.com/css?family=Material+Icons+Outlined" rel="stylesheet">
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<link rel="shortcut icon" href="img/favicon.ico" />
<link rel=”canonical” href=”https://nobuyukiokahashi.github.io/github.io-Isotope_calc_gadgets_tutorial/” />
</head>
<body>
<div class="wrapper">
<!-- header -->
<header class="header ">
<div class="inner">
<h1 class="header-logo">
<a href=".">Isotope Calculation Gadgets</a>
</h1>
<nav class="header-nav">
<ul class="header-nav-list">
<li class="header-nav-item"><a href="index.html#About">About</a></li>
<li class="header-nav-item"><a href="index.html#Overview">Overview</a></li>
<li class="header-nav-item"><a href="index.html#Imprementation">Imprementation</a></li>
<li class="header-nav-item"><a href="index.html#Gadgets">How to use</a></li>
<li class="header-nav-item"><a href="index.html#Contact">Contact</a></li>
</ul>
</nav>
</div>
</header>
<!-- /header -->
<main class="content">
<article class="article">
<div class="article-inner">
<h2 class="article-title">Data mapping</h2>
<div class="profile">
<p class="profile-body">
<img src="img/Overview_after.png">
</p>
</div>
<div class="article-body">
<p>
Processed data by "Isotope Calculation Gadgets" can be visualized on blank maps by using "Shimadzu Multi-Omics Analysis Gadget Pack" and "VANTED".
</p>
<h3 class="article-info-title">Preparation</h3>
<p>
Obtain natural isotope-subtracted labeling data by using <a href="./Natural_Isotope_Subtractor.html">"Natural Isotope Subtractor".</a>
</p>
<h3 class="article-info-title">Procedure</h3>
<p>
Click data to visualize, then click "Discover" Button. Select "Shimadzu MSdata import."
</p>
<img src="img/mapping_start.png">
<p>
<div class ="note">
<h4>Note:</h4>
<li>
If you can't find "Shimadzu MSdata import", download and install it following <a href="index.html #Imprementation">instruction</a> (Step 4 in imprementation).
</li>
</div>
</p>
<p>
Click "Fluxomics" button in the pop-up window.
</p>
<p>
The data will be imported in "Shimadzu MSdata import".
</p>
<p>
<div class ="note">
<h4>Note:</h4>
<li>
If the screen freezes, save the result file of Natural isotope subtractor and reload it in the newly launched Shimadzu MSdata import from "File">"Add Flux quant format file".
</li>
</div>
</p>
<p>
Fill the names of the sample groups in the sample ID row. Check "Sample ID" in the Group box. Click Discover and select "Multiomics Data Mapper".
</p>
<img src="img/data_setting.png">
<p>
"Multiomics Data Mapper" will start up.
</p>
<p>
Click "Pathway GML File" and choose a blank map. Then, click the "Launch" button.
<div class ="note">
<h4>Note:</h4>
<li>
Ready-made blank maps can be obtained from <a href="https://github.com/NobuyukiOkahashi/Isotope_gadgets">here</a>.
</li>
</div>
</p>
<img src="img/data_mapper.png">
<p>
Click the "Disocver" button and select <a href=https://www.cls.uni-konstanz.de/software/vanted/>"VANTED"</a>.
</p>
<img src="img/vanted_transfer.png">
<p>
A map with the data visualized will be displayed.
<div class ="note">
<h4>Note:</h4>
<li>
The map can be modified as you like.
</li>
</div>
</p>
<img src="img/vanted_map.png">
<p>
Saved the map as image.
Click "File" > "Export" > "Network as Image", then choose an extension.
</p>
</div>
<div class="home-link">
<p>Return to <a href="./index.html#Gadgets">How to use</a></p>
</div>
</div>
</article>
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<span class="material-icons-outlined">expand_less</span>
</div>
</main>
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<footer class="footer">
<div class="copyright">©Nobuyuki Okahashi</div>
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