-
Notifications
You must be signed in to change notification settings - Fork 3
/
index-earth-system.html
255 lines (183 loc) · 12.7 KB
/
index-earth-system.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
<!DOCTYPE html>
<html lang="en">
<head>
<title>Galaxy Europe</title>
<meta property="og:title" content="" />
<meta property="og:description" content="" />
<meta property="og:image" content="/assets/media/galaxy-eu-logo.512.png" />
<meta name="description" content="The European Galaxy Instance">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<link rel="stylesheet" href="/assets/css/bootstrap.min.css">
<link rel="stylesheet" href="/assets/css/main.css">
<link rel="canonical" href="https://galaxyproject.eu/index-earth-system.html">
<link rel="shortcut icon" href="/assets/media/galaxy-eu-logo.64.png" type="image/x-icon" />
<link rel="alternate" type="application/rss+xml" title="Galaxy Europe" href="/feed.xml">
<link href="/assets/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-wvfXpqpZZVQGK6TAh5PVlGOfQNHSoD2xbE+QkPxCAFlNEevoEH3Sl0sibVcOQVnN" crossorigin="anonymous">
<script src="/assets/js/jquery-3.2.1.slim.min.js" integrity="sha256-k2WSCIexGzOj3Euiig+TlR8gA0EmPjuc79OEeY5L45g=" crossorigin="anonymous"></script>
<script src="/assets/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
</head>
<body>
<div id="wrap">
<div id="main">
<div class="container" id="maincontainer">
<div class="home">
<p><img src="assets/media/fair_ease_colour.png" alt="Fair-Ease on Galaxy" class="sc-intro-left" /></p>
<h1 id="welcome-to-galaxy-for-earth-system-and-environment">Welcome to Galaxy for Earth System and environment</h1>
<p class="no_toc"><img src="assets/media/earth_system_background.png" alt="Fair-Ease project" /></p>
<p><br />
Galaxy for Earth System and environment was implemented within the project <a href="https://fairease.eu/" target="_blank"><strong>Fair-Ease</strong></a>. It’s a virtual platform to process, analyse and visualize Earth System, Environment and Biodiversity data. It is based on the <a href="https://galaxyproject.org" target="_blank">Galaxy framework</a>, which guarantees simple access, easy extension, flexible adaption to personal and security needs, and sophisticated analyses independent of command-line knowledge.</p>
<p><br /></p>
<h1 class="no_toc" id="content">Content</h1>
<ol id="markdown-toc">
<li><a href="#welcome-to-galaxy-for-earth-system-and-environment" id="markdown-toc-welcome-to-galaxy-for-earth-system-and-environment">Welcome to Galaxy for Earth System and environment</a></li>
<li><a href="#get-started" id="markdown-toc-get-started">Get started</a></li>
<li><a href="#training" id="markdown-toc-training">Training</a></li>
<li><a href="#tools" id="markdown-toc-tools">Tools</a></li>
<li><a href="#workflows" id="markdown-toc-workflows">Workflows</a></li>
<li><a href="#references" id="markdown-toc-references">References</a></li>
</ol>
<h1 id="get-started">Get started</h1>
<p>Are you new to Galaxy for Earth System sciences, or returning after a long time, and looking for help to get started? Take a <a href="https://training.galaxyproject.org/training-material/topics/climate/tutorials/earth_system/tutorial.html" target="_blank"><strong>guided tour</strong></a> through a detailed tutorial on the Galaxy Training Network.</p>
<h1 id="training">Training</h1>
<p>We are working in close collaboration with the <a href="https://training.galaxyproject.org" target="_blank"><strong>Galaxy Training Network (GTN)</strong></a> to develop training materials of data analyses based on Galaxy. If you want to know more about the GTN or how to become part of the Galaxy community, check the videos below!</p>
<p><strong>Training material</strong></p>
<p>All relevant materials for Earth System, Environment and Biodiversity data analysis will be available within the GTN. You can search for them within the GTN by writing <strong>earth-system</strong> in the search bar or directly acces our full <a href="https://training.galaxyproject.org/training-material/search2?query=earth-system">set of tutorials</a>.
A sample of the different tutorials that you can find below but many more are available:</p>
<ul>
<li><a href="https://training.galaxyproject.org/topics/introduction/tutorials/galaxy-intro-short/slides.html">Welcome and introduction to Galaxy</a></li>
<li><a href="https://training.galaxyproject.org/training-material/topics/climate/tutorials/ocean-variables/tutorial.html">How to study Ocean’s variables</a></li>
<li><a href="https://training.galaxyproject.org/training-material/topics/climate/tutorials/argo_pangeo/tutorial.html">Analyse Ocean data (from Argo)</a></li>
<li><a href="https://training.galaxyproject.org/training-material/topics/ecology/tutorials/QGIS_Web_Feature_Services/tutorial.html">How to use QGIS</a></li>
<li><a href="https://training.galaxyproject.org/training-material/topics/climate/tutorials/sentinel5_data/tutorial.html">How to study atmospheric volcanic data</a></li>
<li><a href="https://training.galaxyproject.org/training-material/topics/ecology/tutorials/ndvi_openeo/tutorial.html">Get access to vegetation indices</a></li>
<li><a href="https://training.galaxyproject.org/training-material/topics/ecology/tutorials/obisindicators/tutorial.html">Study Marine biodiversity</a></li>
<li><a href="https://training.galaxyproject.org/training-material/topics/ecology/tutorials/marine_omics_bgc/tutorial.html">Learn in the Marine Omics domain to identify biosynthetic gene clusters</a></li>
</ul>
<h1 id="tools">Tools</h1>
<p>Multiple tools on Earth System, Environment and Biodiversity data analysis will be available in this custom Galaxy instance:</p>
<ul>
<li><strong>General tools</strong>
<ul>
<li><a href="https://earth-system.usegalaxy.eu/root?tool_id=interactive_tool_qgis">QGIS</a></li>
<li><a href="https://earth-system.usegalaxy.eu/root?tool_id=interactive_tool_hdfviewer">HDFviewer</a></li>
<li><a href="https://earth-system.usegalaxy.eu/root?tool_id=interactive_tool_holoviz">Holoviz</a></li>
</ul>
</li>
<li><strong>Coastal Water Dynamics tools</strong>
<ul>
<li>Ocean Data viewer <a href="https://earth-system.usegalaxy.eu/root?tool_id=interactive_tool_odv">ODV</a></li>
<li><a href="https://earth-system.usegalaxy.eu/root?tool_id=interactive_tool_divand">DIVAnd</a></li>
<li><a href="https://earth-system.usegalaxy.eu/root?tool_id=interactive_tool_source">Source</a></li>
</ul>
</li>
<li><strong>Bio-GeoChemical tools</strong>
<ul>
<li><a href="https://earth-system.usegalaxy.eu/root?tool_id=interactive_tool_scoop3_argo">Scoop Argo</a></li>
</ul>
</li>
<li><strong>Marine omics tools</strong></li>
<li><strong>Earth critical zone tools</strong> on land degradation</li>
<li><strong>Volcano tools</strong></li>
</ul>
<h1 id="workflows">Workflows</h1>
<p>To orchestrate tools and help users with their analyses, several <a href="https://galaxyproject.org/learn/advanced-workflow/" target="_blank">workflows</a> will be available. They formally orchestrate tools in a defined order and with defined parameters, but they are customizable (tools, order, parameters).</p>
<h1 id="references">References</h1>
<ol class="bibliography"></ol>
<p><img src="assets/media/en_funded_eu.jpg" alt="European Comission" class="sc-intro-left" /></p>
<h2>Our Data Policy</h2>
<table class="table table-striped">
<thead>
<tr>
<th>Registered Users</th><th>Unregistered Users</th><th>FTP Data</th><th>GDPR Compliance</th>
</tr>
</thead>
<tbody>
<tr>
<td>User data on UseGalaxy.eu (i.e. datasets, histories) will be available as long
as they are not deleted by the user. Once marked as deleted the datasets will
be permanently removed within 14 days. If the user "purges" the dataset in the
Galaxy, it will be removed immediately, permanently.
An <a href="https://docs.google.com/forms/d/e/1FAIpQLSf9w2MOS6KOlu9XdhRSDqWnCDkzoVBqHJ3zH_My4p8D8ZgkIQ/viewform" target="_blank">extended quota can be requested</a>
for a limited time period in special cases.
</td>
<td>Processed data will only be accessible during one browser session, using a
cookie to identify your data. This cookie is not used for any other purposes
(e.g. tracking or analytics).
If UseGalaxy.eu service is not accessed for 90 days, those datasets will be
permanently deleted.
</td>
<td>Any user data uploaded to our <a href="https://galaxyproject.eu/ftp/">FTP server</a> should be imported into Galaxy as soon
as possible. Data left in FTP folders for more than 3 months, will be deleted.
</td>
<td>The Galaxy service complies with the EU General Data Protection Regulation
(GDPR). You can read more about this on our
<a href="https://usegalaxy.eu/terms/">Terms and Conditions</a>.</td>
</tr>
</tbody>
</table>
<!-- <h4>Registered Users</h4>
User data on UseGalaxy.eu (i.e. datasets, histories) will be available as long
as they are not deleted by the user. Once marked as deleted the datasets will
be permanently removed within 14 days. If the user "purges" the dataset in the
Galaxy, it will be removed immediately, permanently.
An <a href="https://docs.google.com/forms/d/e/1FAIpQLSf9w2MOS6KOlu9XdhRSDqWnCDkzoVBqHJ3zH_My4p8D8ZgkIQ/viewform" target="_blank">extended quota can be requested</a>
for a limited time period in special cases.
<h4>Unregistered Users</h4>
Processed data will only be accessible during one browser session, using a
cookie to identify your data. This cookie is not used for any other purposes
(e.g. tracking or analytics).
If UseGalaxy.eu service is not accessed for 90 days, those datasets will be
permanently deleted.
<h4>FTP Data</h4>
Any user data uploaded to our <a href="https://galaxyproject.eu/ftp/">FTP server</a> should be imported into Galaxy as soon
as possible. Data left in FTP folders for more than 3 months, will be deleted.
<h4>GDPR Compliance</h4>
The Galaxy service complies with the EU General Data Protection Regulation
(GDPR). You can read more about this on our
<a href="https://usegalaxy.eu/terms/">Terms and Conditions</a>.
-->
<div>
<iframe style="border: 0px" width="100%" height="150px" src="https://stats.galaxyproject.eu/d-solo/000000034/jobs-dashboard?orgId=1&refresh=1m&panelId=1" ></iframe>
</div>
<div>
<!--<iframe style="border: 0px" width="33%" height="100px" src="https://stats.galaxyproject.eu/d-solo/000000034/jobs-dashboard?orgId=1&refresh=1m&panelId=3" ></iframe>-->
</div>
<div class="row">
<section class="section-content">
<div class="col-md-12">
</div>
</section>
</div>
</div>
</div>
</div>
</div>
<footer class="navbar-default">
<div class="container">
<div class="row">
</div>
<div class="row">
<div class="col-lg-12" style="text-align:center">
<p>UseGalaxy.eu is maintained largely by the <a href="/freiburg/">Freiburg Galaxy Team</a> but also collectively by groups and individuals from across Europe. All of the member sites in this repository contribute to the European Galaxy Project.
For <strong>acknowledgement</strong>, please refer to the <a href="/about">About</a> section.
All content on this site is available under <a href="https://creativecommons.org/share-your-work/public-domain/cc0/">CC0-1.0</a> unless otherwise specified.</p>
</div>
</div>
<div class="row">
<div class="col-lg-12" style="text-align:center">
<ul class="contact-info">
<li><i class="fa fa-github"></i><a href="https://github.com/usegalaxy-eu/website/tree/master/index-earth-system.md">Edit this page on GitHub</a></li>
<li><i class="fa fa-envelope"></i><a href="mailto:[email protected]">[email protected]</a></li>
<li><i class="fa fa-github"></i><a href="https://github.com/usegalaxy-eu">usegalaxy-eu</a></li>
<li><img class="fa-mastodon" src="/assets/media/mastodon.svg" style="width:18px;height:18px;padding-right:4px;filter:grayscale(100%);-webkit-filter:grayscale(100%);"/><a href="https://bawü.social/@galaxyfreiburg">galaxyfreiburg</a></li>
<li><i class="fa fa-rss"></i>Subscribe <a href="/feed.xml">via RSS (UseGalaxy.eu Feed)</a></li>
</ul>
</div>
</div>
</div>
</footer>
<script async defer data-domain="galaxyproject.eu" src="https://plausible.galaxyproject.eu/js/plausible.js"></script>
</body>
</html>