-
Notifications
You must be signed in to change notification settings - Fork 0
/
resources.html
163 lines (162 loc) · 8.33 KB
/
resources.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
<!DOCTYPE HTML>
<html>
<head>
<title>Sandin MM - Resources</title>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1, user-scalable=no" />
<link rel="stylesheet" href="assets/css/main.css" />
</head>
<body class="is-preload">
<div id="page-wrapper">
<!-- Header -->
<div id="header">
<!-- Logo -->
<h1 hidden><a href="index.html" id="logo"><em>Sandin MM - </em>Resources</a></h1>
<!-- Nav -->
<nav id="nav">
<ul>
<li><a href="index.html">Home</a></li>
<li><a href="research.html">Research</a></li>
<li><a href="CV.html">CV</a></li>
<li><a href="publications.html">Publications</a></li>
<li><a href="communication.html">Communication</a></li>
<li class="current"><a href="resources.html">Resources</a></li>
<li><a href="contact.html">Contact</a></li>
</ul>
</nav>
</div>
<!-- Banner -->
<section id="banner" class="resources">
<header>
<h2>Courses, pipelines, protocols, images and other scientific production</h2>
</header>
</section>
<!-- Main -->
<section class="wrapper style1">
<div class="container">
<header class="major">
<h2>Hands-on courses for the exploration of molecular environmental diversity</h2>
</header>
<div class="row">
<section class="col-6 col-12-narrower">
<div class="box post">
<a href="https://github.com/MiguelMSandin/SSNetwork" target="_blank" class="image left"><img src="images/resources_ssn.png" alt="" /></a>
<div class="inner">
<h3><a href="https://github.com/MiguelMSandin/SSNetworks" target="_blank">Sequence Similarity Networks</a></h3>
<p>In the <a href="https://github.com/MiguelMSandin/SSNetworks" target="_blank">SSNetworks</a> GitHub repository you will find all necessary materials for getting started with sequence similarity networks with (mostly) DNA sequences.</p>
</div>
</div>
</section>
<section class="col-6 col-12-narrower">
<div class="box post">
<a href="https://miguelmsandin.github.io/phylogeniesQuickStart/book/01_intro.html" target="_blank" class="image left"><img src="images/resources_phylo.png" alt="" /></a>
<div class="inner">
<h3><a href="https://miguelmsandin.github.io/phylogeniesQuickStart/book/01_intro.html" target="_blank">Phylogenetic analyses</a></h3>
<p>The <a href="https://miguelmsandin.github.io/phylogeniesQuickStart/book/01_intro.html" target="_blank">phylogeniesQuickStart</a> GitHub repository is intended to be a practical guide for the reconstruction and specially the interpretation of phylogentic trees of (mostly) DNA sequences.</p>
</div>
</div>
</section>
</div>
</div>
<div class="container">
<header class="major">
<h2>Scripts and pipelines for the exploration of molecular diversity</h2>
</header>
<div class="row">
<section class="col-6 col-12-narrower">
<div class="box post">
<a href="https://github.com/MiguelMSandin/random" target="_blank" class="image left"><img src="images/resources_bioinfo.png" alt="" /></a>
<div class="inner">
<h3><a href="https://github.com/MiguelMSandin/random" target="_blank">A collection of scripts for bioinformatics</a></h3>
<p>In the <a href="https://github.com/MiguelMSandin/random" target="_blank">random</a> GitHub repository you will find a collection of a set of scripts to deal with common fasta files and phylogenetic tree manipulations from the command line.</p>
</div>
</div>
</section>
<section class="col-6 col-12-narrower">
<div class="box post">
<a href="https://miguelmsandin.github.io/phylogeniesQuickStart/book/01_intro.html" target="_blank" class="image left"><img src="images/resources_oligo.png" style="max-width:100px" alt="" /></a>
<div class="inner">
<h3><a href="https://github.com/MiguelMSandin/oligoN-design" target="_blank">Oligonucleotide design</a></h3>
<p>The <a href="https://github.com/MiguelMSandin/oligoN-design" target="_blank">OligoN-design</a> GitHub repository describes a pipeline for the high-throughput design of specific primers or probes for further molecular analyses, such as Fluorescence <i>in situ</i> Hybridization (FISH) or PCR amplification.</p>
</div>
</div>
</section>
</div>
</div>
<div class="container">
<header class="major">
<h2>Wet-lab protocols for single-cell</h2>
</header>
<div class="row">
<section class="col-6 col-12-narrower">
<div class="box post">
<a href="" target="_blank" class="image left"><img style="max-width:180px; border-radius: 50%" src="images/cover_filtrating.png" alt="" /></a>
<div class="inner">
<h3>DNA amplification</h3>
<p>Here you can find protocols for single-cell ribosomal DNA extraction and amplification of <a href="https://dx.doi.org/10.17504/protocols.io.t5req56" target="_blank">Nassellaria</a> and <a href="https://dx.doi.org/10.17504/protocols.io.xwvfpe6" target="_blank">Spumellaria</a> (Radiolaria).</p>
</div>
</div>
</section>
<section class="col-6 col-12-narrower">
<div class="box post">
<a href="" target="_blank" class="image left"><img style="max-width:180px; border-radius: 50%" src="images/resources_spum.png" style="max-width:100px" alt="" /></a>
<div class="inner">
<h3>Scanning electron and confocal microscopy imaging of silica skeletons</h3>
<p>Here you can find a protocol for cleaning and staining of silica skeletons for confocal microscopy imaging <a href="https://dx.doi.org/10.17504/protocols.io.t5qeq5w" target="_blank">(CM)</a> and a protocol for cleaning and mounting silica skeleton for scanning electron microscopy imaging <a href="https://dx.doi.org/10.17504/protocols.io.ug9etz6" target="_blank">(SEM)</a>. In general this protocols will work for most skeleton that do not dissolve on water.</p>
</div>
</div>
</section>
</div>
</div>
<div class="container">
<header class="major">
<h2>Silhouettes</h2>
</header>
</div>
<div class="container">
<div class="row gtr-200">
<div class="col-3 col-12-narrower">
<div id="sidebar1">
<span class="image fit"><img style="max-width:180px" src="images/resources_silhouette_nass.png" alt="" /></span>
</div>
</div>
<div class="col-6 col-12-narrower imp-narrower imp-narrower">
<div id="content">
<!-- Content -->
<article>
<header>
<h2><a href="https://beta.phylopic.org/contributors/87b1c532-3a40-4dee-aa2b-08c32036a342" target="_blank">16 silhouettes of Radiolaria</a></h2>
</header>
<p>I have deposited in the <a href="https://beta.phylopic.org/contributors/87b1c532-3a40-4dee-aa2b-08c32036a342" target="_blank">PhyloPic</a> database 16 silhouettes of Radiolaria to the public domain for further presentations, manuscripts and outreach purposes.<br>
These silhouettes are rendered from real scanning electron microscopy images, and I'm slowly rendering and uploading more.</p>
</article>
</div>
</div>
<div class="col-3 col-12-narrower">
<div id="sidebar2">
<span class="image fit"><img style="max-width:180px" src="images/resources_silhouette_spum.png" alt="" /></span>
</div>
</div>
</div>
</div>
</section>
<!-- Footer -->
<div id="footer">
<!-- Copyright -->
<div class="copyright">
<ul class="menu">
<li>© Untitled. All rights reserved</li><li>Design from: <a href="http://html5up.net" target="_blank">HTML5 UP</a></li>
</ul>
</div>
</div>
</div>
<!-- Scripts -->
<script src="assets/js/jquery.min.js"></script>
<script src="assets/js/jquery.dropotron.min.js"></script>
<script src="assets/js/browser.min.js"></script>
<script src="assets/js/breakpoints.min.js"></script>
<script src="assets/js/util.js"></script>
<script src="assets/js/main.js"></script>
<script src="https://code.iconify.design/iconify-icon/1.0.1/iconify-icon.min.js"></script>
</body>
</html>