MicroMar: userguide.html

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User Guide from MicroMar explaining unit etc.

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1 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/strict.dtd">
2 <html><head><title>Micro-Mar Database - User Guide</title>
3  
4  
5    
6     <meta name="author" content="Pushker Ravindra">
7     <meta http-equiv="content-type" content="text/html; charset=ISO-8859-1">
8     <meta name="description" content="This is Micro-Mar database User Guide page">
9     <script type="text/javascript" src="userguide_files/checkAll.js"></script> 
10     <script type="text/javascript" src="userguide_files/openInNewWindow.js"></script> 
11     <style media="all" type="text/css">@import url(styleSheet.css);
12     </style><!--[if IE]>
13     <style>
14     #leftNavigation {
15         margin-left: 5px;
16     }
17     </style>
18     <![endif]--></head><body>
19     <div id="topNavigation">
20       <!--<object width="100%" height="50">
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25     <img src="userguide_files/micromar.jpg" alt="Micro-Mar banner" height="50" width="800">
26     </div>
27       <ul id="menu">
28       <li><a href="http://egg.umh.es/micromar/index.php" title="Go to Micro-Mar database main page">Home</a></li>
29       <li><a href="http://egg.umh.es/micromar/mm_search_check_res.php" title="Query the database">Search</a></li>
30       <li><a href="http://egg.umh.es/micromar/mm_blast_check_res.php" title="BLAST your sequence with Micro-Mar database">Local BLAST</a></li>
31       <li><a href="http://egg.umh.es/micromar/mm_map_check_res.php" title="Dynamic map">Dynamic Map</a></li>             
32       <li><a href="http://egg.umh.es/micromar/mm_sequp.php" title="Micro-Mar sequence submission">MMSeqUp</a></li>           
33        
34       <li><a href="http://egg.umh.es/forum/index.php" title="Forums">Forum</a></li>
35      
36      <li><a href="http://egg.umh.es/micromar/guide.php" title="User guide"><strong>User Guide</strong></a></li>
37       <li><a href="http://egg.umh.es/micromar/login.php" title="Administration">Administration</a></li>
38       <li><a href="http://egg.umh.es/micromar/team.php" title="Team">Team</a></li>
39     </ul>
40    
41 <div class="midNavigation">
42 <h1>Variable and Units Used</h1>
43
44 <table id="search">
45 <tbody><tr><td><h3><i>Parameter</i></h3></td><td><h3><i>Unit</i></h3></td></tr>
46 <tr><td>Pressure</td><td>dbar
47 </td></tr><tr><td>Depth</td><td>meter
48
49 </td></tr><tr><td>Temperature</td><td>°C (ITS-90)
50 </td></tr><tr><td>Salinity</td><td>PSU
51 </td></tr><tr><td>Oxygen</td><td>ml/l at STP or µmol/kg
52 </td></tr><tr><td>Phosphate</td><td>µmol/l or µmol/kg
53 </td></tr><tr><td>Total Phosphorous</td><td>µmol/l or µmol/kg
54 </td></tr><tr><td>Silicate</td><td>µmol/l or µmol/kg
55 </td></tr><tr><td>Nitrate</td><td>µmol/l or µmol/kg
56
57 </td></tr><tr><td>Nitrite</td><td>µmol/l or µmol/kg
58 </td></tr><tr><td>Ammonium</td><td>µmol/l or µmol/kg
59 </td></tr><tr><td>Total Nitrogen</td><td>µmol/l or µmol/kg
60 </td></tr><tr><td>Hydrogen Sulphide</td><td>µmol/l or µmol/kg
61 </td></tr><tr><td>pH</td><td>Hydrogen ion concentration in situ
62 </td></tr><tr><td>Alkalinity</td><td>milliequivalents/litre (mEq/l)
63 </td></tr><tr><td>Chlorophyll A</td><td>mg/m^3 at 20°C
64
65 </td></tr><tr><td>Other</td><td>µmol/l or µmol/kg or 'As measured'
66 </td></tr></tbody></table>
67
68
69
70 </div>
71 <div class="midNavigation">
72 <h1>Ambiguous positions</h1>
73
74 <table id="search">
75 <tbody><tr><td><h3><i>Ambiguous <br>Representation</i></h3></td><td><h3><i>Bases</i></h3></td></tr>
76 <tr><td>N</td><td>A + c + T + g</td></tr>
77
78 <tr><td>H</td><td>  A + c + T     </td></tr>
79 <tr><td>V</td><td>  A + c     + g </td></tr>
80 <tr><td>M</td><td>  A + c         </td></tr>
81 <tr><td>D</td><td>  A     + T + g </td></tr>
82 <tr><td>W</td><td>  A     + T     </td></tr>
83 <tr><td>R</td><td>  A         + g </td></tr>
84 <tr><td>B</td><td>      c + T + g </td></tr>
85 <tr><td>Y</td><td>      c + T     </td></tr>
86 <tr><td>S</td><td>      c     + g </td></tr>
87 <tr><td>K</td><td>          T + g </td></tr>
88 </tbody></table>
89
90 </div>
91
92 <div class="midNavigation">
93 <h1>Type of entry</h1>
94
95 <h3>First character</h3>
96
97 <table>
98 <tbody><tr align="center"><td>Off-shore</td><td>  A 
99 </td></tr><tr align="center"><td>In-shore </td><td>  B 
100 </td></tr><tr align="center"><td>Sediments</td><td>  C 
101 </td></tr></tbody></table>
102
103 <h3>Second character</h3>
104
105 <table>
106 <tbody><tr align="center"><td>DNA - PCR </td><td>  A 
107 </td></tr><tr align="center"><td>DNA - Clone </td><td>  B 
108 </td></tr><tr align="center"><td>Isolated strain</td><td>  C 
109 </td></tr></tbody></table>
110
111 </div>
112
113
114 </body></html>