| 1 | <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"> |
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| 2 | <!-- |
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| 3 | $Id: index.html 4509 2008-09-11 20:01:44Z jari $ |
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| 4 | |
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| 5 | Copyright (C) 2005 Jari Hakkinen, Nicklas Nordborg |
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| 6 | Copyright (C) 2006 Jari Hakkinen |
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| 7 | |
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| 8 | This file is part of BASE - BioArray Software Environment. |
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| 9 | Available at http://base.thep.lu.se/ |
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| 10 | |
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| 11 | BASE is free software; you can redistribute it and/or |
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| 12 | modify it under the terms of the GNU General Public License |
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| 13 | as published by the Free Software Foundation; either version 3 |
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| 14 | of the License, or (at your option) any later version. |
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| 15 | |
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| 16 | BASE is distributed in the hope that it will be useful, |
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| 17 | but WITHOUT ANY WARRANTY; without even the implied warranty of |
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| 18 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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| 19 | GNU General Public License for more details. |
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| 20 | |
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| 21 | You should have received a copy of the GNU General Public License |
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| 22 | along with BASE. If not, see <http://www.gnu.org/licenses/>. |
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| 23 | --> |
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| 24 | <html> |
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| 25 | <head> |
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| 26 | <title>BASE - Core specification</title> |
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| 27 | <link rel=stylesheet type="text/css" href="../../styles.css"> |
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| 28 | </head> |
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| 29 | <body> |
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| 30 | <div class="navigation"> |
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| 31 | <a href="../../index.html">BASE</a> |
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| 32 | <img src="../../next.gif"> |
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| 33 | Core specification |
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| 34 | </div> |
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| 35 | |
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| 36 | <h1>Core specification</h1> |
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| 37 | |
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| 38 | <div class="abstract"> |
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| 39 | <p> |
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| 40 | This document contains a detailed specification of the core |
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| 41 | functions in BASE 2. It is based on the |
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| 42 | <a href="../../features_core.html">list of features</a> |
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| 43 | compiled by Carl and will continue to grow. |
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| 44 | </p> |
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| 45 | |
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| 46 | <p class="authors"> |
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| 47 | <b>Last updated:</b> $Date: 2008-09-11 20:01:44 +0000 (Thu, 11 Sep 2008) $ |
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| 48 | </p> |
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| 49 | </div> |
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| 50 | <br> |
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| 51 | |
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| 52 | <dl> |
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| 53 | <dt><a href="authentication.html">User authentication and management</a></dt> |
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| 54 | <dd> |
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| 55 | <p> |
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| 56 | This document covers the details of internal and external user authentication. |
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| 57 | It also discusses user management and how groups and roles are related. |
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| 58 | <br> |
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| 59 | <b>Status:</b> Stable<br> |
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| 60 | </p> |
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| 61 | </dd> |
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| 62 | |
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| 63 | <dt><a href="accesscontrol.html">Access control</a></dt> |
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| 64 | <dd> |
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| 65 | <p> |
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| 66 | This document covers the details of how to control who may access a given |
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| 67 | item and/or function in BASE. |
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| 68 | |
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| 69 | <br> |
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| 70 | <b>Status:</b> Stable<br> |
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| 71 | </p> |
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| 72 | </dd> |
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| 73 | |
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| 74 | <dt><a href="sessionsettings.html">Sessions and application settings</a></dt> |
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| 75 | <dd> |
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| 76 | <p> |
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| 77 | This document covers the details of how client applications should be able to store |
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| 78 | configuration settings and temporary information in BASE. |
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| 79 | |
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| 80 | <br> |
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| 81 | <b>Status:</b> Stable<br> |
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| 82 | </p> |
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| 83 | </dd> |
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| 84 | |
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| 85 | <dt><a href="annotations.html">Annotations</a></dt> |
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| 86 | <dd> |
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| 87 | <p> |
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| 88 | This document covers the details of how the annotation system works. |
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| 89 | |
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| 90 | <br> |
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| 91 | <b>Status:</b> Draft<br> |
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| 92 | </p> |
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| 93 | |
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| 94 | <dt><a href="biomaterials.html">Biomaterials</a></dt> |
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| 95 | <dd> |
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| 96 | <p> |
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| 97 | This document covers the details of how biomaterials are handled in BASE. |
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| 98 | |
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| 99 | <br> |
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| 100 | <b>Status:</b> Stable<br> |
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| 101 | </p> |
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| 102 | |
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| 103 | <dt><a href="protocols.html">Protocols and hardware / software</a></dt> |
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| 104 | <dd> |
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| 105 | <p> |
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| 106 | This document covers the details of how BASE handles protocols and |
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| 107 | information about hardware and software. |
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| 108 | |
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| 109 | <br> |
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| 110 | <b>Status:</b> Stable<br> |
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| 111 | </p> |
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| 112 | |
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| 113 | <dt><a href="reporters.html">Reporters</a></dt> |
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| 114 | <dd> |
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| 115 | <p> |
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| 116 | This document covers the details of how BASE handles reporters |
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| 117 | (clones, oligos, etc.). |
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| 118 | |
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| 119 | <br> |
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| 120 | <b>Status:</b> Stable<br> |
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| 121 | </p> |
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| 122 | |
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| 123 | <dt><a href="arraylims.html">Array LIMS</a></dt> |
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| 124 | <dd> |
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| 125 | <p> |
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| 126 | This document covers the details of how the array LIMS section works. |
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| 127 | |
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| 128 | <br> |
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| 129 | <b>Status:</b> Draft<br> |
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| 130 | </p> |
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| 131 | |
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| 132 | <dt><a href="hybridizations.html">Hybridizations and raw data</a></dt> |
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| 133 | <dd> |
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| 134 | <p> |
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| 135 | This document covers the details of how BASE handles hybridizations |
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| 136 | and raw data. |
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| 137 | |
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| 138 | <br> |
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| 139 | <b>Status:</b> Draft<br> |
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| 140 | </p> |
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| 141 | |
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| 142 | <dt><a href="experiments.html">Experiments and analysis</a></dt> |
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| 143 | <dd> |
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| 144 | <p> |
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| 145 | This document covers the details of how BASE groups data |
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| 146 | into experiments and performs analysis on it. |
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| 147 | |
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| 148 | <br> |
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| 149 | <b>Status:</b> In progress<br> |
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| 150 | </p> |
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| 151 | |
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| 152 | <dt><a href="jobqueue.html">Job controller / queuing system</a></dt> |
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| 153 | <dd> |
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| 154 | <p> |
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| 155 | This document covers the details of how the job controller / queuing system works. |
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| 156 | |
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| 157 | <br> |
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| 158 | <b>Status:</b> In progress<br> |
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| 159 | </p> |
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| 160 | |
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| 161 | <dt><a href="fileupload.html">File upload / disk quota</a></dt> |
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| 162 | <dd> |
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| 163 | <p> |
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| 164 | This document covers the details of how to handle file uploads in BASE. |
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| 165 | A discussion about disk quota is also included. |
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| 166 | |
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| 167 | <br> |
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| 168 | <b>Status:</b> Stable<br> |
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| 169 | </p> |
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| 170 | |
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| 171 | <dt><a href="importexport.html">Data import and export</a></dt> |
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| 172 | <dd> |
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| 173 | <p> |
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| 174 | This document covers details for data import and export and how |
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| 175 | it can be extended to support more file formats by the use of plugins. |
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| 176 | |
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| 177 | <br> |
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| 178 | <b>Status:</b> In progress<br> |
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| 179 | </p> |
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| 180 | |
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| 181 | <dt><a href="defaultdata.html">Default data</a></dt> |
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| 182 | <dd> |
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| 183 | <p> |
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| 184 | This document contains a list of all items |
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| 185 | that are automatically installed into a new BASE 2 installation. |
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| 186 | <br> |
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| 187 | <b>Status:</b> In progress<br> |
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| 188 | </p> |
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| 189 | |
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| 190 | <!-- |
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| 191 | <dt><a href="items.html">Items</a></dt> |
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| 192 | <dd> |
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| 193 | <p> |
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| 194 | This document is not a specification as such, but more |
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| 195 | an idea about how to implement the basic class |
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| 196 | structure in BASE. |
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| 197 | |
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| 198 | <br> |
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| 199 | <b>Status:</b> Draft<br> |
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| 200 | </p> |
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| 201 | --> |
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| 202 | |
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| 203 | |
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| 204 | </dl> |
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| 205 | |
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| 206 | </body> |
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| 207 | </html> |
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