| 1 | |
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| 2 | ========== |
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| 3 | * Overview |
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| 4 | ========== |
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| 5 | |
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| 6 | - Why use BASE |
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| 7 | - Low cost |
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| 8 | - Opensource/GNU-GPL |
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| 9 | - Easy to use |
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| 10 | - Plugin interface |
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| 11 | - Handles massive amount of data |
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| 12 | - All experiment information in one place |
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| 13 | - Coop.s |
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| 14 | |
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| 15 | - Overview of BASE |
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| 16 | - Terminology used in BASE / real world |
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| 17 | - Pre-knowledge |
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| 18 | - For users |
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| 19 | - For admin |
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| 20 | |
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| 21 | ==================== |
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| 22 | * User documentation |
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| 23 | ==================== |
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| 24 | |
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| 25 | - How to use this document |
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| 26 | |
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| 27 | - GUI |
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| 28 | - Introduction |
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| 29 | - Help texts |
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| 30 | - Menu bar |
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| 31 | - Tool bar |
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| 32 | - Ctrl/alt/shift - click |
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| 33 | - Congifuration |
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| 34 | - Main page |
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| 35 | - News |
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| 36 | - List pages |
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| 37 | - Filters |
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| 38 | - Table configuration |
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| 39 | - Hits/page |
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| 40 | - Column config |
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| 41 | - View pages |
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| 42 | - Listed parent, child items, annotations etc. |
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| 43 | |
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| 44 | - Projects and the permission system |
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| 45 | - Introduction |
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| 46 | - How it works (in an users point of view) |
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| 47 | - Permissions on an item |
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| 48 | - Share items |
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| 49 | - The active project |
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| 50 | - Project |
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| 51 | - Project management |
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| 52 | - Items overview |
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| 53 | |
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| 54 | - Trashcan |
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| 55 | - Introduction |
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| 56 | - Manage deleted items |
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| 57 | |
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| 58 | - File upload/File system |
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| 59 | - Introduction |
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| 60 | - Where are the files physically stored |
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| 61 | - Upload file before use |
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| 62 | - File management |
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| 63 | - New directory |
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| 64 | - Uploadfile |
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| 65 | - Edit file |
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| 66 | - Delete/Restore |
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| 67 | - Move offline |
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| 68 | - Move directory |
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| 69 | |
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| 70 | - Reporters |
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| 71 | - Introduction |
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| 72 | - Reporter management |
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| 73 | - New/Edit |
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| 74 | - Delete/Restore |
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| 75 | - Reporter lists |
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| 76 | |
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| 77 | - Annotations |
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| 78 | - Introduction |
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| 79 | - Inherited |
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| 80 | - Types |
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| 81 | - management |
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| 82 | - New/edit |
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| 83 | - Delete/Restore |
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| 84 | - Categories |
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| 85 | - Management |
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| 86 | - New/edit |
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| 87 | - Delete/Restore |
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| 88 | |
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| 89 | - Protocols |
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| 90 | - Types |
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| 91 | - Protocol type management |
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| 92 | - Protocol management |
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| 93 | - Parameters |
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| 94 | |
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| 95 | - Hardware |
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| 96 | - Hardware management |
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| 97 | |
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| 98 | - Software |
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| 99 | - Software management |
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| 100 | |
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| 101 | - Array LIMS |
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| 102 | - Plates |
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| 103 | - Introduction |
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| 104 | - Plate types |
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| 105 | - Plate mappings |
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| 106 | - Merge |
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| 107 | - Plate management |
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| 108 | - Wells |
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| 109 | - Events |
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| 110 | |
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| 111 | - Array designs and slides |
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| 112 | - Introduction |
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| 113 | - Designs |
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| 114 | - Features |
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| 115 | - Slides |
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| 116 | - Batch |
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| 117 | - Slide management |
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| 118 | - Create multiple new |
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| 119 | |
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| 120 | - Biomaterials |
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| 121 | - Introduction |
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| 122 | - Workflow |
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| 123 | - Create children |
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| 124 | - Biomaterial event |
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| 125 | - Biosources |
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| 126 | - Biosource management |
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| 127 | - Create/Edit |
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| 128 | - Delete/Restore |
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| 129 | - Samples |
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| 130 | - Sample management |
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| 131 | - Create/Edit |
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| 132 | - Pool |
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| 133 | - Delete/Restore |
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| 134 | - Extracts |
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| 135 | - Extract management |
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| 136 | - Create/Edit |
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| 137 | - Pool |
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| 138 | - Delete/Restore |
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| 139 | - Labeled extracts |
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| 140 | - Labels |
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| 141 | - Label management |
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| 142 | - Labeled extract management |
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| 143 | - Create/Edit |
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| 144 | - Pool |
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| 145 | - Delete/Restore |
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| 146 | - Hybridizations |
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| 147 | - Hybridization management |
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| 148 | - Create/Edit |
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| 149 | - Delete/Restore |
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| 150 | |
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| 151 | - Experiments and analysis |
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| 152 | - Scans and images |
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| 153 | - Scan management |
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| 154 | - image management |
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| 155 | - Raw bioassays |
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| 156 | - Experiments |
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| 157 | - Raw data types |
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| 158 | - Affymetrix data |
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| 159 | - Creating a root bioassayset |
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| 160 | - Bioassayset |
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| 161 | - Overview plots |
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| 162 | - Filtering |
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| 163 | - Formulas |
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| 164 | - Formula management |
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| 165 | - Normalization |
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| 166 | - Running a (analysis?)plugin |
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| 167 | - Messages |
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| 168 | - Plot tool |
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| 169 | - Scatter plot |
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| 170 | - Histogram plot |
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| 171 | - Experiment overview |
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| 172 | - Validation of an experiment |
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| 173 | - Options |
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| 174 | - Experiment explorer |
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| 175 | - Reporter view |
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| 176 | - Reporter search |
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| 177 | - Using MeV |
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| 178 | |
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| 179 | - Import and export of data |
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| 180 | - Import |
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| 181 | - Plugins |
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| 182 | - Auto detect |
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| 183 | - File Format |
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| 184 | - Auto detect |
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| 185 | - Export |
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| 186 | - Table exporter |
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| 187 | |
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| 188 | ===================== |
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| 189 | * Admin documentation |
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| 190 | ===================== |
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| 191 | |
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| 192 | - Installation and upgrade |
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| 193 | - Requirements |
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| 194 | - MySQL, settings, options, etc. |
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| 195 | - Postgres, settings, options, etc. |
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| 196 | - Configuration |
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| 197 | - Raw data types |
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| 198 | - Extended properties |
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| 199 | - base.config reference |
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| 200 | - other configuration files (log4j.properities, web.xml, etc.) |
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| 201 | - Job agents |
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| 202 | - jobagent.properties reference |
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| 203 | - jobagent.sh reference |
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| 204 | |
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| 205 | - Installing plugins |
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| 206 | - Plugin configurations |
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| 207 | - "Test with file" feature for creating import configurations |
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| 208 | - BASE 1 plugins |
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| 209 | - Core plugins and configurations |
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| 210 | |
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| 211 | - Adding users, groups, roles |
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| 212 | - Projects and the permission system |
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| 213 | - The default roles: admin, power user, user and guest |
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| 214 | - Quota |
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| 215 | |
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| 216 | |
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| 217 | ========================= |
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| 218 | * Developer documentation |
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| 219 | ========================= |
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| 220 | - Overview of BASE2 |
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| 221 | |
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| 222 | - Plugin developer |
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| 223 | - How to organize your plugin project |
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| 224 | - With Ant |
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| 225 | - With Eclipse |
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| 226 | - Packaging and installing the plugin |
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| 227 | - The Plugin API |
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| 228 | - Interfaces |
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| 229 | - Asking for parameters |
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| 230 | - Using custom JSP pages for parameters |
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| 231 | - Import plugins |
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| 232 | - Autodetecting importer |
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| 233 | - The AbstractFlatFileImporter superclass |
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| 234 | - Export plugins |
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| 235 | - Immediate download of exported data |
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| 236 | - Analysis plugins |
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| 237 | - Other plugins |
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| 238 | - Authentication plugins |
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| 239 | - Secondary file storage plugins |
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| 240 | - File unpacker plugins |
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| 241 | - Example plugins (with download) |
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| 242 | |
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| 243 | - API overview (how to use and code examples) |
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| 244 | - Database schema (Data layer API) |
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| 245 | - The Core API |
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| 246 | - The Query API |
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| 247 | - Analysis and the Dynamic and Batch API |
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| 248 | - Other useful classes and methods |
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| 249 | |
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| 250 | - Javadoc |
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| 251 | |
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| 252 | - Core developer reference |
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| 253 | - Important procedures |
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| 254 | - Publishing a new release |
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| 255 | - Subversion / building BASE |
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| 256 | - Coding rules and guidelines |
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| 257 | - Development process |
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| 258 | - General coding style guidelines |
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| 259 | - Data-layer rules |
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| 260 | - Item-class rules |
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| 261 | - Batch-class rules |
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| 262 | - Test-class rules |
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| 263 | - Internals of the Core API |
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| 264 | - Authentication and sessions |
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| 265 | - Access permissions |
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| 266 | - Data validation |
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| 267 | - Transaction handling |
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| 268 | - Create/read/write/delete operations |
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| 269 | - Batch operations |
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| 270 | - Quota |
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| 271 | - Plugin execution / job queue |
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| 272 | |
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| 273 | ======= |
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| 274 | * Index |
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| 275 | ======= |
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| 276 | |
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| 277 | |
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| 278 | |
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| 279 | |
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