Changeset 3048 for trunk/doc/user/coreplugins.html
- Timestamp:
- Jan 5, 2007, 12:11:21 PM (16 years ago)
- File:
-
- 1 edited
-
trunk/doc/user/coreplugins.html (modified) (2 diffs)
Legend:
- Unmodified
- Added
- Removed
-
trunk/doc/user/coreplugins.html
r3047 r3048 42 42 <p> 43 43 This document lists all available core plugins in BASE 2. <br>Each plugin can be downloaded and installed separately.<br> 44 There are also an example of configuration, that can be downloaded and imported, for those plugins that have configuration support. 44 There are also examples of configuration for some of the plugins that support configuration. 45 The plugin configurations are also available in packages for different kind of arrays. 45 46 </p> 46 <b>Plugin types</b>47 <b>Plugins</b> 47 48 <ol> 48 <li><a href="#analyse">Analyse</a></li> 49 <li><a href="#export">Export</a></li> 50 <li><a href="#import">Import</a></li> 51 <li><a href="#intensity">Intensity</a></li> 52 <li><a href="#other">Other</a></li> 49 <li><a href="#types">Types</a> 50 <ol type="a"> 51 <li><a href="#analyze">Analyze</a></li> 52 <li><a href="#export">Export</a></li> 53 <li><a href="#import">Import</a></li> 54 <li><a href="#intensity">Intensity</a></li> 55 <li><a href="#other">Other</a></li> 56 </ol> 57 </li> 58 <li><a href="#config_packages">Configuration packages</a></li> 53 59 </ol> 54 60 … … 59 65 </p> 60 66 </div> 61 62 67 <ol> 63 68 <li> 64 <a name="analyse"></a> 65 <h2>Analyse</h2> 69 <a name="types"></a> 70 <h2>Types</h2> 71 <ol type="a"> 72 <li> 73 <a name="analyze"></a> 74 <b>Analyze</b> 75 <table class="listing"> 76 <tr> 77 <th>Plugin name</th> 78 <th>Download</th> 79 <th>Configuration</th> 80 <th>BASE version</th> 81 </tr> 82 <tr> 83 <td>Base1PluginExecuter</td> 84 <td><a href="">download</a></td> 85 <td><i>-N/A-</i></td> 86 <td> </td> 87 </tr> 88 <tr class="evenrow"> 89 <td>JEP extra value calculator</td> 90 <td><a href="">download</a></td> 91 <td><i>-N/A-</i></td> 92 <td> </td> 93 </tr> 94 <tr> 95 <td>JEP filter plugin</td> 96 <td><a href="">download</a></td> 97 <td><i>-N/A-</i></td> 98 <td> </td> 99 </tr> 100 <tr class="evenrow"> 101 <td>JEP intensity transformer</td> 102 <td><a href="">download</a></td> 103 <td><i>-N/A-</i></td> 104 <td> </td> 105 </tr> 106 <tr> 107 <td>Normalization: Lowess</td> 108 <td><a href="">download</a></td> 109 <td><i>-N/A- </i></td> 110 <td> </td> 111 </tr> 112 <tr class="evenrow"> 113 <td>Normalization: Median ratio</td> 114 <td><a href="">download</a></td> 115 <td><i>-N/A-</i></td> 116 <td> </td> 117 </tr> 118 </table><br> 119 </li> 120 121 <li> 122 <a name="export"></a> 123 <b>Export</b> 124 <table class="listing"> 125 <tr> 126 <th>Plugin name</th> 127 <th>Download</th> 128 <th>Configuration</th> 129 <th>BASE version</th> 130 </tr> 131 <tr> 132 <td>Bioassay set exporter</td> 133 <td><a href="">download</a></td> 134 <td><i>- N/A -</i></td> 135 <td> </td> 136 </tr> 137 <tr class="evenrow"> 138 <td>Help texts exporter</td> 139 <td><a href="">download</a></td> 140 <td><i>- N/A -</i></td> 141 <td> </td> 142 </tr> 143 <tr> 144 <td>Plate mapping exporter</td> 145 <td><a href="">download</a></td> 146 <td><i>- N/A -</i></td> 147 <td> </td> 148 </tr> 149 <tr class="evenrow"> 150 <td>Plugin configuration exporter</td> 151 <td><a href="">download</a></td> 152 <td><i>- N/A -</i></td> 153 <td> </td> 154 </tr> 155 <tr> 156 <td>Table exporter</td> 157 <td><a href="">download</a></td> 158 <td><i>- N/A -</i></td> 159 <td> </td> 160 </tr> 161 </table><br> 162 </li> 163 164 <li> 165 <a name="import"></a> 166 <b>Import</b> 167 <table class="listing"> 168 <tr> 169 <th>Plugin name</th> 170 <th>Download</th> 171 <th>Configuration</th> 172 <th>BASE version</th> 173 </tr> 174 <tr> 175 <td>Help texts exporter</td> 176 <td><a href="">download</a></td> 177 <td><i>- N/A -</i></td> 178 <td> </td> 179 </tr> 180 <tr class="evenrow"> 181 <td>Plate importer</td> 182 <td><a href="">download</a></td> 183 <td> 184 <table cellspacing="0"> 185 <tr> 186 <td><a href="download/plugin_configuration/importer/plate_importer(384wells).xml">384 wells-plate</a></td> 187 </tr> 188 <tr> 189 <td><a href="download/plugin_configuration/importer/plate_importer(96wells).xml">96 wells-plate</a></td> 190 </tr> 191 </table> 192 </td> 193 <td> </td> 194 </tr> 195 <tr> 196 <td>Plate mapping importer</td> 197 <td><a href="">download</a></td> 198 <td><i>- N/A -</i></td> 199 <td> </td> 200 </tr> 201 <tr class="evenrow"> 202 <td>Plugin configuration importer</td> 203 <td><a href="">download</a></td> 204 <td><i>- N/A -</i></td> 205 <td> </td> 206 </tr> 207 <tr> 208 <td>Print map importer</td> 209 <td><a href="">download</a></td> 210 <td><i>- N/A -</i></td> 211 <td> </td> 212 </tr> 213 <tr class="evenrow"> 214 <td>Raw data importer</td> 215 <td><a href="">download</a></td> 216 <td> 217 <table cellspacing="0"> 218 <tr> 219 <td><a href="download/plugin_configuration/importer/rawdata_importer_genepix(cy3_cy5).xml">cy3/cy5 genepix</a></td> 220 </tr> 221 <tr> 222 <td><a href="download/plugin_configuration/importer/rawdata_importer_genepix(cy5_cy3).xml">cy5/cy3 genepix</a></td> 223 </tr> 224 </table> 225 </td> 226 <td> </td> 227 </tr> 228 <tr> 229 <td>Reporter importer</td> 230 <td><a href="">download</a></td> 231 <td> 232 <table cellspacing="0"> 233 <tr> 234 <td><a href="download/plugin_configuration/importer/reporter_importer(96wells).xml">96 wells</a></td> 235 </tr> 236 <tr> 237 <td><a href="download/plugin_configuration/importer/reporter_importer(384wells).xml">384 wells</a></td> 238 </tr> 239 <tr> 240 <td><a href="download/plugin_configuration/importer/reporter_importer(genepix).xml">genepix</a></td> 241 </tr> 242 </table> 243 </td> 244 <td> </td> 245 </tr> 246 <tr class="evenrow"> 247 <td>Reporter map importer</td> 248 <td><a href="">download</a></td> 249 <td> 250 <table cellspacing="0"> 251 <tr> 252 <td><a href="download/plugin_configuration/importer/reporter_map_importer(genepix).xml">genepix</a></td> 253 </tr> 254 </table> 255 </td> 256 <td> </td> 257 </tr> 258 </table><br> 259 </li> 260 261 <li> 262 <a name="intensity"></a> 263 <b>Intensity</b> 264 <table class="listing"> 265 <tr> 266 <th>Plugin name</th> 267 <th>Download</th> 268 <th>Configuration</th> 269 <th>BASE version</th> 270 </tr> 271 <tr> 272 <td>Formula intensity calculator</td> 273 <td><a href="">download</a></td> 274 <td><i>- N/A -</i></td> 275 <td> </td> 276 277 </tr> 278 </table><br> 279 </li> 280 281 <li> 282 <a name="other"></a> 283 <b>Other</b> 284 <table class="listing"> 285 <tr> 286 <th>Plugin name</th> 287 <th>Download</th> 288 <th>Configuration</th> 289 <th>BASE version</th> 290 </tr> 291 <tr> 292 <td>Spot images creator</td> 293 <td><a href="download/plugin_jar/other/spot_image_creator.jar">download</a></td> 294 <td><i>- N/A -</i></td> 295 <td> </td> 296 </tr> 297 <tr class="evenrow"> 298 <td>ZIP file unpacker</td> 299 <td><a href="download/plugin_jar/other/zip_file_unpacker.jar">download</a></td> 300 <td><i>- N/A -</i></td> 301 <td> </td> 302 </tr> 303 </table><br> 304 </li> 305 </ol> 306 </li> 307 <li> 308 <a name="config_packages"></a> 309 <h2>Configuration packages</h2> 66 310 <table class="listing"> 67 311 <tr> 68 <th>Plugin name</th> 69 <th colspan="2">Download/Configuration</th> 70 <th>Description</th> 312 <th>Type</th> 313 <th>Date</th> 314 <th>Download</th> 315 <th>Plugins</th> 71 316 </tr> 72 317 <tr> 73 <td> Base1PluginExecuter</td>74 <td> <a href="">download</a></td>75 <td> <a href="">configuration</a></td>76 <td> This plug-in simulates the plug-in runner from Base 1.2 to enable old plug-ins to be executed.</td>318 <td>Affymetrix</td> 319 <td> </td> 320 <td>download</td> 321 <td> </td> 77 322 </tr> 78 <tr >79 <td> JEP extra value calculator</td>80 <td> <a href="">download</a></td>81 <td> <i>- N/A -</i></td>82 <td> This plugin is used to calculate extra values for a bioassay set. The expressions are parsed with the JEP package.</td>323 <tr class="evenrow"> 324 <td>Genepix</td> 325 <td> </td> 326 <td>download</td> 327 <td> </td> 83 328 </tr> 84 <tr> 85 <td>JEP filter plugin</td> 86 <td><a href="">download</a></td> 87 <td><i>- N/A -</i></td> 88 <td>This filter is based on expressions entered by the user, which are parsed with the JEP package.</td> 89 </tr> 90 <tr> 91 <td>JEP intensity transformer</td> 92 <td><a href="">download</a></td> 93 <td><i>- N/A -</i></td> 94 <td> 95 This plugin is used to transform the intensities of a bioassayset using expressions entered by the user. 96 The expressions are parsed with the JEP package. 97 </td> 98 </tr> 99 <tr> 100 <td>Normalization: Lowess</td> 101 <td><a href="">download</a></td> 102 <td><i>- N/A - </i></td> 103 <td>This is an efficient java implementation by Johan Enell of the LOWESS algorithm. It provides intensity-based normalization.</td> 104 </tr> 105 <tr> 106 <td>Normalization: Median ratio</td> 107 <td><a href="">download</a></td> 108 <td><i>- N/A - </i></td> 109 <td>This normalizer scales the intensities in such a way that their geometric mean (sqrt(i1 * i2)) is kept constant but the median of their ratios (i1/i2) is shifted to 1.</td> 110 </tr> 111 </table> 112 </li> 113 114 <li> 115 <a name="export"></a> 116 <h2>Export</h2> 117 <table class="listing"> 118 <tr> 119 <th>Plugin name</th> 120 <th colspan="2">Download/Configuration</th> 121 <th>Description</th> 122 </tr> 123 <tr> 124 <td>Bioassay set exporter</td> 125 <td><a href="">download</a></td> 126 <td><i>- N/A -</i></td> 127 <td>Exporter for bioassay sets.</td> 128 </tr> 129 <tr> 130 <td>Help texts exporter</td> 131 <td><a href="">download</a></td> 132 <td><i>- N/A -</i></td> 133 <td>This plugin is used to export a client application's help texts.</td> 134 </tr> 135 <tr> 136 <td>Plate mapping exporter</td> 137 <td><a href="">download</a></td> 138 <td><i>- N/A -</i></td> 139 <td>This plugin is used to export plate mappings.</td> 140 </tr> 141 <tr> 142 <td>Plugin configuration exporter</td> 143 <td><a href="">download</a></td> 144 <td><i>- N/A -</i></td> 145 <td>This plugin is used to export plugin configurations to an XML-file.</td> 146 </tr> 147 <tr> 148 <td>Table exporter</td> 149 <td><a href="">download</a></td> 150 <td><i>- N/A -</i></td> 151 <td>Export all table listings in the web interface as tab-separated text files or as XML.</td> 152 </tr> 153 </table> 154 </li> 155 156 <li> 157 <a name="import"></a> 158 <h2>Import</h2> 159 <table class="listing"> 160 <tr> 161 <th>Plugin name</th> 162 <th colspan="2">Download/Configuration</th> 163 <th>Description</th> 164 </tr> 165 <tr> 166 <td>Help texts exporter</td> 167 <td><a href="">download</a></td> 168 <td><i>- N/A -</i></td> 169 <td>This plugin imports help texts from a XML-file to the BASE.</td> 170 </tr> 171 <tr> 172 <td>Plate importer</td> 173 <td><a href="">download</a></td> 174 <td><a href="">configuration</a></td> 175 <td>This plugin is used to import plates from a simple flat file.</td> 176 </tr> 177 <tr> 178 <td>Plate mapping importer</td> 179 <td><a href="">download</a></td> 180 <td><i>- N/A -</i></td> 181 <td>This plugin is used to import plate mappings.</td> 182 </tr> 183 <tr> 184 <td>Plugin configuration importer</td> 185 <td><a href="">download</a></td> 186 <td><i>- N/A -</i></td> 187 <td>This plugin is used to import configuration for a BASE plugin.</td> 188 </tr> 189 <tr> 190 <td>Print map importer</td> 191 <td><a href="">download</a></td> 192 <td><i>- N/A -</i></td> 193 <td>This plugin is used to import arraydesign from a print map.</td> 194 </tr> 195 <tr> 196 <td>Raw data importer</td> 197 <td><a href="">download</a></td> 198 <td><a href="">configuration</a></td> 199 <td>This plugin is used to import raw data from a simple text file.</td> 200 </tr> 201 <tr> 202 <td>Reporter importer</td> 203 <td><a href="">download</a></td> 204 <td><a href="">configuration</a></td> 205 <td>This plugin is used to import reporters from a simple flat file.</td> 206 </tr> 207 <tr> 208 <td>Reporter map importer</td> 209 <td><a href="">download</a></td> 210 <td><a href="">configuration</a></td> 211 <td>This plugin is used to import features to an ArrayDesign from a simple flat file.</td> 212 </tr> 213 </table> 214 </li> 215 216 <li> 217 <a name="intensity"></a> 218 <h2>Intensity</h2> 219 <table class="listing"> 220 <tr> 221 <th>Plugin name</th> 222 <th colspan="2">Download/Configuration</th> 223 <th>Description</th> 224 </tr> 225 <tr> 226 <td>Formula intensity calculator</td> 227 <td><a href="">download</a></td> 228 <td><i>- N/A -</i></td> 229 <td>This plugin is used to calculate intensities from raw data</td> 230 </tr> 231 </table> 232 </li> 233 234 <li> 235 <a name="other"></a> 236 <h2>Other</h2> 237 <table class="listing"> 238 <tr> 239 <th>Plugin name</th> 240 <th colspan="2">Download/Configuration</th> 241 <th>Description</th> 242 </tr> 243 </table> 329 </table> 244 330 </li> 245 331 </ol>
Note: See TracChangeset
for help on using the changeset viewer.
