Changeset 2801
- Timestamp:
- Oct 25, 2006, 1:12:33 AM (16 years ago)
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- 1 edited
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trunk/doc/user/getting_started.html (modified) (3 diffs)
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trunk/doc/user/getting_started.html
r2800 r2801 83 83 84 84 <li> 85 <p> Log in as 'root' using the password you set during 86 BASE initialization. Create an administrator account. Log 87 out, and use the admin account for all administrative 85 <p> <b>Create an administrator account</b> <br> Log in as 86 'root' using the password you set during BASE 87 initialization. Create an administrator account. Log out, 88 and use the admin account for all administrative 88 89 tasks. The root account should not be used as the 89 90 administrator account. </p> … … 91 92 92 93 <li> 93 <p> Create user accounts using the newly created 94 administrator account. You should give your users 95 appropriate roles, most of them should be assigned to the 96 'User' role. (Link to role docs?) You can create new roles 97 if the default ones does not fit your needs. </p> 98 </li> 99 100 <li> 101 <p> Create needed plug-in configurations. Some plug-ins 102 need to be configured before use, whereas other works out 103 of the box. Some external plug-ins as the 94 <p> <b>Create user accounts</b> <br> Create user accounts 95 using the newly created administrator account. You should 96 give your users appropriate roles, most of them should be 97 assigned to the 'User' role. (Link to role docs?) You can 98 create new roles if the default ones does not fit your 99 needs. </p> 100 </li> 101 102 <li> 103 <p> <b>Create essential plug-in configurations</b> <br> 104 Some plug-ins need to be configured before use, whereas 105 other works out of the box. Some external plug-ins as the 104 106 <a 105 107 href=http://baseplugins.thep.lu.se/wiki/thep.lu.se.RMAExpress>RMAExpress … … 129 131 any raw data can be stored in BASE some information has to 130 132 be available in BASE. The slide design (reporter map) and 131 reporter information (probeset information in Affymetrix 132 vocabulary). For these we need to create configurations 133 for the "Reporter map importer" and "Reporter importer" 134 respectively, and a configuration is needed for the raw 135 data import plug-in, "Raw data importer", as well. </p> 133 reporter information (probe set information in Affymetrix 134 vocabulary). For these imports to work for Genepix data we 135 need to create configurations for the "Reporter map 136 importer" and "Reporter importer" respectively, and a 137 configuration is needed for the raw data import plug-in, 138 "Raw data importer", as well. Affymetrix data import works 139 differently and only a "Reporter map importer" 140 configuration is needed.</p> 141 142 <p> The pre-installed plug-in definitions are already 143 shared to group 'Everyone' (all users are member of this 144 group) but the configurations created are not shared by 145 default. The configurations should be shared to the users 146 who should have access to them, normally group 147 'Everyone'. As counterexamples, the reporter importers and 148 reporter map importers do not have to be share to everyone 149 since these imports should only be allowed to be done by a 150 small group of users. Every reporter and reporter map 151 should only be imported once and all users should use the 152 same reporter and reporter map information. The raw data 153 importers should normally be shared to everyone since all 154 users import data into BASE. </p> 155 156 <p> <i>Reporter importer</i> <br> Select the "Reporter 157 importer", and click on the 'New configuration ...' 158 tab. Enter a name in the 'Name' field (Affymetrix probe 159 set importer / ) and click 'Save and configure' 160 button. The next pop-up expects input of regular 161 expression needed to import reporter data. Here we just 162 give the values to add to the panel, but as of version 2.1 163 it is possible to use a import format wizard. The wizard 164 is started by clicking on the 'Test with file ...' 165 button. Here we tabulated the regexp to enter (assuming 166 that the default 167 <a 168 href="../admin/extended-properties.html">extended-properties.xml</a> 169 is used): 170 <table> 171 <tr> 172 <td> <b>Column</b> </td> 173 <td> <b>Regexp</b> (Affymetrix) </td> 174 <td> <b>Regexp</b> (Genepix) </td> 175 </tr> 176 <tr> 177 <td> Data Header </td> 178 <td> "Probe Set ID","GeneChip Array",.* </td> 179 <td> </td> 180 </tr> 181 <tr> 182 <td> Data splitter </td> 183 <td> (?!"),(?=") </td> 184 <td> </td> 185 </tr> 186 <tr> 187 <td> Remove quotes </td> 188 <td> true </td> 189 <td> </td> 190 </tr> 191 <tr> 192 <td> Name </td> 193 <td> \Probe Set ID\ </td> 194 <td> </td> 195 </tr> 196 <tr> 197 <td> Reporter ID </td> 198 <td> \Probe Set ID\ </td> 199 <td> </td> 200 </tr> 201 <tr> 202 <td> Gene symbol </td> 203 <td> \Gene Symbol\ </td> 204 <td> </td> 205 </tr> 206 <tr> 207 <td> Cluster ID </td> 208 <td> \UniGene ID\ </td> 209 <td> </td> 210 </tr> 211 </table> 212 <br> Finalize with clicking 'Next'. You can of course fill 213 the other entries as well. </p> 214 215 <p> <i>Reporter map importer</i> <br> Affymetrix CDF files 216 do not need a configuration since these are not imported 217 to BASE with a plug-in. Genepix data requires a 218 configuration. Select the "Reporter map importer" from the 219 plug-in definition list. Genepix documentation missing 220 here. </p> 221 222 <p> <i>Raw data importer</i> <br> Affymetrix CEL files 223 do not need a configuration since these are not imported 224 to BASE with a plug-in. Genepix data requires a 225 configuration. Select the "Raw data importer" from the 226 plug-in definition list. Genepix documentation missing 227 here. </p> 228 </li> 229 230 <li> 231 <p> (Affymetrix only) <b>Install 232 <a 233 href=http://baseplugins.thep.lu.se/wiki/thep.lu.se.RMAExpress>RMAExpress 234 plug-in for BASE</a></b> <br> This plug-in is required for 235 Affymetrix data. The plug-in will create a bioassay set, 236 i.e., to be able to analyse the data in BASE.</p> 237 </li> 238 239 <li> 240 <p> <b>Upload files</b> <br> Before import you can upload 241 files to the server, or if preferred, files to be imported 242 can be uploaded at import time. To upload files, choose 243 'View' -> 'Files' and click in the 'Upload file...' 244 button. At upload time you assign a type to the file (can 245 be changed later if needed), and batch upload of files is 246 possible in a zip-file or tar archive. </p> 247 248 <p> As administrator you need to upload the reporter map 249 (array design) files and corresponding reporter files. For 250 Affymetrix this translates to Affydesign.cdf files and 251 Affydesign_annot.csv files. </p> 252 </li> 253 254 <li> 255 <p> <b> Reporter import </b> <br> Choose 'View' -> 256 'Reporters' and click on the 'Import...' tab. Click 'Next' 257 in the pop-up without changing anything. Select the file 258 with reporter information and click 'Next'. In the panel 259 you can choose to update reporter information for already 260 stored reporters. Click 'Next'. Set the job name and click 261 'Finish' to start the import. A progress report will be 262 displayed. It is safe to close this page since the job 263 will finish anyway. </p> 264 </li> 265 266 <li> 267 <p> <b> Import reporter maps </b> <br> To create a new 268 design, choose 'Array LIMS' -> 'Array designs' and click 269 on the 'New...' tab. Select a name for the design. If it 270 is an Affymetrix design, mark the 'Affy chip' box and 271 select a 'CDF file'. Hint: For Affymetrix design you 272 should choose the name to be the same as the cdf file 273 name. If you are importing something else than Affymetrix 274 designs make sure that you unmark the 'Affy chip' 275 box. Finalize with 'Save'. For Affymetrix the import is 276 done, whereas Genepix have to perform reporter map 277 import. </p> 278 279 <p> <i>Genepix reporter map import</i> <br> Click on the 280 newly created array design, and click on the 'Import...' 281 tab. More information needed here. </p> 136 282 </li> 137 283
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