Ignore:
Timestamp:
Oct 25, 2006, 1:12:33 AM (16 years ago)
Author:
Jari Häkkinen
Message:

Improving getting started doc.

File:
1 edited

Legend:

Unmodified
Added
Removed
  • trunk/doc/user/getting_started.html

    r2800 r2801  
    8383
    8484          <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
    8889            tasks. The root account should not be used as the
    8990            administrator account. </p>
     
    9192
    9293          <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
    104106            <a
    105107            href=http://baseplugins.thep.lu.se/wiki/thep.lu.se.RMAExpress>RMAExpress
     
    129131            any raw data can be stored in BASE some information has to
    130132            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>
    136282          </li>
    137283
Note: See TracChangeset for help on using the changeset viewer.