Changeset 3414


Ignore:
Timestamp:
May 30, 2007, 11:46:05 PM (14 years ago)
Author:
Martin Svensson
Message:

References #565. Major organizations, will read it one more time before this ticket is closed.

Location:
trunk/doc/src/docbook
Files:
1 deleted
1 edited

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  • trunk/doc/src/docbook/userdoc/array_lims.xml

    r3412 r3414  
    55<!--
    66  $Id$
    7 
     7 
    88  Copyright (C) Authors contributing to this file.
    9 
     9 
    1010  This file is part of BASE - BioArray Software Environment.
    1111  Available at http://base.thep.lu.se/
    12 
     12 
    1313  BASE is free software; you can redistribute it and/or
    1414  modify it under the terms of the GNU General Public License
    1515  as published by the Free Software Foundation; either version 2
    1616  of the License, or (at your option) any later version.
    17 
     17 
    1818  BASE is distributed in the hope that it will be useful,
    1919  but WITHOUT ANY WARRANTY; without even the implied warranty of
    2020  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    2121  GNU General Public License for more details.
    22 
     22 
    2323  You should have received a copy of the GNU General Public License
    2424  along with this program; if not, write to the Free Software
     
    3232  <sect1 id="array_lims.introduction">
    3333    <title>Introduction</title>
    34 
    35     <para>Arrays are at the core of the BASE2 business and are essential elements to describe in
     34    <para>
     35      Arrays are at the core of the BASE2 business and are essential elements to describe in
    3636      order to be MIAME compliant. It is also critical to track and manage information about
    3737      microarray design as accurately as possible since mistakes could prove extremely costly
    38       in downstream analysis.</para>
    39     <para>Finally, as a good practice, all Array related information should be entered into
    40       BASE2 system prior to start describing the sample processing and hybridizations events
    41       making up a microarray experiment.</para>
    42 
    43     <para>BASE2 has been engineered to support microarray printing facilities. The system
     38      in downstream analysis.
     39    </para>
     40    <para>
     41      Finally, as a good practice, all array related information should be entered into BASE2
     42      system prior to start describing the sample processing and hybridizations events making
     43      up a microarray experiment.
     44    </para>
     45
     46    <para>
     47      BASE2 has been engineered to support microarray printing facilities. The system
    4448      therefore offers objects to describe plates, their geometries and the events (merging,
    4549      printing) affected them. The first section of the chapter deals with this functionality.
    46       as well as plate management.</para>
    47 
    48     <para>For users buying their arrays from commercial sources, the Plate Management component
    49       can be ignored and they can go immediately to the second section <xref
    50         linkend="array_lims.arraydesign"/> of the chapter.</para>
     50      as well as plate management.
     51    </para>
     52
     53    <para>
     54      For users buying their arrays from commercial sources, the plate management component
     55      can be ignored and they can go immediately to
     56      <xref linkend="array_lims.arraydesign" />
     57      .
     58    </para>
    5159
    5260  </sect1>
    5361
    5462  <sect1 id="array_lims.platemanagement">
    55     <title>Managing Plates</title>
    56     <para>TO DO</para>
     63    <title>Plates</title>
     64    <para>TODO</para>
    5765  </sect1>
    5866
    5967  <sect1 id="array_lims.arraydesign">
    60     <title>Managing ArrayDesigns</title>
    61     <para> ArrayDesign should be understood as a plan which can be realized during a printing
     68    <title>Array designs</title>
     69    <para>
     70      Array design should be understood as a plan which can be realized during a printing
    6271      process producing microarray slides. During the course of the printing process, reagents
    6372      may run out leading to the interruption of this process. All slides created during this
    64       printing process belong to the same printing 'batch'. It is the array slide that will
    65       eventually be used in a Hybridization event. BASE2 allows user to track those 3 entities
     73      printing process belong to the same printing batch. It is the array slide that will
     74      eventually be used in a hybridization event. BASE2 allows user to track those 3 entities
    6675      with great details. This is an important functionality for users producing their own
    6776      arrays and for those caring for quality control and tracking of microarray slides in a
    6877      printing facility. The following sections detail how to use BASE2 to help in these
    69       tasks. </para>
    70     <sect2 id="array_lims.arraydesign.create">
    71       <title>Creating ArrayDesigns</title>
    72       <para>To create an ArrayDesign, do the following</para>
    73       <para>Go To <menuchoice>
    74           <guimenu>Array LIMS</guimenu>
    75           <guimenuitem>Array designs</guimenuitem>
    76         </menuchoice>
    77       </para>
    78       <para>The ArrayDesign List view now presents all ArrayDesigns available to the user
    79         (shared to or owned by).</para>
    80       <para>Click on &gbNew; button</para>
    81       <para>A 'Create' pop-up window opens. It contains 3 tabs</para>
    82 
     78      tasks.
     79    </para>
     80    <tip>
     81      <para>
     82        It's highly recommended to have read
     83        <xref linkend="webclient.items" />
     84        before continuing with this chapter.
     85      </para>
     86    </tip>
     87    <para>
     88      Use
     89      <menuchoice>
     90        <guimenu>Array LIMS</guimenu>
     91        <guimenuitem>Array designs</guimenuitem>
     92      </menuchoice>
     93      to get to the list page with array designs.
     94    </para>
     95    <sect2 id="array_lims.arraydesign.properties">
     96      <title>Properties</title>
     97      <sect3 id="array_lims.arraydesign.properties.arraydesign">
     98        <title>Array design</title>
     99        <variablelist>
     100          <varlistentry>
     101            <term>
     102              <guilabel>Name</guilabel>
     103            </term>
     104            <listitem>
     105              <para>Provide an unique sensible name for the design (required).</para>
     106            </listitem>
     107          </varlistentry>
     108          <varlistentry>
     109            <term>
     110              <guilabel>Affy chip</guilabel>
     111            </term>
     112            <listitem>
     113              <para>
     114                This is a checkbox for providing a boolean entry, essentially
     115                telling the system whether the array design being created is of
     116                affymetrix technology or not.
     117              </para>
     118              <warning>
     119                <para>
     120                  As indicated on the interface, once saved, this information
     121                  cannot be modified, so if a mistake is made, the entry will have
     122                  to be deleted.
     123                </para>
     124              </warning>
     125            </listitem>
     126          </varlistentry>
     127          <varlistentry>
     128            <term>
     129              <guilabel>CDF file</guilabel>
     130            </term>
     131            <listitem>
     132              <para>
     133                This field allows to upload an affymetrix CDF file. A CDF file is a
     134                binary file describing affymetrix chip layout. This file is
     135                necessary for performing analysis using some BASE2 plugins (e.g
     136                RMAExpress plugin).
     137              </para>
     138              <note>
     139                <para>
     140                  Affymetrix users, you can also upload CLF or BPMAP files defined
     141                  for exon and tiling arrays respectively.
     142                </para>
     143              </note>
     144            </listitem>
     145          </varlistentry>
     146          <varlistentry>
     147            <term>
     148              <guilabel>Description</guilabel>
     149            </term>
     150            <listitem>
     151              <para>
     152                Provide other useful information about the array design in this text
     153                area.
     154              </para>
     155            </listitem>
     156          </varlistentry>
     157        </variablelist>
     158        <para>
     159          Click on the &gbSave; button to store the information in BASE2 or on the
     160          &gbCancel; button to abort.
     161        </para>
     162        <para>
     163          Upon saving, the array design list view page is displayed. Users should pay
     164          attention to the column
     165          <guilabel>Has features</guilabel>
     166          . Unless an affymetrix array design was created, the value will be by default
     167          set to
     168          <guilabel>no</guilabel>
     169          . For all other cases, this value will only be updated following
     170          <guilabel>Importing the features</guilabel>
     171          , a process which is detailed in the next section.
     172        </para>
     173      </sect3>
     174
     175      <sect3 id="array_lims.arraydesign.properties.annotations">
     176        <title>Annotations and inherited annotations</title>
     177        <para>
     178          This allow you to input values associated to annotation types devised to refine
     179          array design description. Read more about annotations in
     180          <xref linkend="annotations" />
     181          .
     182        </para>
     183      </sect3>
     184
     185
     186      <sect3 id="array_lims.arraydesign.properties.importfeature">
     187        <title>Importing features to an array design</title>
     188
     189        <para>
     190          For non-affymetrix arraydesigns, importing features is an important step in
     191          order to fully define an array design. It should be noted that BASE2 does not
     192          enforce the immediate feature import upon creation of array design. However, It
     193          is STRONGLY advised to do so when creating an array design. Doing so enables to
     194          use the array design for downstream analysis with no further trouble. It also
     195          matters when importing raw bioassay data and matching those to the corresponding
     196          array design.
     197        </para>
     198
     199        <para>
     200          This section applies only to non-affymetrix array design since affymetrix
     201          designs are handled differently. For affymetrix platform, features are
     202          considered imported when the affymetrix CDF file is actually uploaded.
     203        </para>
     204        <para>
     205          From the array design item view, click on the &gbImport; button and use the
     206          reporter map importer and an appropriate plugin configuration when following the
     207          instructions in
     208          <xref linkend="import_export_data.import" />
     209          .
     210        </para>
     211        <note>
     212          <para>
     213            The button only shows up if the logged in user has enough permissions.
     214          </para>
     215        </note>
     216        <para>
     217          If the import run is successful, go to the array design list view. The
     218          <guilabel>Has features</guilabel>
     219          column will show
     220          <guilabel>Yes (n)</guilabel>
     221          where n is the number of features actually present on the microarray and now
     222          associated to the newly created ArrayDesign.
     223        </para>
     224      </sect3>
     225    </sect2>
     226  </sect1>
     227
     228
     229  <sect1 id="array_lims.arraybatch">
     230    <title>Array batches</title>
     231
     232    <sect2 id="array_lims.arraybatch.create">
     233      <title>Creating array batches</title>
     234      <para>
     235        Beside the common way of creating items in BASE, an array batch can also be created
     236        directly from an array design, both in list view and single item view.
     237      </para>
    83238      <variablelist>
    84239        <varlistentry>
     240          <term>In list view of array design</term>
     241          <listitem>
     242            <para>
     243              Click on the
     244              <inlinemediaobject>
     245                <imageobject>
     246                  <imagedata fileref="figures/add.png" format="PNG" />
     247                </imageobject>
     248              </inlinemediaobject>
     249              icon available from the
     250              <guilabel>Batches</guilabel>
     251              column of the array design you want to use.
     252              <tip>
     253                <para>
     254                  As default in BASE the
     255                  <guilabel>Batches</guilabel>
     256                  column is hidden and need therefore be made visible first, see
     257                  <xref linkend="webclient.itemlist.columns" />
     258                </para>
     259              </tip>
     260            </para>
     261          </listitem>
     262        </varlistentry>
     263      </variablelist>
     264      <para>
     265        <guibutton>New batch&hellip;</guibutton>
     266        is the corresponding button in single item view. The current array design will
     267        automatically be filled in the array design property for the new batch.
     268      </para>
     269    </sect2>
     270    <sect2 id="array_lims.arraybatch.properties">
     271      <title>Properties</title>
     272      <variablelist>
     273        <varlistentry>
     274          <term>
     275            <guilabel>Name</guilabel>
     276          </term>
     277          <listitem>
     278            <para>The name of the array batch (required).</para>
     279          </listitem>
     280        </varlistentry>
     281        <varlistentry>
    85282          <term>
    86283            <guilabel>Array design</guilabel>
    87284          </term>
    88285          <listitem>
    89 
    90             <para>The tab contains four fields, namely:</para>
    91 
    92             <variablelist>
    93 
    94               <varlistentry>
    95                 <term>
    96                   <guilabel>Name</guilabel>
    97                 </term>
     286            <para>Array design that is used for the batch.</para>
     287          </listitem>
     288        </varlistentry>
     289        <varlistentry>
     290          <term>
     291            <guilabel>Print robot</guilabel>
     292          </term>
     293          <listitem>
     294            <para>The print robot that is used.</para>
     295          </listitem>
     296        </varlistentry>
     297        <varlistentry>
     298          <term>
     299            <guilabel>Protocol</guilabel>
     300          </term>
     301          <listitem>
     302            <para>
     303              The printing protocol that was followed when producing the array batch
     304            </para>
     305          </listitem>
     306        </varlistentry>
     307      </variablelist>
     308      <para>
     309        Click on the &gbSave; button to store the information in BASE2 or on the &gbCancel;
     310        button to abort.
     311      </para>
     312      <para>
     313        See
     314        <xref linkend="annotations" />
     315        for information about annotating items and inherit annotations.
     316      </para>
     317      <para>
     318        Number of slides that belongs to each array batch can be found in the
     319        <guilabel>Slides</guilabel>
     320        column, list view page.
     321      </para>
     322    </sect2>
     323  </sect1>
     324
     325  <sect1 id="array_lims.arrayslide">
     326    <title>Array slides</title>
     327    <para>
     328      Use
     329      <menuchoice>
     330        <guimenu>Array LIMS</guimenu>
     331        <guimenuitem>Array slides</guimenuitem>
     332      </menuchoice>
     333      to get to the list page of array slides.
     334    </para>
     335    <sect2 id="array_lims.arrayslide.create">
     336      <title>Creating array slides</title>
     337      <para>In BASE2, array slides can be created, except the common way, by 2 routes:</para>
     338      <variablelist>
     339        <varlistentry>
     340          <term>from the array batch list page</term>
     341          <listitem>
     342            <para>
     343              Clicking on the
     344              <inlinemediaobject>
     345                <imageobject>
     346                  <imagedata fileref="figures/add.png" format="PNG" />
     347                </imageobject>
     348              </inlinemediaobject>
     349              icon in the
     350              <guilabel>Slides</guilabel>
     351              column for the batch to add a slide to. Corresponding button in the view
     352              page of a batch is
     353              <guibutton>New slide&hellip;</guibutton>
     354              .
     355            </para>
     356          </listitem>
     357        </varlistentry>
     358        <varlistentry>
     359          <term>using a wizard to create multiple slides simultaneously</term>
     360          <listitem>
     361            <para>
     362              This can be started from three different places:
     363              <itemizedlist>
    98364                <listitem>
    99                   <para> Provide a unique sensible name for the design. Possibly
    100                     follow the convention [organisation-species-feature
    101                     number-version] as in EMBL-Hsapiens-wholegenome-45k-v1. For
    102                     commercial platforms such as Agilent and Affymetrix, it is
    103                     probably better to use the commercial names, such as Agilent
    104                     Whole Mouse Genome G4122A or HG_U133A respectively</para>
     365                  <para>
     366                    array batch list view by clicking on
     367                    <inlinemediaobject>
     368                      <imageobject>
     369                        <imagedata fileref="figures/new_wizard.gif"
     370                          format="GIF" />
     371                      </imageobject>
     372                    </inlinemediaobject>
     373                    in the
     374                    <guilabel>Slides</guilabel>
     375                    column of the batch that should be used.
     376                  </para>
    105377                </listitem>
    106               </varlistentry>
    107 
    108               <varlistentry>
    109                 <term>
    110                   <guilabel>Description</guilabel>
    111                 </term>
    112378                <listitem>
    113                   <para>Provide a short but meaningful of the ArrayDesign</para>
     379                  <para>
     380                    Using the
     381                    <guibutton>Create slides</guibutton>
     382                    in a single item view of an array batch.
     383                  </para>
    114384                </listitem>
    115               </varlistentry>
    116 
    117               <varlistentry>
    118                 <term>
    119                   <guilabel>Affy Chip</guilabel>
    120                 </term>
    121385                <listitem>
    122                   <para>This is a radio button for providing a boolean entry,
    123                     essentially telling the system whether the ArrayDesign being
    124                     created is of Affymetrix technology or not.</para>
    125                   <warning>
    126                     <para>As indicated on the interface, once saved, this
    127                       information cannot be modified, so if a mistake is made,
    128                       the entry will have to be deleted.</para>
    129                   </warning>
     386                  <para>
     387                    In the list page of array slides, using the
     388                    <guibutton>Create multiple&hellip;</guibutton>
     389                    button
     390                  </para>
    130391                </listitem>
    131               </varlistentry>
    132 
    133               <varlistentry>
    134                 <term>
    135                   <guilabel>CDF file</guilabel>
    136                 </term>
    137                 <listitem>
    138                   <para>This field allows to upload an Affymetrix CDF file. A CDF
    139                     file is a binary file describing Affymetrix chip layout.
    140                     This file is necessary for performing analysis using BASE2
    141                     plugins (e.g RMAExpress plugin).</para>
    142                   <note>
    143                     <para>Affymetrix users, you can also upload CLF or BPMAP
    144                       files defined for exon and tiling arrays
    145                     respectively.</para>
    146                   </note>
    147                 </listitem>
    148               </varlistentry>
    149 
    150             </variablelist>
    151           </listitem>
    152         </varlistentry>
    153 
    154         <varlistentry>
    155           <term>
    156             <guilabel>Annotations</guilabel>
    157           </term>
    158           <listitem>
    159             <para>This tab allows to input values associated to Annotation Types devised
    160               to refine ArrayDesign description.</para>
    161             <para>The windows will be empty if no Annotation Types have been declared to
    162               annotation ArrayDesign item or if none are shared to the user</para>
    163           </listitem>
    164         </varlistentry>
    165 
    166         <varlistentry>
    167           <term>
    168             <guilabel>Inherited Annotations</guilabel>
    169           </term>
    170           <listitem>
    171             <para>TO DO</para>
    172           </listitem>
    173         </varlistentry>
    174 
     392              </itemizedlist>
     393              The wizard is described further down in this chapter,
     394              <xref linkend="array_lims.arrayslide.properties.wizard" />
     395              .
     396            </para>
     397          </listitem>
     398        </varlistentry>
    175399      </variablelist>
    176       <para>Click on the &gbSave; button to store the information in BASE2 or on the
    177           &gbCancel; button to abort. </para>
    178       <para>Upon saving, the Array Design List View page is displayed. Users should pay
    179         attention to the column <guilabel>Has features</guilabel>. Unless an Affymetrix
    180         ArrayDesign was created, the value will be by default set to
    181         <guilabel>no</guilabel>. For all other cases, this value will only be updated
    182         following <guilabel>Importing the Features</guilabel>, a process which is detailed
    183         in the next section.</para>
    184 
    185400    </sect2>
    186 
    187     <sect2 id="array_lims.arraydesign.importfeature">
    188       <title>Importing Features associated to an ArrayDesign</title>
    189       <important>
    190         <para>For non-Affymetrix ArrayDesigns, Importing Features is an important step in
    191           order to fully define an ArrayDesign. It should be noted that BASE2 does not
    192           enforce the immediate Feature import upon creation of ArrayDesign. However, It
    193           is STRONGLY advised to do so when creating an ArrayDesign. Doing so enables to
    194           use the Array Design for downstream analysis with no further trouble. It also
    195           matters when importing rawBioassay data and matching those to the corresponding
    196           ArrayDesign. It is interesting to note that the processes of importing features
    197           associated to Array Design and importing Data associated to Raw BioAssay are in
    198           essence very similar.</para> Please see section <xref
    199           linkend="experiments_analysis.rawbioassay.rawdata"/> for more information. </important>
    200       <para>This section applies only to non-affymetrix ArrayDesign since Affymetrix designs
    201         are handled differently. For Affymetrix platform, features are considered imported
    202         when the Affymetrix CDF file is actually uploaded.</para>
    203       <para>From the ArrayDesign Item View, click on the &gbImport;
    204       button.</para>.<note>
    205         <para>The button only shows up if the logged in user has enough permissions.</para>
    206       </note>
    207       <para>A plugin interface is launched. One can either run the import using the autodetect
    208         settings or for more control, select a <guilabel>'Reporter Map Importer'</guilabel>
    209         plugin and then choose a <guilabel>plugin configuration</guilabel> available from
    210         the drop-down list populated from configurations shared to or owned by the user.</para>
    211       <para>BASE2 ships with Reporter Map Importer plugin configurations allowing to import
    212         features from Axon gal files and also gpr files (2 configurations_Block/Column/Row
    213         and Block/Row/Column for each file formats) and for Agilent FeatureExtraction files
    214         (to be confirmed). </para>
    215       <para>For more about the plugin configuration, refer to section <xref
    216           linkend="plugins.installation"/>.</para>
    217       <para>If the import run is successful, go to the ArrayDesign List view. The
    218           <guilabel>Has features</guilabel> column will show <guilabel>Yes (n)</guilabel>
    219         where n is the number of features actually present on the microarray and now
    220         associated to the newly created ArrayDesign.</para>
    221       <tip>
    222         <para>A list of Reporter Map Importer plugin configurations is maintained at BASE2
    223           site and each can be downloaded as xml file from
    224           <ulink url="http://base.thep.lu.se/chrome/site/doc/admin/plugin_configuration/coreplugins.html"/>.</para>
    225       </tip>
    226     </sect2>
    227     <para>If both actions have been successfully completed, the ArrayDesign is now fully defined
    228       and ArrayBatches and Array slides items can be created. This process is described in the
    229       following sections.</para>
    230 
    231 
    232     <sect2 id="array_lims.arraydesign.detail_view">
    233       <title>Viewing/Editing ArrayDesigns</title>
    234       <itemizedlist>
    235         <listitem>
    236           <para> Press and hold one of the <keycap>CTRL</keycap>, <keycap>ALT</keycap> or
    237               <keycap>SHIFT</keycap> keys while clicking on the name of an ArrayDesign
    238             Item, which is a live link. </para>
    239         </listitem>
    240         <listitem>
    241           <para> Alternately, navigating to the ArrayDesign Item View, one can hit the
    242               &gbEdit; to performed the task.</para>
    243           <para>In both cases, an Edit pop-up windows opens. It is essentially identical
    244             to a Create window and allows updating information about a particular
    245             ArrayDesign item stored in BASE2.</para>
    246           <figure id="write_docbook_doc.figures.arraydesign-itemview">
    247             <title>ArrayDesign Item View</title>
    248             <screenshot>
    249               <mediaobject>
    250                 <imageobject>
    251                   <imagedata contentwidth="10cm" width="10cm" fileref="figures/arraydesign-itemview.png" format="PNG"/>
    252                 </imageobject>
    253               </mediaobject>
    254             </screenshot>
    255           </figure>
    256         </listitem>
    257         <listitem>
    258           <para>From the ArrayDesign item View, all associated
    259             <guilabel>ArrayBatches</guilabel> are indicated as navigable links. Also
    260             present on the ArrayDesign Item View are the links back to
    261             <guilabel>Plates</guilabel> possibly used to define the ArrayDesign (none
    262             used in the screenshot).</para>
    263         </listitem>
    264       </itemizedlist>
    265     </sect2>
    266     <sect2 id="array_lims.arraydesign.delete">
    267       <title>Deleting/Restoring ArrayDesigns</title>
    268       <para>As for other items in BASE2, ArrayDesigns can be removed and restored. To do so,
    269         do the following:</para>
    270       <itemizedlist>
    271         <listitem>
    272           <para>Select one or more ArrayDesigns and click &gbDelete;
    273             button in the menu bar. </para>
    274           <para>All the selected ArrayDesigns have been marked as deleted and are no
    275             longer available from the interface. </para>
    276           <para>Only by selecting from the <guilabel>view/preset&hellip;</guilabel>
    277             select box the <guilabel>Removed</guilabel> option, one can see those of the
    278             ArrayDesigns earmarked for deletion. They will be shown with a symbol <inlinemediaobject>
    279               <imageobject>
    280                 <imagedata fileref="figures/deleted.gif" format="GIF"/>
    281               </imageobject>
    282             </inlinemediaobject> in front of them. </para>
    283         </listitem>
    284         <listitem>
    285           <para>Alternately, navigating to the ArrayDesign Item View, one can hit the
    286               &gbDelete; to performed the task. </para>
    287         </listitem>
    288         <listitem>
    289           <para>Deletion errors at this stage can be easily recovered. Select the item to
    290             recover from the List View (be sure to check the
    291             <guilabel>Removed</guilabel> option in the
    292             <guilabel>view/preset&hellip;</guilabel> filter) and hit the
    293               &gbRestore; button to performed the task. </para>
    294         </listitem>
    295       </itemizedlist>
    296       <important>
    297         <para>To really delete an item from the database you must use the trashcan. Items
    298           deleted from the Trashcan can not be recovered. To learn more about the trashcan
    299           function, please refer to <xref linkend="trashcan"/>
    300         </para>
    301       </important>
    302     </sect2>
    303 
    304   </sect1>
    305   <sect1 id="array_lims.arraybatch">
    306     <title>Managing Array Batches</title>
    307 
    308     <sect2 id="array_lims.arraybatch.create">
    309       <title>Creating Array Batches </title>
    310       <para>In BASE2, Array Batches can be created by 2 routes:</para>
    311       <orderedlist>
    312         <listitem>
    313           <para>Creating Array Batch from the ArrayDesign List View page</para>
    314           <para>Clicking on the <inlinemediaobject>
    315               <imageobject>
    316                 <imagedata fileref="figures/add.png" format="PNG"/>
    317               </imageobject>
    318             </inlinemediaobject> add Array batch button available from the
    319               <guilabel>Batches</guilabel> column of the ArrayDesign list view page.
    320           </para>
    321         </listitem>
    322         <listitem>
    323           <para>Creating ArrayBatch from the ArrayBatch List View page</para>
    324           <para>Go to <menuchoice>
    325               <guimenu>Array LIMS</guimenu>
    326               <guimenuitem>Array batches</guimenuitem>
    327             </menuchoice></para>
    328           <para>Click on &gbNew; button </para>
    329         </listitem>
    330       </orderedlist>
    331 
    332       <para>In both cases, an ArrayBatch Create pop-up window opens. The window contains 2
    333         mandatory fields:</para>
    334       <figure id="write_docbook_doc.figures.arraybatch-create">
    335         <title>Create New Array batch from the ArrayDesign List View</title>
     401    <sect2 id="array_lims.arrayslide.properties">
     402      <title>Properties</title>
     403
     404      <figure id="write_docbook_doc.figures.arrayslide-single-create">
     405        <title>Create New Array Slide from the ArrayBatch List View</title>
    336406        <screenshot>
    337407          <mediaobject>
    338408            <imageobject>
    339               <imagedata contentwidth="10cm" width="10cm" fileref="figures/arraybatch-create.png" format="PNG"/>
     409              <imagedata contentwidth="10cm" width="10cm"
     410                fileref="figures/arrayslide-single-create.png" format="PNG" />
    340411            </imageobject>
    341412          </mediaobject>
    342413        </screenshot>
    343414      </figure>
    344       <itemizedlist>
    345         <listitem>
    346           <para>
    347             <guilabel>Name</guilabel> and <guilabel>ArrayDesign</guilabel>.</para>
    348           <para>The later is a select-list population from ArrayDesigns owned by or shared
    349             to the user.</para>
    350         </listitem>
    351         <listitem>
    352           <para><guilabel>Print robot</guilabel> and <guilabel>Protocol</guilabel>, the
    353             other 2 fields, are optional and self explanatory.</para>
    354         </listitem>
    355       </itemizedlist>
    356       <para>Click on the &gbSave; button to store the information in BASE2 or on the
    357       &gbCancel; button to abort.</para>
    358     </sect2>
    359 
    360     <sect2 id="array_lims.arraybatch.detail_view">
    361       <title>Viewing/Editing ArrayBatches</title>
    362       <itemizedlist>
    363         <listitem>
    364           <para> Press and hold one of the <keycap>CTRL</keycap>, <keycap>ALT</keycap> or
    365               <keycap>SHIFT</keycap> keys while clicking on the name of an ArrayBatch
    366             Item, which is a live link. </para>
    367         </listitem>
    368         <listitem>
    369           <para> Alternately, navigating to the ArrayBatch Item View, one can hit the
    370               &gbEdit; to performed the task.</para>
    371           <para>In both cases, an Edit pop-up windows opens. It is essentially identical
    372             to a Create window and allows updating information about a particular
    373             ArrayBatch item stored in BASE2</para>
    374           <figure id="write_docbook_doc.figures.arraybatch-itemview">
    375             <title>ArrayBatch Item View</title>
    376             <screenshot>
    377               <mediaobject>
    378                 <imageobject>
    379                   <imagedata contentwidth="10cm" width="10cm" fileref="figures/arraybatch-itemview.png" format="PNG"/>
    380                 </imageobject>
    381               </mediaobject>
    382             </screenshot>
    383           </figure>
    384         </listitem>
    385         <listitem>
    386           <para>From the ArrayBatch item View, all associated <guilabel/>ArraySlides are
    387             indicated as their use in Hybridization events. Both ArraySlides and
    388             Hybridizations are clickable items, enabling easy navigation.</para>
    389         </listitem>
    390       </itemizedlist>
    391     </sect2>
    392     <sect2 id="array_lims.arraybatch.delete">
    393       <title>Deleting/Restoring ArrayBatches</title>
    394       <para>As for other items in BASE2, ArrayBatches can be removed and restored. To do so,
    395         do the following</para>
    396       <itemizedlist>
    397         <listitem>
    398           <para>Select one or more ArrayBatches and click &gbDelete;
    399             button in the menu bar. </para>
    400           <para>All the selected ArrayBatches have been marked as deleted and are no
    401             longer available from the interface. </para>
    402           <para>Only by selecting from the <guilabel>view/preset&hellip;</guilabel>
    403             select box the <guilabel>Removed</guilabel> option, one can see those of the
    404             ArrayBatches earmarked for deletion. They will be shown with a symbol <inlinemediaobject>
     415      <variablelist>
     416        <varlistentry>
     417          <term>
     418            <guilabel>Name</guilabel>
     419          </term>
     420          <listitem>
     421            <para>The name of the array slide (required).</para>
     422          </listitem>
     423        </varlistentry>
     424        <varlistentry>
     425          <term>
     426            <guilabel>Barcode</guilabel>
     427          </term>
     428          <listitem>
     429            <para>Does the array slide have a barcode, it can be put here.</para>
     430          </listitem>
     431        </varlistentry>
     432        <varlistentry>
     433          <term>
     434            <guilabel>Destroyed</guilabel>
     435          </term>
     436          <listitem>
     437            <para>
     438              This check-box can be ticked to mark the slide as destroyed, lost or
     439              damaged.
     440            </para>
     441          </listitem>
     442        </varlistentry>
     443        <varlistentry>
     444          <term>
     445            <guilabel>Array batch</guilabel>
     446          </term>
     447          <listitem>
     448            <para>Array batch that the slide belongs to (required).</para>
     449          </listitem>
     450        </varlistentry>
     451        <varlistentry>
     452          <term>
     453            <guilabel>Index</guilabel>
     454          </term>
     455          <listitem>
     456            <para>Index to mark up the name of the array slide.</para>
     457          </listitem>
     458        </varlistentry>
     459        <varlistentry>
     460          <term>
     461            <guilabel>Description</guilabel>
     462          </term>
     463          <listitem>
     464            <para>
     465              Any information useful information about the slide can be in this field.
     466            </para>
     467          </listitem>
     468        </varlistentry>
     469      </variablelist>
     470      <para>
     471        Click on the &gbSave; button to store the information in BASE2 or on the &gbCancel;
     472        button to abort.
     473      </para>
     474      <sect3 id="array_lims.arrayslide.properties.wizard">
     475        <title>Multiple slides wizard</title>
     476        <para>
     477          As mentioned above there is an alternative to create one slide at a time if you
     478          have many to add. The wizard is in two steps, both showed in the picture
     479          <xref linkend="write_docbook_doc.figures.arrayslide-multiple-create" />
     480          .
     481          <orderedlist>
     482            <listitem>
     483              <para>
     484                The first step reminds alot of the normal edit window of an array
     485                slide, but there are some differences:
     486                <variablelist>
     487                  <varlistentry>
     488                    <term>Quantity</term>
     489                    <listitem>
     490                      <para>
     491                        Number of slides to create with this wizard
     492                        (required and must be between 1 and 999)
     493                      </para>
     494                    </listitem>
     495                  </varlistentry>
     496                  <varlistentry>
     497                    <term>Start at</term>
     498                    <listitem>
     499                      <para>
     500                        The index number to start from when indexing the
     501                        name of the slides.
     502                      </para>
     503                    </listitem>
     504                  </varlistentry>
     505                  <varlistentry>
     506                    <term>Pad size</term>
     507                    <listitem>
     508                      <para>
     509                        The index will be filled out with zeros in front to
     510                        always have this length.
     511                      </para>
     512                    </listitem>
     513                  </varlistentry>
     514                </variablelist>
     515                Press
     516                <guibutton>Next</guibutton>
     517                to continue to next step of the wizard.
     518                <important>
     519                  <para>
     520                    Be sure to get everything right before proceeding, be cause
     521                    it is not possible to go back from step 2.
     522                  </para>
     523                </important>
     524              </para>
     525            </listitem>
     526            <listitem>
     527              <para>
     528                In step 2 should the barcodes for the array slides be entered, for
     529                those which have one. The autogenerated names of the slides can also
     530                be changed if that is wanted, as long as not any name-field is
     531                empty.
     532              </para>
     533            </listitem>
     534          </orderedlist>
     535        </para>
     536        <figure id="write_docbook_doc.figures.arrayslide-multiple-create">
     537          <title>Create multiple array slide</title>
     538          <screenshot>
     539            <mediaobject>
    405540              <imageobject>
    406                 <imagedata fileref="figures/deleted.gif" format="GIF"/>
     541                <imagedata contentwidth="10cm" width="10cm"
     542                  fileref="figures/arrayslide-multiple-create.png" format="PNG" />
    407543              </imageobject>
    408             </inlinemediaobject> in front of them. </para>
    409         </listitem>
    410         <listitem>
    411           <para>Alternately, navigating to the ArrayBatch Item View, one can hit the
    412               &gbDelete; to performed the task. </para>
    413         </listitem>
    414         <listitem>
    415           <para>Deletion errors at this stage can be easily recovered. Select the item to
    416             recover from the List View (be sure to check the
    417             <guilabel>Removed</guilabel> option in the
    418             <guilabel>view/preset&hellip;</guilabel> filter) and hit the
    419               &gbRestore; button to performed the task. </para>
    420         </listitem>
    421       </itemizedlist>
    422       <important>
    423         <para>To really delete an item from the database you must use the trashcan. Items
    424           deleted from the Trashcan can not be recovered. To learn more about the trashcan
    425           function, please refer to <xref linkend="trashcan"/>
    426         </para>
    427       </important>
     544            </mediaobject>
     545          </screenshot>
     546        </figure>
     547        <para>Fill in the necessary information as exhaustively as possible.</para>
     548        <para>
     549          Click on the &gbSave; button to store the information in BASE2 or on the
     550          &gbCancel; button to abort.
     551        </para>
     552      </sect3>
    428553    </sect2>
    429554  </sect1>
    430   <sect1 id="array_lims.arrayslide">
    431     <title>Managing Array Slides</title>
    432     <sect2 id="array_lims.arrayslide.create">
    433       <title>Creating Array Slides </title>
    434       <para>In BASE2, Array Slides can be created by 2 routes:</para>
    435       <orderedlist>
    436         <listitem>
    437           <para>Creating Array Slides from the ArrayBatch View page</para>
    438           <para>Clicking on the <inlinemediaobject>
    439               <imageobject>
    440                 <imagedata fileref="figures/add.png" format="PNG"/>
    441               </imageobject>
    442             </inlinemediaobject> add Array slides button. </para>
    443           <figure id="write_docbook_doc.figures.arrayslide-single-create">
    444             <title>Create New Array Slide from the ArrayBatch List View</title>
    445             <screenshot>
    446               <mediaobject>
    447                 <imageobject>
    448                   <imagedata contentwidth="10cm" width="10cm" fileref="figures/arrayslide-single-create.png" format="PNG"/>
    449                 </imageobject>
    450               </mediaobject>
    451             </screenshot>
    452           </figure>
    453         </listitem>
    454         <listitem>
    455           <para>Creating ArraySlides from the ArrayBatch List View page</para>
    456           <para>Go to <menuchoice>
    457               <guimenu>Array LIMS</guimenu>
    458               <guimenuitem>Array slides</guimenuitem>
    459             </menuchoice></para>
    460           <para>Click on &gbNew; button </para>
    461         </listitem>
    462       </orderedlist>
    463 
    464       <para>In both cases, an ArraySlide Create pop-up window opens. The window contains 2
    465         mandatory fields:</para>
    466       <itemizedlist>
    467         <listitem>
    468           <para>
    469             <guilabel>Name</guilabel> and <guilabel>ArrayBatch</guilabel>.</para>
    470           <para>The later is a select-list populated with ArrayBatches owned by or shared
    471             to the user.</para>
    472         </listitem>
    473         <listitem>
    474           <para><guilabel>Barcode</guilabel>, <guilabel>Index</guilabel> and
    475               <guilabel>Destroyed</guilabel>, a tick box enabling to record microarray
    476             slides lost by accident.</para>
    477         </listitem>
    478       </itemizedlist>
    479       <para>Click on the &gbSave; button to store the information in BASE2 or on the
    480           &gbCancel; button to abort. </para>
    481 
    482       <para> In addition to this classic way of creating BASE items, Arrays Slides can be
    483         created with a wizard available from both the ArraySlide Item view or from the
    484         ArrayBatch List View page. To call the wizard:</para>
    485       <para>Click on the <inlinemediaobject>
    486           <imageobject>
    487             <imagedata fileref="figures/new_wizard.gif" format="GIF"/>
    488           </imageobject>
    489         </inlinemediaobject> add multiple Array slides button in the
    490         <guilabel>Slides</guilabel> column of the ArrayBatch List view page.</para>
    491 
    492       <para> or </para>
    493       <para>Click on the <inlinemediaobject>
    494           <imageobject>
    495             <imagedata fileref="figures/new_wizard.gif" format="GIF"/>
    496           </imageobject>
    497         </inlinemediaobject>
    498         <guibutton>Create multiple&hellip;</guibutton> button from the menu bar of the
    499         ArraySlides List View page </para>
    500 
    501       <para>Either way will open the wizard window as shown below</para>
    502       <figure id="write_docbook_doc.figures.arrayslide-multiple-create">
    503         <title>Create Multiple Array Slide from the ArrayBatch List View wizard</title>
    504         <screenshot>
    505           <mediaobject>
    506             <imageobject>
    507               <imagedata contentwidth="10cm" width="10cm" fileref="figures/arrayslide-multiple-create.png" format="PNG"/>
    508             </imageobject>
    509           </mediaobject>
    510         </screenshot>
    511       </figure>
    512       <para>Fill in the necessary information as exhaustively as possible.</para>
    513       <para>Click on the &gbSave; button to store the information in BASE2
    514       or on the &gbCancel; button to abort. </para>
    515     </sect2>
    516 
    517     <sect2 id="array_lims.arrayslide.detail_view">
    518       <title>Viewing/Editing ArraySlides</title>
    519       <itemizedlist>
    520         <listitem>
    521           <para> Press and hold one of the <keycap>CTRL</keycap>, <keycap>ALT</keycap> or
    522               <keycap>SHIFT</keycap> keys while clicking on the name of an ArraySlide
    523             Item, which is a live link. </para>
    524         </listitem>
    525         <listitem>
    526           <para> Alternately, navigating to the ArraySlide Item View, one can hit the
    527               &gbEdit; to performed the task.</para>
    528           <para>In both cases, an Edit pop-up windows opens. It is essentially identical
    529             to a Create window and allows updating information about a particular
    530             ArraySlide item stored in BASE2</para>
    531           <figure id="write_docbook_doc.figures.arrayslide-itemview">
    532             <title>ArraySlide Item View</title>
    533             <screenshot>
    534               <mediaobject>
    535                 <imageobject>
    536                   <imagedata contentwidth="10cm" width="10cm" fileref="figures/arrayslide-itemview.png" format="PNG"/>
    537                 </imageobject>
    538               </mediaobject>
    539             </screenshot>
    540           </figure>
    541         </listitem>
    542 
    543         <listitem>
    544           <para>From the ArraySlide item View, the associated
    545             <guilabel>Hybridization</guilabel> can be indicated as navigable
    546           links</para>
    547         </listitem>
    548       </itemizedlist>
    549     </sect2>
    550     <sect2 id="array_lims.arrayslide.delete">
    551       <title>Deleting/Restoring ArraySlides</title>
    552       <para>As for other items in BASE2, ArraySlides can be removed and restored. To do so, do
    553         the following</para>
    554       <itemizedlist>
    555         <listitem>
    556           <para>Select one or more ArraySlides and click &gbDelete;
    557             button in the menu bar. </para>
    558           <para>All the selected ArraySlides have been marked as deleted and are no longer
    559             available from the interface. </para>
    560           <para>Only by selecting from the <guilabel>view/preset&hellip;</guilabel>
    561             select box the <guilabel>Removed</guilabel> option, one can see those of the
    562             ArraySlides earmarked for deletion. They will be shown with a symbol <inlinemediaobject>
    563               <imageobject>
    564                 <imagedata fileref="figures/deleted.gif" format="GIF"/>
    565               </imageobject>
    566             </inlinemediaobject> in front of them. </para>
    567         </listitem>
    568         <listitem>
    569           <para>Alternately, navigating to the ArraySlide Item View, one can hit the
    570               &gbDelete; to performed the task. </para>
    571         </listitem>
    572         <listitem>
    573           <para>Deletion errors at this stage can be easily recovered. Select the item to
    574             recover from the List View (be sure to check the
    575             <guilabel>Removed</guilabel> option in the
    576             <guilabel>view/preset&hellip;</guilabel> filter) and hit the
    577               &gbRestore; button to performed the task. </para>
    578         </listitem>
    579       </itemizedlist>
    580       <important>
    581         <para>To really delete an item from the database you must use the trashcan. Items
    582           deleted from the Trashcan can not be recovered. To learn more about the trashcan
    583           function, please refer to <xref linkend="trashcan"/>
    584         </para>
    585       </important>
    586     </sect2>
    587 
    588 
    589   </sect1>
    590 
    591555</chapter>
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