Ignore:
Timestamp:
Oct 10, 2011, 1:38:22 PM (11 years ago)
Author:
Nicklas Nordborg
Message:

References #1590: Documentation cleanup

New and updated screenshots for chapter 15 - Array LIMS.

File:
1 edited

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

    r5783 r5796  
    3636    about microarray design as accurately as possible since mistakes
    3737    could prove extremely costly in downstream analysis.
    38   </para>
    39   <para>
    4038    As a good practice, all array related information should be
    4139    entered into BASE prior to work on describing the sample
    42     processing and hybridizations events making up a microarray
     40    processing and hybridizations or other events making up an
    4341    experiment is begun.
    4442  </para>
    45   <para>
    46     BASE is engineered to support microarray printing facilities. The
    47     system therefore offers objects to describe plates, their
    48     geometries, and the events (<emphasis>e.g.</emphasis>, merging and
    49     printing) affecting them. The first section of this chapter deals
    50     with this functionality as well as plate management. Users buying
    51     arrays from commercial sources can ignore the plate management
    52     component and immediately jump to
    53     <xref linkend="array_lims.arraydesign" />.
    54   </para>
    55 
    56   <sect1 id="array_lims.platemanagement">
    57     <title>Plates</title>
    58     <para>TODO</para>
    59   </sect1>
    6043
    6144  <sect1 id="array_lims.arraydesign">
    … …  
    7356      tasks.
    7457    </para>
    75     <tip>
    76       <para>
    77         It's highly recommended to have read
    78         <xref linkend="webclient.items" />
    79         before continuing with this chapter.
    80       </para>
    81     </tip>
     58
     59    <note>
     60      <title>Non-array platforms also need array designs</title>
     61      <para>
     62        Array designs are needed also for non-array platforms (eg. sequencing). In this
     63        case a "virtual array design" is created which is simply a list of all features
     64        that is of interest in the experiment. Since there are no coordinates or positions
     65        to identify features a unique id need to be constructed in some other way.
     66        For example, in sequencing experiments we may use a GTF file to create a
     67        virtual array design using the <emphasis>transcript_id</emphasis> and
     68        <emphasis>chromosome</emphasis> as a unique identifier.
     69      </para>
     70    </note>
     71
    8272    <para>
    8373      Use
    … …  
    9181    <sect2 id="array_lims.arraydesign.properties">
    9282      <title>Properties</title>
    93       <sect3 id="array_lims.arraydesign.properties.arraydesign">
    94         <title>Array design</title>
    95        
     83
     84        <figure id="array_lims.figures.arraydesign">
     85          <title>Array design properties</title>
     86          <screenshot>
     87            <mediaobject>
     88              <imageobject>
     89                <imagedata
     90                  fileref="figures/arraydesign_edit.png" format="PNG" />
     91              </imageobject>
     92            </mediaobject>
     93          </screenshot>
     94        </figure>
     95
    9696        <helptext external_id="arraydesign.edit" title="Edit array design">
    9797        <variablelist>
    … …  
    126126                single slide. The default value is 1, but some
    127127                platforms, for example Illumina, has slides
    128                 with 6 or 8 arrays.
     128                with 6 or 8 arrays. In sequencing platforms, this value
     129                is the number of lanes on a flow cell.
    129130              </para>
    130131            </listitem>
    … …  
    153154        </helptext>
    154155       
    155       </sect3>
    156 
    157       <sect3 id="array_lims.arraydesign.datafiles">
    158         <title>Data files</title>
    159         <para>
    160           This allows you to select files that contain data for the array design.
    161           Read more about this in <xref linkend="platforms.selectfiles" />.
    162         </para>
    163       </sect3>
     156      <para>
     157        The <guilabel>Data files</guilabel> tab allows BASE users to
     158        attach files to the array design. The possible file types are defined
     159        by the array design's platform. See <xref linkend="platforms.selectfiles"/>
     160        for more information.
     161      </para>
    164162     
    165       <sect3 id="array_lims.arraydesign.annotations">
    166         <title>Annotations and inherited annotations</title>
    167         <para>
    168           This allows you to input values associated to annotation types devised to refine
    169           array design description. Read more about annotations in
    170           <xref linkend="annotations" />.
    171         </para>
    172       </sect3>
     163      <para>
     164        The <guilabel>Annotations</guilabel> tab allows BASE users to use
     165        annotation types to refine array design description. More about annotating items
     166        can be read in <xref linkend="annotations.annotating" />.
     167      </para>
     168     
     169      <para>
     170        This <guilabel>Inherited annotations</guilabel> tab contains a list of those annotations
     171        that are inherited from the array design's parents (eg. plates). Information about
     172        working with inherited annotations can be found in <xref linkend="annotations.inheriting" />.
     173      </para>
     174
    173175    </sect2>
    174176
    … …  
    238240    <title>Array batches</title>
    239241
    240     <sect2 id="array_lims.arraybatch.create">
    241       <title>Creating array batches</title>
    242242      <para>
    243243        Beside the common way of creating items in BASE, an array batch can also be created
    … …  
    277277        automatically be filled in the array design property for the new batch.
    278278      </para>
    279     </sect2>
    280     <sect2 id="array_lims.arraybatch.properties">
    281       <title>Properties</title>
    282       <variablelist>
    283         <varlistentry>
    284           <term>
    285             <guilabel>Name</guilabel>
    286           </term>
    287           <listitem>
    288             <para>The name of the array batch (required).</para>
    289           </listitem>
    290         </varlistentry>
    291         <varlistentry>
    292           <term>
    293             <guilabel>Array design</guilabel>
    294           </term>
    295           <listitem>
    296             <para>Array design that is used for the batch.</para>
    297           </listitem>
    298         </varlistentry>
    299         <varlistentry>
    300           <term>
    301             <guilabel>Print robot</guilabel>
    302           </term>
    303           <listitem>
    304             <para>The print robot that is used.</para>
    305           </listitem>
    306         </varlistentry>
    307         <varlistentry>
    308           <term>
    309             <guilabel>Protocol</guilabel>
    310           </term>
    311           <listitem>
    312             <para>
    313               The printing protocol that was followed when producing the array batch
    314             </para>
    315           </listitem>
    316         </varlistentry>
    317       </variablelist>
    318       <para>
    319         Click on the &gbSave; button to store the information in BASE or on the &gbCancel;
    320         button to abort.
    321       </para>
    322       <para>
    323         See
    324         <xref linkend="annotations" />
    325         for information about annotating items and inherit annotations.
    326       </para>
    327       <para>
    328         How many slides each batch has can be found in the
    329         <guilabel>Slides</guilabel>
    330         column, list view page.
    331       </para>
    332     </sect2>
     279
     280
     281        <figure id="array_lims.figures.arraybatch">
     282          <title>Array batch properties</title>
     283          <screenshot>
     284            <mediaobject>
     285              <imageobject>
     286                <imagedata
     287                  fileref="figures/arraybatch_edit.png" format="PNG" />
     288              </imageobject>
     289            </mediaobject>
     290          </screenshot>
     291        </figure>
     292
     293      <helptext external_id="arraybatch.edit"
     294        title="Edit array batch">
     295     
     296        <variablelist>
     297          <varlistentry>
     298            <term>
     299              <guilabel>Name</guilabel>
     300            </term>
     301            <listitem>
     302              <para>The name of the array batch (required).</para>
     303            </listitem>
     304          </varlistentry>
     305          <varlistentry>
     306            <term>
     307              <guilabel>Array design</guilabel>
     308            </term>
     309            <listitem>
     310              <para>Array design that is used for the batch.</para>
     311            </listitem>
     312          </varlistentry>
     313          <varlistentry>
     314            <term>
     315              <guilabel>Print robot</guilabel>
     316            </term>
     317            <listitem>
     318              <para>The print robot that is used.</para>
     319            </listitem>
     320          </varlistentry>
     321          <varlistentry>
     322            <term>
     323              <guilabel>Protocol</guilabel>
     324            </term>
     325            <listitem>
     326              <para>
     327                The printing protocol that was followed when producing the array batch
     328              </para>
     329            </listitem>
     330          </varlistentry>
     331          <varlistentry>
     332            <term>
     333              <guilabel>Description</guilabel>
     334            </term>
     335            <listitem>
     336              <para>
     337                Provide other useful information about the array batch in this text
     338                area.
     339              </para>
     340            </listitem>
     341          </varlistentry>
     342        </variablelist>
     343        <para>
     344          Click on the &gbSave; button to store the information in BASE or on the &gbCancel;
     345          button to abort.
     346        </para>
     347       
     348        <seeother>
     349          <other external_id="annotations.edit">Annotations</other>
     350          <other external_id="annotations.edit.inerited">Inherit annotations</other>
     351        </seeother>
     352      </helptext>
     353     
    333354  </sect1>
    334355
    … …  
    406427              </itemizedlist>
    407428              The wizard is described further down in
    408               <xref linkend="array_lims.arrayslide.properties.wizard" />
    409               .
     429              <xref linkend="array_lims.arrayslide.wizard" />.
    410430            </para>
    411431          </listitem>
    412432        </varlistentry>
    413433      </variablelist>
    414     </sect2>
    415     <sect2 id="array_lims.arrayslide.properties">
    416       <title>Properties</title>
    417434
    418435      <figure id="write_docbook_doc.figures.arrayslide-single-create">
    … …  
    427444        </screenshot>
    428445      </figure>
     446      <helptext
     447        external_id="arrayslide.edit"
     448        title="Edit array slide">
    429449      <variablelist>
    430450        <varlistentry>
    … …  
    486506        button to abort.
    487507      </para>
    488       <sect3 id="array_lims.arrayslide.properties.wizard">
     508        <seeother>
     509          <other external_id="arrayslide.createwizard.1">Create array slides - step 1</other>
     510          <other external_id="arrayslide.createwizard.2">Create array slides - step 2</other>
     511        </seeother>
     512      </helptext>
     513    </sect2>
     514   
     515    <sect2 id="array_lims.arrayslide.wizard">
    489516        <title>Multiple slides wizard</title>
    490517        <para>
    491518          As mentioned above there is an alternative to create one slide at a time if you
    492519          have many to add. There is a wizard that can help you to create at the most 999
    493           slides in one go. The wizard is in two steps, both showed in the picture
    494           <xref linkend="write_docbook_doc.figures.arrayslide-multiple-create" />
    495           .
    496           <orderedlist>
    497             <listitem>
    498               <para>
    499                 The first step reminds alot of the normal edit window of an array
    500                 slide, but there are some differences:
    501                 <variablelist>
    502                   <varlistentry>
    503                     <term>
    504                       <guilabel>Quantity</guilabel>
    505                     </term>
    506                     <listitem>
    507                       <para>
    508                         Number of slides to create with this wizard
    509                         (required and must be between 1 and 999)
    510                       </para>
    511                     </listitem>
    512                   </varlistentry>
    513                   <varlistentry>
    514                     <term>
    515                       <guilabel>Start at</guilabel>
    516                     </term>
    517                     <listitem>
    518                       <para>
    519                         The index number to start from when indexing the
    520                         name of the slides.
    521                       </para>
    522                     </listitem>
    523                   </varlistentry>
    524                   <varlistentry>
    525                     <term>
    526                       <guilabel>Pad size</guilabel>
    527                     </term>
    528                     <listitem>
    529                       <para>
    530                         The index will be filled out with zeros in front to
    531                         always have this length.
    532                       </para>
    533                     </listitem>
    534                   </varlistentry>
    535                 </variablelist>
    536                 Press
    537                 <guibutton>Next</guibutton>
    538                 to continue to next step of the wizard.
    539                 <important>
    540                   <para>
    541                     Be sure to get everything right before proceeding, because
    542                     it is not possible to go back from step 2.
    543                   </para>
    544                 </important>
    545               </para>
    546             </listitem>
    547             <listitem>
    548               <para>
    549                 In step 2 should the barcodes for the array slides be entered, for
    550                 those which have one. The autogenerated names of the slides can also
    551                 be changed if that is wanted, as long as no name-field is left
    552                 empty.
    553               </para>
    554             </listitem>
    555           </orderedlist>
    556 
    557           <figure id="write_docbook_doc.figures.arrayslide-multiple-create">
    558             <title>Create multiple array slide</title>
     520          slides in one go. The wizard is in two steps:
     521        </para>
     522       
     523          <figure id="array_lims.figures.arrayslide-wizard-step1">
     524            <title>Create multiple array slides - step 1</title>
    559525            <screenshot>
    560526              <mediaobject>
    561527                <imageobject>
    562                   <imagedata scalefit="1" width="100%"
    563                     fileref="figures/arrayslide-multiple-create.png" format="PNG" />
     528                  <imagedata fileref="figures/arrayslide-wizard-step1.png" format="PNG" />
    564529                </imageobject>
    565530              </mediaobject>
    566531            </screenshot>
    567532          </figure>
    568           Fill in the necessary information as exhaustively as possible.
    569         </para>
    570         <para>
    571           Click on the &gbSave; button to store the information in BASE or on the
    572           &gbCancel; button to abort.
    573         </para>
    574         <para>
    575           See
    576           <xref linkend="annotations" />
    577           for information about annotating items and inherit annotations.
    578         </para>
    579       </sect3>
     533
     534          <helptext external_id="arrayslide.createwizard.1"
     535            title="Create array slides - step 1">
     536           
     537            <para>
     538              The first step reminds alot of the normal edit window of an array
     539              slide:
     540            </para>
     541           
     542            <variablelist>
     543              <varlistentry>
     544                <term>
     545                  <guilabel>Name</guilabel>
     546                </term>
     547                <listitem>
     548                  <para>
     549                    The name prefix of the array slides. Each array slide will be
     550                    numbered according to the <emphasis>start at</emphasis> and
     551                    <emphasis>pad size</emphasis> settings below.
     552                  </para>
     553                </listitem>
     554              </varlistentry>
     555              <varlistentry>
     556                <term>
     557                  <guilabel>Array batch</guilabel>
     558                </term>
     559                <listitem>
     560                  <para>Array batch that the slides belongs to (required).</para>
     561                </listitem>
     562              </varlistentry>
     563              <varlistentry>
     564                <term>
     565                  <guilabel>Quantity</guilabel>
     566                </term>
     567                <listitem>
     568                  <para>
     569                    Number of slides to create with this wizard
     570                    (required and must be between 1 and 999)
     571                  </para>
     572                </listitem>
     573              </varlistentry>
     574              <varlistentry>
     575                <term>
     576                  <guilabel>Start at</guilabel>
     577                </term>
     578                <listitem>
     579                  <para>
     580                    The index number to start from when indexing the
     581                    name of the slides.
     582                  </para>
     583                </listitem>
     584              </varlistentry>
     585              <varlistentry>
     586                <term>
     587                  <guilabel>Pad size</guilabel>
     588                </term>
     589                <listitem>
     590                  <para>
     591                    The index will be filled out with zeros in front to
     592                    always have this length.
     593                  </para>
     594                </listitem>
     595              </varlistentry>
     596            </variablelist>
     597           
     598            <para>
     599              Click on &gbNext; to move on to the second step of the wizard.
     600            </para>
     601           
     602            <seeother>
     603              <other external_id="arrayslide.createwizard.2">Create array slides - step 2</other>
     604              <other external_id="arrayslide.edit">Edit array slide</other>
     605            </seeother>
     606           
     607          </helptext>
     608         
     609         
     610          <figure id="array_lims.figures.arrayslide-wizard-step2">
     611            <title>Create multiple array slides - step 2</title>
     612            <screenshot>
     613              <mediaobject>
     614                <imageobject>
     615                  <imagedata fileref="figures/arrayslide-wizard-step2.png" format="PNG" />
     616                </imageobject>
     617              </mediaobject>
     618            </screenshot>
     619          </figure>
     620         
     621          <helptext external_id="arrayslide.createwizard.2" title="Create array slides - step 2">
     622            <para>
     623              This step allows the names of the array slides to be adjusted
     624              if needed. It is also possible to enter barcodes for each of the
     625              new slides. The information can either be filled in one-by-one
     626              or by using the "scratchpad" icon
     627              <guiicon>
     628                <inlinemediaobject>
     629                  <imageobject>
     630                    <imagedata fileref="figures/paste.png"
     631                      format="PNG" />
     632                  </imageobject>
     633                </inlinemediaobject>
     634              </guiicon>. This opens up a larger text window where the names or barcodes
     635              can be entered one per line. This can be useful if the information can be
     636              pasted from an external source.
     637            </para>
     638           
     639            <seeother>
     640              <other external_id="arrayslide.createwizard.1">Create array slides - step 1</other>
     641              <other external_id="arrayslide.edit">Edit array slide</other>
     642            </seeother>
     643           
     644            <para>
     645              Click on the &gbSave; button to store the information in BASE or on the
     646              &gbCancel; button to abort the wizard.
     647            </para>
     648         
     649          </helptext>
     650
    580651    </sect2>
    581652  </sect1>
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