Changeset 3381


Ignore:
Timestamp:
May 25, 2007, 9:45:07 AM (14 years ago)
Author:
Martin Svensson
Message:

References #565. Minor fixes - pictures remain to be checked in before this chapter is finished.

File:
1 edited

Legend:

Unmodified
Added
Removed
  • trunk/doc/src/docbook/userdoc/array_lims.xml

    r3370 r3381  
    3030  <?dbhtml dir="array_lims"?>
    3131  <title>Array LIMS</title>
    32   <sect1>
     32  <sect1 id="array_lims.introduction">
    3333    <title>Introduction</title>
    3434
     
    4747
    4848    <para>For users buying their arrays from commercial sources, the Plate Management component
    49       can be ignored and they can go immediatly to the second section <xref
     49      can be ignored and they can go immediately to the second section <xref
    5050        linkend="array_lims.arraydesign"/> of the chapter.</para>
    5151
     
    7373      <para>Go To <menuchoice>
    7474          <guimenu>Array LIMS</guimenu>
    75           <guimenuitem>ArrayDesign</guimenuitem>
     75          <guimenuitem>Array designs</guimenuitem>
    7676        </menuchoice>
    7777      </para>
     
    174174
    175175      </variablelist>
    176       <para>Click on the <inlinemediaobject>
    177           <imageobject>
    178             <imagedata fileref="figures/save.gif" format="GIF"/>
    179           </imageobject>
    180         </inlinemediaobject> Save button to store the information in BASE2 or on the <inlinemediaobject>
    181           <imageobject>
    182             <imagedata fileref="figures/cancel.gif" format="GIF"/>
    183           </imageobject>
    184         </inlinemediaobject> button to abort. </para>
     176      <para>Click on the <guibutton>Save</guibutton> button to store the information in BASE2 or on the
     177          <guibutton>Cancel</guibutton> button to abort. </para>
    185178      <para>Upon saving, the Array Design List View page is displayed. Users should pay
    186179        attention to the column <guilabel>Has features</guilabel>. Unless an Affymetrix
     
    209202        when the Affymetrix CDF file is actually uploaded.</para>
    210203      <para>From the ArrayDesign Item View, click on the <guibutton>Import</guibutton>
    211       button</para>. <note>
     204      button.</para>.<note>
    212205        <para>The button only shows up if the logged in user has enough permissions.</para>
    213206      </note>
     
    228221      <tip>
    229222        <para>A list of Reporter Map Importer plugin configurations is maintained at BASE2
    230           site and each can be downloaded as xml file from <ulink url="tbd"/>.</para>
     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>
    231225      </tip>
    232226    </sect2>
     
    329323          <para>Creating ArrayBatch from the ArrayBatch List View page</para>
    330324          <para>Go to <menuchoice>
    331               <guimenu>View</guimenu>
    332               <guimenuitem>ArrayBatch</guimenuitem>
     325              <guimenu>Array LIMS</guimenu>
     326              <guimenuitem>Array batches</guimenuitem>
    333327            </menuchoice></para>
    334328          <para>Click on <guibutton>New&hellip;</guibutton> button </para>
     
    360354        </listitem>
    361355      </itemizedlist>
    362       <para>Click on the <inlinemediaobject>
    363           <imageobject>
    364             <imagedata fileref="figures/save.gif" format="GIF"/>
    365           </imageobject>
    366         </inlinemediaobject> Save button to store the information in BASE2 or on the <inlinemediaobject>
    367           <imageobject>
    368             <imagedata fileref="figures/cancel.gif" format="GIF"/>
    369           </imageobject>
    370         </inlinemediaobject> button to abort.</para>
     356      <para>Click on the <guibutton>Save</guibutton> button to store the information in BASE2 or on the
     357      <guibutton>Cancel</guibutton> button to abort.</para>
    371358    </sect2>
    372359
     
    399386          <para>From the ArrayBatch item View, all associated <guilabel/>ArraySlides are
    400387            indicated as their use in Hybridization events. Both ArraySlides and
    401             Hybridations are clickable items, enabling easy navigation.</para>
     388            Hybridizations are clickable items, enabling easy navigation.</para>
    402389        </listitem>
    403390      </itemizedlist>
     
    468455          <para>Creating ArraySlides from the ArrayBatch List View page</para>
    469456          <para>Go to <menuchoice>
    470               <guimenu>View</guimenu>
    471               <guimenuitem>ArraySlides</guimenuitem>
     457              <guimenu>Array LIMS</guimenu>
     458              <guimenuitem>Array slides</guimenuitem>
    472459            </menuchoice></para>
    473460          <para>Click on <guibutton>New&hellip;</guibutton> button </para>
     
    490477        </listitem>
    491478      </itemizedlist>
    492       <para>Click on the <inlinemediaobject>
    493           <imageobject>
    494             <imagedata fileref="figures/save.gif" format="GIF"/>
    495           </imageobject>
    496         </inlinemediaobject> Save button to store the information in BASE2 or on the <inlinemediaobject>
    497           <imageobject>
    498             <imagedata fileref="figures/cancel.gif" format="GIF"/>
    499           </imageobject>
    500         </inlinemediaobject> button to abort. </para>
     479      <para>Click on the <guibutton>Save</guibutton> button to store the information in BASE2 or on the
     480          <guibutton>Cancel</guibutton> button to abort. </para>
    501481
    502482      <para> In addition to this classic way of creating BASE items, Arrays Slides can be
     
    519499        ArraySlides List View page </para>
    520500
    521       <para>Either way ill open the a wizzard window as shown below</para>
     501      <para>Either way will open the wizard window as shown below</para>
    522502      <figure id="write_docbook_doc.figures.arrayslide-multiple-create">
    523         <title>Create Muliple Array Slide from the ArrayBatch List View wizzard</title>
     503        <title>Create Multiple Array Slide from the ArrayBatch List View wizard</title>
    524504        <screenshot>
    525505          <mediaobject>
     
    531511      </figure>
    532512      <para>Fill in the necessary information as exhaustively as possible.</para>
    533       <para>Click on the <inlinemediaobject>
    534           <imageobject>
    535             <imagedata fileref="figures/save.gif" format="GIF"/>
    536           </imageobject>
    537         </inlinemediaobject> Save button to store the information in BASE2 or on the <inlinemediaobject>
    538           <imageobject>
    539             <imagedata fileref="figures/cancel.gif" format="GIF"/>
    540           </imageobject>
    541         </inlinemediaobject> button to abort. </para>
     513      <para>Click on the <guibutton>Save</guibutton> button to store the information in BASE2
     514      or on the <guibutton>Cancel</guibutton> button to abort. </para>
    542515    </sect2>
    543516
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