Changeset 5708


Ignore:
Timestamp:
Aug 25, 2011, 2:48:46 PM (12 years ago)
Author:
Nicklas Nordborg
Message:

References #1590: Documentation cleanup

Biomaterials section. Added empty sections for biomaterial lists and bioplate events that hopefully will be written some day. All screen shots must be updated.

Fixed spelling of "bioplate" in a lot of jsp scripts.

Display well coordinates without brackets. A1 instead of [A,1].

Fixed an issue with the regular expression used to link different help texts in the web client.

Reorganized the biomaterial lims menu so that it is consistent with the documentation.

Location:
trunk
Files:
1 deleted
13 edited

Legend:

Unmodified
Added
Removed

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

    r4889 r5708  
    3232    <para>
    3333      The generic term biomaterial refers to any biological material used in an experiment.
    34       Biomaterial is subdivided in 4 components, biosource, sample, extract and labeled
    35       extract. The order used in presenting those entities is not innocuous as it represents the
     34      Biomaterial is divided in three main components, <emphasis>biosources</emphasis>, <emphasis>samples</emphasis>
     35      and <emphasis>extracts</emphasis>. The biomaterials can then be subclassified further by
     36      the use of subtypes (see <xref linkend="subtypes"/>). BASE has, for example, defined two extracts subtypes:
     37      <emphasis>Labeled extract</emphasis> (used in microarray experiments)
     38      and <emphasis>Library</emphasis> (used in sequencing experiments).   
     39      The order used in presenting those entities is not innocuous as it represents the
    3640      sequence of transformation a source material undergoes until it is in a state compatible
    37       with the realization of a microarray hybridization. This progression is actually
     41      for further exeperimental processing. This progression is actually
    3842      mimicked in the BASE
    3943      <guimenu>Biomaterial LIMS</guimenu>
    … …  
    6064        </simpara>
    6165      </listitem>
    62       <listitem>
    63         <simpara>
    64           Labeled extracts correspond to nucleic acid materials which have undergone a
    65           marking procedure using a fluorescent or radioactive compound for detection in a
    66           microarray assay.
    67         </simpara>
    68       </listitem>
    6966    </itemizedlist>
    7067    <para>
    … …  
    8582
    8683
    87     <sect2 id="biomaterials.biosources.properties">
    88       <title>Properties</title>
    89       <sect3 id="biomaterials.biosources.properties.biosource">
    90         <title>Biosource</title>
    91         <para>This tab allows users to enter essential information about a biosource.</para>
     84    <para>
     85      Biosources correspond to the native biological entity used in an experiment prior to any treatment.
     86      Biosources can be added to BASE by most users and are managed from <menuchoice>
     87        <guimenu>Biomaterial LIMS</guimenu>
     88        <guimenuitem>Biosources</guimenuitem>
     89      </menuchoice>.
     90      Use the &gbNew; button to create a new biosource. This brings up the dialog below.
     91    </para>
     92
     93      <figure id="biomaterials.figures.biosource-tab-1">
     94        <title>Biosource properties</title>
     95        <screenshot>
     96          <mediaobject>
     97            <imageobject>
     98              <imagedata
     99                fileref="figures/biosource-tab-1.png" format="PNG" />
     100            </imageobject>
     101          </mediaobject>
     102        </screenshot>
     103      </figure>
     104      <helptext external_id="biosource.edit" title="Biosource properties">
     105
    92106        <variablelist>
    93107          <varlistentry>
    … …  
    105119          <varlistentry>
    106120            <term>
     121              <guilabel>Type</guilabel>
     122            </term>
     123            <listitem>
     124              <para>
     125              The subtype of the biosource. The list
     126              may evolve depending on additions by the server
     127              administrator. Selecting the proper subtype
     128              is recommended and enables BASE to automatically guess
     129              the most likely subtype when creating child biomaterial.
     130              <nohelp>
     131              See <xref linkend="subtypes" /> for more information.
     132              </nohelp>
     133              </para>
     134            </listitem>
     135          </varlistentry>
     136          <varlistentry>
     137            <term>
    107138              <guilabel>External ID</guilabel>
    108139            </term>
    … …  
    123154          </varlistentry>
    124155        </variablelist>
    125         <figure id="write_docbook_doc.figures.biosource-tab-1">
    126           <title>Biosource properties</title>
    127           <screenshot>
    128             <mediaobject>
    129               <imageobject>
    130                 <imagedata
    131                   fileref="figures/biosource-tab-1.png" format="PNG" />
    132               </imageobject>
    133             </mediaobject>
    134           </screenshot>
    135         </figure>
    136       </sect3>
    137       <sect3 id="biomaterials.biosource.properties.annotations">
    138         <title>Annotations</title>
    139         <para>
    140           This allows BASE users to use annotation types to refine biosource description.
    141           More about annotating items can be read in
    142           <xref linkend="annotations.annotating" />
    143           .
    144         </para>
    145       </sect3>
    146     </sect2>
     156        <seeother>
     157          <other external_id="annotations.edit">Annotations</other>
     158        </seeother>
     159      </helptext>
     160
     161      <para>
     162        The <guilabel>Annotations</guilabel> tab allows BASE users to use
     163        annotation types to refine biosource description. More about annotating items
     164        can be read in <xref linkend="annotations.annotating" />
     165      </para>
     166
    147167  </sect1>
    148168  <sect1 id="biomaterial.samples">
    … …  
    169189      to get to the list of samples.
    170190    </para>
    171     <sect2 id="biomaterials.samples.create">
     191   
     192    <sect2 id="biomaterial.samples.create">
    172193      <title>Create sample</title>
     194   
    173195      <para>
    174196        Beside the common way, using the &gbNew; button, a sample can be created in one of
    175197        the following ways:
     198      </para>
    176199        <variablelist>
    177200          <varlistentry>
    … …  
    189212                  </inlinemediaobject>
    190213                </guiicon>
    191                 in the sample column of the biosource list view. There is also a
     214                in the <guilabel>Samples</guilabel> column of the biosource list view. There is also a
    192215                corresponding button,
    193                 <guibutton>Create sample&hellip;</guibutton>
     216                <guibutton>New sample&hellip;</guibutton>
    194217                in the toolbar when viewing a single biosource.
    195218              </para>
    … …  
    200223            <listitem>
    201224              <para>
    202                 Pooled samples can also be created by first selecting the parents
    203                 from the list of samples and then press
    204                 <guibutton>Pool&hellip;</guibutton>
    205                 in the toolbar.
     225                Child samples can be created from a single parent by clicking on the
     226                <guiicon>
     227                  <inlinemediaobject>
     228                    <imageobject>
     229                      <imagedata fileref="figures/add.png" format="PNG" />
     230                    </imageobject>
     231                  </inlinemediaobject>
     232                </guiicon> icon in the <guilabel>Child samples</guilabel> column.
     233                Pooled samples can be created by first selecting the parents
     234                from the list of samples and then click the <guibutton>Pool&hellip;</guibutton>
     235                button in the toolbar.
    206236              </para>
    207237            </listitem>
    208238          </varlistentry>
    209239        </variablelist>
    210       </para>
    211240    </sect2>
    212     <sect2 id="biomaterials.samples.properties">
    213       <title>Properties</title>
    214       <sect3 id="biomaterials.samples.properties.sample">
    215         <title>Sample</title>
    216         <helptext external_id="sample.edit" title="Edit sample">
    217           <variablelist>
    218             <varlistentry>
    219               <term>
    220                 <guilabel>Name</guilabel>
    221               </term>
    222               <listitem>
    223                 <para>
    224                   The sample's name(required). BASE by default assigns names to
    225                   samples (by suffixing
    226                   <replaceable>s#</replaceable>
    227                   when creating a sample from an existing biosource or
    228                   <replaceable>New Sample</replaceable>
    229                   otherwise) but it is possible to edit at will.
    230                 </para>
    231               </listitem>
    232             </varlistentry>
    233             <varlistentry>
    234               <term>
    235                 <guilabel>External ID</guilabel>
    236               </term>
    237               <listitem>
    238                 <para>
    239                   An identification used to identify the sample outside BASE.
    240                 </para>
    241               </listitem>
    242             </varlistentry>
    243             <varlistentry>
    244               <term>
    245                 <guilabel>Original quantity</guilabel>
    246               </term>
    247               <listitem>
    248                 <para>
    249                   This is meant to report information about the actual mass of
    250                   sample created.
    251                 </para>
    252               </listitem>
    253             </varlistentry>
    254             <varlistentry>
    255               <term>
    256                 <guilabel>Created</guilabel>
    257               </term>
    258               <listitem>
    259                 <para>
    260                   A date when the sample was created. The information can be
    261                   important when running quality controls on data and account for
    262                   potential confounding factor (e.g. day effect).
    263                 </para>
    264               </listitem>
    265             </varlistentry>
    266             <varlistentry>
    267               <term>
    268                 <guilabel>Registered</guilabel>
    269               </term>
    270               <listitem>
    271                 <para>The date at which the sample was entered in BASE.</para>
    272               </listitem>
    273             </varlistentry>
    274             <varlistentry>
    275               <term>
    276                 <guilabel>Protocol</guilabel>
    277               </term>
    278               <listitem>
    279                 <para>The protocol used to produce this sample.</para>
    280               </listitem>
    281             </varlistentry>
    282             <varlistentry>
    283               <term>
    284                 <guilabel>Bioplate</guilabel>
    285               </term>
    286               <listitem>
    287                 <para>The bioplate where this sample is located.</para>
    288               </listitem>             
    289             </varlistentry>
    290             <varlistentry>
    291               <term>
    292                 <guilabel>Biowell</guilabel>
    293               </term>
    294               <listitem>
    295                 <para>
    296                   Biowell that holds this sample.
    297                   <guilabel>Bioplate</guilabel> has to be defined before
    298                   biowell can be selected.
    299                 </para>
    300               </listitem>             
    301             </varlistentry>
    302             <varlistentry>
    303               <term>
    304                 <guilabel>Description</guilabel>
    305               </term>
    306               <listitem>
    307                 <para>
    308                   A text field to report any information that not can be captured
    309                   otherwise.
    310                 </para>
    311               </listitem>
    312             </varlistentry>
    313           </variablelist>
    314         </helptext>
    315         <figure id="write_docbook_doc.figures.biosample-tab-1">
     241     
     242    <sect2 id="biomaterial.samples.properties">
     243      <title>Sample properties</title>
     244        <figure id="biomaterials.figures.biosample-tab-1">
    316245          <title>Sample properties</title>
    317246          <screenshot>
    … …  
    324253          </screenshot>
    325254        </figure>
    326       </sect3>
    327       <sect3 id="biomaterials.samples.properties.parents">
    328         <title>Parents</title>
     255        <helptext external_id="sample.edit" title="Edit sample">
     256          <variablelist>
     257            <varlistentry>
     258              <term>
     259                <guilabel>Name</guilabel>
     260              </term>
     261              <listitem>
     262                <para>
     263                  The sample's name (required). BASE by default assigns names to
     264                  samples (by suffixing
     265                  <replaceable>s#</replaceable>
     266                  when creating a sample from an existing biosource or
     267                  <replaceable>New Sample</replaceable>
     268                  otherwise) but it is possible to edit at will.
     269                </para>
     270              </listitem>
     271            </varlistentry>
     272            <varlistentry>
     273              <term>
     274                <guilabel>Type</guilabel>
     275              </term>
     276              <listitem>
     277                <para>
     278                The subtype of the sample. The list
     279                may evolve depending on additions by the server
     280                administrator. Selecting the proper subtype
     281                is recommended and enables BASE to automatically guess
     282                the most likely subtype when creating child biomaterial.
     283                <nohelp>
     284                See <xref linkend="subtypes" /> for more information.
     285                </nohelp>
     286                </para>
     287              </listitem>
     288            </varlistentry>
     289            <varlistentry>
     290              <term>
     291                <guilabel>External ID</guilabel>
     292              </term>
     293              <listitem>
     294                <para>
     295                  An identification used to identify the sample outside BASE.
     296                </para>
     297              </listitem>
     298            </varlistentry>
     299            <varlistentry>
     300              <term>
     301                <guilabel>Original quantity</guilabel>
     302              </term>
     303              <listitem>
     304                <para>
     305                  This is meant to report information about the actual mass of
     306                  sample created.
     307                </para>
     308              </listitem>
     309            </varlistentry>
     310            <varlistentry>
     311              <term>
     312                <guilabel>Created</guilabel>
     313              </term>
     314              <listitem>
     315                <para>
     316                  A date when the sample was created. The information can be
     317                  important when running quality controls on data and account for
     318                  potential confounding factor (e.g. day effect).
     319                </para>
     320              </listitem>
     321            </varlistentry>
     322            <varlistentry>
     323              <term>
     324                <guilabel>Registered</guilabel>
     325              </term>
     326              <listitem>
     327                <para>The date at which the sample was entered in BASE.</para>
     328              </listitem>
     329            </varlistentry>
     330            <varlistentry>
     331              <term>
     332                <guilabel>Protocol</guilabel>
     333              </term>
     334              <listitem>
     335                <para>The protocol used to produce this sample.</para>
     336              </listitem>
     337            </varlistentry>
     338            <varlistentry>
     339              <term>
     340                <guilabel>Bioplate</guilabel>
     341              </term>
     342              <listitem>
     343                <para>The bioplate where this sample is located.</para>
     344              </listitem>             
     345            </varlistentry>
     346            <varlistentry>
     347              <term>
     348                <guilabel>Biowell</guilabel>
     349              </term>
     350              <listitem>
     351                <para>
     352                  Biowell that holds this sample.
     353                  <guilabel>Bioplate</guilabel> has to be defined before
     354                  biowell can be selected.
     355                </para>
     356              </listitem>             
     357            </varlistentry>
     358            <varlistentry>
     359              <term>
     360                <guilabel>Description</guilabel>
     361              </term>
     362              <listitem>
     363                <para>
     364                  A text field to report any information that not can be captured
     365                  otherwise.
     366                </para>
     367              </listitem>
     368            </varlistentry>
     369          </variablelist>
     370         
     371          <seeother>
     372            <other external_id="sample.parents">Parents</other>
     373            <other external_id="annotations.edit">Annotations &amp; parameters</other>
     374            <other external_id="annotations.edit.inherited">Inherited annotations</other>
     375          </seeother>
     376        </helptext>
     377    </sect2>
     378   
     379    <sect2 id="biomaterial.samples.parents">
     380      <title>Sample parents</title>
     381        <figure id="biomaterials.figures.biosample-tab-2">
     382          <title>Sample parents</title>
     383          <screenshot>
     384            <mediaobject>
     385              <imageobject>
     386                <imagedata
     387                  fileref="figures/biosample-tab-2.png" format="PNG" />
     388              </imageobject>
     389            </mediaobject>
     390          </screenshot>
     391        </figure>
     392       
    329393        <helptext external_id="sample.parents" title="Sample's parents">
    330394          <para>
    331395            This is meant to keep track of the sample origin. BASE
    332             distinguished between two cases which are controlled by the
    333             <guilabel>Pooled</guilabel>
     396            distinguishes between two cases which are controlled by the
     397            <guilabel>Parent type</guilabel>
    334398            radio-button in the edit pop-up window.
    335399          </para>
    … …  
    338402              <para>
    339403                If the parent is a biosource the radio-button is set to
    340                 <guilabel>No</guilabel>
    341                 . This will make the biosource select button active, which allows
    342                 users to point to a biosource from which the sample originates from.
     404                <guilabel>Biosource</guilabel>. Only a single biosource
     405                can be used as the parent. This option is automatically
     406                selected if the user selects a biosource with the
     407                <guibutton>Select biosource</guibutton> button.
    343408              </para>
    344409            </listitem>
    … …  
    346411              <para>
    347412                When the parent is one or several other samples the radio-button is
    348                 set to
    349                 <guilabel>Yes</guilabel>
    350                 . Upon selection, the biosource select button is deactivated and the
    351                 samples box and button are activated. This allows users to specify
    352                 one or more samples to be selected from a sample list view page.
     413                set to <guilabel>Sample</guilabel>. This option is automatically
     414                selected if the user add samples with the <guibutton>Add samples</guibutton> button.           
     415                For each parent sample, it is
     416                possible to specify the amount used in µg. This will automatically
     417                update the <guilabel>remaining quantity</guilabel> of the parent.
    353418              </para>
    354419            </listitem>
    355420          </itemizedlist>
     421         
     422          <seeother>
     423            <other external_id="sample.edit">Sample properties</other>
     424            <other external_id="annotations.edit">Annotations &amp; parameters</other>
     425            <other external_id="annotations.edit.inherited">Inherited annotations</other>
     426          </seeother>
    356427        </helptext>
    357       </sect3>
    358       <sect3 id="biomaterials.samples.properties.annotation_param">
    359         <title>Annotations &amp; parameters</title>
    360         <para>
    361           As seen in the biosource section, this tab allows users to further supply
    362           information about the sample provided they have defined or shared annotation
    363           types to annotate sample items.
    364         </para>
    365         <para>
    366           To learn more about annotation types and how to define a value for a type,
    367           please refer to
    368           <xref linkend="annotations" />
    369         </para>
    370       </sect3>
    371       <sect3 id="biomaterials.samples.properties.inherited">
    372         <title>Inherited annotations</title>
    373         <para>
    374           This tab contains a list of those annotations that are inherited from the
    375           sample's parents. Information about working with inherited annotations can be
    376           found in
    377           <xref linkend="annotations.inheriting" />
    378           .
    379         </para>
    380       </sect3>
    381428    </sect2>
     429    <para>
     430      The <guilabel>Annotations</guilabel> tab allows BASE users to use
     431      annotation types to refine sample description. More about annotating items
     432      can be read in <xref linkend="annotations.annotating" />
     433    </para>
     434       
     435    <para>
     436      This <guilabel>Inherited annotations</guilabel> tab contains a list of those annotations
     437      that are inherited from the sample's parents. Information about working with inherited
     438      annotations can be found in <xref linkend="annotations.inheriting" />.
     439    </para>
    382440  </sect1>
    383441
    … …  
    395453      but it should serve as guidance when devising the granularity of the sample processing
    396454      task. Also, it is good practice to provide protocol information.
     455    </para>
     456    <para>
     457      Use
     458      <menuchoice>
     459        <guimenu>Biomaterial LIMS</guimenu>
     460        <guimenuitem>Extracts</guimenuitem>
     461      </menuchoice>
     462      to get to the list of extracts.
    397463    </para>
    398464    <sect2 id="biomaterials.extracts.create">
    … …  
    416482                  </inlinemediaobject>
    417483                </guiicon>
    418                 in the extracts column for the sample that should be a parent of the
    419                 extract.
    420               </para>
    421               <para>
    422                 There is also a corresponding button,
    423                 <guibutton>Create extract&hellip;</guibutton>
     484                in the <guilabel>Child extracts</guilabel> column for the sample that should be a parent of the
     485                extract.  There is also a corresponding button,
     486                <guibutton>New child extract&hellip;</guibutton>
    424487                in the toolbar when viewing a single sample.
    425488              </para>
    … …  
    430493            <listitem>
    431494              <para>
    432                 Pooled extract can also be created by first selecting the parents
     495                Child extracts can be created from a single parent by clicking on the
     496                <guiicon>
     497                  <inlinemediaobject>
     498                    <imageobject>
     499                      <imagedata fileref="figures/add.png" format="PNG" />
     500                    </imageobject>
     501                  </inlinemediaobject>
     502                </guiicon> icon in the <guilabel>Child extracts</guilabel> column.
     503                Pooled extract can be created by first selecting the parents
    433504                from the list of extracts and then press
    434505                <guibutton>Pool&hellip;</guibutton>
    … …  
    442513    </sect2>
    443514    <sect2 id="biomaterials.extracts.properties">
    444       <title>Properties</title>
    445       <sect3 id="biomaterials.extracts.properties.extract">
    446         <title>Extract</title>
    447         <helptext external_id="extract.edit" title="Edit extract">
    448           <variablelist>
    449             <varlistentry>
    450               <term>
    451                 <guilabel>Name</guilabel>
    452               </term>
    453               <listitem>
    454                 <para>
    455                   A mandatory field for providing the extract name. BASE by
    456                   default assigns names to extract (by suffixing
    457                   <replaceable>e#</replaceable>
    458                   when creating an extract from an existing sample or
    459                   <replaceable>New extract</replaceable>
    460                   otherwise) but it is possible to edit it at will.
    461                 </para>
    462               </listitem>
    463             </varlistentry>
    464             <varlistentry>
    465               <term>
    466                 <guilabel>External ID</guilabel>
    467               </term>
    468               <listitem>
    469                 <para>The extracts identification outside BASE</para>
    470               </listitem>
    471             </varlistentry>
    472             <varlistentry>
    473               <term>
    474                 <guilabel>Original quantity</guilabel>
    475               </term>
    476               <listitem>
    477                 <para>
    478                   Holds information about the original mass of the created
    479                   extract.
    480                 </para>
    481               </listitem>
    482             </varlistentry>
    483             <varlistentry>
    484               <term>
    485                 <guilabel>Created</guilabel>
    486               </term>
    487               <listitem>
    488                 <para>
    489                   The date when the extract was created. The information can be
    490                   important when running quality controls on data and account for
    491                   potential confounding factor (e.g. day effect)
    492                 </para>
    493               </listitem>
    494             </varlistentry>
    495             <varlistentry>
    496               <term>
    497                 <guilabel>Registered</guilabel>
    498               </term>
    499               <listitem>
    500                 <para>
    501                   This is automatically populated with a date at which the sample
    502                   was entered in BASE system.
    503                 </para>
    504               </listitem>
    505             </varlistentry>
    506             <varlistentry>
    507               <term>
    508                 <guilabel>Protocol</guilabel>
    509               </term>
    510               <listitem>
    511                 <para>
    512                   The extraction protocol that was used to produce the extract.
    513                 </para>
    514               </listitem>
    515             </varlistentry>
    516             <varlistentry>
    517               <term>
    518                 <guilabel>Bioplate</guilabel>
    519               </term>
    520               <listitem>
    521                 <para>The bioplate where this extract is located.</para>
    522               </listitem>             
    523             </varlistentry>
    524             <varlistentry>
    525               <term>
    526                 <guilabel>Biowell</guilabel>
    527               </term>
    528               <listitem>
    529                 <para>
    530                   Biowell that holds this extract.
    531                   <guilabel>Bioplate</guilabel> has to be defined before
    532                   biowell can be selected.
    533                 </para>
    534               </listitem>             
    535             </varlistentry>
    536             <varlistentry>
    537               <term>
    538                 <guilabel>Description</guilabel>
    539               </term>
    540               <listitem>
    541                 <para>
    542                   A text field to report any information that not can be captured
    543                   otherwise.
    544                 </para>
    545               </listitem>
    546             </varlistentry>
    547           </variablelist>
    548         </helptext>
    549         <figure id="write_docbook_doc.figures.extract-tab-1">
    550           <title>Extract tab</title>
     515      <title>Extract properties</title>
     516     
     517        <figure id="biomaterials.figures.extract-tab-1">
     518          <title>Extract properties</title>
    551519          <screenshot>
    552520            <mediaobject>
    … …  
    558526          </screenshot>
    559527        </figure>
    560       </sect3>
    561 
    562       <sect3 id="biomaterials.extracts.properties.parents">
    563         <title>Parents</title>
    564         <helptext external_id="extract.parents" title="Extract's parents">
    565           <para>
    566             This important tab allows users to select the extract
    567             origin. BASE distinguished between two cases which are
    568             controlled by the
    569             <guilabel>Pooled</guilabel>
    570             radio-button.
    571           </para>
    572           <itemizedlist>
    573             <listitem>
    574               <para>
    575                 If the parent is a sample the radio-button is set to
    576                 <guilabel>No</guilabel>
    577                 . The Sample select button is active and allows users to point to
    578                 the sample from which the sample originates.
    579               </para>
    580             </listitem>
    581             <listitem>
    582               <para>
    583                 The parent is another extract and the radio-button is set to
    584                 <guilabel>Yes</guilabel>
    585                 . Upon selection, the samples select button is deactivated and the
    586                 extracts box and button are activated. This allows users to specify
    587                 one or more extracts to be selected from an extract list view page.
    588               </para>
    589             </listitem>
    590           </itemizedlist>
    591         </helptext>
    592       </sect3>
    593       <sect3 id="biomaterials.extracts.properties.annotations_param">
    594         <title>Annotations &amp; parameters</title>
    595         <para>
    596           As seen in the biosource and sample sections, this tab allows users to supply
    597           further information about the extract, provided they have defined annotation
    598           types to annotation extract items or have such elements shared to them.
    599         </para>
    600         <para>
    601           To learn more about annotation types, please refer to
    602           <xref linkend="annotations" />
    603         </para>
    604       </sect3>
    605       <sect3 id="biomaterials.extracts.properties.inherited">
    606         <title>Inherited Annotations</title>
    607         <para>
    608           This tab contains a list of those annotations that are inherited from the
    609           extract parents. Information about working with inherited annotations can be
    610           found in
    611           <xref linkend="annotations.inheriting" />
    612           .
    613         </para>
    614       </sect3>
    615     </sect2>
    616   </sect1>
    617 
    618   <sect1 id="biomaterials.labels">
    619     <title>Labels</title>
    620     <para>
    621       Before attempting to create labeled extracts, users should make sure that the
    622       appropriate label object is present in BASE. To browse the list of labels, go to
    623       <menuchoice>
    624         <guimenu>Biomaterial LIMS</guimenu>
    625         <guimenuitem>Labels</guimenuitem>
    626       </menuchoice>
    627     </para>
    628     <sect2 id="biomaterials.labels.properties">
    629       <title>Properties</title>
    630       <helptext external_id="label.edit" title="Edit label">
    631         <para>
    632           The label item is very simple and does not need much explanation. There are only
    633           two properties for a label
     528        <helptext external_id="extract.edit" title="Edit extract">
    634529          <variablelist>
    635530            <varlistentry>
    … …  
    638533              </term>
    639534              <listitem>
    640                 <para>The name of the label(required).</para>
    641               </listitem>
    642             </varlistentry>
    643             <varlistentry>
    644               <term>
    645                 <guilabel>Description</guilabel>
    646               </term>
    647               <listitem>
    648                 <para>
    649                   An explaining text or other information associated with the
    650                   label.
    651                 </para>
    652               </listitem>
    653             </varlistentry>
    654           </variablelist>
    655           .
    656         </para>
    657       </helptext>
    658     </sect2>
    659 
    660   </sect1>
    661   <sect1 id="biomaterials.labeledextracts">
    662     <title>Labeled extracts</title>
    663     <para>
    664       Labeled extract items should be used to describe the event that transformed an extract
    665       material in a labeled extract material. Labeled extracts can be created from extract
    666       items or from one or more labeled extract items. When a labeled extract is created from
    667       several other labeled extracts, a pooling event is performed.
    668     </para>
    669     <para>
    670       During the transformation from extracts to labeled extracts, it is possible to provide
    671       information about the protocol used to perform this task. It is not enforced in BASE
    672       but it should serve as guidance when devising the granularity of the extract processing
    673       task. Also, it is good practice to provide protocol information.
    674     </para>
    675     <sect2 id="biomaterials.labeledextracts.create">
    676       <title>Creating labeled extracts</title>
    677       <para>
    678         Beside the regular way of using the &gbNew; button in
    679         <menuchoice>
    680           <guimenu>Biomaterial LIMS</guimenu>
    681           <guimenuitem>Labeled extracts</guimenuitem>
    682         </menuchoice>
    683         , a labeled extract can be created in one of following ways.
    684       </para>
    685       <variablelist>
    686         <varlistentry>
    687           <term>pooling selected labeled extracts</term>
    688           <listitem>
    689             <para>
    690               The toolbar at the list page of labeled extracts contains an addition
    691               &gbPool; button. This button allows users to create pooled labeled
    692               extracts by selecting the list of labeled extracts used to derived a new
    693               labeled extract and then click on the button.
    694             </para>
    695             <para>
    696               This provides an easy and simple way to create pooled labeled extracts.
    697               The result of such process is the creation of a new labeled extract, in
    698               which, when navigating to the parent tab, shows that all the labeled
    699               extracts involved are already set and listed in the Labeled Extract box
    700               of the tab.
    701             </para>
    702           </listitem>
    703         </varlistentry>
    704         <varlistentry>
    705           <term>from the extract pages.</term>
    706           <listitem>
    707             <para>
    708               Following the laboratory workflow, a natural way to create a labeled
    709               extract from an extract is to click on the
    710               <guiicon>
    711                 <inlinemediaobject>
    712                   <imageobject>
    713                     <imagedata fileref="figures/add.png" format="PNG" />
    714                   </imageobject>
    715                 </inlinemediaobject>
    716               </guiicon>
    717               from the labeled extract column of the extract list view. Corresponding
    718               button,
    719               <guibutton>New labeled extract</guibutton>
    720               is located on the single item view page for each extract. By creating a
    721               labeled extract from an extract page will automatically set the extract
    722               as a parent.
    723             </para>
    724           </listitem>
    725         </varlistentry>
    726         <varlistentry>
    727           <term>from single item view of a label</term>
    728           <listitem>
    729             <para>
    730               Click on the
    731               <guibutton>New labeled extract&hellip;</guibutton>
    732               to use the current label and create a new labeled extract with it
    733               pre-selected as
    734               <guilabel>Label</guilabel>
    735               .
    736             </para>
    737           </listitem>
    738         </varlistentry>
    739       </variablelist>
    740     </sect2>
    741     <sect2 id="biomaterials.labeledextracts.properties">
    742       <title>Properties</title>
    743       <sect3 id="biomaterials.labeledextracts.properties.labeledextract">
    744         <title>Labeled extract</title>
    745         <variablelist>
    746           <varlistentry>
    747             <term>
    748               <guilabel>Name</guilabel>
    749             </term>
    750             <listitem>
    751               <para>
    752                 The name of the labeled extract (required). BASE by default assigns
    753                 names to labeled extract(by suffixing
    754                 <replaceable>lbe#</replaceable>
    755                 when creating a labeled extract from an existing extract or
    756                 <replaceable>New labeled extract</replaceable>
    757                 otherwise) but it is possible to edit it at will
    758               </para>
    759             </listitem>
    760           </varlistentry>
    761           <varlistentry>
    762             <term>
    763               <guilabel>Label</guilabel>
    764             </term>
    765             <listitem>
    766               <para>
    767                 Used to specify which dye or marker was used in the labeling
    768                 reaction (required).
    769               </para>
    770             </listitem>
    771           </varlistentry>
    772           <varlistentry>
    773             <term>
    774               <guilabel>External ID</guilabel>
    775             </term>
    776             <listitem>
    777               <para>An id used to recognize the labeled extract outside BASE.</para>
    778             </listitem>
    779           </varlistentry>
    780           <varlistentry>
    781             <term>
    782               <guilabel>Original quantity</guilabel>
    783             </term>
    784             <listitem>
    785               <para>The mass of labeled extract that was created.</para>
    786             </listitem>
    787           </varlistentry>
    788           <varlistentry>
    789             <term>
    790               <guilabel>Created</guilabel>
    791             </term>
    792             <listitem>
    793               <para>
    794                 A date should be provided. The information can be important when
    795                 running quality controls on data and account for potential
    796                 confounding factor (e.g. day effect).
    797               </para>
    798             </listitem>
    799           </varlistentry>
    800           <varlistentry>
    801             <term>
    802               <guilabel>Registered</guilabel>
    803             </term>
    804             <listitem>
    805               <para>
    806                 This is automatically populated with a date at which the labeled
    807                 extract was actually entered in BASE system.
    808               </para>
    809             </listitem>
    810           </varlistentry>
    811           <varlistentry>
    812             <term>
    813               <guilabel>Protocol</guilabel>
    814             </term>
    815             <listitem>
    816               <para>
    817                 The labeling protocol that was used to produce the labeled extract.
    818               </para>
    819             </listitem>
    820           </varlistentry>
    821           <varlistentry>
     535                <para>
     536                  A mandatory field for providing the extract name. BASE by
     537                  default assigns names to extract (by suffixing
     538                  <replaceable>e#</replaceable>
     539                  when creating an extract from an existing sample or
     540                  <replaceable>New extract</replaceable>
     541                  otherwise) but it is possible to edit it at will.
     542                </para>
     543              </listitem>
     544            </varlistentry>
     545            <varlistentry>
     546              <term>
     547                <guilabel>Type</guilabel>
     548              </term>
     549              <listitem>
     550                <para>
     551                The subtype of the extract. The list
     552                may evolve depending on additions by the server
     553                administrator. Selecting the proper subtype
     554                is recommended and enables BASE to automatically guess
     555                the most likely subtype when creating child biomaterial and
     556                bioassays.
     557                <nohelp>
     558                See <xref linkend="subtypes" /> for more information.
     559                </nohelp>
     560                </para>
     561              </listitem>
     562            </varlistentry>
     563            <varlistentry>
     564              <term>
     565                <guilabel>Tag</guilabel>
     566              </term>
     567              <listitem>
     568                <para>
     569                  If the extract has been marked with a tag, select it here. Note
     570                  that the subtype of the extract usually limits what kind of tag
     571                  that can be used. For example, a <emphasis>labeled extract</emphasis>
     572                  should be tagged with a <emphasis>label</emphasis>.
     573                </para>
     574              </listitem>
     575            </varlistentry>
     576            <varlistentry>
     577              <term>
     578                <guilabel>External ID</guilabel>
     579              </term>
     580              <listitem>
     581                <para>The extracts identification outside BASE</para>
     582              </listitem>
     583            </varlistentry>
     584            <varlistentry>
     585              <term>
     586                <guilabel>Original quantity</guilabel>
     587              </term>
     588              <listitem>
     589                <para>
     590                  Holds information about the original mass of the created
     591                  extract.
     592                </para>
     593              </listitem>
     594            </varlistentry>
     595            <varlistentry>
     596              <term>
     597                <guilabel>Created</guilabel>
     598              </term>
     599              <listitem>
     600                <para>
     601                  The date when the extract was created. The information can be
     602                  important when running quality controls on data and account for
     603                  potential confounding factor (e.g. day effect)
     604                </para>
     605              </listitem>
     606            </varlistentry>
     607            <varlistentry>
     608              <term>
     609                <guilabel>Registered</guilabel>
     610              </term>
     611              <listitem>
     612                <para>
     613                  This is automatically populated with a date at which the sample
     614                  was entered in BASE system.
     615                </para>
     616              </listitem>
     617            </varlistentry>
     618            <varlistentry>
     619              <term>
     620                <guilabel>Protocol</guilabel>
     621              </term>
     622              <listitem>
     623                <para>
     624                  The extraction protocol that was used to produce the extract.
     625                </para>
     626              </listitem>
     627            </varlistentry>
     628            <varlistentry>
    822629              <term>
    823630                <guilabel>Bioplate</guilabel>
    824631              </term>
    825632              <listitem>
    826                 <para>The bioplate where this labeled extract is located.</para>
     633                <para>The bioplate where this extract is located.</para>
    827634              </listitem>             
    828635            </varlistentry>
    … …  
    833640              <listitem>
    834641                <para>
    835                   Biowell that holds this labeled extract.
     642                  Biowell that holds this extract.
    836643                  <guilabel>Bioplate</guilabel> has to be defined before
    837644                  biowell can be selected.
    … …  
    839646              </listitem>             
    840647            </varlistentry>
    841           <varlistentry>
    842             <term>
    843               <guilabel>Description</guilabel>
    844             </term>
    845             <listitem>
    846               <para>
    847                 A free text field to report any information that can not be captured
    848                 otherwise.
    849               </para>
    850             </listitem>
    851           </varlistentry>
    852         </variablelist>
    853         <figure id="write_docbook_doc.figures.labeledextract-properties">
    854           <title>Labeled extract properties</title>
     648            <varlistentry>
     649              <term>
     650                <guilabel>Description</guilabel>
     651              </term>
     652              <listitem>
     653                <para>
     654                  A text field to report any information that not can be captured
     655                  otherwise.
     656                </para>
     657              </listitem>
     658            </varlistentry>
     659          </variablelist>
     660          <seeother>
     661            <other external_id="extract.edit.parents">Parents</other>
     662            <other external_id="annotations.edit">Annotations &amp; parameters</other>
     663            <other external_id="annotations.edit.inherited">Inherited annotations</other>
     664          </seeother>
     665        </helptext>
     666  </sect2>
     667 
     668  <sect2 id="biomaterials.extracts.parents">
     669    <title>Extract parents</title>
     670        <figure id="biomaterials.figures.extract-tab-2">
     671          <title>Extract parents</title>
    855672          <screenshot>
    856673            <mediaobject>
    857674              <imageobject>
    858                 <imagedata contentwidth="10cm" width="10cm"
    859                   fileref="figures/labeledextract-properties.png" format="PNG" />
     675                <imagedata
     676                  fileref="figures/extract-tab-2.png" format="PNG" />
    860677              </imageobject>
    861678            </mediaobject>
    862679          </screenshot>
    863680        </figure>
    864       </sect3>
    865       <sect3 id="biomaterials.labeledextracts.properties.parents">
    866         <title>Parents</title>
    867         <para>
    868           This important tab allows users to select the labeled
    869           extract origin. BASE distinguished between two cases which
    870           are controlled by the
    871           <guilabel>Pooled</guilabel>
    872           radio-button.
    873         </para>
    874         <itemizedlist>
    875           <listitem>
    876             <para>The parent is an extract</para>
    877             <para>
    878               The radio-button is set to
    879               <guilabel>No</guilabel>
    880               . The Extract select button is active and allows users to point to one
    881               and only one extract from which the labeled extract originates from.
    882             </para>
    883           </listitem>
    884           <listitem>
    885             <para>The parent is another labeled extract</para>
    886             <para>
    887               The radio-button has to be set to
    888               <guilabel>Yes</guilabel>
    889               . Upon selection, the extract select button is deactivated and the
    890               labeled extracts box and button are activated. This allows users to
    891               specify one or more extracts to be selected from the labeled extract
    892               list view page.
    893             </para>
    894           </listitem>
    895         </itemizedlist>
    896       </sect3>
    897       <sect3 id="biomaterials.labeledextracts.properties.annotations_param">
    898         <title>Annotations &amp; parameters</title>
    899         <para>
    900           As seen in the biosource and sample sections, this tab allows users to further
    901           supply information about the labeled extract provided they have defined
    902           annotation types to annotate labeled extract items or have such elements shared
    903           to them.
    904         </para>
    905         <important>
     681        <helptext external_id="extract.parents" title="Extract's parents">
    906682          <para>
    907             In order to use this feature, annotation type must be declared and made
    908             available. To learn more about annotation types and how these are set,
    909             please refer to
    910             <xref linkend="annotations" />
    911             .
     683            This is meant to keep track of the extract origin. BASE
     684            distinguishes between two cases which are controlled by the
     685            <guilabel>Parent type</guilabel>
     686            radio-button in the edit pop-up window.
    912687          </para>
    913         </important>
    914       </sect3>
    915       <sect3 id="biomaterials.labeledextracts.properties.inherited">
    916         <title>Inherited annotations</title>
    917         <para>
    918           This tab contains a list of those annotations that are inherited from the
    919           parents of the labeled extract. Information about dealing with inherited
    920           annotations can be found in
    921           <xref linkend="annotations.inheriting" />
    922           .
    923         </para>
    924       </sect3>
    925     </sect2>
     688          <itemizedlist>
     689            <listitem>
     690              <para>
     691                If the parent is a sample the radio-button is set to
     692                <guilabel>Sample</guilabel>. Only a single sample
     693                can be used as the parent. This option is automatically
     694                selected if the user selects a sample with the
     695                <guibutton>Select sample</guibutton> button.
     696              </para>
     697            </listitem>
     698            <listitem>
     699              <para>
     700                When the parent is one or several other extracts the radio-button is
     701                set to <guilabel>Extract</guilabel>. This option is automatically
     702                selected if the user add extracts with the <guibutton>Add extracts</guibutton> button.           
     703              </para>
     704            </listitem>
     705          </itemizedlist>
     706         
     707          <para>
     708            For each parent item, it is
     709            possible to specify the amount used in micrograms. This will automatically
     710            update the <guilabel>remaining quantity</guilabel> of the parent.
     711          </para>
     712         
     713          <seeother>
     714            <other external_id="extract.edit">Extract properties</other>
     715            <other external_id="annotations.edit">Annotations &amp; parameters</other>
     716            <other external_id="annotations.edit.inherited">Inherited annotations</other>
     717          </seeother>
     718        </helptext>
     719
     720    <para>
     721      The <guilabel>Annotations</guilabel> tab allows BASE users to use
     722      annotation types to refine extract description. More about annotating items
     723      can be read in <xref linkend="annotations.annotating" />
     724    </para>
     725       
     726    <para>
     727      This <guilabel>Inherited annotations</guilabel> tab contains a list of those annotations
     728      that are inherited from the extract's parents. Information about working with inherited
     729      annotations can be found in <xref linkend="annotations.inheriting" />.
     730    </para>
     731
     732
     733  </sect2>
     734
     735
    926736  </sect1>
     737
     738  <sect1 id="biomaterials.tags">
     739    <title>Tags</title>
     740    <para>
     741      Before attempting to create tagged extracts, users should make sure that the
     742      appropriate tag object is present in BASE. To browse the list of tags, go to
     743      <menuchoice>
     744        <guimenu>Biomaterial LIMS</guimenu>
     745        <guimenuitem>Tags</guimenuitem>
     746      </menuchoice>
     747    </para>
     748
     749    <figure id="biomaterials.figures.tags">
     750      <title>Tag properties</title>
     751      <screenshot>
     752        <mediaobject>
     753          <imageobject>
     754            <imagedata
     755              fileref="figures/edit_tag.png" format="PNG" />
     756          </imageobject>
     757        </mediaobject>
     758      </screenshot>
     759    </figure>
     760
     761    <helptext external_id="tag.edit" title="Edit tag">
     762      <para>
     763        The tag item is very simple and does not need much explanation. There are only
     764        a few properties for a tag.
     765        <variablelist>
     766          <varlistentry>
     767            <term>
     768              <guilabel>Name</guilabel>
     769            </term>
     770            <listitem>
     771              <para>The name of the tag (required).</para>
     772            </listitem>
     773          </varlistentry>
     774          <varlistentry>
     775            <term>
     776              <guilabel>Type</guilabel>
     777            </term>
     778            <listitem>
     779              <para>
     780              The subtype of the tag. The list
     781              may evolve depending on additions by the server
     782              administrator. Selecting the proper subtype
     783              is important and enables BASE to automatically guess
     784              the most likely tag when creating tagged extracts (eg.
     785              a <emphasis>Label</emphasis> for a <emphasis>Labeled extract</emphasis>
     786              or a <emphasis>Barcode</emphasis> for a <emphasis>Library</emphasis>).
     787              <nohelp>
     788              See <xref linkend="subtypes" /> for more information.
     789              </nohelp>
     790              </para>
     791            </listitem>
     792          </varlistentry>
     793          <varlistentry>
     794            <term>
     795              <guilabel>Description</guilabel>
     796            </term>
     797            <listitem>
     798              <para>
     799                An explaining text or other information associated with the
     800                tag.
     801              </para>
     802            </listitem>
     803          </varlistentry>
     804        </variablelist>
     805      </para>
     806    </helptext>
     807
     808  </sect1>
     809
    927810 
    928   <sect1 id="biomaterials.bioplate">
    929     <title>Bioplate</title>
    930     <para>
    931       With bioplates it is possible to organize biomaterial such as samples, extracts and
    932       labeled extracts into wells. Each plate has a number of wells that is defined by the
    933       plate geometry.
     811  <sect1 id="biomaterials.bioplates">
     812    <title>Bioplates</title>
     813    <para>
     814      With bioplates it is possible to organize biomaterial such as samples and extracts
     815      into wells. Each plate has a number of wells that is defined by the plate geometry.
    934816    </para>
    935817    <para>
    … …  
    937819      <menuchoice>
    938820        <guimenu>Biomaterial LIMS</guimenu>
    939         <guimenuitem>Bioplate</guimenuitem>
     821        <guimenuitem>Bioplates</guimenuitem>
    940822      </menuchoice>
    941823      to get to the list of bioplates.   
    942824    </para>
    943825    <sect2 id="biomaterials.bioplate.properties">
    944       <title>Properties</title>     
    945       <helptext external_id="bioplate.edit" title="Edit bioplate">
    946         <para>
    947           <variablelist>
    948             <varlistentry>
    949               <term><guilabel>Name</guilabel></term>
    950               <listitem>
    951                 <para>
    952                   The bioplate name. The name does not unique but it is
    953                   recommended to keep it unique. BASE by default assigns
    954                   <replaceable>New bioplate</replaceable> as name.
    955                   This field is mandatory.
    956                 </para>
    957               </listitem>
    958             </varlistentry>
    959             <varlistentry>
    960               <term><guilabel>Plate geometry</guilabel></term>
    961               <listitem>
    962                 <para>
    963                   Information about the plate design defining the
    964                   number of  rows and columns on the bioplate.
    965                   This field are mandatory and can only be set for new bioplates.
    966                 </para>
    967               </listitem>             
    968             </varlistentry>
    969             <varlistentry>
    970               <term><guilabel>Freezer</guilabel></term>
    971               <listitem>
    972                 <para>The freezer where the bioplate is stored. Optional.</para>
    973               </listitem>
    974             </varlistentry>
    975             <varlistentry>
    976               <term><guilabel>Barcode</guilabel></term>
    977               <listitem>
    978                 <para>
    979                   Barcode of the bioplate.
    980                   Optional.
    981                 </para>
    982               </listitem>
    983             </varlistentry>
    984             <varlistentry>
    985               <term><guilabel>Description</guilabel></term>
    986               <listitem>
    987                 <para>
    988                   Other useful information about the bioplate. Optional.
    989                 </para>
    990               </listitem>
    991             </varlistentry>
    992           </variablelist>
    993         </para>
    994       </helptext>
    995       <figure id="write_docbook_doc.figures.bioplate-tab-1">
     826      <title>Bioplate properties</title>     
     827
     828      <figure id="biomaterials.figures.bioplate-tab-1">
    996829        <title>Bioplate properties</title>
    997830        <screenshot>
    … …  
    1004837        </screenshot>
    1005838      </figure>
    1006       <sect3 id="biomaterials.bioplate.properties.annotations">
    1007         <title>Annotations</title>
     839
     840      <helptext external_id="bioplate.edit" title="Edit bioplate">
    1008841        <para>
    1009           This allows BASE users to use annotation types to refine bioplate description.
    1010           More about annotating items can be read in
    1011           <xref linkend="annotations.annotating" />
    1012           .
     842          <variablelist>
     843            <varlistentry>
     844              <term><guilabel>Name</guilabel></term>
     845              <listitem>
     846                <para>
     847                  The bioplate name. The name does not have to be unique but it is
     848                  recommended to keep it unique. BASE by default assigns
     849                  <replaceable>New bioplate</replaceable> as name.
     850                  This field is mandatory.
     851                </para>
     852              </listitem>
     853            </varlistentry>
     854            <varlistentry>
     855              <term><guilabel>Bioplate type</guilabel></term>
     856              <listitem>
     857                <para>
     858                  The type of the bioplate may be a generic storage plate that
     859                  can store any type of biomaterial or a locked plate that
     860                  can only store a single type of biomaterial. This field
     861                  is mandatory and can only be set for new bioplates.
     862                  <nohelp>See <xref linkend="biomaterials.bioplatetypes" /> for more
     863                  information.</nohelp>
     864                </para>
     865              </listitem>             
     866            </varlistentry>
     867            <varlistentry>
     868              <term><guilabel>Plate geometry</guilabel></term>
     869              <listitem>
     870                <para>
     871                  Information about the plate design defining the
     872                  number of  rows and columns on the bioplate.
     873                  This field is mandatory and can only be set for new bioplates.
     874                </para>
     875              </listitem>             
     876            </varlistentry>
     877            <varlistentry>
     878              <term><guilabel>Freezer</guilabel></term>
     879              <listitem>
     880                <para>The freezer where the bioplate is stored. Optional.</para>
     881              </listitem>
     882            </varlistentry>
     883            <varlistentry>
     884              <term><guilabel>Barcode</guilabel></term>
     885              <listitem>
     886                <para>
     887                  Barcode of the bioplate.
     888                  Optional.
     889                </para>
     890              </listitem>
     891            </varlistentry>
     892            <varlistentry>
     893              <term><guilabel>Description</guilabel></term>
     894              <listitem>
     895                <para>
     896                  Other useful information about the bioplate. Optional.
     897                </para>
     898              </listitem>
     899            </varlistentry>
     900          </variablelist>
    1013901        </para>
    1014       </sect3>
     902       
     903        <seeother>
     904          <other external_id="annotations.edit">Annotations</other>
     905        </seeother>
     906      </helptext>
     907     
     908    <para>
     909      The <guilabel>Annotations</guilabel> tab allows BASE users to use
     910      annotation types to refine bioplate description. More about annotating items
     911      can be read in <xref linkend="annotations.annotating" />
     912    </para>
     913
    1015914    </sect2>
    1016     <sect2 id="biomaterials.bioplate.biowell">
    1017       <title>Biowell</title>
     915    <sect2 id="biomaterials.bioplate.biowells">
     916      <title>Biowells</title>
    1018917      <para>
    1019918        Biowells existence are managed through the bioplate they
    1020919        belong to. Creating a bioplate will automatically create the
    1021         biowells on the plate, correspondingly deleting a plate will
    1022         also remove the associated biowells. The only thing that can
    1023         be changed for a biowell is the biomaterial it holds. Go to
    1024         the <guilabel>Wells</guilabel>-tab when viewing a bioplate and
    1025         click on
    1026         <guiicon>
    1027           <inlinemediaobject>
    1028             <imageobject>
    1029               <imagedata fileref="figures/edit.gif" format="GIF" />
    1030             </imageobject>
    1031           </inlinemediaobject>
    1032         </guiicon> in the biomaterial column
    1033         for the specific biowell you want to change. Assigning a biomaterial to a biowell
    1034         can also be done when editing a sample, extract or labeled
    1035         extract item.
     920        biowells (as given by the selected geometry) on the plate.
     921        The wells are initially empty. To add biomaterial to the plate
     922        go to the single-item view page for the bioplate. This page
     923        includes an overview of the layout of the plate. Clicking
     924        on an empty well will open a popup dialog that allows you
     925        to select a biomaterial. The same dialog can also be accessed from
     926        the <guilabel>Wells</guilabel> tab. Assigning a biomaterial to a
     927        biowell can also be done when editing a sample or extract.
    1036928      </para>
    1037929     
    1038       <sect3 id="biomaterials.bioplate.biowell.properties">
    1039         <title>Properties</title>       
     930      <figure id="biomaterials.figures.biowell">
     931        <title>Biowell properties</title>
     932        <screenshot>
     933          <mediaobject>
     934            <imageobject>
     935              <imagedata
     936                fileref="figures/biowell.png" format="PNG" />
     937            </imageobject>
     938          </mediaobject>
     939        </screenshot>
     940      </figure>
     941
    1040942        <helptext external_id="biowell.edit" title="Edit biowell">
    1041943          <para>
    … …  
    1051953              </varlistentry>
    1052954              <varlistentry>             
    1053                 <term><guilabel>Coordinate</guilabel></term>
     955                <term><guilabel>Well location</guilabel></term>
    1054956                <listitem>
    1055957                  <para>
    1056                     The biowell location on the bioplate in format [row,column].
     958                    The biowell location on the bioplate in row+column format.
    1057959                    This property is read-only.
    1058960                  </para>
    1059961                </listitem>
    1060962              </varlistentry>
    1061               <varlistentry>             
     963              <varlistentry>
    1062964                <term><guilabel>Biomaterial type</guilabel></term>
    1063965                <listitem>
    … …  
    1065967                    The type of biomaterial stored in this biowell. This
    1066968                    property must be selected before before a
    1067                     biomaterial can be selected.
     969                    biomaterial can be selected. On some plates this
     970                    is locked due to settings in the bioplate's type.
    1068971                  </para>
    1069972                </listitem>
    … …  
    1074977                  <para>
    1075978                    Name of the biomaterial in this biowell. Before changing
    1076                     this you must select the appropriate
    1077                     <guilabel>Biomaterial type</guilabel>.
     979                    this you must select the appropriate <guilabel>Biomaterial type</guilabel>.
     980                    A biomaterial can only be placed in a single well. If the selected
     981                    biomaterial is already placed in another location it will be moved.
    1078982                  </para>
    1079983                </listitem>
    … …  
    1081985            </variablelist>
    1082986          </para>
    1083         </helptext>
    1084         <figure id="write_docbook_doc.figures.biowell">
    1085           <title>Biowell properties</title>
    1086           <screenshot>
    1087             <mediaobject>
    1088               <imageobject>
    1089                 <imagedata
    1090                   fileref="figures/biowell.png" format="PNG" />
    1091               </imageobject>
    1092             </mediaobject>
    1093           </screenshot>
    1094         </figure>
    1095       </sect3>
     987        </helptext>
    1096988    </sect2>
     989   
     990    <sect2 id="biomaterials.bioplatetypes">
     991      <title>Bioplate types</title>
     992     
     993      <helptext external_id="bioplatetype.view.properties" title="Bioplate types">
     994      <para>
     995        Bioplate types are used to subclassify bioplates and may put restrictions on them.
     996        BASE ships with a few pre-defined bioplate types. The <emphasis>Storage plate</emphasis> type
     997        is a generic plate type that can be used for all types of biomaterial and doesn't
     998        have any other restrictions on it. The reaction plate types are locked to a single
     999        type of biomaterial and have a restriction that biomaterial can never be moved out from
     1000        a well once it has been placed there.
     1001      </para>
     1002      </helptext>
     1003     
     1004      <figure id="biomaterials.figures.bioplatetype">
     1005        <title>Bioplate type properties</title>
     1006        <screenshot>
     1007          <mediaobject>
     1008            <imageobject>
     1009              <imagedata
     1010                fileref="figures/edit_bioplatetype.png" format="PNG" />
     1011            </imageobject>
     1012          </mediaobject>
     1013        </screenshot>
     1014      </figure>
     1015     
     1016          <helptext external_id="bioplatetype.edit" title="Edit bioplate type">
     1017          <para>
     1018            <variablelist>
     1019              <varlistentry>
     1020                <term><guilabel>Name</guilabel></term>
     1021                <listitem>
     1022                  <para>
     1023                    The name of the bioplate type.
     1024                  </para>
     1025                </listitem>
     1026              </varlistentry>
     1027              <varlistentry>             
     1028                <term><guilabel>Biomaterial type</guilabel></term>
     1029                <listitem>
     1030                  <para>
     1031                    Select if bioplates using this type should be locked to
     1032                    specific biomaterial type or not. This property can only
     1033                    be set for new bioplate types.
     1034                  </para>
     1035                </listitem>
     1036              </varlistentry>
     1037              <varlistentry>
     1038                <term><guilabel>Well lock mode</guilabel></term>
     1039                <listitem>
     1040                  <para>
     1041                    This option controls the wells on bioplates using this type.
     1042                    There are four options:
     1043                    <itemizedlist>
     1044                      <listitem>
     1045                        <para><guilabel>Unlocked</guilabel>:
     1046                          The wells are unlocked and biomaterial can be added
     1047                          and removed freely any number of times.
     1048                        </para>
     1049                      </listitem>
     1050                      <listitem>
     1051                        <para><guilabel>Locked after add+clear</guilabel>:
     1052                          A biomaterial can be placed once in the well and
     1053                          then moved to another bioplate. After that the well
     1054                          becomes locked and it is not possible to add a
     1055                          different biomaterial to it.
     1056                        </para>
     1057                      </listitem>
     1058                      <listitem>
     1059                        <para><guilabel>Locked after add</guilabel>:
     1060                          The wells are locked as soon as biomaterial is
     1061                          added to them. The biomaterial can't be moved to another
     1062                          place or be replaced with other biomaterial.
     1063                        </para>
     1064                      </listitem>
     1065                      <listitem>
     1066                        <para><guilabel>Locked at plate creation</guilabel>:
     1067                          The wells are locked as soon as the bioplate has been
     1068                          saved to the database. This lock mode is primarily intended
     1069                          to be used when plug-ins are creating and populating the
     1070                          bioplate as a single event.
     1071                        </para>
     1072                      </listitem>
     1073                    </itemizedlist>
     1074                  </para>
     1075                </listitem>
     1076              </varlistentry>
     1077              <varlistentry>             
     1078                <term><guilabel>Description</guilabel></term>
     1079                <listitem>
     1080                  <para>
     1081                    Other useful information about the bioplate type. Optional.
     1082                  </para>
     1083                </listitem>
     1084              </varlistentry>
     1085            </variablelist>
     1086          </para>
     1087        </helptext>
     1088    </sect2>
     1089   
     1090    <sect2 id="biomaterials.bioplateevents">
     1091      <title>Bioplate events</title>
     1092   
     1093      <para>
     1094        TODO
     1095      </para>
     1096   
     1097    </sect2>
     1098   
    10971099  </sect1>
    1098 
    1099   <sect1 id="biomaterials.hybridizations">
    1100     <title>Hybridizations</title>
    1101     <para>
    1102       A hybridization event corresponds to the application of one or more labeled extracts
     1100 
     1101  <sect1 id="biomaterials.lists">
     1102    <title>Biomaterial lists</title>
     1103   
     1104    <para>
     1105      TODO
     1106    </para>
     1107 
     1108  </sect1>
     1109
     1110  <sect1 id="biomaterials.bioassays">
     1111    <title>Physical bioassays</title>
     1112    <para>
     1113      A physical bioassay represents the application of one or more extracts
     1114      to an experimental setup designed to measure quantities that we are
     1115      interested in. For example, a <emphasis>Hybridization</emphasis> event corresponds
     1116      to the application of one or more <emphasis>Labeled extracts</emphasis>
    11031117      materials to a microarray slide under conditions detailed in hybridization protocols.
    11041118      Use
    11051119      <menuchoice>
    11061120        <guimenu>View</guimenu>
    1107         <guimenuitem>Hybridizations</guimenuitem>
     1121        <guimenuitem>Physical bioassays</guimenuitem>
    11081122      </menuchoice>
    1109       to get to the hybridizations.
    1110     </para>
    1111     <sect2 id="biomaterials.hybridizations.create">
    1112       <title>Creating hybridizations</title>
     1123      to get to the bioassays.
     1124    </para>
     1125   
     1126    <sect2 id="biomaterials.bioassays.create">
     1127      <title>Create physical bioassays</title>
    11131128      <para>
    1114         In BASE, there are two possible routes to create an hybridization object except the
    1115         common way with the &gbNew; button at hybridization list page.
     1129        In BASE, there are two possible routes to create a physical bioassay except the
     1130        common way with the &gbNew; button at the list page.
    11161131      </para>
    11171132      <variablelist>
    11181133        <varlistentry>
    1119           <term>from the labeled extract list view page</term>
     1134          <term>from the extract list view page</term>
    11201135          <listitem>
    11211136            <para>
    1122               Select at least one labeled extract, to create a hybridization from, by
     1137              Select at least one extract, to create a bioassay from, by
    11231138              ticking the selection boxes before the name field.
    1124             </para>
    1125             <para>
    1126               Click on the
    1127               <guibutton>New hybridization&hellip;</guibutton>
    1128               from the toolbar of labeled extract list view.
     1139              Click on the <guibutton>New physical bioassay&hellip;</guibutton>
     1140              in the toolbar.
    11291141            </para>
    11301142          </listitem>
    11311143        </varlistentry>
    11321144        <varlistentry>
    1133           <term>from a labeled extract single item page</term>
     1145          <term>from the extract single-item page</term>
    11341146          <listitem>
    11351147            <para>
    1136               When viewing a label extract in single item view, click on the
    1137               <guibutton>New hybridization&hellip;</guibutton>
    1138               button from the toolbar of the labeled extract item view.
     1148              When viewing an extract in single-item view, click on the
     1149              <guibutton>New physical bioassay&hellip;</guibutton>
     1150              button in the toolbar.
    11391151            </para>
    11401152          </listitem>
    … …  
    11421154      </variablelist>
    11431155    </sect2>
    1144     <sect2 id="biomaterials.hybridizations.properties">
    1145       <title>Properties</title>
    1146 
    1147       <sect3 id="biomaterials.hybridizations.hybridization">
    1148         <title>Hybridization</title>
     1156   
     1157    <sect2 id="biomaterials.bioassays.properties">
     1158      <title>Bioassay properties</title>
     1159
    11491160 
    1150         <figure id="write_docbook_doc.figures.hybridization-tab-1">
    1151           <title>Hybridization tab</title>
     1161        <figure id="biomaterials.figures.bioassays-tab-1">
     1162          <title>Physical bioassay properties</title>
    11521163          <screenshot>
    11531164            <mediaobject>
    11541165              <imageobject>
    11551166                <imagedata
    1156                   fileref="figures/hybridization-tab-1.png" format="PNG" />
     1167                  fileref="figures/physicalbioassay-tab-1.png" format="PNG" />
    11571168              </imageobject>
    11581169            </mediaobject>
    … …  
    11601171        </figure>
    11611172       
    1162         <helptext external_id="hybridization.edit" title="Edit hybridization">
     1173        <helptext external_id="physicalbioassay.edit" title="Edit physical bioassay">
    11631174        <variablelist>
    11641175          <varlistentry>
    … …  
    11681179            <listitem>
    11691180              <para>
    1170                 <replaceable>New hybridization</replaceable>
    1171                 is the BASE default name but it is strongly advise to provide a
    1172                 meaningful and unique name (required).
    1173               </para>
    1174             </listitem>
    1175           </varlistentry>
    1176           <varlistentry>
    1177             <term>
    1178               <guilabel>Arrays</guilabel>
    1179             </term>
    1180             <listitem>
    1181               <para>
    1182                 The number of sub-arrays on the slide that was used in
    1183                 this hybridization. The default value is 1, but some
    1184                 platforms, for example Illumina, has slides
    1185                 with 6 or 8 arrays. When the array-slide property below
    1186                 is changed this value will be updated automatically to
    1187                 be consistent with the number of sub-arrays on the used
    1188                 array-design.
     1181                The bioassay's name (required). It is recommended that the default
     1182                name is replaced with something that is unique.
     1183              </para>
     1184            </listitem>
     1185          </varlistentry>
     1186          <varlistentry>
     1187            <term>
     1188              <guilabel>Type</guilabel>
     1189            </term>
     1190            <listitem>
     1191              <para>
     1192              The subtype of the bioassay. The list
     1193              may evolve depending on additions by the server
     1194              administrator. Selecting the proper subtype
     1195              is recommended and enables BASE to automatically guess
     1196              the most likely subtype when assignint source biomaterials
     1197              and when creating derived bioassays.
     1198              <nohelp>
     1199              See <xref linkend="subtypes" /> for more information.
     1200              </nohelp>
     1201              </para>
     1202            </listitem>
     1203          </varlistentry>
     1204          <varlistentry>
     1205            <term>
     1206              <guilabel>Size</guilabel>
     1207            </term>
     1208            <listitem>
     1209              <para>
     1210                The size of the bioassay is the number of independent
     1211                positions on the bioassay. Depending on the
     1212                characteristics of the bioassay, multiple biomaterials
     1213                may share the same position, but are then usually
     1214                required to have different tags. Two biomaterials
     1215                in different positions can use the same tag.
     1216                The default value is 1, but some platforms, for example
     1217                Illumina BeadArrays, has slides with 6 or 8 positions.
    11891218              </para>
    11901219            </listitem>
    … …  
    11991228                A date should be provided. The information can be important when
    12001229                running quality controls on data and account for potential
    1201                 confounding factor (e.g. to account for a day effect)
     1230                confounding factor (e.g. to account for a day effect).
    12021231              </para>
    12031232            </listitem>
    … …  
    12221251            <listitem>
    12231252              <para>
    1224                 The hybridization protocol that was used to do the hybridization.
     1253                The protocol that was used to create the bioassay.
    12251254              </para>
    12261255            </listitem>
    … …  
    12331262            <listitem>
    12341263              <para>
    1235                 The hybridization-station that was used during the hybridization.
     1264                Information about the machine (if any) that was used when creating
     1265                the bioassay.
    12361266              </para>
    12371267            </listitem>
    … …  
    12431273            </term>
    12441274            <listitem>
    1245               <para>The array slide that was used in the hybridization.</para>
    1246               <note>
    1247                 <para>
    1248                   Ideally, The Array Slides should have been created but for those
    1249                   users with permission to do, Array Slides could be generated at
    1250                   that point.
    1251                 </para>
    1252               </note>
     1275              <para>The array slide that was used for the bioassay.</para>
    12531276            </listitem>
    12541277          </varlistentry>
    … …  
    12611284              <para>
    12621285                A free text field to report any information that can not be captured
    1263                 otherwise
     1286                otherwise.
    12641287              </para>
    12651288            </listitem>
    … …  
    12671290        </variablelist>
    12681291        <seeother>
    1269           <other external_id="hybridization.labeledextracts">Labeled extracts</other>
     1292          <other external_id="physicalbioassay.extracts">Extracts</other>
     1293          <other external_id="annotations.edit">Annotations &amp; parameters</other>
     1294          <other external_id="annotations.edit.inherited">Inherited annotations</other>
     1295        </seeother>
     1296        </helptext>
     1297      </sect2>
     1298     
     1299      <sect2 id="biomaterials.bioassays.extracts">
     1300        <title>Parent extracts</title>
     1301       
     1302        <figure id="biomaterials.figures.bioassay-tab-2">
     1303          <title>Parent extracts</title>
     1304          <screenshot>
     1305            <mediaobject>
     1306              <imageobject>
     1307                <imagedata
     1308                  fileref="figures/physicalbioassay-tab-2.png" format="PNG" />
     1309              </imageobject>
     1310            </mediaobject>
     1311          </screenshot>
     1312        </figure>
     1313       
     1314        <helptext external_id="physicalbioassay.extracts" title="Extracts">
     1315        <para>
     1316          This important tab allows users to select the extracts used by the
     1317          bioassay, and specify the amount of material used, expressed in microgram.
     1318        </para>
     1319        <para>
     1320          Use the <guibutton>Add extracts</guibutton> button to add
     1321          items and the <guibutton>Remove</guibutton> button to remove items.
     1322          Select one or several extracts in the list and write the used
     1323          mass and position number in the fields below the list.
     1324        </para>
     1325       
     1326        <seeother>
     1327          <other external_id="physicalbioassay.edit">Edit physical bioassay</other>
     1328          <other external_id="annotations.edit">Annotations &amp; parameters</other>
     1329          <other external_id="annotations.edit.inherited">Inherited annotations</other>
    12701330        </seeother>
    12711331        </helptext>
    12721332       
    1273       </sect3>
     1333      </sect2>
    12741334     
    1275       <sect3 id="biomaterials.hybridizations.properties.labeledextracts">
    1276         <title>Labeled extracts</title>
     1335     
     1336    <para>
     1337      The <guilabel>Annotations</guilabel> tab allows BASE users to use
     1338      annotation types to refine bioassay description. More about annotating items
     1339      can be read in <xref linkend="annotations.annotating" />
     1340    </para>
    12771341       
    1278         <helptext external_id="hybridization.labeledextracts" title="Labeled extracts">
    1279         <para>
    1280           This important tab allows users to select the labeled extracts applied to an
    1281           array slide, and specify the amount of material used, expressed in microgram.
    1282         </para>
    1283         <para>
    1284           Use the <guibutton>Add labeled extracts</guibutton> button to add
    1285           items and the <guibutton>Remove</guibutton> button to remove items.
    1286           Select one or several labeled extracts in the list and write the used
    1287           mass and sub-array index in the fields below.
    1288         </para>
    1289        
    1290         <seeother>
    1291           <other external_id="hybridization.edit">Edit hybridization</other>
    1292         </seeother>
    1293         </helptext>
    1294        
    1295       </sect3>
    1296       <sect3 id="biomaterials.hybridizations.properties.annotations_param">
    1297         <title>Annotations &amp; parameters</title>
    1298         <para>
    1299           As seen in the biosource and sample sections, this tab allows users to supply
    1300           further information about the hybridization provided annotation types have been
    1301           defined or shared to annotate hybridization items.
    1302         </para>
    1303         <important>
    1304           <para>
    1305             In order to use this feature, annotation type must be declared and made
    1306             available. To learn more about annotation types and how these are set,
    1307             please refer to
    1308             <xref linkend="annotations" />
    1309           </para>
    1310         </important>
    1311       </sect3>
    1312       <sect3 id="biomaterials.hybridizations.properties.inherited">
    1313         <title>Inherited annotations</title>
    1314         <para>
    1315           This tab contains a list of those annotations that are inherited from the
    1316           labeled extracts. Information about dealing with inherited annotations can be
    1317           found in
    1318           <xref linkend="annotations.inheriting" />
    1319           .
    1320         </para>
    1321       </sect3>
    1322     </sect2>
     1342    <para>
     1343      This <guilabel>Inherited annotations</guilabel> tab contains a list of those annotations
     1344      that are inherited from the bioassay's parents. Information about working with inherited
     1345      annotations can be found in <xref linkend="annotations.inheriting" />.
     1346    </para>
     1347     
    13231348  </sect1>
    13241349</chapter>

  • trunk/www/biomaterials/bioplates/edit_bioplate.jsp

    r5630 r5708  
    319319      </tr>
    320320      <tr>
    321         <td class="prompt">Bio plate type</td>
     321        <td class="prompt">Bioplate type</td>
    322322        <td>
    323323          <%

  • trunk/www/biomaterials/bioplates/list_bioplates.jsp

    r5674 r5708  
    308308        property="bioPlateType.name"
    309309        datatype="string"
    310         title="Bio plate type"
     310        title="Bioplate type"
    311311        sortable="true"
    312312        filterable="true"

  • trunk/www/biomaterials/bioplates/view_bioplate.jsp

    r5642 r5708  
    385385      </tr>
    386386      <tr>
    387         <td class="prompt">Bio plate type</td>
     387        <td class="prompt">Bioplate type</td>
    388388        <td><base:propertyvalue item="<%=bioplate%>" property="bioPlateType" /></td>
    389389      </tr>

  • trunk/www/biomaterials/bioplates/wells/edit_biowell.jsp

    r5641 r5708  
    6969  WellCoordinateFormatter columnFormatter = new WellCoordinateFormatter(false);
    7070 
    71   title = "Edit biowell -- [" + rowFormatter.format(bioWell.getRow()) + ", " + columnFormatter.format(bioWell.getColumn()) + "] on bioplate " + HTML.encodeTags(bioPlate.getName());
     71  title = "Edit biowell -- " + rowFormatter.format(bioWell.getRow()) + columnFormatter.format(bioWell.getColumn()) + " on " + HTML.encodeTags(bioPlate.getName());
    7272
    7373  final String clazz = "class=\"text\"";
    … …  
    171171      </tr>
    172172      <tr>
    173         <td class="prompt">Coordinate</td>
    174         <td>[<%=rowFormatter.format(bioWell.getRow())%>,<%=columnFormatter.format(bioWell.getColumn())%>]</td>
     173        <td class="prompt">Well location</td>
     174        <td><%=rowFormatter.format(bioWell.getRow())%><%=columnFormatter.format(bioWell.getColumn())%></td>
    175175      </tr>
    176176      <tr>

  • trunk/www/biomaterials/bioplatetypes/edit_platetype.jsp

    r5641 r5708  
    7171  if (itemId == 0)
    7272  {
    73     title = "Create bio plate type";
     73    title = "Create bioplate type";
    7474    cc.removeObject("item");
    7575    int lm = Values.getInt(cc.getPropertyValue("lockMode"));
    … …  
    8282    lockMode = bioPlateType.getLockMode();
    8383    cc.setObject("item", bioPlateType);
    84     title = "Edit bio plate type -- " + HTML.encodeTags(bioPlateType.getName());
     84    title = "Edit bioplate type -- " + HTML.encodeTags(bioPlateType.getName());
    8585  }
    8686  final String clazz = "class=\"text\"";
    … …  
    141141      position="bottom"  remember="<%=bioPlateType != null%>"
    142142      extensions="<%=invoker%>">
    143     <t:tab id="info" title="Bio plate type" validate="validateBioPlateType()" helpid="bioplatetype.edit">
     143    <t:tab id="info" title="Bioplate type" validate="validateBioPlateType()" helpid="bioplatetype.edit">
    144144      <table class="form" cellspacing=0>
    145145      <tr>
    146146        <td class="prompt">Name</td>
    147147        <td><input <%=requiredClazz%> type="text" name="name"
    148           value="<%=HTML.encodeTags(bioPlateType == null ? Values.getString(cc.getPropertyValue("name"), "New bio plate type") : bioPlateType.getName())%>"
     148          value="<%=HTML.encodeTags(bioPlateType == null ? Values.getString(cc.getPropertyValue("name"), "New bioplate type") : bioPlateType.getName())%>"
    149149          size="40" maxlength="<%=BioPlateType.MAX_NAME_LENGTH%>"></td>
    150150      </tr>

  • trunk/www/biomaterials/bioplatetypes/list_platetypes.jsp

    r5641 r5708  
    9393final ModeInfo mode = ModeInfo.get(request.getParameter("mode"));
    9494final String callback = request.getParameter("callback");
    95 final String title = mode.generateTitle("bio plate type", "bio plate types");
     95final String title = mode.generateTitle("bioplate type", "bioplate types");
    9696final DbControl dc = sc.newDbControl();
    9797ItemResultIterator<BioPlateType> bioPlateTypes = null;
    … …  
    112112  ExtensionsInvoker invoker = ToolbarUtil.useExtensions(jspContext);
    113113  %>
    114   <base:page title="<%=title==null ? "Bio plate types" : title%>" type="<%=mode.getPageType()%>">
     114  <base:page title="<%=title==null ? "Bioplate types" : title%>" type="<%=mode.getPageType()%>">
    115115  <base:head scripts="menu.js,table.js" styles="menu.css,table.css">
    116116    <ext:scripts context="<%=jspContext%>" />
    … …  
    270270          onclick="newItem()"
    271271          title="New&hellip;"
    272           tooltip="<%=createPermission ? "Create new bio plate type" : "You do not have permission to create bio plate types"%>"
     272          tooltip="<%=createPermission ? "Create new bioplate type" : "You do not have permission to create bioplate types"%>"
    273273        />
    274274        <tbl:button
    … …  
    422422      {
    423423        %>
    424         <tbl:panel><%=bioPlateTypes == null || bioPlateTypes.getTotalCount() == 0 ? "No bio plate types were found" : "No bio plate types on this page. Please select another page!" %></tbl:panel>
     424        <tbl:panel><%=bioPlateTypes == null || bioPlateTypes.getTotalCount() == 0 ? "No bioplate types were found" : "No bioplate types on this page. Please select another page!" %></tbl:panel>
    425425        <%
    426426      }

  • trunk/www/biomaterials/bioplatetypes/view_platetype.jsp

    r5496 r5708  
    127127    <p>
    128128    <p:path>
    129       <p:pathelement title="Bio plate types" href="<%="index.jsp?ID="+ID%>" />
     129      <p:pathelement title="Bioplate types" href="<%="index.jsp?ID="+ID%>" />
    130130      <p:pathelement title="<%=HTML.encodeTags(plateType.getName())%>" />
    131131    </p:path>
    … …  
    141141        onclick="editItem()"
    142142        title="Edit&hellip;"
    143         tooltip="<%=writePermission ? "Edit this bio plate type" : "You do not have permission to edit this bio plate type"%>"
     143        tooltip="<%=writePermission ? "Edit this bioplate type" : "You do not have permission to edit this bioplate type"%>"
    144144      />
    145145      <tbl:button
    … …  
    149149        title="Delete"
    150150        visible="<%=!plateType.isRemoved()%>"
    151         tooltip="<%=deletePermission ? "Delete this bio plate type" : "You do not have permission to delete this bio plate type"%>"
     151        tooltip="<%=deletePermission ? "Delete this bioplate type" : "You do not have permission to delete this bioplate type"%>"
    152152      />
    153153      <tbl:button
    … …  
    157157        title="Restore"
    158158        visible="<%=plateType.isRemoved()%>"
    159         tooltip="<%=writePermission ? "Restore this bio plate type" : "You do not have permission to restore this bio plate type"%>"
     159        tooltip="<%=writePermission ? "Restore this bioplate type" : "You do not have permission to restore this bioplate type"%>"
    160160      />
    161161      <tbl:button

  • trunk/www/biomaterials/extracts/edit_extract.jsp

    r5701 r5708  
    916916          <tr valign="top">
    917917          <td>
    918             <select name="extracts" size="5" multiple class="selectionlist"
     918            <select name="extracts" size="12" multiple class="selectionlist"
    919919              onchange="extractsOnChange()">
    920920            </select>&nbsp;

  • trunk/www/biomaterials/samples/edit_sample.jsp

    r5701 r5708  
    833833          <tr valign="top">
    834834          <td>
    835             <select name="samples" size="5" multiple class="selectionlist"
     835            <select name="samples" size="12" multiple class="selectionlist"
    836836              onchange="samplesOnChange()">
    837837            </select>&nbsp;

  • trunk/www/common/help/view_help.jsp

    r5426 r5708  
    4343<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
    4444<%!
    45 private static final Pattern findTag = Pattern.compile("\\{\\@(\\w+)\\s([^\\s]+)\\s*(.*)\\}");
     45private static final Pattern findTag = Pattern.compile("\\{\\@(\\w+)\\s([^\\s]+)\\s*(.+?)\\}");
    4646private String parseTags(String ID, Help help, int includeLevel)
    4747{

  • trunk/www/include/menu.jsp

    r5685 r5708  
    701701        />
    702702        <m:menuitem
    703           title="<%=common.getString("item.biomateriallist+")%>"
    704           onclick="<%="Menu.openUrl('"+root+"biomaterials/lists/index.jsp?ID="+ID+"')"%>"
    705           tooltip="<%=menu.getString("biomateriallists.tooltip", hasBioMaterialLists)%>"
    706           enabled="<%=hasBioMaterialLists%>"
    707         />
    708         <m:menuseparator />
    709         <m:menuitem
    710703          title="<%=common.getString("item.bioplatetype+")%>"
    711704          onclick="<%="Menu.openUrl('"+root+"biomaterials/bioplatetypes/index.jsp?ID="+ID+"')"%>"
    … …  
    718711          tooltip="<%=menu.getString("bioplateeventtypes.tooltip", hasBioPlateEventTypes)%>"
    719712          enabled="<%=hasBioPlateEventTypes%>"
     713        />
     714        <m:menuseparator />
     715        <m:menuitem
     716          title="<%=common.getString("item.biomateriallist+")%>"
     717          onclick="<%="Menu.openUrl('"+root+"biomaterials/lists/index.jsp?ID="+ID+"')"%>"
     718          tooltip="<%=menu.getString("biomateriallists.tooltip", hasBioMaterialLists)%>"
     719          enabled="<%=hasBioMaterialLists%>"
    720720        />
    721721      </m:menu>

  • trunk/www/views/physicalbioassays/edit_bioassay.jsp

    r5701 r5708  
    747747          <tr valign="top">
    748748          <td>
    749             <select name="extracts" size="5" multiple style="width: 20em;"
     749            <select name="extracts" size="15" multiple style="width: 20em;"
    750750              onchange="extractsOnChange()">
    751751            </select>&nbsp;<br>
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