source: trunk/doc/src/docbook/user/biomaterials.xml @ 6064

Last change on this file since 6064 was 6064, checked in by Nicklas Nordborg, 10 years ago

References #1695 and #1696.

Updated screen shot and documentation.

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1<?xml version="1.0" encoding="UTF-8"?>
2<!DOCTYPE chapter PUBLIC
3    "-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN"
4    "../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd">
5<!--
6  $Id: biomaterials.xml 6064 2012-06-13 12:29:26Z nicklas $
7 
8  Copyright (C) 2007 Peter Johansson, Nicklas Nordborg, Philippe Rocca-Serra, Martin Svensson
9  Copyright (C) 2008, 2009 Jari Häkkinen, Martin Svensson
10 
11  This file is part of BASE - BioArray Software Environment.
12  Available at http://base.thep.lu.se/
13 
14  BASE is free software; you can redistribute it and/or
15  modify it under the terms of the GNU General Public License
16  as published by the Free Software Foundation; either version 3
17  of the License, or (at your option) any later version.
18 
19  BASE is distributed in the hope that it will be useful,
20  but WITHOUT ANY WARRANTY; without even the implied warranty of
21  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
22  GNU General Public License for more details.
23 
24  You should have received a copy of the GNU General Public License
25  along with BASE. If not, see <http://www.gnu.org/licenses/>.
26-->
27<chapter id="biomaterials">
28  <?dbhtml dir="biomaterials" filename="index.html" ?>
29
30  <title>Biomaterial LIMS</title>
31
32    <para>
33      The generic term biomaterial refers to any biological material used in an experiment.
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
40      sequence of transformation a source material undergoes until it is in a state compatible
41      for further exeperimental processing. This progression is actually
42      mimicked in the BASE
43      <guimenu>Biomaterial LIMS</guimenu>
44      menu again to insist on this natural progression.
45    </para>
46    <itemizedlist>
47      <listitem>
48        <simpara>
49          Biosources correspond to the native biological entity used in an experiment
50          prior to any treatment.
51        </simpara>
52      </listitem>
53      <listitem>
54        <simpara>
55          Samples are central to BASE to describe the sample processing. So samples can
56          be created from other samples if user want to track sample processing event in a
57          finely granular fashion.
58        </simpara>
59      </listitem>
60      <listitem>
61        <simpara>
62          Extracts correspond to nucleic acid material extracted from a tissue sample or a
63          cell culture sample.
64        </simpara>
65      </listitem>
66    </itemizedlist>
67    <para>
68      BASE allows users to create any of the these entities fairly freely, however it is
69      expected that users will follow the natural path of the laboratory workflow.
70    </para>
71
72 
73  <sect1 id="biomaterials.biosources">
74    <?dbhtml filename="biosources.html" ?>
75    <title>Biosources</title>
76
77
78    <para>
79      Biosources correspond to the native biological entity used in an experiment prior to any treatment.
80      Biosources can be added to BASE by most users and are managed from <menuchoice>
81        <guimenu>Biomaterial LIMS</guimenu>
82        <guimenuitem>Biosources</guimenuitem>
83      </menuchoice>.
84      Use the &gbNew; button to create a new biosource. This brings up the dialog below.
85    </para>
86
87      <figure id="biomaterials.figures.biosource-tab-1">
88        <title>Biosource properties</title>
89        <screenshot>
90          <mediaobject>
91            <imageobject>
92              <imagedata 
93                fileref="figures/biosource-tab-1.png" format="PNG" />
94            </imageobject>
95          </mediaobject>
96        </screenshot>
97      </figure>
98      <helptext external_id="biosource.edit" title="Biosource properties">
99
100        <variablelist>
101          <varlistentry>
102            <term>
103              <guilabel>Name</guilabel>
104            </term>
105            <listitem>
106              <para>
107                This is the only mandatory field. BASE by default assigns
108                <replaceable>New biosource</replaceable>
109                as name but it is advised to provide unique sensible names.
110              </para>
111            </listitem>
112          </varlistentry>
113          <varlistentry>
114            <term>
115              <guilabel>Type</guilabel>
116            </term>
117            <listitem>
118              <para>
119              The subtype of the biosource. The list
120              may evolve depending on additions by the server
121              administrator. Selecting the proper subtype
122              is recommended and enables BASE to automatically guess
123              the most likely subtype when creating child biomaterial.
124              <nohelp>
125              See <xref linkend="subtypes" /> for more information.
126              </nohelp>
127              </para>
128            </listitem>
129          </varlistentry>
130          <varlistentry>
131            <term>
132              <guilabel>External ID</guilabel>
133            </term>
134            <listitem>
135              <para>
136                An external reference identifiers (e.g. a patient identification
137                code) can be supplied using this field.
138              </para>
139            </listitem>
140          </varlistentry>
141          <varlistentry>
142            <term>
143              <guilabel>Description</guilabel>
144            </term>
145            <listitem>
146              <para>A free text description can be supplied using this field.</para>
147            </listitem>
148          </varlistentry>
149        </variablelist>
150        <seeother>
151          <other external_id="annotations.edit">Annotations</other>
152        </seeother>
153      </helptext>
154
155      <para>
156        The <guilabel>Annotations</guilabel> tab allows BASE users to use
157        annotation types to refine biosource description. More about annotating items
158        can be read in <xref linkend="annotations.annotating" />
159      </para>
160
161  </sect1>
162  <sect1 id="biomaterial.samples">
163    <?dbhtml filename="samples.html" ?>
164    <title>Samples</title>
165    <para>
166      Samples result from processing events applied to biosource material or other samples
167      before they are turned into an extract. In other words, samples can be created from
168      biosource items or from one or more sample items. When a sample is created from several
169      other samples, a pooling event is performed.
170    </para>
171    <para>
172      For every step of transformation from biosource to sample, it is possible to provide
173      information about the protocol used to perform this task. It is not enforced in BASE
174      but it should serve as guidance when devising the granularity of the sample processing
175      task. Also, it is good practice to provide protocol information to ensure MIAME
176      compliance.
177    </para>
178    <para>
179      Use
180      <menuchoice>
181        <guimenu>Biomaterial LIMS</guimenu>
182        <guimenuitem>Samples</guimenuitem>
183      </menuchoice>
184      to get to the list of samples.
185    </para>
186   
187    <sect2 id="biomaterial.samples.create">
188      <title>Create sample</title>
189   
190      <para>
191        Beside the common way, using the &gbNew; button, a sample can be created in one of
192        the following ways:
193      </para>
194        <variablelist>
195          <varlistentry>
196            <term>from either biosource list- or single view- page.</term>
197            <listitem>
198              <para>
199                No matter how complex the sample processing phase is, at least one
200                sample has to be anchored to a biosource. Therefore, a natural way
201                to create an sample is to click on
202                <guiicon>
203                  <inlinemediaobject>
204                    <imageobject>
205                      <imagedata fileref="figures/add.png" format="PNG" />
206                    </imageobject>
207                  </inlinemediaobject>
208                </guiicon>
209                in the <guilabel>Samples</guilabel> column of the biosource list view. There is also a
210                corresponding button,
211                <guibutton>New sample&hellip;</guibutton>
212                in the toolbar when viewing a single biosource.
213              </para>
214            </listitem>
215          </varlistentry>
216          <varlistentry>
217            <term>from the sample list page</term>
218            <listitem>
219              <para>
220                Child samples can be created from a single parent by clicking on the
221                <guiicon>
222                  <inlinemediaobject>
223                    <imageobject>
224                      <imagedata fileref="figures/add.png" format="PNG" />
225                    </imageobject>
226                  </inlinemediaobject>
227                </guiicon> icon in the <guilabel>Child samples</guilabel> column.
228                Pooled samples can be created by first selecting the parents
229                from the list of samples and then click the <guibutton>Pool&hellip;</guibutton>
230                button in the toolbar.
231              </para>
232            </listitem>
233          </varlistentry>
234        </variablelist>
235    </sect2>
236     
237    <sect2 id="biomaterial.samples.properties">
238      <title>Sample properties</title>
239        <figure id="biomaterials.figures.biosample-tab-1">
240          <title>Sample properties</title>
241          <screenshot>
242            <mediaobject>
243              <imageobject>
244                <imagedata 
245                  fileref="figures/biosample-tab-1.png" format="PNG" />
246              </imageobject>
247            </mediaobject>
248          </screenshot>
249        </figure>
250        <helptext external_id="sample.edit" title="Edit sample">
251          <variablelist>
252            <varlistentry>
253              <term>
254                <guilabel>Name</guilabel>
255              </term>
256              <listitem>
257                <para>
258                  The sample's name (required). BASE by default assigns names to
259                  samples (by suffixing
260                  <replaceable>s#</replaceable>
261                  when creating a sample from an existing biosource or
262                  <replaceable>New Sample</replaceable>
263                  otherwise) but it is possible to edit at will.
264                </para>
265              </listitem>
266            </varlistentry>
267            <varlistentry>
268              <term>
269                <guilabel>Type</guilabel>
270              </term>
271              <listitem>
272                <para>
273                The subtype of the sample. The list
274                may evolve depending on additions by the server
275                administrator. Selecting the proper subtype
276                is recommended and enables BASE to automatically guess
277                the most likely subtype when creating child biomaterial.
278                <nohelp>
279                See <xref linkend="subtypes" /> for more information.
280                </nohelp>
281                </para>
282              </listitem>
283            </varlistentry>
284            <varlistentry>
285              <term>
286                <guilabel>External ID</guilabel>
287              </term>
288              <listitem>
289                <para>
290                  An identification used to identify the sample outside BASE.
291                </para>
292              </listitem>
293            </varlistentry>
294            <varlistentry>
295              <term>
296                <guilabel>Original quantity</guilabel>
297              </term>
298              <listitem>
299                <para>
300                  This is meant to report information about the actual mass of
301                  sample created.
302                </para>
303              </listitem>
304            </varlistentry>
305            <varlistentry>
306              <term>
307                <guilabel>Created</guilabel>
308              </term>
309              <listitem>
310                <para>
311                  A date when the sample was created. The information can be
312                  important when running quality controls on data and account for
313                  potential confounding factor (e.g. day effect).
314                </para>
315              </listitem>
316            </varlistentry>
317            <varlistentry>
318              <term>
319                <guilabel>Registered</guilabel>
320              </term>
321              <listitem>
322                <para>The date at which the sample was entered in BASE.</para>
323              </listitem>
324            </varlistentry>
325            <varlistentry>
326              <term>
327                <guilabel>Protocol</guilabel>
328              </term>
329              <listitem>
330                <para>The protocol used to produce this sample.</para>
331              </listitem>
332            </varlistentry>
333            <varlistentry>
334              <term>
335                <guilabel>Bioplate</guilabel>
336              </term>
337              <listitem>
338                <para>The bioplate where this sample is located.</para>
339              </listitem>             
340            </varlistentry>
341            <varlistentry>
342              <term>
343                <guilabel>Biowell</guilabel>
344              </term>
345              <listitem>
346                <para>
347                  Biowell that holds this sample.
348                  <guilabel>Bioplate</guilabel> has to be defined before
349                  biowell can be selected.
350                </para>
351              </listitem>             
352            </varlistentry>
353            <varlistentry>
354              <term>
355                <guilabel>Description</guilabel>
356              </term>
357              <listitem>
358                <para>
359                  A text field to report any information that not can be captured
360                  otherwise.
361                </para>
362              </listitem>
363            </varlistentry>
364          </variablelist>
365         
366          <seeother>
367            <other external_id="sample.parents">Parents</other>
368            <other external_id="annotations.edit">Annotations &amp; parameters</other>
369            <other external_id="annotations.edit.inherited">Inherited annotations</other>
370          </seeother>
371        </helptext>
372    </sect2>
373   
374    <sect2 id="biomaterial.samples.parents">
375      <title>Sample parents</title>
376        <figure id="biomaterials.figures.biosample-tab-2">
377          <title>Sample parents</title>
378          <screenshot>
379            <mediaobject>
380              <imageobject>
381                <imagedata 
382                  fileref="figures/biosample-tab-2.png" format="PNG" />
383              </imageobject>
384            </mediaobject>
385          </screenshot>
386        </figure>
387       
388        <helptext external_id="sample.parents" title="Sample's parents">
389          <para>
390            This is meant to keep track of the sample origin. BASE
391            distinguishes between two cases which are controlled by the
392            <guilabel>Parent type</guilabel>
393            radio-button in the edit pop-up window.
394          </para>
395          <itemizedlist>
396            <listitem>
397              <para>
398                If the parent is a biosource the radio-button is set to
399                <guilabel>Biosource</guilabel>. Only a single biosource
400                can be used as the parent. This option is automatically
401                selected if the user selects a biosource with the
402                <guibutton>Select biosource</guibutton> button.
403              </para>
404            </listitem>
405            <listitem>
406              <para>
407                When the parent is one or several other samples the radio-button is
408                set to <guilabel>Sample</guilabel>. This option is automatically
409                selected if the user add samples with the <guibutton>Add samples</guibutton> button.           
410                For each parent sample, it is
411                possible to specify the amount used in µg. This will automatically
412                update the <guilabel>remaining quantity</guilabel> of the parent.
413              </para>
414            </listitem>
415          </itemizedlist>
416         
417          <seeother>
418            <other external_id="sample.edit">Sample properties</other>
419            <other external_id="annotations.edit">Annotations &amp; parameters</other>
420            <other external_id="annotations.edit.inherited">Inherited annotations</other>
421          </seeother>
422        </helptext>
423    </sect2>
424    <para>
425      The <guilabel>Annotations</guilabel> tab allows BASE users to use
426      annotation types to refine sample description. More about annotating items
427      can be read in <xref linkend="annotations.annotating" />
428    </para>
429       
430    <para>
431      This <guilabel>Inherited annotations</guilabel> tab contains a list of those annotations
432      that are inherited from the sample's parents. Information about working with inherited
433      annotations can be found in <xref linkend="annotations.inheriting" />.
434    </para>
435  </sect1>
436
437  <sect1 id="biomaterials.extracts">
438    <?dbhtml filename="extracts.html" ?>
439    <title>Extracts</title>
440    <para>
441      Extract items should be used to describe the events that transform a sample material
442      into an extract material. An extract can be created from one sample item or from one or
443      more extract items. When an extract is created from several other extracts, a pooling
444      event is performed.
445    </para>
446    <para>
447      During the transformation from samples to extracts, it is possible to provide
448      information about the protocol used to perform this task. It is not enforced in BASE
449      but it should serve as guidance when devising the granularity of the sample processing
450      task. Also, it is good practice to provide protocol information.
451    </para>
452    <para>
453      Use
454      <menuchoice>
455        <guimenu>Biomaterial LIMS</guimenu>
456        <guimenuitem>Extracts</guimenuitem>
457      </menuchoice>
458      to get to the list of extracts.
459    </para>
460    <sect2 id="biomaterials.extracts.create">
461      <title>Create extract</title>
462      <para>
463        Beside the common way, using the &gbNew; button, an extract can be created in one of
464        the following ways:
465        <variablelist>
466          <varlistentry>
467            <term>from either sample list- or single view- page.</term>
468            <listitem>
469              <para>
470                No matter how complex the extract processing phase is, at least one
471                extract has to be anchored to a sample. Therefore, a natural way to
472                create an extract is to click on
473                <guiicon>
474                  <inlinemediaobject>
475                    <imageobject>
476                      <imagedata fileref="figures/add.png" format="PNG" />
477                    </imageobject>
478                  </inlinemediaobject>
479                </guiicon>
480                in the <guilabel>Child extracts</guilabel> column for the sample that should be a parent of the
481                extract.  There is also a corresponding button,
482                <guibutton>New child extract&hellip;</guibutton>
483                in the toolbar when viewing a single sample.
484              </para>
485            </listitem>
486          </varlistentry>
487          <varlistentry>
488            <term>from the extract list page</term>
489            <listitem>
490              <para>
491                Child extracts can be created from a single parent by clicking on the
492                <guiicon>
493                  <inlinemediaobject>
494                    <imageobject>
495                      <imagedata fileref="figures/add.png" format="PNG" />
496                    </imageobject>
497                  </inlinemediaobject>
498                </guiicon> icon in the <guilabel>Child extracts</guilabel> column.
499                Pooled extract can be created by first selecting the parents
500                from the list of extracts and then press
501                <guibutton>Pool&hellip;</guibutton>
502                in the toolbar. The selected extracts will be put into the parent
503                property.
504              </para>
505            </listitem>
506          </varlistentry>
507        </variablelist>
508      </para>
509    </sect2>
510    <sect2 id="biomaterials.extracts.properties">
511      <title>Extract properties</title>
512     
513        <figure id="biomaterials.figures.extract-tab-1">
514          <title>Extract properties</title>
515          <screenshot>
516            <mediaobject>
517              <imageobject>
518                <imagedata 
519                  fileref="figures/extract-tab-1.png" format="PNG" />
520              </imageobject>
521            </mediaobject>
522          </screenshot>
523        </figure>
524        <helptext external_id="extract.edit" title="Edit extract">
525          <variablelist>
526            <varlistentry>
527              <term>
528                <guilabel>Name</guilabel>
529              </term>
530              <listitem>
531                <para>
532                  A mandatory field for providing the extract name. BASE by
533                  default assigns names to extract (by suffixing
534                  <replaceable>e#</replaceable>
535                  when creating an extract from an existing sample or
536                  <replaceable>New extract</replaceable>
537                  otherwise) but it is possible to edit it at will.
538                </para>
539              </listitem>
540            </varlistentry>
541            <varlistentry>
542              <term>
543                <guilabel>Type</guilabel>
544              </term>
545              <listitem>
546                <para>
547                The subtype of the extract. The list
548                may evolve depending on additions by the server
549                administrator. Selecting the proper subtype
550                is recommended and enables BASE to automatically guess
551                the most likely subtype when creating child biomaterial and
552                bioassays.
553                <nohelp>
554                See <xref linkend="subtypes" /> for more information.
555                </nohelp>
556                </para>
557              </listitem>
558            </varlistentry>
559            <varlistentry>
560              <term>
561                <guilabel>Tag</guilabel>
562              </term>
563              <listitem>
564                <para>
565                  If the extract has been marked with a tag, select it here. Note
566                  that the subtype of the extract usually limits what kind of tag
567                  that can be used. For example, a <emphasis>labeled extract</emphasis>
568                  should be tagged with a <emphasis>label</emphasis>.
569                </para>
570              </listitem>
571            </varlistentry>
572            <varlistentry>
573              <term>
574                <guilabel>External ID</guilabel>
575              </term>
576              <listitem>
577                <para>The extracts identification outside BASE</para>
578              </listitem>
579            </varlistentry>
580            <varlistentry>
581              <term>
582                <guilabel>Original quantity</guilabel>
583              </term>
584              <listitem>
585                <para>
586                  Holds information about the original mass of the created
587                  extract.
588                </para>
589              </listitem>
590            </varlistentry>
591            <varlistentry>
592              <term>
593                <guilabel>Created</guilabel>
594              </term>
595              <listitem>
596                <para>
597                  The date when the extract was created. The information can be
598                  important when running quality controls on data and account for
599                  potential confounding factor (e.g. day effect)
600                </para>
601              </listitem>
602            </varlistentry>
603            <varlistentry>
604              <term>
605                <guilabel>Registered</guilabel>
606              </term>
607              <listitem>
608                <para>
609                  This is automatically populated with a date at which the sample
610                  was entered in BASE system.
611                </para>
612              </listitem>
613            </varlistentry>
614            <varlistentry>
615              <term>
616                <guilabel>Protocol</guilabel>
617              </term>
618              <listitem>
619                <para>
620                  The extraction protocol that was used to produce the extract.
621                </para>
622              </listitem>
623            </varlistentry>
624            <varlistentry>
625              <term>
626                <guilabel>Bioplate</guilabel>
627              </term>
628              <listitem>
629                <para>The bioplate where this extract is located.</para>
630              </listitem>             
631            </varlistentry>
632            <varlistentry>
633              <term>
634                <guilabel>Biowell</guilabel>
635              </term>
636              <listitem>
637                <para>
638                  Biowell that holds this extract.
639                  <guilabel>Bioplate</guilabel> has to be defined before
640                  biowell can be selected.
641                </para>
642              </listitem>             
643            </varlistentry>
644            <varlistentry>
645              <term>
646                <guilabel>Description</guilabel>
647              </term>
648              <listitem>
649                <para>
650                  A text field to report any information that not can be captured
651                  otherwise.
652                </para>
653              </listitem>
654            </varlistentry>
655          </variablelist>
656          <seeother>
657            <other external_id="extract.parents">Parents</other>
658            <other external_id="annotations.edit">Annotations &amp; parameters</other>
659            <other external_id="annotations.edit.inherited">Inherited annotations</other>
660          </seeother>
661        </helptext>
662  </sect2>
663 
664  <sect2 id="biomaterials.extracts.parents">
665    <title>Extract parents</title>
666        <figure id="biomaterials.figures.extract-tab-2">
667          <title>Extract parents</title>
668          <screenshot>
669            <mediaobject>
670              <imageobject>
671                <imagedata 
672                  fileref="figures/extract-tab-2.png" format="PNG" />
673              </imageobject>
674            </mediaobject>
675          </screenshot>
676        </figure>
677        <helptext external_id="extract.parents" title="Extract's parents">
678          <para>
679            This is meant to keep track of the extract origin. BASE
680            distinguishes between two cases which are controlled by the
681            <guilabel>Parent type</guilabel>
682            radio-button in the edit pop-up window.
683          </para>
684          <itemizedlist>
685            <listitem>
686              <para>
687                If the parent is a sample the radio-button is set to
688                <guilabel>Sample</guilabel>. Only a single sample
689                can be used as the parent. This option is automatically
690                selected if the user selects a sample with the
691                <guibutton>Select sample</guibutton> button.
692              </para>
693            </listitem>
694            <listitem>
695              <para>
696                When the parent is one or several other extracts the radio-button is
697                set to <guilabel>Extract</guilabel>. This option is automatically
698                selected if the user add extracts with the <guibutton>Add extracts</guibutton> button.           
699              </para>
700            </listitem>
701          </itemizedlist>
702         
703          <para>
704            For each parent item, it is
705            possible to specify the amount used in micrograms. This will automatically
706            update the <guilabel>remaining quantity</guilabel> of the parent.
707          </para>
708         
709          <seeother>
710            <other external_id="extract.edit">Extract properties</other>
711            <other external_id="annotations.edit">Annotations &amp; parameters</other>
712            <other external_id="annotations.edit.inherited">Inherited annotations</other>
713          </seeother>
714        </helptext>
715
716    <para>
717      The <guilabel>Annotations</guilabel> tab allows BASE users to use
718      annotation types to refine extract description. More about annotating items
719      can be read in <xref linkend="annotations.annotating" />
720    </para>
721       
722    <para>
723      This <guilabel>Inherited annotations</guilabel> tab contains a list of those annotations
724      that are inherited from the extract's parents. Information about working with inherited
725      annotations can be found in <xref linkend="annotations.inheriting" />.
726    </para>
727
728
729  </sect2>
730
731
732  </sect1>
733
734  <sect1 id="biomaterials.tags">
735    <?dbhtml filename="tags.html" ?>
736    <title>Tags</title>
737    <para>
738      Before attempting to create tagged extracts, users should make sure that the
739      appropriate tag object is present in BASE. To browse the list of tags, go to
740      <menuchoice>
741        <guimenu>Biomaterial LIMS</guimenu>
742        <guimenuitem>Tags</guimenuitem>
743      </menuchoice>
744    </para>
745
746    <figure id="biomaterials.figures.tags">
747      <title>Tag properties</title>
748      <screenshot>
749        <mediaobject>
750          <imageobject>
751            <imagedata 
752              fileref="figures/edit_tag.png" format="PNG" />
753          </imageobject>
754        </mediaobject>
755      </screenshot>
756    </figure>
757
758    <helptext external_id="tag.edit" title="Edit tag">
759      <para>
760        The tag item is very simple and does not need much explanation. There are only
761        a few properties for a tag.
762        <variablelist>
763          <varlistentry>
764            <term>
765              <guilabel>Name</guilabel>
766            </term>
767            <listitem>
768              <para>The name of the tag (required).</para>
769            </listitem>
770          </varlistentry>
771          <varlistentry>
772            <term>
773              <guilabel>Type</guilabel>
774            </term>
775            <listitem>
776              <para>
777              The subtype of the tag. The list
778              may evolve depending on additions by the server
779              administrator. Selecting the proper subtype
780              is important and enables BASE to automatically guess
781              the most likely tag when creating tagged extracts (eg.
782              a <emphasis>Label</emphasis> for a <emphasis>Labeled extract</emphasis> 
783              or a <emphasis>Barcode</emphasis> for a <emphasis>Library</emphasis>).
784              <nohelp>
785              See <xref linkend="subtypes" /> for more information.
786              </nohelp>
787              </para>
788            </listitem>
789          </varlistentry>
790          <varlistentry>
791            <term>
792              <guilabel>Description</guilabel>
793            </term>
794            <listitem>
795              <para>
796                An explaining text or other information associated with the
797                tag.
798              </para>
799            </listitem>
800          </varlistentry>
801        </variablelist>
802      </para>
803    </helptext>
804
805  </sect1>
806
807 
808  <sect1 id="biomaterials.bioplates">
809    <?dbhtml filename="bioplates.html" ?>
810    <title>Bioplates</title>
811    <para>
812      With bioplates it is possible to organize biomaterial such as samples and extracts
813      into wells. Each plate has a number of wells that is defined by the plate geometry.
814    </para>
815    <para>
816      Use
817      <menuchoice>
818        <guimenu>Biomaterial LIMS</guimenu>
819        <guimenuitem>Bioplates</guimenuitem>
820      </menuchoice>
821      to get to the list of bioplates.   
822    </para>
823    <sect2 id="biomaterials.bioplate.properties">
824      <title>Bioplate properties</title>     
825
826      <figure id="biomaterials.figures.bioplate-tab-1">
827        <title>Bioplate properties</title>
828        <screenshot>
829          <mediaobject>
830            <imageobject>
831              <imagedata 
832                fileref="figures/bioplate-tab-1.png" format="PNG" />
833            </imageobject>
834          </mediaobject>
835        </screenshot>
836      </figure>
837
838      <helptext external_id="bioplate.edit" title="Edit bioplate">
839        <para>
840          <variablelist>
841            <varlistentry>
842              <term><guilabel>Name</guilabel></term>
843              <listitem>
844                <para>
845                  The bioplate name. The name does not have to be unique but it is
846                  recommended to keep it unique. BASE by default assigns
847                  <replaceable>New bioplate</replaceable> as name.
848                  This field is mandatory.
849                </para>
850              </listitem>
851            </varlistentry>
852            <varlistentry>
853              <term><guilabel>Bioplate type</guilabel></term>
854              <listitem>
855                <para>
856                  The type of the bioplate may be a generic storage plate that
857                  can store any type of biomaterial or a locked plate that
858                  can only store a single type of biomaterial. This field
859                  is mandatory and can only be set for new bioplates.
860                  <nohelp>See <xref linkend="biomaterials.bioplatetypes" /> for more
861                  information.</nohelp>
862                </para>
863              </listitem>             
864            </varlistentry>
865            <varlistentry>
866              <term><guilabel>Plate geometry</guilabel></term>
867              <listitem>
868                <para>
869                  Information about the plate design defining the
870                  number of  rows and columns on the bioplate.
871                  This field is mandatory and can only be set for new bioplates.
872                </para>
873              </listitem>             
874            </varlistentry>
875            <varlistentry>
876              <term><guilabel>Storage location</guilabel></term>
877              <listitem>
878                <para>The location, for example a freezer, where the bioplate is stored. Optional.</para>
879              </listitem>
880            </varlistentry>
881            <varlistentry>
882              <term><guilabel>Section</guilabel></term>
883              <listitem>
884                <para>The section within the freezer where the bioplate is stored. Optional.</para>
885              </listitem>
886            </varlistentry>
887            <varlistentry>
888              <term><guilabel>Tray</guilabel></term>
889              <listitem>
890                <para>The tray within the section where the bioplate is stored. Optional.</para>
891              </listitem>
892            </varlistentry>
893            <varlistentry>
894              <term><guilabel>Position</guilabel></term>
895              <listitem>
896                <para>The position within the tray where the bioplate is stored. Optional.</para>
897              </listitem>
898            </varlistentry>
899            <varlistentry>
900              <term><guilabel>Barcode</guilabel></term>
901              <listitem>
902                <para>
903                  Barcode of the bioplate.
904                  Optional.
905                </para>
906              </listitem>
907            </varlistentry>
908            <varlistentry>
909              <term><guilabel>Description</guilabel></term>
910              <listitem>
911                <para>
912                  Other useful information about the bioplate. Optional.
913                </para>
914              </listitem>
915            </varlistentry>
916          </variablelist>
917        </para>
918       
919        <seeother>
920          <other external_id="annotations.edit">Annotations</other>
921        </seeother>
922      </helptext>
923     
924    <para>
925      The <guilabel>Annotations</guilabel> tab allows BASE users to use
926      annotation types to refine bioplate description. More about annotating items
927      can be read in <xref linkend="annotations.annotating" />
928    </para>
929
930    </sect2>
931    <sect2 id="biomaterials.bioplate.biowells">
932      <title>Biowells</title>
933      <para>
934        Biowells existence are managed through the bioplate they
935        belong to. Creating a bioplate will automatically create the
936        biowells (as given by the selected geometry) on the plate.
937        The wells are initially empty. To add biomaterial to the plate
938        go to the single-item view page for the bioplate. This page
939        includes an overview of the layout of the plate. Clicking
940        on an empty well will open a popup dialog that allows you
941        to select a biomaterial. The same dialog can also be accessed from
942        the <guilabel>Wells</guilabel> tab. Assigning a biomaterial to a
943        biowell can also be done when editing a sample or extract, or
944        by using the <link linkend="biomaterials.placeonplate">Place-on-plate
945        wizard</link>.
946      </para>
947     
948      <figure id="biomaterials.figures.biowell">
949        <title>Biowell properties</title>
950        <screenshot>
951          <mediaobject>
952            <imageobject>
953              <imagedata 
954                fileref="figures/biowell.png" format="PNG" />
955            </imageobject>
956          </mediaobject>
957        </screenshot>
958      </figure>
959
960        <helptext external_id="biowell.edit" title="Edit biowell">
961          <para>
962            <variablelist>
963              <varlistentry>
964                <term><guilabel>Bioplate</guilabel></term>
965                <listitem>
966                  <para>
967                    Shows which bioplate the biowell is located on.
968                    This property is read-only.
969                  </para>
970                </listitem>
971              </varlistentry>
972              <varlistentry>             
973                <term><guilabel>Well location</guilabel></term>
974                <listitem>
975                  <para>
976                    The biowell location on the bioplate in row+column format.
977                    This property is read-only.
978                  </para>
979                </listitem>
980              </varlistentry>
981              <varlistentry>
982                <term><guilabel>Biomaterial type</guilabel></term>
983                <listitem>
984                  <para>
985                    The type of biomaterial stored in this biowell. This
986                    property must be selected before before a
987                    biomaterial can be selected. On some plates this
988                    is locked due to settings in the bioplate's type.
989                  </para>
990                </listitem>
991              </varlistentry>
992              <varlistentry>             
993                <term><guilabel>Biomaterial</guilabel></term>
994                <listitem>
995                  <para>
996                    Name of the biomaterial in this biowell. Before changing
997                    this you must select the appropriate <guilabel>Biomaterial type</guilabel>.
998                    A biomaterial can only be placed in a single well. If the selected
999                    biomaterial is already placed in another location it will be moved.
1000                  </para>
1001                </listitem>
1002              </varlistentry>
1003            </variablelist>
1004          </para>
1005        </helptext> 
1006    </sect2>
1007   
1008    <sect2 id="biomaterials.bioplatetypes">
1009      <title>Bioplate types</title>
1010     
1011      <helptext external_id="bioplatetype.view.properties" title="Bioplate types">
1012      <para>
1013        Bioplate types are used to subclassify bioplates and may put restrictions on them.
1014        BASE ships with a few pre-defined bioplate types. The <emphasis>Storage plate</emphasis> type
1015        is a generic plate type that can be used for all types of biomaterial and doesn't
1016        have any other restrictions on it. The reaction plate types are locked to a single
1017        type of biomaterial and have a restriction that biomaterial can never be moved out from
1018        a well once it has been placed there.
1019      </para>
1020      </helptext>
1021     
1022      <figure id="biomaterials.figures.bioplatetype">
1023        <title>Bioplate type properties</title>
1024        <screenshot>
1025          <mediaobject>
1026            <imageobject>
1027              <imagedata 
1028                fileref="figures/edit_bioplatetype.png" format="PNG" />
1029            </imageobject>
1030          </mediaobject>
1031        </screenshot>
1032      </figure>
1033     
1034          <helptext external_id="bioplatetype.edit" title="Edit bioplate type">
1035          <para>
1036            <variablelist>
1037              <varlistentry>
1038                <term><guilabel>Name</guilabel></term>
1039                <listitem>
1040                  <para>
1041                    The name of the bioplate type.
1042                  </para>
1043                </listitem>
1044              </varlistentry>
1045              <varlistentry>             
1046                <term><guilabel>Biomaterial type</guilabel></term>
1047                <listitem>
1048                  <para>
1049                    Select if bioplates using this type should be locked to
1050                    specific biomaterial type or not. This property can only
1051                    be set for new bioplate types.
1052                  </para>
1053                </listitem>
1054              </varlistentry>
1055              <varlistentry>             
1056                <term><guilabel>Biomaterial subtype</guilabel></term>
1057                <listitem>
1058                  <para>
1059                    If a specific biomaterial type has been selected
1060                    it is also possible to further restrict the use
1061                    of the bioplate to a certain biomaterial subtype.
1062                    The restriction is not enforced by the core but is mainly used
1063                    by the gui to provide smart filters in selection
1064                    lists, in the bioplate event wizards, etc.
1065                  </para>
1066                </listitem>
1067              </varlistentry>
1068              <varlistentry>             
1069                <term><guilabel>Storage type</guilabel></term>
1070                <listitem>
1071                  <para>
1072                    The subtype of the hardware item (eg. freezer, cabinet)
1073                    where bioplates with this bioplate type usually are stored.
1074                  </para>
1075                </listitem>
1076              </varlistentry>
1077              <varlistentry>
1078                <term><guilabel>Well lock mode</guilabel></term>
1079                <listitem>
1080                  <para>
1081                    This option controls the wells on bioplates using this type.
1082                    There are four options:
1083                    <itemizedlist>
1084                      <listitem>
1085                        <para><guilabel>Unlocked</guilabel>:
1086                          The wells are unlocked and biomaterial can be added
1087                          and removed freely any number of times.
1088                        </para>
1089                      </listitem>
1090                      <listitem>
1091                        <para><guilabel>Locked after add+clear</guilabel>:
1092                          A biomaterial can be placed once in the well and
1093                          then moved to another bioplate. After that the well
1094                          becomes locked and it is not possible to add a
1095                          different biomaterial to it.
1096                        </para>
1097                      </listitem>
1098                      <listitem>
1099                        <para><guilabel>Locked after add</guilabel>:
1100                          The wells are locked as soon as biomaterial is
1101                          added to them. The biomaterial can't be moved to another
1102                          place or be replaced with other biomaterial.
1103                        </para>
1104                      </listitem>
1105                      <listitem>
1106                        <para><guilabel>Locked at plate creation</guilabel>:
1107                          The wells are locked as soon as the bioplate has been
1108                          saved to the database. This lock mode is primarily intended
1109                          to be used when plug-ins are creating and populating the
1110                          bioplate as a single event.
1111                        </para>
1112                      </listitem>
1113                    </itemizedlist>
1114                  </para>
1115                </listitem>
1116              </varlistentry>
1117              <varlistentry>             
1118                <term><guilabel>Description</guilabel></term>
1119                <listitem>
1120                  <para>
1121                    Other useful information about the bioplate type. Optional.
1122                  </para>
1123                </listitem>
1124              </varlistentry>
1125            </variablelist>
1126          </para>
1127        </helptext> 
1128    </sect2>
1129   
1130    <sect2 id="biomaterials.bioplateevents">
1131      <title>Bioplate events</title>
1132   
1133      <para>
1134        Certain actions can be applied collectively to the biomaterial on a bioplate,
1135        either as a whole or a subset that is picked by the user.
1136        A list of the available actions can be found on the list page
1137        <menuchoice>
1138          <guimenu>Biomaterial LIMS</guimenu>
1139          <guimenuitem>Bioplate event types</guimenuitem>
1140        </menuchoice>.
1141       
1142        Although it is possible to create more event types here there is usually no
1143        meaning to do so, since each event needs a specailized GUI wizard to take
1144        care of it. The possibility to add more event types should be seen as an
1145        opportunity for extension development.
1146      </para>
1147     
1148      <sect3 id="biomaterials.placeonplate">
1149        <title>The place-on-plate event</title>
1150     
1151        <figure id="biomaterials.figures.placeonplate">
1152          <title>Place on plate wizard</title>
1153          <screenshot>
1154            <mediaobject>
1155              <imageobject>
1156                <imagedata 
1157                  fileref="figures/place_on_plate.png" format="PNG" />
1158              </imageobject>
1159            </mediaobject>
1160          </screenshot>
1161        </figure>
1162     
1163        <helptext external_id="bioplateevent.place-on-plate" title="Place on plate">
1164        <para>
1165          This event is available on the sample and extract list pages and can be used
1166          to place multiple biomaterial on a bioplate in one go. Click on
1167          the <guibutton>Place on plate</guibutton> button to start the wizard.
1168          The wizard will automatically use the selected biomaterials or, if none
1169          are selected, all listed biomaterials that aren't alredy located on a
1170          plate.
1171
1172          <variablelist>
1173            <varlistentry>
1174              <term><guilabel>Event name</guilabel></term>
1175              <listitem>
1176                <para>
1177                  Give a name to the event, or keep the suggested name.
1178                </para>
1179              </listitem>
1180            </varlistentry>
1181            <varlistentry>
1182              <term><guilabel>Event date</guilabel></term>
1183              <listitem>
1184                <para>
1185                  The date of the event.
1186                </para>
1187              </listitem>
1188            </varlistentry>
1189            <varlistentry>
1190              <term><guilabel>Protocol</guilabel></term>
1191              <listitem>
1192                <para>
1193                  The protocol used in the event, if any.
1194                </para>
1195              </listitem>
1196            </varlistentry>
1197            <varlistentry>
1198              <term><guilabel>Hardware</guilabel></term>
1199              <listitem>
1200                <para>
1201                  The hardware item used in the event, if any.
1202                </para>
1203              </listitem>
1204            </varlistentry>
1205            <varlistentry>
1206              <term><guilabel>Description</guilabel></term>
1207              <listitem>
1208                <para>
1209                  Other comments about the event.
1210                </para>
1211              </listitem>
1212            </varlistentry>
1213            <varlistentry>
1214              <term><guilabel>Select plate...</guilabel></term>
1215              <listitem>
1216                <para>
1217                  You need to select an existing plate on which the
1218                  biomaterial should be placed. It is only possible to
1219                  use one plate in each event. If you want to place biomaterial
1220                  on more than one plate, the wizard must be repeated for
1221                  each destination plate.
1222                </para>
1223              </listitem>
1224            </varlistentry>
1225            <varlistentry>
1226              <term><guilabel>Clear</guilabel></term>
1227              <listitem>
1228                <para>
1229                  Clear all current placement.
1230                </para>
1231              </listitem>
1232            </varlistentry>
1233            <varlistentry>
1234              <term><guilabel>Place by row/column</guilabel></term>
1235              <listitem>
1236                <para>
1237                  Automatically place the remaining biomaterial by filling empty wells,
1238                  starting with rows or columns.
1239                </para>
1240              </listitem>
1241            </varlistentry>
1242            <varlistentry>
1243              <term><guilabel>Items to place</guilabel></term>
1244              <listitem>
1245                <para>
1246                  This column contains the biomaterial that should be placed on the plate.
1247                  When a destination plate has been selected, it is displayed as a grid to
1248                  the right. To place a biomaterial either use the <guibutton>Place by row</guibutton>
1249                  or <guibutton>Place by column</guibutton> buttons, or select an item in this
1250                  list. When an item has been selected, click on the destination well on the
1251                  plate. The coordinate of the well is displayed in the gray area before the
1252                  biomaterial name and a line is drawn between it and the destination well.
1253                  The destination well is also marked with an icon.
1254                  If the <guilabel>Auto-select next unmapped item</guilabel> is selected
1255                  the selection is automatically moved to the next biomaterial which can then
1256                  be placed by selecting another destination well. If a mistake is made it is
1257                  easy to correct. Simply re-select the item and then click on the correct well.
1258                </para>
1259              </listitem>
1260            </varlistentry>
1261
1262          </variablelist>
1263         
1264          When the biomaterial has been placed on the plate (it is not neccessary to place all of them)
1265          click on <guibutton>Save</guibutton> to store everything. BASE will create a plate event
1266          for the selected destination plate and "other"-type events for each biomaterial that was
1267          placed on it.
1268        </para>
1269        </helptext> 
1270      </sect3>
1271
1272      <sect3 id="biomaterials.move">
1273        <title>The move biomaterials event</title>
1274     
1275        <figure id="biomaterials.figures.move">
1276          <title>Move biomaterials wizard</title>
1277          <screenshot>
1278            <mediaobject>
1279              <imageobject>
1280                <imagedata 
1281                  fileref="figures/move_biomaterials.png" format="PNG" />
1282              </imageobject>
1283            </mediaobject>
1284          </screenshot>
1285        </figure>
1286     
1287        <helptext external_id="bioplateevent.move" title="Move biomaterials">
1288        <para>
1289          This event is available on the single-item view page of a bioplate
1290          and can be used to move biomaterial from one plate to another. Click on
1291          the <guibutton>Move biomaterial</guibutton> button to start the wizard.
1292          <variablelist>
1293            <varlistentry>
1294              <term><guilabel>Event name</guilabel></term>
1295              <listitem>
1296                <para>
1297                  Give a name to the event, or keep the suggested name.
1298                </para>
1299              </listitem>
1300            </varlistentry>
1301            <varlistentry>
1302              <term><guilabel>Event date</guilabel></term>
1303              <listitem>
1304                <para>
1305                  The date of the event.
1306                </para>
1307              </listitem>
1308            </varlistentry>
1309            <varlistentry>
1310              <term><guilabel>Protocol</guilabel></term>
1311              <listitem>
1312                <para>
1313                  The protocol used in the event, if any.
1314                </para>
1315              </listitem>
1316            </varlistentry>
1317            <varlistentry>
1318              <term><guilabel>Hardware</guilabel></term>
1319              <listitem>
1320                <para>
1321                  The hardware item used in the event, if any.
1322                </para>
1323              </listitem>
1324            </varlistentry>
1325            <varlistentry>
1326              <term><guilabel>Description</guilabel></term>
1327              <listitem>
1328                <para>
1329                  Other comments about the event.
1330                </para>
1331              </listitem>
1332            </varlistentry>
1333            <varlistentry>
1334              <term><guilabel>Select plate...</guilabel></term>
1335              <listitem>
1336                <para>
1337                  You need to select an existing plate to which the
1338                  biomaterial should be moved. It is only possible to
1339                  use one plate in each event. If you want to move biomaterial
1340                  to more than one plate, the wizard must be repeated for
1341                  each destination plate.
1342                </para>
1343              </listitem>
1344            </varlistentry>
1345            <varlistentry>
1346              <term><guilabel>Clear</guilabel></term>
1347              <listitem>
1348                <para>
1349                  Clear all current mapping between the source and destination plates.
1350                </para>
1351              </listitem>
1352            </varlistentry>
1353            <varlistentry>
1354              <term><guilabel>Place by row/column</guilabel></term>
1355              <listitem>
1356                <para>
1357                  Automatically move the remaining biomaterial by filling empty wells,
1358                  starting with rows or columns.
1359                </para>
1360              </listitem>
1361            </varlistentry>
1362            <varlistentry>
1363              <term><guilabel>Predefined mapping</guilabel></term>
1364              <listitem>
1365                <para>
1366                  Use this button to select a predefined mapping between source
1367                  and destination wells. The biomaterial will be moved according
1368                  to the mapping.
1369                </para>
1370              </listitem>
1371            </varlistentry>
1372            <varlistentry>
1373              <term><guilabel>Source plate</guilabel></term>
1374              <listitem>
1375                <para>
1376                  This displays the source plate as a grid with icons that indicate
1377                  filled and movable wells.
1378                 
1379                  When a destination plate has been selected, it is displayed as a similar grid to
1380                  the right. To move a biomaterial either use the <guibutton>Place by row</guibutton>,
1381                  <guibutton>Place by column</guibutton> or <guibutton>Predefined mapping</guibutton>
1382                  buttons, or select a well on the source plate. When a source well has been selected,
1383                  click on a well on the destination plate. A line is drawn between the source and
1384                  destination wells and the icons are updated to show what is going on. The
1385                  wells on the destination plate will also show the coordinate of the mapped
1386                  source well unless the <guilabel>Show source coordinates</guilabel>
1387                  checkbox is deselected. If a mistake is made it is
1388                  easy to correct. Simply re-select the source well and then click on the correct
1389                  destination well.
1390                   
1391                </para>
1392              </listitem>
1393            </varlistentry>
1394          </variablelist>
1395
1396          When the biomaterial has been mapped between the source and destination plates
1397          (it is not neccessary to map all of them) click on <guibutton>Save</guibutton> to store everything.
1398          BASE will create a plate event for the selected plates and "other"-type events for each
1399          biomaterial that was moved.
1400
1401        </para>
1402        </helptext>
1403      </sect3>
1404     
1405      <sect3 id="biomaterials.create_child">
1406        <title>The create child plate event</title>
1407     
1408        <figure id="biomaterials.figures.create_child_1">
1409          <title>Create child plate wizard - step 1</title>
1410          <screenshot>
1411            <mediaobject>
1412              <imageobject>
1413                <imagedata 
1414                  fileref="figures/create_child_plate_1.png" format="PNG" />
1415              </imageobject>
1416            </mediaobject>
1417          </screenshot>
1418        </figure>
1419     
1420        <helptext external_id="bioplateevent.create-child-1" title="Create child plate - step 1">
1421        <para>
1422          This event is available on the single-item view page of a bioplate
1423          when the bioplate is limited to a single type of biomaterial (eg.
1424          only samples or only extracts). The event is used to create either
1425          a child bioplate with biomaterial that is derived from the biomaterial
1426          on the parent plate or to create one or more physical bioassays. Click on
1427          the <guibutton>Create child bioplate</guibutton> button to start the wizard.
1428        </para>
1429       
1430        <para>
1431          The wizard has two steps. In the first step you set properties that
1432          are related to the event and to the creation of child plates and
1433          biomaterial. The first step is divied into three main sections.
1434        </para>
1435       
1436       
1437        <bridgehead>Event</bridgehead>
1438       
1439        <variablelist>
1440          <varlistentry>
1441            <term><guilabel>Event name</guilabel></term>
1442            <listitem>
1443              <para>
1444                Give a name to the event, or keep the suggested name.
1445              </para>
1446            </listitem>
1447          </varlistentry>
1448          <varlistentry>
1449            <term><guilabel>Event date</guilabel></term>
1450            <listitem>
1451              <para>
1452                The date of the event.
1453              </para>
1454            </listitem>
1455          </varlistentry>
1456          <varlistentry>
1457            <term><guilabel>Protocol</guilabel></term>
1458            <listitem>
1459              <para>
1460                The protocol used in the event, if any.
1461              </para>
1462            </listitem>
1463          </varlistentry>
1464          <varlistentry>
1465            <term><guilabel>Hardware</guilabel></term>
1466            <listitem>
1467              <para>
1468                The hardware item used in the event, if any.
1469              </para>
1470            </listitem>
1471          </varlistentry>
1472          <varlistentry>
1473            <term><guilabel>Description</guilabel></term>
1474            <listitem>
1475              <para>
1476                Other comments about the event.
1477              </para>
1478            </listitem>
1479          </varlistentry>
1480        </variablelist>
1481         
1482        <bridgehead>Child biomaterial</bridgehead>
1483        <variablelist>
1484          <varlistentry>
1485            <term><guilabel>Type</guilabel></term>
1486            <listitem>
1487              <para>
1488                The type of child items to create. If the source plate
1489                contains samples, you can select between sample and
1490                extract and if the source plate contains extract you
1491                can select between extract and physical bioassay.
1492              </para>
1493            </listitem>
1494          </varlistentry>
1495          <varlistentry>
1496            <term><guilabel>Subtype</guilabel></term>
1497            <listitem>
1498              <para>
1499                The subtype to assign to the newly created biomaterial
1500                (or physical bioassay). The list of options is automatically
1501                updated based on the selection in the <guilabel>Type</guilabel>
1502                list.
1503              </para>
1504            </listitem>
1505          </varlistentry>
1506          <varlistentry>
1507            <term><guilabel>Tag</guilabel></term>
1508            <listitem>
1509              <para>
1510                Visible when creating child extracts only. Select the tag to
1511                assign to the new extract. If no tag is selected and the
1512                source biomaterial is also extracts, the children will get the
1513                same tag as their parents.
1514              </para>
1515            </listitem>
1516          </varlistentry>
1517          <varlistentry>
1518            <term><guilabel>Original quantity</guilabel></term>
1519            <listitem>
1520              <para>
1521                The original quantity of the new biomaterial. Not visible when
1522                creating a physical bioassay.
1523              </para>
1524            </listitem>
1525          </varlistentry>
1526          <varlistentry>
1527            <term><guilabel>Used quantity</guilabel></term>
1528            <listitem>
1529              <para>
1530                The quantity that was used from the parent biomaterial
1531                in the process of creating child biomaterial.
1532              </para>
1533            </listitem>
1534          </varlistentry>
1535          <varlistentry>
1536            <term><guilabel>Description</guilabel></term>
1537            <listitem>
1538              <para>
1539                Other comments about the new biomaterial.
1540              </para>
1541            </listitem>
1542          </varlistentry>
1543        </variablelist>
1544       
1545       
1546        <bridgehead>Child plates</bridgehead>
1547        <variablelist>
1548          <varlistentry>
1549            <term><guilabel>No. of plates</guilabel></term>
1550            <listitem>
1551              <para>
1552                The number of child plates to create. The default value is 1.
1553              </para>
1554            </listitem>
1555          </varlistentry>
1556          <varlistentry>
1557            <term><guilabel>Name prefix</guilabel></term>
1558            <listitem>
1559              <para>
1560                The child plates will be named using the prefix plus a running number
1561                starting with 0. Eg. New plate.0.
1562              </para>
1563            </listitem>
1564          </varlistentry>
1565          <varlistentry>
1566            <term><guilabel>Geometry</guilabel></term>
1567            <listitem>
1568              <para>
1569                The geometry of the child plates. The default is the same
1570                geometry as the parent plate. This option is replaced with
1571                <guilabel>Size of bioassay</guilabel> when creating a
1572                physical bioassay.
1573              </para>
1574            </listitem>
1575          </varlistentry>
1576          <varlistentry>
1577            <term><guilabel>Plate type</guilabel></term>
1578            <listitem>
1579              <para>
1580                The plate type of the child plates. Not used when creating a
1581                physical bioassay.
1582              </para>
1583            </listitem>
1584          </varlistentry>
1585          <varlistentry>
1586            <term><guilabel>Freezer</guilabel></term>
1587            <listitem>
1588              <para>
1589                The freezer in which the new child plates are located. Not used
1590                when creating a physical bioassay.
1591              </para>
1592            </listitem>
1593          </varlistentry>
1594          <varlistentry>
1595            <term><guilabel>Description</guilabel></term>
1596            <listitem>
1597              <para>
1598                Other comments about the new child plates.
1599              </para>
1600            </listitem>
1601          </varlistentry>
1602        </variablelist>
1603       
1604        <seeother>
1605          <other external_id="bioplateevent.create-child-2">Create child plate - step 2</other>
1606        </seeother>
1607        </helptext>
1608
1609        <figure id="biomaterials.figures.create_child_2">
1610          <title>Create child plate wizard - step 2</title>
1611          <screenshot>
1612            <mediaobject>
1613              <imageobject>
1614                <imagedata 
1615                  fileref="figures/create_child_plate_2.png" format="PNG" />
1616              </imageobject>
1617            </mediaobject>
1618          </screenshot>
1619        </figure>
1620     
1621        <helptext external_id="bioplateevent.create-child-2" title="Create child plate - step 2">
1622        <para>
1623          The second step display the source plate and new child plates as a grid.
1624          To create child biomaterial either use the <guibutton>Place by row</guibutton>,
1625          <guibutton>Place by column</guibutton> or <guibutton>Predefined mapping</guibutton>
1626          buttons, or select a well on the source plate. When a source well has been selected,
1627          click on a well on the destination plate. A line is drawn between the source and
1628          destination wells and the icons are updated to show what is going on. The
1629          wells on the destination plate will also show the coordinate of the mapped
1630          source well unless the <guilabel>Show source coordinates</guilabel>
1631          checkbox is deselected. If a mistake is made it is
1632          easy to correct. Simply re-select the source well and then click on the correct
1633          destination well.
1634        </para>
1635       
1636        <para>
1637          When a child biomaterial is selected you have the option to override the
1638          automatially generated name. It is also possible to change the name
1639          and barcode of the child plate.
1640        </para>
1641       
1642        <note>
1643          The principle is the same when creating physical bioassays, except that no
1644          new child biomaterial is created.
1645        </note>
1646       
1647        <para>
1648          When the biomaterial has been mapped between the source and destination plates
1649          (it is not neccessary to map all of them) click on <guibutton>Save</guibutton> 
1650          to store everything. BASE will create a plate event for the selected plates
1651          and "create" or "bioassay"-type events for each biomaterial that was used.
1652        </para>
1653       
1654        <seeother>
1655          <other external_id="bioplateevent.create-child-1">Create child plate - step 1</other>
1656        </seeother>
1657       
1658        </helptext>
1659      </sect3>
1660    </sect2>
1661   
1662  </sect1>
1663 
1664  <sect1 id="biomaterials.lists">
1665    <?dbhtml filename="lists.html" ?>
1666    <title>Biomaterial lists</title>
1667   
1668    <para>
1669      TODO
1670    </para>
1671 
1672  </sect1>
1673
1674  <sect1 id="biomaterials.bioassays">
1675    <?dbhtml filename="bioassays.html" ?>
1676    <title>Physical bioassays</title>
1677    <para>
1678      A physical bioassay represents the application of one or more extracts
1679      to an experimental setup designed to measure quantities that we are
1680      interested in. For example, a <emphasis>Hybridization</emphasis> event corresponds
1681      to the application of one or more <emphasis>Labeled extracts</emphasis>
1682      materials to a microarray slide under conditions detailed in hybridization protocols.
1683      Use
1684      <menuchoice>
1685        <guimenu>View</guimenu>
1686        <guimenuitem>Physical bioassays</guimenuitem>
1687      </menuchoice>
1688      to get to the bioassays.
1689    </para>
1690   
1691    <sect2 id="biomaterials.bioassays.create">
1692      <title>Create physical bioassays</title>
1693      <para>
1694        In BASE, there are two possible routes to create a physical bioassay except the
1695        common way with the &gbNew; button at the list page.
1696      </para>
1697      <variablelist>
1698        <varlistentry>
1699          <term>from the extract list view page</term>
1700          <listitem>
1701            <para>
1702              Select at least one extract, to create a bioassay from, by
1703              ticking the selection boxes before the name field.
1704              Click on the <guibutton>New physical bioassay&hellip;</guibutton>
1705              in the toolbar.
1706            </para>
1707          </listitem>
1708        </varlistentry>
1709        <varlistentry>
1710          <term>from the extract single-item page</term>
1711          <listitem>
1712            <para>
1713              When viewing an extract in single-item view, click on the
1714              <guibutton>New physical bioassay&hellip;</guibutton>
1715              button in the toolbar.
1716            </para>
1717          </listitem>
1718        </varlistentry>
1719      </variablelist>
1720    </sect2>
1721   
1722    <sect2 id="biomaterials.bioassays.properties">
1723      <title>Bioassay properties</title>
1724
1725 
1726        <figure id="biomaterials.figures.bioassays-tab-1">
1727          <title>Physical bioassay properties</title>
1728          <screenshot>
1729            <mediaobject>
1730              <imageobject>
1731                <imagedata 
1732                  fileref="figures/physicalbioassay-tab-1.png" format="PNG" />
1733              </imageobject>
1734            </mediaobject>
1735          </screenshot>
1736        </figure> 
1737       
1738        <helptext external_id="physicalbioassay.edit" title="Edit physical bioassay">
1739        <variablelist>
1740          <varlistentry>
1741            <term>
1742              <guilabel>Name</guilabel>
1743            </term>
1744            <listitem>
1745              <para>
1746                The bioassay's name (required). It is recommended that the default
1747                name is replaced with something that is unique.
1748              </para>
1749            </listitem>
1750          </varlistentry>
1751          <varlistentry>
1752            <term>
1753              <guilabel>Type</guilabel>
1754            </term>
1755            <listitem>
1756              <para>
1757              The subtype of the bioassay. The list
1758              may evolve depending on additions by the server
1759              administrator. Selecting the proper subtype
1760              is recommended and enables BASE to automatically guess
1761              the most likely subtype when assignint source biomaterials
1762              and when creating derived bioassays.
1763              <nohelp>
1764              See <xref linkend="subtypes" /> for more information.
1765              </nohelp>
1766              </para>
1767            </listitem>
1768          </varlistentry>
1769          <varlistentry>
1770            <term>
1771              <guilabel>Size</guilabel>
1772            </term>
1773            <listitem>
1774              <para>
1775                The size of the bioassay is the number of independent
1776                positions on the bioassay. Depending on the
1777                characteristics of the bioassay, multiple biomaterials
1778                may share the same position, but are then usually
1779                required to have different tags. Two biomaterials
1780                in different positions can use the same tag.
1781                The default value is 1, but some platforms, for example
1782                Illumina BeadArrays, has slides with 6 or 8 positions
1783                and sequencing flow cells have 8 lanes.
1784              </para>
1785            </listitem>
1786          </varlistentry>
1787
1788          <varlistentry>
1789            <term>
1790              <guilabel>Created</guilabel>
1791            </term>
1792            <listitem>
1793              <para>
1794                A date should be provided. The information can be important when
1795                running quality controls on data and account for potential
1796                confounding factor (e.g. to account for a day effect).
1797              </para>
1798            </listitem>
1799          </varlistentry>
1800
1801          <varlistentry>
1802            <term>
1803              <guilabel>Registered</guilabel>
1804            </term>
1805            <listitem>
1806              <para>
1807                This field is automatically populated with a date at which the
1808                hybridization was entered in BASE system.
1809              </para>
1810            </listitem>
1811          </varlistentry>
1812
1813          <varlistentry>
1814            <term>
1815              <guilabel>Protocol</guilabel>
1816            </term>
1817            <listitem>
1818              <para>
1819                The protocol that was used to create the bioassay.
1820              </para>
1821            </listitem>
1822          </varlistentry>
1823
1824          <varlistentry>
1825            <term>
1826              <guilabel>Hardware</guilabel>
1827            </term>
1828            <listitem>
1829              <para>
1830                Information about the machine (if any) that was used when creating
1831                the bioassay.
1832              </para>
1833            </listitem>
1834          </varlistentry>
1835
1836          <varlistentry>
1837            <term>
1838              <guilabel>Array slide</guilabel>
1839            </term>
1840            <listitem>
1841              <para>The array slide that was used for the bioassay.</para>
1842            </listitem>
1843          </varlistentry>
1844
1845          <varlistentry>
1846            <term>
1847              <guilabel>Description</guilabel>
1848            </term>
1849            <listitem>
1850              <para>
1851                A free text field to report any information that can not be captured
1852                otherwise.
1853              </para>
1854            </listitem>
1855          </varlistentry>
1856        </variablelist>
1857        <seeother>
1858          <other external_id="physicalbioassay.extracts">Extracts</other>
1859          <other external_id="annotations.edit">Annotations &amp; parameters</other>
1860          <other external_id="annotations.edit.inherited">Inherited annotations</other>
1861        </seeother>
1862        </helptext>
1863      </sect2>
1864     
1865      <sect2 id="biomaterials.bioassays.extracts">
1866        <title>Parent extracts</title>
1867       
1868        <figure id="biomaterials.figures.bioassay-tab-2">
1869          <title>Parent extracts</title>
1870          <screenshot>
1871            <mediaobject>
1872              <imageobject>
1873                <imagedata 
1874                  fileref="figures/physicalbioassay-tab-2.png" format="PNG" />
1875              </imageobject>
1876            </mediaobject>
1877          </screenshot>
1878        </figure>
1879       
1880        <helptext external_id="physicalbioassay.extracts" title="Extracts">
1881        <para>
1882          This important tab allows users to select the extracts used by the
1883          bioassay, and specify the amount of material used, expressed in microgram.
1884        </para>
1885        <para>
1886          Use the <guibutton>Add extracts</guibutton> button to add
1887          items and the <guibutton>Remove</guibutton> button to remove items.
1888          Select one or several extracts in the list and write the used
1889          mass and position number in the fields below the list.
1890        </para>
1891       
1892        <seeother>
1893          <other external_id="physicalbioassay.edit">Edit physical bioassay</other>
1894          <other external_id="annotations.edit">Annotations &amp; parameters</other>
1895          <other external_id="annotations.edit.inherited">Inherited annotations</other>
1896        </seeother>
1897        </helptext>
1898       
1899      </sect2>
1900     
1901     
1902    <para>
1903      The <guilabel>Annotations</guilabel> tab allows BASE users to use
1904      annotation types to refine bioassay description. More about annotating items
1905      can be read in <xref linkend="annotations.annotating" />
1906    </para>
1907       
1908    <para>
1909      This <guilabel>Inherited annotations</guilabel> tab contains a list of those annotations
1910      that are inherited from the bioassay's parents. Information about working with inherited
1911      annotations can be found in <xref linkend="annotations.inheriting" />.
1912    </para>
1913     
1914  </sect1>
1915</chapter>
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