source: trunk/doc/src/docbook/user/biomaterials.xml @ 5738

Last change on this file since 5738 was 5738, checked in by Nicklas Nordborg, 10 years ago

References #1590: Documentation cleanup

Re-orgarnized file/directory structure of documentation to make the paths a little bit shorter.

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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 5738 2011-09-15 06:53:11Z 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  <title>Biomaterial</title>
29  <sect1 id="biomaterial.introduction">
30    <title>Introduction</title>
31    <para>
32      The generic term biomaterial refers to any biological material used in an experiment.
33      Biomaterial is divided in three main components, <emphasis>biosources</emphasis>, <emphasis>samples</emphasis>
34      and <emphasis>extracts</emphasis>. The biomaterials can then be subclassified further by
35      the use of subtypes (see <xref linkend="subtypes"/>). BASE has, for example, defined two extracts subtypes:
36      <emphasis>Labeled extract</emphasis> (used in microarray experiments)
37      and <emphasis>Library</emphasis> (used in sequencing experiments).   
38      The order used in presenting those entities is not innocuous as it represents the
39      sequence of transformation a source material undergoes until it is in a state compatible
40      for further exeperimental processing. This progression is actually
41      mimicked in the BASE
42      <guimenu>Biomaterial LIMS</guimenu>
43      menu again to insist on this natural progression.
44    </para>
45    <itemizedlist>
46      <listitem>
47        <simpara>
48          Biosources correspond to the native biological entity used in an experiment
49          prior to any treatment.
50        </simpara>
51      </listitem>
52      <listitem>
53        <simpara>
54          Samples are central to BASE to describe the sample processing. So samples can
55          be created from other samples if user want to track sample processing event in a
56          finely granular fashion.
57        </simpara>
58      </listitem>
59      <listitem>
60        <simpara>
61          Extracts correspond to nucleic acid material extracted from a tissue sample or a
62          cell culture sample.
63        </simpara>
64      </listitem>
65    </itemizedlist>
66    <para>
67      BASE allows users to create any of the these entities fairly freely, however it is
68      expected that users will follow the natural path of the laboratory workflow.
69    </para>
70    <tip>
71      <para>
72        It is highly recommended that you have read
73        <xref linkend="webclient.items" />
74        before continuing with this chapter.
75      </para>
76    </tip>
77  </sect1>
78 
79  <sect1 id="biomaterials.biosources">
80    <title>Biosources</title>
81
82
83    <para>
84      Biosources correspond to the native biological entity used in an experiment prior to any treatment.
85      Biosources can be added to BASE by most users and are managed from <menuchoice>
86        <guimenu>Biomaterial LIMS</guimenu>
87        <guimenuitem>Biosources</guimenuitem>
88      </menuchoice>.
89      Use the &gbNew; button to create a new biosource. This brings up the dialog below.
90    </para>
91
92      <figure id="biomaterials.figures.biosource-tab-1">
93        <title>Biosource properties</title>
94        <screenshot>
95          <mediaobject>
96            <imageobject>
97              <imagedata 
98                fileref="figures/biosource-tab-1.png" format="PNG" />
99            </imageobject>
100          </mediaobject>
101        </screenshot>
102      </figure>
103      <helptext external_id="biosource.edit" title="Biosource properties">
104
105        <variablelist>
106          <varlistentry>
107            <term>
108              <guilabel>Name</guilabel>
109            </term>
110            <listitem>
111              <para>
112                This is the only mandatory field. BASE by default assigns
113                <replaceable>New biosource</replaceable>
114                as name but it is advised to provide unique sensible names.
115              </para>
116            </listitem>
117          </varlistentry>
118          <varlistentry>
119            <term>
120              <guilabel>Type</guilabel>
121            </term>
122            <listitem>
123              <para>
124              The subtype of the biosource. The list
125              may evolve depending on additions by the server
126              administrator. Selecting the proper subtype
127              is recommended and enables BASE to automatically guess
128              the most likely subtype when creating child biomaterial.
129              <nohelp>
130              See <xref linkend="subtypes" /> for more information.
131              </nohelp>
132              </para>
133            </listitem>
134          </varlistentry>
135          <varlistentry>
136            <term>
137              <guilabel>External ID</guilabel>
138            </term>
139            <listitem>
140              <para>
141                An external reference identifiers (e.g. a patient identification
142                code) can be supplied using this field.
143              </para>
144            </listitem>
145          </varlistentry>
146          <varlistentry>
147            <term>
148              <guilabel>Description</guilabel>
149            </term>
150            <listitem>
151              <para>A free text description can be supplied using this field.</para>
152            </listitem>
153          </varlistentry>
154        </variablelist>
155        <seeother>
156          <other external_id="annotations.edit">Annotations</other>
157        </seeother>
158      </helptext>
159
160      <para>
161        The <guilabel>Annotations</guilabel> tab allows BASE users to use
162        annotation types to refine biosource description. More about annotating items
163        can be read in <xref linkend="annotations.annotating" />
164      </para>
165
166  </sect1>
167  <sect1 id="biomaterial.samples">
168    <title>Samples</title>
169    <para>
170      Samples result from processing events applied to biosource material or other samples
171      before they are turned into an extract. In other words, samples can be created from
172      biosource items or from one or more sample items. When a sample is created from several
173      other samples, a pooling event is performed.
174    </para>
175    <para>
176      For every step of transformation from biosource to sample, it is possible to provide
177      information about the protocol used to perform this task. It is not enforced in BASE
178      but it should serve as guidance when devising the granularity of the sample processing
179      task. Also, it is good practice to provide protocol information to ensure MIAME
180      compliance.
181    </para>
182    <para>
183      Use
184      <menuchoice>
185        <guimenu>Biomaterial LIMS</guimenu>
186        <guimenuitem>Samples</guimenuitem>
187      </menuchoice>
188      to get to the list of samples.
189    </para>
190   
191    <sect2 id="biomaterial.samples.create">
192      <title>Create sample</title>
193   
194      <para>
195        Beside the common way, using the &gbNew; button, a sample can be created in one of
196        the following ways:
197      </para>
198        <variablelist>
199          <varlistentry>
200            <term>from either biosource list- or single view- page.</term>
201            <listitem>
202              <para>
203                No matter how complex the sample processing phase is, at least one
204                sample has to be anchored to a biosource. Therefore, a natural way
205                to create an sample is to click on
206                <guiicon>
207                  <inlinemediaobject>
208                    <imageobject>
209                      <imagedata fileref="figures/add.png" format="PNG" />
210                    </imageobject>
211                  </inlinemediaobject>
212                </guiicon>
213                in the <guilabel>Samples</guilabel> column of the biosource list view. There is also a
214                corresponding button,
215                <guibutton>New sample&hellip;</guibutton>
216                in the toolbar when viewing a single biosource.
217              </para>
218            </listitem>
219          </varlistentry>
220          <varlistentry>
221            <term>from the sample list page</term>
222            <listitem>
223              <para>
224                Child samples can be created from a single parent by clicking on the
225                <guiicon>
226                  <inlinemediaobject>
227                    <imageobject>
228                      <imagedata fileref="figures/add.png" format="PNG" />
229                    </imageobject>
230                  </inlinemediaobject>
231                </guiicon> icon in the <guilabel>Child samples</guilabel> column.
232                Pooled samples can be created by first selecting the parents
233                from the list of samples and then click the <guibutton>Pool&hellip;</guibutton>
234                button in the toolbar.
235              </para>
236            </listitem>
237          </varlistentry>
238        </variablelist>
239    </sect2>
240     
241    <sect2 id="biomaterial.samples.properties">
242      <title>Sample properties</title>
243        <figure id="biomaterials.figures.biosample-tab-1">
244          <title>Sample properties</title>
245          <screenshot>
246            <mediaobject>
247              <imageobject>
248                <imagedata 
249                  fileref="figures/biosample-tab-1.png" format="PNG" />
250              </imageobject>
251            </mediaobject>
252          </screenshot>
253        </figure>
254        <helptext external_id="sample.edit" title="Edit sample">
255          <variablelist>
256            <varlistentry>
257              <term>
258                <guilabel>Name</guilabel>
259              </term>
260              <listitem>
261                <para>
262                  The sample's name (required). BASE by default assigns names to
263                  samples (by suffixing
264                  <replaceable>s#</replaceable>
265                  when creating a sample from an existing biosource or
266                  <replaceable>New Sample</replaceable>
267                  otherwise) but it is possible to edit at will.
268                </para>
269              </listitem>
270            </varlistentry>
271            <varlistentry>
272              <term>
273                <guilabel>Type</guilabel>
274              </term>
275              <listitem>
276                <para>
277                The subtype of the sample. The list
278                may evolve depending on additions by the server
279                administrator. Selecting the proper subtype
280                is recommended and enables BASE to automatically guess
281                the most likely subtype when creating child biomaterial.
282                <nohelp>
283                See <xref linkend="subtypes" /> for more information.
284                </nohelp>
285                </para>
286              </listitem>
287            </varlistentry>
288            <varlistentry>
289              <term>
290                <guilabel>External ID</guilabel>
291              </term>
292              <listitem>
293                <para>
294                  An identification used to identify the sample outside BASE.
295                </para>
296              </listitem>
297            </varlistentry>
298            <varlistentry>
299              <term>
300                <guilabel>Original quantity</guilabel>
301              </term>
302              <listitem>
303                <para>
304                  This is meant to report information about the actual mass of
305                  sample created.
306                </para>
307              </listitem>
308            </varlistentry>
309            <varlistentry>
310              <term>
311                <guilabel>Created</guilabel>
312              </term>
313              <listitem>
314                <para>
315                  A date when the sample was created. The information can be
316                  important when running quality controls on data and account for
317                  potential confounding factor (e.g. day effect).
318                </para>
319              </listitem>
320            </varlistentry>
321            <varlistentry>
322              <term>
323                <guilabel>Registered</guilabel>
324              </term>
325              <listitem>
326                <para>The date at which the sample was entered in BASE.</para>
327              </listitem>
328            </varlistentry>
329            <varlistentry>
330              <term>
331                <guilabel>Protocol</guilabel>
332              </term>
333              <listitem>
334                <para>The protocol used to produce this sample.</para>
335              </listitem>
336            </varlistentry>
337            <varlistentry>
338              <term>
339                <guilabel>Bioplate</guilabel>
340              </term>
341              <listitem>
342                <para>The bioplate where this sample is located.</para>
343              </listitem>             
344            </varlistentry>
345            <varlistentry>
346              <term>
347                <guilabel>Biowell</guilabel>
348              </term>
349              <listitem>
350                <para>
351                  Biowell that holds this sample.
352                  <guilabel>Bioplate</guilabel> has to be defined before
353                  biowell can be selected.
354                </para>
355              </listitem>             
356            </varlistentry>
357            <varlistentry>
358              <term>
359                <guilabel>Description</guilabel>
360              </term>
361              <listitem>
362                <para>
363                  A text field to report any information that not can be captured
364                  otherwise.
365                </para>
366              </listitem>
367            </varlistentry>
368          </variablelist>
369         
370          <seeother>
371            <other external_id="sample.parents">Parents</other>
372            <other external_id="annotations.edit">Annotations &amp; parameters</other>
373            <other external_id="annotations.edit.inherited">Inherited annotations</other>
374          </seeother>
375        </helptext>
376    </sect2>
377   
378    <sect2 id="biomaterial.samples.parents">
379      <title>Sample parents</title>
380        <figure id="biomaterials.figures.biosample-tab-2">
381          <title>Sample parents</title>
382          <screenshot>
383            <mediaobject>
384              <imageobject>
385                <imagedata 
386                  fileref="figures/biosample-tab-2.png" format="PNG" />
387              </imageobject>
388            </mediaobject>
389          </screenshot>
390        </figure>
391       
392        <helptext external_id="sample.parents" title="Sample's parents">
393          <para>
394            This is meant to keep track of the sample origin. BASE
395            distinguishes between two cases which are controlled by the
396            <guilabel>Parent type</guilabel>
397            radio-button in the edit pop-up window.
398          </para>
399          <itemizedlist>
400            <listitem>
401              <para>
402                If the parent is a biosource the radio-button is set to
403                <guilabel>Biosource</guilabel>. Only a single biosource
404                can be used as the parent. This option is automatically
405                selected if the user selects a biosource with the
406                <guibutton>Select biosource</guibutton> button.
407              </para>
408            </listitem>
409            <listitem>
410              <para>
411                When the parent is one or several other samples the radio-button is
412                set to <guilabel>Sample</guilabel>. This option is automatically
413                selected if the user add samples with the <guibutton>Add samples</guibutton> button.           
414                For each parent sample, it is
415                possible to specify the amount used in µg. This will automatically
416                update the <guilabel>remaining quantity</guilabel> of the parent.
417              </para>
418            </listitem>
419          </itemizedlist>
420         
421          <seeother>
422            <other external_id="sample.edit">Sample properties</other>
423            <other external_id="annotations.edit">Annotations &amp; parameters</other>
424            <other external_id="annotations.edit.inherited">Inherited annotations</other>
425          </seeother>
426        </helptext>
427    </sect2>
428    <para>
429      The <guilabel>Annotations</guilabel> tab allows BASE users to use
430      annotation types to refine sample description. More about annotating items
431      can be read in <xref linkend="annotations.annotating" />
432    </para>
433       
434    <para>
435      This <guilabel>Inherited annotations</guilabel> tab contains a list of those annotations
436      that are inherited from the sample's parents. Information about working with inherited
437      annotations can be found in <xref linkend="annotations.inheriting" />.
438    </para>
439  </sect1>
440
441  <sect1 id="biomaterials.extracts">
442    <title>Extracts</title>
443    <para>
444      Extract items should be used to describe the events that transform a sample material
445      into an extract material. An extract can be created from one sample item or from one or
446      more extract items. When an extract is created from several other extracts, a pooling
447      event is performed.
448    </para>
449    <para>
450      During the transformation from samples to extracts, it is possible to provide
451      information about the protocol used to perform this task. It is not enforced in BASE
452      but it should serve as guidance when devising the granularity of the sample processing
453      task. Also, it is good practice to provide protocol information.
454    </para>
455    <para>
456      Use
457      <menuchoice>
458        <guimenu>Biomaterial LIMS</guimenu>
459        <guimenuitem>Extracts</guimenuitem>
460      </menuchoice>
461      to get to the list of extracts.
462    </para>
463    <sect2 id="biomaterials.extracts.create">
464      <title>Create extract</title>
465      <para>
466        Beside the common way, using the &gbNew; button, an extract can be created in one of
467        the following ways:
468        <variablelist>
469          <varlistentry>
470            <term>from either sample list- or single view- page.</term>
471            <listitem>
472              <para>
473                No matter how complex the extract processing phase is, at least one
474                extract has to be anchored to a sample. Therefore, a natural way to
475                create an extract is to click on
476                <guiicon>
477                  <inlinemediaobject>
478                    <imageobject>
479                      <imagedata fileref="figures/add.png" format="PNG" />
480                    </imageobject>
481                  </inlinemediaobject>
482                </guiicon>
483                in the <guilabel>Child extracts</guilabel> column for the sample that should be a parent of the
484                extract.  There is also a corresponding button,
485                <guibutton>New child extract&hellip;</guibutton>
486                in the toolbar when viewing a single sample.
487              </para>
488            </listitem>
489          </varlistentry>
490          <varlistentry>
491            <term>from the extract list page</term>
492            <listitem>
493              <para>
494                Child extracts can be created from a single parent by clicking on the
495                <guiicon>
496                  <inlinemediaobject>
497                    <imageobject>
498                      <imagedata fileref="figures/add.png" format="PNG" />
499                    </imageobject>
500                  </inlinemediaobject>
501                </guiicon> icon in the <guilabel>Child extracts</guilabel> column.
502                Pooled extract can be created by first selecting the parents
503                from the list of extracts and then press
504                <guibutton>Pool&hellip;</guibutton>
505                in the toolbar. The selected extracts will be put into the parent
506                property.
507              </para>
508            </listitem>
509          </varlistentry>
510        </variablelist>
511      </para>
512    </sect2>
513    <sect2 id="biomaterials.extracts.properties">
514      <title>Extract properties</title>
515     
516        <figure id="biomaterials.figures.extract-tab-1">
517          <title>Extract properties</title>
518          <screenshot>
519            <mediaobject>
520              <imageobject>
521                <imagedata 
522                  fileref="figures/extract-tab-1.png" format="PNG" />
523              </imageobject>
524            </mediaobject>
525          </screenshot>
526        </figure>
527        <helptext external_id="extract.edit" title="Edit extract">
528          <variablelist>
529            <varlistentry>
530              <term>
531                <guilabel>Name</guilabel>
532              </term>
533              <listitem>
534                <para>
535                  A mandatory field for providing the extract name. BASE by
536                  default assigns names to extract (by suffixing
537                  <replaceable>e#</replaceable>
538                  when creating an extract from an existing sample or
539                  <replaceable>New extract</replaceable>
540                  otherwise) but it is possible to edit it at will.
541                </para>
542              </listitem>
543            </varlistentry>
544            <varlistentry>
545              <term>
546                <guilabel>Type</guilabel>
547              </term>
548              <listitem>
549                <para>
550                The subtype of the extract. The list
551                may evolve depending on additions by the server
552                administrator. Selecting the proper subtype
553                is recommended and enables BASE to automatically guess
554                the most likely subtype when creating child biomaterial and
555                bioassays.
556                <nohelp>
557                See <xref linkend="subtypes" /> for more information.
558                </nohelp>
559                </para>
560              </listitem>
561            </varlistentry>
562            <varlistentry>
563              <term>
564                <guilabel>Tag</guilabel>
565              </term>
566              <listitem>
567                <para>
568                  If the extract has been marked with a tag, select it here. Note
569                  that the subtype of the extract usually limits what kind of tag
570                  that can be used. For example, a <emphasis>labeled extract</emphasis>
571                  should be tagged with a <emphasis>label</emphasis>.
572                </para>
573              </listitem>
574            </varlistentry>
575            <varlistentry>
576              <term>
577                <guilabel>External ID</guilabel>
578              </term>
579              <listitem>
580                <para>The extracts identification outside BASE</para>
581              </listitem>
582            </varlistentry>
583            <varlistentry>
584              <term>
585                <guilabel>Original quantity</guilabel>
586              </term>
587              <listitem>
588                <para>
589                  Holds information about the original mass of the created
590                  extract.
591                </para>
592              </listitem>
593            </varlistentry>
594            <varlistentry>
595              <term>
596                <guilabel>Created</guilabel>
597              </term>
598              <listitem>
599                <para>
600                  The date when the extract was created. The information can be
601                  important when running quality controls on data and account for
602                  potential confounding factor (e.g. day effect)
603                </para>
604              </listitem>
605            </varlistentry>
606            <varlistentry>
607              <term>
608                <guilabel>Registered</guilabel>
609              </term>
610              <listitem>
611                <para>
612                  This is automatically populated with a date at which the sample
613                  was entered in BASE system.
614                </para>
615              </listitem>
616            </varlistentry>
617            <varlistentry>
618              <term>
619                <guilabel>Protocol</guilabel>
620              </term>
621              <listitem>
622                <para>
623                  The extraction protocol that was used to produce the extract.
624                </para>
625              </listitem>
626            </varlistentry>
627            <varlistentry>
628              <term>
629                <guilabel>Bioplate</guilabel>
630              </term>
631              <listitem>
632                <para>The bioplate where this extract is located.</para>
633              </listitem>             
634            </varlistentry>
635            <varlistentry>
636              <term>
637                <guilabel>Biowell</guilabel>
638              </term>
639              <listitem>
640                <para>
641                  Biowell that holds this extract.
642                  <guilabel>Bioplate</guilabel> has to be defined before
643                  biowell can be selected.
644                </para>
645              </listitem>             
646            </varlistentry>
647            <varlistentry>
648              <term>
649                <guilabel>Description</guilabel>
650              </term>
651              <listitem>
652                <para>
653                  A text field to report any information that not can be captured
654                  otherwise.
655                </para>
656              </listitem>
657            </varlistentry>
658          </variablelist>
659          <seeother>
660            <other external_id="extract.edit.parents">Parents</other>
661            <other external_id="annotations.edit">Annotations &amp; parameters</other>
662            <other external_id="annotations.edit.inherited">Inherited annotations</other>
663          </seeother>
664        </helptext>
665  </sect2>
666 
667  <sect2 id="biomaterials.extracts.parents">
668    <title>Extract parents</title>
669        <figure id="biomaterials.figures.extract-tab-2">
670          <title>Extract parents</title>
671          <screenshot>
672            <mediaobject>
673              <imageobject>
674                <imagedata 
675                  fileref="figures/extract-tab-2.png" format="PNG" />
676              </imageobject>
677            </mediaobject>
678          </screenshot>
679        </figure>
680        <helptext external_id="extract.parents" title="Extract's parents">
681          <para>
682            This is meant to keep track of the extract origin. BASE
683            distinguishes between two cases which are controlled by the
684            <guilabel>Parent type</guilabel>
685            radio-button in the edit pop-up window.
686          </para>
687          <itemizedlist>
688            <listitem>
689              <para>
690                If the parent is a sample the radio-button is set to
691                <guilabel>Sample</guilabel>. Only a single sample
692                can be used as the parent. This option is automatically
693                selected if the user selects a sample with the
694                <guibutton>Select sample</guibutton> button.
695              </para>
696            </listitem>
697            <listitem>
698              <para>
699                When the parent is one or several other extracts the radio-button is
700                set to <guilabel>Extract</guilabel>. This option is automatically
701                selected if the user add extracts with the <guibutton>Add extracts</guibutton> button.           
702              </para>
703            </listitem>
704          </itemizedlist>
705         
706          <para>
707            For each parent item, it is
708            possible to specify the amount used in micrograms. This will automatically
709            update the <guilabel>remaining quantity</guilabel> of the parent.
710          </para>
711         
712          <seeother>
713            <other external_id="extract.edit">Extract properties</other>
714            <other external_id="annotations.edit">Annotations &amp; parameters</other>
715            <other external_id="annotations.edit.inherited">Inherited annotations</other>
716          </seeother>
717        </helptext>
718
719    <para>
720      The <guilabel>Annotations</guilabel> tab allows BASE users to use
721      annotation types to refine extract description. More about annotating items
722      can be read in <xref linkend="annotations.annotating" />
723    </para>
724       
725    <para>
726      This <guilabel>Inherited annotations</guilabel> tab contains a list of those annotations
727      that are inherited from the extract's parents. Information about working with inherited
728      annotations can be found in <xref linkend="annotations.inheriting" />.
729    </para>
730
731
732  </sect2>
733
734
735  </sect1>
736
737  <sect1 id="biomaterials.tags">
738    <title>Tags</title>
739    <para>
740      Before attempting to create tagged extracts, users should make sure that the
741      appropriate tag object is present in BASE. To browse the list of tags, go to
742      <menuchoice>
743        <guimenu>Biomaterial LIMS</guimenu>
744        <guimenuitem>Tags</guimenuitem>
745      </menuchoice>
746    </para>
747
748    <figure id="biomaterials.figures.tags">
749      <title>Tag properties</title>
750      <screenshot>
751        <mediaobject>
752          <imageobject>
753            <imagedata 
754              fileref="figures/edit_tag.png" format="PNG" />
755          </imageobject>
756        </mediaobject>
757      </screenshot>
758    </figure>
759
760    <helptext external_id="tag.edit" title="Edit tag">
761      <para>
762        The tag item is very simple and does not need much explanation. There are only
763        a few properties for a tag.
764        <variablelist>
765          <varlistentry>
766            <term>
767              <guilabel>Name</guilabel>
768            </term>
769            <listitem>
770              <para>The name of the tag (required).</para>
771            </listitem>
772          </varlistentry>
773          <varlistentry>
774            <term>
775              <guilabel>Type</guilabel>
776            </term>
777            <listitem>
778              <para>
779              The subtype of the tag. The list
780              may evolve depending on additions by the server
781              administrator. Selecting the proper subtype
782              is important and enables BASE to automatically guess
783              the most likely tag when creating tagged extracts (eg.
784              a <emphasis>Label</emphasis> for a <emphasis>Labeled extract</emphasis> 
785              or a <emphasis>Barcode</emphasis> for a <emphasis>Library</emphasis>).
786              <nohelp>
787              See <xref linkend="subtypes" /> for more information.
788              </nohelp>
789              </para>
790            </listitem>
791          </varlistentry>
792          <varlistentry>
793            <term>
794              <guilabel>Description</guilabel>
795            </term>
796            <listitem>
797              <para>
798                An explaining text or other information associated with the
799                tag.
800              </para>
801            </listitem>
802          </varlistentry>
803        </variablelist>
804      </para>
805    </helptext>
806
807  </sect1>
808
809 
810  <sect1 id="biomaterials.bioplates">
811    <title>Bioplates</title>
812    <para>
813      With bioplates it is possible to organize biomaterial such as samples and extracts
814      into wells. Each plate has a number of wells that is defined by the plate geometry.
815    </para>
816    <para>
817      Use
818      <menuchoice>
819        <guimenu>Biomaterial LIMS</guimenu>
820        <guimenuitem>Bioplates</guimenuitem>
821      </menuchoice>
822      to get to the list of bioplates.   
823    </para>
824    <sect2 id="biomaterials.bioplate.properties">
825      <title>Bioplate properties</title>     
826
827      <figure id="biomaterials.figures.bioplate-tab-1">
828        <title>Bioplate properties</title>
829        <screenshot>
830          <mediaobject>
831            <imageobject>
832              <imagedata 
833                fileref="figures/bioplate-tab-1.png" format="PNG" />
834            </imageobject>
835          </mediaobject>
836        </screenshot>
837      </figure>
838
839      <helptext external_id="bioplate.edit" title="Edit bioplate">
840        <para>
841          <variablelist>
842            <varlistentry>
843              <term><guilabel>Name</guilabel></term>
844              <listitem>
845                <para>
846                  The bioplate name. The name does not have to be unique but it is
847                  recommended to keep it unique. BASE by default assigns
848                  <replaceable>New bioplate</replaceable> as name.
849                  This field is mandatory.
850                </para>
851              </listitem>
852            </varlistentry>
853            <varlistentry>
854              <term><guilabel>Bioplate type</guilabel></term>
855              <listitem>
856                <para>
857                  The type of the bioplate may be a generic storage plate that
858                  can store any type of biomaterial or a locked plate that
859                  can only store a single type of biomaterial. This field
860                  is mandatory and can only be set for new bioplates.
861                  <nohelp>See <xref linkend="biomaterials.bioplatetypes" /> for more
862                  information.</nohelp>
863                </para>
864              </listitem>             
865            </varlistentry>
866            <varlistentry>
867              <term><guilabel>Plate geometry</guilabel></term>
868              <listitem>
869                <para>
870                  Information about the plate design defining the
871                  number of  rows and columns on the bioplate.
872                  This field is mandatory and can only be set for new bioplates.
873                </para>
874              </listitem>             
875            </varlistentry>
876            <varlistentry>
877              <term><guilabel>Freezer</guilabel></term>
878              <listitem>
879                <para>The freezer where the bioplate is stored. Optional.</para>
880              </listitem>
881            </varlistentry>
882            <varlistentry>
883              <term><guilabel>Barcode</guilabel></term>
884              <listitem>
885                <para>
886                  Barcode of the bioplate.
887                  Optional.
888                </para>
889              </listitem>
890            </varlistentry>
891            <varlistentry>
892              <term><guilabel>Description</guilabel></term>
893              <listitem>
894                <para>
895                  Other useful information about the bioplate. Optional.
896                </para>
897              </listitem>
898            </varlistentry>
899          </variablelist>
900        </para>
901       
902        <seeother>
903          <other external_id="annotations.edit">Annotations</other>
904        </seeother>
905      </helptext>
906     
907    <para>
908      The <guilabel>Annotations</guilabel> tab allows BASE users to use
909      annotation types to refine bioplate description. More about annotating items
910      can be read in <xref linkend="annotations.annotating" />
911    </para>
912
913    </sect2>
914    <sect2 id="biomaterials.bioplate.biowells">
915      <title>Biowells</title>
916      <para>
917        Biowells existence are managed through the bioplate they
918        belong to. Creating a bioplate will automatically create the
919        biowells (as given by the selected geometry) on the plate.
920        The wells are initially empty. To add biomaterial to the plate
921        go to the single-item view page for the bioplate. This page
922        includes an overview of the layout of the plate. Clicking
923        on an empty well will open a popup dialog that allows you
924        to select a biomaterial. The same dialog can also be accessed from
925        the <guilabel>Wells</guilabel> tab. Assigning a biomaterial to a
926        biowell can also be done when editing a sample or extract, or
927        by using the <link linkend="biomaterials.placeonplate">Place-on-plate
928        wizard</link>.
929      </para>
930     
931      <figure id="biomaterials.figures.biowell">
932        <title>Biowell properties</title>
933        <screenshot>
934          <mediaobject>
935            <imageobject>
936              <imagedata 
937                fileref="figures/biowell.png" format="PNG" />
938            </imageobject>
939          </mediaobject>
940        </screenshot>
941      </figure>
942
943        <helptext external_id="biowell.edit" title="Edit biowell">
944          <para>
945            <variablelist>
946              <varlistentry>
947                <term><guilabel>Bioplate</guilabel></term>
948                <listitem>
949                  <para>
950                    Shows which bioplate the biowell is located on.
951                    This property is read-only.
952                  </para>
953                </listitem>
954              </varlistentry>
955              <varlistentry>             
956                <term><guilabel>Well location</guilabel></term>
957                <listitem>
958                  <para>
959                    The biowell location on the bioplate in row+column format.
960                    This property is read-only.
961                  </para>
962                </listitem>
963              </varlistentry>
964              <varlistentry>
965                <term><guilabel>Biomaterial type</guilabel></term>
966                <listitem>
967                  <para>
968                    The type of biomaterial stored in this biowell. This
969                    property must be selected before before a
970                    biomaterial can be selected. On some plates this
971                    is locked due to settings in the bioplate's type.
972                  </para>
973                </listitem>
974              </varlistentry>
975              <varlistentry>             
976                <term><guilabel>Biomaterial</guilabel></term>
977                <listitem>
978                  <para>
979                    Name of the biomaterial in this biowell. Before changing
980                    this you must select the appropriate <guilabel>Biomaterial type</guilabel>.
981                    A biomaterial can only be placed in a single well. If the selected
982                    biomaterial is already placed in another location it will be moved.
983                  </para>
984                </listitem>
985              </varlistentry>
986            </variablelist>
987          </para>
988        </helptext> 
989    </sect2>
990   
991    <sect2 id="biomaterials.bioplatetypes">
992      <title>Bioplate types</title>
993     
994      <helptext external_id="bioplatetype.view.properties" title="Bioplate types">
995      <para>
996        Bioplate types are used to subclassify bioplates and may put restrictions on them.
997        BASE ships with a few pre-defined bioplate types. The <emphasis>Storage plate</emphasis> type
998        is a generic plate type that can be used for all types of biomaterial and doesn't
999        have any other restrictions on it. The reaction plate types are locked to a single
1000        type of biomaterial and have a restriction that biomaterial can never be moved out from
1001        a well once it has been placed there.
1002      </para>
1003      </helptext>
1004     
1005      <figure id="biomaterials.figures.bioplatetype">
1006        <title>Bioplate type properties</title>
1007        <screenshot>
1008          <mediaobject>
1009            <imageobject>
1010              <imagedata 
1011                fileref="figures/edit_bioplatetype.png" format="PNG" />
1012            </imageobject>
1013          </mediaobject>
1014        </screenshot>
1015      </figure>
1016     
1017          <helptext external_id="bioplatetype.edit" title="Edit bioplate type">
1018          <para>
1019            <variablelist>
1020              <varlistentry>
1021                <term><guilabel>Name</guilabel></term>
1022                <listitem>
1023                  <para>
1024                    The name of the bioplate type.
1025                  </para>
1026                </listitem>
1027              </varlistentry>
1028              <varlistentry>             
1029                <term><guilabel>Biomaterial type</guilabel></term>
1030                <listitem>
1031                  <para>
1032                    Select if bioplates using this type should be locked to
1033                    specific biomaterial type or not. This property can only
1034                    be set for new bioplate types.
1035                  </para>
1036                </listitem>
1037              </varlistentry>
1038              <varlistentry>
1039                <term><guilabel>Well lock mode</guilabel></term>
1040                <listitem>
1041                  <para>
1042                    This option controls the wells on bioplates using this type.
1043                    There are four options:
1044                    <itemizedlist>
1045                      <listitem>
1046                        <para><guilabel>Unlocked</guilabel>:
1047                          The wells are unlocked and biomaterial can be added
1048                          and removed freely any number of times.
1049                        </para>
1050                      </listitem>
1051                      <listitem>
1052                        <para><guilabel>Locked after add+clear</guilabel>:
1053                          A biomaterial can be placed once in the well and
1054                          then moved to another bioplate. After that the well
1055                          becomes locked and it is not possible to add a
1056                          different biomaterial to it.
1057                        </para>
1058                      </listitem>
1059                      <listitem>
1060                        <para><guilabel>Locked after add</guilabel>:
1061                          The wells are locked as soon as biomaterial is
1062                          added to them. The biomaterial can't be moved to another
1063                          place or be replaced with other biomaterial.
1064                        </para>
1065                      </listitem>
1066                      <listitem>
1067                        <para><guilabel>Locked at plate creation</guilabel>:
1068                          The wells are locked as soon as the bioplate has been
1069                          saved to the database. This lock mode is primarily intended
1070                          to be used when plug-ins are creating and populating the
1071                          bioplate as a single event.
1072                        </para>
1073                      </listitem>
1074                    </itemizedlist>
1075                  </para>
1076                </listitem>
1077              </varlistentry>
1078              <varlistentry>             
1079                <term><guilabel>Description</guilabel></term>
1080                <listitem>
1081                  <para>
1082                    Other useful information about the bioplate type. Optional.
1083                  </para>
1084                </listitem>
1085              </varlistentry>
1086            </variablelist>
1087          </para>
1088        </helptext> 
1089    </sect2>
1090   
1091    <sect2 id="biomaterials.bioplateevents">
1092      <title>Bioplate events</title>
1093   
1094      <para>
1095        Certain actions can be applied collectively to the biomaterial on a bioplate,
1096        either as a whole or a subset that is picked by the user.
1097        A list of the available actions can be found on the list page
1098        <menuchoice>
1099          <guimenu>Biomaterial LIMS</guimenu>
1100          <guimenuitem>Bioplate event types</guimenuitem>
1101        </menuchoice>.
1102       
1103        Although it is possible to create more event types here there is usually no
1104        meaning to do so, since each event needs a specailized GUI wizard to take
1105        care of it. The possibility to add more event types should be seen as an
1106        opportunity for extension development.
1107      </para>
1108     
1109      <sect3 id="biomaterials.placeonplate">
1110        <title>The place-on-plate event</title>
1111     
1112        <figure id="biomaterials.figures.placeonplate">
1113          <title>Place on plate wizard</title>
1114          <screenshot>
1115            <mediaobject>
1116              <imageobject>
1117                <imagedata 
1118                  fileref="figures/place_on_plate.png" format="PNG" />
1119              </imageobject>
1120            </mediaobject>
1121          </screenshot>
1122        </figure>
1123     
1124        <helptext external_id="bioplateevent.place-on-plate" title="Place on plate">
1125        <para>
1126          This event is available on the sample and extract list pages and can be used
1127          to place multiple biomaterial on a bioplate in one go. Click on
1128          the <guibutton>Place on plate</guibutton> button to start the wizard.
1129          The wizard will automatically use the selected biomaterials or, if none
1130          are selected, all listed biomaterials that aren't alredy located on a
1131          plate.
1132
1133          <variablelist>
1134            <varlistentry>
1135              <term><guilabel>Event name</guilabel></term>
1136              <listitem>
1137                <para>
1138                  Give a name to the event, or keep the suggested name.
1139                </para>
1140              </listitem>
1141            </varlistentry>
1142            <varlistentry>
1143              <term><guilabel>Event date</guilabel></term>
1144              <listitem>
1145                <para>
1146                  The date of the event.
1147                </para>
1148              </listitem>
1149            </varlistentry>
1150            <varlistentry>
1151              <term><guilabel>Protocol</guilabel></term>
1152              <listitem>
1153                <para>
1154                  The protocol used in the event, if any.
1155                </para>
1156              </listitem>
1157            </varlistentry>
1158            <varlistentry>
1159              <term><guilabel>Hardware</guilabel></term>
1160              <listitem>
1161                <para>
1162                  The hardware item used in the event, if any.
1163                </para>
1164              </listitem>
1165            </varlistentry>
1166            <varlistentry>
1167              <term><guilabel>Description</guilabel></term>
1168              <listitem>
1169                <para>
1170                  Other comments about the event.
1171                </para>
1172              </listitem>
1173            </varlistentry>
1174            <varlistentry>
1175              <term><guilabel>Select plate...</guilabel></term>
1176              <listitem>
1177                <para>
1178                  You need to select an existing plate on which the
1179                  biomaterial should be placed. It is only possible to
1180                  use one plate in each event. If you want to place biomaterial
1181                  on more than one plate, the wizard must be repeated for
1182                  each destination plate.
1183                </para>
1184              </listitem>
1185            </varlistentry>
1186            <varlistentry>
1187              <term><guilabel>Clear</guilabel></term>
1188              <listitem>
1189                <para>
1190                  Clear all current placement.
1191                </para>
1192              </listitem>
1193            </varlistentry>
1194            <varlistentry>
1195              <term><guilabel>Place by row/column</guilabel></term>
1196              <listitem>
1197                <para>
1198                  Automatically place the remaining biomaterial by filling empty wells,
1199                  starting with rows or columns.
1200                </para>
1201              </listitem>
1202            </varlistentry>
1203            <varlistentry>
1204              <term><guilabel>Items to place</guilabel></term>
1205              <listitem>
1206                <para>
1207                  This column contains the biomaterial that should be placed on the plate.
1208                  When a destination plate has been selected, it is displayed as a grid to
1209                  the right. To place a biomaterial either use the <guibutton>Plate by row</guibutton>
1210                  or <guibutton>Place by column</guibutton> buttons, or select an item in this
1211                  list. When an item has been selected, click on the destination well on the
1212                  plate. The coordinate of the well is displayed in the gray area before the
1213                  biomaterial name and a line is drawn between it and the destination well.
1214                  The destination well is also marked with an icon.
1215                  If the <guilabel>Auto-select next unmapped item</guilabel> is selected
1216                  the selection is automatically moved to the next biomaterial which can then
1217                  be placed by selecting another destination well. If a mistake is made it is
1218                  easy to correct. Simply re-select the item and then click on the correct well.
1219                </para>
1220              </listitem>
1221            </varlistentry>
1222
1223          </variablelist>
1224         
1225          When the biomaterial has been placed on the plate (it is not neccessary to place all of them)
1226          click on <guibutton>Save</guibutton> to store everything. BASE will create a plate event
1227          for the selected destination plate and "other"-type events for each biomaterial that was
1228          placed on it.
1229        </para>
1230        </helptext> 
1231      </sect3>
1232
1233      <sect3 id="biomaterials.move">
1234        <title>The move biomaterials event</title>
1235     
1236        <figure id="biomaterials.figures.move">
1237          <title>Move biomaterials wizard</title>
1238          <screenshot>
1239            <mediaobject>
1240              <imageobject>
1241                <imagedata 
1242                  fileref="figures/move_biomaterials.png" format="PNG" />
1243              </imageobject>
1244            </mediaobject>
1245          </screenshot>
1246        </figure>
1247     
1248        <helptext external_id="bioplateevent.move" title="Move biomaterials">
1249        <para>
1250          This event is available on the single-item view page of a bioplate
1251          and can be used to move biomaterial from one plate to another. Click on
1252          the <guibutton>Move biomaterial</guibutton> button to start the wizard.
1253          <variablelist>
1254            <varlistentry>
1255              <term><guilabel>Event name</guilabel></term>
1256              <listitem>
1257                <para>
1258                  Give a name to the event, or keep the suggested name.
1259                </para>
1260              </listitem>
1261            </varlistentry>
1262            <varlistentry>
1263              <term><guilabel>Event date</guilabel></term>
1264              <listitem>
1265                <para>
1266                  The date of the event.
1267                </para>
1268              </listitem>
1269            </varlistentry>
1270            <varlistentry>
1271              <term><guilabel>Protocol</guilabel></term>
1272              <listitem>
1273                <para>
1274                  The protocol used in the event, if any.
1275                </para>
1276              </listitem>
1277            </varlistentry>
1278            <varlistentry>
1279              <term><guilabel>Hardware</guilabel></term>
1280              <listitem>
1281                <para>
1282                  The hardware item used in the event, if any.
1283                </para>
1284              </listitem>
1285            </varlistentry>
1286            <varlistentry>
1287              <term><guilabel>Description</guilabel></term>
1288              <listitem>
1289                <para>
1290                  Other comments about the event.
1291                </para>
1292              </listitem>
1293            </varlistentry>
1294            <varlistentry>
1295              <term><guilabel>Select plate...</guilabel></term>
1296              <listitem>
1297                <para>
1298                  You need to select an existing plate to which the
1299                  biomaterial should be moved. It is only possible to
1300                  use one plate in each event. If you want to move biomaterial
1301                  to more than one plate, the wizard must be repeated for
1302                  each destination plate.
1303                </para>
1304              </listitem>
1305            </varlistentry>
1306            <varlistentry>
1307              <term><guilabel>Clear</guilabel></term>
1308              <listitem>
1309                <para>
1310                  Clear all current mapping between the source and destination plates.
1311                </para>
1312              </listitem>
1313            </varlistentry>
1314            <varlistentry>
1315              <term><guilabel>Place by row/column</guilabel></term>
1316              <listitem>
1317                <para>
1318                  Automatically move the remaining biomaterial by filling empty wells,
1319                  starting with rows or columns.
1320                </para>
1321              </listitem>
1322            </varlistentry>
1323            <varlistentry>
1324              <term><guilabel>Predefined mapping</guilabel></term>
1325              <listitem>
1326                <para>
1327                  Use this button to select a predefined mapping between source
1328                  and destination wells. The biomaterial will be moved according
1329                  to the mapping.
1330                </para>
1331              </listitem>
1332            </varlistentry>
1333            <varlistentry>
1334              <term><guilabel>Source plate</guilabel></term>
1335              <listitem>
1336                <para>
1337                  This displays the source plate as a grid with icons that indicate
1338                  filled and movable wells.
1339                 
1340                  When a destination plate has been selected, it is displayed as a similar grid to
1341                  the right. To move a biomaterial either use the <guibutton>Place by row</guibutton>,
1342                  <guibutton>Place by column</guibutton> or <guibutton>Predefined mapping</guibutton>
1343                  buttons, or select a well on the source plate. When a source well has been selected,
1344                  click on a well on the destination plate. A line is drawn between the source and
1345                  destination wells and the icons are updated to show what is going on. The
1346                  wells on the destination plate will also show the coordinate of the mapped
1347                  source well unless the <guilabel>Show source coordinates</guilabel>
1348                  checkbox is deselected. If a mistake is made it is
1349                  easy to correct. Simply re-select the source well and then click on the correct
1350                  destination well.
1351                   
1352                </para>
1353              </listitem>
1354            </varlistentry>
1355          </variablelist>
1356
1357          When the biomaterial has been mapped between the source and destination plates
1358          (it is not neccessary to map all of them) click on <guibutton>Save</guibutton> to store everything.
1359          BASE will create a plate event for the selected plates and "other"-type events for each
1360          biomaterial that was moved.
1361
1362        </para>
1363        </helptext>
1364      </sect3>
1365     
1366      <sect3 id="biomaterials.create_child">
1367        <title>The create child plate event</title>
1368     
1369        <figure id="biomaterials.figures.create_child_1">
1370          <title>Create child plate wizard - step 1</title>
1371          <screenshot>
1372            <mediaobject>
1373              <imageobject>
1374                <imagedata 
1375                  fileref="figures/create_child_plate_1.png" format="PNG" />
1376              </imageobject>
1377            </mediaobject>
1378          </screenshot>
1379        </figure>
1380     
1381        <helptext external_id="bioplateevent.create-child-1" title="Create child plate - step 1">
1382        <para>
1383          This event is available on the single-item view page of a bioplate
1384          when the bioplate is limited to a single type of biomaterial (eg.
1385          only samples or only extracts). The event is used to create either
1386          a child bioplate with biomaterial that is derived from the biomaterial
1387          on the parent plate or to create one or more physical bioassays. Click on
1388          the <guibutton>Create child bioplate</guibutton> button to start the wizard.
1389        </para>
1390       
1391        <para>
1392          The wizard has two steps. In the first step you set properties that
1393          are related to the event and to the creation of child plates and
1394          biomaterial. The first step is divied into three main sections.
1395        </para>
1396       
1397       
1398        <bridgehead>Event</bridgehead>
1399       
1400        <variablelist>
1401          <varlistentry>
1402            <term><guilabel>Event name</guilabel></term>
1403            <listitem>
1404              <para>
1405                Give a name to the event, or keep the suggested name.
1406              </para>
1407            </listitem>
1408          </varlistentry>
1409          <varlistentry>
1410            <term><guilabel>Event date</guilabel></term>
1411            <listitem>
1412              <para>
1413                The date of the event.
1414              </para>
1415            </listitem>
1416          </varlistentry>
1417          <varlistentry>
1418            <term><guilabel>Protocol</guilabel></term>
1419            <listitem>
1420              <para>
1421                The protocol used in the event, if any.
1422              </para>
1423            </listitem>
1424          </varlistentry>
1425          <varlistentry>
1426            <term><guilabel>Hardware</guilabel></term>
1427            <listitem>
1428              <para>
1429                The hardware item used in the event, if any.
1430              </para>
1431            </listitem>
1432          </varlistentry>
1433          <varlistentry>
1434            <term><guilabel>Description</guilabel></term>
1435            <listitem>
1436              <para>
1437                Other comments about the event.
1438              </para>
1439            </listitem>
1440          </varlistentry>
1441        </variablelist>
1442         
1443        <bridgehead>Child biomaterial</bridgehead>
1444        <variablelist>
1445          <varlistentry>
1446            <term><guilabel>Type</guilabel></term>
1447            <listitem>
1448              <para>
1449                The type of child items to create. If the source plate
1450                contains samples, you can select between sample and
1451                extract and if the source plate contains extract you
1452                can select between extract and physical bioassay.
1453              </para>
1454            </listitem>
1455          </varlistentry>
1456          <varlistentry>
1457            <term><guilabel>Subtype</guilabel></term>
1458            <listitem>
1459              <para>
1460                The subtype to assign to the newly created biomaterial
1461                (or physical bioassay). The list of options is automatically
1462                updated based on the selection in the <guilabel>Type</guilabel>
1463                list.
1464              </para>
1465            </listitem>
1466          </varlistentry>
1467          <varlistentry>
1468            <term><guilabel>Tag</guilabel></term>
1469            <listitem>
1470              <para>
1471                Visible when creating child extracts only. Select the tag to
1472                assign to the new extract. If no tag is selected and the
1473                source biomaterial is also extracts, the children will get the
1474                same tag as their parents.
1475              </para>
1476            </listitem>
1477          </varlistentry>
1478          <varlistentry>
1479            <term><guilabel>Original quantity</guilabel></term>
1480            <listitem>
1481              <para>
1482                The original quantity of the new biomaterial. Not visible when
1483                creating a physical bioassay.
1484              </para>
1485            </listitem>
1486          </varlistentry>
1487          <varlistentry>
1488            <term><guilabel>Used quantity</guilabel></term>
1489            <listitem>
1490              <para>
1491                The quantity that was used from the parent biomaterial
1492                in the process of creating child biomaterial.
1493              </para>
1494            </listitem>
1495          </varlistentry>
1496          <varlistentry>
1497            <term><guilabel>Description</guilabel></term>
1498            <listitem>
1499              <para>
1500                Other comments about the new biomaterial.
1501              </para>
1502            </listitem>
1503          </varlistentry>
1504        </variablelist>
1505       
1506       
1507        <bridgehead>Child plates</bridgehead>
1508        <variablelist>
1509          <varlistentry>
1510            <term><guilabel>No. of plates</guilabel></term>
1511            <listitem>
1512              <para>
1513                The number of child plates to create. The default value is 1.
1514              </para>
1515            </listitem>
1516          </varlistentry>
1517          <varlistentry>
1518            <term><guilabel>Name prefix</guilabel></term>
1519            <listitem>
1520              <para>
1521                The child plates will be named using the prefix plus a running number
1522                starting with 0. Eg. New plate.0.
1523              </para>
1524            </listitem>
1525          </varlistentry>
1526          <varlistentry>
1527            <term><guilabel>Geometry</guilabel></term>
1528            <listitem>
1529              <para>
1530                The geometry of the child plates. The default is the same
1531                geometry as the parent plate. This option is replaced with
1532                <guilabel>Size of bioassay</guilabel> when creating a
1533                physical bioassay.
1534              </para>
1535            </listitem>
1536          </varlistentry>
1537          <varlistentry>
1538            <term><guilabel>Plate type</guilabel></term>
1539            <listitem>
1540              <para>
1541                The plate type of the child plates. Not used when creating a
1542                physical bioassay.
1543              </para>
1544            </listitem>
1545          </varlistentry>
1546          <varlistentry>
1547            <term><guilabel>Freezer</guilabel></term>
1548            <listitem>
1549              <para>
1550                The freezer in which the new child plates are located. Not used
1551                when creating a physical bioassay.
1552              </para>
1553            </listitem>
1554          </varlistentry>
1555          <varlistentry>
1556            <term><guilabel>Description</guilabel></term>
1557            <listitem>
1558              <para>
1559                Other comments about the new child plates.
1560              </para>
1561            </listitem>
1562          </varlistentry>
1563        </variablelist>
1564       
1565        <seeother>
1566          <other external_id="bioplateevent.create-child-2">Create child plate - step 2</other>
1567        </seeother>
1568        </helptext>
1569
1570        <figure id="biomaterials.figures.create_child_2">
1571          <title>Create child plate wizard - step 2</title>
1572          <screenshot>
1573            <mediaobject>
1574              <imageobject>
1575                <imagedata 
1576                  fileref="figures/create_child_plate_2.png" format="PNG" />
1577              </imageobject>
1578            </mediaobject>
1579          </screenshot>
1580        </figure>
1581     
1582        <helptext external_id="bioplateevent.create-child-2" title="Create child plate - step 2">
1583        <para>
1584          The second step display the source plate and new child plates as a grid.
1585          To create child biomaterial either use the <guibutton>Place by row</guibutton>,
1586          <guibutton>Place by column</guibutton> or <guibutton>Predefined mapping</guibutton>
1587          buttons, or select a well on the source plate. When a source well has been selected,
1588          click on a well on the destination plate. A line is drawn between the source and
1589          destination wells and the icons are updated to show what is going on. The
1590          wells on the destination plate will also show the coordinate of the mapped
1591          source well unless the <guilabel>Show source coordinates</guilabel>
1592          checkbox is deselected. If a mistake is made it is
1593          easy to correct. Simply re-select the source well and then click on the correct
1594          destination well.
1595        </para>
1596       
1597        <para>
1598          When a child biomaterial is selected you have the option to override the
1599          automatially generated name. It is also possible to change the name
1600          and barcode of the child plate.
1601        </para>
1602       
1603        <note>
1604          The principle is the same when creating physical bioassays, except that no
1605          new child biomaterial is created.
1606        </note>
1607       
1608        <para>
1609          When the biomaterial has been mapped between the source and destination plates
1610          (it is not neccessary to map all of them) click on <guibutton>Save</guibutton> 
1611          to store everything. BASE will create a plate event for the selected plates
1612          and "create" or "bioassay"-type events for each biomaterial that was used.
1613        </para>
1614       
1615        <seeother>
1616          <other external_id="bioplateevent.create-child-1">Create child plate - step 1</other>
1617        </seeother>
1618       
1619        </helptext>
1620      </sect3>
1621    </sect2>
1622   
1623  </sect1>
1624 
1625  <sect1 id="biomaterials.lists">
1626    <title>Biomaterial lists</title>
1627   
1628    <para>
1629      TODO
1630    </para>
1631 
1632  </sect1>
1633
1634  <sect1 id="biomaterials.bioassays">
1635    <title>Physical bioassays</title>
1636    <para>
1637      A physical bioassay represents the application of one or more extracts
1638      to an experimental setup designed to measure quantities that we are
1639      interested in. For example, a <emphasis>Hybridization</emphasis> event corresponds
1640      to the application of one or more <emphasis>Labeled extracts</emphasis>
1641      materials to a microarray slide under conditions detailed in hybridization protocols.
1642      Use
1643      <menuchoice>
1644        <guimenu>View</guimenu>
1645        <guimenuitem>Physical bioassays</guimenuitem>
1646      </menuchoice>
1647      to get to the bioassays.
1648    </para>
1649   
1650    <sect2 id="biomaterials.bioassays.create">
1651      <title>Create physical bioassays</title>
1652      <para>
1653        In BASE, there are two possible routes to create a physical bioassay except the
1654        common way with the &gbNew; button at the list page.
1655      </para>
1656      <variablelist>
1657        <varlistentry>
1658          <term>from the extract list view page</term>
1659          <listitem>
1660            <para>
1661              Select at least one extract, to create a bioassay from, by
1662              ticking the selection boxes before the name field.
1663              Click on the <guibutton>New physical bioassay&hellip;</guibutton>
1664              in the toolbar.
1665            </para>
1666          </listitem>
1667        </varlistentry>
1668        <varlistentry>
1669          <term>from the extract single-item page</term>
1670          <listitem>
1671            <para>
1672              When viewing an extract in single-item view, click on the
1673              <guibutton>New physical bioassay&hellip;</guibutton>
1674              button in the toolbar.
1675            </para>
1676          </listitem>
1677        </varlistentry>
1678      </variablelist>
1679    </sect2>
1680   
1681    <sect2 id="biomaterials.bioassays.properties">
1682      <title>Bioassay properties</title>
1683
1684 
1685        <figure id="biomaterials.figures.bioassays-tab-1">
1686          <title>Physical bioassay properties</title>
1687          <screenshot>
1688            <mediaobject>
1689              <imageobject>
1690                <imagedata 
1691                  fileref="figures/physicalbioassay-tab-1.png" format="PNG" />
1692              </imageobject>
1693            </mediaobject>
1694          </screenshot>
1695        </figure> 
1696       
1697        <helptext external_id="physicalbioassay.edit" title="Edit physical bioassay">
1698        <variablelist>
1699          <varlistentry>
1700            <term>
1701              <guilabel>Name</guilabel>
1702            </term>
1703            <listitem>
1704              <para>
1705                The bioassay's name (required). It is recommended that the default
1706                name is replaced with something that is unique.
1707              </para>
1708            </listitem>
1709          </varlistentry>
1710          <varlistentry>
1711            <term>
1712              <guilabel>Type</guilabel>
1713            </term>
1714            <listitem>
1715              <para>
1716              The subtype of the bioassay. The list
1717              may evolve depending on additions by the server
1718              administrator. Selecting the proper subtype
1719              is recommended and enables BASE to automatically guess
1720              the most likely subtype when assignint source biomaterials
1721              and when creating derived bioassays.
1722              <nohelp>
1723              See <xref linkend="subtypes" /> for more information.
1724              </nohelp>
1725              </para>
1726            </listitem>
1727          </varlistentry>
1728          <varlistentry>
1729            <term>
1730              <guilabel>Size</guilabel>
1731            </term>
1732            <listitem>
1733              <para>
1734                The size of the bioassay is the number of independent
1735                positions on the bioassay. Depending on the
1736                characteristics of the bioassay, multiple biomaterials
1737                may share the same position, but are then usually
1738                required to have different tags. Two biomaterials
1739                in different positions can use the same tag.
1740                The default value is 1, but some platforms, for example
1741                Illumina BeadArrays, has slides with 6 or 8 positions.
1742              </para>
1743            </listitem>
1744          </varlistentry>
1745
1746          <varlistentry>
1747            <term>
1748              <guilabel>Created</guilabel>
1749            </term>
1750            <listitem>
1751              <para>
1752                A date should be provided. The information can be important when
1753                running quality controls on data and account for potential
1754                confounding factor (e.g. to account for a day effect).
1755              </para>
1756            </listitem>
1757          </varlistentry>
1758
1759          <varlistentry>
1760            <term>
1761              <guilabel>Registered</guilabel>
1762            </term>
1763            <listitem>
1764              <para>
1765                This field is automatically populated with a date at which the
1766                hybridization was entered in BASE system.
1767              </para>
1768            </listitem>
1769          </varlistentry>
1770
1771          <varlistentry>
1772            <term>
1773              <guilabel>Protocol</guilabel>
1774            </term>
1775            <listitem>
1776              <para>
1777                The protocol that was used to create the bioassay.
1778              </para>
1779            </listitem>
1780          </varlistentry>
1781
1782          <varlistentry>
1783            <term>
1784              <guilabel>Hardware</guilabel>
1785            </term>
1786            <listitem>
1787              <para>
1788                Information about the machine (if any) that was used when creating
1789                the bioassay.
1790              </para>
1791            </listitem>
1792          </varlistentry>
1793
1794          <varlistentry>
1795            <term>
1796              <guilabel>Array slide</guilabel>
1797            </term>
1798            <listitem>
1799              <para>The array slide that was used for the bioassay.</para>
1800            </listitem>
1801          </varlistentry>
1802
1803          <varlistentry>
1804            <term>
1805              <guilabel>Description</guilabel>
1806            </term>
1807            <listitem>
1808              <para>
1809                A free text field to report any information that can not be captured
1810                otherwise.
1811              </para>
1812            </listitem>
1813          </varlistentry>
1814        </variablelist>
1815        <seeother>
1816          <other external_id="physicalbioassay.extracts">Extracts</other>
1817          <other external_id="annotations.edit">Annotations &amp; parameters</other>
1818          <other external_id="annotations.edit.inherited">Inherited annotations</other>
1819        </seeother>
1820        </helptext>
1821      </sect2>
1822     
1823      <sect2 id="biomaterials.bioassays.extracts">
1824        <title>Parent extracts</title>
1825       
1826        <figure id="biomaterials.figures.bioassay-tab-2">
1827          <title>Parent extracts</title>
1828          <screenshot>
1829            <mediaobject>
1830              <imageobject>
1831                <imagedata 
1832                  fileref="figures/physicalbioassay-tab-2.png" format="PNG" />
1833              </imageobject>
1834            </mediaobject>
1835          </screenshot>
1836        </figure>
1837       
1838        <helptext external_id="physicalbioassay.extracts" title="Extracts">
1839        <para>
1840          This important tab allows users to select the extracts used by the
1841          bioassay, and specify the amount of material used, expressed in microgram.
1842        </para>
1843        <para>
1844          Use the <guibutton>Add extracts</guibutton> button to add
1845          items and the <guibutton>Remove</guibutton> button to remove items.
1846          Select one or several extracts in the list and write the used
1847          mass and position number in the fields below the list.
1848        </para>
1849       
1850        <seeother>
1851          <other external_id="physicalbioassay.edit">Edit physical bioassay</other>
1852          <other external_id="annotations.edit">Annotations &amp; parameters</other>
1853          <other external_id="annotations.edit.inherited">Inherited annotations</other>
1854        </seeother>
1855        </helptext>
1856       
1857      </sect2>
1858     
1859     
1860    <para>
1861      The <guilabel>Annotations</guilabel> tab allows BASE users to use
1862      annotation types to refine bioassay description. More about annotating items
1863      can be read in <xref linkend="annotations.annotating" />
1864    </para>
1865       
1866    <para>
1867      This <guilabel>Inherited annotations</guilabel> tab contains a list of those annotations
1868      that are inherited from the bioassay's parents. Information about working with inherited
1869      annotations can be found in <xref linkend="annotations.inheriting" />.
1870    </para>
1871     
1872  </sect1>
1873</chapter>
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