source: trunk/doc/src/docbook/user/biomaterials.xml @ 5782

Last change on this file since 5782 was 5782, checked in by Nicklas Nordborg, 10 years ago

References #1590: Documentation cleanup

Restructured documentation to generate shorter filenames.

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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 5782 2011-10-04 13:43:16Z 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</title>
31  <sect1 id="biomaterial.introduction">
32    <?dbhtml filename="introduction.html" ?>
33    <title>Introduction</title>
34    <para>
35      The generic term biomaterial refers to any biological material used in an experiment.
36      Biomaterial is divided in three main components, <emphasis>biosources</emphasis>, <emphasis>samples</emphasis>
37      and <emphasis>extracts</emphasis>. The biomaterials can then be subclassified further by
38      the use of subtypes (see <xref linkend="subtypes"/>). BASE has, for example, defined two extracts subtypes:
39      <emphasis>Labeled extract</emphasis> (used in microarray experiments)
40      and <emphasis>Library</emphasis> (used in sequencing experiments).   
41      The order used in presenting those entities is not innocuous as it represents the
42      sequence of transformation a source material undergoes until it is in a state compatible
43      for further exeperimental processing. This progression is actually
44      mimicked in the BASE
45      <guimenu>Biomaterial LIMS</guimenu>
46      menu again to insist on this natural progression.
47    </para>
48    <itemizedlist>
49      <listitem>
50        <simpara>
51          Biosources correspond to the native biological entity used in an experiment
52          prior to any treatment.
53        </simpara>
54      </listitem>
55      <listitem>
56        <simpara>
57          Samples are central to BASE to describe the sample processing. So samples can
58          be created from other samples if user want to track sample processing event in a
59          finely granular fashion.
60        </simpara>
61      </listitem>
62      <listitem>
63        <simpara>
64          Extracts correspond to nucleic acid material extracted from a tissue sample or a
65          cell culture sample.
66        </simpara>
67      </listitem>
68    </itemizedlist>
69    <para>
70      BASE allows users to create any of the these entities fairly freely, however it is
71      expected that users will follow the natural path of the laboratory workflow.
72    </para>
73    <tip>
74      <para>
75        It is highly recommended that you have read
76        <xref linkend="webclient.items" />
77        before continuing with this chapter.
78      </para>
79    </tip>
80  </sect1>
81 
82  <sect1 id="biomaterials.biosources">
83    <?dbhtml filename="biosources.html" ?>
84    <title>Biosources</title>
85
86
87    <para>
88      Biosources correspond to the native biological entity used in an experiment prior to any treatment.
89      Biosources can be added to BASE by most users and are managed from <menuchoice>
90        <guimenu>Biomaterial LIMS</guimenu>
91        <guimenuitem>Biosources</guimenuitem>
92      </menuchoice>.
93      Use the &gbNew; button to create a new biosource. This brings up the dialog below.
94    </para>
95
96      <figure id="biomaterials.figures.biosource-tab-1">
97        <title>Biosource properties</title>
98        <screenshot>
99          <mediaobject>
100            <imageobject>
101              <imagedata 
102                fileref="figures/biosource-tab-1.png" format="PNG" />
103            </imageobject>
104          </mediaobject>
105        </screenshot>
106      </figure>
107      <helptext external_id="biosource.edit" title="Biosource properties">
108
109        <variablelist>
110          <varlistentry>
111            <term>
112              <guilabel>Name</guilabel>
113            </term>
114            <listitem>
115              <para>
116                This is the only mandatory field. BASE by default assigns
117                <replaceable>New biosource</replaceable>
118                as name but it is advised to provide unique sensible names.
119              </para>
120            </listitem>
121          </varlistentry>
122          <varlistentry>
123            <term>
124              <guilabel>Type</guilabel>
125            </term>
126            <listitem>
127              <para>
128              The subtype of the biosource. The list
129              may evolve depending on additions by the server
130              administrator. Selecting the proper subtype
131              is recommended and enables BASE to automatically guess
132              the most likely subtype when creating child biomaterial.
133              <nohelp>
134              See <xref linkend="subtypes" /> for more information.
135              </nohelp>
136              </para>
137            </listitem>
138          </varlistentry>
139          <varlistentry>
140            <term>
141              <guilabel>External ID</guilabel>
142            </term>
143            <listitem>
144              <para>
145                An external reference identifiers (e.g. a patient identification
146                code) can be supplied using this field.
147              </para>
148            </listitem>
149          </varlistentry>
150          <varlistentry>
151            <term>
152              <guilabel>Description</guilabel>
153            </term>
154            <listitem>
155              <para>A free text description can be supplied using this field.</para>
156            </listitem>
157          </varlistentry>
158        </variablelist>
159        <seeother>
160          <other external_id="annotations.edit">Annotations</other>
161        </seeother>
162      </helptext>
163
164      <para>
165        The <guilabel>Annotations</guilabel> tab allows BASE users to use
166        annotation types to refine biosource description. More about annotating items
167        can be read in <xref linkend="annotations.annotating" />
168      </para>
169
170  </sect1>
171  <sect1 id="biomaterial.samples">
172    <?dbhtml filename="samples.html" ?>
173    <title>Samples</title>
174    <para>
175      Samples result from processing events applied to biosource material or other samples
176      before they are turned into an extract. In other words, samples can be created from
177      biosource items or from one or more sample items. When a sample is created from several
178      other samples, a pooling event is performed.
179    </para>
180    <para>
181      For every step of transformation from biosource to sample, it is possible to provide
182      information about the protocol used to perform this task. It is not enforced in BASE
183      but it should serve as guidance when devising the granularity of the sample processing
184      task. Also, it is good practice to provide protocol information to ensure MIAME
185      compliance.
186    </para>
187    <para>
188      Use
189      <menuchoice>
190        <guimenu>Biomaterial LIMS</guimenu>
191        <guimenuitem>Samples</guimenuitem>
192      </menuchoice>
193      to get to the list of samples.
194    </para>
195   
196    <sect2 id="biomaterial.samples.create">
197      <title>Create sample</title>
198   
199      <para>
200        Beside the common way, using the &gbNew; button, a sample can be created in one of
201        the following ways:
202      </para>
203        <variablelist>
204          <varlistentry>
205            <term>from either biosource list- or single view- page.</term>
206            <listitem>
207              <para>
208                No matter how complex the sample processing phase is, at least one
209                sample has to be anchored to a biosource. Therefore, a natural way
210                to create an sample is to click on
211                <guiicon>
212                  <inlinemediaobject>
213                    <imageobject>
214                      <imagedata fileref="figures/add.png" format="PNG" />
215                    </imageobject>
216                  </inlinemediaobject>
217                </guiicon>
218                in the <guilabel>Samples</guilabel> column of the biosource list view. There is also a
219                corresponding button,
220                <guibutton>New sample&hellip;</guibutton>
221                in the toolbar when viewing a single biosource.
222              </para>
223            </listitem>
224          </varlistentry>
225          <varlistentry>
226            <term>from the sample list page</term>
227            <listitem>
228              <para>
229                Child samples can be created from a single parent by clicking on the
230                <guiicon>
231                  <inlinemediaobject>
232                    <imageobject>
233                      <imagedata fileref="figures/add.png" format="PNG" />
234                    </imageobject>
235                  </inlinemediaobject>
236                </guiicon> icon in the <guilabel>Child samples</guilabel> column.
237                Pooled samples can be created by first selecting the parents
238                from the list of samples and then click the <guibutton>Pool&hellip;</guibutton>
239                button in the toolbar.
240              </para>
241            </listitem>
242          </varlistentry>
243        </variablelist>
244    </sect2>
245     
246    <sect2 id="biomaterial.samples.properties">
247      <title>Sample properties</title>
248        <figure id="biomaterials.figures.biosample-tab-1">
249          <title>Sample properties</title>
250          <screenshot>
251            <mediaobject>
252              <imageobject>
253                <imagedata 
254                  fileref="figures/biosample-tab-1.png" format="PNG" />
255              </imageobject>
256            </mediaobject>
257          </screenshot>
258        </figure>
259        <helptext external_id="sample.edit" title="Edit sample">
260          <variablelist>
261            <varlistentry>
262              <term>
263                <guilabel>Name</guilabel>
264              </term>
265              <listitem>
266                <para>
267                  The sample's name (required). BASE by default assigns names to
268                  samples (by suffixing
269                  <replaceable>s#</replaceable>
270                  when creating a sample from an existing biosource or
271                  <replaceable>New Sample</replaceable>
272                  otherwise) but it is possible to edit at will.
273                </para>
274              </listitem>
275            </varlistentry>
276            <varlistentry>
277              <term>
278                <guilabel>Type</guilabel>
279              </term>
280              <listitem>
281                <para>
282                The subtype of the sample. The list
283                may evolve depending on additions by the server
284                administrator. Selecting the proper subtype
285                is recommended and enables BASE to automatically guess
286                the most likely subtype when creating child biomaterial.
287                <nohelp>
288                See <xref linkend="subtypes" /> for more information.
289                </nohelp>
290                </para>
291              </listitem>
292            </varlistentry>
293            <varlistentry>
294              <term>
295                <guilabel>External ID</guilabel>
296              </term>
297              <listitem>
298                <para>
299                  An identification used to identify the sample outside BASE.
300                </para>
301              </listitem>
302            </varlistentry>
303            <varlistentry>
304              <term>
305                <guilabel>Original quantity</guilabel>
306              </term>
307              <listitem>
308                <para>
309                  This is meant to report information about the actual mass of
310                  sample created.
311                </para>
312              </listitem>
313            </varlistentry>
314            <varlistentry>
315              <term>
316                <guilabel>Created</guilabel>
317              </term>
318              <listitem>
319                <para>
320                  A date when the sample was created. The information can be
321                  important when running quality controls on data and account for
322                  potential confounding factor (e.g. day effect).
323                </para>
324              </listitem>
325            </varlistentry>
326            <varlistentry>
327              <term>
328                <guilabel>Registered</guilabel>
329              </term>
330              <listitem>
331                <para>The date at which the sample was entered in BASE.</para>
332              </listitem>
333            </varlistentry>
334            <varlistentry>
335              <term>
336                <guilabel>Protocol</guilabel>
337              </term>
338              <listitem>
339                <para>The protocol used to produce this sample.</para>
340              </listitem>
341            </varlistentry>
342            <varlistentry>
343              <term>
344                <guilabel>Bioplate</guilabel>
345              </term>
346              <listitem>
347                <para>The bioplate where this sample is located.</para>
348              </listitem>             
349            </varlistentry>
350            <varlistentry>
351              <term>
352                <guilabel>Biowell</guilabel>
353              </term>
354              <listitem>
355                <para>
356                  Biowell that holds this sample.
357                  <guilabel>Bioplate</guilabel> has to be defined before
358                  biowell can be selected.
359                </para>
360              </listitem>             
361            </varlistentry>
362            <varlistentry>
363              <term>
364                <guilabel>Description</guilabel>
365              </term>
366              <listitem>
367                <para>
368                  A text field to report any information that not can be captured
369                  otherwise.
370                </para>
371              </listitem>
372            </varlistentry>
373          </variablelist>
374         
375          <seeother>
376            <other external_id="sample.parents">Parents</other>
377            <other external_id="annotations.edit">Annotations &amp; parameters</other>
378            <other external_id="annotations.edit.inherited">Inherited annotations</other>
379          </seeother>
380        </helptext>
381    </sect2>
382   
383    <sect2 id="biomaterial.samples.parents">
384      <title>Sample parents</title>
385        <figure id="biomaterials.figures.biosample-tab-2">
386          <title>Sample parents</title>
387          <screenshot>
388            <mediaobject>
389              <imageobject>
390                <imagedata 
391                  fileref="figures/biosample-tab-2.png" format="PNG" />
392              </imageobject>
393            </mediaobject>
394          </screenshot>
395        </figure>
396       
397        <helptext external_id="sample.parents" title="Sample's parents">
398          <para>
399            This is meant to keep track of the sample origin. BASE
400            distinguishes between two cases which are controlled by the
401            <guilabel>Parent type</guilabel>
402            radio-button in the edit pop-up window.
403          </para>
404          <itemizedlist>
405            <listitem>
406              <para>
407                If the parent is a biosource the radio-button is set to
408                <guilabel>Biosource</guilabel>. Only a single biosource
409                can be used as the parent. This option is automatically
410                selected if the user selects a biosource with the
411                <guibutton>Select biosource</guibutton> button.
412              </para>
413            </listitem>
414            <listitem>
415              <para>
416                When the parent is one or several other samples the radio-button is
417                set to <guilabel>Sample</guilabel>. This option is automatically
418                selected if the user add samples with the <guibutton>Add samples</guibutton> button.           
419                For each parent sample, it is
420                possible to specify the amount used in µg. This will automatically
421                update the <guilabel>remaining quantity</guilabel> of the parent.
422              </para>
423            </listitem>
424          </itemizedlist>
425         
426          <seeother>
427            <other external_id="sample.edit">Sample properties</other>
428            <other external_id="annotations.edit">Annotations &amp; parameters</other>
429            <other external_id="annotations.edit.inherited">Inherited annotations</other>
430          </seeother>
431        </helptext>
432    </sect2>
433    <para>
434      The <guilabel>Annotations</guilabel> tab allows BASE users to use
435      annotation types to refine sample description. More about annotating items
436      can be read in <xref linkend="annotations.annotating" />
437    </para>
438       
439    <para>
440      This <guilabel>Inherited annotations</guilabel> tab contains a list of those annotations
441      that are inherited from the sample's parents. Information about working with inherited
442      annotations can be found in <xref linkend="annotations.inheriting" />.
443    </para>
444  </sect1>
445
446  <sect1 id="biomaterials.extracts">
447    <?dbhtml filename="extracts.html" ?>
448    <title>Extracts</title>
449    <para>
450      Extract items should be used to describe the events that transform a sample material
451      into an extract material. An extract can be created from one sample item or from one or
452      more extract items. When an extract is created from several other extracts, a pooling
453      event is performed.
454    </para>
455    <para>
456      During the transformation from samples to extracts, it is possible to provide
457      information about the protocol used to perform this task. It is not enforced in BASE
458      but it should serve as guidance when devising the granularity of the sample processing
459      task. Also, it is good practice to provide protocol information.
460    </para>
461    <para>
462      Use
463      <menuchoice>
464        <guimenu>Biomaterial LIMS</guimenu>
465        <guimenuitem>Extracts</guimenuitem>
466      </menuchoice>
467      to get to the list of extracts.
468    </para>
469    <sect2 id="biomaterials.extracts.create">
470      <title>Create extract</title>
471      <para>
472        Beside the common way, using the &gbNew; button, an extract can be created in one of
473        the following ways:
474        <variablelist>
475          <varlistentry>
476            <term>from either sample list- or single view- page.</term>
477            <listitem>
478              <para>
479                No matter how complex the extract processing phase is, at least one
480                extract has to be anchored to a sample. Therefore, a natural way to
481                create an extract is to click on
482                <guiicon>
483                  <inlinemediaobject>
484                    <imageobject>
485                      <imagedata fileref="figures/add.png" format="PNG" />
486                    </imageobject>
487                  </inlinemediaobject>
488                </guiicon>
489                in the <guilabel>Child extracts</guilabel> column for the sample that should be a parent of the
490                extract.  There is also a corresponding button,
491                <guibutton>New child extract&hellip;</guibutton>
492                in the toolbar when viewing a single sample.
493              </para>
494            </listitem>
495          </varlistentry>
496          <varlistentry>
497            <term>from the extract list page</term>
498            <listitem>
499              <para>
500                Child extracts can be created from a single parent by clicking on the
501                <guiicon>
502                  <inlinemediaobject>
503                    <imageobject>
504                      <imagedata fileref="figures/add.png" format="PNG" />
505                    </imageobject>
506                  </inlinemediaobject>
507                </guiicon> icon in the <guilabel>Child extracts</guilabel> column.
508                Pooled extract can be created by first selecting the parents
509                from the list of extracts and then press
510                <guibutton>Pool&hellip;</guibutton>
511                in the toolbar. The selected extracts will be put into the parent
512                property.
513              </para>
514            </listitem>
515          </varlistentry>
516        </variablelist>
517      </para>
518    </sect2>
519    <sect2 id="biomaterials.extracts.properties">
520      <title>Extract properties</title>
521     
522        <figure id="biomaterials.figures.extract-tab-1">
523          <title>Extract properties</title>
524          <screenshot>
525            <mediaobject>
526              <imageobject>
527                <imagedata 
528                  fileref="figures/extract-tab-1.png" format="PNG" />
529              </imageobject>
530            </mediaobject>
531          </screenshot>
532        </figure>
533        <helptext external_id="extract.edit" title="Edit extract">
534          <variablelist>
535            <varlistentry>
536              <term>
537                <guilabel>Name</guilabel>
538              </term>
539              <listitem>
540                <para>
541                  A mandatory field for providing the extract name. BASE by
542                  default assigns names to extract (by suffixing
543                  <replaceable>e#</replaceable>
544                  when creating an extract from an existing sample or
545                  <replaceable>New extract</replaceable>
546                  otherwise) but it is possible to edit it at will.
547                </para>
548              </listitem>
549            </varlistentry>
550            <varlistentry>
551              <term>
552                <guilabel>Type</guilabel>
553              </term>
554              <listitem>
555                <para>
556                The subtype of the extract. The list
557                may evolve depending on additions by the server
558                administrator. Selecting the proper subtype
559                is recommended and enables BASE to automatically guess
560                the most likely subtype when creating child biomaterial and
561                bioassays.
562                <nohelp>
563                See <xref linkend="subtypes" /> for more information.
564                </nohelp>
565                </para>
566              </listitem>
567            </varlistentry>
568            <varlistentry>
569              <term>
570                <guilabel>Tag</guilabel>
571              </term>
572              <listitem>
573                <para>
574                  If the extract has been marked with a tag, select it here. Note
575                  that the subtype of the extract usually limits what kind of tag
576                  that can be used. For example, a <emphasis>labeled extract</emphasis>
577                  should be tagged with a <emphasis>label</emphasis>.
578                </para>
579              </listitem>
580            </varlistentry>
581            <varlistentry>
582              <term>
583                <guilabel>External ID</guilabel>
584              </term>
585              <listitem>
586                <para>The extracts identification outside BASE</para>
587              </listitem>
588            </varlistentry>
589            <varlistentry>
590              <term>
591                <guilabel>Original quantity</guilabel>
592              </term>
593              <listitem>
594                <para>
595                  Holds information about the original mass of the created
596                  extract.
597                </para>
598              </listitem>
599            </varlistentry>
600            <varlistentry>
601              <term>
602                <guilabel>Created</guilabel>
603              </term>
604              <listitem>
605                <para>
606                  The date when the extract was created. The information can be
607                  important when running quality controls on data and account for
608                  potential confounding factor (e.g. day effect)
609                </para>
610              </listitem>
611            </varlistentry>
612            <varlistentry>
613              <term>
614                <guilabel>Registered</guilabel>
615              </term>
616              <listitem>
617                <para>
618                  This is automatically populated with a date at which the sample
619                  was entered in BASE system.
620                </para>
621              </listitem>
622            </varlistentry>
623            <varlistentry>
624              <term>
625                <guilabel>Protocol</guilabel>
626              </term>
627              <listitem>
628                <para>
629                  The extraction protocol that was used to produce the extract.
630                </para>
631              </listitem>
632            </varlistentry>
633            <varlistentry>
634              <term>
635                <guilabel>Bioplate</guilabel>
636              </term>
637              <listitem>
638                <para>The bioplate where this extract is located.</para>
639              </listitem>             
640            </varlistentry>
641            <varlistentry>
642              <term>
643                <guilabel>Biowell</guilabel>
644              </term>
645              <listitem>
646                <para>
647                  Biowell that holds this extract.
648                  <guilabel>Bioplate</guilabel> has to be defined before
649                  biowell can be selected.
650                </para>
651              </listitem>             
652            </varlistentry>
653            <varlistentry>
654              <term>
655                <guilabel>Description</guilabel>
656              </term>
657              <listitem>
658                <para>
659                  A text field to report any information that not can be captured
660                  otherwise.
661                </para>
662              </listitem>
663            </varlistentry>
664          </variablelist>
665          <seeother>
666            <other external_id="extract.edit.parents">Parents</other>
667            <other external_id="annotations.edit">Annotations &amp; parameters</other>
668            <other external_id="annotations.edit.inherited">Inherited annotations</other>
669          </seeother>
670        </helptext>
671  </sect2>
672 
673  <sect2 id="biomaterials.extracts.parents">
674    <title>Extract parents</title>
675        <figure id="biomaterials.figures.extract-tab-2">
676          <title>Extract parents</title>
677          <screenshot>
678            <mediaobject>
679              <imageobject>
680                <imagedata 
681                  fileref="figures/extract-tab-2.png" format="PNG" />
682              </imageobject>
683            </mediaobject>
684          </screenshot>
685        </figure>
686        <helptext external_id="extract.parents" title="Extract's parents">
687          <para>
688            This is meant to keep track of the extract origin. BASE
689            distinguishes between two cases which are controlled by the
690            <guilabel>Parent type</guilabel>
691            radio-button in the edit pop-up window.
692          </para>
693          <itemizedlist>
694            <listitem>
695              <para>
696                If the parent is a sample the radio-button is set to
697                <guilabel>Sample</guilabel>. Only a single sample
698                can be used as the parent. This option is automatically
699                selected if the user selects a sample with the
700                <guibutton>Select sample</guibutton> button.
701              </para>
702            </listitem>
703            <listitem>
704              <para>
705                When the parent is one or several other extracts the radio-button is
706                set to <guilabel>Extract</guilabel>. This option is automatically
707                selected if the user add extracts with the <guibutton>Add extracts</guibutton> button.           
708              </para>
709            </listitem>
710          </itemizedlist>
711         
712          <para>
713            For each parent item, it is
714            possible to specify the amount used in micrograms. This will automatically
715            update the <guilabel>remaining quantity</guilabel> of the parent.
716          </para>
717         
718          <seeother>
719            <other external_id="extract.edit">Extract properties</other>
720            <other external_id="annotations.edit">Annotations &amp; parameters</other>
721            <other external_id="annotations.edit.inherited">Inherited annotations</other>
722          </seeother>
723        </helptext>
724
725    <para>
726      The <guilabel>Annotations</guilabel> tab allows BASE users to use
727      annotation types to refine extract description. More about annotating items
728      can be read in <xref linkend="annotations.annotating" />
729    </para>
730       
731    <para>
732      This <guilabel>Inherited annotations</guilabel> tab contains a list of those annotations
733      that are inherited from the extract's parents. Information about working with inherited
734      annotations can be found in <xref linkend="annotations.inheriting" />.
735    </para>
736
737
738  </sect2>
739
740
741  </sect1>
742
743  <sect1 id="biomaterials.tags">
744    <?dbhtml filename="tags.html" ?>
745    <title>Tags</title>
746    <para>
747      Before attempting to create tagged extracts, users should make sure that the
748      appropriate tag object is present in BASE. To browse the list of tags, go to
749      <menuchoice>
750        <guimenu>Biomaterial LIMS</guimenu>
751        <guimenuitem>Tags</guimenuitem>
752      </menuchoice>
753    </para>
754
755    <figure id="biomaterials.figures.tags">
756      <title>Tag properties</title>
757      <screenshot>
758        <mediaobject>
759          <imageobject>
760            <imagedata 
761              fileref="figures/edit_tag.png" format="PNG" />
762          </imageobject>
763        </mediaobject>
764      </screenshot>
765    </figure>
766
767    <helptext external_id="tag.edit" title="Edit tag">
768      <para>
769        The tag item is very simple and does not need much explanation. There are only
770        a few properties for a tag.
771        <variablelist>
772          <varlistentry>
773            <term>
774              <guilabel>Name</guilabel>
775            </term>
776            <listitem>
777              <para>The name of the tag (required).</para>
778            </listitem>
779          </varlistentry>
780          <varlistentry>
781            <term>
782              <guilabel>Type</guilabel>
783            </term>
784            <listitem>
785              <para>
786              The subtype of the tag. The list
787              may evolve depending on additions by the server
788              administrator. Selecting the proper subtype
789              is important and enables BASE to automatically guess
790              the most likely tag when creating tagged extracts (eg.
791              a <emphasis>Label</emphasis> for a <emphasis>Labeled extract</emphasis> 
792              or a <emphasis>Barcode</emphasis> for a <emphasis>Library</emphasis>).
793              <nohelp>
794              See <xref linkend="subtypes" /> for more information.
795              </nohelp>
796              </para>
797            </listitem>
798          </varlistentry>
799          <varlistentry>
800            <term>
801              <guilabel>Description</guilabel>
802            </term>
803            <listitem>
804              <para>
805                An explaining text or other information associated with the
806                tag.
807              </para>
808            </listitem>
809          </varlistentry>
810        </variablelist>
811      </para>
812    </helptext>
813
814  </sect1>
815
816 
817  <sect1 id="biomaterials.bioplates">
818    <?dbhtml filename="bioplates.html" ?>
819    <title>Bioplates</title>
820    <para>
821      With bioplates it is possible to organize biomaterial such as samples and extracts
822      into wells. Each plate has a number of wells that is defined by the plate geometry.
823    </para>
824    <para>
825      Use
826      <menuchoice>
827        <guimenu>Biomaterial LIMS</guimenu>
828        <guimenuitem>Bioplates</guimenuitem>
829      </menuchoice>
830      to get to the list of bioplates.   
831    </para>
832    <sect2 id="biomaterials.bioplate.properties">
833      <title>Bioplate properties</title>     
834
835      <figure id="biomaterials.figures.bioplate-tab-1">
836        <title>Bioplate properties</title>
837        <screenshot>
838          <mediaobject>
839            <imageobject>
840              <imagedata 
841                fileref="figures/bioplate-tab-1.png" format="PNG" />
842            </imageobject>
843          </mediaobject>
844        </screenshot>
845      </figure>
846
847      <helptext external_id="bioplate.edit" title="Edit bioplate">
848        <para>
849          <variablelist>
850            <varlistentry>
851              <term><guilabel>Name</guilabel></term>
852              <listitem>
853                <para>
854                  The bioplate name. The name does not have to be unique but it is
855                  recommended to keep it unique. BASE by default assigns
856                  <replaceable>New bioplate</replaceable> as name.
857                  This field is mandatory.
858                </para>
859              </listitem>
860            </varlistentry>
861            <varlistentry>
862              <term><guilabel>Bioplate type</guilabel></term>
863              <listitem>
864                <para>
865                  The type of the bioplate may be a generic storage plate that
866                  can store any type of biomaterial or a locked plate that
867                  can only store a single type of biomaterial. This field
868                  is mandatory and can only be set for new bioplates.
869                  <nohelp>See <xref linkend="biomaterials.bioplatetypes" /> for more
870                  information.</nohelp>
871                </para>
872              </listitem>             
873            </varlistentry>
874            <varlistentry>
875              <term><guilabel>Plate geometry</guilabel></term>
876              <listitem>
877                <para>
878                  Information about the plate design defining the
879                  number of  rows and columns on the bioplate.
880                  This field is mandatory and can only be set for new bioplates.
881                </para>
882              </listitem>             
883            </varlistentry>
884            <varlistentry>
885              <term><guilabel>Freezer</guilabel></term>
886              <listitem>
887                <para>The freezer where the bioplate is stored. Optional.</para>
888              </listitem>
889            </varlistentry>
890            <varlistentry>
891              <term><guilabel>Barcode</guilabel></term>
892              <listitem>
893                <para>
894                  Barcode of the bioplate.
895                  Optional.
896                </para>
897              </listitem>
898            </varlistentry>
899            <varlistentry>
900              <term><guilabel>Description</guilabel></term>
901              <listitem>
902                <para>
903                  Other useful information about the bioplate. Optional.
904                </para>
905              </listitem>
906            </varlistentry>
907          </variablelist>
908        </para>
909       
910        <seeother>
911          <other external_id="annotations.edit">Annotations</other>
912        </seeother>
913      </helptext>
914     
915    <para>
916      The <guilabel>Annotations</guilabel> tab allows BASE users to use
917      annotation types to refine bioplate description. More about annotating items
918      can be read in <xref linkend="annotations.annotating" />
919    </para>
920
921    </sect2>
922    <sect2 id="biomaterials.bioplate.biowells">
923      <title>Biowells</title>
924      <para>
925        Biowells existence are managed through the bioplate they
926        belong to. Creating a bioplate will automatically create the
927        biowells (as given by the selected geometry) on the plate.
928        The wells are initially empty. To add biomaterial to the plate
929        go to the single-item view page for the bioplate. This page
930        includes an overview of the layout of the plate. Clicking
931        on an empty well will open a popup dialog that allows you
932        to select a biomaterial. The same dialog can also be accessed from
933        the <guilabel>Wells</guilabel> tab. Assigning a biomaterial to a
934        biowell can also be done when editing a sample or extract, or
935        by using the <link linkend="biomaterials.placeonplate">Place-on-plate
936        wizard</link>.
937      </para>
938     
939      <figure id="biomaterials.figures.biowell">
940        <title>Biowell properties</title>
941        <screenshot>
942          <mediaobject>
943            <imageobject>
944              <imagedata 
945                fileref="figures/biowell.png" format="PNG" />
946            </imageobject>
947          </mediaobject>
948        </screenshot>
949      </figure>
950
951        <helptext external_id="biowell.edit" title="Edit biowell">
952          <para>
953            <variablelist>
954              <varlistentry>
955                <term><guilabel>Bioplate</guilabel></term>
956                <listitem>
957                  <para>
958                    Shows which bioplate the biowell is located on.
959                    This property is read-only.
960                  </para>
961                </listitem>
962              </varlistentry>
963              <varlistentry>             
964                <term><guilabel>Well location</guilabel></term>
965                <listitem>
966                  <para>
967                    The biowell location on the bioplate in row+column format.
968                    This property is read-only.
969                  </para>
970                </listitem>
971              </varlistentry>
972              <varlistentry>
973                <term><guilabel>Biomaterial type</guilabel></term>
974                <listitem>
975                  <para>
976                    The type of biomaterial stored in this biowell. This
977                    property must be selected before before a
978                    biomaterial can be selected. On some plates this
979                    is locked due to settings in the bioplate's type.
980                  </para>
981                </listitem>
982              </varlistentry>
983              <varlistentry>             
984                <term><guilabel>Biomaterial</guilabel></term>
985                <listitem>
986                  <para>
987                    Name of the biomaterial in this biowell. Before changing
988                    this you must select the appropriate <guilabel>Biomaterial type</guilabel>.
989                    A biomaterial can only be placed in a single well. If the selected
990                    biomaterial is already placed in another location it will be moved.
991                  </para>
992                </listitem>
993              </varlistentry>
994            </variablelist>
995          </para>
996        </helptext> 
997    </sect2>
998   
999    <sect2 id="biomaterials.bioplatetypes">
1000      <title>Bioplate types</title>
1001     
1002      <helptext external_id="bioplatetype.view.properties" title="Bioplate types">
1003      <para>
1004        Bioplate types are used to subclassify bioplates and may put restrictions on them.
1005        BASE ships with a few pre-defined bioplate types. The <emphasis>Storage plate</emphasis> type
1006        is a generic plate type that can be used for all types of biomaterial and doesn't
1007        have any other restrictions on it. The reaction plate types are locked to a single
1008        type of biomaterial and have a restriction that biomaterial can never be moved out from
1009        a well once it has been placed there.
1010      </para>
1011      </helptext>
1012     
1013      <figure id="biomaterials.figures.bioplatetype">
1014        <title>Bioplate type properties</title>
1015        <screenshot>
1016          <mediaobject>
1017            <imageobject>
1018              <imagedata 
1019                fileref="figures/edit_bioplatetype.png" format="PNG" />
1020            </imageobject>
1021          </mediaobject>
1022        </screenshot>
1023      </figure>
1024     
1025          <helptext external_id="bioplatetype.edit" title="Edit bioplate type">
1026          <para>
1027            <variablelist>
1028              <varlistentry>
1029                <term><guilabel>Name</guilabel></term>
1030                <listitem>
1031                  <para>
1032                    The name of the bioplate type.
1033                  </para>
1034                </listitem>
1035              </varlistentry>
1036              <varlistentry>             
1037                <term><guilabel>Biomaterial type</guilabel></term>
1038                <listitem>
1039                  <para>
1040                    Select if bioplates using this type should be locked to
1041                    specific biomaterial type or not. This property can only
1042                    be set for new bioplate types.
1043                  </para>
1044                </listitem>
1045              </varlistentry>
1046              <varlistentry>
1047                <term><guilabel>Well lock mode</guilabel></term>
1048                <listitem>
1049                  <para>
1050                    This option controls the wells on bioplates using this type.
1051                    There are four options:
1052                    <itemizedlist>
1053                      <listitem>
1054                        <para><guilabel>Unlocked</guilabel>:
1055                          The wells are unlocked and biomaterial can be added
1056                          and removed freely any number of times.
1057                        </para>
1058                      </listitem>
1059                      <listitem>
1060                        <para><guilabel>Locked after add+clear</guilabel>:
1061                          A biomaterial can be placed once in the well and
1062                          then moved to another bioplate. After that the well
1063                          becomes locked and it is not possible to add a
1064                          different biomaterial to it.
1065                        </para>
1066                      </listitem>
1067                      <listitem>
1068                        <para><guilabel>Locked after add</guilabel>:
1069                          The wells are locked as soon as biomaterial is
1070                          added to them. The biomaterial can't be moved to another
1071                          place or be replaced with other biomaterial.
1072                        </para>
1073                      </listitem>
1074                      <listitem>
1075                        <para><guilabel>Locked at plate creation</guilabel>:
1076                          The wells are locked as soon as the bioplate has been
1077                          saved to the database. This lock mode is primarily intended
1078                          to be used when plug-ins are creating and populating the
1079                          bioplate as a single event.
1080                        </para>
1081                      </listitem>
1082                    </itemizedlist>
1083                  </para>
1084                </listitem>
1085              </varlistentry>
1086              <varlistentry>             
1087                <term><guilabel>Description</guilabel></term>
1088                <listitem>
1089                  <para>
1090                    Other useful information about the bioplate type. Optional.
1091                  </para>
1092                </listitem>
1093              </varlistentry>
1094            </variablelist>
1095          </para>
1096        </helptext> 
1097    </sect2>
1098   
1099    <sect2 id="biomaterials.bioplateevents">
1100      <title>Bioplate events</title>
1101   
1102      <para>
1103        Certain actions can be applied collectively to the biomaterial on a bioplate,
1104        either as a whole or a subset that is picked by the user.
1105        A list of the available actions can be found on the list page
1106        <menuchoice>
1107          <guimenu>Biomaterial LIMS</guimenu>
1108          <guimenuitem>Bioplate event types</guimenuitem>
1109        </menuchoice>.
1110       
1111        Although it is possible to create more event types here there is usually no
1112        meaning to do so, since each event needs a specailized GUI wizard to take
1113        care of it. The possibility to add more event types should be seen as an
1114        opportunity for extension development.
1115      </para>
1116     
1117      <sect3 id="biomaterials.placeonplate">
1118        <title>The place-on-plate event</title>
1119     
1120        <figure id="biomaterials.figures.placeonplate">
1121          <title>Place on plate wizard</title>
1122          <screenshot>
1123            <mediaobject>
1124              <imageobject>
1125                <imagedata 
1126                  fileref="figures/place_on_plate.png" format="PNG" />
1127              </imageobject>
1128            </mediaobject>
1129          </screenshot>
1130        </figure>
1131     
1132        <helptext external_id="bioplateevent.place-on-plate" title="Place on plate">
1133        <para>
1134          This event is available on the sample and extract list pages and can be used
1135          to place multiple biomaterial on a bioplate in one go. Click on
1136          the <guibutton>Place on plate</guibutton> button to start the wizard.
1137          The wizard will automatically use the selected biomaterials or, if none
1138          are selected, all listed biomaterials that aren't alredy located on a
1139          plate.
1140
1141          <variablelist>
1142            <varlistentry>
1143              <term><guilabel>Event name</guilabel></term>
1144              <listitem>
1145                <para>
1146                  Give a name to the event, or keep the suggested name.
1147                </para>
1148              </listitem>
1149            </varlistentry>
1150            <varlistentry>
1151              <term><guilabel>Event date</guilabel></term>
1152              <listitem>
1153                <para>
1154                  The date of the event.
1155                </para>
1156              </listitem>
1157            </varlistentry>
1158            <varlistentry>
1159              <term><guilabel>Protocol</guilabel></term>
1160              <listitem>
1161                <para>
1162                  The protocol used in the event, if any.
1163                </para>
1164              </listitem>
1165            </varlistentry>
1166            <varlistentry>
1167              <term><guilabel>Hardware</guilabel></term>
1168              <listitem>
1169                <para>
1170                  The hardware item used in the event, if any.
1171                </para>
1172              </listitem>
1173            </varlistentry>
1174            <varlistentry>
1175              <term><guilabel>Description</guilabel></term>
1176              <listitem>
1177                <para>
1178                  Other comments about the event.
1179                </para>
1180              </listitem>
1181            </varlistentry>
1182            <varlistentry>
1183              <term><guilabel>Select plate...</guilabel></term>
1184              <listitem>
1185                <para>
1186                  You need to select an existing plate on which the
1187                  biomaterial should be placed. It is only possible to
1188                  use one plate in each event. If you want to place biomaterial
1189                  on more than one plate, the wizard must be repeated for
1190                  each destination plate.
1191                </para>
1192              </listitem>
1193            </varlistentry>
1194            <varlistentry>
1195              <term><guilabel>Clear</guilabel></term>
1196              <listitem>
1197                <para>
1198                  Clear all current placement.
1199                </para>
1200              </listitem>
1201            </varlistentry>
1202            <varlistentry>
1203              <term><guilabel>Place by row/column</guilabel></term>
1204              <listitem>
1205                <para>
1206                  Automatically place the remaining biomaterial by filling empty wells,
1207                  starting with rows or columns.
1208                </para>
1209              </listitem>
1210            </varlistentry>
1211            <varlistentry>
1212              <term><guilabel>Items to place</guilabel></term>
1213              <listitem>
1214                <para>
1215                  This column contains the biomaterial that should be placed on the plate.
1216                  When a destination plate has been selected, it is displayed as a grid to
1217                  the right. To place a biomaterial either use the <guibutton>Plate by row</guibutton>
1218                  or <guibutton>Place by column</guibutton> buttons, or select an item in this
1219                  list. When an item has been selected, click on the destination well on the
1220                  plate. The coordinate of the well is displayed in the gray area before the
1221                  biomaterial name and a line is drawn between it and the destination well.
1222                  The destination well is also marked with an icon.
1223                  If the <guilabel>Auto-select next unmapped item</guilabel> is selected
1224                  the selection is automatically moved to the next biomaterial which can then
1225                  be placed by selecting another destination well. If a mistake is made it is
1226                  easy to correct. Simply re-select the item and then click on the correct well.
1227                </para>
1228              </listitem>
1229            </varlistentry>
1230
1231          </variablelist>
1232         
1233          When the biomaterial has been placed on the plate (it is not neccessary to place all of them)
1234          click on <guibutton>Save</guibutton> to store everything. BASE will create a plate event
1235          for the selected destination plate and "other"-type events for each biomaterial that was
1236          placed on it.
1237        </para>
1238        </helptext> 
1239      </sect3>
1240
1241      <sect3 id="biomaterials.move">
1242        <title>The move biomaterials event</title>
1243     
1244        <figure id="biomaterials.figures.move">
1245          <title>Move biomaterials wizard</title>
1246          <screenshot>
1247            <mediaobject>
1248              <imageobject>
1249                <imagedata 
1250                  fileref="figures/move_biomaterials.png" format="PNG" />
1251              </imageobject>
1252            </mediaobject>
1253          </screenshot>
1254        </figure>
1255     
1256        <helptext external_id="bioplateevent.move" title="Move biomaterials">
1257        <para>
1258          This event is available on the single-item view page of a bioplate
1259          and can be used to move biomaterial from one plate to another. Click on
1260          the <guibutton>Move biomaterial</guibutton> button to start the wizard.
1261          <variablelist>
1262            <varlistentry>
1263              <term><guilabel>Event name</guilabel></term>
1264              <listitem>
1265                <para>
1266                  Give a name to the event, or keep the suggested name.
1267                </para>
1268              </listitem>
1269            </varlistentry>
1270            <varlistentry>
1271              <term><guilabel>Event date</guilabel></term>
1272              <listitem>
1273                <para>
1274                  The date of the event.
1275                </para>
1276              </listitem>
1277            </varlistentry>
1278            <varlistentry>
1279              <term><guilabel>Protocol</guilabel></term>
1280              <listitem>
1281                <para>
1282                  The protocol used in the event, if any.
1283                </para>
1284              </listitem>
1285            </varlistentry>
1286            <varlistentry>
1287              <term><guilabel>Hardware</guilabel></term>
1288              <listitem>
1289                <para>
1290                  The hardware item used in the event, if any.
1291                </para>
1292              </listitem>
1293            </varlistentry>
1294            <varlistentry>
1295              <term><guilabel>Description</guilabel></term>
1296              <listitem>
1297                <para>
1298                  Other comments about the event.
1299                </para>
1300              </listitem>
1301            </varlistentry>
1302            <varlistentry>
1303              <term><guilabel>Select plate...</guilabel></term>
1304              <listitem>
1305                <para>
1306                  You need to select an existing plate to which the
1307                  biomaterial should be moved. It is only possible to
1308                  use one plate in each event. If you want to move biomaterial
1309                  to more than one plate, the wizard must be repeated for
1310                  each destination plate.
1311                </para>
1312              </listitem>
1313            </varlistentry>
1314            <varlistentry>
1315              <term><guilabel>Clear</guilabel></term>
1316              <listitem>
1317                <para>
1318                  Clear all current mapping between the source and destination plates.
1319                </para>
1320              </listitem>
1321            </varlistentry>
1322            <varlistentry>
1323              <term><guilabel>Place by row/column</guilabel></term>
1324              <listitem>
1325                <para>
1326                  Automatically move the remaining biomaterial by filling empty wells,
1327                  starting with rows or columns.
1328                </para>
1329              </listitem>
1330            </varlistentry>
1331            <varlistentry>
1332              <term><guilabel>Predefined mapping</guilabel></term>
1333              <listitem>
1334                <para>
1335                  Use this button to select a predefined mapping between source
1336                  and destination wells. The biomaterial will be moved according
1337                  to the mapping.
1338                </para>
1339              </listitem>
1340            </varlistentry>
1341            <varlistentry>
1342              <term><guilabel>Source plate</guilabel></term>
1343              <listitem>
1344                <para>
1345                  This displays the source plate as a grid with icons that indicate
1346                  filled and movable wells.
1347                 
1348                  When a destination plate has been selected, it is displayed as a similar grid to
1349                  the right. To move a biomaterial either use the <guibutton>Place by row</guibutton>,
1350                  <guibutton>Place by column</guibutton> or <guibutton>Predefined mapping</guibutton>
1351                  buttons, or select a well on the source plate. When a source well has been selected,
1352                  click on a well on the destination plate. A line is drawn between the source and
1353                  destination wells and the icons are updated to show what is going on. The
1354                  wells on the destination plate will also show the coordinate of the mapped
1355                  source well unless the <guilabel>Show source coordinates</guilabel>
1356                  checkbox is deselected. If a mistake is made it is
1357                  easy to correct. Simply re-select the source well and then click on the correct
1358                  destination well.
1359                   
1360                </para>
1361              </listitem>
1362            </varlistentry>
1363          </variablelist>
1364
1365          When the biomaterial has been mapped between the source and destination plates
1366          (it is not neccessary to map all of them) click on <guibutton>Save</guibutton> to store everything.
1367          BASE will create a plate event for the selected plates and "other"-type events for each
1368          biomaterial that was moved.
1369
1370        </para>
1371        </helptext>
1372      </sect3>
1373     
1374      <sect3 id="biomaterials.create_child">
1375        <title>The create child plate event</title>
1376     
1377        <figure id="biomaterials.figures.create_child_1">
1378          <title>Create child plate wizard - step 1</title>
1379          <screenshot>
1380            <mediaobject>
1381              <imageobject>
1382                <imagedata 
1383                  fileref="figures/create_child_plate_1.png" format="PNG" />
1384              </imageobject>
1385            </mediaobject>
1386          </screenshot>
1387        </figure>
1388     
1389        <helptext external_id="bioplateevent.create-child-1" title="Create child plate - step 1">
1390        <para>
1391          This event is available on the single-item view page of a bioplate
1392          when the bioplate is limited to a single type of biomaterial (eg.
1393          only samples or only extracts). The event is used to create either
1394          a child bioplate with biomaterial that is derived from the biomaterial
1395          on the parent plate or to create one or more physical bioassays. Click on
1396          the <guibutton>Create child bioplate</guibutton> button to start the wizard.
1397        </para>
1398       
1399        <para>
1400          The wizard has two steps. In the first step you set properties that
1401          are related to the event and to the creation of child plates and
1402          biomaterial. The first step is divied into three main sections.
1403        </para>
1404       
1405       
1406        <bridgehead>Event</bridgehead>
1407       
1408        <variablelist>
1409          <varlistentry>
1410            <term><guilabel>Event name</guilabel></term>
1411            <listitem>
1412              <para>
1413                Give a name to the event, or keep the suggested name.
1414              </para>
1415            </listitem>
1416          </varlistentry>
1417          <varlistentry>
1418            <term><guilabel>Event date</guilabel></term>
1419            <listitem>
1420              <para>
1421                The date of the event.
1422              </para>
1423            </listitem>
1424          </varlistentry>
1425          <varlistentry>
1426            <term><guilabel>Protocol</guilabel></term>
1427            <listitem>
1428              <para>
1429                The protocol used in the event, if any.
1430              </para>
1431            </listitem>
1432          </varlistentry>
1433          <varlistentry>
1434            <term><guilabel>Hardware</guilabel></term>
1435            <listitem>
1436              <para>
1437                The hardware item used in the event, if any.
1438              </para>
1439            </listitem>
1440          </varlistentry>
1441          <varlistentry>
1442            <term><guilabel>Description</guilabel></term>
1443            <listitem>
1444              <para>
1445                Other comments about the event.
1446              </para>
1447            </listitem>
1448          </varlistentry>
1449        </variablelist>
1450         
1451        <bridgehead>Child biomaterial</bridgehead>
1452        <variablelist>
1453          <varlistentry>
1454            <term><guilabel>Type</guilabel></term>
1455            <listitem>
1456              <para>
1457                The type of child items to create. If the source plate
1458                contains samples, you can select between sample and
1459                extract and if the source plate contains extract you
1460                can select between extract and physical bioassay.
1461              </para>
1462            </listitem>
1463          </varlistentry>
1464          <varlistentry>
1465            <term><guilabel>Subtype</guilabel></term>
1466            <listitem>
1467              <para>
1468                The subtype to assign to the newly created biomaterial
1469                (or physical bioassay). The list of options is automatically
1470                updated based on the selection in the <guilabel>Type</guilabel>
1471                list.
1472              </para>
1473            </listitem>
1474          </varlistentry>
1475          <varlistentry>
1476            <term><guilabel>Tag</guilabel></term>
1477            <listitem>
1478              <para>
1479                Visible when creating child extracts only. Select the tag to
1480                assign to the new extract. If no tag is selected and the
1481                source biomaterial is also extracts, the children will get the
1482                same tag as their parents.
1483              </para>
1484            </listitem>
1485          </varlistentry>
1486          <varlistentry>
1487            <term><guilabel>Original quantity</guilabel></term>
1488            <listitem>
1489              <para>
1490                The original quantity of the new biomaterial. Not visible when
1491                creating a physical bioassay.
1492              </para>
1493            </listitem>
1494          </varlistentry>
1495          <varlistentry>
1496            <term><guilabel>Used quantity</guilabel></term>
1497            <listitem>
1498              <para>
1499                The quantity that was used from the parent biomaterial
1500                in the process of creating child biomaterial.
1501              </para>
1502            </listitem>
1503          </varlistentry>
1504          <varlistentry>
1505            <term><guilabel>Description</guilabel></term>
1506            <listitem>
1507              <para>
1508                Other comments about the new biomaterial.
1509              </para>
1510            </listitem>
1511          </varlistentry>
1512        </variablelist>
1513       
1514       
1515        <bridgehead>Child plates</bridgehead>
1516        <variablelist>
1517          <varlistentry>
1518            <term><guilabel>No. of plates</guilabel></term>
1519            <listitem>
1520              <para>
1521                The number of child plates to create. The default value is 1.
1522              </para>
1523            </listitem>
1524          </varlistentry>
1525          <varlistentry>
1526            <term><guilabel>Name prefix</guilabel></term>
1527            <listitem>
1528              <para>
1529                The child plates will be named using the prefix plus a running number
1530                starting with 0. Eg. New plate.0.
1531              </para>
1532            </listitem>
1533          </varlistentry>
1534          <varlistentry>
1535            <term><guilabel>Geometry</guilabel></term>
1536            <listitem>
1537              <para>
1538                The geometry of the child plates. The default is the same
1539                geometry as the parent plate. This option is replaced with
1540                <guilabel>Size of bioassay</guilabel> when creating a
1541                physical bioassay.
1542              </para>
1543            </listitem>
1544          </varlistentry>
1545          <varlistentry>
1546            <term><guilabel>Plate type</guilabel></term>
1547            <listitem>
1548              <para>
1549                The plate type of the child plates. Not used when creating a
1550                physical bioassay.
1551              </para>
1552            </listitem>
1553          </varlistentry>
1554          <varlistentry>
1555            <term><guilabel>Freezer</guilabel></term>
1556            <listitem>
1557              <para>
1558                The freezer in which the new child plates are located. Not used
1559                when creating a physical bioassay.
1560              </para>
1561            </listitem>
1562          </varlistentry>
1563          <varlistentry>
1564            <term><guilabel>Description</guilabel></term>
1565            <listitem>
1566              <para>
1567                Other comments about the new child plates.
1568              </para>
1569            </listitem>
1570          </varlistentry>
1571        </variablelist>
1572       
1573        <seeother>
1574          <other external_id="bioplateevent.create-child-2">Create child plate - step 2</other>
1575        </seeother>
1576        </helptext>
1577
1578        <figure id="biomaterials.figures.create_child_2">
1579          <title>Create child plate wizard - step 2</title>
1580          <screenshot>
1581            <mediaobject>
1582              <imageobject>
1583                <imagedata 
1584                  fileref="figures/create_child_plate_2.png" format="PNG" />
1585              </imageobject>
1586            </mediaobject>
1587          </screenshot>
1588        </figure>
1589     
1590        <helptext external_id="bioplateevent.create-child-2" title="Create child plate - step 2">
1591        <para>
1592          The second step display the source plate and new child plates as a grid.
1593          To create child biomaterial either use the <guibutton>Place by row</guibutton>,
1594          <guibutton>Place by column</guibutton> or <guibutton>Predefined mapping</guibutton>
1595          buttons, or select a well on the source plate. When a source well has been selected,
1596          click on a well on the destination plate. A line is drawn between the source and
1597          destination wells and the icons are updated to show what is going on. The
1598          wells on the destination plate will also show the coordinate of the mapped
1599          source well unless the <guilabel>Show source coordinates</guilabel>
1600          checkbox is deselected. If a mistake is made it is
1601          easy to correct. Simply re-select the source well and then click on the correct
1602          destination well.
1603        </para>
1604       
1605        <para>
1606          When a child biomaterial is selected you have the option to override the
1607          automatially generated name. It is also possible to change the name
1608          and barcode of the child plate.
1609        </para>
1610       
1611        <note>
1612          The principle is the same when creating physical bioassays, except that no
1613          new child biomaterial is created.
1614        </note>
1615       
1616        <para>
1617          When the biomaterial has been mapped between the source and destination plates
1618          (it is not neccessary to map all of them) click on <guibutton>Save</guibutton> 
1619          to store everything. BASE will create a plate event for the selected plates
1620          and "create" or "bioassay"-type events for each biomaterial that was used.
1621        </para>
1622       
1623        <seeother>
1624          <other external_id="bioplateevent.create-child-1">Create child plate - step 1</other>
1625        </seeother>
1626       
1627        </helptext>
1628      </sect3>
1629    </sect2>
1630   
1631  </sect1>
1632 
1633  <sect1 id="biomaterials.lists">
1634    <?dbhtml filename="lists.html" ?>
1635    <title>Biomaterial lists</title>
1636   
1637    <para>
1638      TODO
1639    </para>
1640 
1641  </sect1>
1642
1643  <sect1 id="biomaterials.bioassays">
1644    <?dbhtml filename="bioassays.html" ?>
1645    <title>Physical bioassays</title>
1646    <para>
1647      A physical bioassay represents the application of one or more extracts
1648      to an experimental setup designed to measure quantities that we are
1649      interested in. For example, a <emphasis>Hybridization</emphasis> event corresponds
1650      to the application of one or more <emphasis>Labeled extracts</emphasis>
1651      materials to a microarray slide under conditions detailed in hybridization protocols.
1652      Use
1653      <menuchoice>
1654        <guimenu>View</guimenu>
1655        <guimenuitem>Physical bioassays</guimenuitem>
1656      </menuchoice>
1657      to get to the bioassays.
1658    </para>
1659   
1660    <sect2 id="biomaterials.bioassays.create">
1661      <title>Create physical bioassays</title>
1662      <para>
1663        In BASE, there are two possible routes to create a physical bioassay except the
1664        common way with the &gbNew; button at the list page.
1665      </para>
1666      <variablelist>
1667        <varlistentry>
1668          <term>from the extract list view page</term>
1669          <listitem>
1670            <para>
1671              Select at least one extract, to create a bioassay from, by
1672              ticking the selection boxes before the name field.
1673              Click on the <guibutton>New physical bioassay&hellip;</guibutton>
1674              in the toolbar.
1675            </para>
1676          </listitem>
1677        </varlistentry>
1678        <varlistentry>
1679          <term>from the extract single-item page</term>
1680          <listitem>
1681            <para>
1682              When viewing an extract in single-item view, click on the
1683              <guibutton>New physical bioassay&hellip;</guibutton>
1684              button in the toolbar.
1685            </para>
1686          </listitem>
1687        </varlistentry>
1688      </variablelist>
1689    </sect2>
1690   
1691    <sect2 id="biomaterials.bioassays.properties">
1692      <title>Bioassay properties</title>
1693
1694 
1695        <figure id="biomaterials.figures.bioassays-tab-1">
1696          <title>Physical bioassay properties</title>
1697          <screenshot>
1698            <mediaobject>
1699              <imageobject>
1700                <imagedata 
1701                  fileref="figures/physicalbioassay-tab-1.png" format="PNG" />
1702              </imageobject>
1703            </mediaobject>
1704          </screenshot>
1705        </figure> 
1706       
1707        <helptext external_id="physicalbioassay.edit" title="Edit physical bioassay">
1708        <variablelist>
1709          <varlistentry>
1710            <term>
1711              <guilabel>Name</guilabel>
1712            </term>
1713            <listitem>
1714              <para>
1715                The bioassay's name (required). It is recommended that the default
1716                name is replaced with something that is unique.
1717              </para>
1718            </listitem>
1719          </varlistentry>
1720          <varlistentry>
1721            <term>
1722              <guilabel>Type</guilabel>
1723            </term>
1724            <listitem>
1725              <para>
1726              The subtype of the bioassay. The list
1727              may evolve depending on additions by the server
1728              administrator. Selecting the proper subtype
1729              is recommended and enables BASE to automatically guess
1730              the most likely subtype when assignint source biomaterials
1731              and when creating derived bioassays.
1732              <nohelp>
1733              See <xref linkend="subtypes" /> for more information.
1734              </nohelp>
1735              </para>
1736            </listitem>
1737          </varlistentry>
1738          <varlistentry>
1739            <term>
1740              <guilabel>Size</guilabel>
1741            </term>
1742            <listitem>
1743              <para>
1744                The size of the bioassay is the number of independent
1745                positions on the bioassay. Depending on the
1746                characteristics of the bioassay, multiple biomaterials
1747                may share the same position, but are then usually
1748                required to have different tags. Two biomaterials
1749                in different positions can use the same tag.
1750                The default value is 1, but some platforms, for example
1751                Illumina BeadArrays, has slides with 6 or 8 positions.
1752              </para>
1753            </listitem>
1754          </varlistentry>
1755
1756          <varlistentry>
1757            <term>
1758              <guilabel>Created</guilabel>
1759            </term>
1760            <listitem>
1761              <para>
1762                A date should be provided. The information can be important when
1763                running quality controls on data and account for potential
1764                confounding factor (e.g. to account for a day effect).
1765              </para>
1766            </listitem>
1767          </varlistentry>
1768
1769          <varlistentry>
1770            <term>
1771              <guilabel>Registered</guilabel>
1772            </term>
1773            <listitem>
1774              <para>
1775                This field is automatically populated with a date at which the
1776                hybridization was entered in BASE system.
1777              </para>
1778            </listitem>
1779          </varlistentry>
1780
1781          <varlistentry>
1782            <term>
1783              <guilabel>Protocol</guilabel>
1784            </term>
1785            <listitem>
1786              <para>
1787                The protocol that was used to create the bioassay.
1788              </para>
1789            </listitem>
1790          </varlistentry>
1791
1792          <varlistentry>
1793            <term>
1794              <guilabel>Hardware</guilabel>
1795            </term>
1796            <listitem>
1797              <para>
1798                Information about the machine (if any) that was used when creating
1799                the bioassay.
1800              </para>
1801            </listitem>
1802          </varlistentry>
1803
1804          <varlistentry>
1805            <term>
1806              <guilabel>Array slide</guilabel>
1807            </term>
1808            <listitem>
1809              <para>The array slide that was used for the bioassay.</para>
1810            </listitem>
1811          </varlistentry>
1812
1813          <varlistentry>
1814            <term>
1815              <guilabel>Description</guilabel>
1816            </term>
1817            <listitem>
1818              <para>
1819                A free text field to report any information that can not be captured
1820                otherwise.
1821              </para>
1822            </listitem>
1823          </varlistentry>
1824        </variablelist>
1825        <seeother>
1826          <other external_id="physicalbioassay.extracts">Extracts</other>
1827          <other external_id="annotations.edit">Annotations &amp; parameters</other>
1828          <other external_id="annotations.edit.inherited">Inherited annotations</other>
1829        </seeother>
1830        </helptext>
1831      </sect2>
1832     
1833      <sect2 id="biomaterials.bioassays.extracts">
1834        <title>Parent extracts</title>
1835       
1836        <figure id="biomaterials.figures.bioassay-tab-2">
1837          <title>Parent extracts</title>
1838          <screenshot>
1839            <mediaobject>
1840              <imageobject>
1841                <imagedata 
1842                  fileref="figures/physicalbioassay-tab-2.png" format="PNG" />
1843              </imageobject>
1844            </mediaobject>
1845          </screenshot>
1846        </figure>
1847       
1848        <helptext external_id="physicalbioassay.extracts" title="Extracts">
1849        <para>
1850          This important tab allows users to select the extracts used by the
1851          bioassay, and specify the amount of material used, expressed in microgram.
1852        </para>
1853        <para>
1854          Use the <guibutton>Add extracts</guibutton> button to add
1855          items and the <guibutton>Remove</guibutton> button to remove items.
1856          Select one or several extracts in the list and write the used
1857          mass and position number in the fields below the list.
1858        </para>
1859       
1860        <seeother>
1861          <other external_id="physicalbioassay.edit">Edit physical bioassay</other>
1862          <other external_id="annotations.edit">Annotations &amp; parameters</other>
1863          <other external_id="annotations.edit.inherited">Inherited annotations</other>
1864        </seeother>
1865        </helptext>
1866       
1867      </sect2>
1868     
1869     
1870    <para>
1871      The <guilabel>Annotations</guilabel> tab allows BASE users to use
1872      annotation types to refine bioassay description. More about annotating items
1873      can be read in <xref linkend="annotations.annotating" />
1874    </para>
1875       
1876    <para>
1877      This <guilabel>Inherited annotations</guilabel> tab contains a list of those annotations
1878      that are inherited from the bioassay's parents. Information about working with inherited
1879      annotations can be found in <xref linkend="annotations.inheriting" />.
1880    </para>
1881     
1882  </sect1>
1883</chapter>
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