| 3157 |
05 Mar 07 |
martin |
1 |
<?xml version="1.0" encoding="UTF-8"?> |
| 3159 |
05 Mar 07 |
martin |
2 |
<!DOCTYPE chapter PUBLIC |
| 3159 |
05 Mar 07 |
martin |
3 |
"-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN" |
| 3192 |
13 Mar 07 |
martin |
4 |
"../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd"> |
| 3399 |
28 May 07 |
martin |
5 |
<!-- |
| 3399 |
28 May 07 |
martin |
$Id$ |
| 3399 |
28 May 07 |
martin |
7 |
|
| 3675 |
16 Aug 07 |
jari |
Copyright (C) 2007 Peter Johansson, Nicklas Nordborg, Philippe Rocca-Serra, Martin Svensson |
| 4889 |
06 Apr 09 |
nicklas |
Copyright (C) 2008, 2009 Jari Häkkinen, Martin Svensson |
| 3399 |
28 May 07 |
martin |
10 |
|
| 3399 |
28 May 07 |
martin |
This file is part of BASE - BioArray Software Environment. |
| 3399 |
28 May 07 |
martin |
Available at http://base.thep.lu.se/ |
| 3399 |
28 May 07 |
martin |
13 |
|
| 3399 |
28 May 07 |
martin |
BASE is free software; you can redistribute it and/or |
| 3399 |
28 May 07 |
martin |
modify it under the terms of the GNU General Public License |
| 4477 |
05 Sep 08 |
jari |
as published by the Free Software Foundation; either version 3 |
| 3399 |
28 May 07 |
martin |
of the License, or (at your option) any later version. |
| 3399 |
28 May 07 |
martin |
18 |
|
| 3399 |
28 May 07 |
martin |
BASE is distributed in the hope that it will be useful, |
| 3399 |
28 May 07 |
martin |
but WITHOUT ANY WARRANTY; without even the implied warranty of |
| 3399 |
28 May 07 |
martin |
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
| 3399 |
28 May 07 |
martin |
GNU General Public License for more details. |
| 3399 |
28 May 07 |
martin |
23 |
|
| 3399 |
28 May 07 |
martin |
You should have received a copy of the GNU General Public License |
| 4509 |
11 Sep 08 |
jari |
along with BASE. If not, see <http://www.gnu.org/licenses/>. |
| 3399 |
28 May 07 |
martin |
26 |
--> |
| 3373 |
24 May 07 |
martin |
27 |
<chapter id="biomaterials"> |
| 5782 |
04 Oct 11 |
nicklas |
28 |
<?dbhtml dir="biomaterials" filename="index.html" ?> |
| 5782 |
04 Oct 11 |
nicklas |
29 |
|
| 5797 |
11 Oct 11 |
nicklas |
30 |
<title>Biomaterial LIMS</title> |
| 5797 |
11 Oct 11 |
nicklas |
31 |
|
| 3399 |
28 May 07 |
martin |
32 |
<para> |
| 3399 |
28 May 07 |
martin |
33 |
The generic term biomaterial refers to any biological material used in an experiment. |
| 5708 |
25 Aug 11 |
nicklas |
34 |
Biomaterial is divided in three main components, <emphasis>biosources</emphasis>, <emphasis>samples</emphasis> |
| 5708 |
25 Aug 11 |
nicklas |
35 |
and <emphasis>extracts</emphasis>. The biomaterials can then be subclassified further by |
| 5708 |
25 Aug 11 |
nicklas |
36 |
the use of subtypes (see <xref linkend="subtypes"/>). BASE has, for example, defined two extracts subtypes: |
| 5708 |
25 Aug 11 |
nicklas |
37 |
<emphasis>Labeled extract</emphasis> (used in microarray experiments) |
| 5708 |
25 Aug 11 |
nicklas |
38 |
and <emphasis>Library</emphasis> (used in sequencing experiments). |
| 5708 |
25 Aug 11 |
nicklas |
39 |
The order used in presenting those entities is not innocuous as it represents the |
| 3399 |
28 May 07 |
martin |
40 |
sequence of transformation a source material undergoes until it is in a state compatible |
| 5708 |
25 Aug 11 |
nicklas |
41 |
for further exeperimental processing. This progression is actually |
| 4487 |
08 Sep 08 |
jari |
42 |
mimicked in the BASE |
| 4732 |
21 Jan 09 |
martin |
43 |
<guimenu>Biomaterial LIMS</guimenu> |
| 3399 |
28 May 07 |
martin |
44 |
menu again to insist on this natural progression. |
| 3399 |
28 May 07 |
martin |
45 |
</para> |
| 3412 |
30 May 07 |
martin |
46 |
<itemizedlist> |
| 3412 |
30 May 07 |
martin |
47 |
<listitem> |
| 3412 |
30 May 07 |
martin |
48 |
<simpara> |
| 3412 |
30 May 07 |
martin |
49 |
Biosources correspond to the native biological entity used in an experiment |
| 3412 |
30 May 07 |
martin |
50 |
prior to any treatment. |
| 3412 |
30 May 07 |
martin |
51 |
</simpara> |
| 3412 |
30 May 07 |
martin |
52 |
</listitem> |
| 3412 |
30 May 07 |
martin |
53 |
<listitem> |
| 3412 |
30 May 07 |
martin |
54 |
<simpara> |
| 4487 |
08 Sep 08 |
jari |
55 |
Samples are central to BASE to describe the sample processing. So samples can |
| 3412 |
30 May 07 |
martin |
56 |
be created from other samples if user want to track sample processing event in a |
| 3412 |
30 May 07 |
martin |
57 |
finely granular fashion. |
| 3412 |
30 May 07 |
martin |
58 |
</simpara> |
| 3412 |
30 May 07 |
martin |
59 |
</listitem> |
| 3412 |
30 May 07 |
martin |
60 |
<listitem> |
| 3412 |
30 May 07 |
martin |
61 |
<simpara> |
| 3412 |
30 May 07 |
martin |
62 |
Extracts correspond to nucleic acid material extracted from a tissue sample or a |
| 3412 |
30 May 07 |
martin |
63 |
cell culture sample. |
| 3412 |
30 May 07 |
martin |
64 |
</simpara> |
| 3412 |
30 May 07 |
martin |
65 |
</listitem> |
| 3412 |
30 May 07 |
martin |
66 |
</itemizedlist> |
| 3399 |
28 May 07 |
martin |
67 |
<para> |
| 4487 |
08 Sep 08 |
jari |
68 |
BASE allows users to create any of the these entities fairly freely, however it is |
| 3399 |
28 May 07 |
martin |
69 |
expected that users will follow the natural path of the laboratory workflow. |
| 3399 |
28 May 07 |
martin |
70 |
</para> |
| 5797 |
11 Oct 11 |
nicklas |
71 |
|
| 4732 |
21 Jan 09 |
martin |
72 |
|
| 3412 |
30 May 07 |
martin |
73 |
<sect1 id="biomaterials.biosources"> |
| 5782 |
04 Oct 11 |
nicklas |
74 |
<?dbhtml filename="biosources.html" ?> |
| 4149 |
19 Feb 08 |
martin |
75 |
<title>Biosources</title> |
| 3412 |
30 May 07 |
martin |
76 |
|
| 3412 |
30 May 07 |
martin |
77 |
|
| 5708 |
25 Aug 11 |
nicklas |
78 |
<para> |
| 5708 |
25 Aug 11 |
nicklas |
79 |
Biosources correspond to the native biological entity used in an experiment prior to any treatment. |
| 5708 |
25 Aug 11 |
nicklas |
80 |
Biosources can be added to BASE by most users and are managed from <menuchoice> |
| 5708 |
25 Aug 11 |
nicklas |
81 |
<guimenu>Biomaterial LIMS</guimenu> |
| 5708 |
25 Aug 11 |
nicklas |
82 |
<guimenuitem>Biosources</guimenuitem> |
| 5708 |
25 Aug 11 |
nicklas |
83 |
</menuchoice>. |
| 5708 |
25 Aug 11 |
nicklas |
84 |
Use the &gbNew; button to create a new biosource. This brings up the dialog below. |
| 5708 |
25 Aug 11 |
nicklas |
85 |
</para> |
| 5708 |
25 Aug 11 |
nicklas |
86 |
|
| 5708 |
25 Aug 11 |
nicklas |
87 |
<figure id="biomaterials.figures.biosource-tab-1"> |
| 5708 |
25 Aug 11 |
nicklas |
88 |
<title>Biosource properties</title> |
| 5708 |
25 Aug 11 |
nicklas |
89 |
<screenshot> |
| 5708 |
25 Aug 11 |
nicklas |
90 |
<mediaobject> |
| 5708 |
25 Aug 11 |
nicklas |
91 |
<imageobject> |
| 5708 |
25 Aug 11 |
nicklas |
92 |
<imagedata |
| 5708 |
25 Aug 11 |
nicklas |
93 |
fileref="figures/biosource-tab-1.png" format="PNG" /> |
| 5708 |
25 Aug 11 |
nicklas |
94 |
</imageobject> |
| 5708 |
25 Aug 11 |
nicklas |
95 |
</mediaobject> |
| 5708 |
25 Aug 11 |
nicklas |
96 |
</screenshot> |
| 5708 |
25 Aug 11 |
nicklas |
97 |
</figure> |
| 5708 |
25 Aug 11 |
nicklas |
98 |
<helptext external_id="biosource.edit" title="Biosource properties"> |
| 5708 |
25 Aug 11 |
nicklas |
99 |
|
| 3412 |
30 May 07 |
martin |
100 |
<variablelist> |
| 3412 |
30 May 07 |
martin |
101 |
<varlistentry> |
| 3412 |
30 May 07 |
martin |
102 |
<term> |
| 3412 |
30 May 07 |
martin |
103 |
<guilabel>Name</guilabel> |
| 3412 |
30 May 07 |
martin |
104 |
</term> |
| 3412 |
30 May 07 |
martin |
105 |
<listitem> |
| 3412 |
30 May 07 |
martin |
106 |
<para> |
| 4487 |
08 Sep 08 |
jari |
107 |
This is the only mandatory field. BASE by default assigns |
| 3412 |
30 May 07 |
martin |
108 |
<replaceable>New biosource</replaceable> |
| 3412 |
30 May 07 |
martin |
109 |
as name but it is advised to provide unique sensible names. |
| 3412 |
30 May 07 |
martin |
110 |
</para> |
| 3412 |
30 May 07 |
martin |
111 |
</listitem> |
| 3412 |
30 May 07 |
martin |
112 |
</varlistentry> |
| 3412 |
30 May 07 |
martin |
113 |
<varlistentry> |
| 3412 |
30 May 07 |
martin |
114 |
<term> |
| 5708 |
25 Aug 11 |
nicklas |
115 |
<guilabel>Type</guilabel> |
| 5708 |
25 Aug 11 |
nicklas |
116 |
</term> |
| 5708 |
25 Aug 11 |
nicklas |
117 |
<listitem> |
| 5708 |
25 Aug 11 |
nicklas |
118 |
<para> |
| 5708 |
25 Aug 11 |
nicklas |
119 |
The subtype of the biosource. The list |
| 5708 |
25 Aug 11 |
nicklas |
120 |
may evolve depending on additions by the server |
| 5708 |
25 Aug 11 |
nicklas |
121 |
administrator. Selecting the proper subtype |
| 5708 |
25 Aug 11 |
nicklas |
122 |
is recommended and enables BASE to automatically guess |
| 5708 |
25 Aug 11 |
nicklas |
123 |
the most likely subtype when creating child biomaterial. |
| 5708 |
25 Aug 11 |
nicklas |
124 |
<nohelp> |
| 5708 |
25 Aug 11 |
nicklas |
125 |
See <xref linkend="subtypes" /> for more information. |
| 5708 |
25 Aug 11 |
nicklas |
126 |
</nohelp> |
| 5708 |
25 Aug 11 |
nicklas |
127 |
</para> |
| 5708 |
25 Aug 11 |
nicklas |
128 |
</listitem> |
| 5708 |
25 Aug 11 |
nicklas |
129 |
</varlistentry> |
| 5708 |
25 Aug 11 |
nicklas |
130 |
<varlistentry> |
| 5708 |
25 Aug 11 |
nicklas |
131 |
<term> |
| 3412 |
30 May 07 |
martin |
132 |
<guilabel>External ID</guilabel> |
| 3412 |
30 May 07 |
martin |
133 |
</term> |
| 3412 |
30 May 07 |
martin |
134 |
<listitem> |
| 3412 |
30 May 07 |
martin |
135 |
<para> |
| 3412 |
30 May 07 |
martin |
136 |
An external reference identifiers (e.g. a patient identification |
| 3412 |
30 May 07 |
martin |
137 |
code) can be supplied using this field. |
| 3412 |
30 May 07 |
martin |
138 |
</para> |
| 3412 |
30 May 07 |
martin |
139 |
</listitem> |
| 3412 |
30 May 07 |
martin |
140 |
</varlistentry> |
| 3412 |
30 May 07 |
martin |
141 |
<varlistentry> |
| 3412 |
30 May 07 |
martin |
142 |
<term> |
| 3412 |
30 May 07 |
martin |
143 |
<guilabel>Description</guilabel> |
| 3412 |
30 May 07 |
martin |
144 |
</term> |
| 3412 |
30 May 07 |
martin |
145 |
<listitem> |
| 3412 |
30 May 07 |
martin |
146 |
<para>A free text description can be supplied using this field.</para> |
| 3412 |
30 May 07 |
martin |
147 |
</listitem> |
| 3412 |
30 May 07 |
martin |
148 |
</varlistentry> |
| 3412 |
30 May 07 |
martin |
149 |
</variablelist> |
| 5708 |
25 Aug 11 |
nicklas |
150 |
<seeother> |
| 5708 |
25 Aug 11 |
nicklas |
151 |
<other external_id="annotations.edit">Annotations</other> |
| 5708 |
25 Aug 11 |
nicklas |
152 |
</seeother> |
| 5708 |
25 Aug 11 |
nicklas |
153 |
</helptext> |
| 5708 |
25 Aug 11 |
nicklas |
154 |
|
| 5708 |
25 Aug 11 |
nicklas |
155 |
<para> |
| 5708 |
25 Aug 11 |
nicklas |
156 |
The <guilabel>Annotations</guilabel> tab allows BASE users to use |
| 5708 |
25 Aug 11 |
nicklas |
157 |
annotation types to refine biosource description. More about annotating items |
| 5708 |
25 Aug 11 |
nicklas |
158 |
can be read in <xref linkend="annotations.annotating" /> |
| 5708 |
25 Aug 11 |
nicklas |
159 |
</para> |
| 5708 |
25 Aug 11 |
nicklas |
160 |
|
| 3412 |
30 May 07 |
martin |
161 |
</sect1> |
| 3412 |
30 May 07 |
martin |
162 |
<sect1 id="biomaterial.samples"> |
| 5782 |
04 Oct 11 |
nicklas |
163 |
<?dbhtml filename="samples.html" ?> |
| 3412 |
30 May 07 |
martin |
164 |
<title>Samples</title> |
| 3399 |
28 May 07 |
martin |
165 |
<para> |
| 3412 |
30 May 07 |
martin |
166 |
Samples result from processing events applied to biosource material or other samples |
| 3412 |
30 May 07 |
martin |
167 |
before they are turned into an extract. In other words, samples can be created from |
| 4616 |
29 Oct 08 |
jari |
168 |
biosource items or from one or more sample items. When a sample is created from several |
| 3412 |
30 May 07 |
martin |
169 |
other samples, a pooling event is performed. |
| 3412 |
30 May 07 |
martin |
170 |
</para> |
| 3412 |
30 May 07 |
martin |
171 |
<para> |
| 3412 |
30 May 07 |
martin |
172 |
For every step of transformation from biosource to sample, it is possible to provide |
| 4487 |
08 Sep 08 |
jari |
173 |
information about the protocol used to perform this task. It is not enforced in BASE |
| 3412 |
30 May 07 |
martin |
174 |
but it should serve as guidance when devising the granularity of the sample processing |
| 3412 |
30 May 07 |
martin |
175 |
task. Also, it is good practice to provide protocol information to ensure MIAME |
| 3412 |
30 May 07 |
martin |
176 |
compliance. |
| 3412 |
30 May 07 |
martin |
177 |
</para> |
| 3412 |
30 May 07 |
martin |
178 |
<para> |
| 3412 |
30 May 07 |
martin |
179 |
Use |
| 3399 |
28 May 07 |
martin |
180 |
<menuchoice> |
| 4732 |
21 Jan 09 |
martin |
181 |
<guimenu>Biomaterial LIMS</guimenu> |
| 4732 |
21 Jan 09 |
martin |
182 |
<guimenuitem>Samples</guimenuitem> |
| 3399 |
28 May 07 |
martin |
183 |
</menuchoice> |
| 4732 |
21 Jan 09 |
martin |
184 |
to get to the list of samples. |
| 3399 |
28 May 07 |
martin |
185 |
</para> |
| 5708 |
25 Aug 11 |
nicklas |
186 |
|
| 5708 |
25 Aug 11 |
nicklas |
187 |
<sect2 id="biomaterial.samples.create"> |
| 3412 |
30 May 07 |
martin |
188 |
<title>Create sample</title> |
| 5708 |
25 Aug 11 |
nicklas |
189 |
|
| 3412 |
30 May 07 |
martin |
190 |
<para> |
| 3412 |
30 May 07 |
martin |
191 |
Beside the common way, using the &gbNew; button, a sample can be created in one of |
| 3412 |
30 May 07 |
martin |
192 |
the following ways: |
| 5708 |
25 Aug 11 |
nicklas |
193 |
</para> |
| 3412 |
30 May 07 |
martin |
194 |
<variablelist> |
| 3412 |
30 May 07 |
martin |
195 |
<varlistentry> |
| 3412 |
30 May 07 |
martin |
196 |
<term>from either biosource list- or single view- page.</term> |
| 3412 |
30 May 07 |
martin |
197 |
<listitem> |
| 3412 |
30 May 07 |
martin |
198 |
<para> |
| 3412 |
30 May 07 |
martin |
199 |
No matter how complex the sample processing phase is, at least one |
| 3412 |
30 May 07 |
martin |
200 |
sample has to be anchored to a biosource. Therefore, a natural way |
| 3412 |
30 May 07 |
martin |
201 |
to create an sample is to click on |
| 3950 |
12 Nov 07 |
martin |
202 |
<guiicon> |
| 3950 |
12 Nov 07 |
martin |
203 |
<inlinemediaobject> |
| 3950 |
12 Nov 07 |
martin |
204 |
<imageobject> |
| 3950 |
12 Nov 07 |
martin |
205 |
<imagedata fileref="figures/add.png" format="PNG" /> |
| 3950 |
12 Nov 07 |
martin |
206 |
</imageobject> |
| 3950 |
12 Nov 07 |
martin |
207 |
</inlinemediaobject> |
| 3950 |
12 Nov 07 |
martin |
208 |
</guiicon> |
| 5708 |
25 Aug 11 |
nicklas |
209 |
in the <guilabel>Samples</guilabel> column of the biosource list view. There is also a |
| 3412 |
30 May 07 |
martin |
210 |
corresponding button, |
| 5708 |
25 Aug 11 |
nicklas |
211 |
<guibutton>New sample…</guibutton> |
| 3412 |
30 May 07 |
martin |
212 |
in the toolbar when viewing a single biosource. |
| 3412 |
30 May 07 |
martin |
213 |
</para> |
| 3412 |
30 May 07 |
martin |
214 |
</listitem> |
| 3412 |
30 May 07 |
martin |
215 |
</varlistentry> |
| 3412 |
30 May 07 |
martin |
216 |
<varlistentry> |
| 3412 |
30 May 07 |
martin |
217 |
<term>from the sample list page</term> |
| 3412 |
30 May 07 |
martin |
218 |
<listitem> |
| 3412 |
30 May 07 |
martin |
219 |
<para> |
| 5708 |
25 Aug 11 |
nicklas |
220 |
Child samples can be created from a single parent by clicking on the |
| 5708 |
25 Aug 11 |
nicklas |
221 |
<guiicon> |
| 5708 |
25 Aug 11 |
nicklas |
222 |
<inlinemediaobject> |
| 5708 |
25 Aug 11 |
nicklas |
223 |
<imageobject> |
| 5708 |
25 Aug 11 |
nicklas |
224 |
<imagedata fileref="figures/add.png" format="PNG" /> |
| 5708 |
25 Aug 11 |
nicklas |
225 |
</imageobject> |
| 5708 |
25 Aug 11 |
nicklas |
226 |
</inlinemediaobject> |
| 5708 |
25 Aug 11 |
nicklas |
227 |
</guiicon> icon in the <guilabel>Child samples</guilabel> column. |
| 5708 |
25 Aug 11 |
nicklas |
228 |
Pooled samples can be created by first selecting the parents |
| 5708 |
25 Aug 11 |
nicklas |
229 |
from the list of samples and then click the <guibutton>Pool…</guibutton> |
| 5708 |
25 Aug 11 |
nicklas |
230 |
button in the toolbar. |
| 3412 |
30 May 07 |
martin |
231 |
</para> |
| 3412 |
30 May 07 |
martin |
232 |
</listitem> |
| 3412 |
30 May 07 |
martin |
233 |
</varlistentry> |
| 3412 |
30 May 07 |
martin |
234 |
</variablelist> |
| 3412 |
30 May 07 |
martin |
235 |
</sect2> |
| 5708 |
25 Aug 11 |
nicklas |
236 |
|
| 5708 |
25 Aug 11 |
nicklas |
237 |
<sect2 id="biomaterial.samples.properties"> |
| 5708 |
25 Aug 11 |
nicklas |
238 |
<title>Sample properties</title> |
| 5708 |
25 Aug 11 |
nicklas |
239 |
<figure id="biomaterials.figures.biosample-tab-1"> |
| 5708 |
25 Aug 11 |
nicklas |
240 |
<title>Sample properties</title> |
| 5708 |
25 Aug 11 |
nicklas |
241 |
<screenshot> |
| 5708 |
25 Aug 11 |
nicklas |
242 |
<mediaobject> |
| 5708 |
25 Aug 11 |
nicklas |
243 |
<imageobject> |
| 5708 |
25 Aug 11 |
nicklas |
244 |
<imagedata |
| 5708 |
25 Aug 11 |
nicklas |
245 |
fileref="figures/biosample-tab-1.png" format="PNG" /> |
| 5708 |
25 Aug 11 |
nicklas |
246 |
</imageobject> |
| 5708 |
25 Aug 11 |
nicklas |
247 |
</mediaobject> |
| 5708 |
25 Aug 11 |
nicklas |
248 |
</screenshot> |
| 5708 |
25 Aug 11 |
nicklas |
249 |
</figure> |
| 3412 |
30 May 07 |
martin |
250 |
<helptext external_id="sample.edit" title="Edit sample"> |
| 3399 |
28 May 07 |
martin |
251 |
<variablelist> |
| 3399 |
28 May 07 |
martin |
252 |
<varlistentry> |
| 3399 |
28 May 07 |
martin |
253 |
<term> |
| 3399 |
28 May 07 |
martin |
254 |
<guilabel>Name</guilabel> |
| 3399 |
28 May 07 |
martin |
255 |
</term> |
| 3399 |
28 May 07 |
martin |
256 |
<listitem> |
| 3399 |
28 May 07 |
martin |
257 |
<para> |
| 5708 |
25 Aug 11 |
nicklas |
258 |
The sample's name (required). BASE by default assigns names to |
| 3412 |
30 May 07 |
martin |
259 |
samples (by suffixing |
| 3412 |
30 May 07 |
martin |
260 |
<replaceable>s#</replaceable> |
| 3412 |
30 May 07 |
martin |
261 |
when creating a sample from an existing biosource or |
| 3412 |
30 May 07 |
martin |
262 |
<replaceable>New Sample</replaceable> |
| 3412 |
30 May 07 |
martin |
263 |
otherwise) but it is possible to edit at will. |
| 3399 |
28 May 07 |
martin |
264 |
</para> |
| 3399 |
28 May 07 |
martin |
265 |
</listitem> |
| 3399 |
28 May 07 |
martin |
266 |
</varlistentry> |
| 3399 |
28 May 07 |
martin |
267 |
<varlistentry> |
| 3399 |
28 May 07 |
martin |
268 |
<term> |
| 5708 |
25 Aug 11 |
nicklas |
269 |
<guilabel>Type</guilabel> |
| 5708 |
25 Aug 11 |
nicklas |
270 |
</term> |
| 5708 |
25 Aug 11 |
nicklas |
271 |
<listitem> |
| 5708 |
25 Aug 11 |
nicklas |
272 |
<para> |
| 5708 |
25 Aug 11 |
nicklas |
273 |
The subtype of the sample. The list |
| 5708 |
25 Aug 11 |
nicklas |
274 |
may evolve depending on additions by the server |
| 5708 |
25 Aug 11 |
nicklas |
275 |
administrator. Selecting the proper subtype |
| 5708 |
25 Aug 11 |
nicklas |
276 |
is recommended and enables BASE to automatically guess |
| 5708 |
25 Aug 11 |
nicklas |
277 |
the most likely subtype when creating child biomaterial. |
| 5708 |
25 Aug 11 |
nicklas |
278 |
<nohelp> |
| 5708 |
25 Aug 11 |
nicklas |
279 |
See <xref linkend="subtypes" /> for more information. |
| 5708 |
25 Aug 11 |
nicklas |
280 |
</nohelp> |
| 5708 |
25 Aug 11 |
nicklas |
281 |
</para> |
| 5708 |
25 Aug 11 |
nicklas |
282 |
</listitem> |
| 5708 |
25 Aug 11 |
nicklas |
283 |
</varlistentry> |
| 5708 |
25 Aug 11 |
nicklas |
284 |
<varlistentry> |
| 5708 |
25 Aug 11 |
nicklas |
285 |
<term> |
| 3412 |
30 May 07 |
martin |
286 |
<guilabel>External ID</guilabel> |
| 3399 |
28 May 07 |
martin |
287 |
</term> |
| 3399 |
28 May 07 |
martin |
288 |
<listitem> |
| 3399 |
28 May 07 |
martin |
289 |
<para> |
| 3412 |
30 May 07 |
martin |
290 |
An identification used to identify the sample outside BASE. |
| 3399 |
28 May 07 |
martin |
291 |
</para> |
| 3399 |
28 May 07 |
martin |
292 |
</listitem> |
| 3399 |
28 May 07 |
martin |
293 |
</varlistentry> |
| 3399 |
28 May 07 |
martin |
294 |
<varlistentry> |
| 3399 |
28 May 07 |
martin |
295 |
<term> |
| 3412 |
30 May 07 |
martin |
296 |
<guilabel>Original quantity</guilabel> |
| 3412 |
30 May 07 |
martin |
297 |
</term> |
| 3412 |
30 May 07 |
martin |
298 |
<listitem> |
| 3412 |
30 May 07 |
martin |
299 |
<para> |
| 3412 |
30 May 07 |
martin |
300 |
This is meant to report information about the actual mass of |
| 3412 |
30 May 07 |
martin |
301 |
sample created. |
| 3412 |
30 May 07 |
martin |
302 |
</para> |
| 3412 |
30 May 07 |
martin |
303 |
</listitem> |
| 3412 |
30 May 07 |
martin |
304 |
</varlistentry> |
| 3412 |
30 May 07 |
martin |
305 |
<varlistentry> |
| 3412 |
30 May 07 |
martin |
306 |
<term> |
| 3412 |
30 May 07 |
martin |
307 |
<guilabel>Created</guilabel> |
| 3412 |
30 May 07 |
martin |
308 |
</term> |
| 3412 |
30 May 07 |
martin |
309 |
<listitem> |
| 3412 |
30 May 07 |
martin |
310 |
<para> |
| 3412 |
30 May 07 |
martin |
311 |
A date when the sample was created. The information can be |
| 3412 |
30 May 07 |
martin |
312 |
important when running quality controls on data and account for |
| 3412 |
30 May 07 |
martin |
313 |
potential confounding factor (e.g. day effect). |
| 3412 |
30 May 07 |
martin |
314 |
</para> |
| 3412 |
30 May 07 |
martin |
315 |
</listitem> |
| 3412 |
30 May 07 |
martin |
316 |
</varlistentry> |
| 3412 |
30 May 07 |
martin |
317 |
<varlistentry> |
| 3412 |
30 May 07 |
martin |
318 |
<term> |
| 3412 |
30 May 07 |
martin |
319 |
<guilabel>Registered</guilabel> |
| 3412 |
30 May 07 |
martin |
320 |
</term> |
| 3412 |
30 May 07 |
martin |
321 |
<listitem> |
| 4487 |
08 Sep 08 |
jari |
322 |
<para>The date at which the sample was entered in BASE.</para> |
| 3412 |
30 May 07 |
martin |
323 |
</listitem> |
| 3412 |
30 May 07 |
martin |
324 |
</varlistentry> |
| 3412 |
30 May 07 |
martin |
325 |
<varlistentry> |
| 3412 |
30 May 07 |
martin |
326 |
<term> |
| 3412 |
30 May 07 |
martin |
327 |
<guilabel>Protocol</guilabel> |
| 3412 |
30 May 07 |
martin |
328 |
</term> |
| 3412 |
30 May 07 |
martin |
329 |
<listitem> |
| 3412 |
30 May 07 |
martin |
330 |
<para>The protocol used to produce this sample.</para> |
| 3412 |
30 May 07 |
martin |
331 |
</listitem> |
| 3412 |
30 May 07 |
martin |
332 |
</varlistentry> |
| 3412 |
30 May 07 |
martin |
333 |
<varlistentry> |
| 3412 |
30 May 07 |
martin |
334 |
<term> |
| 4732 |
21 Jan 09 |
martin |
335 |
<guilabel>Bioplate</guilabel> |
| 4732 |
21 Jan 09 |
martin |
336 |
</term> |
| 4732 |
21 Jan 09 |
martin |
337 |
<listitem> |
| 4732 |
21 Jan 09 |
martin |
338 |
<para>The bioplate where this sample is located.</para> |
| 4732 |
21 Jan 09 |
martin |
339 |
</listitem> |
| 4732 |
21 Jan 09 |
martin |
340 |
</varlistentry> |
| 4732 |
21 Jan 09 |
martin |
341 |
<varlistentry> |
| 4732 |
21 Jan 09 |
martin |
342 |
<term> |
| 4732 |
21 Jan 09 |
martin |
343 |
<guilabel>Biowell</guilabel> |
| 4732 |
21 Jan 09 |
martin |
344 |
</term> |
| 4732 |
21 Jan 09 |
martin |
345 |
<listitem> |
| 4732 |
21 Jan 09 |
martin |
346 |
<para> |
| 4732 |
21 Jan 09 |
martin |
347 |
Biowell that holds this sample. |
| 4732 |
21 Jan 09 |
martin |
348 |
<guilabel>Bioplate</guilabel> has to be defined before |
| 4732 |
21 Jan 09 |
martin |
349 |
biowell can be selected. |
| 4732 |
21 Jan 09 |
martin |
350 |
</para> |
| 4732 |
21 Jan 09 |
martin |
351 |
</listitem> |
| 4732 |
21 Jan 09 |
martin |
352 |
</varlistentry> |
| 4732 |
21 Jan 09 |
martin |
353 |
<varlistentry> |
| 4732 |
21 Jan 09 |
martin |
354 |
<term> |
| 3399 |
28 May 07 |
martin |
355 |
<guilabel>Description</guilabel> |
| 3399 |
28 May 07 |
martin |
356 |
</term> |
| 3399 |
28 May 07 |
martin |
357 |
<listitem> |
| 3399 |
28 May 07 |
martin |
358 |
<para> |
| 3412 |
30 May 07 |
martin |
359 |
A text field to report any information that not can be captured |
| 3412 |
30 May 07 |
martin |
360 |
otherwise. |
| 3399 |
28 May 07 |
martin |
361 |
</para> |
| 3399 |
28 May 07 |
martin |
362 |
</listitem> |
| 3399 |
28 May 07 |
martin |
363 |
</varlistentry> |
| 3399 |
28 May 07 |
martin |
364 |
</variablelist> |
| 5708 |
25 Aug 11 |
nicklas |
365 |
|
| 5708 |
25 Aug 11 |
nicklas |
366 |
<seeother> |
| 5708 |
25 Aug 11 |
nicklas |
367 |
<other external_id="sample.parents">Parents</other> |
| 5708 |
25 Aug 11 |
nicklas |
368 |
<other external_id="annotations.edit">Annotations & parameters</other> |
| 5708 |
25 Aug 11 |
nicklas |
369 |
<other external_id="annotations.edit.inherited">Inherited annotations</other> |
| 5708 |
25 Aug 11 |
nicklas |
370 |
</seeother> |
| 3412 |
30 May 07 |
martin |
371 |
</helptext> |
| 5708 |
25 Aug 11 |
nicklas |
372 |
</sect2> |
| 5708 |
25 Aug 11 |
nicklas |
373 |
|
| 5708 |
25 Aug 11 |
nicklas |
374 |
<sect2 id="biomaterial.samples.parents"> |
| 5708 |
25 Aug 11 |
nicklas |
375 |
<title>Sample parents</title> |
| 5708 |
25 Aug 11 |
nicklas |
376 |
<figure id="biomaterials.figures.biosample-tab-2"> |
| 5708 |
25 Aug 11 |
nicklas |
377 |
<title>Sample parents</title> |
| 3420 |
31 May 07 |
martin |
378 |
<screenshot> |
| 3420 |
31 May 07 |
martin |
379 |
<mediaobject> |
| 3420 |
31 May 07 |
martin |
380 |
<imageobject> |
| 3423 |
31 May 07 |
nicklas |
381 |
<imagedata |
| 5708 |
25 Aug 11 |
nicklas |
382 |
fileref="figures/biosample-tab-2.png" format="PNG" /> |
| 3420 |
31 May 07 |
martin |
383 |
</imageobject> |
| 3420 |
31 May 07 |
martin |
384 |
</mediaobject> |
| 3420 |
31 May 07 |
martin |
385 |
</screenshot> |
| 3420 |
31 May 07 |
martin |
386 |
</figure> |
| 5708 |
25 Aug 11 |
nicklas |
387 |
|
| 3412 |
30 May 07 |
martin |
388 |
<helptext external_id="sample.parents" title="Sample's parents"> |
| 3399 |
28 May 07 |
martin |
389 |
<para> |
| 4487 |
08 Sep 08 |
jari |
390 |
This is meant to keep track of the sample origin. BASE |
| 5708 |
25 Aug 11 |
nicklas |
391 |
distinguishes between two cases which are controlled by the |
| 5708 |
25 Aug 11 |
nicklas |
392 |
<guilabel>Parent type</guilabel> |
| 3412 |
30 May 07 |
martin |
393 |
radio-button in the edit pop-up window. |
| 3399 |
28 May 07 |
martin |
394 |
</para> |
| 3412 |
30 May 07 |
martin |
395 |
<itemizedlist> |
| 3412 |
30 May 07 |
martin |
396 |
<listitem> |
| 3412 |
30 May 07 |
martin |
397 |
<para> |
| 3412 |
30 May 07 |
martin |
398 |
If the parent is a biosource the radio-button is set to |
| 5708 |
25 Aug 11 |
nicklas |
399 |
<guilabel>Biosource</guilabel>. Only a single biosource |
| 5708 |
25 Aug 11 |
nicklas |
400 |
can be used as the parent. This option is automatically |
| 5708 |
25 Aug 11 |
nicklas |
401 |
selected if the user selects a biosource with the |
| 5708 |
25 Aug 11 |
nicklas |
402 |
<guibutton>Select biosource</guibutton> button. |
| 3412 |
30 May 07 |
martin |
403 |
</para> |
| 3412 |
30 May 07 |
martin |
404 |
</listitem> |
| 3412 |
30 May 07 |
martin |
405 |
<listitem> |
| 3412 |
30 May 07 |
martin |
406 |
<para> |
| 3412 |
30 May 07 |
martin |
407 |
When the parent is one or several other samples the radio-button is |
| 5708 |
25 Aug 11 |
nicklas |
408 |
set to <guilabel>Sample</guilabel>. This option is automatically |
| 5708 |
25 Aug 11 |
nicklas |
409 |
selected if the user add samples with the <guibutton>Add samples</guibutton> button. |
| 5708 |
25 Aug 11 |
nicklas |
410 |
For each parent sample, it is |
| 5708 |
25 Aug 11 |
nicklas |
411 |
possible to specify the amount used in µg. This will automatically |
| 5708 |
25 Aug 11 |
nicklas |
412 |
update the <guilabel>remaining quantity</guilabel> of the parent. |
| 3412 |
30 May 07 |
martin |
413 |
</para> |
| 3412 |
30 May 07 |
martin |
414 |
</listitem> |
| 3412 |
30 May 07 |
martin |
415 |
</itemizedlist> |
| 5708 |
25 Aug 11 |
nicklas |
416 |
|
| 5708 |
25 Aug 11 |
nicklas |
417 |
<seeother> |
| 5708 |
25 Aug 11 |
nicklas |
418 |
<other external_id="sample.edit">Sample properties</other> |
| 5708 |
25 Aug 11 |
nicklas |
419 |
<other external_id="annotations.edit">Annotations & parameters</other> |
| 5708 |
25 Aug 11 |
nicklas |
420 |
<other external_id="annotations.edit.inherited">Inherited annotations</other> |
| 5708 |
25 Aug 11 |
nicklas |
421 |
</seeother> |
| 3399 |
28 May 07 |
martin |
422 |
</helptext> |
| 3399 |
28 May 07 |
martin |
423 |
</sect2> |
| 5708 |
25 Aug 11 |
nicklas |
424 |
<para> |
| 5708 |
25 Aug 11 |
nicklas |
425 |
The <guilabel>Annotations</guilabel> tab allows BASE users to use |
| 5708 |
25 Aug 11 |
nicklas |
426 |
annotation types to refine sample description. More about annotating items |
| 5708 |
25 Aug 11 |
nicklas |
427 |
can be read in <xref linkend="annotations.annotating" /> |
| 5708 |
25 Aug 11 |
nicklas |
428 |
</para> |
| 5708 |
25 Aug 11 |
nicklas |
429 |
|
| 5708 |
25 Aug 11 |
nicklas |
430 |
<para> |
| 5708 |
25 Aug 11 |
nicklas |
431 |
This <guilabel>Inherited annotations</guilabel> tab contains a list of those annotations |
| 5708 |
25 Aug 11 |
nicklas |
432 |
that are inherited from the sample's parents. Information about working with inherited |
| 5708 |
25 Aug 11 |
nicklas |
433 |
annotations can be found in <xref linkend="annotations.inheriting" />. |
| 5708 |
25 Aug 11 |
nicklas |
434 |
</para> |
| 3399 |
28 May 07 |
martin |
435 |
</sect1> |
| 3412 |
30 May 07 |
martin |
436 |
|
| 3412 |
30 May 07 |
martin |
437 |
<sect1 id="biomaterials.extracts"> |
| 5782 |
04 Oct 11 |
nicklas |
438 |
<?dbhtml filename="extracts.html" ?> |
| 3412 |
30 May 07 |
martin |
439 |
<title>Extracts</title> |
| 3399 |
28 May 07 |
martin |
440 |
<para> |
| 3412 |
30 May 07 |
martin |
441 |
Extract items should be used to describe the events that transform a sample material |
| 3412 |
30 May 07 |
martin |
442 |
into an extract material. An extract can be created from one sample item or from one or |
| 3412 |
30 May 07 |
martin |
443 |
more extract items. When an extract is created from several other extracts, a pooling |
| 3412 |
30 May 07 |
martin |
444 |
event is performed. |
| 3399 |
28 May 07 |
martin |
445 |
</para> |
| 3399 |
28 May 07 |
martin |
446 |
<para> |
| 3412 |
30 May 07 |
martin |
447 |
During the transformation from samples to extracts, it is possible to provide |
| 4487 |
08 Sep 08 |
jari |
448 |
information about the protocol used to perform this task. It is not enforced in BASE |
| 3399 |
28 May 07 |
martin |
449 |
but it should serve as guidance when devising the granularity of the sample processing |
| 3412 |
30 May 07 |
martin |
450 |
task. Also, it is good practice to provide protocol information. |
| 3399 |
28 May 07 |
martin |
451 |
</para> |
| 5708 |
25 Aug 11 |
nicklas |
452 |
<para> |
| 5708 |
25 Aug 11 |
nicklas |
453 |
Use |
| 5708 |
25 Aug 11 |
nicklas |
454 |
<menuchoice> |
| 5708 |
25 Aug 11 |
nicklas |
455 |
<guimenu>Biomaterial LIMS</guimenu> |
| 5708 |
25 Aug 11 |
nicklas |
456 |
<guimenuitem>Extracts</guimenuitem> |
| 5708 |
25 Aug 11 |
nicklas |
457 |
</menuchoice> |
| 5708 |
25 Aug 11 |
nicklas |
458 |
to get to the list of extracts. |
| 5708 |
25 Aug 11 |
nicklas |
459 |
</para> |
| 3412 |
30 May 07 |
martin |
460 |
<sect2 id="biomaterials.extracts.create"> |
| 3412 |
30 May 07 |
martin |
461 |
<title>Create extract</title> |
| 3412 |
30 May 07 |
martin |
462 |
<para> |
| 3412 |
30 May 07 |
martin |
463 |
Beside the common way, using the &gbNew; button, an extract can be created in one of |
| 3412 |
30 May 07 |
martin |
464 |
the following ways: |
| 3412 |
30 May 07 |
martin |
465 |
<variablelist> |
| 3412 |
30 May 07 |
martin |
466 |
<varlistentry> |
| 3412 |
30 May 07 |
martin |
467 |
<term>from either sample list- or single view- page.</term> |
| 3399 |
28 May 07 |
martin |
468 |
<listitem> |
| 3399 |
28 May 07 |
martin |
469 |
<para> |
| 3412 |
30 May 07 |
martin |
470 |
No matter how complex the extract processing phase is, at least one |
| 3412 |
30 May 07 |
martin |
471 |
extract has to be anchored to a sample. Therefore, a natural way to |
| 3412 |
30 May 07 |
martin |
472 |
create an extract is to click on |
| 3950 |
12 Nov 07 |
martin |
473 |
<guiicon> |
| 3950 |
12 Nov 07 |
martin |
474 |
<inlinemediaobject> |
| 3950 |
12 Nov 07 |
martin |
475 |
<imageobject> |
| 3950 |
12 Nov 07 |
martin |
476 |
<imagedata fileref="figures/add.png" format="PNG" /> |
| 3950 |
12 Nov 07 |
martin |
477 |
</imageobject> |
| 3950 |
12 Nov 07 |
martin |
478 |
</inlinemediaobject> |
| 3950 |
12 Nov 07 |
martin |
479 |
</guiicon> |
| 5708 |
25 Aug 11 |
nicklas |
480 |
in the <guilabel>Child extracts</guilabel> column for the sample that should be a parent of the |
| 5708 |
25 Aug 11 |
nicklas |
481 |
extract. There is also a corresponding button, |
| 5708 |
25 Aug 11 |
nicklas |
482 |
<guibutton>New child extract…</guibutton> |
| 3412 |
30 May 07 |
martin |
483 |
in the toolbar when viewing a single sample. |
| 3399 |
28 May 07 |
martin |
484 |
</para> |
| 3399 |
28 May 07 |
martin |
485 |
</listitem> |
| 3412 |
30 May 07 |
martin |
486 |
</varlistentry> |
| 3412 |
30 May 07 |
martin |
487 |
<varlistentry> |
| 3412 |
30 May 07 |
martin |
488 |
<term>from the extract list page</term> |
| 3399 |
28 May 07 |
martin |
489 |
<listitem> |
| 3399 |
28 May 07 |
martin |
490 |
<para> |
| 5708 |
25 Aug 11 |
nicklas |
491 |
Child extracts can be created from a single parent by clicking on the |
| 5708 |
25 Aug 11 |
nicklas |
492 |
<guiicon> |
| 5708 |
25 Aug 11 |
nicklas |
493 |
<inlinemediaobject> |
| 5708 |
25 Aug 11 |
nicklas |
494 |
<imageobject> |
| 5708 |
25 Aug 11 |
nicklas |
495 |
<imagedata fileref="figures/add.png" format="PNG" /> |
| 5708 |
25 Aug 11 |
nicklas |
496 |
</imageobject> |
| 5708 |
25 Aug 11 |
nicklas |
497 |
</inlinemediaobject> |
| 5708 |
25 Aug 11 |
nicklas |
498 |
</guiicon> icon in the <guilabel>Child extracts</guilabel> column. |
| 5708 |
25 Aug 11 |
nicklas |
499 |
Pooled extract can be created by first selecting the parents |
| 3412 |
30 May 07 |
martin |
500 |
from the list of extracts and then press |
| 3412 |
30 May 07 |
martin |
501 |
<guibutton>Pool…</guibutton> |
| 3412 |
30 May 07 |
martin |
502 |
in the toolbar. The selected extracts will be put into the parent |
| 3412 |
30 May 07 |
martin |
503 |
property. |
| 3399 |
28 May 07 |
martin |
504 |
</para> |
| 3399 |
28 May 07 |
martin |
505 |
</listitem> |
| 3412 |
30 May 07 |
martin |
506 |
</varlistentry> |
| 3412 |
30 May 07 |
martin |
507 |
</variablelist> |
| 3412 |
30 May 07 |
martin |
508 |
</para> |
| 3412 |
30 May 07 |
martin |
509 |
</sect2> |
| 3412 |
30 May 07 |
martin |
510 |
<sect2 id="biomaterials.extracts.properties"> |
| 5708 |
25 Aug 11 |
nicklas |
511 |
<title>Extract properties</title> |
| 5708 |
25 Aug 11 |
nicklas |
512 |
|
| 5708 |
25 Aug 11 |
nicklas |
513 |
<figure id="biomaterials.figures.extract-tab-1"> |
| 5708 |
25 Aug 11 |
nicklas |
514 |
<title>Extract properties</title> |
| 5708 |
25 Aug 11 |
nicklas |
515 |
<screenshot> |
| 5708 |
25 Aug 11 |
nicklas |
516 |
<mediaobject> |
| 5708 |
25 Aug 11 |
nicklas |
517 |
<imageobject> |
| 5708 |
25 Aug 11 |
nicklas |
518 |
<imagedata |
| 5708 |
25 Aug 11 |
nicklas |
519 |
fileref="figures/extract-tab-1.png" format="PNG" /> |
| 5708 |
25 Aug 11 |
nicklas |
520 |
</imageobject> |
| 5708 |
25 Aug 11 |
nicklas |
521 |
</mediaobject> |
| 5708 |
25 Aug 11 |
nicklas |
522 |
</screenshot> |
| 5708 |
25 Aug 11 |
nicklas |
523 |
</figure> |
| 3412 |
30 May 07 |
martin |
524 |
<helptext external_id="extract.edit" title="Edit extract"> |
| 3412 |
30 May 07 |
martin |
525 |
<variablelist> |
| 3412 |
30 May 07 |
martin |
526 |
<varlistentry> |
| 3412 |
30 May 07 |
martin |
527 |
<term> |
| 3412 |
30 May 07 |
martin |
528 |
<guilabel>Name</guilabel> |
| 3412 |
30 May 07 |
martin |
529 |
</term> |
| 3412 |
30 May 07 |
martin |
530 |
<listitem> |
| 3399 |
28 May 07 |
martin |
531 |
<para> |
| 4487 |
08 Sep 08 |
jari |
532 |
A mandatory field for providing the extract name. BASE by |
| 3412 |
30 May 07 |
martin |
533 |
default assigns names to extract (by suffixing |
| 3412 |
30 May 07 |
martin |
534 |
<replaceable>e#</replaceable> |
| 3412 |
30 May 07 |
martin |
535 |
when creating an extract from an existing sample or |
| 3412 |
30 May 07 |
martin |
536 |
<replaceable>New extract</replaceable> |
| 3412 |
30 May 07 |
martin |
537 |
otherwise) but it is possible to edit it at will. |
| 3399 |
28 May 07 |
martin |
538 |
</para> |
| 3412 |
30 May 07 |
martin |
539 |
</listitem> |
| 3412 |
30 May 07 |
martin |
540 |
</varlistentry> |
| 3412 |
30 May 07 |
martin |
541 |
<varlistentry> |
| 3412 |
30 May 07 |
martin |
542 |
<term> |
| 5708 |
25 Aug 11 |
nicklas |
543 |
<guilabel>Type</guilabel> |
| 5708 |
25 Aug 11 |
nicklas |
544 |
</term> |
| 5708 |
25 Aug 11 |
nicklas |
545 |
<listitem> |
| 5708 |
25 Aug 11 |
nicklas |
546 |
<para> |
| 5708 |
25 Aug 11 |
nicklas |
547 |
The subtype of the extract. The list |
| 5708 |
25 Aug 11 |
nicklas |
548 |
may evolve depending on additions by the server |
| 5708 |
25 Aug 11 |
nicklas |
549 |
administrator. Selecting the proper subtype |
| 5708 |
25 Aug 11 |
nicklas |
550 |
is recommended and enables BASE to automatically guess |
| 5708 |
25 Aug 11 |
nicklas |
551 |
the most likely subtype when creating child biomaterial and |
| 5708 |
25 Aug 11 |
nicklas |
552 |
bioassays. |
| 5708 |
25 Aug 11 |
nicklas |
553 |
<nohelp> |
| 5708 |
25 Aug 11 |
nicklas |
554 |
See <xref linkend="subtypes" /> for more information. |
| 5708 |
25 Aug 11 |
nicklas |
555 |
</nohelp> |
| 5708 |
25 Aug 11 |
nicklas |
556 |
</para> |
| 5708 |
25 Aug 11 |
nicklas |
557 |
</listitem> |
| 5708 |
25 Aug 11 |
nicklas |
558 |
</varlistentry> |
| 5708 |
25 Aug 11 |
nicklas |
559 |
<varlistentry> |
| 5708 |
25 Aug 11 |
nicklas |
560 |
<term> |
| 5708 |
25 Aug 11 |
nicklas |
561 |
<guilabel>Tag</guilabel> |
| 5708 |
25 Aug 11 |
nicklas |
562 |
</term> |
| 5708 |
25 Aug 11 |
nicklas |
563 |
<listitem> |
| 5708 |
25 Aug 11 |
nicklas |
564 |
<para> |
| 5708 |
25 Aug 11 |
nicklas |
565 |
If the extract has been marked with a tag, select it here. Note |
| 5708 |
25 Aug 11 |
nicklas |
566 |
that the subtype of the extract usually limits what kind of tag |
| 5708 |
25 Aug 11 |
nicklas |
567 |
that can be used. For example, a <emphasis>labeled extract</emphasis> |
| 5708 |
25 Aug 11 |
nicklas |
568 |
should be tagged with a <emphasis>label</emphasis>. |
| 5708 |
25 Aug 11 |
nicklas |
569 |
</para> |
| 5708 |
25 Aug 11 |
nicklas |
570 |
</listitem> |
| 5708 |
25 Aug 11 |
nicklas |
571 |
</varlistentry> |
| 5708 |
25 Aug 11 |
nicklas |
572 |
<varlistentry> |
| 5708 |
25 Aug 11 |
nicklas |
573 |
<term> |
| 3412 |
30 May 07 |
martin |
574 |
<guilabel>External ID</guilabel> |
| 3412 |
30 May 07 |
martin |
575 |
</term> |
| 3412 |
30 May 07 |
martin |
576 |
<listitem> |
| 3412 |
30 May 07 |
martin |
577 |
<para>The extracts identification outside BASE</para> |
| 3412 |
30 May 07 |
martin |
578 |
</listitem> |
| 3412 |
30 May 07 |
martin |
579 |
</varlistentry> |
| 3412 |
30 May 07 |
martin |
580 |
<varlistentry> |
| 3412 |
30 May 07 |
martin |
581 |
<term> |
| 3412 |
30 May 07 |
martin |
582 |
<guilabel>Original quantity</guilabel> |
| 3412 |
30 May 07 |
martin |
583 |
</term> |
| 3412 |
30 May 07 |
martin |
584 |
<listitem> |
| 3412 |
30 May 07 |
martin |
585 |
<para> |
| 3412 |
30 May 07 |
martin |
586 |
Holds information about the original mass of the created |
| 3412 |
30 May 07 |
martin |
587 |
extract. |
| 3412 |
30 May 07 |
martin |
588 |
</para> |
| 3412 |
30 May 07 |
martin |
589 |
</listitem> |
| 3412 |
30 May 07 |
martin |
590 |
</varlistentry> |
| 3412 |
30 May 07 |
martin |
591 |
<varlistentry> |
| 3412 |
30 May 07 |
martin |
592 |
<term> |
| 3412 |
30 May 07 |
martin |
593 |
<guilabel>Created</guilabel> |
| 3412 |
30 May 07 |
martin |
594 |
</term> |
| 3412 |
30 May 07 |
martin |
595 |
<listitem> |
| 3412 |
30 May 07 |
martin |
596 |
<para> |
| 3412 |
30 May 07 |
martin |
597 |
The date when the extract was created. The information can be |
| 3412 |
30 May 07 |
martin |
598 |
important when running quality controls on data and account for |
| 3412 |
30 May 07 |
martin |
599 |
potential confounding factor (e.g. day effect) |
| 3412 |
30 May 07 |
martin |
600 |
</para> |
| 3412 |
30 May 07 |
martin |
601 |
</listitem> |
| 3412 |
30 May 07 |
martin |
602 |
</varlistentry> |
| 3412 |
30 May 07 |
martin |
603 |
<varlistentry> |
| 3412 |
30 May 07 |
martin |
604 |
<term> |
| 3412 |
30 May 07 |
martin |
605 |
<guilabel>Registered</guilabel> |
| 3412 |
30 May 07 |
martin |
606 |
</term> |
| 3412 |
30 May 07 |
martin |
607 |
<listitem> |
| 3412 |
30 May 07 |
martin |
608 |
<para> |
| 3412 |
30 May 07 |
martin |
609 |
This is automatically populated with a date at which the sample |
| 4487 |
08 Sep 08 |
jari |
610 |
was entered in BASE system. |
| 3412 |
30 May 07 |
martin |
611 |
</para> |
| 3412 |
30 May 07 |
martin |
612 |
</listitem> |
| 3412 |
30 May 07 |
martin |
613 |
</varlistentry> |
| 3412 |
30 May 07 |
martin |
614 |
<varlistentry> |
| 3412 |
30 May 07 |
martin |
615 |
<term> |
| 3412 |
30 May 07 |
martin |
616 |
<guilabel>Protocol</guilabel> |
| 3412 |
30 May 07 |
martin |
617 |
</term> |
| 3412 |
30 May 07 |
martin |
618 |
<listitem> |
| 3412 |
30 May 07 |
martin |
619 |
<para> |
| 3412 |
30 May 07 |
martin |
620 |
The extraction protocol that was used to produce the extract. |
| 3412 |
30 May 07 |
martin |
621 |
</para> |
| 3412 |
30 May 07 |
martin |
622 |
</listitem> |
| 3412 |
30 May 07 |
martin |
623 |
</varlistentry> |
| 3412 |
30 May 07 |
martin |
624 |
<varlistentry> |
| 3412 |
30 May 07 |
martin |
625 |
<term> |
| 4732 |
21 Jan 09 |
martin |
626 |
<guilabel>Bioplate</guilabel> |
| 4732 |
21 Jan 09 |
martin |
627 |
</term> |
| 4732 |
21 Jan 09 |
martin |
628 |
<listitem> |
| 4732 |
21 Jan 09 |
martin |
629 |
<para>The bioplate where this extract is located.</para> |
| 4732 |
21 Jan 09 |
martin |
630 |
</listitem> |
| 4732 |
21 Jan 09 |
martin |
631 |
</varlistentry> |
| 4732 |
21 Jan 09 |
martin |
632 |
<varlistentry> |
| 4732 |
21 Jan 09 |
martin |
633 |
<term> |
| 4732 |
21 Jan 09 |
martin |
634 |
<guilabel>Biowell</guilabel> |
| 4732 |
21 Jan 09 |
martin |
635 |
</term> |
| 4732 |
21 Jan 09 |
martin |
636 |
<listitem> |
| 4732 |
21 Jan 09 |
martin |
637 |
<para> |
| 4732 |
21 Jan 09 |
martin |
638 |
Biowell that holds this extract. |
| 4732 |
21 Jan 09 |
martin |
639 |
<guilabel>Bioplate</guilabel> has to be defined before |
| 4732 |
21 Jan 09 |
martin |
640 |
biowell can be selected. |
| 4732 |
21 Jan 09 |
martin |
641 |
</para> |
| 4732 |
21 Jan 09 |
martin |
642 |
</listitem> |
| 4732 |
21 Jan 09 |
martin |
643 |
</varlistentry> |
| 4732 |
21 Jan 09 |
martin |
644 |
<varlistentry> |
| 4732 |
21 Jan 09 |
martin |
645 |
<term> |
| 3412 |
30 May 07 |
martin |
646 |
<guilabel>Description</guilabel> |
| 3412 |
30 May 07 |
martin |
647 |
</term> |
| 3412 |
30 May 07 |
martin |
648 |
<listitem> |
| 3412 |
30 May 07 |
martin |
649 |
<para> |
| 3412 |
30 May 07 |
martin |
650 |
A text field to report any information that not can be captured |
| 3412 |
30 May 07 |
martin |
651 |
otherwise. |
| 3412 |
30 May 07 |
martin |
652 |
</para> |
| 3412 |
30 May 07 |
martin |
653 |
</listitem> |
| 3412 |
30 May 07 |
martin |
654 |
</varlistentry> |
| 3412 |
30 May 07 |
martin |
655 |
</variablelist> |
| 5708 |
25 Aug 11 |
nicklas |
656 |
<seeother> |
| 5799 |
12 Oct 11 |
nicklas |
657 |
<other external_id="extract.parents">Parents</other> |
| 5708 |
25 Aug 11 |
nicklas |
658 |
<other external_id="annotations.edit">Annotations & parameters</other> |
| 5708 |
25 Aug 11 |
nicklas |
659 |
<other external_id="annotations.edit.inherited">Inherited annotations</other> |
| 5708 |
25 Aug 11 |
nicklas |
660 |
</seeother> |
| 3412 |
30 May 07 |
martin |
661 |
</helptext> |
| 5708 |
25 Aug 11 |
nicklas |
662 |
</sect2> |
| 5708 |
25 Aug 11 |
nicklas |
663 |
|
| 5708 |
25 Aug 11 |
nicklas |
664 |
<sect2 id="biomaterials.extracts.parents"> |
| 5708 |
25 Aug 11 |
nicklas |
665 |
<title>Extract parents</title> |
| 5708 |
25 Aug 11 |
nicklas |
666 |
<figure id="biomaterials.figures.extract-tab-2"> |
| 5708 |
25 Aug 11 |
nicklas |
667 |
<title>Extract parents</title> |
| 3412 |
30 May 07 |
martin |
668 |
<screenshot> |
| 3412 |
30 May 07 |
martin |
669 |
<mediaobject> |
| 3412 |
30 May 07 |
martin |
670 |
<imageobject> |
| 3423 |
31 May 07 |
nicklas |
671 |
<imagedata |
| 5708 |
25 Aug 11 |
nicklas |
672 |
fileref="figures/extract-tab-2.png" format="PNG" /> |
| 3412 |
30 May 07 |
martin |
673 |
</imageobject> |
| 3412 |
30 May 07 |
martin |
674 |
</mediaobject> |
| 3412 |
30 May 07 |
martin |
675 |
</screenshot> |
| 3412 |
30 May 07 |
martin |
676 |
</figure> |
| 3412 |
30 May 07 |
martin |
677 |
<helptext external_id="extract.parents" title="Extract's parents"> |
| 3412 |
30 May 07 |
martin |
678 |
<para> |
| 5708 |
25 Aug 11 |
nicklas |
679 |
This is meant to keep track of the extract origin. BASE |
| 5708 |
25 Aug 11 |
nicklas |
680 |
distinguishes between two cases which are controlled by the |
| 5708 |
25 Aug 11 |
nicklas |
681 |
<guilabel>Parent type</guilabel> |
| 5708 |
25 Aug 11 |
nicklas |
682 |
radio-button in the edit pop-up window. |
| 3412 |
30 May 07 |
martin |
683 |
</para> |
| 3412 |
30 May 07 |
martin |
684 |
<itemizedlist> |
| 3412 |
30 May 07 |
martin |
685 |
<listitem> |
| 3399 |
28 May 07 |
martin |
686 |
<para> |
| 3412 |
30 May 07 |
martin |
687 |
If the parent is a sample the radio-button is set to |
| 5708 |
25 Aug 11 |
nicklas |
688 |
<guilabel>Sample</guilabel>. Only a single sample |
| 5708 |
25 Aug 11 |
nicklas |
689 |
can be used as the parent. This option is automatically |
| 5708 |
25 Aug 11 |
nicklas |
690 |
selected if the user selects a sample with the |
| 5708 |
25 Aug 11 |
nicklas |
691 |
<guibutton>Select sample</guibutton> button. |
| 3399 |
28 May 07 |
martin |
692 |
</para> |
| 3399 |
28 May 07 |
martin |
693 |
</listitem> |
| 3399 |
28 May 07 |
martin |
694 |
<listitem> |
| 3412 |
30 May 07 |
martin |
695 |
<para> |
| 5708 |
25 Aug 11 |
nicklas |
696 |
When the parent is one or several other extracts the radio-button is |
| 5708 |
25 Aug 11 |
nicklas |
697 |
set to <guilabel>Extract</guilabel>. This option is automatically |
| 5708 |
25 Aug 11 |
nicklas |
698 |
selected if the user add extracts with the <guibutton>Add extracts</guibutton> button. |
| 3412 |
30 May 07 |
martin |
699 |
</para> |
| 3399 |
28 May 07 |
martin |
700 |
</listitem> |
| 3399 |
28 May 07 |
martin |
701 |
</itemizedlist> |
| 5708 |
25 Aug 11 |
nicklas |
702 |
|
| 5708 |
25 Aug 11 |
nicklas |
703 |
<para> |
| 5708 |
25 Aug 11 |
nicklas |
704 |
For each parent item, it is |
| 5708 |
25 Aug 11 |
nicklas |
705 |
possible to specify the amount used in micrograms. This will automatically |
| 5708 |
25 Aug 11 |
nicklas |
706 |
update the <guilabel>remaining quantity</guilabel> of the parent. |
| 5708 |
25 Aug 11 |
nicklas |
707 |
</para> |
| 5708 |
25 Aug 11 |
nicklas |
708 |
|
| 5708 |
25 Aug 11 |
nicklas |
709 |
<seeother> |
| 5708 |
25 Aug 11 |
nicklas |
710 |
<other external_id="extract.edit">Extract properties</other> |
| 5708 |
25 Aug 11 |
nicklas |
711 |
<other external_id="annotations.edit">Annotations & parameters</other> |
| 5708 |
25 Aug 11 |
nicklas |
712 |
<other external_id="annotations.edit.inherited">Inherited annotations</other> |
| 5708 |
25 Aug 11 |
nicklas |
713 |
</seeother> |
| 3412 |
30 May 07 |
martin |
714 |
</helptext> |
| 5708 |
25 Aug 11 |
nicklas |
715 |
|
| 5708 |
25 Aug 11 |
nicklas |
716 |
<para> |
| 5708 |
25 Aug 11 |
nicklas |
717 |
The <guilabel>Annotations</guilabel> tab allows BASE users to use |
| 5708 |
25 Aug 11 |
nicklas |
718 |
annotation types to refine extract description. More about annotating items |
| 5708 |
25 Aug 11 |
nicklas |
719 |
can be read in <xref linkend="annotations.annotating" /> |
| 5708 |
25 Aug 11 |
nicklas |
720 |
</para> |
| 5708 |
25 Aug 11 |
nicklas |
721 |
|
| 5708 |
25 Aug 11 |
nicklas |
722 |
<para> |
| 5708 |
25 Aug 11 |
nicklas |
723 |
This <guilabel>Inherited annotations</guilabel> tab contains a list of those annotations |
| 5708 |
25 Aug 11 |
nicklas |
724 |
that are inherited from the extract's parents. Information about working with inherited |
| 5708 |
25 Aug 11 |
nicklas |
725 |
annotations can be found in <xref linkend="annotations.inheriting" />. |
| 5708 |
25 Aug 11 |
nicklas |
726 |
</para> |
| 5708 |
25 Aug 11 |
nicklas |
727 |
|
| 5708 |
25 Aug 11 |
nicklas |
728 |
|
| 5708 |
25 Aug 11 |
nicklas |
729 |
</sect2> |
| 5708 |
25 Aug 11 |
nicklas |
730 |
|
| 5708 |
25 Aug 11 |
nicklas |
731 |
|
| 3399 |
28 May 07 |
martin |
732 |
</sect1> |
| 3157 |
05 Mar 07 |
martin |
733 |
|
| 5708 |
25 Aug 11 |
nicklas |
734 |
<sect1 id="biomaterials.tags"> |
| 5782 |
04 Oct 11 |
nicklas |
735 |
<?dbhtml filename="tags.html" ?> |
| 5708 |
25 Aug 11 |
nicklas |
736 |
<title>Tags</title> |
| 3399 |
28 May 07 |
martin |
737 |
<para> |
| 5708 |
25 Aug 11 |
nicklas |
738 |
Before attempting to create tagged extracts, users should make sure that the |
| 5708 |
25 Aug 11 |
nicklas |
739 |
appropriate tag object is present in BASE. To browse the list of tags, go to |
| 3412 |
30 May 07 |
martin |
740 |
<menuchoice> |
| 4789 |
24 Feb 09 |
nicklas |
741 |
<guimenu>Biomaterial LIMS</guimenu> |
| 5708 |
25 Aug 11 |
nicklas |
742 |
<guimenuitem>Tags</guimenuitem> |
| 3412 |
30 May 07 |
martin |
743 |
</menuchoice> |
| 3399 |
28 May 07 |
martin |
744 |
</para> |
| 3412 |
30 May 07 |
martin |
745 |
|
| 5708 |
25 Aug 11 |
nicklas |
746 |
<figure id="biomaterials.figures.tags"> |
| 5708 |
25 Aug 11 |
nicklas |
747 |
<title>Tag properties</title> |
| 5708 |
25 Aug 11 |
nicklas |
748 |
<screenshot> |
| 5708 |
25 Aug 11 |
nicklas |
749 |
<mediaobject> |
| 5708 |
25 Aug 11 |
nicklas |
750 |
<imageobject> |
| 5708 |
25 Aug 11 |
nicklas |
751 |
<imagedata |
| 5708 |
25 Aug 11 |
nicklas |
752 |
fileref="figures/edit_tag.png" format="PNG" /> |
| 5708 |
25 Aug 11 |
nicklas |
753 |
</imageobject> |
| 5708 |
25 Aug 11 |
nicklas |
754 |
</mediaobject> |
| 5708 |
25 Aug 11 |
nicklas |
755 |
</screenshot> |
| 5708 |
25 Aug 11 |
nicklas |
756 |
</figure> |
| 5708 |
25 Aug 11 |
nicklas |
757 |
|
| 5708 |
25 Aug 11 |
nicklas |
758 |
<helptext external_id="tag.edit" title="Edit tag"> |
| 3412 |
30 May 07 |
martin |
759 |
<para> |
| 5708 |
25 Aug 11 |
nicklas |
760 |
The tag item is very simple and does not need much explanation. There are only |
| 5708 |
25 Aug 11 |
nicklas |
761 |
a few properties for a tag. |
| 3412 |
30 May 07 |
martin |
762 |
<variablelist> |
| 3412 |
30 May 07 |
martin |
763 |
<varlistentry> |
| 3412 |
30 May 07 |
martin |
764 |
<term> |
| 3412 |
30 May 07 |
martin |
765 |
<guilabel>Name</guilabel> |
| 3412 |
30 May 07 |
martin |
766 |
</term> |
| 3399 |
28 May 07 |
martin |
767 |
<listitem> |
| 5708 |
25 Aug 11 |
nicklas |
768 |
<para>The name of the tag (required).</para> |
| 3412 |
30 May 07 |
martin |
769 |
</listitem> |
| 3412 |
30 May 07 |
martin |
770 |
</varlistentry> |
| 3412 |
30 May 07 |
martin |
771 |
<varlistentry> |
| 3412 |
30 May 07 |
martin |
772 |
<term> |
| 5708 |
25 Aug 11 |
nicklas |
773 |
<guilabel>Type</guilabel> |
| 3412 |
30 May 07 |
martin |
774 |
</term> |
| 3412 |
30 May 07 |
martin |
775 |
<listitem> |
| 3399 |
28 May 07 |
martin |
776 |
<para> |
| 5708 |
25 Aug 11 |
nicklas |
777 |
The subtype of the tag. The list |
| 5708 |
25 Aug 11 |
nicklas |
778 |
may evolve depending on additions by the server |
| 5708 |
25 Aug 11 |
nicklas |
779 |
administrator. Selecting the proper subtype |
| 5708 |
25 Aug 11 |
nicklas |
780 |
is important and enables BASE to automatically guess |
| 5708 |
25 Aug 11 |
nicklas |
781 |
the most likely tag when creating tagged extracts (eg. |
| 5708 |
25 Aug 11 |
nicklas |
782 |
a <emphasis>Label</emphasis> for a <emphasis>Labeled extract</emphasis> |
| 5708 |
25 Aug 11 |
nicklas |
783 |
or a <emphasis>Barcode</emphasis> for a <emphasis>Library</emphasis>). |
| 5708 |
25 Aug 11 |
nicklas |
784 |
<nohelp> |
| 5708 |
25 Aug 11 |
nicklas |
785 |
See <xref linkend="subtypes" /> for more information. |
| 5708 |
25 Aug 11 |
nicklas |
786 |
</nohelp> |
| 3399 |
28 May 07 |
martin |
787 |
</para> |
| 3412 |
30 May 07 |
martin |
788 |
</listitem> |
| 3412 |
30 May 07 |
martin |
789 |
</varlistentry> |
| 3412 |
30 May 07 |
martin |
790 |
<varlistentry> |
| 3412 |
30 May 07 |
martin |
791 |
<term> |
| 3412 |
30 May 07 |
martin |
792 |
<guilabel>Description</guilabel> |
| 3412 |
30 May 07 |
martin |
793 |
</term> |
| 3412 |
30 May 07 |
martin |
794 |
<listitem> |
| 3399 |
28 May 07 |
martin |
795 |
<para> |
| 5708 |
25 Aug 11 |
nicklas |
796 |
An explaining text or other information associated with the |
| 5708 |
25 Aug 11 |
nicklas |
797 |
tag. |
| 3399 |
28 May 07 |
martin |
798 |
</para> |
| 3399 |
28 May 07 |
martin |
799 |
</listitem> |
| 3412 |
30 May 07 |
martin |
800 |
</varlistentry> |
| 3412 |
30 May 07 |
martin |
801 |
</variablelist> |
| 5708 |
25 Aug 11 |
nicklas |
802 |
</para> |
| 5708 |
25 Aug 11 |
nicklas |
803 |
</helptext> |
| 5708 |
25 Aug 11 |
nicklas |
804 |
|
| 3399 |
28 May 07 |
martin |
805 |
</sect1> |
| 5708 |
25 Aug 11 |
nicklas |
806 |
|
| 4732 |
21 Jan 09 |
martin |
807 |
|
| 5708 |
25 Aug 11 |
nicklas |
808 |
<sect1 id="biomaterials.bioplates"> |
| 5782 |
04 Oct 11 |
nicklas |
809 |
<?dbhtml filename="bioplates.html" ?> |
| 5708 |
25 Aug 11 |
nicklas |
810 |
<title>Bioplates</title> |
| 4732 |
21 Jan 09 |
martin |
811 |
<para> |
| 5708 |
25 Aug 11 |
nicklas |
812 |
With bioplates it is possible to organize biomaterial such as samples and extracts |
| 5708 |
25 Aug 11 |
nicklas |
813 |
into wells. Each plate has a number of wells that is defined by the plate geometry. |
| 4732 |
21 Jan 09 |
martin |
814 |
</para> |
| 4732 |
21 Jan 09 |
martin |
815 |
<para> |
| 4732 |
21 Jan 09 |
martin |
816 |
Use |
| 4732 |
21 Jan 09 |
martin |
817 |
<menuchoice> |
| 4732 |
21 Jan 09 |
martin |
818 |
<guimenu>Biomaterial LIMS</guimenu> |
| 5708 |
25 Aug 11 |
nicklas |
819 |
<guimenuitem>Bioplates</guimenuitem> |
| 4732 |
21 Jan 09 |
martin |
820 |
</menuchoice> |
| 4732 |
21 Jan 09 |
martin |
821 |
to get to the list of bioplates. |
| 4732 |
21 Jan 09 |
martin |
822 |
</para> |
| 4732 |
21 Jan 09 |
martin |
823 |
<sect2 id="biomaterials.bioplate.properties"> |
| 5708 |
25 Aug 11 |
nicklas |
824 |
<title>Bioplate properties</title> |
| 5708 |
25 Aug 11 |
nicklas |
825 |
|
| 5708 |
25 Aug 11 |
nicklas |
826 |
<figure id="biomaterials.figures.bioplate-tab-1"> |
| 5708 |
25 Aug 11 |
nicklas |
827 |
<title>Bioplate properties</title> |
| 5708 |
25 Aug 11 |
nicklas |
828 |
<screenshot> |
| 5708 |
25 Aug 11 |
nicklas |
829 |
<mediaobject> |
| 5708 |
25 Aug 11 |
nicklas |
830 |
<imageobject> |
| 5708 |
25 Aug 11 |
nicklas |
831 |
<imagedata |
| 5708 |
25 Aug 11 |
nicklas |
832 |
fileref="figures/bioplate-tab-1.png" format="PNG" /> |
| 5708 |
25 Aug 11 |
nicklas |
833 |
</imageobject> |
| 5708 |
25 Aug 11 |
nicklas |
834 |
</mediaobject> |
| 5708 |
25 Aug 11 |
nicklas |
835 |
</screenshot> |
| 5708 |
25 Aug 11 |
nicklas |
836 |
</figure> |
| 5708 |
25 Aug 11 |
nicklas |
837 |
|
| 4732 |
21 Jan 09 |
martin |
838 |
<helptext external_id="bioplate.edit" title="Edit bioplate"> |
| 4732 |
21 Jan 09 |
martin |
839 |
<para> |
| 4732 |
21 Jan 09 |
martin |
840 |
<variablelist> |
| 4732 |
21 Jan 09 |
martin |
841 |
<varlistentry> |
| 4732 |
21 Jan 09 |
martin |
842 |
<term><guilabel>Name</guilabel></term> |
| 4732 |
21 Jan 09 |
martin |
843 |
<listitem> |
| 4732 |
21 Jan 09 |
martin |
844 |
<para> |
| 5708 |
25 Aug 11 |
nicklas |
845 |
The bioplate name. The name does not have to be unique but it is |
| 4789 |
24 Feb 09 |
nicklas |
846 |
recommended to keep it unique. BASE by default assigns |
| 4732 |
21 Jan 09 |
martin |
847 |
<replaceable>New bioplate</replaceable> as name. |
| 4732 |
21 Jan 09 |
martin |
848 |
This field is mandatory. |
| 4732 |
21 Jan 09 |
martin |
849 |
</para> |
| 4732 |
21 Jan 09 |
martin |
850 |
</listitem> |
| 4732 |
21 Jan 09 |
martin |
851 |
</varlistentry> |
| 4732 |
21 Jan 09 |
martin |
852 |
<varlistentry> |
| 5708 |
25 Aug 11 |
nicklas |
853 |
<term><guilabel>Bioplate type</guilabel></term> |
| 5708 |
25 Aug 11 |
nicklas |
854 |
<listitem> |
| 5708 |
25 Aug 11 |
nicklas |
855 |
<para> |
| 5708 |
25 Aug 11 |
nicklas |
856 |
The type of the bioplate may be a generic storage plate that |
| 5708 |
25 Aug 11 |
nicklas |
857 |
can store any type of biomaterial or a locked plate that |
| 5708 |
25 Aug 11 |
nicklas |
858 |
can only store a single type of biomaterial. This field |
| 5708 |
25 Aug 11 |
nicklas |
859 |
is mandatory and can only be set for new bioplates. |
| 5708 |
25 Aug 11 |
nicklas |
860 |
<nohelp>See <xref linkend="biomaterials.bioplatetypes" /> for more |
| 5708 |
25 Aug 11 |
nicklas |
861 |
information.</nohelp> |
| 5708 |
25 Aug 11 |
nicklas |
862 |
</para> |
| 5708 |
25 Aug 11 |
nicklas |
863 |
</listitem> |
| 5708 |
25 Aug 11 |
nicklas |
864 |
</varlistentry> |
| 5708 |
25 Aug 11 |
nicklas |
865 |
<varlistentry> |
| 4732 |
21 Jan 09 |
martin |
866 |
<term><guilabel>Plate geometry</guilabel></term> |
| 4732 |
21 Jan 09 |
martin |
867 |
<listitem> |
| 4732 |
21 Jan 09 |
martin |
868 |
<para> |
| 4789 |
24 Feb 09 |
nicklas |
869 |
Information about the plate design defining the |
| 4789 |
24 Feb 09 |
nicklas |
870 |
number of rows and columns on the bioplate. |
| 5708 |
25 Aug 11 |
nicklas |
871 |
This field is mandatory and can only be set for new bioplates. |
| 4732 |
21 Jan 09 |
martin |
872 |
</para> |
| 4732 |
21 Jan 09 |
martin |
873 |
</listitem> |
| 4732 |
21 Jan 09 |
martin |
874 |
</varlistentry> |
| 4732 |
21 Jan 09 |
martin |
875 |
<varlistentry> |
| 6064 |
13 Jun 12 |
nicklas |
876 |
<term><guilabel>Storage location</guilabel></term> |
| 4732 |
21 Jan 09 |
martin |
877 |
<listitem> |
| 6064 |
13 Jun 12 |
nicklas |
878 |
<para>The location, for example a freezer, where the bioplate is stored. Optional.</para> |
| 4732 |
21 Jan 09 |
martin |
879 |
</listitem> |
| 4732 |
21 Jan 09 |
martin |
880 |
</varlistentry> |
| 4732 |
21 Jan 09 |
martin |
881 |
<varlistentry> |
| 6064 |
13 Jun 12 |
nicklas |
882 |
<term><guilabel>Section</guilabel></term> |
| 6064 |
13 Jun 12 |
nicklas |
883 |
<listitem> |
| 6064 |
13 Jun 12 |
nicklas |
884 |
<para>The section within the freezer where the bioplate is stored. Optional.</para> |
| 6064 |
13 Jun 12 |
nicklas |
885 |
</listitem> |
| 6064 |
13 Jun 12 |
nicklas |
886 |
</varlistentry> |
| 6064 |
13 Jun 12 |
nicklas |
887 |
<varlistentry> |
| 6064 |
13 Jun 12 |
nicklas |
888 |
<term><guilabel>Tray</guilabel></term> |
| 6064 |
13 Jun 12 |
nicklas |
889 |
<listitem> |
| 6064 |
13 Jun 12 |
nicklas |
890 |
<para>The tray within the section where the bioplate is stored. Optional.</para> |
| 6064 |
13 Jun 12 |
nicklas |
891 |
</listitem> |
| 6064 |
13 Jun 12 |
nicklas |
892 |
</varlistentry> |
| 6064 |
13 Jun 12 |
nicklas |
893 |
<varlistentry> |
| 6064 |
13 Jun 12 |
nicklas |
894 |
<term><guilabel>Position</guilabel></term> |
| 6064 |
13 Jun 12 |
nicklas |
895 |
<listitem> |
| 6064 |
13 Jun 12 |
nicklas |
896 |
<para>The position within the tray where the bioplate is stored. Optional.</para> |
| 6064 |
13 Jun 12 |
nicklas |
897 |
</listitem> |
| 6064 |
13 Jun 12 |
nicklas |
898 |
</varlistentry> |
| 6064 |
13 Jun 12 |
nicklas |
899 |
<varlistentry> |
| 4732 |
21 Jan 09 |
martin |
900 |
<term><guilabel>Barcode</guilabel></term> |
| 4732 |
21 Jan 09 |
martin |
901 |
<listitem> |
| 4732 |
21 Jan 09 |
martin |
902 |
<para> |
| 4789 |
24 Feb 09 |
nicklas |
903 |
Barcode of the bioplate. |
| 4732 |
21 Jan 09 |
martin |
904 |
Optional. |
| 4732 |
21 Jan 09 |
martin |
905 |
</para> |
| 4732 |
21 Jan 09 |
martin |
906 |
</listitem> |
| 4732 |
21 Jan 09 |
martin |
907 |
</varlistentry> |
| 4732 |
21 Jan 09 |
martin |
908 |
<varlistentry> |
| 4732 |
21 Jan 09 |
martin |
909 |
<term><guilabel>Description</guilabel></term> |
| 4732 |
21 Jan 09 |
martin |
910 |
<listitem> |
| 4732 |
21 Jan 09 |
martin |
911 |
<para> |
| 4789 |
24 Feb 09 |
nicklas |
912 |
Other useful information about the bioplate. Optional. |
| 4732 |
21 Jan 09 |
martin |
913 |
</para> |
| 4732 |
21 Jan 09 |
martin |
914 |
</listitem> |
| 4732 |
21 Jan 09 |
martin |
915 |
</varlistentry> |
| 4732 |
21 Jan 09 |
martin |
916 |
</variablelist> |
| 4732 |
21 Jan 09 |
martin |
917 |
</para> |
| 5708 |
25 Aug 11 |
nicklas |
918 |
|
| 5708 |
25 Aug 11 |
nicklas |
919 |
<seeother> |
| 5708 |
25 Aug 11 |
nicklas |
920 |
<other external_id="annotations.edit">Annotations</other> |
| 5708 |
25 Aug 11 |
nicklas |
921 |
</seeother> |
| 4732 |
21 Jan 09 |
martin |
922 |
</helptext> |
| 5708 |
25 Aug 11 |
nicklas |
923 |
|
| 5708 |
25 Aug 11 |
nicklas |
924 |
<para> |
| 5708 |
25 Aug 11 |
nicklas |
925 |
The <guilabel>Annotations</guilabel> tab allows BASE users to use |
| 5708 |
25 Aug 11 |
nicklas |
926 |
annotation types to refine bioplate description. More about annotating items |
| 5708 |
25 Aug 11 |
nicklas |
927 |
can be read in <xref linkend="annotations.annotating" /> |
| 5708 |
25 Aug 11 |
nicklas |
928 |
</para> |
| 5708 |
25 Aug 11 |
nicklas |
929 |
|
| 5708 |
25 Aug 11 |
nicklas |
930 |
</sect2> |
| 5708 |
25 Aug 11 |
nicklas |
931 |
<sect2 id="biomaterials.bioplate.biowells"> |
| 5708 |
25 Aug 11 |
nicklas |
932 |
<title>Biowells</title> |
| 5708 |
25 Aug 11 |
nicklas |
933 |
<para> |
| 5708 |
25 Aug 11 |
nicklas |
934 |
Biowells existence are managed through the bioplate they |
| 5708 |
25 Aug 11 |
nicklas |
935 |
belong to. Creating a bioplate will automatically create the |
| 5708 |
25 Aug 11 |
nicklas |
936 |
biowells (as given by the selected geometry) on the plate. |
| 5708 |
25 Aug 11 |
nicklas |
937 |
The wells are initially empty. To add biomaterial to the plate |
| 5708 |
25 Aug 11 |
nicklas |
938 |
go to the single-item view page for the bioplate. This page |
| 5708 |
25 Aug 11 |
nicklas |
939 |
includes an overview of the layout of the plate. Clicking |
| 5708 |
25 Aug 11 |
nicklas |
940 |
on an empty well will open a popup dialog that allows you |
| 5708 |
25 Aug 11 |
nicklas |
941 |
to select a biomaterial. The same dialog can also be accessed from |
| 5708 |
25 Aug 11 |
nicklas |
942 |
the <guilabel>Wells</guilabel> tab. Assigning a biomaterial to a |
| 5724 |
08 Sep 11 |
nicklas |
943 |
biowell can also be done when editing a sample or extract, or |
| 5724 |
08 Sep 11 |
nicklas |
944 |
by using the <link linkend="biomaterials.placeonplate">Place-on-plate |
| 5724 |
08 Sep 11 |
nicklas |
945 |
wizard</link>. |
| 5708 |
25 Aug 11 |
nicklas |
946 |
</para> |
| 5708 |
25 Aug 11 |
nicklas |
947 |
|
| 5708 |
25 Aug 11 |
nicklas |
948 |
<figure id="biomaterials.figures.biowell"> |
| 5708 |
25 Aug 11 |
nicklas |
949 |
<title>Biowell properties</title> |
| 4732 |
21 Jan 09 |
martin |
950 |
<screenshot> |
| 4732 |
21 Jan 09 |
martin |
951 |
<mediaobject> |
| 4732 |
21 Jan 09 |
martin |
952 |
<imageobject> |
| 4732 |
21 Jan 09 |
martin |
953 |
<imagedata |
| 5708 |
25 Aug 11 |
nicklas |
954 |
fileref="figures/biowell.png" format="PNG" /> |
| 4732 |
21 Jan 09 |
martin |
955 |
</imageobject> |
| 4732 |
21 Jan 09 |
martin |
956 |
</mediaobject> |
| 4732 |
21 Jan 09 |
martin |
957 |
</screenshot> |
| 4732 |
21 Jan 09 |
martin |
958 |
</figure> |
| 5708 |
25 Aug 11 |
nicklas |
959 |
|
| 4732 |
21 Jan 09 |
martin |
960 |
<helptext external_id="biowell.edit" title="Edit biowell"> |
| 4732 |
21 Jan 09 |
martin |
961 |
<para> |
| 4732 |
21 Jan 09 |
martin |
962 |
<variablelist> |
| 4732 |
21 Jan 09 |
martin |
963 |
<varlistentry> |
| 4732 |
21 Jan 09 |
martin |
964 |
<term><guilabel>Bioplate</guilabel></term> |
| 4732 |
21 Jan 09 |
martin |
965 |
<listitem> |
| 4732 |
21 Jan 09 |
martin |
966 |
<para> |
| 4789 |
24 Feb 09 |
nicklas |
967 |
Shows which bioplate the biowell is located on. |
| 4732 |
21 Jan 09 |
martin |
968 |
This property is read-only. |
| 4732 |
21 Jan 09 |
martin |
969 |
</para> |
| 4732 |
21 Jan 09 |
martin |
970 |
</listitem> |
| 4732 |
21 Jan 09 |
martin |
971 |
</varlistentry> |
| 4732 |
21 Jan 09 |
martin |
972 |
<varlistentry> |
| 5708 |
25 Aug 11 |
nicklas |
973 |
<term><guilabel>Well location</guilabel></term> |
| 4732 |
21 Jan 09 |
martin |
974 |
<listitem> |
| 4732 |
21 Jan 09 |
martin |
975 |
<para> |
| 5708 |
25 Aug 11 |
nicklas |
976 |
The biowell location on the bioplate in row+column format. |
| 4732 |
21 Jan 09 |
martin |
977 |
This property is read-only. |
| 4732 |
21 Jan 09 |
martin |
978 |
</para> |
| 4732 |
21 Jan 09 |
martin |
979 |
</listitem> |
| 4732 |
21 Jan 09 |
martin |
980 |
</varlistentry> |
| 5708 |
25 Aug 11 |
nicklas |
981 |
<varlistentry> |
| 4732 |
21 Jan 09 |
martin |
982 |
<term><guilabel>Biomaterial type</guilabel></term> |
| 4732 |
21 Jan 09 |
martin |
983 |
<listitem> |
| 4732 |
21 Jan 09 |
martin |
984 |
<para> |
| 4732 |
21 Jan 09 |
martin |
985 |
The type of biomaterial stored in this biowell. This |
| 4789 |
24 Feb 09 |
nicklas |
986 |
property must be selected before before a |
| 5708 |
25 Aug 11 |
nicklas |
987 |
biomaterial can be selected. On some plates this |
| 5708 |
25 Aug 11 |
nicklas |
988 |
is locked due to settings in the bioplate's type. |
| 4732 |
21 Jan 09 |
martin |
989 |
</para> |
| 4732 |
21 Jan 09 |
martin |
990 |
</listitem> |
| 4732 |
21 Jan 09 |
martin |
991 |
</varlistentry> |
| 4732 |
21 Jan 09 |
martin |
992 |
<varlistentry> |
| 4732 |
21 Jan 09 |
martin |
993 |
<term><guilabel>Biomaterial</guilabel></term> |
| 4732 |
21 Jan 09 |
martin |
994 |
<listitem> |
| 4732 |
21 Jan 09 |
martin |
995 |
<para> |
| 4732 |
21 Jan 09 |
martin |
996 |
Name of the biomaterial in this biowell. Before changing |
| 5708 |
25 Aug 11 |
nicklas |
997 |
this you must select the appropriate <guilabel>Biomaterial type</guilabel>. |
| 5708 |
25 Aug 11 |
nicklas |
998 |
A biomaterial can only be placed in a single well. If the selected |
| 5708 |
25 Aug 11 |
nicklas |
999 |
biomaterial is already placed in another location it will be moved. |
| 4732 |
21 Jan 09 |
martin |
1000 |
</para> |
| 4732 |
21 Jan 09 |
martin |
1001 |
</listitem> |
| 4732 |
21 Jan 09 |
martin |
1002 |
</varlistentry> |
| 4732 |
21 Jan 09 |
martin |
1003 |
</variablelist> |
| 4732 |
21 Jan 09 |
martin |
1004 |
</para> |
| 5708 |
25 Aug 11 |
nicklas |
1005 |
</helptext> |
| 4732 |
21 Jan 09 |
martin |
1006 |
</sect2> |
| 5708 |
25 Aug 11 |
nicklas |
1007 |
|
| 5708 |
25 Aug 11 |
nicklas |
1008 |
<sect2 id="biomaterials.bioplatetypes"> |
| 5708 |
25 Aug 11 |
nicklas |
1009 |
<title>Bioplate types</title> |
| 5708 |
25 Aug 11 |
nicklas |
1010 |
|
| 5708 |
25 Aug 11 |
nicklas |
1011 |
<helptext external_id="bioplatetype.view.properties" title="Bioplate types"> |
| 5708 |
25 Aug 11 |
nicklas |
1012 |
<para> |
| 5708 |
25 Aug 11 |
nicklas |
1013 |
Bioplate types are used to subclassify bioplates and may put restrictions on them. |
| 5708 |
25 Aug 11 |
nicklas |
1014 |
BASE ships with a few pre-defined bioplate types. The <emphasis>Storage plate</emphasis> type |
| 5708 |
25 Aug 11 |
nicklas |
1015 |
is a generic plate type that can be used for all types of biomaterial and doesn't |
| 5708 |
25 Aug 11 |
nicklas |
1016 |
have any other restrictions on it. The reaction plate types are locked to a single |
| 5708 |
25 Aug 11 |
nicklas |
1017 |
type of biomaterial and have a restriction that biomaterial can never be moved out from |
| 5708 |
25 Aug 11 |
nicklas |
1018 |
a well once it has been placed there. |
| 5708 |
25 Aug 11 |
nicklas |
1019 |
</para> |
| 5708 |
25 Aug 11 |
nicklas |
1020 |
</helptext> |
| 5708 |
25 Aug 11 |
nicklas |
1021 |
|
| 5708 |
25 Aug 11 |
nicklas |
1022 |
<figure id="biomaterials.figures.bioplatetype"> |
| 5708 |
25 Aug 11 |
nicklas |
1023 |
<title>Bioplate type properties</title> |
| 5708 |
25 Aug 11 |
nicklas |
1024 |
<screenshot> |
| 5708 |
25 Aug 11 |
nicklas |
1025 |
<mediaobject> |
| 5708 |
25 Aug 11 |
nicklas |
1026 |
<imageobject> |
| 5708 |
25 Aug 11 |
nicklas |
1027 |
<imagedata |
| 5708 |
25 Aug 11 |
nicklas |
1028 |
fileref="figures/edit_bioplatetype.png" format="PNG" /> |
| 5708 |
25 Aug 11 |
nicklas |
1029 |
</imageobject> |
| 5708 |
25 Aug 11 |
nicklas |
1030 |
</mediaobject> |
| 5708 |
25 Aug 11 |
nicklas |
1031 |
</screenshot> |
| 5708 |
25 Aug 11 |
nicklas |
1032 |
</figure> |
| 5708 |
25 Aug 11 |
nicklas |
1033 |
|
| 5708 |
25 Aug 11 |
nicklas |
1034 |
<helptext external_id="bioplatetype.edit" title="Edit bioplate type"> |
| 5708 |
25 Aug 11 |
nicklas |
1035 |
<para> |
| 5708 |
25 Aug 11 |
nicklas |
1036 |
<variablelist> |
| 5708 |
25 Aug 11 |
nicklas |
1037 |
<varlistentry> |
| 5708 |
25 Aug 11 |
nicklas |
1038 |
<term><guilabel>Name</guilabel></term> |
| 5708 |
25 Aug 11 |
nicklas |
1039 |
<listitem> |
| 5708 |
25 Aug 11 |
nicklas |
1040 |
<para> |
| 5708 |
25 Aug 11 |
nicklas |
1041 |
The name of the bioplate type. |
| 5708 |
25 Aug 11 |
nicklas |
1042 |
</para> |
| 5708 |
25 Aug 11 |
nicklas |
1043 |
</listitem> |
| 5708 |
25 Aug 11 |
nicklas |
1044 |
</varlistentry> |
| 5708 |
25 Aug 11 |
nicklas |
1045 |
<varlistentry> |
| 5708 |
25 Aug 11 |
nicklas |
1046 |
<term><guilabel>Biomaterial type</guilabel></term> |
| 5708 |
25 Aug 11 |
nicklas |
1047 |
<listitem> |
| 5708 |
25 Aug 11 |
nicklas |
1048 |
<para> |
| 5708 |
25 Aug 11 |
nicklas |
1049 |
Select if bioplates using this type should be locked to |
| 5708 |
25 Aug 11 |
nicklas |
1050 |
specific biomaterial type or not. This property can only |
| 5708 |
25 Aug 11 |
nicklas |
1051 |
be set for new bioplate types. |
| 5708 |
25 Aug 11 |
nicklas |
1052 |
</para> |
| 5708 |
25 Aug 11 |
nicklas |
1053 |
</listitem> |
| 5708 |
25 Aug 11 |
nicklas |
1054 |
</varlistentry> |
| 5797 |
11 Oct 11 |
nicklas |
1055 |
<varlistentry> |
| 5797 |
11 Oct 11 |
nicklas |
1056 |
<term><guilabel>Biomaterial subtype</guilabel></term> |
| 5797 |
11 Oct 11 |
nicklas |
1057 |
<listitem> |
| 5797 |
11 Oct 11 |
nicklas |
1058 |
<para> |
| 5797 |
11 Oct 11 |
nicklas |
1059 |
If a specific biomaterial type has been selected |
| 5797 |
11 Oct 11 |
nicklas |
1060 |
it is also possible to further restrict the use |
| 5797 |
11 Oct 11 |
nicklas |
1061 |
of the bioplate to a certain biomaterial subtype. |
| 5797 |
11 Oct 11 |
nicklas |
1062 |
The restriction is not enforced by the core but is mainly used |
| 5797 |
11 Oct 11 |
nicklas |
1063 |
by the gui to provide smart filters in selection |
| 5797 |
11 Oct 11 |
nicklas |
1064 |
lists, in the bioplate event wizards, etc. |
| 5797 |
11 Oct 11 |
nicklas |
1065 |
</para> |
| 5797 |
11 Oct 11 |
nicklas |
1066 |
</listitem> |
| 5797 |
11 Oct 11 |
nicklas |
1067 |
</varlistentry> |
| 6064 |
13 Jun 12 |
nicklas |
1068 |
<varlistentry> |
| 6064 |
13 Jun 12 |
nicklas |
1069 |
<term><guilabel>Storage type</guilabel></term> |
| 6064 |
13 Jun 12 |
nicklas |
1070 |
<listitem> |
| 6064 |
13 Jun 12 |
nicklas |
1071 |
<para> |
| 6064 |
13 Jun 12 |
nicklas |
1072 |
The subtype of the hardware item (eg. freezer, cabinet) |
| 6064 |
13 Jun 12 |
nicklas |
1073 |
where bioplates with this bioplate type usually are stored. |
| 6064 |
13 Jun 12 |
nicklas |
1074 |
</para> |
| 6064 |
13 Jun 12 |
nicklas |
1075 |
</listitem> |
| 6064 |
13 Jun 12 |
nicklas |
1076 |
</varlistentry> |
| 5708 |
25 Aug 11 |
nicklas |
1077 |
<varlistentry> |
| 5708 |
25 Aug 11 |
nicklas |
1078 |
<term><guilabel>Well lock mode</guilabel></term> |
| 5708 |
25 Aug 11 |
nicklas |
1079 |
<listitem> |
| 5708 |
25 Aug 11 |
nicklas |
1080 |
<para> |
| 5708 |
25 Aug 11 |
nicklas |
1081 |
This option controls the wells on bioplates using this type. |
| 5708 |
25 Aug 11 |
nicklas |
1082 |
There are four options: |
| 5708 |
25 Aug 11 |
nicklas |
1083 |
<itemizedlist> |
| 5708 |
25 Aug 11 |
nicklas |
1084 |
<listitem> |
| 5708 |
25 Aug 11 |
nicklas |
1085 |
<para><guilabel>Unlocked</guilabel>: |
| 5708 |
25 Aug 11 |
nicklas |
1086 |
The wells are unlocked and biomaterial can be added |
| 5708 |
25 Aug 11 |
nicklas |
1087 |
and removed freely any number of times. |
| 5708 |
25 Aug 11 |
nicklas |
1088 |
</para> |
| 5708 |
25 Aug 11 |
nicklas |
1089 |
</listitem> |
| 5708 |
25 Aug 11 |
nicklas |
1090 |
<listitem> |
| 5708 |
25 Aug 11 |
nicklas |
1091 |
<para><guilabel>Locked after add+clear</guilabel>: |
| 5708 |
25 Aug 11 |
nicklas |
1092 |
A biomaterial can be placed once in the well and |
| 5708 |
25 Aug 11 |
nicklas |
1093 |
then moved to another bioplate. After that the well |
| 5708 |
25 Aug 11 |
nicklas |
1094 |
becomes locked and it is not possible to add a |
| 5708 |
25 Aug 11 |
nicklas |
1095 |
different biomaterial to it. |
| 5708 |
25 Aug 11 |
nicklas |
1096 |
</para> |
| 5708 |
25 Aug 11 |
nicklas |
1097 |
</listitem> |
| 5708 |
25 Aug 11 |
nicklas |
1098 |
<listitem> |
| 5708 |
25 Aug 11 |
nicklas |
1099 |
<para><guilabel>Locked after add</guilabel>: |
| 5708 |
25 Aug 11 |
nicklas |
1100 |
The wells are locked as soon as biomaterial is |
| 5708 |
25 Aug 11 |
nicklas |
1101 |
added to them. The biomaterial can't be moved to another |
| 5708 |
25 Aug 11 |
nicklas |
1102 |
place or be replaced with other biomaterial. |
| 5708 |
25 Aug 11 |
nicklas |
1103 |
</para> |
| 5708 |
25 Aug 11 |
nicklas |
1104 |
</listitem> |
| 5708 |
25 Aug 11 |
nicklas |
1105 |
<listitem> |
| 5708 |
25 Aug 11 |
nicklas |
1106 |
<para><guilabel>Locked at plate creation</guilabel>: |
| 5708 |
25 Aug 11 |
nicklas |
1107 |
The wells are locked as soon as the bioplate has been |
| 5708 |
25 Aug 11 |
nicklas |
1108 |
saved to the database. This lock mode is primarily intended |
| 5708 |
25 Aug 11 |
nicklas |
1109 |
to be used when plug-ins are creating and populating the |
| 5708 |
25 Aug 11 |
nicklas |
1110 |
bioplate as a single event. |
| 5708 |
25 Aug 11 |
nicklas |
1111 |
</para> |
| 5708 |
25 Aug 11 |
nicklas |
1112 |
</listitem> |
| 5708 |
25 Aug 11 |
nicklas |
1113 |
</itemizedlist> |
| 5708 |
25 Aug 11 |
nicklas |
1114 |
</para> |
| 5708 |
25 Aug 11 |
nicklas |
1115 |
</listitem> |
| 5708 |
25 Aug 11 |
nicklas |
1116 |
</varlistentry> |
| 5708 |
25 Aug 11 |
nicklas |
1117 |
<varlistentry> |
| 5708 |
25 Aug 11 |
nicklas |
1118 |
<term><guilabel>Description</guilabel></term> |
| 5708 |
25 Aug 11 |
nicklas |
1119 |
<listitem> |
| 5708 |
25 Aug 11 |
nicklas |
1120 |
<para> |
| 5708 |
25 Aug 11 |
nicklas |
1121 |
Other useful information about the bioplate type. Optional. |
| 5708 |
25 Aug 11 |
nicklas |
1122 |
</para> |
| 5708 |
25 Aug 11 |
nicklas |
1123 |
</listitem> |
| 5708 |
25 Aug 11 |
nicklas |
1124 |
</varlistentry> |
| 5708 |
25 Aug 11 |
nicklas |
1125 |
</variablelist> |
| 5708 |
25 Aug 11 |
nicklas |
1126 |
</para> |
| 5708 |
25 Aug 11 |
nicklas |
1127 |
</helptext> |
| 5708 |
25 Aug 11 |
nicklas |
1128 |
</sect2> |
| 5708 |
25 Aug 11 |
nicklas |
1129 |
|
| 5708 |
25 Aug 11 |
nicklas |
1130 |
<sect2 id="biomaterials.bioplateevents"> |
| 5708 |
25 Aug 11 |
nicklas |
1131 |
<title>Bioplate events</title> |
| 5708 |
25 Aug 11 |
nicklas |
1132 |
|
| 5708 |
25 Aug 11 |
nicklas |
1133 |
<para> |
| 5724 |
08 Sep 11 |
nicklas |
1134 |
Certain actions can be applied collectively to the biomaterial on a bioplate, |
| 5724 |
08 Sep 11 |
nicklas |
1135 |
either as a whole or a subset that is picked by the user. |
| 5724 |
08 Sep 11 |
nicklas |
1136 |
A list of the available actions can be found on the list page |
| 5724 |
08 Sep 11 |
nicklas |
1137 |
<menuchoice> |
| 5724 |
08 Sep 11 |
nicklas |
1138 |
<guimenu>Biomaterial LIMS</guimenu> |
| 5724 |
08 Sep 11 |
nicklas |
1139 |
<guimenuitem>Bioplate event types</guimenuitem> |
| 5724 |
08 Sep 11 |
nicklas |
1140 |
</menuchoice>. |
| 5724 |
08 Sep 11 |
nicklas |
1141 |
|
| 5724 |
08 Sep 11 |
nicklas |
1142 |
Although it is possible to create more event types here there is usually no |
| 5724 |
08 Sep 11 |
nicklas |
1143 |
meaning to do so, since each event needs a specailized GUI wizard to take |
| 5724 |
08 Sep 11 |
nicklas |
1144 |
care of it. The possibility to add more event types should be seen as an |
| 5724 |
08 Sep 11 |
nicklas |
1145 |
opportunity for extension development. |
| 5708 |
25 Aug 11 |
nicklas |
1146 |
</para> |
| 5724 |
08 Sep 11 |
nicklas |
1147 |
|
| 5724 |
08 Sep 11 |
nicklas |
1148 |
<sect3 id="biomaterials.placeonplate"> |
| 5724 |
08 Sep 11 |
nicklas |
1149 |
<title>The place-on-plate event</title> |
| 5724 |
08 Sep 11 |
nicklas |
1150 |
|
| 5724 |
08 Sep 11 |
nicklas |
1151 |
<figure id="biomaterials.figures.placeonplate"> |
| 5724 |
08 Sep 11 |
nicklas |
1152 |
<title>Place on plate wizard</title> |
| 5724 |
08 Sep 11 |
nicklas |
1153 |
<screenshot> |
| 5724 |
08 Sep 11 |
nicklas |
1154 |
<mediaobject> |
| 5724 |
08 Sep 11 |
nicklas |
1155 |
<imageobject> |
| 5724 |
08 Sep 11 |
nicklas |
1156 |
<imagedata |
| 5724 |
08 Sep 11 |
nicklas |
1157 |
fileref="figures/place_on_plate.png" format="PNG" /> |
| 5724 |
08 Sep 11 |
nicklas |
1158 |
</imageobject> |
| 5724 |
08 Sep 11 |
nicklas |
1159 |
</mediaobject> |
| 5724 |
08 Sep 11 |
nicklas |
1160 |
</screenshot> |
| 5724 |
08 Sep 11 |
nicklas |
1161 |
</figure> |
| 5724 |
08 Sep 11 |
nicklas |
1162 |
|
| 5724 |
08 Sep 11 |
nicklas |
1163 |
<helptext external_id="bioplateevent.place-on-plate" title="Place on plate"> |
| 5724 |
08 Sep 11 |
nicklas |
1164 |
<para> |
| 5724 |
08 Sep 11 |
nicklas |
1165 |
This event is available on the sample and extract list pages and can be used |
| 5724 |
08 Sep 11 |
nicklas |
1166 |
to place multiple biomaterial on a bioplate in one go. Click on |
| 5724 |
08 Sep 11 |
nicklas |
1167 |
the <guibutton>Place on plate</guibutton> button to start the wizard. |
| 5724 |
08 Sep 11 |
nicklas |
1168 |
The wizard will automatically use the selected biomaterials or, if none |
| 5724 |
08 Sep 11 |
nicklas |
1169 |
are selected, all listed biomaterials that aren't alredy located on a |
| 5724 |
08 Sep 11 |
nicklas |
1170 |
plate. |
| 5724 |
08 Sep 11 |
nicklas |
1171 |
|
| 5724 |
08 Sep 11 |
nicklas |
1172 |
<variablelist> |
| 5724 |
08 Sep 11 |
nicklas |
1173 |
<varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1174 |
<term><guilabel>Event name</guilabel></term> |
| 5724 |
08 Sep 11 |
nicklas |
1175 |
<listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1176 |
<para> |
| 5724 |
08 Sep 11 |
nicklas |
1177 |
Give a name to the event, or keep the suggested name. |
| 5724 |
08 Sep 11 |
nicklas |
1178 |
</para> |
| 5724 |
08 Sep 11 |
nicklas |
1179 |
</listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1180 |
</varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1181 |
<varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1182 |
<term><guilabel>Event date</guilabel></term> |
| 5724 |
08 Sep 11 |
nicklas |
1183 |
<listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1184 |
<para> |
| 5724 |
08 Sep 11 |
nicklas |
1185 |
The date of the event. |
| 5724 |
08 Sep 11 |
nicklas |
1186 |
</para> |
| 5724 |
08 Sep 11 |
nicklas |
1187 |
</listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1188 |
</varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1189 |
<varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1190 |
<term><guilabel>Protocol</guilabel></term> |
| 5724 |
08 Sep 11 |
nicklas |
1191 |
<listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1192 |
<para> |
| 5724 |
08 Sep 11 |
nicklas |
1193 |
The protocol used in the event, if any. |
| 5724 |
08 Sep 11 |
nicklas |
1194 |
</para> |
| 5724 |
08 Sep 11 |
nicklas |
1195 |
</listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1196 |
</varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1197 |
<varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1198 |
<term><guilabel>Hardware</guilabel></term> |
| 5724 |
08 Sep 11 |
nicklas |
1199 |
<listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1200 |
<para> |
| 5724 |
08 Sep 11 |
nicklas |
1201 |
The hardware item used in the event, if any. |
| 5724 |
08 Sep 11 |
nicklas |
1202 |
</para> |
| 5724 |
08 Sep 11 |
nicklas |
1203 |
</listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1204 |
</varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1205 |
<varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1206 |
<term><guilabel>Description</guilabel></term> |
| 5724 |
08 Sep 11 |
nicklas |
1207 |
<listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1208 |
<para> |
| 5724 |
08 Sep 11 |
nicklas |
1209 |
Other comments about the event. |
| 5724 |
08 Sep 11 |
nicklas |
1210 |
</para> |
| 5724 |
08 Sep 11 |
nicklas |
1211 |
</listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1212 |
</varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1213 |
<varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1214 |
<term><guilabel>Select plate...</guilabel></term> |
| 5724 |
08 Sep 11 |
nicklas |
1215 |
<listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1216 |
<para> |
| 5724 |
08 Sep 11 |
nicklas |
1217 |
You need to select an existing plate on which the |
| 5724 |
08 Sep 11 |
nicklas |
1218 |
biomaterial should be placed. It is only possible to |
| 5724 |
08 Sep 11 |
nicklas |
1219 |
use one plate in each event. If you want to place biomaterial |
| 5724 |
08 Sep 11 |
nicklas |
1220 |
on more than one plate, the wizard must be repeated for |
| 5724 |
08 Sep 11 |
nicklas |
1221 |
each destination plate. |
| 5724 |
08 Sep 11 |
nicklas |
1222 |
</para> |
| 5724 |
08 Sep 11 |
nicklas |
1223 |
</listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1224 |
</varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1225 |
<varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1226 |
<term><guilabel>Clear</guilabel></term> |
| 5724 |
08 Sep 11 |
nicklas |
1227 |
<listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1228 |
<para> |
| 5724 |
08 Sep 11 |
nicklas |
1229 |
Clear all current placement. |
| 5724 |
08 Sep 11 |
nicklas |
1230 |
</para> |
| 5724 |
08 Sep 11 |
nicklas |
1231 |
</listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1232 |
</varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1233 |
<varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1234 |
<term><guilabel>Place by row/column</guilabel></term> |
| 5724 |
08 Sep 11 |
nicklas |
1235 |
<listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1236 |
<para> |
| 5724 |
08 Sep 11 |
nicklas |
1237 |
Automatically place the remaining biomaterial by filling empty wells, |
| 5724 |
08 Sep 11 |
nicklas |
1238 |
starting with rows or columns. |
| 5724 |
08 Sep 11 |
nicklas |
1239 |
</para> |
| 5724 |
08 Sep 11 |
nicklas |
1240 |
</listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1241 |
</varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1242 |
<varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1243 |
<term><guilabel>Items to place</guilabel></term> |
| 5724 |
08 Sep 11 |
nicklas |
1244 |
<listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1245 |
<para> |
| 5724 |
08 Sep 11 |
nicklas |
1246 |
This column contains the biomaterial that should be placed on the plate. |
| 5724 |
08 Sep 11 |
nicklas |
1247 |
When a destination plate has been selected, it is displayed as a grid to |
| 5797 |
11 Oct 11 |
nicklas |
1248 |
the right. To place a biomaterial either use the <guibutton>Place by row</guibutton> |
| 5724 |
08 Sep 11 |
nicklas |
1249 |
or <guibutton>Place by column</guibutton> buttons, or select an item in this |
| 5724 |
08 Sep 11 |
nicklas |
1250 |
list. When an item has been selected, click on the destination well on the |
| 5724 |
08 Sep 11 |
nicklas |
1251 |
plate. The coordinate of the well is displayed in the gray area before the |
| 5724 |
08 Sep 11 |
nicklas |
1252 |
biomaterial name and a line is drawn between it and the destination well. |
| 5724 |
08 Sep 11 |
nicklas |
1253 |
The destination well is also marked with an icon. |
| 5724 |
08 Sep 11 |
nicklas |
1254 |
If the <guilabel>Auto-select next unmapped item</guilabel> is selected |
| 5724 |
08 Sep 11 |
nicklas |
1255 |
the selection is automatically moved to the next biomaterial which can then |
| 5724 |
08 Sep 11 |
nicklas |
1256 |
be placed by selecting another destination well. If a mistake is made it is |
| 5724 |
08 Sep 11 |
nicklas |
1257 |
easy to correct. Simply re-select the item and then click on the correct well. |
| 5724 |
08 Sep 11 |
nicklas |
1258 |
</para> |
| 5724 |
08 Sep 11 |
nicklas |
1259 |
</listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1260 |
</varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1261 |
|
| 5724 |
08 Sep 11 |
nicklas |
1262 |
</variablelist> |
| 5724 |
08 Sep 11 |
nicklas |
1263 |
|
| 5724 |
08 Sep 11 |
nicklas |
1264 |
When the biomaterial has been placed on the plate (it is not neccessary to place all of them) |
| 5724 |
08 Sep 11 |
nicklas |
1265 |
click on <guibutton>Save</guibutton> to store everything. BASE will create a plate event |
| 5724 |
08 Sep 11 |
nicklas |
1266 |
for the selected destination plate and "other"-type events for each biomaterial that was |
| 5724 |
08 Sep 11 |
nicklas |
1267 |
placed on it. |
| 5724 |
08 Sep 11 |
nicklas |
1268 |
</para> |
| 5724 |
08 Sep 11 |
nicklas |
1269 |
</helptext> |
| 5724 |
08 Sep 11 |
nicklas |
1270 |
</sect3> |
| 5724 |
08 Sep 11 |
nicklas |
1271 |
|
| 5724 |
08 Sep 11 |
nicklas |
1272 |
<sect3 id="biomaterials.move"> |
| 5724 |
08 Sep 11 |
nicklas |
1273 |
<title>The move biomaterials event</title> |
| 5724 |
08 Sep 11 |
nicklas |
1274 |
|
| 5724 |
08 Sep 11 |
nicklas |
1275 |
<figure id="biomaterials.figures.move"> |
| 5724 |
08 Sep 11 |
nicklas |
1276 |
<title>Move biomaterials wizard</title> |
| 5724 |
08 Sep 11 |
nicklas |
1277 |
<screenshot> |
| 5724 |
08 Sep 11 |
nicklas |
1278 |
<mediaobject> |
| 5724 |
08 Sep 11 |
nicklas |
1279 |
<imageobject> |
| 5724 |
08 Sep 11 |
nicklas |
1280 |
<imagedata |
| 5724 |
08 Sep 11 |
nicklas |
1281 |
fileref="figures/move_biomaterials.png" format="PNG" /> |
| 5724 |
08 Sep 11 |
nicklas |
1282 |
</imageobject> |
| 5724 |
08 Sep 11 |
nicklas |
1283 |
</mediaobject> |
| 5724 |
08 Sep 11 |
nicklas |
1284 |
</screenshot> |
| 5724 |
08 Sep 11 |
nicklas |
1285 |
</figure> |
| 5724 |
08 Sep 11 |
nicklas |
1286 |
|
| 5724 |
08 Sep 11 |
nicklas |
1287 |
<helptext external_id="bioplateevent.move" title="Move biomaterials"> |
| 5724 |
08 Sep 11 |
nicklas |
1288 |
<para> |
| 5724 |
08 Sep 11 |
nicklas |
1289 |
This event is available on the single-item view page of a bioplate |
| 5724 |
08 Sep 11 |
nicklas |
1290 |
and can be used to move biomaterial from one plate to another. Click on |
| 5724 |
08 Sep 11 |
nicklas |
1291 |
the <guibutton>Move biomaterial</guibutton> button to start the wizard. |
| 5724 |
08 Sep 11 |
nicklas |
1292 |
<variablelist> |
| 5724 |
08 Sep 11 |
nicklas |
1293 |
<varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1294 |
<term><guilabel>Event name</guilabel></term> |
| 5724 |
08 Sep 11 |
nicklas |
1295 |
<listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1296 |
<para> |
| 5724 |
08 Sep 11 |
nicklas |
1297 |
Give a name to the event, or keep the suggested name. |
| 5724 |
08 Sep 11 |
nicklas |
1298 |
</para> |
| 5724 |
08 Sep 11 |
nicklas |
1299 |
</listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1300 |
</varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1301 |
<varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1302 |
<term><guilabel>Event date</guilabel></term> |
| 5724 |
08 Sep 11 |
nicklas |
1303 |
<listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1304 |
<para> |
| 5724 |
08 Sep 11 |
nicklas |
1305 |
The date of the event. |
| 5724 |
08 Sep 11 |
nicklas |
1306 |
</para> |
| 5724 |
08 Sep 11 |
nicklas |
1307 |
</listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1308 |
</varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1309 |
<varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1310 |
<term><guilabel>Protocol</guilabel></term> |
| 5724 |
08 Sep 11 |
nicklas |
1311 |
<listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1312 |
<para> |
| 5724 |
08 Sep 11 |
nicklas |
1313 |
The protocol used in the event, if any. |
| 5724 |
08 Sep 11 |
nicklas |
1314 |
</para> |
| 5724 |
08 Sep 11 |
nicklas |
1315 |
</listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1316 |
</varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1317 |
<varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1318 |
<term><guilabel>Hardware</guilabel></term> |
| 5724 |
08 Sep 11 |
nicklas |
1319 |
<listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1320 |
<para> |
| 5724 |
08 Sep 11 |
nicklas |
1321 |
The hardware item used in the event, if any. |
| 5724 |
08 Sep 11 |
nicklas |
1322 |
</para> |
| 5724 |
08 Sep 11 |
nicklas |
1323 |
</listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1324 |
</varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1325 |
<varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1326 |
<term><guilabel>Description</guilabel></term> |
| 5724 |
08 Sep 11 |
nicklas |
1327 |
<listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1328 |
<para> |
| 5724 |
08 Sep 11 |
nicklas |
1329 |
Other comments about the event. |
| 5724 |
08 Sep 11 |
nicklas |
1330 |
</para> |
| 5724 |
08 Sep 11 |
nicklas |
1331 |
</listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1332 |
</varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1333 |
<varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1334 |
<term><guilabel>Select plate...</guilabel></term> |
| 5724 |
08 Sep 11 |
nicklas |
1335 |
<listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1336 |
<para> |
| 5724 |
08 Sep 11 |
nicklas |
1337 |
You need to select an existing plate to which the |
| 5724 |
08 Sep 11 |
nicklas |
1338 |
biomaterial should be moved. It is only possible to |
| 5724 |
08 Sep 11 |
nicklas |
1339 |
use one plate in each event. If you want to move biomaterial |
| 5724 |
08 Sep 11 |
nicklas |
1340 |
to more than one plate, the wizard must be repeated for |
| 5724 |
08 Sep 11 |
nicklas |
1341 |
each destination plate. |
| 5724 |
08 Sep 11 |
nicklas |
1342 |
</para> |
| 5724 |
08 Sep 11 |
nicklas |
1343 |
</listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1344 |
</varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1345 |
<varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1346 |
<term><guilabel>Clear</guilabel></term> |
| 5724 |
08 Sep 11 |
nicklas |
1347 |
<listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1348 |
<para> |
| 5724 |
08 Sep 11 |
nicklas |
1349 |
Clear all current mapping between the source and destination plates. |
| 5724 |
08 Sep 11 |
nicklas |
1350 |
</para> |
| 5724 |
08 Sep 11 |
nicklas |
1351 |
</listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1352 |
</varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1353 |
<varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1354 |
<term><guilabel>Place by row/column</guilabel></term> |
| 5724 |
08 Sep 11 |
nicklas |
1355 |
<listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1356 |
<para> |
| 5724 |
08 Sep 11 |
nicklas |
1357 |
Automatically move the remaining biomaterial by filling empty wells, |
| 5724 |
08 Sep 11 |
nicklas |
1358 |
starting with rows or columns. |
| 5724 |
08 Sep 11 |
nicklas |
1359 |
</para> |
| 5724 |
08 Sep 11 |
nicklas |
1360 |
</listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1361 |
</varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1362 |
<varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1363 |
<term><guilabel>Predefined mapping</guilabel></term> |
| 5724 |
08 Sep 11 |
nicklas |
1364 |
<listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1365 |
<para> |
| 5724 |
08 Sep 11 |
nicklas |
1366 |
Use this button to select a predefined mapping between source |
| 5724 |
08 Sep 11 |
nicklas |
1367 |
and destination wells. The biomaterial will be moved according |
| 5724 |
08 Sep 11 |
nicklas |
1368 |
to the mapping. |
| 5724 |
08 Sep 11 |
nicklas |
1369 |
</para> |
| 5724 |
08 Sep 11 |
nicklas |
1370 |
</listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1371 |
</varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1372 |
<varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1373 |
<term><guilabel>Source plate</guilabel></term> |
| 5724 |
08 Sep 11 |
nicklas |
1374 |
<listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1375 |
<para> |
| 5724 |
08 Sep 11 |
nicklas |
1376 |
This displays the source plate as a grid with icons that indicate |
| 5724 |
08 Sep 11 |
nicklas |
1377 |
filled and movable wells. |
| 5724 |
08 Sep 11 |
nicklas |
1378 |
|
| 5724 |
08 Sep 11 |
nicklas |
1379 |
When a destination plate has been selected, it is displayed as a similar grid to |
| 5724 |
08 Sep 11 |
nicklas |
1380 |
the right. To move a biomaterial either use the <guibutton>Place by row</guibutton>, |
| 5724 |
08 Sep 11 |
nicklas |
1381 |
<guibutton>Place by column</guibutton> or <guibutton>Predefined mapping</guibutton> |
| 5724 |
08 Sep 11 |
nicklas |
1382 |
buttons, or select a well on the source plate. When a source well has been selected, |
| 5724 |
08 Sep 11 |
nicklas |
1383 |
click on a well on the destination plate. A line is drawn between the source and |
| 5724 |
08 Sep 11 |
nicklas |
1384 |
destination wells and the icons are updated to show what is going on. The |
| 5724 |
08 Sep 11 |
nicklas |
1385 |
wells on the destination plate will also show the coordinate of the mapped |
| 5724 |
08 Sep 11 |
nicklas |
1386 |
source well unless the <guilabel>Show source coordinates</guilabel> |
| 5724 |
08 Sep 11 |
nicklas |
1387 |
checkbox is deselected. If a mistake is made it is |
| 5724 |
08 Sep 11 |
nicklas |
1388 |
easy to correct. Simply re-select the source well and then click on the correct |
| 5724 |
08 Sep 11 |
nicklas |
1389 |
destination well. |
| 5724 |
08 Sep 11 |
nicklas |
1390 |
|
| 5724 |
08 Sep 11 |
nicklas |
1391 |
</para> |
| 5724 |
08 Sep 11 |
nicklas |
1392 |
</listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1393 |
</varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1394 |
</variablelist> |
| 5724 |
08 Sep 11 |
nicklas |
1395 |
|
| 5724 |
08 Sep 11 |
nicklas |
1396 |
When the biomaterial has been mapped between the source and destination plates |
| 5724 |
08 Sep 11 |
nicklas |
1397 |
(it is not neccessary to map all of them) click on <guibutton>Save</guibutton> to store everything. |
| 5724 |
08 Sep 11 |
nicklas |
1398 |
BASE will create a plate event for the selected plates and "other"-type events for each |
| 5724 |
08 Sep 11 |
nicklas |
1399 |
biomaterial that was moved. |
| 5724 |
08 Sep 11 |
nicklas |
1400 |
|
| 5724 |
08 Sep 11 |
nicklas |
1401 |
</para> |
| 5724 |
08 Sep 11 |
nicklas |
1402 |
</helptext> |
| 5724 |
08 Sep 11 |
nicklas |
1403 |
</sect3> |
| 5724 |
08 Sep 11 |
nicklas |
1404 |
|
| 5724 |
08 Sep 11 |
nicklas |
1405 |
<sect3 id="biomaterials.create_child"> |
| 5724 |
08 Sep 11 |
nicklas |
1406 |
<title>The create child plate event</title> |
| 5724 |
08 Sep 11 |
nicklas |
1407 |
|
| 5724 |
08 Sep 11 |
nicklas |
1408 |
<figure id="biomaterials.figures.create_child_1"> |
| 5724 |
08 Sep 11 |
nicklas |
1409 |
<title>Create child plate wizard - step 1</title> |
| 5724 |
08 Sep 11 |
nicklas |
1410 |
<screenshot> |
| 5724 |
08 Sep 11 |
nicklas |
1411 |
<mediaobject> |
| 5724 |
08 Sep 11 |
nicklas |
1412 |
<imageobject> |
| 5724 |
08 Sep 11 |
nicklas |
1413 |
<imagedata |
| 5724 |
08 Sep 11 |
nicklas |
1414 |
fileref="figures/create_child_plate_1.png" format="PNG" /> |
| 5724 |
08 Sep 11 |
nicklas |
1415 |
</imageobject> |
| 5724 |
08 Sep 11 |
nicklas |
1416 |
</mediaobject> |
| 5724 |
08 Sep 11 |
nicklas |
1417 |
</screenshot> |
| 5724 |
08 Sep 11 |
nicklas |
1418 |
</figure> |
| 5724 |
08 Sep 11 |
nicklas |
1419 |
|
| 5724 |
08 Sep 11 |
nicklas |
1420 |
<helptext external_id="bioplateevent.create-child-1" title="Create child plate - step 1"> |
| 5724 |
08 Sep 11 |
nicklas |
1421 |
<para> |
| 5724 |
08 Sep 11 |
nicklas |
1422 |
This event is available on the single-item view page of a bioplate |
| 5724 |
08 Sep 11 |
nicklas |
1423 |
when the bioplate is limited to a single type of biomaterial (eg. |
| 5724 |
08 Sep 11 |
nicklas |
1424 |
only samples or only extracts). The event is used to create either |
| 5724 |
08 Sep 11 |
nicklas |
1425 |
a child bioplate with biomaterial that is derived from the biomaterial |
| 5724 |
08 Sep 11 |
nicklas |
1426 |
on the parent plate or to create one or more physical bioassays. Click on |
| 5724 |
08 Sep 11 |
nicklas |
1427 |
the <guibutton>Create child bioplate</guibutton> button to start the wizard. |
| 5724 |
08 Sep 11 |
nicklas |
1428 |
</para> |
| 5724 |
08 Sep 11 |
nicklas |
1429 |
|
| 5724 |
08 Sep 11 |
nicklas |
1430 |
<para> |
| 5724 |
08 Sep 11 |
nicklas |
1431 |
The wizard has two steps. In the first step you set properties that |
| 5724 |
08 Sep 11 |
nicklas |
1432 |
are related to the event and to the creation of child plates and |
| 5724 |
08 Sep 11 |
nicklas |
1433 |
biomaterial. The first step is divied into three main sections. |
| 5724 |
08 Sep 11 |
nicklas |
1434 |
</para> |
| 5724 |
08 Sep 11 |
nicklas |
1435 |
|
| 5724 |
08 Sep 11 |
nicklas |
1436 |
|
| 5724 |
08 Sep 11 |
nicklas |
1437 |
<bridgehead>Event</bridgehead> |
| 5724 |
08 Sep 11 |
nicklas |
1438 |
|
| 5724 |
08 Sep 11 |
nicklas |
1439 |
<variablelist> |
| 5724 |
08 Sep 11 |
nicklas |
1440 |
<varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1441 |
<term><guilabel>Event name</guilabel></term> |
| 5724 |
08 Sep 11 |
nicklas |
1442 |
<listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1443 |
<para> |
| 5724 |
08 Sep 11 |
nicklas |
1444 |
Give a name to the event, or keep the suggested name. |
| 5724 |
08 Sep 11 |
nicklas |
1445 |
</para> |
| 5724 |
08 Sep 11 |
nicklas |
1446 |
</listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1447 |
</varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1448 |
<varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1449 |
<term><guilabel>Event date</guilabel></term> |
| 5724 |
08 Sep 11 |
nicklas |
1450 |
<listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1451 |
<para> |
| 5724 |
08 Sep 11 |
nicklas |
1452 |
The date of the event. |
| 5724 |
08 Sep 11 |
nicklas |
1453 |
</para> |
| 5724 |
08 Sep 11 |
nicklas |
1454 |
</listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1455 |
</varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1456 |
<varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1457 |
<term><guilabel>Protocol</guilabel></term> |
| 5724 |
08 Sep 11 |
nicklas |
1458 |
<listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1459 |
<para> |
| 5724 |
08 Sep 11 |
nicklas |
1460 |
The protocol used in the event, if any. |
| 5724 |
08 Sep 11 |
nicklas |
1461 |
</para> |
| 5724 |
08 Sep 11 |
nicklas |
1462 |
</listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1463 |
</varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1464 |
<varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1465 |
<term><guilabel>Hardware</guilabel></term> |
| 5724 |
08 Sep 11 |
nicklas |
1466 |
<listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1467 |
<para> |
| 5724 |
08 Sep 11 |
nicklas |
1468 |
The hardware item used in the event, if any. |
| 5724 |
08 Sep 11 |
nicklas |
1469 |
</para> |
| 5724 |
08 Sep 11 |
nicklas |
1470 |
</listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1471 |
</varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1472 |
<varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1473 |
<term><guilabel>Description</guilabel></term> |
| 5724 |
08 Sep 11 |
nicklas |
1474 |
<listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1475 |
<para> |
| 5724 |
08 Sep 11 |
nicklas |
1476 |
Other comments about the event. |
| 5724 |
08 Sep 11 |
nicklas |
1477 |
</para> |
| 5724 |
08 Sep 11 |
nicklas |
1478 |
</listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1479 |
</varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1480 |
</variablelist> |
| 5724 |
08 Sep 11 |
nicklas |
1481 |
|
| 5724 |
08 Sep 11 |
nicklas |
1482 |
<bridgehead>Child biomaterial</bridgehead> |
| 5724 |
08 Sep 11 |
nicklas |
1483 |
<variablelist> |
| 5724 |
08 Sep 11 |
nicklas |
1484 |
<varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1485 |
<term><guilabel>Type</guilabel></term> |
| 5724 |
08 Sep 11 |
nicklas |
1486 |
<listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1487 |
<para> |
| 5724 |
08 Sep 11 |
nicklas |
1488 |
The type of child items to create. If the source plate |
| 5724 |
08 Sep 11 |
nicklas |
1489 |
contains samples, you can select between sample and |
| 5724 |
08 Sep 11 |
nicklas |
1490 |
extract and if the source plate contains extract you |
| 5724 |
08 Sep 11 |
nicklas |
1491 |
can select between extract and physical bioassay. |
| 5724 |
08 Sep 11 |
nicklas |
1492 |
</para> |
| 5724 |
08 Sep 11 |
nicklas |
1493 |
</listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1494 |
</varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1495 |
<varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1496 |
<term><guilabel>Subtype</guilabel></term> |
| 5724 |
08 Sep 11 |
nicklas |
1497 |
<listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1498 |
<para> |
| 5724 |
08 Sep 11 |
nicklas |
1499 |
The subtype to assign to the newly created biomaterial |
| 5724 |
08 Sep 11 |
nicklas |
1500 |
(or physical bioassay). The list of options is automatically |
| 5724 |
08 Sep 11 |
nicklas |
1501 |
updated based on the selection in the <guilabel>Type</guilabel> |
| 5724 |
08 Sep 11 |
nicklas |
1502 |
list. |
| 5724 |
08 Sep 11 |
nicklas |
1503 |
</para> |
| 5724 |
08 Sep 11 |
nicklas |
1504 |
</listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1505 |
</varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1506 |
<varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1507 |
<term><guilabel>Tag</guilabel></term> |
| 5724 |
08 Sep 11 |
nicklas |
1508 |
<listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1509 |
<para> |
| 5724 |
08 Sep 11 |
nicklas |
1510 |
Visible when creating child extracts only. Select the tag to |
| 5724 |
08 Sep 11 |
nicklas |
1511 |
assign to the new extract. If no tag is selected and the |
| 5724 |
08 Sep 11 |
nicklas |
1512 |
source biomaterial is also extracts, the children will get the |
| 5724 |
08 Sep 11 |
nicklas |
1513 |
same tag as their parents. |
| 5724 |
08 Sep 11 |
nicklas |
1514 |
</para> |
| 5724 |
08 Sep 11 |
nicklas |
1515 |
</listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1516 |
</varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1517 |
<varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1518 |
<term><guilabel>Original quantity</guilabel></term> |
| 5724 |
08 Sep 11 |
nicklas |
1519 |
<listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1520 |
<para> |
| 5724 |
08 Sep 11 |
nicklas |
1521 |
The original quantity of the new biomaterial. Not visible when |
| 5724 |
08 Sep 11 |
nicklas |
1522 |
creating a physical bioassay. |
| 5724 |
08 Sep 11 |
nicklas |
1523 |
</para> |
| 5724 |
08 Sep 11 |
nicklas |
1524 |
</listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1525 |
</varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1526 |
<varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1527 |
<term><guilabel>Used quantity</guilabel></term> |
| 5724 |
08 Sep 11 |
nicklas |
1528 |
<listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1529 |
<para> |
| 5724 |
08 Sep 11 |
nicklas |
1530 |
The quantity that was used from the parent biomaterial |
| 5724 |
08 Sep 11 |
nicklas |
1531 |
in the process of creating child biomaterial. |
| 5724 |
08 Sep 11 |
nicklas |
1532 |
</para> |
| 5724 |
08 Sep 11 |
nicklas |
1533 |
</listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1534 |
</varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1535 |
<varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1536 |
<term><guilabel>Description</guilabel></term> |
| 5724 |
08 Sep 11 |
nicklas |
1537 |
<listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1538 |
<para> |
| 5724 |
08 Sep 11 |
nicklas |
1539 |
Other comments about the new biomaterial. |
| 5724 |
08 Sep 11 |
nicklas |
1540 |
</para> |
| 5724 |
08 Sep 11 |
nicklas |
1541 |
</listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1542 |
</varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1543 |
</variablelist> |
| 5724 |
08 Sep 11 |
nicklas |
1544 |
|
| 5724 |
08 Sep 11 |
nicklas |
1545 |
|
| 5724 |
08 Sep 11 |
nicklas |
1546 |
<bridgehead>Child plates</bridgehead> |
| 5724 |
08 Sep 11 |
nicklas |
1547 |
<variablelist> |
| 5724 |
08 Sep 11 |
nicklas |
1548 |
<varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1549 |
<term><guilabel>No. of plates</guilabel></term> |
| 5724 |
08 Sep 11 |
nicklas |
1550 |
<listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1551 |
<para> |
| 5724 |
08 Sep 11 |
nicklas |
1552 |
The number of child plates to create. The default value is 1. |
| 5724 |
08 Sep 11 |
nicklas |
1553 |
</para> |
| 5724 |
08 Sep 11 |
nicklas |
1554 |
</listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1555 |
</varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1556 |
<varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1557 |
<term><guilabel>Name prefix</guilabel></term> |
| 5724 |
08 Sep 11 |
nicklas |
1558 |
<listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1559 |
<para> |
| 5724 |
08 Sep 11 |
nicklas |
1560 |
The child plates will be named using the prefix plus a running number |
| 5724 |
08 Sep 11 |
nicklas |
1561 |
starting with 0. Eg. New plate.0. |
| 5724 |
08 Sep 11 |
nicklas |
1562 |
</para> |
| 5724 |
08 Sep 11 |
nicklas |
1563 |
</listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1564 |
</varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1565 |
<varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1566 |
<term><guilabel>Geometry</guilabel></term> |
| 5724 |
08 Sep 11 |
nicklas |
1567 |
<listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1568 |
<para> |
| 5724 |
08 Sep 11 |
nicklas |
1569 |
The geometry of the child plates. The default is the same |
| 5724 |
08 Sep 11 |
nicklas |
1570 |
geometry as the parent plate. This option is replaced with |
| 5724 |
08 Sep 11 |
nicklas |
1571 |
<guilabel>Size of bioassay</guilabel> when creating a |
| 5724 |
08 Sep 11 |
nicklas |
1572 |
physical bioassay. |
| 5724 |
08 Sep 11 |
nicklas |
1573 |
</para> |
| 5724 |
08 Sep 11 |
nicklas |
1574 |
</listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1575 |
</varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1576 |
<varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1577 |
<term><guilabel>Plate type</guilabel></term> |
| 5724 |
08 Sep 11 |
nicklas |
1578 |
<listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1579 |
<para> |
| 5724 |
08 Sep 11 |
nicklas |
1580 |
The plate type of the child plates. Not used when creating a |
| 5724 |
08 Sep 11 |
nicklas |
1581 |
physical bioassay. |
| 5724 |
08 Sep 11 |
nicklas |
1582 |
</para> |
| 5724 |
08 Sep 11 |
nicklas |
1583 |
</listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1584 |
</varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1585 |
<varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1586 |
<term><guilabel>Freezer</guilabel></term> |
| 5724 |
08 Sep 11 |
nicklas |
1587 |
<listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1588 |
<para> |
| 5724 |
08 Sep 11 |
nicklas |
1589 |
The freezer in which the new child plates are located. Not used |
| 5724 |
08 Sep 11 |
nicklas |
1590 |
when creating a physical bioassay. |
| 5724 |
08 Sep 11 |
nicklas |
1591 |
</para> |
| 5724 |
08 Sep 11 |
nicklas |
1592 |
</listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1593 |
</varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1594 |
<varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1595 |
<term><guilabel>Description</guilabel></term> |
| 5724 |
08 Sep 11 |
nicklas |
1596 |
<listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1597 |
<para> |
| 5724 |
08 Sep 11 |
nicklas |
1598 |
Other comments about the new child plates. |
| 5724 |
08 Sep 11 |
nicklas |
1599 |
</para> |
| 5724 |
08 Sep 11 |
nicklas |
1600 |
</listitem> |
| 5724 |
08 Sep 11 |
nicklas |
1601 |
</varlistentry> |
| 5724 |
08 Sep 11 |
nicklas |
1602 |
</variablelist> |
| 5724 |
08 Sep 11 |
nicklas |
1603 |
|
| 5724 |
08 Sep 11 |
nicklas |
1604 |
<seeother> |
| 5724 |
08 Sep 11 |
nicklas |
1605 |
<other external_id="bioplateevent.create-child-2">Create child plate - step 2</other> |
| 5724 |
08 Sep 11 |
nicklas |
1606 |
</seeother> |
| 5724 |
08 Sep 11 |
nicklas |
1607 |
</helptext> |
| 5724 |
08 Sep 11 |
nicklas |
1608 |
|
| 5724 |
08 Sep 11 |
nicklas |
1609 |
<figure id="biomaterials.figures.create_child_2"> |
| 5724 |
08 Sep 11 |
nicklas |
1610 |
<title>Create child plate wizard - step 2</title> |
| 5724 |
08 Sep 11 |
nicklas |
1611 |
<screenshot> |
| 5724 |
08 Sep 11 |
nicklas |
1612 |
<mediaobject> |
| 5724 |
08 Sep 11 |
nicklas |
1613 |
<imageobject> |
| 5724 |
08 Sep 11 |
nicklas |
1614 |
<imagedata |
| 5724 |
08 Sep 11 |
nicklas |
1615 |
fileref="figures/create_child_plate_2.png" format="PNG" /> |
| 5724 |
08 Sep 11 |
nicklas |
1616 |
</imageobject> |
| 5724 |
08 Sep 11 |
nicklas |
1617 |
</mediaobject> |
| 5724 |
08 Sep 11 |
nicklas |
1618 |
</screenshot> |
| 5724 |
08 Sep 11 |
nicklas |
1619 |
</figure> |
| 5724 |
08 Sep 11 |
nicklas |
1620 |
|
| 5724 |
08 Sep 11 |
nicklas |
1621 |
<helptext external_id="bioplateevent.create-child-2" title="Create child plate - step 2"> |
| 5724 |
08 Sep 11 |
nicklas |
1622 |
<para> |
| 5724 |
08 Sep 11 |
nicklas |
1623 |
The second step display the source plate and new child plates as a grid. |
| 5724 |
08 Sep 11 |
nicklas |
1624 |
To create child biomaterial either use the <guibutton>Place by row</guibutton>, |
| 5724 |
08 Sep 11 |
nicklas |
1625 |
<guibutton>Place by column</guibutton> or <guibutton>Predefined mapping</guibutton> |
| 5724 |
08 Sep 11 |
nicklas |
1626 |
buttons, or select a well on the source plate. When a source well has been selected, |
| 5724 |
08 Sep 11 |
nicklas |
1627 |
click on a well on the destination plate. A line is drawn between the source and |
| 5724 |
08 Sep 11 |
nicklas |
1628 |
destination wells and the icons are updated to show what is going on. The |
| 5724 |
08 Sep 11 |
nicklas |
1629 |
wells on the destination plate will also show the coordinate of the mapped |
| 5724 |
08 Sep 11 |
nicklas |
1630 |
source well unless the <guilabel>Show source coordinates</guilabel> |
| 5724 |
08 Sep 11 |
nicklas |
1631 |
checkbox is deselected. If a mistake is made it is |
| 5724 |
08 Sep 11 |
nicklas |
1632 |
easy to correct. Simply re-select the source well and then click on the correct |
| 5724 |
08 Sep 11 |
nicklas |
1633 |
destination well. |
| 5724 |
08 Sep 11 |
nicklas |
1634 |
</para> |
| 5724 |
08 Sep 11 |
nicklas |
1635 |
|
| 5724 |
08 Sep 11 |
nicklas |
1636 |
<para> |
| 5724 |
08 Sep 11 |
nicklas |
1637 |
When a child biomaterial is selected you have the option to override the |
| 5724 |
08 Sep 11 |
nicklas |
1638 |
automatially generated name. It is also possible to change the name |
| 5724 |
08 Sep 11 |
nicklas |
1639 |
and barcode of the child plate. |
| 5724 |
08 Sep 11 |
nicklas |
1640 |
</para> |
| 5724 |
08 Sep 11 |
nicklas |
1641 |
|
| 5724 |
08 Sep 11 |
nicklas |
1642 |
<note> |
| 5724 |
08 Sep 11 |
nicklas |
1643 |
The principle is the same when creating physical bioassays, except that no |
| 5724 |
08 Sep 11 |
nicklas |
1644 |
new child biomaterial is created. |
| 5724 |
08 Sep 11 |
nicklas |
1645 |
</note> |
| 5724 |
08 Sep 11 |
nicklas |
1646 |
|
| 5724 |
08 Sep 11 |
nicklas |
1647 |
<para> |
| 5724 |
08 Sep 11 |
nicklas |
1648 |
When the biomaterial has been mapped between the source and destination plates |
| 5724 |
08 Sep 11 |
nicklas |
1649 |
(it is not neccessary to map all of them) click on <guibutton>Save</guibutton> |
| 5724 |
08 Sep 11 |
nicklas |
1650 |
to store everything. BASE will create a plate event for the selected plates |
| 5724 |
08 Sep 11 |
nicklas |
1651 |
and "create" or "bioassay"-type events for each biomaterial that was used. |
| 5724 |
08 Sep 11 |
nicklas |
1652 |
</para> |
| 5724 |
08 Sep 11 |
nicklas |
1653 |
|
| 5724 |
08 Sep 11 |
nicklas |
1654 |
<seeother> |
| 5724 |
08 Sep 11 |
nicklas |
1655 |
<other external_id="bioplateevent.create-child-1">Create child plate - step 1</other> |
| 5724 |
08 Sep 11 |
nicklas |
1656 |
</seeother> |
| 5724 |
08 Sep 11 |
nicklas |
1657 |
|
| 5724 |
08 Sep 11 |
nicklas |
1658 |
</helptext> |
| 5724 |
08 Sep 11 |
nicklas |
1659 |
</sect3> |
| 5708 |
25 Aug 11 |
nicklas |
1660 |
</sect2> |
| 5708 |
25 Aug 11 |
nicklas |
1661 |
|
| 4732 |
21 Jan 09 |
martin |
1662 |
</sect1> |
| 3157 |
05 Mar 07 |
martin |
1663 |
|
| 5708 |
25 Aug 11 |
nicklas |
1664 |
<sect1 id="biomaterials.bioassays"> |
| 5782 |
04 Oct 11 |
nicklas |
1665 |
<?dbhtml filename="bioassays.html" ?> |
| 5708 |
25 Aug 11 |
nicklas |
1666 |
<title>Physical bioassays</title> |
| 3412 |
30 May 07 |
martin |
1667 |
<para> |
| 5708 |
25 Aug 11 |
nicklas |
1668 |
A physical bioassay represents the application of one or more extracts |
| 5708 |
25 Aug 11 |
nicklas |
1669 |
to an experimental setup designed to measure quantities that we are |
| 5708 |
25 Aug 11 |
nicklas |
1670 |
interested in. For example, a <emphasis>Hybridization</emphasis> event corresponds |
| 5708 |
25 Aug 11 |
nicklas |
1671 |
to the application of one or more <emphasis>Labeled extracts</emphasis> |
| 3412 |
30 May 07 |
martin |
1672 |
materials to a microarray slide under conditions detailed in hybridization protocols. |
| 3412 |
30 May 07 |
martin |
1673 |
Use |
| 3412 |
30 May 07 |
martin |
1674 |
<menuchoice> |
| 3412 |
30 May 07 |
martin |
1675 |
<guimenu>View</guimenu> |
| 5708 |
25 Aug 11 |
nicklas |
1676 |
<guimenuitem>Physical bioassays</guimenuitem> |
| 3412 |
30 May 07 |
martin |
1677 |
</menuchoice> |
| 5708 |
25 Aug 11 |
nicklas |
1678 |
to get to the bioassays. |
| 3412 |
30 May 07 |
martin |
1679 |
</para> |
| 5708 |
25 Aug 11 |
nicklas |
1680 |
|
| 5708 |
25 Aug 11 |
nicklas |
1681 |
<sect2 id="biomaterials.bioassays.create"> |
| 5708 |
25 Aug 11 |
nicklas |
1682 |
<title>Create physical bioassays</title> |
| 3399 |
28 May 07 |
martin |
1683 |
<para> |
| 5708 |
25 Aug 11 |
nicklas |
1684 |
In BASE, there are two possible routes to create a physical bioassay except the |
| 5708 |
25 Aug 11 |
nicklas |
1685 |
common way with the &gbNew; button at the list page. |
| 3399 |
28 May 07 |
martin |
1686 |
</para> |
| 3412 |
30 May 07 |
martin |
1687 |
<variablelist> |
| 3412 |
30 May 07 |
martin |
1688 |
<varlistentry> |
| 5708 |
25 Aug 11 |
nicklas |
1689 |
<term>from the extract list view page</term> |
| 3412 |
30 May 07 |
martin |
1690 |
<listitem> |
| 3412 |
30 May 07 |
martin |
1691 |
<para> |
| 5708 |
25 Aug 11 |
nicklas |
1692 |
Select at least one extract, to create a bioassay from, by |
| 3412 |
30 May 07 |
martin |
1693 |
ticking the selection boxes before the name field. |
| 5708 |
25 Aug 11 |
nicklas |
1694 |
Click on the <guibutton>New physical bioassay…</guibutton> |
| 5708 |
25 Aug 11 |
nicklas |
1695 |
in the toolbar. |
| 3412 |
30 May 07 |
martin |
1696 |
</para> |
| 3412 |
30 May 07 |
martin |
1697 |
</listitem> |
| 3412 |
30 May 07 |
martin |
1698 |
</varlistentry> |
| 3412 |
30 May 07 |
martin |
1699 |
<varlistentry> |
| 5708 |
25 Aug 11 |
nicklas |
1700 |
<term>from the extract single-item page</term> |
| 3412 |
30 May 07 |
martin |
1701 |
<listitem> |
| 3412 |
30 May 07 |
martin |
1702 |
<para> |
| 5708 |
25 Aug 11 |
nicklas |
1703 |
When viewing an extract in single-item view, click on the |
| 5708 |
25 Aug 11 |
nicklas |
1704 |
<guibutton>New physical bioassay…</guibutton> |
| 5708 |
25 Aug 11 |
nicklas |
1705 |
button in the toolbar. |
| 3412 |
30 May 07 |
martin |
1706 |
</para> |
| 3412 |
30 May 07 |
martin |
1707 |
</listitem> |
| 3412 |
30 May 07 |
martin |
1708 |
</varlistentry> |
| 3412 |
30 May 07 |
martin |
1709 |
</variablelist> |
| 3412 |
30 May 07 |
martin |
1710 |
</sect2> |
| 5708 |
25 Aug 11 |
nicklas |
1711 |
|
| 5708 |
25 Aug 11 |
nicklas |
1712 |
<sect2 id="biomaterials.bioassays.properties"> |
| 5708 |
25 Aug 11 |
nicklas |
1713 |
<title>Bioassay properties</title> |
| 3372 |
24 May 07 |
philippe |
1714 |
|
| 4131 |
08 Feb 08 |
nicklas |
1715 |
|
| 5708 |
25 Aug 11 |
nicklas |
1716 |
<figure id="biomaterials.figures.bioassays-tab-1"> |
| 5708 |
25 Aug 11 |
nicklas |
1717 |
<title>Physical bioassay properties</title> |
| 4131 |
08 Feb 08 |
nicklas |
1718 |
<screenshot> |
| 4131 |
08 Feb 08 |
nicklas |
1719 |
<mediaobject> |
| 4131 |
08 Feb 08 |
nicklas |
1720 |
<imageobject> |
| 4131 |
08 Feb 08 |
nicklas |
1721 |
<imagedata |
| 5708 |
25 Aug 11 |
nicklas |
1722 |
fileref="figures/physicalbioassay-tab-1.png" format="PNG" /> |
| 4131 |
08 Feb 08 |
nicklas |
1723 |
</imageobject> |
| 4131 |
08 Feb 08 |
nicklas |
1724 |
</mediaobject> |
| 4131 |
08 Feb 08 |
nicklas |
1725 |
</screenshot> |
| 4131 |
08 Feb 08 |
nicklas |
1726 |
</figure> |
| 4131 |
08 Feb 08 |
nicklas |
1727 |
|
| 5708 |
25 Aug 11 |
nicklas |
1728 |
<helptext external_id="physicalbioassay.edit" title="Edit physical bioassay"> |
| 3412 |
30 May 07 |
martin |
1729 |
<variablelist> |
| 3412 |
30 May 07 |
martin |
1730 |
<varlistentry> |
| 3412 |
30 May 07 |
martin |
1731 |
<term> |
| 3412 |
30 May 07 |
martin |
1732 |
<guilabel>Name</guilabel> |
| 3412 |
30 May 07 |
martin |
1733 |
</term> |
| 3399 |
28 May 07 |
martin |
1734 |
<listitem> |
| 3399 |
28 May 07 |
martin |
1735 |
<para> |
| 5708 |
25 Aug 11 |
nicklas |
1736 |
The bioassay's name (required). It is recommended that the default |
| 5708 |
25 Aug 11 |
nicklas |
1737 |
name is replaced with something that is unique. |
| 3399 |
28 May 07 |
martin |
1738 |
</para> |
| 3412 |
30 May 07 |
martin |
1739 |
</listitem> |
| 3412 |
30 May 07 |
martin |
1740 |
</varlistentry> |
| 4131 |
08 Feb 08 |
nicklas |
1741 |
<varlistentry> |
| 4131 |
08 Feb 08 |
nicklas |
1742 |
<term> |
| 5708 |
25 Aug 11 |
nicklas |
1743 |
<guilabel>Type</guilabel> |
| 4131 |
08 Feb 08 |
nicklas |
1744 |
</term> |
| 4131 |
08 Feb 08 |
nicklas |
1745 |
<listitem> |
| 4131 |
08 Feb 08 |
nicklas |
1746 |
<para> |
| 5708 |
25 Aug 11 |
nicklas |
1747 |
The subtype of the bioassay. The list |
| 5708 |
25 Aug 11 |
nicklas |
1748 |
may evolve depending on additions by the server |
| 5708 |
25 Aug 11 |
nicklas |
1749 |
administrator. Selecting the proper subtype |
| 5708 |
25 Aug 11 |
nicklas |
1750 |
is recommended and enables BASE to automatically guess |
| 5708 |
25 Aug 11 |
nicklas |
1751 |
the most likely subtype when assignint source biomaterials |
| 5708 |
25 Aug 11 |
nicklas |
1752 |
and when creating derived bioassays. |
| 5708 |
25 Aug 11 |
nicklas |
1753 |
<nohelp> |
| 5708 |
25 Aug 11 |
nicklas |
1754 |
See <xref linkend="subtypes" /> for more information. |
| 5708 |
25 Aug 11 |
nicklas |
1755 |
</nohelp> |
| 4131 |
08 Feb 08 |
nicklas |
1756 |
</para> |
| 4131 |
08 Feb 08 |
nicklas |
1757 |
</listitem> |
| 4131 |
08 Feb 08 |
nicklas |
1758 |
</varlistentry> |
| 5708 |
25 Aug 11 |
nicklas |
1759 |
<varlistentry> |
| 5708 |
25 Aug 11 |
nicklas |
1760 |
<term> |
| 5708 |
25 Aug 11 |
nicklas |
1761 |
<guilabel>Size</guilabel> |
| 5708 |
25 Aug 11 |
nicklas |
1762 |
</term> |
| 5708 |
25 Aug 11 |
nicklas |
1763 |
<listitem> |
| 5708 |
25 Aug 11 |
nicklas |
1764 |
<para> |
| 5708 |
25 Aug 11 |
nicklas |
1765 |
The size of the bioassay is the number of independent |
| 5708 |
25 Aug 11 |
nicklas |
1766 |
positions on the bioassay. Depending on the |
| 5708 |
25 Aug 11 |
nicklas |
1767 |
characteristics of the bioassay, multiple biomaterials |
| 5708 |
25 Aug 11 |
nicklas |
1768 |
may share the same position, but are then usually |
| 5708 |
25 Aug 11 |
nicklas |
1769 |
required to have different tags. Two biomaterials |
| 5708 |
25 Aug 11 |
nicklas |
1770 |
in different positions can use the same tag. |
| 5708 |
25 Aug 11 |
nicklas |
1771 |
The default value is 1, but some platforms, for example |
| 5797 |
11 Oct 11 |
nicklas |
1772 |
Illumina BeadArrays, has slides with 6 or 8 positions |
| 5797 |
11 Oct 11 |
nicklas |
1773 |
and sequencing flow cells have 8 lanes. |
| 5708 |
25 Aug 11 |
nicklas |
1774 |
</para> |
| 5708 |
25 Aug 11 |
nicklas |
1775 |
</listitem> |
| 5708 |
25 Aug 11 |
nicklas |
1776 |
</varlistentry> |
| 3412 |
30 May 07 |
martin |
1777 |
|
| 3412 |
30 May 07 |
martin |
1778 |
<varlistentry> |
| 3412 |
30 May 07 |
martin |
1779 |
<term> |
| 3412 |
30 May 07 |
martin |
1780 |
<guilabel>Created</guilabel> |
| 3412 |
30 May 07 |
martin |
1781 |
</term> |
| 3412 |
30 May 07 |
martin |
1782 |
<listitem> |
| 3399 |
28 May 07 |
martin |
1783 |
<para> |
| 3412 |
30 May 07 |
martin |
1784 |
A date should be provided. The information can be important when |
| 3412 |
30 May 07 |
martin |
1785 |
running quality controls on data and account for potential |
| 5708 |
25 Aug 11 |
nicklas |
1786 |
confounding factor (e.g. to account for a day effect). |
| 3399 |
28 May 07 |
martin |
1787 |
</para> |
| 3399 |
28 May 07 |
martin |
1788 |
</listitem> |
| 3412 |
30 May 07 |
martin |
1789 |
</varlistentry> |
| 3412 |
30 May 07 |
martin |
1790 |
|
| 3412 |
30 May 07 |
martin |
1791 |
<varlistentry> |
| 3412 |
30 May 07 |
martin |
1792 |
<term> |
| 3412 |
30 May 07 |
martin |
1793 |
<guilabel>Registered</guilabel> |
| 3412 |
30 May 07 |
martin |
1794 |
</term> |
| 3399 |
28 May 07 |
martin |
1795 |
<listitem> |
| 3399 |
28 May 07 |
martin |
1796 |
<para> |
| 3412 |
30 May 07 |
martin |
1797 |
This field is automatically populated with a date at which the |
| 4487 |
08 Sep 08 |
jari |
1798 |
hybridization was entered in BASE system. |
| 3399 |
28 May 07 |
martin |
1799 |
</para> |
| 3399 |
28 May 07 |
martin |
1800 |
</listitem> |
| 3412 |
30 May 07 |
martin |
1801 |
</varlistentry> |
| 3412 |
30 May 07 |
martin |
1802 |
|
| 3412 |
30 May 07 |
martin |
1803 |
<varlistentry> |
| 3412 |
30 May 07 |
martin |
1804 |
<term> |
| 3412 |
30 May 07 |
martin |
1805 |
<guilabel>Protocol</guilabel> |
| 3412 |
30 May 07 |
martin |
1806 |
</term> |
| 3399 |
28 May 07 |
martin |
1807 |
<listitem> |
| 3399 |
28 May 07 |
martin |
1808 |
<para> |
| 5708 |
25 Aug 11 |
nicklas |
1809 |
The protocol that was used to create the bioassay. |
| 3399 |
28 May 07 |
martin |
1810 |
</para> |
| 3399 |
28 May 07 |
martin |
1811 |
</listitem> |
| 3412 |
30 May 07 |
martin |
1812 |
</varlistentry> |
| 3372 |
24 May 07 |
philippe |
1813 |
|
| 3412 |
30 May 07 |
martin |
1814 |
<varlistentry> |
| 3412 |
30 May 07 |
martin |
1815 |
<term> |
| 3412 |
30 May 07 |
martin |
1816 |
<guilabel>Hardware</guilabel> |
| 3412 |
30 May 07 |
martin |
1817 |
</term> |
| 3399 |
28 May 07 |
martin |
1818 |
<listitem> |
| 3399 |
28 May 07 |
martin |
1819 |
<para> |
| 5708 |
25 Aug 11 |
nicklas |
1820 |
Information about the machine (if any) that was used when creating |
| 5708 |
25 Aug 11 |
nicklas |
1821 |
the bioassay. |
| 3399 |
28 May 07 |
martin |
1822 |
</para> |
| 3399 |
28 May 07 |
martin |
1823 |
</listitem> |
| 3412 |
30 May 07 |
martin |
1824 |
</varlistentry> |
| 3412 |
30 May 07 |
martin |
1825 |
|
| 3412 |
30 May 07 |
martin |
1826 |
<varlistentry> |
| 3412 |
30 May 07 |
martin |
1827 |
<term> |
| 3412 |
30 May 07 |
martin |
1828 |
<guilabel>Array slide</guilabel> |
| 3412 |
30 May 07 |
martin |
1829 |
</term> |
| 3399 |
28 May 07 |
martin |
1830 |
<listitem> |
| 5708 |
25 Aug 11 |
nicklas |
1831 |
<para>The array slide that was used for the bioassay.</para> |
| 3399 |
28 May 07 |
martin |
1832 |
</listitem> |
| 3412 |
30 May 07 |
martin |
1833 |
</varlistentry> |
| 3412 |
30 May 07 |
martin |
1834 |
|
| 3412 |
30 May 07 |
martin |
1835 |
<varlistentry> |
| 3412 |
30 May 07 |
martin |
1836 |
<term> |
| 3412 |
30 May 07 |
martin |
1837 |
<guilabel>Description</guilabel> |
| 3412 |
30 May 07 |
martin |
1838 |
</term> |
| 3399 |
28 May 07 |
martin |
1839 |
<listitem> |
| 3399 |
28 May 07 |
martin |
1840 |
<para> |
| 3412 |
30 May 07 |
martin |
1841 |
A free text field to report any information that can not be captured |
| 5708 |
25 Aug 11 |
nicklas |
1842 |
otherwise. |
| 3399 |
28 May 07 |
martin |
1843 |
</para> |
| 3399 |
28 May 07 |
martin |
1844 |
</listitem> |
| 3412 |
30 May 07 |
martin |
1845 |
</varlistentry> |
| 3412 |
30 May 07 |
martin |
1846 |
</variablelist> |
| 4131 |
08 Feb 08 |
nicklas |
1847 |
<seeother> |
| 5708 |
25 Aug 11 |
nicklas |
1848 |
<other external_id="physicalbioassay.extracts">Extracts</other> |
| 5708 |
25 Aug 11 |
nicklas |
1849 |
<other external_id="annotations.edit">Annotations & parameters</other> |
| 5708 |
25 Aug 11 |
nicklas |
1850 |
<other external_id="annotations.edit.inherited">Inherited annotations</other> |
| 4131 |
08 Feb 08 |
nicklas |
1851 |
</seeother> |
| 4131 |
08 Feb 08 |
nicklas |
1852 |
</helptext> |
| 5708 |
25 Aug 11 |
nicklas |
1853 |
</sect2> |
| 4131 |
08 Feb 08 |
nicklas |
1854 |
|
| 5708 |
25 Aug 11 |
nicklas |
1855 |
<sect2 id="biomaterials.bioassays.extracts"> |
| 5708 |
25 Aug 11 |
nicklas |
1856 |
<title>Parent extracts</title> |
| 4131 |
08 Feb 08 |
nicklas |
1857 |
|
| 5708 |
25 Aug 11 |
nicklas |
1858 |
<figure id="biomaterials.figures.bioassay-tab-2"> |
| 5708 |
25 Aug 11 |
nicklas |
1859 |
<title>Parent extracts</title> |
| 5708 |
25 Aug 11 |
nicklas |
1860 |
<screenshot> |
| 5708 |
25 Aug 11 |
nicklas |
1861 |
<mediaobject> |
| 5708 |
25 Aug 11 |
nicklas |
1862 |
<imageobject> |
| 5708 |
25 Aug 11 |
nicklas |
1863 |
<imagedata |
| 5708 |
25 Aug 11 |
nicklas |
1864 |
fileref="figures/physicalbioassay-tab-2.png" format="PNG" /> |
| 5708 |
25 Aug 11 |
nicklas |
1865 |
</imageobject> |
| 5708 |
25 Aug 11 |
nicklas |
1866 |
</mediaobject> |
| 5708 |
25 Aug 11 |
nicklas |
1867 |
</screenshot> |
| 5708 |
25 Aug 11 |
nicklas |
1868 |
</figure> |
| 5708 |
25 Aug 11 |
nicklas |
1869 |
|
| 5708 |
25 Aug 11 |
nicklas |
1870 |
<helptext external_id="physicalbioassay.extracts" title="Extracts"> |
| 3412 |
30 May 07 |
martin |
1871 |
<para> |
| 5708 |
25 Aug 11 |
nicklas |
1872 |
This important tab allows users to select the extracts used by the |
| 5708 |
25 Aug 11 |
nicklas |
1873 |
bioassay, and specify the amount of material used, expressed in microgram. |
| 3412 |
30 May 07 |
martin |
1874 |
</para> |
| 3412 |
30 May 07 |
martin |
1875 |
<para> |
| 5708 |
25 Aug 11 |
nicklas |
1876 |
Use the <guibutton>Add extracts</guibutton> button to add |
| 4131 |
08 Feb 08 |
nicklas |
1877 |
items and the <guibutton>Remove</guibutton> button to remove items. |
| 5708 |
25 Aug 11 |
nicklas |
1878 |
Select one or several extracts in the list and write the used |
| 5708 |
25 Aug 11 |
nicklas |
1879 |
mass and position number in the fields below the list. |
| 3412 |
30 May 07 |
martin |
1880 |
</para> |
| 4131 |
08 Feb 08 |
nicklas |
1881 |
|
| 4131 |
08 Feb 08 |
nicklas |
1882 |
<seeother> |
| 5708 |
25 Aug 11 |
nicklas |
1883 |
<other external_id="physicalbioassay.edit">Edit physical bioassay</other> |
| 5708 |
25 Aug 11 |
nicklas |
1884 |
<other external_id="annotations.edit">Annotations & parameters</other> |
| 5708 |
25 Aug 11 |
nicklas |
1885 |
<other external_id="annotations.edit.inherited">Inherited annotations</other> |
| 4131 |
08 Feb 08 |
nicklas |
1886 |
</seeother> |
| 4131 |
08 Feb 08 |
nicklas |
1887 |
</helptext> |
| 4131 |
08 Feb 08 |
nicklas |
1888 |
|
| 5708 |
25 Aug 11 |
nicklas |
1889 |
</sect2> |
| 5708 |
25 Aug 11 |
nicklas |
1890 |
|
| 5708 |
25 Aug 11 |
nicklas |
1891 |
|
| 5708 |
25 Aug 11 |
nicklas |
1892 |
<para> |
| 5708 |
25 Aug 11 |
nicklas |
1893 |
The <guilabel>Annotations</guilabel> tab allows BASE users to use |
| 5708 |
25 Aug 11 |
nicklas |
1894 |
annotation types to refine bioassay description. More about annotating items |
| 5708 |
25 Aug 11 |
nicklas |
1895 |
can be read in <xref linkend="annotations.annotating" /> |
| 5708 |
25 Aug 11 |
nicklas |
1896 |
</para> |
| 5708 |
25 Aug 11 |
nicklas |
1897 |
|
| 5708 |
25 Aug 11 |
nicklas |
1898 |
<para> |
| 5708 |
25 Aug 11 |
nicklas |
1899 |
This <guilabel>Inherited annotations</guilabel> tab contains a list of those annotations |
| 5708 |
25 Aug 11 |
nicklas |
1900 |
that are inherited from the bioassay's parents. Information about working with inherited |
| 5708 |
25 Aug 11 |
nicklas |
1901 |
annotations can be found in <xref linkend="annotations.inheriting" />. |
| 5708 |
25 Aug 11 |
nicklas |
1902 |
</para> |
| 5708 |
25 Aug 11 |
nicklas |
1903 |
|
| 3399 |
28 May 07 |
martin |
1904 |
</sect1> |
| 3372 |
24 May 07 |
philippe |
1905 |
</chapter> |