source: trunk/doc/src/docbook/user/derivedbioassays.xml @ 5783

Last change on this file since 5783 was 5783, checked in by Nicklas Nordborg, 10 years ago

References #1590: Documentation cleanup

Experiments and analysis chapter.

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1<?xml version="1.0" encoding="UTF-8"?>
2<!DOCTYPE sect1 PUBLIC
3    "-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN"
4    "../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd">
5<!--
6  $Id: derivedbioassays.xml 5783 2011-10-05 10:34:24Z nicklas $
7
8  Copyright (C) 2007 Peter Johansson, Nicklas Nordborg
9
10  This file is part of BASE - BioArray Software Environment.
11  Available at http://base.thep.lu.se/
12
13  BASE is free software; you can redistribute it and/or
14  modify it under the terms of the GNU General Public License
15  as published by the Free Software Foundation; either version 3
16  of the License, or (at your option) any later version.
17
18  BASE is distributed in the hope that it will be useful,
19  but WITHOUT ANY WARRANTY; without even the implied warranty of
20  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
21  GNU General Public License for more details.
22
23  You should have received a copy of the GNU General Public License
24  along with BASE. If not, see <http://www.gnu.org/licenses/>.
25-->
26<sect1 id="experiments_analysis.derivedbioassays">
27  <?dbhtml filename="derivedbioassays.html" ?>
28 
29  <title>Derived bioassays</title>
30  <para>
31    When you have processed your physical bioassay you can
32    register any information that you have gathered as
33    <guilabel>Derived bioassay</guilabel> items in BASE.
34    The derived bioassay can represent both a physical process,
35    such as scanning a microarray slide, or a software
36    process such as aligning sequence data against a reference
37    genome. It is even possible to register child derived
38    bioassays if there are multiple steps involved that you want
39    to register independently. Each derived bioassay can
40    specify a protocol (with parameters if needed) and a hardware
41    or software item that was used to create it.
42  </para>
43 
44  <para>
45    It is also possible to link one or more files to the derived
46    bioassay. This feature requires that a subtype is selected and
47    that the subtype has been linked with the file types that
48    are useful in that context. For example, the <guilabel>Scan</guilabel>
49    subtype is linked with <guilabel>Image</guilabel> files.
50  </para>
51 
52  <note>
53    <para>
54    A derived bioassay can only hold data in the form of files.
55    When the data has been processed enough to make it a sensible
56    option (performance-wise) to import into the database a
57    <guilabel>Raw bioassay</guilabel> should be created.
58    </para>
59  </note>
60 
61  <sect2 id="experiments_analysis.derivedbioassays.create">
62    <title>Create derived bioassays</title>
63 
64    <para>
65      Beside the common way, using the &gbNew; button, a derived bioassay can be created in one of
66      the following ways:
67    </para>
68      <variablelist>
69        <varlistentry>
70          <term>from either physical bioassay list- or single view- page.</term>
71          <listitem>
72            <para>
73              A derived bioassay must always have a physical bioassay as it's
74              parent. Therefore, a natural way to create a derived bioassay is to click on
75              <guiicon>
76                <inlinemediaobject>
77                  <imageobject>
78                    <imagedata fileref="figures/add.png" format="PNG" />
79                  </imageobject>
80                </inlinemediaobject>
81              </guiicon>
82              in the <guilabel>Derived bioassays</guilabel> column in the list view. There is also a
83              corresponding button, <guibutton>New derived bioassay&hellip;</guibutton>
84              in the toolbar when viewing a single physical bioassay.
85            </para>
86          </listitem>
87        </varlistentry>
88        <varlistentry>
89          <term>from either derived bioassays list- or single view- page</term>
90          <listitem>
91            <para>
92              A child derived bioassay must always have another derived bioassay
93              as it's parent. Click on the
94              <guiicon>
95                <inlinemediaobject>
96                  <imageobject>
97                    <imagedata fileref="figures/add.png" format="PNG" />
98                  </imageobject>
99                </inlinemediaobject>
100              </guiicon> icon in the <guilabel>Child bioassays</guilabel> column
101              to create a new child derived bioassay. There is also a
102              corresponding button, <guibutton>New child bioassay&hellip;</guibutton>
103              in the toolbar when viewing a single derived bioassay.
104            </para>
105          </listitem>
106        </varlistentry>
107      </variablelist>
108  </sect2>
109 
110  <sect2 id="experiment_analysis.derivedbioassay.properties">
111    <title>Derived bioassay properties</title>
112   
113    <para>
114      A derived bioassay has the following properties:
115    </para>
116   
117    <helptext external_id="derivedbioassay.edit" title="Edit derived bioassay">
118    <variablelist>
119      <varlistentry>
120        <term><guilabel>Name</guilabel></term>
121        <listitem>
122          <para>
123            The name of the derived bioassay.
124          </para>
125        </listitem>
126      </varlistentry>
127      <varlistentry>
128        <term><guilabel>Type</guilabel></term>
129        <listitem>
130          <para>
131            The subtype of the derived bioassay. The list may evolve depending on additions by
132            the server administrator. Selecting the proper subtype is required
133            to be able to attach data files to the bioassay. It will also help BASE
134            to automatically guess the most likely subtype when creating child bioassays.
135            <nohelp>
136            See <xref linkend="subtypes" /> for more information.
137            </nohelp>
138          </para>
139        </listitem>
140      </varlistentry>
141      <varlistentry>
142        <term><guilabel>Parent type</guilabel></term>
143        <listitem>
144          <para>
145            Select if the parent item is a physical bioassay or
146            another derived bioassay. This option is only available when creating new
147            derived bioassays. Once created it is not possible to change
148            the parent.
149          </para>
150        </listitem>
151      </varlistentry>
152      <varlistentry>
153        <term><guilabel>Extract</guilabel></term>
154        <listitem>
155          <para>
156            Select the extract that this derived bioassay is linked with. The list
157            contains all the extracts that are present on the physical bioassay.
158            Do not select an extract if the derived bioassay represents more than
159            one extract at this stage.
160          </para>
161        </listitem>
162      </varlistentry>
163      <varlistentry>
164        <term><guilabel>Protocol</guilabel></term>
165        <listitem>
166          <para>
167            The protocol used in the process that created this derived bioassay (optional).
168            Parameters may be registered as part of the protocol.
169          </para>
170        </listitem>
171      </varlistentry>
172      <varlistentry>
173        <term><guilabel>Hardware</guilabel></term>
174        <listitem>
175          <para>
176            The machine used in the process that created this derived bioassay (optional).
177          </para>
178        </listitem>
179      </varlistentry>
180      <varlistentry>
181        <term><guilabel>Software</guilabel></term>
182        <listitem>
183          <para>
184            The software used in the process that created this derived bioassay (optional).
185          </para>
186        </listitem>
187      </varlistentry>
188      <varlistentry>
189        <term><guilabel>Description</guilabel></term>
190        <listitem>
191          <para>
192            A decription of the derived bioassay (optional).
193          </para>
194        </listitem>
195      </varlistentry>
196    </variablelist>
197   
198    <seeother>
199      <other external_id="datafiles.edit">Data files</other>
200      <other external_id="annotations.edit">Annotations</other>
201      <other external_id="annotations.edit.inerited">Inherit annotations</other>
202    </seeother>
203   
204    </helptext>
205   
206    <sect3 id="experiment_analysis.derivedbioassay.datafiles">
207      <title>Data files</title>
208      <para>
209        This allows you to select files that contain data for the derived bioassay.
210        Read more about this in <xref linkend="platforms.selectfiles" />.
211      </para>
212    </sect3>
213   
214    <sect3 id="experiment_analysis.derivedbioassay.annotations">
215      <title>Annotations and inherited annotations</title>
216      <para>
217        This allows you to input values associated to annotation types devised to refine
218        the description. Read more about annotations in
219        <xref linkend="annotations" />.
220      </para>
221    </sect3>
222   
223  </sect2>
224
225 
226</sect1>
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