source: trunk/doc/src/docbook/userdoc/protocols.xml @ 4509

Last change on this file since 4509 was 4509, checked in by Jari Häkkinen, 13 years ago

Addresses #1106. Missed to change reference wherefrom retrive GPLv3 license text. And some other changes.

  • Property svn:eol-style set to native
  • Property svn:keywords set to Id
File size: 7.6 KB
Line 
1<?xml version="1.0" encoding="UTF-8"?>
2<!DOCTYPE chapter PUBLIC
3    "-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN"
4    "../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd">
5<!--
6  $Id: protocols.xml 4509 2008-09-11 20:01:44Z jari $
7 
8  Copyright (C) 2007 Nicklas Nordborg, Philippe Rocca-Serra, Martin Svensson
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<chapter id="protocols_protocoltypes">
27  <?dbhtml dir="protocols"?>
28  <title>Protocols and protocol types</title>
29  <para>
30    Information about laboratory standard operating procedure
31    and protocols can be tracked in BASE using two structures,
32    the use of which is detailed in the following sections.
33  </para>
34  <sect1 id="protocoltypes">
35    <title>Protocol types</title>
36
37    <helptext external_id="protocoltype.view.properties"
38      title="Protocol Types">
39      <para>
40        <guilabel>Protocol Type</guilabel>
41        allows classification of protocols based on their
42        usage and purpose in the laboratory workflow. By
43        default, BASE creates the 8 main Protocol types and
44        those correspond to the main protocol families
45        identified by MIAME requirements and applied in a
46        canonical DNA microarray experiment meant for
47        surveying gene expression. These 8 protocol types
48        are namely
49        <guilabel>Printing</guilabel>,
50        <guilabel>Sampling</guilabel>,
51        <guilabel>Pooling</guilabel>,
52        <guilabel>Extraction</guilabel>,
53        <guilabel>Labeling</guilabel>,
54        <guilabel>Hybridization</guilabel>,
55        <guilabel>Scanning</guilabel> and
56        <guilabel>Feature extraction</guilabel>.
57      </para>
58      <para>
59        New applications of DNA microarray technology, for
60        instance DNA binding site identification, imposes
61        the creation of new protocol type in addition to
62        those built-in in BASE.
63      </para>
64      <tip>
65        <title>Follow MIAME recommendations</title>
66        <para>
67          It is advised to define the protocol type
68          <guilabel>Name</guilabel>
69          so that it is compatible with the
70          MIAME requirements and recommendations issues by
71          microarray data repositories.
72        </para>
73      </tip>
74    </helptext>
75   
76    <para>
77      You can manage the protocol types by going to
78      <menuchoice>
79        <guimenu>Administrate</guimenu>
80        <guimenuitem>Types</guimenuitem>
81        <guisubmenu>Protocol Type</guisubmenu>
82      </menuchoice>.
83    </para>
84    <figure
85      id="protocols.figures.protocoltype">
86      <title>Protocol type properties</title>
87      <screenshot>
88        <mediaobject>
89          <imageobject>
90            <imagedata
91              fileref="figures/edit_protocoltype.png" format="PNG" />
92          </imageobject>
93        </mediaobject>
94      </screenshot>
95    </figure>
96   
97    <helptext external_id="protocoltype.edit" 
98      title="Edit protocol type">
99   
100      <variablelist>
101      <varlistentry>
102        <term><guilabel>Name</guilabel></term>
103        <listitem>
104          <para>
105            The name of the protocol type.
106          </para>
107        </listitem>
108      </varlistentry>
109      <varlistentry>
110        <term><guilabel>Description</guilabel></term>
111        <listitem>
112          <para>
113            A description of the protocol type.
114          </para>
115        </listitem>
116      </varlistentry>
117      </variablelist>
118    </helptext>
119  </sect1>
120
121  <sect1 id="protocols">
122    <title>Protocols</title>
123    <para>
124      In BASE, protocols can be created by two routes. Either
125      from the single-item view of a protocol type or from the
126      list view of protocols.
127    </para>
128    <sect2 id="protocols.properties">
129      <title>Protocol properties</title>
130     
131      <figure
132        id="protocols.figures.edit_protocol">
133        <title>Protocol properties</title>
134        <screenshot>
135          <mediaobject>
136            <imageobject>
137              <imagedata
138                fileref="figures/edit_protocol.png" format="PNG" />
139            </imageobject>
140          </mediaobject>
141        </screenshot>
142      </figure>
143     
144      <helptext external_id="protocol.edit" 
145        title="Edit protocol">
146       
147        <para>
148        This tab allows users to enter essential
149        information about a protocol.
150       
151        <variablelist>
152        <varlistentry>
153          <term><guilabel>Name</guilabel></term>
154          <listitem>
155            <para>
156            The name of the protocol.
157            </para>
158          </listitem>
159        </varlistentry>
160        <varlistentry>
161          <term><guilabel>Type</guilabel></term>
162          <listitem>
163            <para>
164            The protocol type of the protocol. The list
165            may evolve depending on additions by the server
166            administrator.
167            </para>
168          </listitem>
169        </varlistentry>
170        <varlistentry>
171          <term><guilabel>File</guilabel></term>
172          <listitem>
173            <para>
174            A document containing the protocol description,     
175            e.g. pdf documents from kit providers to
176            the protocol. Use the <guibutton>Select</guibutton>
177            button to select or upload a file.
178            </para>
179          </listitem>
180        </varlistentry>
181        <varlistentry>
182          <term><guilabel>Description</guilabel></term>
183          <listitem>
184            <para>
185            A description of the protocol.
186            </para>
187          </listitem>
188        </varlistentry>
189        </variablelist>
190        </para>   
191       
192        <seeother>
193          <other external_id="protocol.edit.parameters">Protocol parameters</other>
194        </seeother>
195      </helptext>
196    </sect2>
197   
198    <sect2 id="protocols.parameters">
199      <title>Protocol parameters</title>
200
201      <helptext external_id="protocol.edit.parameters" 
202        title="Protocol parameters">
203
204        <para>
205          BASE users may declare parameters attached to a particular
206          protocol. Parameters are selected from a list of annotation
207          types which have been flagged as parameters. Annotation
208          types which has been selected as parameters show up in the
209          regular annotation dialog whenever the protocol is used for
210          an item. <nohelp>For more information see
211          <xref linkend="annotations" />.</nohelp>
212        </para>
213   
214        <nohelp>
215        <figure
216          id="protocols.figures.protocol_parameters">
217          <title>Protocol parameters</title>
218          <screenshot>
219            <mediaobject>
220              <imageobject>
221                <imagedata
222                  fileref="figures/protocol_parameters.png" format="PNG" />
223              </imageobject>
224            </mediaobject>
225          </screenshot>
226        </figure>
227        </nohelp>
228
229        <variablelist>
230        <varlistentry>
231          <term><guilabel>Annotation types</guilabel></term>
232          <listitem>
233            <para>
234            This list contains the annotation types selected
235            as parameters for the protocol.
236            </para>
237          </listitem>
238        </varlistentry>
239        <varlistentry>
240          <term><guibutton>Add annotation types</guibutton></term>
241          <listitem>
242            <para>
243            Use this button to open a pop-up where you can select
244            annotation type to use for parameters. The list only
245            shows annotations types which has the
246            <guilabel>Protocol parameter</guilabel> flag set.
247            </para>
248          </listitem>
249        </varlistentry>
250        <varlistentry>
251          <term><guibutton>Remove</guibutton></term>
252          <listitem>
253            <para>
254            Removes the selected annotation types from the list.
255            </para>
256          </listitem>
257        </varlistentry>
258        </variablelist>
259     
260        <seeother>
261          <other external_id="protocol.edit">Edit protocol</other>
262          <other external_id="annotations.edit">Annotations &amp; parameters</other>
263        </seeother>
264     
265      </helptext>
266    </sect2>
267
268  </sect1>
269</chapter>
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