source: trunk/doc/src/docbook/userdoc/protocols.xml @ 3387

Last change on this file since 3387 was 3387, checked in by Nicklas Nordborg, 14 years ago

Fixes #540. Major reorganisation. Added screen shots.

  • Property svn:eol-style set to native
  • Property svn:keywords set to Id
File size: 7.6 KB
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1<?xml version="1.0" encoding="UTF-8"?>
2<!DOCTYPE chapter PUBLIC
3    "-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN"
4    "../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd">
5<!--
6  $Id: protocols.xml 3387 2007-05-28 06:53:04Z nicklas $
7 
8  Copyright (C) Authors contributing to this file.
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 2
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 this program; if not, write to the Free Software
25  Foundation, Inc., 59 Temple Place - Suite 330,
26  Boston, MA  02111-1307, USA.
27-->
28<chapter id="protocols_protocoltypes">
29  <?dbhtml dir="protocols"?>
30  <title>Protocols and protocol types</title>
31  <para>
32    Information about laboratory standard operating procedure
33    and protocols can be tracked in BASE2 using two structures,
34    the use of which is detailed in the following sections.
35  </para>
36  <sect1 id="protocoltypes">
37    <title>Protocol types</title>
38
39    <helptext external_id="protocoltype.view.properties"
40      title="Protocol Types">
41      <para>
42        <guilabel>Protocol Type</guilabel>
43        allows classification of protocols based on their
44        usage and purpose in the laboratory workflow. By
45        default, BASE2 creates the 8 main pProtocol types and
46        those correspond to the main protocol families
47        identified by MIAME requirements and applied in a
48        canonical DNA microarray experiment meant for
49        surveying gene expression. These 8 protocol types
50        are namely
51        <guilabel>Printing</guilabel>,
52        <guilabel>Sampling</guilabel>,
53        <guilabel>Pooling</guilabel>,
54        <guilabel>Extraction</guilabel>,
55        <guilabel>Labeling</guilabel>,
56        <guilabel>Hybridization</guilabel>,
57        <guilabel>Scanning</guilabel> and
58        <guilabel>Feature extraction</guilabel>.
59      </para>
60      <para>
61        New applications of DNA microarray technology, for
62        instance DNA binding site identification, imposes
63        the creation of new protocol type in addition to
64        those built-in in BASE2.
65      </para>
66      <tip>
67        <title>Follow MIAME recommendations</title>
68        <para>
69          It is advised to define the protocol type
70          <guilabel>Name</guilabel>
71          so that it is compatible with the
72          MIAME requirements and recommendations issues by
73          microarray data repositories.
74        </para>
75      </tip>
76    </helptext>
77   
78    <para>
79      You can manage the protocol types by going to
80      <menuchoice>
81        <guimenu>Administrate</guimenu>
82        <guimenuitem>Types</guimenuitem>
83        <guisubmenu>Protocol Type</guisubmenu>
84      </menuchoice>.
85    </para>
86    <figure
87      id="protocols.figures.protocoltype">
88      <title>Protocol type properties</title>
89      <screenshot>
90        <mediaobject>
91          <imageobject>
92            <imagedata
93              fileref="figures/edit_protocoltype.png" format="PNG" />
94          </imageobject>
95        </mediaobject>
96      </screenshot>
97    </figure>
98   
99    <helptext external_id="protocoltype.edit" 
100      title="Edit protocol type">
101   
102      <variablelist>
103      <varlistentry>
104        <term><guilabel>Name</guilabel></term>
105        <listitem>
106          <para>
107            The name of the protocol type.
108          </para>
109        </listitem>
110      </varlistentry>
111      <varlistentry>
112        <term><guilabel>Description</guilabel></term>
113        <listitem>
114          <para>
115            A description of the protocol type.
116          </para>
117        </listitem>
118      </varlistentry>
119      </variablelist>
120    </helptext>
121  </sect1>
122
123  <sect1 id="protocols">
124    <title>Protocols</title>
125    <para>
126      In BASE, protocols can be created by 2 routes. Either
127      from the single-item view of a protocol type or from the
128      list view of protocols.
129    </para>
130    <sect2 id="protocols.properties">
131      <title>Protocol properties</title>
132     
133      <figure
134        id="protocols.figures.edit_protocol">
135        <title>Protocol properties</title>
136        <screenshot>
137          <mediaobject>
138            <imageobject>
139              <imagedata
140                fileref="figures/edit_protocol.png" format="PNG" />
141            </imageobject>
142          </mediaobject>
143        </screenshot>
144      </figure>
145     
146      <helptext external_id="protocol.edit" 
147        title="Edit protocol">
148       
149        <para>
150        This tab allows users to enter essential
151        information about a protocol.
152       
153        <variablelist>
154        <varlistentry>
155          <term><guilabel>Name</guilabel></term>
156          <listitem>
157            <para>
158            The name of the protocol.
159            </para>
160          </listitem>
161        </varlistentry>
162        <varlistentry>
163          <term><guilabel>Type</guilabel></term>
164          <listitem>
165            <para>
166            The protocol type of the protocol. The list
167            may evolve depending on additions by the server
168            administrator.
169            </para>
170          </listitem>
171        </varlistentry>
172        <varlistentry>
173          <term><guilabel>File</guilabel></term>
174          <listitem>
175            <para>
176            A document containing the protocol description,     
177            e.g. pdf documents from kit providers to
178            the protocol. Use the <guibutton>Select</guibutton>
179            button to select or upload a file.
180            </para>
181          </listitem>
182        </varlistentry>
183        <varlistentry>
184          <term><guilabel>Description</guilabel></term>
185          <listitem>
186            <para>
187            A description of the protocol.
188            </para>
189          </listitem>
190        </varlistentry>
191        </variablelist>
192        </para>   
193       
194        <seeother>
195          <other external_id="protocol.edit.parameters">Protocol parameters</other>
196        </seeother>
197      </helptext>
198    </sect2>
199   
200    <sect2 id="protocols.parameters">
201      <title>Protocol parameters</title>
202
203      <helptext external_id="protocol.edit.parameters" 
204        title="Protocol parameters">
205
206        <para>
207          BASE users may declare parameters attached to a particular
208          protocol. Parameters are selected from a list of annotation
209          types which have been flagged as parameters. Annotation
210          types which has been selected as parameters show up in the
211          regular annotation dialog whenever the protocol is used for
212          an item. <nohelp>For more information see
213          <xref linkend="annotations" />.</nohelp>
214        </para>
215   
216        <nohelp>
217        <figure
218          id="protocols.figures.protocol_parameters">
219          <title>Protocol parameters</title>
220          <screenshot>
221            <mediaobject>
222              <imageobject>
223                <imagedata
224                  fileref="figures/protocol_parameters.png" format="PNG" />
225              </imageobject>
226            </mediaobject>
227          </screenshot>
228        </figure>
229        </nohelp>
230
231        <variablelist>
232        <varlistentry>
233          <term><guilabel>Annotation types</guilabel></term>
234          <listitem>
235            <para>
236            This list contains the annotation types selected
237            as parameters for the protocol.
238            </para>
239          </listitem>
240        </varlistentry>
241        <varlistentry>
242          <term><guibutton>Add annotation types</guibutton></term>
243          <listitem>
244            <para>
245            Use this button to open a popup where you can select
246            annotation type to use for parameters. The list only
247            shows annotations types which has the
248            <guilabel>Protocol parameter</guilabel> flag set.
249            </para>
250          </listitem>
251        </varlistentry>
252        <varlistentry>
253          <term><guibutton>Remove</guibutton></term>
254          <listitem>
255            <para>
256            Removes the selected annotation types from the list.
257            </para>
258          </listitem>
259        </varlistentry>
260        </variablelist>
261     
262        <seeother>
263          <other external_id="protocol.edit">Edit protocol</other>
264          <other external_id="annotations.edit">Annotations &amp; parameters</other>
265        </seeother>
266     
267      </helptext>
268    </sect2>
269
270  </sect1>
271</chapter>
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