source: trunk/doc/src/docbook/userdoc/protocols.xml @ 5706

Last change on this file since 5706 was 5706, checked in by Nicklas Nordborg, 10 years ago

References #1590: Documentation cleanup

User documentation chapter 10 to 15. Added new chapter about "Item subtypes". Removed sections about protocol types, hardware types and software types. Merged "Hardware" and "Software" into a single chapter.

Added some menu separators in the New annotation type menu.

As usual, screen shots have not yet been updated.

  • Property svn:eol-style set to native
  • Property svn:keywords set to Id
File size: 5.9 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 5706 2011-08-23 13:20:30Z nicklas $
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" chunked="0">
27  <?dbhtml dir="protocols"?>
28  <title>Protocols</title>
29
30    <para>
31      A protocol is a document describing some kind of process that
32      is typically performed in the lab to create an item
33      of some type (for example, how to create an extract from a sample).
34      It can also represent a procedure for running software programs to
35      extract measured data (for example, from a scanned microarray image).
36      A protocol in the simplest form is just a name with an optional link to a file.
37      The file may for example be a PDF or some other document with a more
38      detailed description.
39    </para>
40   
41    <para>
42      Protocols are typically added to a BASE server by an administrator
43      and can be managed from <menuchoice>
44        <guimenu>Administrate</guimenu>
45        <guimenuitem>Protocols</guimenuitem>
46      </menuchoice>.
47    </para>
48
49     
50    <figure
51      id="protocols.figures.edit_protocol">
52      <title>Protocol properties</title>
53      <screenshot>
54        <mediaobject>
55          <imageobject>
56            <imagedata
57              fileref="figures/edit_protocol.png" format="PNG" />
58          </imageobject>
59        </mediaobject>
60      </screenshot>
61    </figure>
62     
63      <helptext external_id="protocol.edit" 
64        title="Edit protocol">
65       
66        <para>
67        This tab allows users to enter essential
68        information about a protocol.
69        </para>
70       
71        <variablelist>
72        <varlistentry>
73          <term><guilabel>Name</guilabel></term>
74          <listitem>
75            <para>
76            The name of the protocol.
77            </para>
78          </listitem>
79        </varlistentry>
80        <varlistentry>
81          <term><guilabel>Type</guilabel></term>
82          <listitem>
83            <para>
84            The protocol type of the protocol. The list
85            may evolve depending on additions by the server
86            administrator. Selecting the proper protocol type
87            is important and enables BASE to automatically guess
88            the most likely protocol when creating new items.
89            <nohelp>
90            See <xref linkend="subtypes" /> for more information.
91            </nohelp>
92            </para>
93          </listitem>
94        </varlistentry>
95        <varlistentry>
96          <term><guilabel>External ID</guilabel></term>
97          <listitem>
98            <para>
99            An ID identifying this protocol in an external
100            database. The value does not have to be unique.
101            </para>
102          </listitem>
103        </varlistentry>
104        <varlistentry>
105          <term><guilabel>File</guilabel></term>
106          <listitem>
107            <para>
108            A document containing the protocol description,     
109            e.g. PDF documents from kit providers to
110            the protocol. Use the <guibutton>Select</guibutton>
111            button to select or upload a file.
112            </para>
113          </listitem>
114        </varlistentry>
115        <varlistentry>
116          <term><guilabel>Description</guilabel></term>
117          <listitem>
118            <para>
119            A description of the protocol.
120            </para>
121          </listitem>
122        </varlistentry>
123        </variablelist>
124       
125        <seeother>
126          <other external_id="protocol.edit.parameters">Protocol parameters</other>
127        </seeother>
128      </helptext>
129   
130    <sect1 id="protocols.parameters">
131      <title>Protocol parameters</title>
132
133      <helptext external_id="protocol.edit.parameters" 
134        title="Protocol parameters">
135
136        <para>
137          BASE users may declare parameters attached to a particular
138          protocol. Parameters are selected from a list of annotation
139          types which have been flagged as parameters. Annotation
140          types which has been selected as parameters show up in the
141          regular annotation dialog whenever the protocol is used for
142          an item. <nohelp>For more information see
143          <xref linkend="annotations" />.</nohelp>
144        </para>
145   
146        <nohelp>
147        <figure
148          id="protocols.figures.protocol_parameters">
149          <title>Protocol parameters</title>
150          <screenshot>
151            <mediaobject>
152              <imageobject>
153                <imagedata
154                  fileref="figures/protocol_parameters.png" format="PNG" />
155              </imageobject>
156            </mediaobject>
157          </screenshot>
158        </figure>
159        </nohelp>
160
161        <variablelist>
162        <varlistentry>
163          <term><guilabel>Annotation types</guilabel></term>
164          <listitem>
165            <para>
166            This list contains the annotation types selected
167            as parameters for the protocol.
168            </para>
169          </listitem>
170        </varlistentry>
171        <varlistentry>
172          <term><guibutton>Add annotation types</guibutton></term>
173          <listitem>
174            <para>
175            Use this button to open a pop-up where you can select
176            annotation type to use for parameters. The list only
177            shows annotations types which has the
178            <guilabel>Protocol parameter</guilabel> flag set.
179            </para>
180          </listitem>
181        </varlistentry>
182        <varlistentry>
183          <term><guibutton>Remove</guibutton></term>
184          <listitem>
185            <para>
186            Removes the selected annotation types from the list.
187            </para>
188          </listitem>
189        </varlistentry>
190        </variablelist>
191     
192        <seeother>
193          <other external_id="protocol.edit">Edit protocol</other>
194          <other external_id="annotations.edit">Annotations &amp; parameters</other>
195        </seeother>
196     
197      </helptext>
198  </sect1>
199</chapter>
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