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1<?xml version="1.0" encoding="UTF-8"?>
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 3372 2007-05-24 08:45:06Z philippe $
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28<chapter id="protocol">
29 <title>Protocols</title>
30 <sect1 id="protocol.introduction">
31  <title>Introduction</title>
32  <para>Information about laboratory standard operating procedure and protocols can be tracked in
33   BASE2 using two structures, the use of which is detailed in the following sections. </para>
34 </sect1>
35 <sect1 id="protocol.manage">
36  <title>Managing Protocols</title>
37  <para> </para>
39  <helptext external_id="" title="Protocol Types">
41   <sect2 id="protocoltype.create">
42    <title>Creating Protocol Types</title>
43    <para><guilabel>Protocol Type</guilabel> allows classification of protocols based on their usage
44     and purpose in the laboratory workflow. By default, BASE2 creates the 8 main Protocol Types and
45     those correspond to the main protocol families identified by MIAME requirements and applied in
46     a canonical DNA microarray experiment meant for surveying gene expression. These 8 protocol
47     types are namely <guilabel>Printing</guilabel>,
48      <guilabel>Sampling</guilabel>,<guilabel>Pooling</guilabel>,<guilabel>Extraction</guilabel>,
49      <guilabel>Labeling</guilabel>, <guilabel>Hybridization</guilabel>,
50     <guilabel>Scanning</guilabel>, <guilabel>Feature extraction</guilabel>
51    </para>
52    <para>New applications of DNA microarray technology, for instance DNA binding site
53     identification, imposes the creation of new Protocol Type in addition to those built-in in
54     BASE2.</para>
55    <para>In order to do so</para>
56    <para>Go To <menuchoice>
57      <guimenu>Administrate</guimenu>
58      <guimenuitem>Types</guimenuitem>
59      <guisubmenu>Protocol Type</guisubmenu>
60     </menuchoice>
61    </para>
62    <para> Click on <guibutton>New&hellip;</guibutton>. </para>
63    <para>A 'Create' pop-up window opens and allow to fill in name and description</para>
64    <tip>
65     <para>It is advised to define the Protocol Type <guilabel>Name</guilabel> attribute so that it
66      is compatible with the MIAME requirements and recommendations issues by microarray data
67      repositories.</para>
68    </tip>
69    <itemizedlist>
70     <listitem>
71      <figure id="write_docbook_doc.figures.protocoltype">
72       <title>The Protocol Type Create Window</title>
73       <screenshot>
74    <mediaobject>
75     <imageobject>
76      <imagedata fileref="figures/protocoltype.png" format="PNG"/>
77     </imageobject>
78    </mediaobject>
79   </screenshot>
80      </figure>
81     </listitem>
82    </itemizedlist>
83   </sect2>
85  </helptext>
87  <sect2 id="protocol.create">
88   <title>Creating Protocols</title>
89   <para>In BASE2, Protocols can be created by 2 routes. Either from the Protocol Type page or from
90    the Protocol Page. </para>
91   <orderedlist>
92    <listitem>
93     <para>Creating Protocols from the Protocol Type View</para>
94     <para> Clicking on the <guibutton>(+) add protocol</guibutton> button. </para>
95     <figure id="write_docbook_doc.figures.protocol-frompt">
96      <title>Create New Protocol from the Protocol Type list view</title>
97      <screenshot>
98       <mediaobject>
99        <imageobject>
100         <imagedata fileref="figures/protocol-frompt.png" format="PNG"/>
101        </imageobject>
102       </mediaobject>
103      </screenshot>
104     </figure>
105    </listitem>
106    <listitem>
107     <para>Creating Protocols from the Protocol View</para>
108     <para>Go to <menuchoice>
109       <guimenu>View</guimenu>
110       <guimenuitem>Protocol</guimenuitem>
111      </menuchoice> Click on <guibutton>New&hellip;</guibutton> button </para>
112     <para> Either way causes a 'Create' pop-up window to open, it contains 2 tabs:
113       <guilabel>Protocol</guilabel> and <guilabel>Parameters</guilabel>. </para>
114     <itemizedlist>
115      <listitem>
116       <para>
117        <guilabel>Protocol</guilabel>
118       </para>
119       <para> This tab allows users to enter essential information about a protocol. Mandatory tags
120        are Protocol <guilabel>Name</guilabel> and <guilabel>Protocol Type</guilabel>, the later
121        being in the form of a drop-down list populated by Protocol Types shared to the users. This
122        list therefore varies and may evolve depending on additions and permissions. The tab has
123        also a dedicated field <guilabel>File</guilabel> to enable linking of external files, e.g.
124        pdf documents from kit providers to the protocol.</para>
125       <figure id="write_docbook_doc.figures.protocol-1">
126        <title>The Protocol tab in the Protocol Create Window</title>
127        <screenshot>
128      <mediaobject>
129       <imageobject>
130        <imagedata fileref="figures/protocol-1.png" format="PNG"/>
131       </imageobject>
132      </mediaobject>
133     </screenshot>
134       </figure>
135      </listitem>
136      <listitem>
137       <para>
138        <guilabel>Parameters</guilabel>
139       </para>
140       <para> This tab allows BASE2 users to declare parameters attached to a particular protocol.
141        Parameters are selected from a list of Annotation Types which have been flagged as
142        parameters. Only those Annotation Types are available for selection using the <guibutton>Add
143         annotation types&hellip;</guibutton>
144       </para>
145       <figure id="write_docbook_doc.figures.protocol-2">
146        <title>The Paramater tab from the Protocol Create Window</title>
147        <screenshot>
148      <mediaobject>
149       <imageobject>
150        <imagedata fileref="figures/protocol-2.png" format="PNG"/>
151       </imageobject>
152      </mediaobject>
153     </screenshot>
154       </figure>
155      </listitem>
156     </itemizedlist>
157    </listitem>
158   </orderedlist>
159  </sect2>
160  <sect2 id="protocol.detail_view">
161   <title>Viewing/Editing Protocols</title>
162   <itemizedlist>
163    <listitem>
164     <para>From the Protocol List View, clicking on the Protocol <guilabel>Name</guilabel> opens a
165      detail view for that protocol, showing a summary of all information available in BASE2 about
166      that entity</para>
167    </listitem>
168    <listitem>
169     <para>Alternately, from the Protocol Item View, clicking the
170      <guibutton>Edit&hellip;</guibutton> performs the same task. </para>
171     <figure id="write_docbook_doc.figures.protocol-itemview">
172      <title>Protocol Item View</title>
173      <screenshot>
174      <mediaobject>
175       <imageobject>
176        <imagedata fileref="figures/protocol-itemview.png" format="PNG"/>
177       </imageobject>
178      </mediaobject>
179     </screenshot>
180     </figure>
181    </listitem>
182    <listitem>
183     <para> Note from the Protocol Item view how protocol <guilabel>Paramaters</guilabel> are
184      listed. Clicking on the <guilabel>Parameter name</guilabel> will open the corresponding
185      Annotation Type element in an item view </para>
186    </listitem>
187   </itemizedlist>
189  </sect2>
190  <sect2 id="protocol.delete">
191   <title>Deleting/Restoring Protocols</title>
192   <para>As for other items in BASE2, some can be removed and restored. To do so, do the following</para>
193   <itemizedlist>
194    <listitem>
195     <para>Select one or more protocols and click the <guibutton>Delete</guibutton> button in the
196      menu bar. </para>
197     <para>All the selected protocols have been marked as deleted and are no longer available from
198      the interface. </para>
199     <para>Only by selecting from the <guilabel>view/preset&hellip;</guilabel> select box the
200       <guilabel>Removed</guilabel> option, one can see those of the protocols earmarked for
201      deletion. They will be shown with a symbol in front of them. </para>
202    </listitem>
203    <listitem>
204     <para>Alternately, navigating to the Protocol Item View, one can hit the
205      <guibutton>Delete</guibutton> to performed the task. </para>
206    </listitem>
207    <listitem>
208     <para>Deletion errors at this stage can be easily recovered. Select the item to recover from
209      the List View (be sure to check the <guilabel>Removed</guilabel> option in the
210       <guilabel>view/preset&hellip;</guilabel> filter) and hit the
211      <guibutton>Restore</guibutton> button to performed the task. </para>
212    </listitem>
213   </itemizedlist>
214   <important>
215    <para>To really delete an item from the database you must use the <link linkend="trashcan"
216      >trashcan</link>. Items deleted from the Trashcan can not be recovered. </para>
217   </important>
218  </sect2>
219 </sect1>
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