source: trunk/doc/src/docbook/userdoc/protocols.xml @ 3382

Last change on this file since 3382 was 3382, checked in by Martin Svensson, 14 years ago

Fixed the organization of the output-files

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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 3382 2007-05-25 09:11:55Z martin $
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28<chapter id="protocol">
29<?dbhtml dir="protocols"?>
30 <title>Protocols</title>
31 <sect1 id="protocol.introduction">
32  <title>Introduction</title>
33  <para>Information about laboratory standard operating procedure and protocols can be tracked in
34   BASE2 using two structures, the use of which is detailed in the following sections. </para>
35 </sect1>
36 <sect1 id="protocol.manage">
37  <title>Managing Protocols</title>
38  <para> </para>
39
40 
41
42   <sect2 id="protocoltype.create">
43    <title>Creating Protocol Types</title>
44    <helptext external_id="protocol.view.properties" title="Protocol Types">
45    <para><guilabel>Protocol Type</guilabel> allows classification of protocols based on their usage
46     and purpose in the laboratory workflow. By default, BASE2 creates the 8 main Protocol Types and
47     those correspond to the main protocol families identified by MIAME requirements and applied in
48     a canonical DNA microarray experiment meant for surveying gene expression. These 8 protocol
49     types are namely <guilabel>Printing</guilabel>,
50      <guilabel>Sampling</guilabel>,<guilabel>Pooling</guilabel>,<guilabel>Extraction</guilabel>,
51      <guilabel>Labeling</guilabel>, <guilabel>Hybridization</guilabel>,
52     <guilabel>Scanning</guilabel>, <guilabel>Feature extraction</guilabel>
53    </para>
54    <para>New applications of DNA microarray technology, for instance DNA binding site
55     identification, imposes the creation of new Protocol Type in addition to those built-in in
56     BASE2.</para>
57    <para>In order to do so</para>
58    <para>Go To <menuchoice>
59      <guimenu>Administrate</guimenu>
60      <guimenuitem>Types</guimenuitem>
61      <guisubmenu>Protocol Type</guisubmenu>
62     </menuchoice>
63    </para>
64    <para> Click on <guibutton>New&hellip;</guibutton>. </para>
65    <para>A 'Create' pop-up window opens and allow to fill in name and description</para>
66    <tip>
67     <para>It is advised to define the Protocol Type <guilabel>Name</guilabel> attribute so that it
68      is compatible with the MIAME requirements and recommendations issues by microarray data
69      repositories.</para>
70    </tip>
71    <itemizedlist>
72     <listitem>
73      <figure id="write_docbook_doc.figures.protocoltype">
74       <title>The Protocol Type Create Window</title>
75       <screenshot>
76    <mediaobject>
77     <imageobject>
78      <imagedata fileref="figures/protocoltype.png" format="PNG"/>
79     </imageobject>
80    </mediaobject>
81   </screenshot>
82      </figure>
83     </listitem>
84    </itemizedlist>
85    </helptext>
86   </sect2>
87
88 
89
90  <sect2 id="protocol.create">
91   <title>Creating Protocols</title>
92   <para>In BASE2, Protocols can be created by 2 routes. Either from the Protocol Type page or from
93    the Protocol Page. </para>
94   <orderedlist>
95    <listitem>
96     <para>Creating Protocols from the Protocol Type View</para>
97     <para> Clicking on the <guibutton>(+) add protocol</guibutton> button. </para>
98     <figure id="write_docbook_doc.figures.protocol-frompt">
99      <title>Create New Protocol from the Protocol Type list view</title>
100      <screenshot>
101       <mediaobject>
102        <imageobject>
103         <imagedata fileref="figures/protocol-frompt.png" format="PNG"/>
104        </imageobject>
105       </mediaobject>
106      </screenshot>
107     </figure>
108    </listitem>
109    <listitem>
110     <para>Creating Protocols from the Protocol View</para>
111     <para>Go to <menuchoice>
112       <guimenu>View</guimenu>
113       <guimenuitem>Protocol</guimenuitem>
114      </menuchoice> Click on <guibutton>New&hellip;</guibutton> button </para>
115     <para> Either way causes a 'Create' pop-up window to open, it contains 2 tabs:
116       <guilabel>Protocol</guilabel> and <guilabel>Parameters</guilabel>. </para>
117     <itemizedlist>
118      <listitem>
119       <para>
120        <guilabel>Protocol</guilabel>
121       </para>
122       <para> This tab allows users to enter essential information about a protocol. Mandatory tags
123        are Protocol <guilabel>Name</guilabel> and <guilabel>Protocol Type</guilabel>, the later
124        being in the form of a drop-down list populated by Protocol Types shared to the users. This
125        list therefore varies and may evolve depending on additions and permissions. The tab has
126        also a dedicated field <guilabel>File</guilabel> to enable linking of external files, e.g.
127        pdf documents from kit providers to the protocol.</para>
128       <figure id="write_docbook_doc.figures.protocol-1">
129        <title>The Protocol tab in the Protocol Create Window</title>
130        <screenshot>
131      <mediaobject>
132       <imageobject>
133        <imagedata fileref="figures/protocol-1.png" format="PNG"/>
134       </imageobject>
135      </mediaobject>
136     </screenshot>
137       </figure>
138      </listitem>
139      <listitem>
140       <para>
141        <guilabel>Parameters</guilabel>
142       </para>
143       <para> This tab allows BASE2 users to declare parameters attached to a particular protocol.
144        Parameters are selected from a list of Annotation Types which have been flagged as
145        parameters. Only those Annotation Types are available for selection using the <guibutton>Add
146         annotation types&hellip;</guibutton>
147       </para>
148       <figure id="write_docbook_doc.figures.protocol-2">
149        <title>The Paramater tab from the Protocol Create Window</title>
150        <screenshot>
151      <mediaobject>
152       <imageobject>
153        <imagedata fileref="figures/protocol-2.png" format="PNG"/>
154       </imageobject>
155      </mediaobject>
156     </screenshot>
157       </figure>
158      </listitem>
159     </itemizedlist>
160    </listitem>
161   </orderedlist>
162  </sect2>
163  <sect2 id="protocol.detail_view">
164   <title>Viewing/Editing Protocols</title>
165   <itemizedlist>
166    <listitem>
167     <para>From the Protocol List View, clicking on the Protocol <guilabel>Name</guilabel> opens a
168      detail view for that protocol, showing a summary of all information available in BASE2 about
169      that entity</para>
170    </listitem>
171    <listitem>
172     <para>Alternately, from the Protocol Item View, clicking the
173      <guibutton>Edit&hellip;</guibutton> performs the same task. </para>
174     <figure id="write_docbook_doc.figures.protocol-itemview">
175      <title>Protocol Item View</title>
176      <screenshot>
177      <mediaobject>
178       <imageobject>
179        <imagedata fileref="figures/protocol-itemview.png" format="PNG"/>
180       </imageobject>
181      </mediaobject>
182     </screenshot>
183     </figure>
184    </listitem>
185    <listitem>
186     <para> Note from the Protocol Item view how protocol <guilabel>Paramaters</guilabel> are
187      listed. Clicking on the <guilabel>Parameter name</guilabel> will open the corresponding
188      Annotation Type element in an item view </para>
189    </listitem>
190   </itemizedlist>
191
192  </sect2>
193  <sect2 id="protocol.delete">
194   <title>Deleting/Restoring Protocols</title>
195   <para>As for other items in BASE2, some can be removed and restored. To do so, do the following</para>
196   <itemizedlist>
197    <listitem>
198     <para>Select one or more protocols and click the <guibutton>Delete</guibutton> button in the
199      menu bar. </para>
200     <para>All the selected protocols have been marked as deleted and are no longer available from
201      the interface. </para>
202     <para>Only by selecting from the <guilabel>view/preset&hellip;</guilabel> select box the
203       <guilabel>Removed</guilabel> option, one can see those of the protocols earmarked for
204      deletion. They will be shown with a symbol in front of them. </para>
205    </listitem>
206    <listitem>
207     <para>Alternately, navigating to the Protocol Item View, one can hit the
208      <guibutton>Delete</guibutton> to performed the task. </para>
209    </listitem>
210    <listitem>
211     <para>Deletion errors at this stage can be easily recovered. Select the item to recover from
212      the List View (be sure to check the <guilabel>Removed</guilabel> option in the
213       <guilabel>view/preset&hellip;</guilabel> filter) and hit the
214      <guibutton>Restore</guibutton> button to performed the task. </para>
215    </listitem>
216   </itemizedlist>
217   <important>
218    <para>To really delete an item from the database you must use the <link linkend="trashcan"
219      >trashcan</link>. Items deleted from the Trashcan can not be recovered. </para>
220   </important>
221  </sect2>
222 </sect1>
223</chapter>
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