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Timestamp:
May 24, 2007, 10:45:06 AM (16 years ago)
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philippe
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  • trunk/doc/src/docbook/userdoc/protocols.xml

    r3246 r3372  
    33    "-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN"
    44    "../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd">
    5 <!--
    6   $Id$
    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 
    29 <chapter id="protocols">
    30   <?dbhtml dir="protocols"?>
    31   <title>Protocols</title>
    32     <sect1>
    33       <title></title>
    34       <para></para>
    35     </sect1>
     5    <!--
     6     $Id$
     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="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>
     38
     39  <helptext external_id="protocol.view.properties" title="Protocol Types">
     40
     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>
     84
     85  </helptext>
     86
     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>
     188
     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>
    36220</chapter>
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