source: trunk/doc/src/docbook/userdoc/overview.xml @ 4509

Last change on this file since 4509 was 4509, checked in by Jari Häkkinen, 15 years ago

Addresses #1106. Missed to change reference wherefrom retrive GPLv3 license text. And some other changes.

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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">
6  $Id: overview.xml 4509 2008-09-11 20:01:44Z jari $
8  Copyright (C) 2007 Nicklas Nordborg, Martin
10  This file is part of BASE - BioArray Software Environment.
11  Available at
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.
18  BASE is distributed in the hope that it will be useful,
19  but WITHOUT ANY WARRANTY; without even the implied warranty of
21  GNU General Public License for more details.
23  You should have received a copy of the GNU General Public License
24  along with BASE. If not, see <>.
27<chapter id="userdoc_overview" chunked="0">
28  <?dbhtml dir="overview"?>
29  <title>Overview of user documentation</title>
30  <para> The 'User documentation' part is quite extensive and covers everything from how to Log in on
31    a BASE server and find your way through the program, to working with experiments and doing some
32    useful analysis. The intention with this chapter is to give an overview of the following chapters
33    so it will be easier for you to know where to look for certain information in case you don't want
34    to read the whole part from the beginning to the end.</para>
35  <sect1 id="userdoc_overview.environment">
36    <title>Working environment</title>
37    <para> Before you start working with any big experiment or project in BASE it could be a good idea
38      to get to know the environment and perhaps personalize some behavior and appearance of the
39      program. When this is done your daily work in BASE will be much easier and you will feel more
40      comfortable working with the program.</para>
41    <para>
42      Most of the things that have to do with the working environment are gathered in one chapter,
43      where the first subsection,
44      <xref linkend="webclient.introduction" />
45      , gives a good guidance how to start using BASE including a general explanation how to navigate
46      your way through the program.
47    </para>
48    <para>
49      The second subsection,
50      <xref linkend="webclient.configuration" />
51      , describes how to personalize BASE with contact information, preferences and changing password.
52      The preferences are for instance some appearance like date format, text size or the look of the
53      toolbar buttons.
54    </para>
55    <para>
56      The last two subsections,
57      <xref linkend="webclient.items" />
58      and
59      <xref linkend="webclient.itemlist" />
60      , in the web client chapter explains how to work with BASE. No matter what you are going to do the
61      user interface contains a lot of common functions that works the same everywhere. For example,
62      how to list and search for items, how to create new items and modify and delete existing items.
63      Subsequent chapters with detailed information about each type of item will usually not include
64      descriptions of the common functionality.
65    </para>
66  </sect1>
67  <sect1 id="userdoc_overview.start2work">
68    <title>Start working with BASE</title>
69    <para>
70      There are some working principles that need to be understood by all users in BASE. These concern
71      the permission system and how to get the workflow to move on without any disturbance caused by
72      insufficient permissions. The key is to work in projects, which is covered in detail in
73      <xref linkend="project_permission" />
74      .
75    </para>
76    <para> 
77      Understanding the permission system and how to work in projects will not only make it more
78      simple for you to work in BASE but also for your co-workers who want access to your data.
79    </para>
80    <para>
81      The next thing to do is to add some relevant data to work with. Most of the different items can
82      be created manually from the web client, but some items and data must be imported from files.
83      Before importing a file, it has to be uploaded on the BASE-server's file system.
84      <xref linkend="file_system" />
85      gives you information about the server's file system and how to upload the files.
86    </para>
87    <para>
88      <xref linkend="import_data" /> explains how the import is done
89      and <xref linkend="export_data" /> covers how data later on can
90      be exported from the database back into files, often simple text
91      files or xml files.
92    </para>
93    <para> 
94      Each different item has it's own section in this part of the documentation, where more
95      specific information and also some screen shots can be found. Go back to the table of contents
96      for this part and look up the item you want to know more about.
97    </para>
100    <sect2 id="userdoc_overview.start2work.getgoing">
101      <title>Get going</title>
102      <para> 
103        This description will guide you from the initiating tasks of creating the first account to
104        running an analysis plug-in. Most of the steps below ends with a reference to somewhere in the
105        documentation where more information can be found.
106      </para>
108      <sect3 id="userdoc_overview.start2work.getgoing.administrative">
109        <title>Administrative tasks</title>
110        <para> 
111          Most of the tasks in this section require more privileges than the normal user
112          credentials. As always, there are many ways to do things so steps presented here is the path
113          to get going with BASE as fast as possible without creating havoc in future use of the BASE
114          server.
115        </para>
116        <orderedlist>
117          <listitem>
118            <para>
119              Log in as
120              <prompt>root</prompt>
121              using the password you set during BASE initialization. Create an account and give it the
122              administrator-role. Switch user to the new admin account and use this for all future
123              administrative tasks.
124            </para>
125            <note>
126              <para> 
127                The root-account should only be used to create the first administrator account and
128                nothing else.
129              </para>
130            </note>
131          </listitem>
132          <listitem>
133            <para> 
134              First thing to do, when logged in as administrator, is to create other user-accounts
135              and give them appropriate roles, most of them should be assigned to the User-role.
136            </para>
137            <para>
138              Information related to user-accounts can be found at
139              <xref linkend="user_administration" />
140              .
141            </para>
142          </listitem>
143          <listitem>
144            <para>
145              Next step for you as an administrator is to import reporter-map and corresponding reporters
146              to BASE. For import of Genepix data you can use the
147              <prompt>Reporter importer</prompt>
148              plug-in and
149              <prompt>Reporter map importer</prompt>
150              plug-in that come with BASE. Go to
151              <menuchoice>
152                <guimenuitem>Array LIMS</guimenuitem>
153                <guimenuitem>Array designs</guimenuitem>
154              </menuchoice>
155              or
156              <menuchoice>
157                <guimenuitem>View</guimenuitem>
158                <guimenuitem>Reporters</guimenuitem>
159              </menuchoice>
160              respectively and start the import from there. You can read more about data-import in
161              <xref linkend="import_data" />
162            </para>
163          </listitem>
164        </orderedlist>
165      </sect3>
166      <sect3 id="userdoc_overview.start2work.getgoing.user">
167        <title>User tasks</title>
168        <para> 
169          A normal user is not allowed to add array design, reporter information, and a lot of
170          other information to BASE. The reason for this is that a lot of information should only exist
171          as one copy in the database. For example, reporters should only exist in one copy because
172          everyone uses the same reporters. There is no need to store several copies of the same array
173          design.
174        </para>
175        <para> 
176          A user will normally upload experimental data to BASE for import into the database. To be
177          able to import the data, the array design which is used, must be available in BASE at import
178          time. If the array design is not available, a user with the proper credential must add the
179          array design to BASE.
180        </para>
181        <orderedlist>
182          <listitem>
183            <para>
184              The first thing for an user to do is creating a project to work in and set this as
185              <prompt>active project</prompt>
186              . This should be done before any other items are created.
187              <xref linkend="project_permission.projects" />
188              tell you more how working in project can help you and your co-workers.
189            </para>
190          </listitem>
191          <listitem>
192            <para>
193              Next step is to create raw bioassays and up-load raw data to BASE. This is done in the raw
194              bioassay section.(
195              <menuchoice>
196                <guimenuitem>View</guimenuitem>
197                <guimenuitem>Raw bioassays</guimenuitem>
198              </menuchoice>
199              ) . More information see
200              <xref linkend="experiments_analysis.rawbioassay" />
201            </para>
202          </listitem>
203          <listitem>
204            <para>
205              Now when there are data to work with, you can create your first experiment. You reach the
206              experiment section through the menu
207              <menuchoice>
208                <guimenuitem>View</guimenuitem>
209                <guimenuitem>Experiments</guimenuitem>
210              </menuchoice>
211              Further reading in
212              <xref linkend="experiments_analysis.experiments" />
213            </para>
214          </listitem>
215          <listitem>
216            <orderedlist>
217              <listitem>
218                <para>
219                  The analysis often starts with the creation of a root bioassay set. Open the recently
220                  created experiment and go to the
221                  <guilabel>Bioassay sets</guilabel>
222                  tab. Click on the
223                  <guibutton>New root bioassay set</guibutton>
224                  button to start the creation.
225                </para>
226              </listitem>
227              <listitem>
228                <para>
229                  With a root bioassay set you can now continue your analysis with different kinds of
230                  analysis plug-in. To the right of the each listed bioassay set is a set of icons for the
231                  actions that can be performed.
232                  <xref linkend="experiments_analysis.analysis" />
233                  goes to the bottom of analysis in BASE.
234                </para>
235              </listitem>
236            </orderedlist>
237          </listitem>
238        </orderedlist>
239        <para> 
240          This concludes the short step-by-step get going text. Far from all functionality in BASE
241          has been covered here. E.g. nothing about LIMS or biomaterials have been mentioned. But you
242          should now at least be familiar with getting to that point when it is possible to do some
243          analysis.
244        </para>
245      </sect3>
246    </sect2>
247  </sect1>
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