source: trunk/doc/src/docbook/userdoc/overview.xml @ 3892

Last change on this file since 3892 was 3892, checked in by Nicklas Nordborg, 14 years ago

Fixes #524: Read "Overview of user documentation" section

  • Property svn:eol-style set to native
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File size: 4.8 KB
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 3892 2007-10-30 13:33:19Z nicklas $
8  Copyright (C) 2007 Nicklas Nordborg, Martin Svensson
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 2
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 this program; if not, write to the Free Software
25  Foundation, Inc., 59 Temple Place - Suite 330,
26  Boston, MA  02111-1307, USA.
29<chapter id="userdoc_overview" chunked="0">
30  <?dbhtml dir="overview"?>
31  <title>Overview of user documentation</title>
32  <para>
33    The 'User documentation' part is quite extensive and covers everything from how to login on a
34    BASE2 server and find your way through the program, to working with experiments and doing
35    some useful analysis. The intention with this chapter is to give an overview of the
36    following chapters so it will be easier for you to know where to look for certain
37    information in case you don't want to read the whole part from the beginning to the end.
38  </para>
40  <sect1 id="userdoc_overview.environment">
41    <title>Working environment</title>
42    <para>
43      Before you start working with any big experiment or project in BASE it could be a good
44      idea to get to know the environment and perhaps personalize some behavior and appearance
45      of the program. When this is done your daily work in BASE will be much easier and you
46      will feel more comfortable working with the program.
47    </para>
49    <para>
50      Most of the things that have to do with the working environment are gathered in one
51      chapter, where the first subsection,
52      <xref linkend="webclient.introduction" />,
53      gives a good guidance how to start using BASE including a general explanation
54      how to navigate your way through the program.
55    </para>
57    <para>
58      The second subsection,
59      <xref linkend="webclient.configuration" />,
60      describes how to personlize BASE with contact information, preferences and changing
61      password. The preferences are for instance some appearance like date format, text size
62      or the look of the toolbar buttons.
63    </para>
65    <para>
66      The last two subsections,
67      <xref linkend="webclient.items" />
68      and
69      <xref linkend="webclient.itemlist" />,
70      in the webclient chapter explains how to work with BASE. No matter what you
71      are going to do the user interface contains a lot of common functions that
72      works the same everywhere. For example, how to list and search for items,
73      how to create new items and modify and delete existing items. Subsequent
74      chapters with detailed information about each type of item will usually
75      not include descriptions of the common functionality.
76    </para>
77  </sect1>
79  <sect1 id="userdoc_overview.start2work">
80    <title>Start working with BASE</title>
81    <para>
82      There are some working principles that need to be understood by all users in BASE. These
83      concern the permission system and how to get the workflow to move on without any
84      disturbance caused by insufficient permissions. The key is to work in projects, which
85      is covered in detail in <xref linkend="project_permission" />.
86    </para>
87    <para>
88      Understanding the permission system and how to work in projects will not only make it
89      more simple for you to work in BASE but also for your co-workers who want access to your
90      data.
91    </para>
92    <para>
93      The next thing to do is to add some relevant
94      data to work with. Most of the different items can be created manually from the
95      web client, but some items and data must be imported from files. Before importing a file,
96      it has to be uploaded on the BASE-server's filesystem.
97      <xref linkend="file_system" />
98      gives you information about the server's file system and how to upload the files.
99    </para>
101    <para>
103      <xref linkend="import_export_data" />
104      explains how the import is done. This chapter also covers how the data later on
105      can be exported from the database back into files, often simple text files or xml files.
106    </para>
108    <para>
109      Each different item has it's own section in this part of the documentation, where more specific
110      information and also some screen shots can be found. Go back to the table
111      of contents for this part and look up the item you want to know more about.
112    </para>
113  </sect1>
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