source: trunk/doc/src/docbook/userdoc/userdoc_overview.xml @ 3790

Last change on this file since 3790 was 3790, checked in by Martin Svensson, 15 years ago

References #524 Some small changes to finish the writing.

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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: userdoc_overview.xml 3790 2007-09-26 09:24:20Z martin $
7 
8  Copyright (C) 2007 Nicklas Nordborg, Martin Svensson
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="userdoc_overview">
30  <?dbhtml dir="userdoc_overview"?>
31  <title>Overview of user documentation</title>
32  <para>
33    The 'User documentation' part is quite extensive and covers all 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. It is possible to find anything a normal user wants to
36    know about BASE in this part. The intention with this chapter is to give an overview of the
37    following chapters so it will be easier for you to know where to look for certain
38    information in case you don't want to read the whole part from the beginning to the end.
39  </para>
40
41  <sect1 id="userdoc_overview.environment">
42    <title>Working environment</title>
43    <para>
44      Before you start working with any big experiment or project in BASE it could be a good
45      idea to get to know the environment and perhaps personalize some behavior and appearance
46      of the program. When this is done your daily work in BASE will be much easier and you
47      will feel more comfortable working with the program.
48    </para>
49
50    <para>
51      Most of the things that have to do with the working environment are gathered in one
52      chapter, where the first subsection,
53      <xref linkend="webclient.introduction" />
54      , gives a good guidance how to start using BASE including a general explanation
55      how to navigate your way through the program.
56    </para>
57
58    <para>
59      The second subsection,
60      <xref linkend="webclient.configuration" />
61      , describes how to personlize BASE with contact information, preferences and changing
62      password. The preferences are for instance some appearance like date-format, text-size
63      or the look of the toolbar-buttons.
64    </para>
65
66    <para>
67      The last two subsections,
68      <xref linkend="webclient.items" />
69      and
70      <xref linkend="webclient.itemlist" />
71      , in the webclient chapter explain how to work with items in BASE. Things explained here
72      are general in BASE and give e.g information about itemlists and in which ways they can
73      be adjusted to become easier to overlook. Here is also described some single item issue,
74      like creating, editing and deleting. Each item type has also a section of it's own later
75      in this part, where more detailed information can be found.
76    </para>
77  </sect1>
78
79  <sect1 id="userdoc_overview.think_base">
80    <title>How to think like 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 permission. The key is to work in projects, that and
85      the permission system are covered in
86      <xref linkend="project_permission" />
87    </para>
88    <para>
89      Understanding the permission system and how to work in projects will not only make it
90      simpliar for you to work in BASE but also for your co-workers who want access to your
91      items.
92    </para>
93  </sect1>
94
95  <sect1 id="userdoc_overview.start2work">
96    <title>Start working with BASE</title>
97    <para>
98      The first thing to do in BASE, to get started with your work, is to put in some relevant
99      data to work with. Most of the different items are created in the same way in the
100      webclient, but some items and data must be imported from files. Before importing a file,
101      it has to be uploaded on the BASE-server's filesystem.
102      <xref linkend="file_system" />
103      gives you information about the server's file system and how to upload the files.
104    </para>
105
106    <para>
107     
108      <xref linkend="import_export_data" />
109      explains then how the import is done . This chapter also covers how the data later on
110      can be exported from the database back into files, often simple text files or xml files.
111    </para>
112   
113    <para>
114      Each different item has it's own section in this part of the documentation, where more specific
115      information can be found, such as properties, they are created and so on. Go back to the table
116      of contents for this part and look up the item you want to know more about.
117    </para>
118  </sect1>
119</chapter>
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