source: trunk/doc/src/docbook/userdoc/userdoc_overview.xml @ 3782

Last change on this file since 3782 was 3782, checked in by Martin Svensson, 15 years ago

References #524 Mostly done, will read it one more time and correct misspellings before closing

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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: userdoc_overview.xml 3782 2007-09-25 12:28:03Z martin $
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">
30  <?dbhtml dir="userdoc_overview"?>
31  <title>Overview of user documentation</title>
32  <para>
33    This part of the documentation 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. In other words it is possible to find anything a normal user wants to
36    know about BASE. The intention with this first 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>
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 handy to
45      get to know the environment and perhaps personalize some behavior and appearance of the
46      program. When this is done your daily work in BASE will be much easier and you will feel
47      more comfortable working with the program.
48    </para>
50    <para>
51      Most of the things that have to do with the working environment are gathered in one
52      chapter,
53      <xref linkend="webclient" />
54      where the first subsection,
55      <xref linkend="webclient.introduction" />
56      , gives a good guidance how to start using BASE including a general explanation
57      how to navigate your way through the program.
58    </para>
60    <para>
61      The second subsection,
62      <xref linkend="webclient.configuration" />
63      , describes how to personlize BASE with contact information, preferences and changing
64      password. The preferences are for instance some appearance like date-format, text-size
65      or the look of buttons in the toolbar.
66    </para>
68    <para>
69      The last two subsections in the webclient chapter explain how to work with items in
70      BASE. Things explained here are general in BASE and give e.g information about item
71      lists and in which ways they can be adjusted to become easier to overlook. Here is also
72      described the general way of working with a single item, like creating, editing and
73      deleting. Each item type has also a section of it's own later in this part, where more
74      detailed information can be found.
75    </para>
76  </sect1>
78  <sect1 id="userdoc_overview.think_base">
79    <title>How to think like BASE</title>
80    <para>
81      There are some working principles that need to be understood by all users in BASE. These
82      are about the permission system and how to get the workflow to move on without any
83      disturbance caused by insufficient permission. The key is to work in projects, that and
84      the permission system are covered in
85      <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      simpliar for you to work in BASE but also for your colleagues who needs access to your
90      items when you are working together.
91    </para>
92  </sect1>
94  <sect1 id="userdoc_overview.start2work">
95    <title>Start working with BASE</title>
96    <para>
97      The first thing to do in BASE, to get started with your work, is to put in some relevant
98      data to work with. Most of the different items are created in the same way, but some
99      items and data must be imported from files. The files to import from have to be on the
100      BASE-server's file system.
101      <xref linkend="file_system" />
102      explains how the server's file system works and how to upload the files.
103    </para>
105    <para>
106      In most cases it's not enough to just keep the data in files on the server. To be able
107      to use the data it has to be imported into the database.
108      <xref linkend="import_export" />
109      explains how this is done . This chapter also covers how the data later on are exported
110      from the database back into files, often simple text or xml files.
111    </para>
112  </sect1>
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