Changeset 3782

Sep 25, 2007, 2:28:03 PM (16 years ago)
Martin Svensson

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

1 edited


  • trunk/doc/src/docbook/userdoc/userdoc_overview.xml

    r3766 r3782  
    66  $Id$
    88  Copyright (C) 2007 Nicklas Nordborg, Martin Svensson
    1010  This file is part of BASE - BioArray Software Environment.
    1111  Available at
    1313  BASE is free software; you can redistribute it and/or
    1414  modify it under the terms of the GNU General Public License
    1515  as published by the Free Software Foundation; either version 2
    1616  of the License, or (at your option) any later version.
    1818  BASE is distributed in the hope that it will be useful,
    1919  but WITHOUT ANY WARRANTY; without even the implied warranty of
    2121  GNU General Public License for more details.
    2323  You should have received a copy of the GNU General Public License
    2424  along with this program; if not, write to the Free Software
    3030  <?dbhtml dir="userdoc_overview"?>
    3131  <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>
    3243    <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.
    3448    </para>
    35     <sect1 id="userdoc_overview.environment">
    36       <title>Working environment</title>
    37       <para></para>
    38     </sect1>
     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>
    40     <sect1 id="userdoc_overview.think_base">
    41       <title>How to think like BASE</title>
    42       <para></para>
    43     </sect1>
    45     <sect1 id="userdoc_overview.start2work">
    46       <title>Start working with BASE</title>
    47       <para></para>
    48     </sect1>
     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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