Changeset 4395


Ignore:
Timestamp:
Aug 15, 2008, 1:10:59 PM (14 years ago)
Author:
Martin Svensson
Message:

References #725 Transferred the getting_started document to docbook format and added to the user section in the documentation. Moved the old getting_started' file to the historical folder

Location:
trunk/doc
Files:
2 edited
1 moved

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

    r3892 r4395  
    33    "-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN"
    44    "../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd">
    5 <!--
    6   $Id$
    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 
     5  <!--
     6    $Id$ Copyright (C) 2007 Nicklas Nordborg, Martin
     7    Svensson This file is part of BASE - BioArray Software Environment. Available at
     8    http://base.thep.lu.se/ BASE is free software; you can redistribute it and/or modify it under the
     9    terms of the GNU General Public License as published by the Free Software Foundation; either
     10    version 2 of the License, or (at your option) any later version. BASE is distributed in the hope
     11    that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
     12    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
     13    details. You should have received a copy of the GNU General Public License along with this
     14    program; if not, write to the Free Software Foundation, Inc., 59 Temple Place - Suite 330, Boston,
     15    MA 02111-1307, USA.
     16  -->
    2917<chapter id="userdoc_overview" chunked="0">
    3018  <?dbhtml dir="overview"?>
    3119  <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>
    39 
     20  <para> The 'User documentation' part is quite extensive and covers everything from how to login on
     21    a BASE2 server and find your way through the program, to working with experiments and doing some
     22    useful analysis. The intention with this chapter is to give an overview of the following chapters
     23    so it will be easier for you to know where to look for certain information in case you don't want
     24    to read the whole part from the beginning to the end.</para>
    4025  <sect1 id="userdoc_overview.environment">
    4126    <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>
    48 
    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>
    56 
     27    <para> Before you start working with any big experiment or project in BASE it could be a good idea
     28      to get to know the environment and perhaps personalize some behavior and appearance of the
     29      program. When this is done your daily work in BASE will be much easier and you will feel more
     30      comfortable working with the program.</para>
     31    <para>
     32      Most of the things that have to do with the working environment are gathered in one chapter,
     33      where the first subsection,
     34      <xref linkend="webclient.introduction" />
     35      , gives a good guidance how to start using BASE including a general explanation how to navigate
     36      your way through the program.
     37    </para>
    5738    <para>
    5839      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>
    64 
     40      <xref linkend="webclient.configuration" />
     41      , describes how to personlize BASE with contact information, preferences and changing password.
     42      The preferences are for instance some appearance like date format, text size or the look of the
     43      toolbar buttons.
     44    </para>
    6545    <para>
    6646      The last two subsections,
    6747      <xref linkend="webclient.items" />
    6848      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.
     49      <xref linkend="webclient.itemlist" />
     50      , in the webclient chapter explains how to work with BASE. No matter what you are going to do the
     51      user interface contains a lot of common functions that works the same everywhere. For example,
     52      how to list and search for items, how to create new items and modify and delete existing items.
     53      Subsequent chapters with detailed information about each type of item will usually not include
     54      descriptions of the common functionality.
    7655    </para>
    7756  </sect1>
    78 
    7957  <sect1 id="userdoc_overview.start2work">
    8058    <title>Start working with BASE</title>
    8159    <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.
     60      There are some working principles that need to be understood by all users in BASE. These concern
     61      the permission system and how to get the workflow to move on without any disturbance caused by
     62      insufficient permissions. The key is to work in projects, which is covered in detail in
     63      <xref linkend="project_permission" />
     64      .
     65    </para>
     66    <para>
     67      Understanding the permission system and how to work in projects will not only make it more
     68      simple for you to work in BASE but also for your co-workers who want access to your data.
     69    </para>
     70    <para>
     71      The next thing to do is to add some relevant data to work with. Most of the different items can
     72      be created manually from the web client, but some items and data must be imported from files.
     73      Before importing a file, it has to be uploaded on the BASE-server's filesystem.
    9774      <xref linkend="file_system" />
    9875      gives you information about the server's file system and how to upload the files.
    9976    </para>
    100 
    101     <para>
     77    <para>
     78      <xref linkend="import_export_data" />
     79      explains how the import is done. This chapter also covers how the data later on can be exported
     80      from the database back into files, often simple text files or xml files.
     81    </para>
     82    <para>
     83      Each different item has it's own section in this part of the documentation, where more
     84      specific information and also some screen shots can be found. Go back to the table of contents
     85      for this part and look up the item you want to know more about.
     86    </para>
     87   
     88   
     89    <sect2 id="userdoc_overview.start2work.getgoing">
     90      <title>Get going</title>
     91      <para>
     92        This description will guide you from the initiating tasks of creating the first account to
     93        running an analysis plug-in. Most of the steps below ends with a reference to somewhere in the
     94        documentation where more information can be found.
     95      </para>
    10296     
    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>
    107    
    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>
     97      <sect3 id="userdoc_overview.start2work.getgoing.administrative">
     98        <title>Administrative tasks</title>
     99        <para>
     100          Most of the tasks in this section require more privileges than the normal user
     101          credentials. As always, there are many ways to do things so steps presented here is the path
     102          to get going with BASE as fast as possible without creating havoc in future use of the BASE
     103          server.
     104        </para>
     105        <orderedlist>
     106          <listitem>
     107            <para>
     108              Log in as
     109              <prompt>root</prompt>
     110              using the password you set during BASE initialization. Create an account and give it the
     111              administrator-role. Switch user to the new admin account and use this for all future
     112              administrative tasks.
     113            </para>
     114            <note>
     115              <para>
     116                The root-account should only be used to create the first administrator account and
     117                nothing else.
     118              </para>
     119            </note>
     120          </listitem>
     121          <listitem>
     122            <para>
     123              First thing to do, when logged in as administrator, is to create other user-accounts
     124              and give them appropriate roles, most of them should be assigned to the User-role.
     125            </para>
     126            <para>
     127              Information related to user-accounts can be found at
     128              <xref linkend="user_administration" />
     129              .
     130            </para>
     131          </listitem>
     132          <listitem>
     133            <para>
     134              Next step for you as an administrator is to import reporter-map and corresponding reporters
     135              to BASE. For import of Genepix data you can use the
     136              <prompt>Reporter importer</prompt>
     137              plug-in and
     138              <prompt>Reporter map importer</prompt>
     139              plug-in that come with BASE. Go to
     140              <menuchoice>
     141                <guimenuitem>Array LIMS</guimenuitem>
     142                <guimenuitem>Array designs</guimenuitem>
     143              </menuchoice>
     144              or
     145              <menuchoice>
     146                <guimenuitem>View</guimenuitem>
     147                <guimenuitem>Reporters</guimenuitem>
     148              </menuchoice>
     149              respectively and start the import from there. You can read more about data-import in
     150              <xref linkend="import_export_data" />
     151            </para>
     152          </listitem>
     153        </orderedlist>
     154      </sect3>
     155      <sect3 id="userdoc_overview.start2work.getgoing.user">
     156        <title>User tasks</title>
     157        <para>
     158          A normal user is not allowed to add array design, reporter information, and a lot of
     159          other information to BASE. The reason for this is that a lot of information should only exist
     160          as one copy in the database. For example, reporters should only exist in one copy because
     161          everyone uses the same reporters. There is no need to store several copies of the same array
     162          design.
     163        </para>
     164        <para>
     165          A user will normally upload experimental data to BASE for import into the database. To be
     166          able to import the data, the array design which is used, must be available in BASE at import
     167          time. If the array design is not available, a user with the proper credential must add the
     168          array design to BASE.
     169        </para>
     170        <orderedlist>
     171          <listitem>
     172            <para>
     173              The first thing for an user to do is creating a project to work in and set this as
     174              <prompt>active project</prompt>
     175              . This should be done before any other items are created.
     176              <xref linkend="project_permission.projects" />
     177              tell you more how working in project can help you and your co-workers.
     178            </para>
     179          </listitem>
     180          <listitem>
     181            <para>
     182              Next step is to create raw bioassays and up-load raw data to BASE. This is done in the raw
     183              bioassay section.(
     184              <menuchoice>
     185                <guimenuitem>View</guimenuitem>
     186                <guimenuitem>Raw bioassays</guimenuitem>
     187              </menuchoice>
     188              ) . More information see
     189              <xref linkend="experiments_analysis.rawbioassay" />
     190            </para>
     191          </listitem>
     192          <listitem>
     193            <para>
     194              Now when there are data to work with, you can create your first experiment. You reach the
     195              experiment section through the menu
     196              <menuchoice>
     197                <guimenuitem>View</guimenuitem>
     198                <guimenuitem>Experiments</guimenuitem>
     199              </menuchoice>
     200              Further reading in
     201              <xref linkend="experiments_analysis.experiments" />
     202            </para>
     203          </listitem>
     204          <listitem>
     205            <orderedlist>
     206              <listitem>
     207                <para>
     208                  The analysis often starts with the creation of a root bioassay set. Open the recently
     209                  created experiment and go to the
     210                  <guilabel>Bioassay sets</guilabel>
     211                  tab. Click on the
     212                  <guibutton>New root bioassay set</guibutton>
     213                  button to start the creation.
     214                </para>
     215              </listitem>
     216              <listitem>
     217                <para>
     218                  With a root bioassay set you can now continue your analysis with different kinds of
     219                  analysis plug-in. To the right of the each listed bioassay set is a set of icons for the
     220                  actions that can be performed.
     221                  <xref linkend="experiments_analysis.analysis" />
     222                  goes to the bottom of analysis in BASE.
     223                </para>
     224              </listitem>
     225            </orderedlist>
     226          </listitem>
     227        </orderedlist>
     228        <para>
     229          This concludes the short step-by-step get going text. Far from all functionallity in BASE
     230          has been convered here. E.g. nothing about LIMS or biomaterials have been mentioned. But you
     231          should now at least be familiar with getting to that point when it is possible to do some
     232          analysis.
     233        </para>
     234      </sect3>
     235    </sect2>
    113236  </sect1>
    114237</chapter>
  • trunk/doc/test/index.html

    r4394 r4395  
    5656  <ol>
    5757  <li><a href="performance/index.html">Performance tests</a>:
    58     Test one item/aspect at a time</li>
     58    Test the performance of BASE</li>
    5959  <li><a href="roles/index.html">Roles</a>: Big test for checking that the predefined
    6060    roles has correct permissions and can do their work as intended. This test goes
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