Ignore:
Timestamp:
Aug 20, 2008, 3:58:58 PM (14 years ago)
Author:
Jari Häkkinen
Message:

Improved text and minor change to section order.

File:
1 edited

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

    r4131 r4401  
    77 
    88  Copyright (C) 2007 Nicklas Nordborg, Philippe Rocca-Serra, Martin Svensson
     9  Copyright (C) 2007 Jari Hakkinen, Nicklas Nordborg
    910 
    1011  This file is part of BASE - BioArray Software Environment.
    … …  
    2728-->
    2829
    29 <chapter id="array_lims">
     30<chapter id="array_lims" chunked="0">
    3031  <?dbhtml dir="array_lims"?>
    3132  <title>Array LIMS</title>
    32   <sect1 id="array_lims.introduction">
    33     <title>Introduction</title>
    34     <para>
    35       Arrays are at the core of the BASE2 business and are essential elements to describe in
    36       order to be MIAME compliant. It is also critical to track and manage information about
    37       microarray design as accurately as possible since mistakes could prove extremely costly
    38       in downstream analysis.
    39     </para>
    40     <para>
    41       Finally, as a good practice, all array related information should be entered into BASE2
    42       system prior to start describing the sample processing and hybridizations events making
    43       up a microarray experiment.
    44     </para>
    45 
    46     <para>
    47       BASE2 has been engineered to support microarray printing facilities. The system
    48       therefore offers objects to describe plates, their geometries and the events (merging,
    49       printing) affected them. The first section of the chapter deals with this functionality.
    50       as well as plate management.
    51     </para>
    52 
    53     <para>
    54       For users buying their arrays from commercial sources, the plate management component
    55       can be ignored and they can go immediately to
    56       <xref linkend="array_lims.arraydesign" />.
    57     </para>
    58 
    59   </sect1>
     33
     34  <para>
     35    Arrays are at the core of the BASE business and are essential
     36    elements to describe in order to
     37    be <ulink url='http://www.mged.org/Workgroups/MIAME/miame.html'>MIAME</ulink>
     38    compliant. It is also critical to track and manage information
     39    about microarray design as accurately as possible since mistakes
     40    could prove extremely costly in downstream analysis.
     41  </para>
     42  <para>
     43    As a good practice, all array related information should be
     44    entered into BASE prior to work on describing the sample
     45    processing and hybridizations events making up a microarray
     46    experiment is begun.
     47  </para>
     48  <para>
     49    BASE is engineered to support microarray printing facilities. The
     50    system therefore offers objects to describe plates, their
     51    geometries, and the events (<emphasis>e.g.</emphasis>, merging and
     52    printing) affecting them. The first section of this chapter deals
     53    with this functionality as well as plate management. Users buying
     54    arrays from commercial sources can ignore the plate management
     55    component and immediately jump to
     56    <xref linkend="array_lims.arraydesign" />.
     57  </para>
    6058
    6159  <sect1 id="array_lims.platemanagement">
    … …  
    7270      may run out leading to the interruption of this process. All slides created during this
    7371      printing process belong to the same printing batch. It is the array slide that will
    74       eventually be used in a hybridization event. BASE2 allows user to track those 3 entities
     72      eventually be used in a hybridization event. BASE allows user to track those 3 entities
    7573      with great details. This is an important functionality for users producing their own
    7674      arrays and for those caring for quality control and tracking of microarray slides in a
    77       printing facility. The following sections detail how to use BASE2 to help in these
     75      printing facility. The following sections detail how to use BASE to help in these
    7876      tasks.
    7977    </para>
    … …  
    148146        </variablelist>
    149147        <para>
    150           Click on the &gbSave; button to store the information in BASE2 or on the
     148          Click on the &gbSave; button to store the information in BASE or on the
    151149          &gbCancel; button to abort.
    152150        </para>
    … …  
    175173
    176174      <para>
    177         Importing features is an important step in
    178         order to fully define an array design. It should be noted that BASE2 does not
    179         enforce the immediate feature import upon creation of array design. However, it
    180         is STRONGLY advised to do so when creating an array design. Doing so enables to
    181         use the array design for downstream analysis with no further trouble. It also
    182         matters when importing raw bioassay data and matching those to the corresponding
    183         array design.
     175        Importing features is an important step in order to fully
     176        define an array design. It should be noted that BASE does not
     177        enforce the immediate feature import upon creation of array
     178        design. However, it is STRONGLY advised to do so when creating
     179        an array design. Performing the import enables use of the
     180        array design in downstream analysis with no further
     181        trouble. It also matters when importing raw bioassay data and
     182        matching those to the corresponding array design.
    184183      </para>
    185184
    … …  
    313312      </variablelist>
    314313      <para>
    315         Click on the &gbSave; button to store the information in BASE2 or on the &gbCancel;
     314        Click on the &gbSave; button to store the information in BASE or on the &gbCancel;
    316315        button to abort.
    317316      </para>
    … …  
    341340    <sect2 id="array_lims.arrayslide.create">
    342341      <title>Creating array slides</title>
    343       <para>In BASE2, array slides can be created, except the common way, by 2 routes:</para>
     342      <para>In BASE, array slides can be created, except the common way, by 2 routes:</para>
    344343      <variablelist>
    345344        <varlistentry>
    … …  
    479478      </variablelist>
    480479      <para>
    481         Click on the &gbSave; button to store the information in BASE2 or on the &gbCancel;
     480        Click on the &gbSave; button to store the information in BASE or on the &gbCancel;
    482481        button to abort.
    483482      </para>
    … …  
    565564        </para>
    566565        <para>
    567           Click on the &gbSave; button to store the information in BASE2 or on the
     566          Click on the &gbSave; button to store the information in BASE or on the
    568567          &gbCancel; button to abort.
    569568        </para>
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