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  Copyright (C) 2008 Jari Häkkinen

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<chapter id="features" chunked="0">
  <?dbhtml filename="features.html"?>
  <title>BASE features</title>

  <para>
    This chapter will explain the important features of BASE.
  </para>

  <sect1 id="features.supportedarrays">
    <title>Supported array platforms and raw data formats</title>

    <para>
      BASE supports many different vendor specific and custom printing
      microarray platforms and data formats, there are even users that
      use BASE for protein arrays. For 2 channel array platforms it is
      straightforward to customize BASE for a specific array platform,
      the platform simply needs to be adapted to the (BASE) Generic
      platform. The adaptation is to create a raw data format
      definition and to configure raw data importers, or make use of
      already available raw data formats. However, it is not always
      possible to make an natural mapping of a platform to the Generic
      platform. Platforms such as Affymetrix and Illumina platforms
      cannot naturally be mapped on to the Generic 2 channel
      platform. For Affymetrix, BASE comes with a specific Affymetrix
      platform and Illumina can be supported by customizing BASE.
    </para>

    <para>
      How to adapt new array platforms to the Generic platform format
      or how to create a new platform type in BASE can be read
      elsewhere in this document. Here we list different array
      platforms used in BASE and also list raw data types supported
      by BASE. However, not all platforms nor raw data types listed
      below are available out-of-the box and a BASE administrator must
      customize his local BASE installation for their specific
      need. What comes pre-configured when BASE is installed is
      indicated in the lists below.
    </para>

    <sect2 id="features.supportedarrays.platforms">
      <title>Vendor specific and custom printing array
      platforms</title>

      <para>
        Not all array platforms listed below are available by
        default. The comments to specific platforms explain how to
        enable the use of the array platform in BASE. In some cases
        there is no confirmed usage of a platform but we believe it
        has been tested by anonymous users.
      </para>

      <variablelist>
        <varlistentry>
          <term>Affymetrix</term>
          <listitem>
            <para>
              The Affymetrix platform comes pre-configured with a
              new BASE installation. Affymetrix platform in this
              context are the Affymetrix expression arrays. So far
              there has been no reason for expanding the Array
              platform to other chip-types. In principle any
              Affymetrix chip type can be stored in BASE but current
              plug-ins will always assume that expression data is
              stored and analyzed. This can be resolved by adding
              variants of the Affymetrix platform but the Lund BASE
              team currently has no plans to create Affymetrix
              variants.
            </para>
          </listitem>
        </varlistentry>

        <varlistentry>
          <term>Agilent</term>
          <listitem>
            <para>
            </para>
          </listitem>
        </varlistentry>

        <varlistentry>
          <term>Custom printing</term>
          <listitem>
            <para>
              The array layout options are endless and imagination is
              the only limitation ... almost. BASE can import many
              in-house array designs and platforms. The custom arrays
              usually fall back on one of the raw data types already
              available such as GenePix.
            </para>
          </listitem>
        </varlistentry>

        <varlistentry>
          <term>Illumina</term>
          <listitem>
            <para>
              There are several variants of the Illumina platform. Using
              several variants allows BASE to adapt its handling of
              different Illumina chip types. Illumina platform support
              is not included in a standard BASE installation but there
              is
              a <ulink url="http://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina">
                Illumina plug-in</ulink> available for seamless
              integration of the Illumina array platform to BASE.
            </para>
          </listitem>
        </varlistentry>

        <varlistentry>
          <term>ImaGene</term>
          <listitem>
            <para>
              No successful use confirmed but ImaGene raw data is
              available in BASE.
            </para>
          </listitem>
        </varlistentry>

        <varlistentry>
          <term>Unlisted</term>
          <listitem>
            <para>
              In principle any platform generating a matrix of data can
              be imported into BASE. Simply utilize the available raw
              data formats and data importers.
            </para>
          </listitem>
        </varlistentry>
      </variablelist>

    </sect2>

    <sect2 id="features.supportedarrays.rawdatatypes">
      <title>Available raw data types</title>

      <para>
        Raw data comes in many different formats. These formats are
        usually defined by scanner software vendors and BASE must keep
        track of the different formats for analysis and plotting. BASE
        supports many formats out the box, but some formats need to
        be added manually by the BASE administrator (indicated in the
        list below).
      </para>

      <variablelist>

        <varlistentry>
          <term>Affymetrix</term>
          <listitem>
            <para>
            </para>
          </listitem>
        </varlistentry>

        <varlistentry>
          <term>AIDA</term>
          <listitem>
            <para>
            </para>
          </listitem>
        </varlistentry>

        <varlistentry>
          <term>Agilent</term>
          <listitem>
            <para>
            </para>
          </listitem>
        </varlistentry>

        <varlistentry>
          <term>BZScan</term>
          <listitem>
            <para>
            </para>
          </listitem>
        </varlistentry>

        <varlistentry>
          <term>ChipSkipper</term>
          <listitem>
            <para>
            </para>
          </listitem>
        </varlistentry>

        <varlistentry>
          <term>GenePix</term>
          <listitem>
            <para>
            </para>
          </listitem>
        </varlistentry>

        <varlistentry>
          <term>GeneTAC</term>
          <listitem>
            <para>
            </para>
          </listitem>
        </varlistentry>

        <varlistentry>
          <term>Illumina</term>
          <listitem>
            <para>
              The Illumina array platform usage is recommended to be
              based on the <emphasis>Illumina Bead Summary
              (IBS)</emphasis> raw data format below.
            </para>
          </listitem>
        </varlistentry>

        <varlistentry>
          <term>Illumina Bead Summary (IBS)</term>
          <listitem>
            <para>
              Not available in BASE directly but it is added with
              the <ulink url="http://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina">
              Illumina plug-in</ulink> that adds Illumina array
              platform support to BASE.
            </para>
          </listitem>
        </varlistentry>

        <varlistentry>
          <term>ImaGene</term>
          <listitem>
            <para>
            </para>
          </listitem>
        </varlistentry>

        <varlistentry>
          <term>QuantArray Biotin</term>
          <listitem>
            <para>
            </para>
          </listitem>
        </varlistentry>

        <varlistentry>
          <term>QuantArray Cy</term>
          <listitem>
          <para>
          </para>
          </listitem>
        </varlistentry>

        <varlistentry>
          <term>SpotFinder</term>
          <listitem>
            <para>
            </para>
          </listitem>
        </varlistentry>

      </variablelist>

    </sect2>

  </sect1>

</chapter>