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  Copyright (C) 2007 Martin Svensson, Jari Häkkinen
  Copyright (C) 2008 Jari Häkkinen
  Copyright (C) 2011 Jari Häkkinen, Nicklas Nordborg

  This file is part of BASE - BioArray Software Environment.
  Available at http://base.thep.lu.se/

  BASE is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License
  as published by the Free Software Foundation; either version 3
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  but WITHOUT ANY WARRANTY; without even the implied warranty of
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<chapter id="why_base" chunked="0">
  <?dbhtml filename="why_base.html"?>
  <title>Why use BASE</title>

  <para>
    BASE was initially developed to manage array-based data but is now
    extended to support storage and analysis of sequencing data. The
    first sequencing application is RNAseq.
  </para>

  <para>
    We outline two different uses of BASE to give a flavour why you
    should consider to use BASE. The first example describes a
    research project involving sequencing based gene expression
    analysis and the second example describes a microarray service
    facility use of BASE.
  </para>

  <sect1 id="whybase.scanb">
    <title>Case I: The SCAN-B BASE installation at Department of
    Oncology, Lund University</title>

    <para>
      <ulink
      url='http://www.med.lu.se/english/klinvetlund/canceromics/consortia/scan_b'>SCAN-B</ulink>
      is a project and network of researchers and clinicians that was
      initialised in the fall 2009. The project is centred on a
      prospective study where all new breast cancer patients in
      southern Sweden are asked to enrol. Within the covered region
      approximately 1500 patients are diagnosed with breast cancer
      annually. The overall aim is to continuously collect and analyse
      the consecutive, population-based, breast cancer
      cohort. Analyses include generation of gene expression and
      sequencing data with the ultimate goal to build an
      infrastructure for future real-time clinical implementation.
    </para>

    <para>
      SCAN-B uses BASE to store and manage all information related to
      enrolled patients and collected sample material including
      clinical information and experimental data. Analysis and
      execution of standard analysis pipelines for sequencing data
      will be performed through BASE.
    </para>

    <para>
      The SCAN-B BASE installation consists of three main parts;
      first, the hardware on which the system runs; secondly, the BASE
      software and database, as well as configured analysis plugins;
      thirdly, an external file system for storage of sequencing data
      that are referenced from BASE. In addition, maintenance of the
      hardware and configured database/software is required. The
      server hardware comprises one main computer and raided hard
      drive system. It also includes a backup solution configured to
      backup the entire database 2 times per week. Computational nodes
      are connected to the main computer and used to run configured
      analysis plugins in a seamless integrated fashion. Maintenance
      includes managing the backup-schedule, updating the main BASE
      software, developing, configuring, and maintaining analysis
      plugins, and maintaining the underlying database and external
      storage file systems.
    </para>

    <para>
      Whereas the BASE software itself is freely available to anyone,
      a particular BASE installation at a research site is in general
      not freely accessible. Although BASE can be downloaded and
      installed on a regular of-the-shelf personal computer with
      relative ease by anyone, considerable effort and costs are
      associated with maintaining a BASE installation of the size and
      scope of the SCAN-B BASE installation. A pristine BASE
      installation includes generic features and functionality to
      support a framework of procedures to manage data collection in
      large projects. Within SCAN-B large effort is spent on defining
      the required procedures where laboratory work is mirrored in
      BASE. This implies interplay with adopting the BASE software
      (the <ulink
      url='http://baseplugins.thep.lu.se/wiki/net.sf.basedb.reggie'>Reggie
      extension</ulink> is an example of adaptation on BASE to
      specific needs in SCAN-B) and the laboratory work to achieve
      efficient data collection. To achieve high quality data
      production, measures for continuous quality assurance and
      collection of data associated with patients, samples, and
      laboratory processing must also be implemented.
    </para>

  </sect1>


  <sect1 id="whybase.sciblu">
    <title>Case II: The BASE installation at SCIBLU, Department of
    Oncology, Lund University</title>

    <para>
      In the spring of 2004, Lund University created Swegene Centre
      for Integrative Biology at Lund University (<ulink
      href='http://www.lth.se/sciblu'>SCIBLU</ulink>), which comprise
      the merger of five of the most successful Swegene resource and
      development platforms into one unit, located in the Lund
      University Biomedical Centre (BMC). SCIBLU offers integrated
      service within the main -omics areas. The DNA microarray
      technology within SCIBLU was initially established in 2000 as a
      cancer research resource at the department of Oncology and in
      conjunction with this the development of BASE was initiated.
    </para>

    <para>
      At SCIBLU a BASE installation is maintained and used as a
      production installation that manages information surrounding
      array fabrication (array LIMS) as well as array data generated
      by the SCIBLU provided services. This particular BASE
      installation was initially set up in 2003 and to date manage
      array data from more than 13 000 hybridisation covering a
      variety of technical platforms such as cDNA, oligo, and BeadChip
      expression arrays, as well as BAC and oligo aCGH arrays.
    </para>

    <para>
      The SCIBLU BASE installation consists of two main parts; first,
      the hardware on which the system runs; secondly, the BASE
      software and database, as well as configured analysis plugins.
      Regular maintenance of the hardware and configured
      database/software is also required. The hardware comprises one
      main computer and raided hard drive system. It also includes a
      backup solution configured to backup the entire database 2 times
      per week. Finally, the hardware includes 2 computational servers
      connected to the main computer and used to run configured
      analysis plugins in a seamless integrated fashion. The software
      used for the SCIBLU BASE installation is freely available from
      the BASE project site. Maintenance include managing the
      backup-schedule, updating the main BASE software, updating and
      managing probe annotations, management of user accounts,
      configuring and maintaining analysis plugins, and maintaining
      the underlying database.
    </para>

    <para>
      Users of the microarray services offered by SCIBLU, e.g.,
      expression analysis or aCGH, are provided access to the SCIBLU
      production BASE installation as part of the included
      services. The access comprises user account, access to array
      LIMS (when in-house produced arrays are utilised), and hard
      drive space to cover space needed for storing the data generated
      through the SCIBLU provided service. Additional disk space can
      be acquired and is associated with an additional cost for the
      user. Examples of when additional disk space is needed include
      scenarios where users want to perform extensive data analysis
      within BASE and decide to store the analysis results within
      BASE, e.g., many parallel analysis branches or extensive
      generation of data plots and figures. Other examples include
      when users want to import data from third party providers
      (public data repositories or alternative array data providers)
      to perform meta-analysis with their data generated within
      SCIBLU.
    </para>

  </sect1>
      
</chapter>