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Timestamp:
Nov 1, 2011, 5:05:58 PM (12 years ago)
Author:
Jari Häkkinen
Message:

Fixes #522. After five years ...

File:
1 edited

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

    r5782 r5844  
    66  $Id$
    77
    8   Copyright (C) 2007 Martin Svensson
     8  Copyright (C) 2007 Martin Svensson, Jari Häkkinen
     9  Copyright (C) 2008 Jari Häkkinen
     10  Copyright (C) 2011 Jari Häkkinen, Nicklas Nordborg
    911
    1012  This file is part of BASE - BioArray Software Environment.
    … …  
    1820  BASE is distributed in the hope that it will be useful,
    1921  but WITHOUT ANY WARRANTY; without even the implied warranty of
    20   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
     22  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
    2123  GNU General Public License for more details.
    2224
    … …  
    2830  <?dbhtml filename="why_base.html"?>
    2931  <title>Why use BASE</title>
    30     <sect1 id="nolabelhereyet">
    31       <title></title>
    32       <para></para>
    33     </sect1>
     32
     33  <para>
     34    BASE was initially developed to manage array-based data but is now
     35    extended to support storage and analysis of sequencing data. The
     36    first sequencing application is RNAseq.
     37  </para>
     38
     39  <para>
     40    We outline two different uses of BASE to give a flavour why you
     41    should consider to use BASE. The first example describes a
     42    research project involving sequencing based gene expression
     43    analysis and the second example describes a microarray service
     44    facility use of BASE.
     45  </para>
     46
     47  <sect1 id="whybase.scanb">
     48    <title>Case I: The SCAN-B BASE installation at Department of
     49    Oncology, Lund University</title>
     50
     51    <para>
     52      <ulink
     53      url='http://www.med.lu.se/english/klinvetlund/canceromics/consortia/scan_b'>SCAN-B</ulink>
     54      is a project and network of researchers and clinicians that was
     55      initialised in the fall 2009. The project is centred on a
     56      prospective study where all new breast cancer patients in
     57      southern Sweden are asked to enrol. Within the covered region
     58      approximately 1500 patients are diagnosed with breast cancer
     59      annually. The overall aim is to continuously collect and analyse
     60      the consecutive, population-based, breast cancer
     61      cohort. Analyses include generation of gene expression and
     62      sequencing data with the ultimate goal to build an
     63      infrastructure for future real-time clinical implementation.
     64    </para>
     65
     66    <para>
     67      SCAN-B uses BASE to store and manage all information related to
     68      enrolled patients and collected sample material including
     69      clinical information and experimental data. Analysis and
     70      execution of standard analysis pipelines for sequencing data
     71      will be performed through BASE.
     72    </para>
     73
     74    <para>
     75      The SCAN-B BASE installation consists of three main parts;
     76      first, the hardware on which the system runs; secondly, the BASE
     77      software and database, as well as configured analysis plugins;
     78      thirdly, an external file system for storage of sequencing data
     79      that are referenced from BASE. In addition, maintenance of the
     80      hardware and configured database/software is required. The
     81      server hardware comprises one main computer and raided hard
     82      drive system. It also includes a backup solution configured to
     83      backup the entire database 2 times per week. Computational nodes
     84      are connected to the main computer and used to run configured
     85      analysis plugins in a seamless integrated fashion. Maintenance
     86      includes managing the backup-schedule, updating the main BASE
     87      software, developing, configuring, and maintaining analysis
     88      plugins, and maintaining the underlying database and external
     89      storage file systems.
     90    </para>
     91
     92    <para>
     93      Whereas the BASE software itself is freely available to anyone,
     94      a particular BASE installation at a research site is in general
     95      not freely accessible. Although BASE can be downloaded and
     96      installed on a regular of-the-shelf personal computer with
     97      relative ease by anyone, considerable effort and costs are
     98      associated with maintaining a BASE installation of the size and
     99      scope of the SCAN-B BASE installation. A pristine BASE
     100      installation includes generic features and functionality to
     101      support a framework of procedures to manage data collection in
     102      large projects. Within SCAN-B large effort is spent on defining
     103      the required procedures where laboratory work is mirrored in
     104      BASE. This implies interplay with adopting the BASE software
     105      (the <ulink
     106      url='http://baseplugins.thep.lu.se/wiki/net.sf.basedb.reggie'>Reggie
     107      extension</ulink> is an example of adaptation on BASE to
     108      specific needs in SCAN-B) and the laboratory work to achieve
     109      efficient data collection. To achieve high quality data
     110      production, measures for continuous quality assurance and
     111      collection of data associated with patients, samples, and
     112      laboratory processing must also be implemented.
     113    </para>
     114
     115  </sect1>
     116
     117
     118  <sect1 id="whybase.sciblu">
     119    <title>Case II: The BASE installation at SCIBLU, Department of
     120    Oncology, Lund University</title>
     121
     122    <para>
     123      In the spring of 2004, Lund University created Swegene Centre
     124      for Integrative Biology at Lund University (<ulink
     125      href='http://www.lth.se/sciblu'>SCIBLU</ulink>), which comprise
     126      the merger of five of the most successful Swegene resource and
     127      development platforms into one unit, located in the Lund
     128      University Biomedical Centre (BMC). SCIBLU offers integrated
     129      service within the main -omics areas. The DNA microarray
     130      technology within SCIBLU was initially established in 2000 as a
     131      cancer research resource at the department of Oncology and in
     132      conjunction with this the development of BASE was initiated.
     133    </para>
     134
     135    <para>
     136      At SCIBLU a BASE installation is maintained and used as a
     137      production installation that manages information surrounding
     138      array fabrication (array LIMS) as well as array data generated
     139      by the SCIBLU provided services. This particular BASE
     140      installation was initially set up in 2003 and to date manage
     141      array data from more than 13 000 hybridisation covering a
     142      variety of technical platforms such as cDNA, oligo, and BeadChip
     143      expression arrays, as well as BAC and oligo aCGH arrays.
     144    </para>
     145
     146    <para>
     147      The SCIBLU BASE installation consists of two main parts; first,
     148      the hardware on which the system runs; secondly, the BASE
     149      software and database, as well as configured analysis plugins.
     150      Regular maintenance of the hardware and configured
     151      database/software is also required. The hardware comprises one
     152      main computer and raided hard drive system. It also includes a
     153      backup solution configured to backup the entire database 2 times
     154      per week. Finally, the hardware includes 2 computational servers
     155      connected to the main computer and used to run configured
     156      analysis plugins in a seamless integrated fashion. The software
     157      used for the SCIBLU BASE installation is freely available from
     158      the BASE project site. Maintenance include managing the
     159      backup-schedule, updating the main BASE software, updating and
     160      managing probe annotations, management of user accounts,
     161      configuring and maintaining analysis plugins, and maintaining
     162      the underlying database.
     163    </para>
     164
     165    <para>
     166      Users of the microarray services offered by SCIBLU, e.g.,
     167      expression analysis or aCGH, are provided access to the SCIBLU
     168      production BASE installation as part of the included
     169      services. The access comprises user account, access to array
     170      LIMS (when in-house produced arrays are utilised), and hard
     171      drive space to cover space needed for storing the data generated
     172      through the SCIBLU provided service. Additional disk space can
     173      be acquired and is associated with an additional cost for the
     174      user. Examples of when additional disk space is needed include
     175      scenarios where users want to perform extensive data analysis
     176      within BASE and decide to store the analysis results within
     177      BASE, e.g., many parallel analysis branches or extensive
     178      generation of data plots and figures. Other examples include
     179      when users want to import data from third party providers
     180      (public data repositories or alternative array data providers)
     181      to perform meta-analysis with their data generated within
     182      SCIBLU.
     183    </para>
     184
     185  </sect1>
     186     
    34187</chapter>
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