source: trunk/doc/src/docbook/overview/why_base.xml @ 6807

Last change on this file since 6807 was 5844, checked in by Jari Häkkinen, 11 years ago

Fixes #522. After five years ...

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1<?xml version="1.0" encoding="UTF-8"?>
3    "-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN"
4    "../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd">
6  $Id: why_base.xml 5844 2011-11-01 16:05:58Z jari $
8  Copyright (C) 2007 Martin Svensson, Jari Häkkinen
9  Copyright (C) 2008 Jari Häkkinen
10  Copyright (C) 2011 Jari Häkkinen, Nicklas Nordborg
12  This file is part of BASE - BioArray Software Environment.
13  Available at
15  BASE is free software; you can redistribute it and/or
16  modify it under the terms of the GNU General Public License
17  as published by the Free Software Foundation; either version 3
18  of the License, or (at your option) any later version.
20  BASE is distributed in the hope that it will be useful,
21  but WITHOUT ANY WARRANTY; without even the implied warranty of
23  GNU General Public License for more details.
25  You should have received a copy of the GNU General Public License
26  along with BASE. If not, see <>.
29<chapter id="why_base" chunked="0">
30  <?dbhtml filename="why_base.html"?>
31  <title>Why use BASE</title>
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>
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>
47  <sect1 id="whybase.scanb">
48    <title>Case I: The SCAN-B BASE installation at Department of
49    Oncology, Lund University</title>
51    <para>
52      <ulink
53      url=''>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>
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>
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>
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=''>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>
115  </sect1>
118  <sect1 id="whybase.sciblu">
119    <title>Case II: The BASE installation at SCIBLU, Department of
120    Oncology, Lund University</title>
122    <para>
123      In the spring of 2004, Lund University created Swegene Centre
124      for Integrative Biology at Lund University (<ulink
125      href=''>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>
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>
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>
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>
185  </sect1>
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