source: trunk/doc/src/docbook/overview/features.xml @ 5782

Last change on this file since 5782 was 5782, checked in by Nicklas Nordborg, 10 years ago

References #1590: Documentation cleanup

Restructured documentation to generate shorter filenames.

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1<?xml version="1.0" encoding="UTF-8"?>
2<!DOCTYPE chapter PUBLIC
3    "-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN"
4    "../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd">
5
6<!--
7  $Id: features.xml 5782 2011-10-04 13:43:16Z nicklas $
8
9  Copyright (C) 2008 Jari Häkkinen
10
11  This file is part of BASE - BioArray Software Environment.
12  Available at http://base.thep.lu.se/
13
14  BASE is free software; you can redistribute it and/or
15  modify it under the terms of the GNU General Public License
16  as published by the Free Software Foundation; either version 3
17  of the License, or (at your option) any later version.
18
19  BASE is distributed in the hope that it will be useful,
20  but WITHOUT ANY WARRANTY; without even the implied warranty of
21  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
22  GNU General Public License for more details.
23
24  You should have received a copy of the GNU General Public License
25  along with BASE. If not, see <http://www.gnu.org/licenses/>.
26-->
27
28<chapter id="features" chunked="0">
29  <?dbhtml filename="features.html"?>
30  <title>BASE features</title>
31
32  <para>
33    This chapter will explain the important features of BASE.
34  </para>
35
36  <sect1 id="features.supportedarrays">
37    <title>Supported array platforms and raw data formats</title>
38
39    <para>
40      BASE supports many different vendor specific and custom printing
41      microarray platforms and data formats, there are even users that
42      use BASE for protein arrays. For 2 channel array platforms it is
43      straightforward to customize BASE for a specific array platform,
44      the platform simply needs to be adapted to the (BASE) Generic
45      platform. The adaptation is to create a raw data format
46      definition and to configure raw data importers, or make use of
47      already available raw data formats. However, it is not always
48      possible to make an natural mapping of a platform to the Generic
49      platform. Platforms such as Affymetrix and Illumina platforms
50      cannot naturally be mapped on to the Generic 2 channel
51      platform. For Affymetrix, BASE comes with a specific Affymetrix
52      platform and Illumina can be supported by customizing BASE.
53    </para>
54
55    <para>
56      How to adapt new array platforms to the Generic platform format
57      or how to create a new platform type in BASE can be read
58      elsewhere in this document. Here we list different array
59      platforms used in BASE and also list raw data types supported
60      by BASE. However, not all platforms nor raw data types listed
61      below are available out-of-the box and a BASE administrator must
62      customize his local BASE installation for their specific
63      need. What comes pre-configured when BASE is installed is
64      indicated in the lists below.
65    </para>
66
67    <sect2 id="features.supportedarrays.platforms">
68      <title>Vendor specific and custom printing array
69      platforms</title>
70
71      <para>
72        Not all array platforms listed below are available by
73        default. The comments to specific platforms explain how to
74        enable the use of the array platform in BASE. In some cases
75        there is no confirmed usage of a platform but we believe it
76        has been tested by anonymous users.
77      </para>
78
79      <variablelist>
80        <varlistentry>
81          <term>Affymetrix</term>
82          <listitem>
83            <para>
84              The Affymetrix platform comes pre-configured with a
85              new BASE installation. Affymetrix platform in this
86              context are the Affymetrix expression arrays. So far
87              there has been no reason for expanding the Array
88              platform to other chip-types. In principle any
89              Affymetrix chip type can be stored in BASE but current
90              plug-ins will always assume that expression data is
91              stored and analyzed. This can be resolved by adding
92              variants of the Affymetrix platform but the Lund BASE
93              team currently has no plans to create Affymetrix
94              variants.
95            </para>
96          </listitem>
97        </varlistentry>
98
99        <varlistentry>
100          <term>Agilent</term>
101          <listitem>
102            <para>
103            </para>
104          </listitem>
105        </varlistentry>
106
107        <varlistentry>
108          <term>Custom printing</term>
109          <listitem>
110            <para>
111              The array layout options are endless and imagination is
112              the only limitation ... almost. BASE can import many
113              in-house array designs and platforms. The custom arrays
114              usually fall back on one of the raw data types already
115              available such as GenePix.
116            </para>
117          </listitem>
118        </varlistentry>
119
120        <varlistentry>
121          <term>Illumina</term>
122          <listitem>
123            <para>
124              There are several variants of the Illumina platform. Using
125              several variants allows BASE to adapt its handling of
126              different Illumina chip types. Illumina platform support
127              is not included in a standard BASE installation but there
128              is
129              a <ulink url="http://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina">
130                Illumina plug-in</ulink> available for seamless
131              integration of the Illumina array platform to BASE.
132            </para>
133          </listitem>
134        </varlistentry>
135
136        <varlistentry>
137          <term>ImaGene</term>
138          <listitem>
139            <para>
140              No successful use confirmed but ImaGene raw data is
141              available in BASE.
142            </para>
143          </listitem>
144        </varlistentry>
145
146        <varlistentry>
147          <term>Unlisted</term>
148          <listitem>
149            <para>
150              In principle any platform generating a matrix of data can
151              be imported into BASE. Simply utilize the available raw
152              data formats and data importers.
153            </para>
154          </listitem>
155        </varlistentry>
156      </variablelist>
157
158    </sect2>
159
160    <sect2 id="features.supportedarrays.rawdatatypes">
161      <title>Available raw data types</title>
162
163      <para>
164        Raw data comes in many different formats. These formats are
165        usually defined by scanner software vendors and BASE must keep
166        track of the different formats for analysis and plotting. BASE
167        supports many formats out the box, but some formats need to
168        be added manually by the BASE administrator (indicated in the
169        list below).
170      </para>
171
172      <variablelist>
173
174        <varlistentry>
175          <term>Affymetrix</term>
176          <listitem>
177            <para>
178            </para>
179          </listitem>
180        </varlistentry>
181
182        <varlistentry>
183          <term>AIDA</term>
184          <listitem>
185            <para>
186            </para>
187          </listitem>
188        </varlistentry>
189
190        <varlistentry>
191          <term>Agilent</term>
192          <listitem>
193            <para>
194            </para>
195          </listitem>
196        </varlistentry>
197
198        <varlistentry>
199          <term>BZScan</term>
200          <listitem>
201            <para>
202            </para>
203          </listitem>
204        </varlistentry>
205
206        <varlistentry>
207          <term>ChipSkipper</term>
208          <listitem>
209            <para>
210            </para>
211          </listitem>
212        </varlistentry>
213
214        <varlistentry>
215          <term>GenePix</term>
216          <listitem>
217            <para>
218            </para>
219          </listitem>
220        </varlistentry>
221
222        <varlistentry>
223          <term>GeneTAC</term>
224          <listitem>
225            <para>
226            </para>
227          </listitem>
228        </varlistentry>
229
230        <varlistentry>
231          <term>Illumina</term>
232          <listitem>
233            <para>
234              The Illumina array platform usage is recommended to be
235              based on the <emphasis>Illumina Bead Summary
236              (IBS)</emphasis> raw data format below.
237            </para>
238          </listitem>
239        </varlistentry>
240
241        <varlistentry>
242          <term>Illumina Bead Summary (IBS)</term>
243          <listitem>
244            <para>
245              Not available in BASE directly but it is added with
246              the <ulink url="http://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina">
247              Illumina plug-in</ulink> that adds Illumina array
248              platform support to BASE.
249            </para>
250          </listitem>
251        </varlistentry>
252
253        <varlistentry>
254          <term>ImaGene</term>
255          <listitem>
256            <para>
257            </para>
258          </listitem>
259        </varlistentry>
260
261        <varlistentry>
262          <term>QuantArray Biotin</term>
263          <listitem>
264            <para>
265            </para>
266          </listitem>
267        </varlistentry>
268
269        <varlistentry>
270          <term>QuantArray Cy</term>
271          <listitem>
272          <para>
273          </para>
274          </listitem>
275        </varlistentry>
276
277        <varlistentry>
278          <term>SpotFinder</term>
279          <listitem>
280            <para>
281            </para>
282          </listitem>
283        </varlistentry>
284
285      </variablelist>
286
287    </sect2>
288
289  </sect1>
290
291</chapter>
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