source: trunk/doc/user/coreplugins.html @ 3047

Last change on this file since 3047 was 3047, checked in by Martin Svensson, 16 years ago

First version of a list with all core plugins in BASE2
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3  $Id: coreplugins.html 3047 2007-01-02 15:35:45Z martin $
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25<html>
26  <head>
27      <title>BASE 2 - Core plugins</title>
28    <link rel=stylesheet type="text/css" href="../styles.css">
29  </head>
30  <body>
31    <div class="navigation">
32      <a href="../index.html">BASE</a>
33      <img src="../next.gif">
34      <a href="index.html">User documentation</a>
35      <img src="../next.gif">
36      Core plugins
37    </div>
38   
39    <h1>BASE 2 - Core plugins</h1>
40   
41    <div class="abstract">
42      <p>
43        This document lists all available core plugins in BASE 2. <br>Each plugin can be downloaded and installed separately.<br>
44        There are also an example of configuration, that can be downloaded and imported, for those plugins that have configuration support.
45      </p>
46      <b>Plugin types</b>
47      <ol>
48        <li><a href="#analyse">Analyse</a></li>
49        <li><a href="#export">Export</a></li>
50        <li><a href="#import">Import</a></li>
51        <li><a href="#intensity">Intensity</a></li>
52        <li><a href="#other">Other</a></li>
53      </ol>
54
55      <p class="authors">
56        <b>Last updated:</b> $Date: 2007-01-02 $ <br>
57        <b>Copyright &copy;</b> 2007 The respective authors. All
58        rights reserved.
59      </p>
60    </div>
61   
62    <ol>
63      <li>
64        <a name="analyse"></a>
65        <h2>Analyse</h2>
66        <table class="listing">
67          <tr>
68            <th>Plugin&nbsp;name</th>
69            <th colspan="2">Download/Configuration</th>
70            <th>Description</th>
71          </tr>
72          <tr>
73            <td>Base1PluginExecuter</td>
74            <td><a href="">download</a></td>
75            <td><a href="">configuration</a></td>
76            <td>This plug-in simulates the plug-in runner from Base 1.2 to enable old plug-ins to be executed.</td>
77          </tr>
78          <tr>
79            <td>JEP&nbsp;extra&nbsp;value calculator</td>
80            <td><a href="">download</a></td>
81            <td><i>- N/A -</i></td>
82            <td>This plugin is used to calculate extra values for a bioassay set. The expressions are parsed with the JEP package.</td>
83          </tr>
84          <tr>
85            <td>JEP&nbsp;filter plugin</td>
86            <td><a href="">download</a></td>
87            <td><i>- N/A -</i></td>
88            <td>This filter is based on expressions entered by the user, which are parsed with the JEP package.</td>
89          </tr>
90          <tr>
91            <td>JEP&nbsp;intensity transformer</td>
92            <td><a href="">download</a></td>
93            <td><i>- N/A -</i></td>
94            <td>
95              This plugin is used to transform the intensities of a bioassayset using expressions entered by the user.
96              The expressions are parsed with the JEP package.
97            </td>
98          </tr>
99          <tr>
100            <td>Normalization: Lowess</td>
101            <td><a href="">download</a></td>
102            <td><i>- N/A - </i></td>
103            <td>This is an efficient java implementation by Johan Enell of the LOWESS algorithm. It provides intensity-based normalization.</td>                       
104          </tr>
105          <tr>
106            <td>Normalization: Median&nbsp;ratio</td>
107            <td><a href="">download</a></td>
108            <td><i>- N/A - </i></td>
109            <td>This normalizer scales the intensities in such a way that their geometric mean (sqrt(i1 * i2)) is kept constant but the median of their ratios (i1/i2) is shifted to 1.</td>
110          </tr>
111        </table>           
112      </li>
113     
114      <li>
115        <a name="export"></a>     
116        <h2>Export</h2>
117        <table class="listing">
118          <tr>
119            <th>Plugin&nbsp;name</th>           
120            <th colspan="2">Download/Configuration</th>
121            <th>Description</th>
122          </tr>
123          <tr>
124            <td>Bioassay&nbsp;set&nbsp;exporter</td>
125            <td><a href="">download</a></td>
126            <td><i>- N/A -</i></td>             
127            <td>Exporter for bioassay sets.</td>
128          </tr>         
129          <tr>
130            <td>Help&nbsp;texts&nbsp;exporter</td>
131            <td><a href="">download</a></td>
132            <td><i>- N/A -</i></td>             
133            <td>This plugin is used to export a client application's help texts.</td>
134          </tr>
135          <tr>
136            <td>Plate&nbsp;mapping&nbsp;exporter</td>
137            <td><a href="">download</a></td>
138            <td><i>- N/A -</i></td>             
139            <td>This plugin is used to export plate mappings.</td>
140          </tr> 
141          <tr>
142            <td>Plugin&nbsp;configuration exporter</td>
143            <td><a href="">download</a></td>
144            <td><i>- N/A -</i></td>             
145            <td>This plugin is used to export plugin configurations to an XML-file.</td>
146          </tr> 
147          <tr>
148            <td>Table&nbsp;exporter</td>
149            <td><a href="">download</a></td>
150            <td><i>- N/A -</i></td>             
151            <td>Export all table listings in the web interface as tab-separated text files or as XML.</td>
152          </tr>     
153        </table> 
154      </li>
155           
156      <li>
157        <a name="import"></a>
158        <h2>Import</h2>
159        <table class="listing">
160          <tr>
161            <th>Plugin&nbsp;name</th>
162            <th colspan="2">Download/Configuration</th>
163            <th>Description</th>
164          </tr>
165          <tr>
166            <td>Help&nbsp;texts&nbsp;exporter</td>
167            <td><a href="">download</a></td>
168            <td><i>- N/A -</i></td>
169            <td>This plugin imports help texts from a XML-file to the BASE.</td>
170          </tr>
171          <tr>
172            <td>Plate&nbsp;importer</td>
173            <td><a href="">download</a></td>
174            <td><a href="">configuration</a></td>
175            <td>This plugin is used to import plates from a simple flat file.</td>
176          </tr>
177          <tr>
178            <td>Plate&nbsp;mapping&nbsp;importer</td>
179            <td><a href="">download</a></td>
180            <td><i>- N/A -</i></td>
181            <td>This plugin is used to import plate mappings.</td>
182          </tr>
183          <tr>
184            <td>Plugin&nbsp;configuration importer</td>
185            <td><a href="">download</a></td>
186            <td><i>- N/A -</i></td>
187            <td>This plugin is used to import configuration for a BASE plugin.</td>
188          </tr>
189          <tr>
190            <td>Print&nbsp;map&nbsp;importer</td>
191            <td><a href="">download</a></td>
192            <td><i>- N/A -</i></td>
193            <td>This plugin is used to import arraydesign from a print map.</td>
194          </tr>         
195          <tr>
196            <td>Raw&nbsp;data&nbsp;importer</td>
197            <td><a href="">download</a></td>
198            <td><a href="">configuration</a></td>
199            <td>This plugin is used to import raw data from a simple text file.</td>
200          </tr>
201          <tr>
202            <td>Reporter&nbsp;importer</td>
203            <td><a href="">download</a></td>
204            <td><a href="">configuration</a></td>
205            <td>This plugin is used to import reporters from a simple flat file.</td>
206          </tr>
207          <tr>
208            <td>Reporter&nbsp;map&nbsp;importer</td>
209            <td><a href="">download</a></td>
210            <td><a href="">configuration</a></td>
211            <td>This plugin is used to import features to an ArrayDesign from a simple flat file.</td>
212          </tr>
213        </table> 
214      </li>
215     
216      <li>
217        <a name="intensity"></a>
218        <h2>Intensity</h2>
219        <table class="listing">
220          <tr>
221            <th>Plugin&nbsp;name</th>
222            <th colspan="2">Download/Configuration</th>
223            <th>Description</th>
224          </tr>
225          <tr>
226            <td>Formula&nbsp;intensity calculator</td>
227            <td><a href="">download</a></td>
228            <td><i>- N/A -</i></td>
229            <td>This plugin is used to calculate intensities from raw data</td>
230          </tr>
231        </table>           
232      </li>
233     
234      <li>
235        <a name="other"></a>
236        <h2>Other</h2>
237        <table class="listing">
238          <tr>
239            <th>Plugin&nbsp;name</th>
240            <th colspan="2">Download/Configuration</th>
241            <th>Description</th>
242          </tr>
243        </table>           
244      </li>
245    </ol>
246  </body>
247</html>
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