source: trunk/doc/historical/specifications/core/defaultdata.html @ 4509

Last change on this file since 4509 was 4509, checked in by Jari Häkkinen, 15 years ago

Addresses #1106. Missed to change reference wherefrom retrive GPLv3 license text. And some other changes.
  • Property svn:eol-style set to native
  • Property svn:keywords set to Id Date
File size: 9.0 KB
Line 
1<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
2<!--
3  $Id: defaultdata.html 4509 2008-09-11 20:01:44Z jari $
4
5  Copyright (C) 2005, 2006 Jari Hakkinen, Nicklas Nordborg
6
7  This file is part of BASE - BioArray Software Environment.
8  Available at http://base.thep.lu.se/
9
10  BASE is free software; you can redistribute it and/or
11  modify it under the terms of the GNU General Public License
12  as published by the Free Software Foundation; either version 3
13  of the License, or (at your option) any later version.
14
15  BASE is distributed in the hope that it will be useful,
16  but WITHOUT ANY WARRANTY; without even the implied warranty of
17  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
18  GNU General Public License for more details.
19
20  You should have received a copy of the GNU General Public License
21  along with BASE. If not, see <http://www.gnu.org/licenses/>.
22-->
23<html>
24  <head>
25    <title>BASE - Core specification - Default data for a new installations</title>
26  <link rel=stylesheet type="text/css" href="../../styles.css">
27  </head>
28<body>
29
30<div class="navigation">
31  <a href="../../index.html">BASE</a>
32  <img src="../../next.gif">
33  <a href="index.html">Core specification</a>
34  <img src="../../next.gif">
35  Default data for a new installations
36</div>
37
38  <h1>Default data for a new installations</h1>
39
40  <div class="abstract">
41    <p>
42    This document contains a list of all items
43    that are automatically installed into a new BASE 2 installation.
44    </p>
45
46    <b>Contents</b><br>
47    <ol>
48    <li><a href="#users">Users</a>
49    <li><a href="#groups">Groups</a>
50    <li><a href="#roles">Roles</a>
51    <li><a href="#keys">Keys</a>
52    <li><a href="#quota">Quota and quota types</a>
53    <li><a href="#protocoltypes">Protocol types</a>
54    <li><a href="#hardware">Hardware and hardware types</a>
55    <li><a href="#software">Software and software types</a>
56    <li><a href="#filetypes">File types</a>
57    <li><a href="#mimetypes">MIME types</a>
58    <li><a href="#annotationtypes">Annotation types</a>
59    <li><a href="#plategeometries">Plate geometries</a>
60    <li><a href="#platemappings">Plate mappings</a>
61    <li><a href="#labels">Labels</a>
62    <li><a href="#clients">Client applications</a>
63    </ol>
64
65    <p class="authors">
66    <b>Last updated:</b> $Date: 2008-09-11 20:01:44 +0000 (Thu, 11 Sep 2008) $
67    </p>
68  </div>
69
70  <a name="users">
71  <h2>1. Users</h2>
72  </a>
73    <ul>
74    <li>Root
75    </ul>
76    <b>Status:</b> Ok
77
78  <a name="groups">
79  <h2>2. Groups</h2>
80  </a>
81    <ul>
82    <li>Everyone
83    </ul>
84    <b>Status:</b> Ok
85
86  <a name="roles">
87  <h2>3. Roles</h2>
88  </a>
89    <ul>
90    <li>Administrator
91    <li>Supervisor
92    <li>Power user (may be split into two types: "biological" and
93    "technical". How should a split like this be done (JVC)?).
94    <li>User
95    <li>Guest
96    </ul>
97    <b>Status:</b> Ok
98
99  <a name="keys">
100  <h2>4. Keys</h2>
101  </a>
102    Anonymous item keys:
103    <ul>
104    <li>READ to Everyone
105    <li>USE to Everyone
106    </ul>
107    <p>
108    Role keys
109    <ul>
110    <li>One role key for each item type. For permissions
111    see the <a href="../../api/net/sf/basedb/core/doc-files/item_permissions.html">
112    Item permissions</a> document
113    </ul>
114    <b>Status:</b> Ok
115
116  <a name="quota">
117  <h2>5. Quota and quota types</h2>
118  </a>
119    Quota types:
120    <ul>
121    <li>Total
122    <li>File
123    <li>Raw data
124    <li>Experiment
125    </ul>
126    <b>Status:</b> Ok
127    <p>
128    Quota
129    <ul>
130    <li>Default (system quota, is assigened to new users)
131    <li>Unlimited (system quota)
132    <li>100 MB total (not system quota)
133    <li>200 MB total (not system quota)
134    <li>500 MB total (not system quota)
135    <li>1 GB total (not system quota)
136    </ul>
137    <b>Status:</b> Ok
138
139  <a name="protocoltypes">
140  <h2>6. Protocol types</h2>
141  </a>
142    <ul>
143    <li>Sampling
144    <li>Extraction
145    <li>Labeling
146    <li>Pooling
147    <li>Hybridization
148    <li>Printing
149    <li>Scanning
150    <li>Feature extraction
151    </ul>
152    <b>Status:</b> Ok
153
154  <a name="hardware">
155  <h2>7. Hardware and hardware types</h2>
156  </a>
157    Hardware types:
158    <ul>
159    <li>Scanner
160    <li>Print robot
161    </ul>
162    <b>Status:</b> Ok
163    <p>
164    Hardware: To be done (JVC)
165
166
167  <a name="software">
168  <h2>8. Software and software types</h2>
169  </a>
170    Software types:
171    <ul>
172    <li>Feature extraction
173    </ul>
174    <b>Status:</b> Ok
175    <p>
176    Software: To be done (JVC)
177
178
179  <a name="filetypes">
180  <h2>9. File types</h2>
181  </a>
182    One type for each item that can be linked with a file.
183    This list may change when the "FileAttachable" interface
184    is developed.
185    <ul>
186    <li>Protocol
187    <li>Raw data
188    <li>Plate mapping
189    <li>Array design
190    <li>Image
191    </ul>
192    <b>Status:</b> Array design to be done, otherwise ok.
193
194  <a name="mimetypes">
195  <h2>10. MIME types</h2>
196  </a>
197
198    General Mime types
199    <table border=1>
200    <tr>
201      <th>Mime type</th>
202      <th>Description</th>
203      <th>Extension</th>
204    </tr>
205    <tr><td>text/plain</td><td>Text files</td><td>txt</td></tr>
206    <tr><td>text/html</td><td>Hypertext markup language files</td><td>htm</td></tr>
207    <tr><td>text/html</td><td>Hypertext markup language files</td><td>html</td></tr>
208    <tr><td>image/jpeg</td><td>JPEG image</td><td>jpg</td></tr>
209    <tr><td>image/jpeg</td><td>JPEG image</td><td>jpeg</td></tr>
210    <tr><td>image/jpeg</td><td>JPEG image</td><td>jpe</td></tr>
211    <tr><td>image/gif</td><td>GIF image</td><td>gif</td></tr>
212    <tr><td>image/png</td><td>PNG image</td><td>png</td></tr>
213    <tr><td>image/tiff</td><td>TIFF image</td><td>tiff</td></tr>
214    <tr><td>image/tiff</td><td>TIFF image</td><td>tif</td></tr>
215    <tr><td>image/rgb</td><td>RGB image</td><td>rgb</td></tr>
216    <tr><td>image/x-pict</td><td>Macintosh PICT format</td><td>pict</td></tr>
217    <tr><td>image/x-ms-bmp</td><td>Microsoft Windows bitmap</td><td>bmp</td></tr>
218    <tr><td>application/postscript</td><td>PostScript</td><td>ai</td></tr>
219    <tr><td>application/postscript</td><td>PostScript</td><td>eps</td></tr>
220    <tr><td>application/postscript</td><td>PostScript</td><td>ps</td></tr>
221    <tr><td>application/pdf</td><td>Adobe Acrobat PDF</td><td>pdf</td></tr>
222    <tr><td>application/x-latex</td><td>LaTeX document</td><td>latex</td></tr>
223    <tr><td>application/msword</td><td>MS word document</td><td>doc</td></tr>
224    <tr><td>application/rtf</td><td>Microsoft Rich Text Format</td><td>rtf</td></tr>
225    <tr><td>application/octet-stream</td><td>PC executable</td><td>exe</td></tr>
226    <tr><td>application/x-perl</td><td>Perl program</td><td>pl</td></tr>
227    <tr><td>application/vnd.ms-powerpoint</td><td>PowerPoint (Microsoft)</td><td>ppt</td></tr>
228    <tr><td>application/vnd.ms-powerpoint</td><td>PowerPoint (Microsoft)</td><td>ppz</td></tr>
229    <tr><td>application/vnd.ms-powerpoint</td><td>PowerPoint (Microsoft)</td><td>pps</td></tr>
230    <tr><td>application/vnd.ms-powerpoint</td><td>PowerPoint (Microsoft)</td><td>pot</td></tr>
231    <tr><td>application/vnd.ms-excel</td><td>Excel spreadsheet (Microsoft)</td><td>xls</td></tr>
232    <tr><td>application/vnd.ms-excel</td><td>Excel spreadsheet (Microsoft)</td><td>xlc</td></tr>
233    <tr><td>application/vnd.ms-excel</td><td>Excel spreadsheet (Microsoft)</td><td>xll</td></tr>
234    <tr><td>application/vnd.ms-excel</td><td>Excel spreadsheet (Microsoft)</td><td>xlm</td></tr>
235    <tr><td>application/vnd.ms-excel</td><td>Excel spreadsheet (Microsoft)</td><td>xlw</td></tr>
236    <tr><td>application/x-compress</td><td>Unix compressed file</td><td>z</td></tr>
237    <tr><td>application/zip</td><td>DOS/PC - Pkzipped archive</td><td>zip</td></tr>
238    <tr><td>application/x-compressed</td><td>Gzip compressed archive</td><td>tgz</td></tr>
239    <tr><td>application/x-gtar</td><td>Gzipped archive</td><td>gtar</td></tr>
240    <tr><td>application/x-gzip</td><td>Gzip compressed file</td><td>gz</td></tr>
241    </table>
242    <p>
243    Microarray/BASE-specific mime types
244    <table border=1>
245    <tr>
246      <th>Mime type</th>
247      <th>Description</th>
248      <th>Extension</th>
249    </tr>
250    <tr><td>text/plain</td><td>GenePix Results file</td><td>gpr</td></tr>
251    <tr><td>text/plain</td><td>GenePix Array List file</td><td>gal</td></tr>
252    <tr><td>text/plain</td><td>Spot file format</td><td>spot</td></tr>
253    <tr><td>text/plain</td><td>Spotfinder file format</td><td>tav</td></tr>
254    <tr><td>text/plain</td><td>Affymetrix CEL file</td><td>cel</td></tr>
255    <tr><td>text/plain</td><td>FASTA formatted file</td><td>fasta</td></tr>
256    <tr><td>text/plain</td><td>BASEfile formatted file</td><td>base</td></tr>
257    <tr><td>text/plain</td><td>Biorobotics TAM format</td><td>tam</td></tr>
258    <tr><td>text/plain</td><td>Molecularware MWBR format</td><td>mvbr</td></tr>
259    </table>
260    <p>
261    <b>Status:</b> Ok
262
263
264  <a name="annotationtypes">
265  <h2>11. Annotation types</h2>
266  </a>
267    All annotations required for MIAME comatibility should
268    be defined. This requires that it is possible to
269    import MGED ontologies.
270    <p>
271    <b>Status:</b> To be done
272
273  <a name="plategeometries">
274  <h2>12. Plate geometries</h2>
275  </a>
276    <ul>
277    <li>96-well (8 rows x 12 columns)
278    <li>384-well (16 x 24)
279    <li>1536-well (32 x 48)
280    </ul>
281    <b>Status:</b> Ok
282
283  <a name="platemappings">
284  <h2>13. Plate mappings</h2>
285  </a>
286    <ul>
287    <li>96 to 96
288    <li>96 to 384
289    <li>384 to 384
290    <li>384 to 1536
291    <li>1536 to 1536
292    </ul>
293    <b>Status:</b> To be done
294
295  <a name="labels">
296  <h2>14. Labels</h2>
297  </a>
298    <ul>
299    <li>cy3
300    <li>cy5
301    </ul>
302    <b>Status:</b> Ok
303
304  <a name="clients">
305  <h2>15. Client applications</h2>
306  </a>
307    <ul>
308    <li>The web client
309    <li>The test programs
310    <li>The migration client
311    </ul>
312    <b>Status:</b> Ok
313
314</body>
315</html>
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