source: branches/2.10-stable/doc/test/roles/index.html @ 4780

Last change on this file since 4780 was 4780, checked in by Nicklas Nordborg, 14 years ago

Updated the 'roles' test program and instructions.
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1<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
2<!--
3  $Id: index.html 4780 2009-02-23 12:40:28Z nicklas $
4
5  Copyright (C) 2006 Jari Hakkinen, Nicklas Nordborg, Martin Svensson
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 - Test procedures for predefined roles</title>
26  <link rel=stylesheet type="text/css" href="../../historical/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">Test procedures</a>
34  <img src="../../next.gif">
35  Predefined roles
36</div>
37
38  <h1>Test procedures for predefined roles</h1>
39
40  <div class="abstract">
41    <p>
42      This document defines a procedure for testing that
43      the predefined roles can perform their work as intended. The main
44      purpose is to weed out permission problems resulting from:
45    </p>
46   
47    <ul>
48    <li>Incorrect permissions installed by installation program</li>
49    <li>Bugs in the permission handling in the core</li>
50    <li>Incorrect handling of permissions in the web client</li>
51    </ul>
52   
53    <p>
54      The test procedure also tests that the
55      basic functionality is working:
56    </p>
57   
58    <ul>
59      <li>Creating items and linking them to other items</li>
60      <li>Defining import file formats</li>
61      <li>Importing array LIMS data</li>
62      <li>Importing and validating raw data against array LIMS data</li>
63      <li>Running analysis plug-ins</li>
64      <li>Using files instead of the database for storing data</li>
65    </ul>
66   
67    <b>Contents</b><br>
68    <ol>
69    <li><a href="#summary">Summary of the test procedure</a></li>
70    <li><a href="#root">Root user tests</a></li>
71    <li><a href="#admin">Administrator tests</a></li>
72    <li><a href="#power">Power user tests</a></li>
73    <li><a href="#user">User tests</a></li>
74    <li><a href="#analysis">Analysis tests</a></li>
75    </ol>
76   
77    <p class="authors">
78    <b>Last updated:</b> $Date: 2009-02-23 12:40:28 +0000 (Mon, 23 Feb 2009) $
79    </p>
80  </div>
81
82 
83  <a name="summary"></a>
84  <h2>1. Summary of the test procedure</h2>
85
86  <p>
87    Here is a summary of the test procedure:
88  </p>
89
90  <ol>
91  <li>Always start with a fresh installation.</li>
92 
93  <li>The root user creates an administrator.</li>
94 
95  <li>The administrator creates more users and some global resources:
96    <ul>
97    <li>A group and three other users. One power user, one user and one guest.</li>
98    <li>File formats for importing reporters</li>
99    <li>Imports reporters</li>
100    </ul>
101  </li>
102   
103  <li>The power user creates item related to the project management:
104    <ul>
105    <li>A project</li>
106    <li>Protocols, one for each type of action: sampling, extraction, etc.</li>
107    <li>Hardware and software that are used in the project</li>
108    <li>Annotation types for annotations used in the project</li>
109    <li>File formats for importing plates, print maps and raw data</li>
110    <li>LIMS information - plate type, plates, array design, array batch and array slides</li>
111    </ul>
112  </li>
113 
114  <li>The user creates items related to an actual experiment:
115    <ul>
116    <li>Biomaterials: biosources, samples, extracts, etc.</li>
117    <li>Experiment: hybridizations, scans, images, raw bioassays</li>
118    <li>Import raw data</li>
119    </ul>
120  </li>
121 
122  <li>Both the user and the guest then do some analysis:
123    <ul>
124    <li>Create a root bioassay set</li>
125    <li>Filter the bioassay set</li>
126    <li>Run a normalization plug-in</li>
127    <li>Check the result by listing and plotting the data</li>
128    </ul>
129  </li>
130  </ol>
131
132  <p>
133    These tests can also be run in automated mode by test programs. This will of
134    course not test the web client, but are useful if one quickly needs to do
135    parts of the test and then continue with, for example, the user or analysis tests
136    on the web.
137  </p>
138 
139  <p>
140    The data files needed by the tests are NOT included in the subversion repository.
141    The main reason is that they are too large, and that we don't have permission to
142    make them publicly available for download. To get the test file you need to be a
143    core developer. Read the instructions on the
144    <a href="http://base.thep.lu.se/wiki/DeveloperInformation">DeveloperInformation</a>
145    page, <code>Test data</code> section on the Base 2 web site. The automated
146    test programs require that file are placed (checked out) in the 'testdata'
147    directory located in the BASE root directory. NOTE! Some test data files are
148    bzip-compressed. These need to be uncompressed before they are uploaded to BASE.
149  </p>
150 
151  <p>
152    To run the tests do the following:
153  </p>
154  <ol>
155   
156    <li>Compile the core and the test programs: <code>ant main test</code>.</li>
157
158    <li>Change to the <code>build/test/</code> directory.</li>
159
160    <li>Run test programs: <code>./test.sh roles [OPTION] &lt;cmds&gt;</code> where
161      <code>&lt;cmds&gt;</code> is one or more of the following:
162      <ul>
163      <li><code>all</code>: run all tests</li>
164      <li><code>root</code>: run the root user tests</li>
165      <li><code>admin</code>: run the administrator tests</li>
166      <li><code>power</code>: run the power user tests</li>
167      <li><code>user</code>: run the regular user tests</li>
168      <li><code>guest</code>: run the guest user tests</li>
169      </ul>
170      and <code>OPTION</code> can be none or more of:
171      <ul>
172      <li><code>-b</code>: if the batch importers should be tested</li>
173      <li><code>-w</code>: if the test program should wait for ENTER before emptying the database.</li>
174      </ul>
175    </li>
176   
177  </ol>
178   
179  <a name="root"></a>
180  <h2>2. Root user tests</h2>
181  <p>
182    The root user creates an administrator which is a server-wide admin.
183  </p>
184 
185  <ol>
186  <li>
187    Create a new user and set the following
188    properties. All other properties may remain unchanged.
189   
190    <table class="listing" cellspacing="0" cellpadding="2" border="0">
191    <tr>
192      <th>Name</th>
193      <th>Login/Password</th>
194      <th>Quota</th>
195      <th>Quota group</th>
196      <th>Membership</th>
197    </tr>
198    <tr>
199      <td>Admin</td>
200      <td>admin/admin</td>
201      <td>Unlimited</td>
202      <td>-</td>
203      <td>Roles: Administrator</td>
204    </tr>
205    </table>
206  </li>
207  </ol>
208
209  <a name="admin"></a>
210  <h2>3. Administrator tests</h2>
211  <p>
212    The administrator creates users for a project and gives them permissions
213    that are suitable for their role in the project. The administrator also
214    sets up quota and group membership.
215  </p>
216
217  <ol>
218  <li>
219    Create a new group and set the following properties:
220 
221    <table class="listing" cellspacing="0" cellpadding="2" border="0">
222    <tr>
223      <th>Name</th>
224      <th>Quota</th>
225    </tr>
226    <tr>
227      <td>Group A</td>
228      <td>1GB</td>
229    </tr>
230    </table>
231    <p>
232  </li>
233 
234  <li>
235    Create the following users:
236
237    <table class="listing" cellspacing="0" cellpadding="2" border="0">
238    <tr>
239      <th>Name</th>
240      <th>Login/Password</th>
241      <th>Quota</th>
242      <th>Quota group</th>
243      <th>Membership</th>
244      <th>Other</th>
245    </tr>
246    <tr>
247      <td>Power user</td>
248      <td>power/power</td>
249      <td>1GB</td>
250      <td>Group A</td>
251      <td>Roles: Power user</td>
252      <td>-</td>
253    </tr>
254    <tr>
255      <td>User</td>
256      <td>user/user</td>
257      <td>1GB</td>
258      <td>Group A</td>
259      <td>Roles: User</td>
260      <td>-</td>
261    </tr>
262    <tr>
263      <td>Guest</td>
264      <td>guest/guest</td>
265      <td>10MB</td>
266      <td>Group A</td>
267      <td>Roles: Guest</td>
268      <td><i>Multi-user account</i> checked</td>
269    </tr>
270    </table>
271    <p>
272  </li>
273 
274  <li>Give USE permission for the listed users to the following plugins:
275 
276    <table class="listing" cellspacing="0" cellpadding="2" border="0">
277    <tr>
278      <th>User</th>
279      <th>Plugins</th>
280    </tr>
281    <tr>
282      <td>Power user</td>
283      <td>
284        <ul>
285        <li>Plate importer</li>
286        <li>Reporter map importer</li>
287        <li>Print map importer</li>
288        </ul>
289      </td>
290    </tr>
291    </table>
292    <p>
293  </li>
294
295  <li>
296    Create file formats (<i>i.e.</i>, plug-in configurations) for importing
297    reporters. The formats marked as
298    optional are not used in the test procedure, but may be useful to weed
299    out import problems, since they allow importing all info from the raw
300    data files. You may either enter the regular expressions as specified or
301    use the "Test with file" feature.
302   
303    <table class="listing" cellspacing="0" cellpadding="2" border="0">
304    <tr>
305      <th>Name</th>
306      <th>Plugin</th>
307      <th>Configuration values</th>
308    </tr>
309    <tr class="oddrow">
310      <td>Reporters for project A</td>
311      <td>Reporter importer</td>
312      <td>
313      <b>Test with file:</b> <code>plates_and_reporters.mouse.v4.37k.txt</code>
314      <table border="0" cellspacing="0" cellpadding="2">
315      <tr>
316        <td><i>Data header</i></td>
317        <td>384_number\t384_column\t384_row\t384_position\toligo_id.*</td>
318      </tr>
319      <tr>
320        <td><i>Data splitter</i></td>
321        <td>\t</td>
322      </tr>
323      <tr>
324        <td><i>Min data columns</i></td>
325        <td>5</td>
326      </tr>
327      <tr>
328        <td><i>Name</i></td>
329        <td>\oligo_id\</td>
330      </tr>
331      <tr>
332        <td><i>External ID</i></td>
333        <td>\oligo_id\</td>
334      </tr>
335      <tr>
336        <td><i>Description</i></td>
337        <td>\description_Ensembl*\</td>
338      </tr>
339      <tr>
340        <td><i>Gene symbol</i></td>
341        <td>\gene_symbol_Ensembl*\</td>
342      </tr>
343      <tr>
344        <td><i>Sequence</i></td>
345        <td>\oligo_sequence\</td>
346      </tr>
347      </table>
348     
349      </td>
350    </tr>
351   
352    <tr class="evenrow">
353      <td>GenePix reporter importer<br>(optional)</td>
354      <td>Reporter importer</td>
355      <td>
356
357      <b>Test with file:</b> <code>genepix.mouse.v4.37k.00h.gpr</code>
358      <table border="0" cellspacing="0" cellpadding="2">
359      <tr>
360        <td><i>Data header</i></td>
361        <td>"Block"\t"Column"\t"Row"\t"Name"\t"ID"\t.*</td>
362      </tr>
363      <tr>
364        <td><i>Data splitter</i></td>
365        <td>\t</td>
366      </tr>
367      <tr>
368        <td><i>Min data columns</i></td>
369        <td>48</td>
370      </tr>
371      <tr>
372        <td><i>Max data columns</i></td>
373        <td>48</td>
374      </tr>
375      <tr>
376        <td><i>Name</i></td>
377        <td>\Name\</td>
378      </tr>
379      <tr>
380        <td><i>External ID</i></td>
381        <td>\ID\</td>
382      </tr>
383      </table>
384
385      </td>
386    </tr>
387    <tr class="oddrow">
388      <td>Reporters from Affymetrix annotations file</td>
389      <td>Reporter importer</td>
390      <td>
391      <b>Test with file:</b> <code>MG_U74Av2_annot.csv.bz2</code>
392      <table border="0" cellspacing="0" cellpadding="2">
393      <tr>
394        <td><i>Data header</i></td>
395        <td>"Probe Set ID","GeneChip Array".*</td>
396      </tr>
397      <tr>
398        <td><i>Data splitter</i></td>
399        <td>(?!"),(?=")</td>
400      </tr>
401      <tr>
402        <td><i>Name</i></td>
403        <td>\Probe Set ID\</td>
404      </tr>
405      <tr>
406        <td><i>External ID</i></td>
407        <td>\Probe Set ID\</td>
408      </tr>
409      <tr>
410        <td><i>Description</i></td>
411        <td>\Target Description\</td>
412      </tr>
413      <tr>
414        <td><i>Gene symbol</i></td>
415        <td>\Gene Symbol\</td>
416      </tr>
417      </table>
418     
419      </td>
420    </tr>   
421    </table>
422    <p>
423    </li>
424
425    <li>
426      Import reporters:
427      <ol>
428      <li>Go to the <code>View -> Reporters</code> page.</li>
429      <li>Click on the <code>Import</code> button.</li>
430      <li>Choose <code>auto-detect</code> and then upload
431        the file <code>plates_and_reporters.mouse.v4.37k.txt</code>.</li>
432      <li>The <code>Reporters for project A</code> format should be
433        found.</li>
434      <li>Select the <code>skip</code> option for the "Missing a required" value
435        since the file contains rows with empty reporter ID:s.
436      <li>Continue and wait for the import to finish. It should create 35,912 new reporters.</li>
437      <li>
438        Repeat the procedure with the <code>MG_U74Av2_annot.csv</code> file. This time
439        also select <code>crop</code> for the "String too long" setting since
440        the file contains data that is too large for the datbase.
441        12,488 new reporters should be created.
442      </ol>
443      <p>
444 
445    </li>
446
447
448  </ol>
449
450
451  <a name="power"></a>
452  <h2>4. Power user tests</h2>
453  <p>
454    The power user is the typical owner/administrator of a project. The power user sets
455    up common resources used in the project, such as hardware, software, protocols,
456    file formats and annotation types. In this case the power user is also responsible for
457    managing the LIMS.
458  </p>
459 
460  <ol>
461  <li>
462    Create a project:
463   
464    <table class="listing" cellspacing="0" cellpadding="2" border="0">
465    <tr>
466      <th>Name</th>
467      <th>Members</th>
468    </tr>
469    <tr>
470      <td>Project A</td>
471      <td>Groups: Group A (Use permission)</td>
472    </tr>
473    </table>
474    <p>
475  </li>
476 
477  <li>Activate the project.<p></li>
478 
479  <li>
480    Create protocols:
481    <table class="listing" cellspacing="0" cellpadding="2" border="0">
482    <tr>
483      <th>Name</th>
484      <th>Type</th>
485    </tr>
486    <tr>
487      <td>Sampling A</td>
488      <td>Sampling</td>
489    </tr>
490    <tr>
491      <td>Extraction A</td>
492      <td>Extraction</td>
493    </tr>
494    <tr>
495      <td>Labeling A</td>
496      <td>Labeling</td>
497    </tr>
498    <tr>
499      <td>Hybridization A</td>
500      <td>Hybridization</td>
501    </tr>
502    <tr>
503      <td>Scanning A</td>
504      <td>Scanning</td>
505    </tr>
506    <tr>
507      <td>Feature extraction A</td>
508      <td>Feature extraction</td>
509    </tr>
510    <tr>
511      <td>Printing A</td>
512      <td>Printing</td>
513    </tr>
514    </table>
515    <p>
516  </li>
517
518  <li>
519    Create hardware:
520    <table class="listing" cellspacing="0" cellpadding="2" border="0">
521    <tr>
522      <th>Name</th>
523      <th>Type</th>
524    </tr>
525    <tr>
526      <td>Hybridization station A</td>
527      <td>Hybridization station</td>
528    </tr>
529    <tr>
530      <td>Scanner A</td>
531      <td>Scanner</td>
532    </tr>
533    <tr>
534      <td>Print robot A</td>
535      <td>Print robot</td>
536    </tr>
537    </table>
538    <p>
539  </li>
540 
541  <li>
542    Create software:
543    <table class="listing" cellspacing="0" cellpadding="2" border="0">
544    <tr>
545      <th>Name</th>
546      <th>Type</th>
547    </tr>
548    <tr>
549      <td>Software A</td>
550      <td>Feature extraction</td>
551    </tr>
552    </table>
553    <p>
554  </li>
555 
556  <li>
557    Create annotation types:
558    <table class="listing" cellspacing="0" cellpadding="2" border="0">
559    <tr>
560      <th>Name</th>
561      <th>Type</th>
562      <th>Unit</th>
563      <th>Interface</th>
564      <th>Values</th>
565      <th>Item types</th>
566    </tr>
567    <tr>
568      <td>Drug resistance</td>
569      <td>String</td>
570      <td>-</td>
571      <td>radiobuttons</td>
572      <td>high, medium, low</td>
573      <td>Biosource</td>
574    </tr>
575    <tr>
576      <td>Time</td>
577      <td>Integer</td>
578      <td>Hour</td>
579      <td>text box</td>
580      <td>-</td>
581      <td>Sample</td>
582    </tr>
583    <tr>
584      <td>Dye swap</td>
585      <td>Boolean</td>
586      <td>-</td>
587      <td>-</td>
588      <td>-</td>
589      <td>Raw bioassay</td>
590    </tr>
591    </table>
592    <p>
593   
594  <li>
595    Create file formats (<i>i.e.</i>, plug-in configurations). The formats marked as
596    optional are not used in the test procedure, but may be useful to weed
597    out import problems, since they allow importing all info from the raw
598    data files. You may either enter the regular expressions as specified or
599    use the "Test with file" feature.
600   
601    <table class="listing" cellspacing="0" cellpadding="2" border="0">
602    <tr>
603      <th>Name</th>
604      <th>Plugin</th>
605      <th>Configuration values</th>
606    </tr>
607   
608    <tr class="oddrow">
609      <td>Plates for project A</td>
610      <td>Plate importer</td>
611      <td>
612     
613      <b>Test with file:</b> <code>plates_and_reporters.mouse.v4.37k.txt</code>
614      <table border="0" cellspacing="0" cellpadding="2">
615      <tr>
616        <td><i>Data header</i></td>
617        <td>384_number\t384_column\t384_row\t384_position\toligo_id.*</td>
618      </tr>
619      <tr>
620        <td><i>Data splitter</i></td>
621        <td>\t</td>
622      </tr>
623      <tr>
624        <td><i>Min data columns</i></td>
625        <td>5</td>
626      </tr>
627      <tr>
628        <td><i>Plate number/name</i></td>
629        <td>\384_number\</td>
630      </tr>
631      <tr>
632        <td><i>Row</i></td>
633        <td>\384_row\</td>
634      </tr>
635      <tr>
636        <td><i>Column</i></td>
637        <td>\384_column\</td>
638      </tr>
639      <tr>
640        <td><i>Reporter ID</i></td>
641        <td>\oligo_id\</td>
642      </tr>
643      </table>
644
645      </td>
646    </tr>
647   
648    <tr class="evenrow">
649      <td>GenePix feature importer<br>(optional)</td>
650      <td>Reporter map importer</td>
651      <td>
652     
653      <b>Test with file:</b> <code>genepix.mouse.v4.37k.00h.gpr</code>
654      <table border="0" cellspacing="0" cellpadding="2">
655      <tr>
656        <td><i>Data header</i></td>
657        <td>"Block"\t"Column"\t"Row"\t"Name"\t"ID"\t.*</td>
658      </tr>
659      <tr>
660        <td><i>Data splitter</i></td>
661        <td>\t</td>
662      </tr>
663      <tr>
664        <td><i>Min data columns</i></td>
665        <td>48</td>
666      </tr>
667      <tr>
668        <td><i>Max data columns</i></td>
669        <td>48</td>
670      </tr>
671      <tr>
672        <td><i>Reporter ID</i></td>
673        <td>\ID\</td>
674      </tr>
675      <tr>
676        <td><i>Block</i></td>
677        <td>\Block\</td>
678      </tr>
679      <tr>
680        <td><i>Column</i></td>
681        <td>\Column\</td>
682      </tr>
683      <tr>
684        <td><i>Row</i></td>
685        <td>\Row\</td>
686      </tr>
687      </table>
688
689      </td>
690    </tr>
691   
692    <tr class="oddrow">
693      <td>Raw data for project A</td>
694      <td>Raw data importer</td>
695      <td>
696     
697      <b>Test with file:</b> <code>genepix.mouse.v4.37k.00h.gpr</code>
698      <table border="0" cellspacing="0" cellpadding="2">
699      <tr>
700        <td><i>Raw data type</i></td>
701        <td>Genepix</td>
702      </tr>
703      <tr>
704        <td><i>Header</i></td>
705        <td>"(.+)=(.*)"</td>
706      </tr>
707      <tr>
708        <td><i>Data header</i></td>
709        <td>"Block"\t"Column"\t"Row"\t"Name"\t"ID"\t.*"Ratio of Medians \(532\/635\)".*</td>
710      </tr>
711      <tr>
712        <td><i>Data splitter</i></td>
713        <td>\t</td>
714      </tr>
715      <tr>
716        <td><i>Min data columns</i></td>
717        <td>48</td>
718      </tr>
719      <tr>
720        <td><i>Max data columns</i></td>
721        <td>48</td>
722      </tr>
723
724      <tr>
725        <td><i>Block</i></td>
726        <td>\Block\</td>
727      </tr>
728      <tr>
729        <td><i>Column</i></td>
730        <td>\Column\</td>
731      </tr>
732      <tr>
733        <td><i>Row</i></td>
734        <td>\Row\</td>
735      </tr>
736      <tr>
737        <td><i>X</i></td>
738        <td>\X\</td>
739      </tr>
740      <tr>
741        <td><i>Y</i></td>
742        <td>\Y\</td>
743      </tr>
744      <tr>
745        <td><i>Reporter ID</i></td>
746        <td>\ID\</td>
747      </tr>
748      <tr>
749        <td><i>Spot diameter</i></td>
750        <td>\Dia.\</td>
751      </tr>
752      <tr>
753        <td><i>Channel 1 foreground median</i></td>
754        <td>\F635 Median\</td>
755      </tr>
756      <tr>
757        <td><i>Channel 1 foreground mean</i></td>
758        <td>\F635 Mean\</td>
759      </tr>
760      <tr>
761        <td><i>Channel 1 foreground standard deviation</i></td>
762        <td>\F635 SD\</td>
763      </tr>
764      <tr>
765        <td><i>Channel 1 background median</i></td>
766        <td>\B635 Median\</td>
767      </tr>
768      <tr>
769        <td><i>Channel 1 background mean</i></td>
770        <td>\B635 Mean\</td>
771      </tr>
772      <tr>
773        <td><i>Channel 1 background standard deviation</i></td>
774        <td>\B635 SD\</td>
775      </tr>
776      <tr>
777        <td><i>Percent pixels within 1 standard deviation</i></td>
778        <td>\% > B635+1SD\</td>
779      </tr>
780      <tr>
781        <td><i>Percent pixels within 2 standard deviations</i></td>
782        <td>\% > B635+2SD\</td>
783      </tr>
784      <tr>
785        <td><i>Percent saturated pixels</i></td>
786        <td>\F635 % Sat.\</td>
787      </tr>
788      <tr>
789        <td><i>Channel 2 foreground median</i></td>
790        <td>\F532 Median\</td>
791      </tr>
792      <tr>
793        <td><i>Channel 2 foreground mean</i></td>
794        <td>\F532 Mean\</td>
795      </tr>
796      <tr>
797        <td><i>Channel 2 foreground standard deviation</i></td>
798        <td>\F532 SD\</td>
799      </tr>
800      <tr>
801        <td><i>Channel 2 background median</i></td>
802        <td>\B532 Median\</td>
803      </tr>
804      <tr>
805        <td><i>Channel 2 background mean</i></td>
806        <td>\B532 Mean\</td>
807      </tr>
808      <tr>
809        <td><i>Channel 2 background standard deviation</i></td>
810        <td>\B532 SD\</td>
811      </tr>
812      <tr>
813        <td><i>Percent pixels within 1 standard deviation</i></td>
814        <td>\% > B532+1SD\</td>
815      </tr>
816      <tr>
817        <td><i>Percent pixels within 2 standard deviations</i></td>
818        <td>\% > B532+2SD\</td>
819      </tr>
820      <tr>
821        <td><i>Percent saturated pixels</i></td>
822        <td>\F532 % Sat.\</td>
823      </tr>
824      <tr>
825        <td><i>Foreground pixels</i></td>
826        <td>\F Pixels\</td>
827      </tr>
828      <tr>
829        <td><i>Background pixels</i></td>
830        <td>\B Pixels\</td>
831      </tr>
832      <tr>
833        <td><i>Flags</i></td>
834        <td>\Flags\</td>
835      </tr>
836      </table>
837
838      </td>
839    </tr>
840   
841    <tr class="evenrow">
842      <td>Raw data for project A (dye-swap)</td>
843      <td>Raw data importer</td>
844      <td>
845
846      <b>Test with file:</b> <code>genepix.mouse.v4.37k.00h.dyeswap.gpr</code>
847      <table border="0" cellspacing="0" cellpadding="2">
848      <tr>
849        <td><i>Raw data type</i></td>
850        <td>Genepix</td>
851      </tr>
852      <tr>
853        <td><i>Header</i></td>
854        <td>"(.+)=(.*)"</td>
855      </tr>
856      <tr>
857        <td><i>Data header</i></td>
858        <td>"Block"\t"Column"\t"Row"\t"Name"\t"ID"\t.*"Ratio of Medians \(635\/532\)".*</td>
859      </tr>
860      <tr>
861        <td><i>Data splitter</i></td>
862        <td>\t</td>
863      </tr>
864      <tr>
865        <td><i>Min data columns</i></td>
866        <td>48</td>
867      </tr>
868      <tr>
869        <td><i>Max data columns</i></td>
870        <td>48</td>
871      </tr>
872
873      <tr>
874        <td><i>Block</i></td>
875        <td>\Block\</td>
876      </tr>
877      <tr>
878        <td><i>Column</i></td>
879        <td>\Column\</td>
880      </tr>
881      <tr>
882        <td><i>Row</i></td>
883        <td>\Row\</td>
884      </tr>
885      <tr>
886        <td><i>X</i></td>
887        <td>\X\</td>
888      </tr>
889      <tr>
890        <td><i>Y</i></td>
891        <td>\Y\</td>
892      </tr>
893      <tr>
894        <td><i>Reporter ID</i></td>
895        <td>\ID\</td>
896      </tr>
897      <tr>
898        <td><i>Spot diameter</i></td>
899        <td>\Dia.\</td>
900      </tr>
901      <tr>
902        <td><i>Channel 1 foreground median</i></td>
903        <td>\F532 Median\</td>
904      </tr>
905      <tr>
906        <td><i>Channel 1 foreground mean</i></td>
907        <td>\F532 Mean\</td>
908      </tr>
909      <tr>
910        <td><i>Channel 1 foreground standard deviation</i></td>
911        <td>\F532 SD\</td>
912      </tr>
913      <tr>
914        <td><i>Channel 1 background median</i></td>
915        <td>\B532 Median\</td>
916      </tr>
917      <tr>
918        <td><i>Channel 1 background mean</i></td>
919        <td>\B532 Mean\</td>
920      </tr>
921      <tr>
922        <td><i>Channel 1 background standard deviation</i></td>
923        <td>\B532 SD\</td>
924      </tr>
925      <tr>
926        <td><i>Percent pixels within 1 standard deviation</i></td>
927        <td>\% > B532+1SD\</td>
928      </tr>
929      <tr>
930        <td><i>Percent pixels within 2 standard deviations</i></td>
931        <td>\% > B532+2SD\</td>
932      </tr>
933      <tr>
934        <td><i>Percent saturated pixels</i></td>
935        <td>\F532 % Sat.\</td>
936      </tr>
937      <tr>
938        <td><i>Channel 2 foreground median</i></td>
939        <td>\F635 Median\</td>
940      </tr>
941      <tr>
942        <td><i>Channel 2 foreground mean</i></td>
943        <td>\F635 Mean\</td>
944      </tr>
945      <tr>
946        <td><i>Channel 2 foreground standard deviation</i></td>
947        <td>\F635 SD\</td>
948      </tr>
949      <tr>
950        <td><i>Channel 2 background median</i></td>
951        <td>\B635 Median\</td>
952      </tr>
953      <tr>
954        <td><i>Channel 2 background mean</i></td>
955        <td>\B635 Mean\</td>
956      </tr>
957      <tr>
958        <td><i>Channel 2 background standard deviation</i></td>
959        <td>\B635 SD\</td>
960      </tr>
961      <tr>
962        <td><i>Percent pixels within 1 standard deviation</i></td>
963        <td>\% > B635+1SD\</td>
964      </tr>
965      <tr>
966        <td><i>Percent pixels within 2 standard deviations</i></td>
967        <td>\% > B635+2SD\</td>
968      </tr>
969      <tr>
970        <td><i>Percent saturated pixels</i></td>
971        <td>\F635 % Sat.\</td>
972      </tr>
973      <tr>
974        <td><i>Foreground pixels</i></td>
975        <td>\F Pixels\</td>
976      </tr>
977      <tr>
978        <td><i>Background pixels</i></td>
979        <td>\B Pixels\</td>
980      </tr>
981      <tr>
982        <td><i>Flags</i></td>
983        <td>\Flags\</td>
984      </tr>
985      </table>
986
987      </td>
988    </tr>
989    </table>
990    <p>
991  </li>
992 
993  <li>
994    Annotate the file formats:
995    <table class="listing" cellspacing="0" cellpadding="2" border="0">
996    <tr>
997      <th>File format</th>
998      <th>Annotation</th>
999      <th>Value</th>
1000    </tr>
1001    <tr>
1002      <td>Raw data for project A</td>
1003      <td>Dye swap</td>
1004      <td>false</td>
1005    </tr>
1006    <tr>
1007      <td>Raw data for project A (dye swap)</td>
1008      <td>Dye swap</td>
1009      <td>true</td>
1010    </tr>
1011    </table>
1012    This will make the raw data importer automatically annotate the
1013    raw bioassays with the specified annotations.
1014    <p>
1015  </li>
1016 
1017  <li>
1018    Create plate type:
1019    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1020    <tr>
1021      <th>Name</th>
1022      <th>Geometry</th>
1023    </tr>
1024    <tr>
1025      <td>Plate type A</td>
1026      <td>384-well (16 x 24)</td>
1027    </tr>
1028    </table>
1029    <p>
1030  </li>
1031 
1032  <li>
1033    Import plates:
1034    <ol>
1035    <li>Go to the <code>Array LIMS -> Plates</code> page.</li>
1036    <li>Click on the <code>Import</code> button.</li>
1037    <li>Choose <code>auto-detect</code> and select
1038      the file <code>plates_and_reporters.mouse.v4.37k.txt</code>.</li>
1039    <li>The <code>Plates for project A</code> format should be
1040      found.</li>
1041    <li>Specify the following parameters:
1042   
1043      <table border="0" cellspacing="0" cellpadding="2">
1044      <tr>
1045        <td><i>Plate type</i></td>
1046        <td>Plate type A</td>
1047      </tr>
1048      <tr>
1049        <td><i>Plate name prefix</i></td>
1050        <td>Plate A</td>
1051      </tr>
1052      <tr>
1053        <td><i>Plate name padding</i></td>
1054        <td>4</td>
1055      </tr>
1056      </table>
1057    </li>
1058    <li>Continue and wait for the import to finish. It should create 96 plates.</li>
1059    </ol>
1060    <p>
1061  </li>
1062
1063  <li>
1064    Create array designs and upload data files to them:
1065    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1066    <tr>
1067      <th>Name</th>
1068      <th>Platform</th>
1069      <th>File(s)</th>
1070    </tr>
1071    <tr>
1072      <td>Array design A</td>
1073      <td>Generic</td>
1074      <td><i>Print map</i>: printmap.mouse.v4.37k.tam</td>
1075    </tr>
1076    <tr>
1077      <td>Affymetrix A</td>
1078      <td>Affymetrix</td>
1079      <td><i>CDF file</i>: MG_U74Av2.cdf.bz2</td>
1080    </tr>
1081    </table>
1082    <p>
1083    Or
1084    <p>
1085    Import array designs with the ArrayDesignImporter plug-in.
1086    <ol>
1087      <li>Make sure the data-files, mentioned in table above, are located in <code>/home/power/</code>, upload them if not</li>
1088      <li>Click on the <code>Import</code> button on the array design list page.</li>
1089      <li>Choose ArrayDesignImporter in the plug-in drop-down list.</li>
1090      <li><b>Test with file:</b> <code>arraydesign_out.txt</code> and set
1091        the parsing parameters with help of the <code>Auto generate</code> button on the <code>Column mapping</code>
1092        tab.</li>
1093      <li>Start the import-job by clicking on the <code>Finish</code> button on the third wizard-page.</li>     
1094    </ol>
1095    <p>
1096  </li>
1097 
1098  <li>
1099    Connect <code>Array design A</code> with plates. Select the imported plates (plate names starting
1100    with <code>Plate A</code>) and sort them in the correct order (as indicated by their names).
1101    <p>
1102  </li>
1103 
1104  <li>
1105    Import features:
1106    <ol>
1107    <li>Click on the <code>Import</code> button when viewing properties for the array design.</li>
1108    <li>Choose <code>auto-detect</code> and upload the file
1109      <code>printmap.mouse.v4.37k.tam</code>.</li>
1110    <li>The <code>Print map importer</code> plug-in should be
1111      found.</li>
1112    <li>Continue and wait for the import to finish. It should create 36,864 features and 48 blocks.</li>
1113    </ol>
1114    <p>
1115  </li>
1116
1117  <li>
1118    Set project defaults. Go to the projects page and edit the
1119    <code>Project A</code> project. On the <code>Defaults</code>
1120    tab, set the following defaults:
1121   
1122    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1123    <tr>
1124      <th>Setting</th>
1125      <th>Value</th>
1126    </tr>
1127    <tr>
1128      <td>Platform / raw data type</td>
1129      <td>Generic / Genepix</td>
1130    </tr>
1131    <tr>
1132      <td>Software</td>
1133      <td>Software A</td>
1134    </tr>
1135    <tr>
1136      <td>Array design</td>
1137      <td>Array design A</td>
1138    </tr>
1139    <tr>
1140      <td>Hybridization station</td>
1141      <td>Hybridization station A</td>
1142    </tr>
1143    <tr>
1144      <td>Scanner</td>
1145      <td>Scanner A</td>
1146    </tr>
1147    <tr>
1148      <td>Print robot</td>
1149      <td>Print robot A</td>
1150    </tr>
1151    <tr>
1152      <td>Scanning protocol</td>
1153      <td>Scanning A</td>
1154    </tr>
1155    <tr>
1156      <td>Sampling protocol</td>
1157      <td>Sampling A</td>
1158    </tr>
1159    <tr>
1160      <td>Extraction protocol</td>
1161      <td>Extraction A</td>
1162    </tr>
1163    <tr>
1164      <td>Labeling protocol</td>
1165      <td>Labeling A</td>
1166    </tr>
1167    <tr>
1168      <td>Hybridization protocol</td>
1169      <td>Hybridization A</td>
1170    </tr>
1171    <tr>
1172      <td>Feat. extraction protocol</td>
1173      <td>Feature extraction A</td>
1174    </tr>
1175    <tr>
1176      <td>Printing protocol</td>
1177      <td>Printing A</td>
1178    </tr>
1179    </table>
1180   
1181    <p>
1182  </li>
1183
1184  <li>
1185    Create array batches:
1186    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1187    <tr>
1188      <th>Name</th>
1189      <th>Array design</th>
1190      <th>Print robot</th>
1191      <th>Protocol</th>
1192    </tr>
1193    <tr>
1194      <td>Array batch A</td>
1195      <td>Array design A</td>
1196      <td>Robot A</td>
1197      <td>Printing A</td>
1198    </tr>
1199    <tr>
1200      <td>Affymetrix batch A</td>
1201      <td>Affymetrix A</td>
1202      <td></td>
1203      <td></td>
1204    </tr>
1205    </table>
1206    <p>
1207    Or
1208    <p>
1209    Import array batches with the ArrayBatchImporter plug-in.
1210    <ol>
1211      <li>Click on the <code>Import</code> button on the array batch list page.</li>
1212      <li>Select ArrayBatchImporter in the plug-in drop-down list and click <code>Next</code></li>
1213      <li><b>Test with file:</b> <code>arraybatch_out.txt</code> and set  the parsing parameters
1214        with help of the <code>Auto generate</code> button on the <code>Column mapping</code>
1215        tab.</li>
1216      <li>Start the import-job by clicking on the <code>Finish</code> button on the third wizzard-page.</li>     
1217    </ol>
1218    <p>   
1219  </li>
1220
1221  <li>
1222    Create array slides with the <code>Create slides</code>
1223    wizard.
1224   
1225    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1226    <tr>
1227      <th>Name</th>
1228      <th>Array batch</th>
1229      <th>Quantity</th>
1230    </tr>
1231    <tr>
1232      <td>Array slide A.</td>
1233      <td>Array batch A</td>
1234      <td>4</td>
1235    </tr>
1236    <tr>
1237      <td>Affymetrix slide A.</td>
1238      <td>Affymetrix batch A</td>
1239      <td>3</td>
1240    </tr>
1241    </table>
1242    <p>
1243    Or
1244    <p>
1245    Import array slides with the ArraySlideImporter plug-in.
1246    <ol>
1247      <li>Click on the <code>Import</code> button on the array slide list page.</li>
1248      <li>Select ArraySlideImporter in the plug-in drop-down list and click <code>Next</code></li>
1249      <li><b>Test with file:</b> <code>arrayslide_out.txt</code> and set  the parsing parameters
1250        with help of the <code>Auto generate</code> button on the <code>Column mapping</code>
1251        tab.</li>
1252      <li>Start the import-job by clicking on the <code>Finish</code> button on the third wizzard-page.</li>     
1253    </ol>
1254    <p>
1255  </li>
1256  </ol>
1257
1258  <a name="user"></a>
1259  <h2>5. User tests</h2>
1260  <p>
1261    The user is a typical worker in the project. The user does the actual experimentation in the
1262    lab, which includes collecting samples, doing extraction, labeling and hybridizations.
1263    The user also scans and analyses the raw data resulting from the images. Inserting items can be
1264    done in two different ways, .
1265  </p>
1266 
1267  <p>
1268    First activate the <code>Project A</code> project and then do one of following proceedures.
1269  </p>
1270  <p>
1271    Use the batch importers for each item type.
1272    <ol>
1273      <li>Click on the <code>Import</code> button on the list page.</li>
1274      <li>Select &lt;itemtype&gt;Importer in the plug-in drop-down list and click <code>Next</code></li>
1275      <li><b>Test with file:</b> using the right file(listed below) and set the parsing parameters
1276        by using the <code>Auto generate</code> button on the <code>Column mapping</code> tab.
1277        <table class="listing" cellspacing="0" cellpadding="2" border="0">
1278        <tr>
1279          <th>Itemtype</th>
1280          <th>File</th>
1281        </tr>
1282        <tr>
1283          <td>Biosource</td>
1284          <td>biosource_out.txt</td>       
1285        </tr>
1286        <tr>
1287          <td>Samples</td>
1288          <td>sample_out.txt</td>
1289        </tr>
1290        <tr>
1291          <td>Extracts</td>
1292          <td>extract_out.txt</td>
1293        </tr>
1294        <tr>
1295          <td>Labeled extracts</td>
1296          <td>labeledextract_out.txt</td>
1297        </tr>
1298        <tr>
1299          <td>Hybridizations</td>
1300          <td>hybridization_out.txt</td>
1301        </tr>
1302        <tr>
1303          <td>Scans</td>
1304          <td>scan_out.txt</td>
1305        </tr>
1306        <tr>
1307          <td>Raw bioassays</td>
1308          <td>rawbioassay_out.txt</td>
1309        </tr>
1310        </table>
1311        The files listed for biosource and samples also contains annotations
1312        for the items and these files should also be used with the annotation importer.
1313        The procedure is the same as for batch importers except that only <code>\\Name\\</code>
1314        is needed in the column mapping. The annotation column should be selected by default in
1315        the second wizzard-step.       
1316      </li>
1317      <li>Start the import-job by clicking on the <code>Finish</code> button on the third wizzard-page.</li>
1318      <li>Then <a href="#inheritannotations">go to the step</a> in the next list where inherited annotations are set to the raw data
1319        and proceed from there.</li>     
1320    </ol>
1321  </p>
1322  <p>
1323  Inserting each item manually
1324  <ol>
1325  <li>
1326    Create a bioplate:
1327    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1328    <tr>
1329      <th>Name</th>
1330      <th>Plate geometry</th>
1331    </tr>
1332    <tr>
1333      <td>Bioplate A</td>
1334      <td>96-well (8 x 12)</td>
1335    </tr>
1336    </table>
1337    <p>
1338  <li>
1339    Create a biosource:
1340    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1341    <tr>
1342      <th>Name</th>
1343      <th>Annotations</th>
1344    </tr>
1345    <tr>
1346      <td>Biosource A</td>
1347      <td>
1348        <table border="0" cellspacing="0" cellpadding="2">
1349        <tr>
1350          <td><i>Drug resistance:</i></td>
1351          <td>medium</td>
1352        </tr>
1353        </table>
1354      </td>
1355    </tr>
1356    </table>
1357    <p>
1358  </li>
1359 
1360  <li>
1361    Create samples:
1362    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1363    <tr>
1364      <th>Name</th>
1365      <th>Protocol</th>
1366      <th>Biosource</th>
1367      <th>Bioplate [well]</th>
1368      <th>Annotations</th>
1369    </tr>
1370    <tr>
1371      <td>Sample A.00h</td>
1372      <td>Sampling A</td>
1373      <td>Biosource A</td>
1374      <td>Bioplate A [0, 0]</td>
1375      <td>
1376        <table border="0" cellspacing="0" cellpadding="2">
1377        <tr>
1378          <td><i>Time:</i></td>
1379          <td>0h</td>
1380        </tr>
1381        </table>
1382      </td>
1383    </tr>
1384    <tr>
1385      <td>Sample A.24h</td>
1386      <td>Sampling A</td>
1387      <td>Biosource A</td>
1388      <td>Bioplate A [0, 1]</td>
1389      <td>
1390        <table border="0" cellspacing="0" cellpadding="2">
1391        <tr>
1392          <td><i>Time:</i></td>
1393          <td>24h</td>
1394        </tr>
1395        </table>
1396      </td>
1397    </tr>
1398    <tr>
1399      <td>Sample A.ref</td>
1400      <td>Sampling A</td>
1401      <td>-</td>
1402      <td>Bioplate A [0, 2]</td>
1403      <td>-</td>
1404    </tr>
1405    </table>
1406    <p>
1407  </li>
1408
1409  <li>
1410    Create extracts:
1411    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1412    <tr>
1413      <th>Name</th>
1414      <th>Protocol</th>
1415      <th>Sample</th>
1416      <th>Bioplate [well]</th>
1417    </tr>
1418    <tr>
1419      <td>Extract A.00h</td>
1420      <td>Extraction A</td>
1421      <td>Sample A.00h</td>
1422      <td>Bioplate A [1, 0]</td>
1423    </tr>
1424    <tr>
1425      <td>Extract A.24h</td>
1426      <td>Extraction A</td>
1427      <td>Sample A.24h</td>
1428      <td>Bioplate A [1, 1]</td>
1429    </tr>
1430    <tr>
1431      <td>Extract A.ref</td>
1432      <td>Extraction A</td>
1433      <td>Sample A.ref</td>
1434      <td>Bioplate A [1, 2]</td>
1435    </tr>
1436    </table>
1437    <p>
1438  </li>
1439
1440  <li>
1441    Create labeled extracts:
1442    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1443    <tr>
1444      <th>Name</th>
1445      <th>Label</th>
1446      <th>Protocol</th>
1447      <th>Extract</th>
1448      <th>Bioplate [well]</th>
1449    </tr>
1450    <tr>
1451      <td>Labeled extract A.00h</td>
1452      <td>cy3</td>
1453      <td>Labeling A</td>
1454      <td>Extract A.00h</td>
1455      <td>Bioplate A [2, 0]</td>
1456    </tr>
1457    <tr>
1458      <td>Labeled extract A.24h</td>
1459      <td>cy3</td>
1460      <td>Labeling A</td>
1461      <td>Extract A.24h</td>
1462      <td>Bioplate A [2, 1]</td>
1463    </tr>
1464    <tr>
1465      <td>Labeled extract A.ref</td>
1466      <td>cy5</td>
1467      <td>Labeling A</td>
1468      <td>Extract A.ref</td>
1469      <td>Bioplate A [2, 2]</td>
1470    </tr>
1471    <tr class="shaded">
1472      <td>Labeled extract A.00h (dye-swap)</td>
1473      <td>cy5</td>
1474      <td>Labeling A</td>
1475      <td>Extract A.00h</td>
1476      <td>Bioplate A [3, 0]</td>
1477    </tr>
1478    <tr class="shaded">
1479      <td>Labeled extract A.24h (dye-swap)</td>
1480      <td>cy5</td>
1481      <td>Labeling A</td>
1482      <td>Extract A.24h</td>
1483      <td>Bioplate A [3, 1]</td>
1484    </tr>
1485    <tr class="shaded">
1486      <td>Labeled extract A.ref (dye-swap)</td>
1487      <td>cy3</td>
1488      <td>Labeling A</td>
1489      <td>Extract A.ref</td>
1490      <td>Bioplate A [3, 2]</td>
1491    </tr>
1492    </table>
1493    <p>
1494  </li>
1495
1496  <li>
1497    Create hybridizations:
1498    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1499    <tr>
1500      <th>Name</th>
1501      <th>Protocol</th>
1502      <th>Hardware</th>
1503      <th>Array slide</th>
1504      <th>Labeled extracts</th>
1505    </tr>
1506    <tr>
1507      <td>Hybridization A.00h</td>
1508      <td>Hybridization A</td>
1509      <td>Hybridization station A</td>
1510      <td>Array slide A.1</td>
1511      <td>Labeled extract A.00h,<br>Labeled extract A.ref</td>
1512    </tr>
1513    <tr>
1514      <td>Hybridization A.24h</td>
1515      <td>Hybridization A</td>
1516      <td>Hybridization station A</td>
1517      <td>Array slide A.2</td>
1518      <td>Labeled extract A.24h,<br>Labeled extract A.ref</td>
1519    </tr>
1520    <tr class="shaded">
1521      <td>Hybridization A.00h (dye-swap)</td>
1522      <td>Hybridization A</td>
1523      <td>Hybridization station A</td>
1524      <td>Array slide A.3</td>
1525      <td>Labeled extract A.00h (dye-swap),<br>Labeled extract A.ref (dye-swap)</td>
1526    </tr>
1527    <tr class="shaded">
1528      <td>Hybridization A.24h (dye-swap)</td>
1529      <td>Hybridization A</td>
1530      <td>Hybridization station A</td>
1531      <td>Array slide A.4</td>
1532      <td>Labeled extract A.24h (dye-swap),<br>Labeled extract A.ref (dye-swap)</td>
1533    </tr>
1534    <tr>
1535      <td>Affymetrix hyb A.1</td>
1536      <td>Hybridization A</td>
1537      <td>Hybridization station A</td>
1538      <td>Affymetrix slide A.1</td>
1539      <td>Labeled extract A.00h</td>
1540    </tr>
1541    <tr>
1542      <td>Affymetrix hyb A.2</td>
1543      <td>Hybridization A</td>
1544      <td>Hybridization station A</td>
1545      <td>Affymetrix slide A.2</td>
1546      <td>Labeled extract A.24h</td>
1547    </tr>
1548    <tr>
1549      <td>Affymetrix hyb A.3</td>
1550      <td>Hybridization A</td>
1551      <td>Hybridization station A</td>
1552      <td>Affymetrix slide A.3</td>
1553      <td>Labeled extract A.ref</td>
1554    </tr>
1555    </table>
1556    <p>
1557  </li>
1558 
1559  <li>
1560    Create scans:
1561    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1562    <tr>
1563      <th>Name</th>
1564      <th>Hybridization</th>
1565      <th>Scanner</th>
1566      <th>Protocol</th>
1567    </tr>
1568    <tr>
1569      <td>Scan A.00h</td>
1570      <td>Hybridization A.00h</td>
1571      <td>Scanner A</td>
1572      <td>Scanning A</td>
1573    </tr>
1574    <tr>
1575      <td>Scan A.24h</td>
1576      <td>Hybridization A.24h</td>
1577      <td>Scanner A</td>
1578      <td>Scanning A</td>
1579    </tr>
1580    <tr class="shaded">
1581      <td>Scan A.00h (dye-swap)</td>
1582      <td>Hybridization A.00h (dye-swap)</td>
1583      <td>Scanner A</td>
1584      <td>Scanning A</td>
1585    </tr>
1586    <tr class="shaded">
1587      <td>Scan A.24h (dye-swap)</td>
1588      <td>Hybridization A.24h (dye-swap)</td>
1589      <td>Scanner A</td>
1590      <td>Scanning A</td>
1591    </tr>
1592    <tr>
1593      <td>Affymetrix scan A.1</td>
1594      <td>Affymetrix hyb A.1</td>
1595      <td>Scanner A</td>
1596      <td>Scanning A</td>
1597    </tr>
1598    <tr>
1599      <td>Affymetrix scan A.2</td>
1600      <td>Affymetrix hyb A.2</td>
1601      <td>Scanner A</td>
1602      <td>Scanning A</td>
1603    </tr>
1604    <tr>
1605      <td>Affymetrix scan A.3</td>
1606      <td>Affymetrix hyb A.3</td>
1607      <td>Scanner A</td>
1608      <td>Scanning A</td>
1609    </tr>
1610    </table>
1611    <p>
1612  </li>
1613 
1614  <li>
1615    Add images to the scans (TODO - we don't have any images yet):
1616    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1617    <tr>
1618      <th>Scan</th>
1619      <th>Image files</th>
1620    </tr>
1621    <tr>
1622      <td>Scan A.00h</td>
1623      <td>-</td>
1624    </tr>
1625    <tr>
1626      <td>Scan A.24h</td>
1627      <td>-</td>
1628    </tr>
1629    <tr class="shaded">
1630      <td>Scan A.00h (dye-swap)</td>
1631      <td>-</td>
1632    </tr>
1633    <tr class="shaded">
1634      <td>Scan A.24h (dye-swap)</td>
1635      <td>-</td>
1636    </tr>
1637    </table>
1638    <p>
1639  </li>
1640
1641  <li>
1642    Create raw bioassays:
1643    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1644    <tr>
1645      <th>Name</th>
1646      <th>Platform/Raw data type</th>
1647      <th>Array design</th>
1648      <th>Protocol</th>
1649      <th>Scan</th>
1650      <th>Software</th>
1651      <th>File(s)</th>
1652    </tr>
1653    <tr>
1654      <td>Raw bioassay A.00h</td>
1655      <td>Generic/GenePix</td>
1656      <td>Array design A</td>
1657      <td>Feature extraction A</td>
1658      <td>Scan A.00h</td>
1659      <td>Software A</td>
1660      <td><i>Raw data</i>: genepix.mouse.v4.37k.00h.gpr</td>
1661    </tr>
1662    <tr>
1663      <td>Raw bioassay A.24h</td>
1664      <td>Generic/GenePix</td>
1665      <td>Array design A</td>
1666      <td>Feature extraction A</td>
1667      <td>Scan A.24h</td>
1668      <td>Software A</td>
1669      <td><i>Raw data</i>: genepix.mouse.v4.37k.24h.gpr</td>
1670    </tr>   
1671    <tr class="shaded">
1672      <td>Raw bioassay A.00h (dye-swap)</td>
1673      <td>Generic/GenePix</td>
1674      <td>Array design A</td>
1675      <td>Feature extraction A</td>
1676      <td>Scan A.00h (dye-swap)</td>
1677      <td>Software A</td>
1678      <td><i>Raw data</i>: genepix.mouse.v4.37k.00h.dyeswap.gpr</td>
1679    </tr> 
1680    <tr class="shaded">
1681      <td>Raw bioassay A.24h (dye-swap)</td>
1682      <td>Generic/GenePix</td>
1683      <td>Array design A</td>
1684      <td>Feature extraction A</td>
1685      <td>Scan A.24h (dye-swap)</td>
1686      <td>Software A</td>
1687      <td><i>Raw data</i>: genepix.mouse.v4.37k.24h.dyeswap.gpr</td>
1688    </tr>
1689    <tr>
1690      <td>Affymetrix raw A.1</td>
1691      <td>Affymetrix</td>
1692      <td>Affymetrix A</td>
1693      <td>Feature extraction A</td>
1694      <td>Affymetrix scan A.1</td>
1695      <td>Software A</td>
1696      <td><i>CEL file</i>: jos1761.cel.bz2</td>
1697    </tr>   
1698    <tr>
1699      <td>Affymetrix raw A.2</td>
1700      <td>Affymetrix</td>
1701      <td>Affymetrix A</td>
1702      <td>Feature extraction A</td>
1703      <td>Affymetrix scan A.2</td>
1704      <td>Software A</td>
1705      <td><i>CEL file</i>: jos1762.cel.bz2</td>
1706    </tr>   
1707    <tr>
1708      <td>Affymetrix raw A.3</td>
1709      <td>Affymetrix</td>
1710      <td>Affymetrix A</td>
1711      <td>Feature extraction A</td>
1712      <td>Affymetrix scan A.3</td>
1713      <td>Software A</td>
1714      <td><i>CEL file</i>: jos1763.cel.bz2</td>
1715    </tr>   
1716    </table>
1717    <p>
1718  </li>
1719 
1720  <li>
1721    Create experiments:
1722    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1723    <tr>
1724      <th>Name</th>
1725      <th>Raw data type</th>
1726      <th>Raw bioassays</th>
1727      <th>Experimental factors</th>
1728    </tr>
1729    <tr>
1730      <td>Experiment A</td>
1731      <td>GenePix</td>
1732      <td>Raw bioassay A.00h,<br>Raw bioassay A.24h,<br>Raw bioassay A.00h (dye-swap),<br>
1733        Raw bioassay A.24h (dye-swap)</td>
1734      <td>Drug resistance, Time, Dye swap</td>
1735    </tr>
1736    <tr>
1737      <td>Affymetrix A</td>
1738      <td>Affymetrix</td>
1739      <td>Affymetrix raw A.1,<br>Affymetrix raw A.2,<br>Affymetrix raw A.3</td>
1740      <td>Drug resistance, Time</td>
1741    </tr>
1742    </table>
1743    <p>
1744  </li>
1745 
1746  <li><a name="inheritannotations"></a>
1747    Inherit the annotations from the samples and biosource for each raw bioassay.
1748    Use the <i>auto-inherit</i> function that exists on the experiment properties
1749    tab. The <i>Status</i> column in <i>Experimental factors</i> table should indicate
1750    the number of raw bioassays that is missing a value. Click on this warning to
1751    automatically inherit annotations from the parents. Note! The <i>Dye swap</i>
1752    annotation will not get values until the next step, and the <i>Affymetrix raw A.3</i>
1753    data set doesn't have any parents with annotations.
1754    <p>
1755
1756  </li>
1757 
1758  <li>
1759    Import GenePix raw data. There are two possible ways to do this:
1760    <ol>
1761    <li>Manually import to each raw bioassay.
1762    <li>Batch import to multiple raw bioassays.
1763    </ol>
1764    <p>
1765    <b>Manual import:</b> Go to the properties tab for each raw bioassay.
1766    Click on the <i>Import</i> button and use the auto-detect feature to
1767    import the raw data. Use the default configuration values except for
1768    those listed in the table below.
1769    <p>
1770   
1771    <b>Batch import:</b> The batch import is started from the
1772    properties tab of the <i>experiment</i>. Click on "Import" and
1773    use the auto-detect feature with one of the used files. Use the default
1774    configuration values except for those listed in the table below.
1775    The batch import should import two raw data sets in one go (since it can
1776    only work with a single file format at a time and the dye-swap files uses
1777    a different file format). Repeat the batch import a second time to import
1778    the remaining two raw data sets.
1779    <p>
1780   
1781    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1782    <tr>
1783      <th>Parameter</th>
1784      <th>Value</th>
1785      <th>Mode</th>
1786    </tr>
1787    <tr>
1788      <td>Feature mismatch</td>
1789      <td>smart</td>
1790      <td>both</td>
1791    </tr>
1792    <tr>
1793      <td>Invalid numeric value</td>
1794      <td>null</td>
1795      <td>both</td>
1796    </tr>
1797    <tr>
1798      <td>Log file</td>
1799      <td>~/import.log</td>
1800      <td>batch import</td>
1801    </tr>
1802    </table>
1803    <p>
1804       
1805    In both cases, the import should produce the same results
1806    as in the table below. When using the batch import mode, the
1807    detailed information for each raw bioassay is only found in
1808    the log file.
1809    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1810    <tr>
1811      <th>Raw bioassay</th>
1812      <th>Raw data file</th>
1813      <th>Spots inserted/with null reporter/skipped)</th>
1814      <th>Annotations created</th>
1815    </tr>
1816    <tr>
1817      <td>Raw bioassay A.00h</td>
1818      <td>genepix.mouse.v4.37k.00h.gpr</td>
1819      <td>36,864/632/768</td>
1820      <td><i>Dye swap</i>: false</td>
1821    </tr>
1822    <tr>
1823      <td>Raw bioassay A.24h</td>
1824      <td>genepix.mouse.v4.37k.24h.gpr</td>
1825      <td>36,864/632/768</td>
1826      <td><i>Dye swap</i>: false</td>
1827    </tr>   
1828    <tr class="shaded">
1829      <td>Raw bioassay A.00h (dye-swap)</td>
1830      <td>genepix.mouse.v4.37k.00h.dyeswap.gpr</td>
1831      <td>36,864/632/768</td>
1832      <td><i>Dye swap</i>: true</td>
1833    </tr> 
1834    <tr class="shaded">
1835      <td>Raw bioassay A.24h (dye-swap)</td>
1836      <td>genepix.mouse.v4.37k.24h.dyeswap.gpr</td>
1837      <td>36,864/632/768</td>
1838      <td><i>Dye swap</i>: true</td>
1839    </tr>
1840    </table>
1841    <p>
1842   
1843  </li>
1844 
1845  <li>
1846    Check the experiment overview page. It should display one warnings for the
1847    Genepix experiment. The warning is related to a missing biosurce
1848    on the reference sample.
1849    <p>
1850    The Affymetrix experiment gives some more warnings. Most of them are
1851    related to not using the project default items, missing protocols
1852    and missing hardware. There should also be an error about missing
1853    experimental factor values for the <code>Affymetrix.3</code>
1854    raw bioassay. It is expected since this comes from the reference sample
1855    which doesn't have values for those annotations.
1856    <p>
1857   
1858    Change validation options to reduce the number of warnings:
1859    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1860    <tr>
1861      <th>Validation option</th>
1862      <th>Setting</th>
1863    </tr>
1864    <tr>
1865      <td>Project defaults</td>
1866      <td>Set all to <code>Ignore</code></td>
1867    </tr>
1868    <tr>
1869      <td>Missing items</td>
1870      <td>Set all to <code>Ignore</code></td>
1871    </tr>
1872    <tr>
1873      <td>Annotations - Missing factor value</td>
1874      <td><code>Warning</code></td>
1875    </tr>
1876    </table>
1877   
1878    After the changes there should now only be two warnings about the
1879    missing factor values.
1880   
1881    <p>
1882  </li>
1883 
1884  </ol>
1885  </li>
1886  </ol>
1887
1888  <a name="analysis"></a>
1889  <h2>6. Analysis tests</h2>
1890  <p>
1891    Now it is time to analyse the data. The analysis test should be done
1892    by both a regular user and a guest.
1893  </p>
1894 
1895  <ol>
1896  <li>
1897    Activate the <code>Project A</code> project<p>
1898  </li>
1899   
1900  <li>
1901    Go to the <code>Experiment A</code> experiment and select
1902    the <code>Bioassay sets</code> tab.
1903    <p>
1904  </li>
1905 
1906  <li>
1907    Create a new root bioassay set:
1908    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1909    <tr>
1910      <th>Bioassay set name</th>
1911      <th>Raw bioassays</th>
1912      <th>Formula</th>
1913    </tr>
1914    <tr>
1915      <td>Root bioassay set</td>
1916      <td>all</td>
1917      <td>Mean FG - Mean BG</td>
1918    </tr>
1919    </table>
1920    Wait for the plug-in to finish.
1921    <p>
1922  </li>
1923 
1924  <li>
1925    Select the created bioassay set and create a filtered bioassayset:
1926    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1927    <tr>
1928      <th>Child name</th>
1929      <th>Filter preset</th>
1930      <th>Expression</th>
1931    </tr>
1932    <tr>
1933      <td>Filtered bioassay set</td>
1934      <td>-</td>
1935      <td>ch(1) &gt; 0 &amp;&amp; ch(2) &gt; 0 &amp;&amp; rep('id') != null</td>
1936    </tr>
1937    </table>
1938    Wait for the plug-in to finish. It should report that 136,498 spots remain and
1939    that 10,958 spots has been removed.
1940    <p>
1941  </li>
1942
1943  <li>
1944    Select the filtered bioassay set and run a normalization plug-in:
1945    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1946    <tr>
1947      <th>Plugin</th>
1948      <th>Parameters</th>
1949    </tr>
1950    <tr>
1951      <td>Normalization: Lowess</td>
1952      <td>Accept the default parameters.</td>
1953    </tr>
1954    </table>
1955    Wait for the plug in to finish. It should report that 136,498 spots has been
1956    normalized and 0 spots has been removed.
1957    <p>
1958  </li>
1959   
1960  <li>
1961    Select the normalized bioassay set and check the overview plots and
1962    the correction factor plots. Here are four examples:
1963    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1964    <tr>
1965      <th>Overview plots</th>
1966      <th>Correction factor plots</th>
1967    </tr>
1968    <tr>
1969      <td><img src="overview.png"><br><img src="overview.dyeswap.png"></td>
1970      <td><img src="correction.png"><br><img src="correction.dyeswap.png"></td>
1971    </tr>
1972    </table>
1973    <p>
1974  </li>
1975 
1976  <li>
1977    Try the plot tool with the following plots. Use the <code>Save</code> function
1978    to save one them as a file in the BASE file system, and the <code>Download</code> 
1979    function  to download a plot to your computer.
1980    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1981    <tr>
1982      <th>Plot type</th>
1983      <th>Y-axis preset</th>
1984      <th>X-axis preset</th>
1985      <th>Other options</th>
1986    </tr>
1987    <tr>
1988      <td>Scatter plot</td>
1989      <td>M, log2(ch1 / ch2)</td>
1990      <td>A, log10(ch1 * ch2) / 2</td>
1991      <td>-</td>
1992    </tr>
1993    <tr>
1994      <td>Histogram plot</td>
1995      <td>Count</td>
1996      <td>Ratio, ch1 / ch2</td>
1997      <td>
1998        <table border="0" cellspacing="0" cellpadding="2">
1999        <tr>
2000          <td><i>Log scale</i></td>
2001          <td>checked</td>
2002        </tr>
2003        <tr>
2004          <td><i>Bin size</i></td>
2005          <td>0.1</td>
2006        </tr>
2007        <tr>
2008          <td><i>Annotation</i></td>
2009          <td>Time</td>
2010        </tr>
2011        </table>
2012      </td>
2013    </tr>
2014    </table>
2015    <p>
2016    Here are two examples:
2017    <table class="listing" cellspacing="0" cellpadding="2" border="0">
2018    <tr>
2019      <th>Scatter plot</th>
2020    </tr>
2021    <tr>
2022      <td><img src="scatter.png"></td>
2023    </tr>
2024    </table>
2025    <p>
2026    <table class="listing" cellspacing="0" cellpadding="2" border="0">
2027    <tr>
2028      <th>Histogram plot</th>
2029    </tr>
2030    <tr>
2031      <td><img src="histogram.png"></td>
2032    </tr>
2033    </table>
2034    <p>
2035  </li>
2036 
2037  </ol>
2038
2039
2040</body>
2041</html>
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