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Last change on this file since 2935 was 2935, checked in by Nicklas Nordborg, 17 years ago
Test program now sets USE permission to plugins since the default has changed and everyone no longer has permission.
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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 2935 2006-11-17 13:12:27Z nicklas $
4
5	Copyright (C) 2005-2006 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 2
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 this program; if not, write to the Free Software
22	Foundation, Inc., 59 Temple Place - Suite 330,
23	Boston, MA 02111-1307, USA.
24	-->
25	<html>
26	<head>
27	<title>BASE - Test procedures for predefined roles</title>
28	<link rel=stylesheet type="text/css" href="../../styles.css">
29	</head>
30	<body>
31
32	<div class="navigation">
33	<a href="../../index.html">BASE</a>
34	<img src="../../next.gif">
35	<a href="../index.html">Test procedures</a>
36	<img src="../../next.gif">
37	Predefined roles
38	</div>
39
40	<h1>Test procedures for predefined roles</h1>
41
42	<div class="abstract">
43	<p>
44	This document defines a procedure for testing that
45	the predefined roles can perform their work as intended. The main
46	purpose is to weed out permission problems resulting from:
47	</p>
48
49	<ul>
50	<li>Incorrect permissions installed by installation program</li>
51	<li>Bugs in the permission handling in the core</li>
52	<li>Incorrect handling of permissions in the web client</li>
53	</ul>
54
55	<p>
56	The test procedure also tests that the
57	basic functionality is working:
58	</p>
59
60	<ul>
61	<li>Creating items and linking them to other items</li>
62	<li>Defining import file formats</li>
63	<li>Importing array LIMS data</li>
64	<li>Importing and validating raw data against array LIMS data</li>
65	<li>Running analysis plug-ins</li>
66	</ul>
67
68	<b>Contents</b><br>
69	<ol>
70	<li><a href="#summary">Summary of the test procedure</a></li>
71	<li><a href="#root">Root user tests</a></li>
72	<li><a href="#admin">Administrator tests</a></li>
73	<li><a href="#power">Power user tests</a></li>
74	<li><a href="#user">User tests</a></li>
75	<li><a href="#analysis">Analysis tests</a></li>
76	</ol>
77
78	<p class="authors">
79	<b>Last updated:</b> $Date: 2006-11-17 13:12:27 +0000 (Fri, 17 Nov 2006) $
80	</p>
81	</div>
82
83
84	<a name="summary"></a>
85	<h2>1. Summary of the test procedure</h2>
86
87	<p>
88	Here is a summary of the test procedure:
89	</p>
90
91	<ol>
92	<li>Always start with a fresh installation.</li>
93
94	<li>The root user creates an administrator.</li>
95
96	<li>The administrator creates a group and three other users. One
97	power user, one user and one guest.</li>
98
99	<li>The power user creates item related to the project management:
100	<ul>
101	<li>A project</li>
102	<li>Protocols, one for each type of action: sampling, extraction, etc.</li>
103	<li>Hardware and software that are used in the project</li>
104	<li>Annotation types for annotations used in the project</li>
105	<li>File formats for importing reporters, plates, print maps and raw data</li>
106	<li>LIMS information - plate type, plates, array design, array batch and array slides</li>
107	</ul>
108	</li>
109
110	<li>The user creates items related to an actual experiment:
111	<ul>
112	<li>Biomaterials: biosources, samples, extracts, etc.</li>
113	<li>Experiment: hybridizations, scans, images, raw bioassays</li>
114	<li>Import raw data</li>
115	</ul>
116	</li>
117
118	<li>Both the user and the guest then do some analysis:
119	<ul>
120	<li>Create a root bioassay set</li>
121	<li>Filter the bioassay set</li>
122	<li>Run a normalization plug-in</li>
123	<li>Check the result by listing and plotting the data</li>
124	</ul>
125	</li>
126	</ol>
127
128	<p>
129	These tests can also be run in automated mode by test programs. This will of
130	course not test the web client, but are useful if one quickly needs to do
131	parts of the test and then continue with, for example, the user or analysis tests
132	on the web.
133	</p>
134
135	<p>
136	The data files needed by the tests are NOT included in the subversion repository.
137	The main reason is that they are too large, and that we don't have permission to
138	make them publicly available for download. To get the test file you need to be a
139	core developer. Read the instructions on the
140	<a href="http://base.thep.lu.se/wiki/DeveloperInformation">DeveloperInformation</a>
141	page, <code>Test data</code> section on the Base 2 web site.
142	</p>
143
144	<p>
145	To run the test do the following:
146	</p>
147	<ol>
148
149	<li>Compile the core and the test programs: <code>ant main test</code>.</li>
150
151	<li>Change to the <code>build/test/</code> directory.</li>
152
153	<li>Run test programs: <code>./test.sh roles <cmds></code> where
154	<code><cmds></code> is one or more of the following:
155	<ul>
156	<li><code>all</code>: run all tests</li>
157	<li><code>root</code>: run the root user tests</li>
158	<li><code>admin</code>: run the administrator tests</li>
159	<li><code>power</code>: run the power user tests</li>
160	<li><code>user</code>: run the regular user tests</li>
161	<li><code>guest</code>: run the guest user tests</li>
162	</ul>
163	</li>
164
165	</ol>
166
167	<a name="root"></a>
168	<h2>2. Root user tests</h2>
169	<p>
170	The root user creates an administrator which is a server-wide admin.
171	</p>
172
173	<ol>
174	<li>
175	Create a new user and set the following
176	properties. All other properties may remain unchanged.
177
178	<table class="listing" cellspacing="0" cellpadding="2" border="0">
179	<tr>
180	<th>Name</th>
181	<th>Login/Password</th>
182	<th>Quota</th>
183	<th>Quota group</th>
184	<th>Membership</th>
185	</tr>
186	<tr>
187	<td>Admin</td>
188	<td>admin/admin</td>
189	<td>Unlimited</td>
190	<td>-</td>
191	<td>Roles: Administrator</td>
192	</tr>
193	</table>
194	</li>
195	</ol>
196
197	<a name="admin"></a>
198	<h2>3. Administrator tests</h2>
199	<p>
200	The administrator creates users for a project and gives them permissions
201	that are suitable for their role in the project. The administrator also
202	sets up quota and group membership.
203	</p>
204
205	<ol>
206	<li>
207	Create a new group and set the following properties:
208
209	<table class="listing" cellspacing="0" cellpadding="2" border="0">
210	<tr>
211	<th>Name</th>
212	<th>Quota</th>
213	</tr>
214	<tr>
215	<td>Group A</td>
216	<td>1GB</td>
217	</tr>
218	</table>
219	<p>
220	</li>
221
222	<li>
223	Create the following users:
224
225	<table class="listing" cellspacing="0" cellpadding="2" border="0">
226	<tr>
227	<th>Name</th>
228	<th>Login/Password</th>
229	<th>Quota</th>
230	<th>Quota group</th>
231	<th>Membership</th>
232	<th>Other</th>
233	</tr>
234	<tr>
235	<td>Power user</td>
236	<td>power/power</td>
237	<td>1GB</td>
238	<td>Group A</td>
239	<td>Roles: Power user</td>
240	<td>-</td>
241	</tr>
242	<tr>
243	<td>User</td>
244	<td>user/user</td>
245	<td>1GB</td>
246	<td>Group A</td>
247	<td>Roles: User</td>
248	<td>-</td>
249	</tr>
250	<tr>
251	<td>Guest</td>
252	<td>guest/guest</td>
253	<td>10MB</td>
254	<td>Group A</td>
255	<td>Roles: Guest</td>
256	<td><i>Multi-user account</i> checked</td>
257	</tr>
258	</table>
259	<p>
260	</li>
261
262	<li>Give USE permission for the listed users to the following plugins:
263
264	<table class="listing" cellspacing="0" cellpadding="2" border="0">
265	<tr>
266	<th>User</th>
267	<th>Plugins</th>
268	</tr>
269	<tr>
270	<td>Power user</td>
271	<td>
272	<ul>
273	<li>Reporter importer</li>
274	<li>Plate importer</li>
275	<li>Reporter map importer</li>
276	<li>Print map importer</li>
277	</ul>
278	</td>
279	</tr>
280	</table>
281	</li>
282
283	</ol>
284
285
286	<a name="power"></a>
287	<h2>4. Power user tests</h2>
288	<p>
289	The power user is the typical owner/administrator of a project. The power user sets
290	up common resources used in the project, such as hardware, software, protocols,
291	file formats and annotation types. In this case the power user is also responsible for
292	managing the LIMS.
293	</p>
294
295	<ol>
296	<li>
297	Create a project:
298
299	<table class="listing" cellspacing="0" cellpadding="2" border="0">
300	<tr>
301	<th>Name</th>
302	<th>Members</th>
303	</tr>
304	<tr>
305	<td>Project A</td>
306	<td>Groups: Group A (Use permission)</td>
307	</tr>
308	</table>
309	<p>
310	</li>
311
312	<li>Activate the project.<p></li>
313
314	<li>
315	Create protocols:
316	<table class="listing" cellspacing="0" cellpadding="2" border="0">
317	<tr>
318	<th>Name</th>
319	<th>Type</th>
320	</tr>
321	<tr>
322	<td>Sampling A</td>
323	<td>Sampling</td>
324	</tr>
325	<tr>
326	<td>Extraction A</td>
327	<td>Extraction</td>
328	</tr>
329	<tr>
330	<td>Labeling A</td>
331	<td>Labeling</td>
332	</tr>
333	<tr>
334	<td>Hybridization A</td>
335	<td>Hybridization</td>
336	</tr>
337	<tr>
338	<td>Scanning A</td>
339	<td>Scanning</td>
340	</tr>
341	<tr>
342	<td>Feature extraction A</td>
343	<td>Feature extraction</td>
344	</tr>
345	<tr>
346	<td>Printing A</td>
347	<td>Printing</td>
348	</tr>
349	</table>
350	<p>
351	</li>
352
353	<li>
354	Create hardware:
355	<table class="listing" cellspacing="0" cellpadding="2" border="0">
356	<tr>
357	<th>Name</th>
358	<th>Type</th>
359	</tr>
360	<tr>
361	<td>Hybridization station A</td>
362	<td>Hybridization station</td>
363	</tr>
364	<tr>
365	<td>Scanner A</td>
366	<td>Scanner</td>
367	</tr>
368	<tr>
369	<td>Print robot A</td>
370	<td>Print robot</td>
371	</tr>
372	</table>
373	<p>
374	</li>
375
376	<li>
377	Create software:
378	<table class="listing" cellspacing="0" cellpadding="2" border="0">
379	<tr>
380	<th>Name</th>
381	<th>Type</th>
382	</tr>
383	<tr>
384	<td>Software A</td>
385	<td>Feature extraction</td>
386	</tr>
387	</table>
388	<p>
389	</li>
390
391	<li>
392	Create annotation types:
393	<table class="listing" cellspacing="0" cellpadding="2" border="0">
394	<tr>
395	<th>Name</th>
396	<th>Type</th>
397	<th>Interface</th>
398	<th>Values</th>
399	<th>Item types</th>
400	</tr>
401	<tr>
402	<td>Drug resistance</td>
403	<td>String</td>
404	<td>radiobuttons</td>
405	<td>high, medium, low</td>
406	<td>Biosource</td>
407	</tr>
408	<tr>
409	<td>Time (hours)</td>
410	<td>Integer</td>
411	<td>text box</td>
412	<td>-</td>
413	<td>Sample</td>
414	</tr>
415	</table>
416	<p>
417
418	<li>
419	Create file formats (<i>i.e.</i>, plug-in configurations). The formats marked as
420	optional are not used in the test procedure, but may be useful to weed
421	out import problems, since they allow importing all info from the raw
422	data files. You may either enter the regular expressions as specified or
423	use the "Test with file" feature.
424
425	<table class="listing" cellspacing="0" cellpadding="2" border="0">
426	<tr>
427	<th>Name</th>
428	<th>Plugin</th>
429	<th>Configuration values</th>
430	</tr>
431	<tr class="oddrow">
432	<td>Reporters for project A</td>
433	<td>Reporter importer</td>
434	<td>
435	<b>Test with file:</b> <code>plates_and_reporters.mouse.v4.37k.txt</code>
436	<table border="0" cellspacing="0" cellpadding="2">
437	<tr>
438	<td><i>Data header</i></td>
439	<td>384_number\t384_column\t384_row\t384_position\toligo_id.*</td>
440	</tr>
441	<tr>
442	<td><i>Data splitter</i></td>
443	<td>\t</td>
444	</tr>
445	<tr>
446	<td><i>Min data columns</i></td>
447	<td>5</td>
448	</tr>
449	<tr>
450	<td><i>Name</i></td>
451	<td>\oligo_id\</td>
452	</tr>
453	<tr>
454	<td><i>Reporter ID</i></td>
455	<td>\oligo_id\</td>
456	</tr>
457	<tr>
458	<td><i>Description</i></td>
459	<td>\description_Ensembl*\</td>
460	</tr>
461	<tr>
462	<td><i>Gene symbol</i></td>
463	<td>\gene_symbol_Ensembl*\</td>
464	</tr>
465	<tr>
466	<td><i>Sequence</i></td>
467	<td>\oligo_sequence\</td>
468	</tr>
469	</table>
470
471	</td>
472	</tr>
473
474	<tr class="evenrow">
475	<td>GenePix reporter importer<br>(optional)</td>
476	<td>Reporter importer</td>
477	<td>
478
479	<b>Test with file:</b> <code>genepix.mouse.v4.37k.00h.gpr</code>
480	<table border="0" cellspacing="0" cellpadding="2">
481	<tr>
482	<td><i>Data header</i></td>
483	<td>"Block"\t"Column"\t"Row"\t"Name"\t"ID"\t.*</td>
484	</tr>
485	<tr>
486	<td><i>Data splitter</i></td>
487	<td>\t</td>
488	</tr>
489	<tr>
490	<td><i>Min data columns</i></td>
491	<td>48</td>
492	</tr>
493	<tr>
494	<td><i>Max data columns</i></td>
495	<td>48</td>
496	</tr>
497	<tr>
498	<td><i>Name</i></td>
499	<td>\Name\</td>
500	</tr>
501	<tr>
502	<td><i>Reporter ID</i></td>
503	<td>\ID\</td>
504	</tr>
505	</table>
506
507	</td>
508	</tr>
509
510	<tr class="oddrow">
511	<td>Plates for project A</td>
512	<td>Plate importer</td>
513	<td>
514
515	<b>Test with file:</b> <code>plates_and_reporters.mouse.v4.37k.txt</code>
516	<table border="0" cellspacing="0" cellpadding="2">
517	<tr>
518	<td><i>Data header</i></td>
519	<td>384_number\t384_column\t384_row\t384_position\toligo_id.*</td>
520	</tr>
521	<tr>
522	<td><i>Data splitter</i></td>
523	<td>\t</td>
524	</tr>
525	<tr>
526	<td><i>Min data columns</i></td>
527	<td>5</td>
528	</tr>
529	<tr>
530	<td><i>Plate number/name</i></td>
531	<td>\384_number\</td>
532	</tr>
533	<tr>
534	<td><i>Row</i></td>
535	<td>\384_row\</td>
536	</tr>
537	<tr>
538	<td><i>Column</i></td>
539	<td>\384_column\</td>
540	</tr>
541	<tr>
542	<td><i>Reporter ID</i></td>
543	<td>\oligo_id\</td>
544	</tr>
545	</table>
546
547	</td>
548	</tr>
549
550	<tr class="evenrow">
551	<td>GenePix feature importer<br>(optional)</td>
552	<td>Reporter map importer</td>
553	<td>
554
555	<b>Test with file:</b> <code>genepix.mouse.v4.37k.00h.gpr</code>
556	<table border="0" cellspacing="0" cellpadding="2">
557	<tr>
558	<td><i>Data header</i></td>
559	<td>"Block"\t"Column"\t"Row"\t"Name"\t"ID"\t.*</td>
560	</tr>
561	<tr>
562	<td><i>Data splitter</i></td>
563	<td>\t</td>
564	</tr>
565	<tr>
566	<td><i>Min data columns</i></td>
567	<td>48</td>
568	</tr>
569	<tr>
570	<td><i>Max data columns</i></td>
571	<td>48</td>
572	</tr>
573	<tr>
574	<td><i>Reporter ID</i></td>
575	<td>\ID\</td>
576	</tr>
577	<tr>
578	<td><i>Block</i></td>
579	<td>\Block\</td>
580	</tr>
581	<tr>
582	<td><i>Column</i></td>
583	<td>\Column\</td>
584	</tr>
585	<tr>
586	<td><i>Row</i></td>
587	<td>\Row\</td>
588	</tr>
589	</table>
590
591	</td>
592	</tr>
593
594	<tr class="oddrow">
595	<td>Raw data for project A</td>
596	<td>Raw data importer</td>
597	<td>
598
599	<b>Test with file:</b> <code>genepix.mouse.v4.37k.00h.gpr</code>
600	<table border="0" cellspacing="0" cellpadding="2">
601	<tr>
602	<td><i>Raw data type</i></td>
603	<td>Genepix</td>
604	</tr>
605	<tr>
606	<td><i>Header</i></td>
607	<td>"(.+)=(.*)"</td>
608	</tr>
609	<tr>
610	<td><i>Data header</i></td>
611	<td>"Block"\t"Column"\t"Row"\t"Name"\t"ID"\t."Ratio of Medians \(532\/635\)".</td>
612	</tr>
613	<tr>
614	<td><i>Data splitter</i></td>
615	<td>\t</td>
616	</tr>
617	<tr>
618	<td><i>Min data columns</i></td>
619	<td>48</td>
620	</tr>
621	<tr>
622	<td><i>Max data columns</i></td>
623	<td>48</td>
624	</tr>
625
626	<tr>
627	<td><i>Block</i></td>
628	<td>\Block\</td>
629	</tr>
630	<tr>
631	<td><i>Column</i></td>
632	<td>\Column\</td>
633	</tr>
634	<tr>
635	<td><i>Row</i></td>
636	<td>\Row\</td>
637	</tr>
638	<tr>
639	<td><i>X</i></td>
640	<td>\X\</td>
641	</tr>
642	<tr>
643	<td><i>Y</i></td>
644	<td>\Y\</td>
645	</tr>
646	<tr>
647	<td><i>Reporter ID</i></td>
648	<td>\ID\</td>
649	</tr>
650	<tr>
651	<td><i>Spot diameter</i></td>
652	<td>\Dia.\</td>
653	</tr>
654	<tr>
655	<td><i>Channel 1 foreground median</i></td>
656	<td>\F635 Median\</td>
657	</tr>
658	<tr>
659	<td><i>Channel 1 foreground mean</i></td>
660	<td>\F635 Mean\</td>
661	</tr>
662	<tr>
663	<td><i>Channel 1 foreground standard deviation</i></td>
664	<td>\F635 SD\</td>
665	</tr>
666	<tr>
667	<td><i>Channel 1 background median</i></td>
668	<td>\B635 Median\</td>
669	</tr>
670	<tr>
671	<td><i>Channel 1 background mean</i></td>
672	<td>\B635 Mean\</td>
673	</tr>
674	<tr>
675	<td><i>Channel 1 background standard deviation</i></td>
676	<td>\B635 SD\</td>
677	</tr>
678	<tr>
679	<td><i>Percent pixels within 1 standard deviation</i></td>
680	<td>\% > B635+1SD\</td>
681	</tr>
682	<tr>
683	<td><i>Percent pixels within 2 standard deviations</i></td>
684	<td>\% > B635+2SD\</td>
685	</tr>
686	<tr>
687	<td><i>Percent saturated pixels</i></td>
688	<td>\F635 % Sat.\</td>
689	</tr>
690	<tr>
691	<td><i>Channel 2 foreground median</i></td>
692	<td>\F532 Median\</td>
693	</tr>
694	<tr>
695	<td><i>Channel 2 foreground mean</i></td>
696	<td>\F532 Mean\</td>
697	</tr>
698	<tr>
699	<td><i>Channel 2 foreground standard deviation</i></td>
700	<td>\F532 SD\</td>
701	</tr>
702	<tr>
703	<td><i>Channel 2 background median</i></td>
704	<td>\B532 Median\</td>
705	</tr>
706	<tr>
707	<td><i>Channel 2 background mean</i></td>
708	<td>\B532 Mean\</td>
709	</tr>
710	<tr>
711	<td><i>Channel 2 background standard deviation</i></td>
712	<td>\B532 SD\</td>
713	</tr>
714	<tr>
715	<td><i>Percent pixels within 1 standard deviation</i></td>
716	<td>\% > B532+1SD\</td>
717	</tr>
718	<tr>
719	<td><i>Percent pixels within 2 standard deviations</i></td>
720	<td>\% > B532+2SD\</td>
721	</tr>
722	<tr>
723	<td><i>Percent saturated pixels</i></td>
724	<td>\F532 % Sat.\</td>
725	</tr>
726	<tr>
727	<td><i>Foreground pixels</i></td>
728	<td>\F Pixels\</td>
729	</tr>
730	<tr>
731	<td><i>Background pixels</i></td>
732	<td>\B Pixels\</td>
733	</tr>
734	<tr>
735	<td><i>Flags</i></td>
736	<td>\Flags\</td>
737	</tr>
738	</table>
739
740	</td>
741	</tr>
742
743	<tr class="evenrow">
744	<td>Raw data for project A (dye-swap)</td>
745	<td>Raw data importer</td>
746	<td>
747
748	<b>Test with file:</b> <code>genepix.mouse.v4.37k.00h.dyeswap.gpr</code>
749	<table border="0" cellspacing="0" cellpadding="2">
750	<tr>
751	<td><i>Raw data type</i></td>
752	<td>Genepix</td>
753	</tr>
754	<tr>
755	<td><i>Header</i></td>
756	<td>"(.+)=(.*)"</td>
757	</tr>
758	<tr>
759	<td><i>Data header</i></td>
760	<td>"Block"\t"Column"\t"Row"\t"Name"\t"ID"\t."Ratio of Medians \(635\/532\)".</td>
761	</tr>
762	<tr>
763	<td><i>Data splitter</i></td>
764	<td>\t</td>
765	</tr>
766	<tr>
767	<td><i>Min data columns</i></td>
768	<td>48</td>
769	</tr>
770	<tr>
771	<td><i>Max data columns</i></td>
772	<td>48</td>
773	</tr>
774
775	<tr>
776	<td><i>Block</i></td>
777	<td>\Block\</td>
778	</tr>
779	<tr>
780	<td><i>Column</i></td>
781	<td>\Column\</td>
782	</tr>
783	<tr>
784	<td><i>Row</i></td>
785	<td>\Row\</td>
786	</tr>
787	<tr>
788	<td><i>X</i></td>
789	<td>\X\</td>
790	</tr>
791	<tr>
792	<td><i>Y</i></td>
793	<td>\Y\</td>
794	</tr>
795	<tr>
796	<td><i>Reporter ID</i></td>
797	<td>\ID\</td>
798	</tr>
799	<tr>
800	<td><i>Spot diameter</i></td>
801	<td>\Dia.\</td>
802	</tr>
803	<tr>
804	<td><i>Channel 1 foreground median</i></td>
805	<td>\F532 Median\</td>
806	</tr>
807	<tr>
808	<td><i>Channel 1 foreground mean</i></td>
809	<td>\F532 Mean\</td>
810	</tr>
811	<tr>
812	<td><i>Channel 1 foreground standard deviation</i></td>
813	<td>\F532 SD\</td>
814	</tr>
815	<tr>
816	<td><i>Channel 1 background median</i></td>
817	<td>\B532 Median\</td>
818	</tr>
819	<tr>
820	<td><i>Channel 1 background mean</i></td>
821	<td>\B532 Mean\</td>
822	</tr>
823	<tr>
824	<td><i>Channel 1 background standard deviation</i></td>
825	<td>\B532 SD\</td>
826	</tr>
827	<tr>
828	<td><i>Percent pixels within 1 standard deviation</i></td>
829	<td>\% > B532+1SD\</td>
830	</tr>
831	<tr>
832	<td><i>Percent pixels within 2 standard deviations</i></td>
833	<td>\% > B532+2SD\</td>
834	</tr>
835	<tr>
836	<td><i>Percent saturated pixels</i></td>
837	<td>\F532 % Sat.\</td>
838	</tr>
839	<tr>
840	<td><i>Channel 2 foreground median</i></td>
841	<td>\F635 Median\</td>
842	</tr>
843	<tr>
844	<td><i>Channel 2 foreground mean</i></td>
845	<td>\F635 Mean\</td>
846	</tr>
847	<tr>
848	<td><i>Channel 2 foreground standard deviation</i></td>
849	<td>\F635 SD\</td>
850	</tr>
851	<tr>
852	<td><i>Channel 2 background median</i></td>
853	<td>\B635 Median\</td>
854	</tr>
855	<tr>
856	<td><i>Channel 2 background mean</i></td>
857	<td>\B635 Mean\</td>
858	</tr>
859	<tr>
860	<td><i>Channel 2 background standard deviation</i></td>
861	<td>\B635 SD\</td>
862	</tr>
863	<tr>
864	<td><i>Percent pixels within 1 standard deviation</i></td>
865	<td>\% > B635+1SD\</td>
866	</tr>
867	<tr>
868	<td><i>Percent pixels within 2 standard deviations</i></td>
869	<td>\% > B635+2SD\</td>
870	</tr>
871	<tr>
872	<td><i>Percent saturated pixels</i></td>
873	<td>\F635 % Sat.\</td>
874	</tr>
875	<tr>
876	<td><i>Foreground pixels</i></td>
877	<td>\F Pixels\</td>
878	</tr>
879	<tr>
880	<td><i>Background pixels</i></td>
881	<td>\B Pixels\</td>
882	</tr>
883	<tr>
884	<td><i>Flags</i></td>
885	<td>\Flags\</td>
886	</tr>
887	</table>
888
889	</td>
890	</tr>
891	</table>
892	<p>
893	</li>
894
895	<li>
896	Import reporters:
897	<ol>
898	<li>Go to the <code>View -> Reporters</code> page.</li>
899	<li>Click on the <code>Import</code> button.</li>
900	<li>Choose <code>auto-detect</code> and then upload
901	the file <code>plates_and_reporters.mouse.v4.37k.txt</code>.</li>
902	<li>The <code>Reporters for project A</code> format should be
903	found.</li>
904	<li>Select the <code>skip</code> option for the "Missing a required" value
905	since the file contains rows with empty reporter ID:s.
906	<li>Continue and wait for the import to finish. It should create 35,912 new reporters.</li>
907	</ol>
908	<p>
909
910	</li>
911
912	<li>
913	Create plate type:
914	<table class="listing" cellspacing="0" cellpadding="2" border="0">
915	<tr>
916	<th>Name</th>
917	<th>Geometry</th>
918	</tr>
919	<tr>
920	<td>Plate type A</td>
921	<td>384-well (16 x 24)</td>
922	</tr>
923	</table>
924	<p>
925	</li>
926
927	<li>
928	Import plates:
929	<ol>
930	<li>Go to the <code>Array LIMS -> Plates</code> page.</li>
931	<li>Click on the <code>Import</code> button.</li>
932	<li>Choose <code>auto-detect</code> and select
933	the file <code>plates_and_reporters.mouse.v4.37k.txt</code>.</li>
934	<li>The <code>Plates for project A</code> format should be
935	found.</li>
936	<li>Specify the following parameters:
937
938	<table border="0" cellspacing="0" cellpadding="2">
939	<tr>
940	<td><i>Plate type</i></td>
941	<td>Plate type A</td>
942	</tr>
943	<tr>
944	<td><i>Plate name prefix</i></td>
945	<td>Plate A</td>
946	</tr>
947	<tr>
948	<td><i>Plate name padding</i></td>
949	<td>4</td>
950	</tr>
951	</table>
952	</li>
953	<li>Continue and wait for the import to finish. It should create 96 plates.</li>
954	</ol>
955	<p>
956	</li>
957
958	<li>
959	Create array design:
960	<table class="listing" cellspacing="0" cellpadding="2" border="0">
961	<tr>
962	<th>Name</th>
963	</tr>
964	<tr>
965	<td>Array design A</td>
966	</tr>
967	</table>
968	<p>
969	</li>
970
971	<li>
972	Connect the array design with plates. Select the imported plates (plate names starting
973	with Plate A) and sort them in the correct order (as indicated by their names).
974	<p>
975	</li>
976
977	<li>
978	Import features:
979	<ol>
980	<li>Click on the <code>Import</code> button when viewing properties for the array design.</li>
981	<li>Choose <code>auto-detect</code> and upload the file
982	<code>printmap.mouse.v4.37k.tam</code>.</li>
983	<li>The <code>Print map importer</code> plug-in should be
984	found.</li>
985	<li>Continue and wait for the import to finish. It should create 36,864 features and 48 blocks.</li>
986	</ol>
987	<p>
988	</li>
989
990	<li>
991	Create array batch:
992	<table class="listing" cellspacing="0" cellpadding="2" border="0">
993	<tr>
994	<th>Name</th>
995	<th>Array design</th>
996	<th>Print robot</th>
997	<th>Protocol</th>
998	</tr>
999	<tr>
1000	<td>Array batch A</td>
1001	<td>Array design A</td>
1002	<td>Robot A</td>
1003	<td>Printing A</td>
1004	</tr>
1005	</table>
1006	<p>
1007	</li>
1008
1009	<li>
1010	Create array slides with the <code>Create slides</code>
1011	wizard.
1012
1013	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1014	<tr>
1015	<th>Name</th>
1016	<th>Array batch</th>
1017	<th>Quantity</th>
1018	</tr>
1019	<tr>
1020	<td>Array slide A.</td>
1021	<td>Array batch A</td>
1022	<td>4</td>
1023	</tr>
1024	</table>
1025	<p>
1026	</li>
1027	</ol>
1028
1029	<a name="user"></a>
1030	<h2>5. User tests</h2>
1031	<p>
1032	The user is a typical worker in the project. The user does the actual experimentation in the
1033	lab, which includes collecting samples, doing extraction, labeling and hybridizations.
1034	The user also scans and analyses the raw data resulting from the images.
1035	</p>
1036
1037	<ol>
1038	<li>
1039	Activate the <code>Project A</code> project<p></li>
1040
1041	<li>
1042	Create a biosource:
1043	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1044	<tr>
1045	<th>Name</th>
1046	<th>Annotations</th>
1047	</tr>
1048	<tr>
1049	<td>Biosource A</td>
1050	<td>
1051	<table border="0" cellspacing="0" cellpadding="2">
1052	<tr>
1053	<td><i>Drug resistance:</i></td>
1054	<td>medium</td>
1055	</tr>
1056	</table>
1057	</td>
1058	</tr>
1059	</table>
1060	<p>
1061	</li>
1062
1063	<li>
1064	Create samples:
1065	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1066	<tr>
1067	<th>Name</th>
1068	<th>Protocol</th>
1069	<th>Biosource</th>
1070	<th>Annotations</th>
1071	</tr>
1072	<tr>
1073	<td>Sample A.00h</td>
1074	<td>Sampling A</td>
1075	<td>Biosource A</td>
1076	<td>
1077	<table border="0" cellspacing="0" cellpadding="2">
1078	<tr>
1079	<td><i>Time (hours):</i></td>
1080	<td>0</td>
1081	</tr>
1082	</table>
1083	</td>
1084	</tr>
1085	<tr>
1086	<td>Sample A.24h</td>
1087	<td>Sampling A</td>
1088	<td>Biosource A</td>
1089	<td>
1090	<table border="0" cellspacing="0" cellpadding="2">
1091	<tr>
1092	<td><i>Time (hours):</i></td>
1093	<td>24</td>
1094	</tr>
1095	</table>
1096	</td>
1097	</tr>
1098	<tr>
1099	<td>Sample A.ref</td>
1100	<td>Sampling A</td>
1101	<td>-</td>
1102	<td>-</td>
1103	</tr>
1104	</table>
1105	<p>
1106	</li>
1107
1108	<li>
1109	Create extracts:
1110	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1111	<tr>
1112	<th>Name</th>
1113	<th>Protocol</th>
1114	<th>Sample</th>
1115	</tr>
1116	<tr>
1117	<td>Extract A.00h</td>
1118	<td>Extraction A</td>
1119	<td>Sample A.00h</td>
1120	</tr>
1121	<tr>
1122	<td>Extract A.24h</td>
1123	<td>Extraction A</td>
1124	<td>Sample A.24h</td>
1125	</tr>
1126	<tr>
1127	<td>Extract A.ref</td>
1128	<td>Extraction A</td>
1129	<td>Sample A.ref</td>
1130	</tr>
1131	</table>
1132	<p>
1133	</li>
1134
1135	<li>
1136	Create labeled extracts:
1137	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1138	<tr>
1139	<th>Name</th>
1140	<th>Label</th>
1141	<th>Protocol</th>
1142	<th>Extract</th>
1143	</tr>
1144	<tr>
1145	<td>Labeled extract A.00h</td>
1146	<td>cy3</td>
1147	<td>Labeling A</td>
1148	<td>Extract A.00h</td>
1149	</tr>
1150	<tr>
1151	<td>Labeled extract A.24h</td>
1152	<td>cy3</td>
1153	<td>Labeling A</td>
1154	<td>Extract A.24h</td>
1155	</tr>
1156	<tr>
1157	<td>Labeled extract A.ref</td>
1158	<td>cy5</td>
1159	<td>Labeling A</td>
1160	<td>Extract A.ref</td>
1161	</tr>
1162	<tr class="shaded">
1163	<td>Labeled extract A.00h (dye-swap)</td>
1164	<td>cy5</td>
1165	<td>Labeling A</td>
1166	<td>Extract A.00h</td>
1167	</tr>
1168	<tr class="shaded">
1169	<td>Labeled extract A.24h (dye-swap)</td>
1170	<td>cy5</td>
1171	<td>Labeling A</td>
1172	<td>Extract A.24h</td>
1173	</tr>
1174	<tr class="shaded">
1175	<td>Labeled extract A.ref (dye-swap)</td>
1176	<td>cy3</td>
1177	<td>Labeling A</td>
1178	<td>Extract A.ref</td>
1179	</tr>
1180	</table>
1181	<p>
1182	</li>
1183
1184	<li>
1185	Create hybridizations:
1186	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1187	<tr>
1188	<th>Name</th>
1189	<th>Protocol</th>
1190	<th>Hardware</th>
1191	<th>Array slide</th>
1192	<th>Labeled extracts</th>
1193	</tr>
1194	<tr>
1195	<td>Hybridization A.00h</td>
1196	<td>Hybridization A</td>
1197	<td>Hybridization station A</td>
1198	<td>Array slide A.1</td>
1199	<td>Labeled extract A.00h,<br>Labeled extract A.ref</td>
1200	</tr>
1201	<tr>
1202	<td>Hybridization A.24h</td>
1203	<td>Hybridization A</td>
1204	<td>Hybridization station A</td>
1205	<td>Array slide A.2</td>
1206	<td>Labeled extract A.24h,<br>Labeled extract A.ref</td>
1207	</tr>
1208	<tr class="shaded">
1209	<td>Hybridization A.00h (dye-swap)</td>
1210	<td>Hybridization A</td>
1211	<td>Hybridization station A</td>
1212	<td>Array slide A.3</td>
1213	<td>Labeled extract A.00h (dye-swap),<br>Labeled extract A.ref (dye-swap)</td>
1214	</tr>
1215	<tr class="shaded">
1216	<td>Hybridization A.24h (dye-swap)</td>
1217	<td>Hybridization A</td>
1218	<td>Hybridization station A</td>
1219	<td>Array slide A.4</td>
1220	<td>Labeled extract A.24h (dye-swap),<br>Labeled extract A.ref (dye-swap)</td>
1221	</tr>
1222	</table>
1223	<p>
1224	</li>
1225
1226	<li>
1227	Create scans:
1228	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1229	<tr>
1230	<th>Name</th>
1231	<th>Hybridization</th>
1232	<th>Scanner</th>
1233	<th>Protocol</th>
1234	</tr>
1235	<tr>
1236	<td>Scan A.00h</td>
1237	<td>Hybridization A.00h</td>
1238	<td>Scanner A</td>
1239	<td>Scanning A</td>
1240	</tr>
1241	<tr>
1242	<td>Scan A.24h</td>
1243	<td>Hybridization A.24h</td>
1244	<td>Scanner A</td>
1245	<td>Scanning A</td>
1246	</tr>
1247	<tr class="shaded">
1248	<td>Scan A.00h (dye-swap)</td>
1249	<td>Hybridization A.00h (dye-swap)</td>
1250	<td>Scanner A</td>
1251	<td>Scanning A</td>
1252	</tr>
1253	<tr class="shaded">
1254	<td>Scan A.24h (dye-swap)</td>
1255	<td>Hybridization A.24h (dye-swap)</td>
1256	<td>Scanner A</td>
1257	<td>Scanning A</td>
1258	</tr>
1259	</table>
1260	<p>
1261	</li>
1262
1263	<li>
1264	Add images to the scans (TODO - we don't have any images yet):
1265	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1266	<tr>
1267	<th>Scan</th>
1268	<th>Image files</th>
1269	</tr>
1270	<tr>
1271	<td>Scan A.00h</td>
1272	<td>-</td>
1273	</tr>
1274	<tr>
1275	<td>Scan A.24h</td>
1276	<td>-</td>
1277	</tr>
1278	<tr class="shaded">
1279	<td>Scan A.00h (dye-swap)</td>
1280	<td>-</td>
1281	</tr>
1282	<tr class="shaded">
1283	<td>Scan A.24h (dye-swap)</td>
1284	<td>-</td>
1285	</tr>
1286	</table>
1287	<p>
1288	</li>
1289
1290	<li>
1291	Create raw bioassays:
1292	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1293	<tr>
1294	<th>Name</th>
1295	<th>Raw data type</th>
1296	<th>Array design</th>
1297	<th>Protocol</th>
1298	<th>Scan</th>
1299	<th>Software</th>
1300	</tr>
1301	<tr>
1302	<td>Raw bioassay A.00h</td>
1303	<td>GenePix</td>
1304	<td>Array design A</td>
1305	<td>Feature extraction A</td>
1306	<td>Scan A.00h</td>
1307	<td>Software A</td>
1308	</tr>
1309	<tr>
1310	<td>Raw bioassay A.24h</td>
1311	<td>GenePix</td>
1312	<td>Array design A</td>
1313	<td>Feature extraction A</td>
1314	<td>Scan A.24h</td>
1315	<td>Software A</td>
1316	</tr>
1317	<tr class="shaded">
1318	<td>Raw bioassay A.00h (dye-swap)</td>
1319	<td>GenePix</td>
1320	<td>Array design A</td>
1321	<td>Feature extraction A</td>
1322	<td>Scan A.00h (dye-swap)</td>
1323	<td>Software A</td>
1324	</tr>
1325	<tr class="shaded">
1326	<td>Raw bioassay A.24h (dye-swap)</td>
1327	<td>GenePix</td>
1328	<td>Array design A</td>
1329	<td>Feature extraction A</td>
1330	<td>Scan A.24h (dye-swap)</td>
1331	<td>Software A</td>
1332	</tr>
1333	</table>
1334	<p>
1335	</li>
1336
1337	<li>
1338	Inherit the annotations from the samples and biosource for each raw bioassay.
1339	<p>
1340
1341	</li>
1342
1343	<li>
1344	Use the auto-detect feature to upload and import raw data for each
1345	raw bioassay. Select the <code>skip</code> option for the "Feature mismatch"
1346	parameter since the file contains rows with bogus reporter ID:s.
1347
1348	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1349	<tr>
1350	<th>Raw bioassay</th>
1351	<th>Raw data file</th>
1352	<th>Spots inserted</th>
1353	</tr>
1354	<tr>
1355	<td>Raw bioassay A.00h</td>
1356	<td>genepix.mouse.v4.37k.00h.gpr</td>
1357	<td>36,232</td>
1358	</tr>
1359	<tr>
1360	<td>Raw bioassay A.24h</td>
1361	<td>genepix.mouse.v4.37k.24h.gpr</td>
1362	<td>36,232</td>
1363	</tr>
1364	<tr class="shaded">
1365	<td>Raw bioassay A.00h (dye-swap)</td>
1366	<td>genepix.mouse.v4.37k.00h.dyeswap.gpr</td>
1367	<td>36,232</td>
1368	</tr>
1369	<tr class="shaded">
1370	<td>Raw bioassay A.24h (dye-swap)</td>
1371	<td>genepix.mouse.v4.37k.24h.dyeswap.gpr</td>
1372	<td>36,232</td>
1373	</tr>
1374	</table>
1375	<p>
1376	</li>
1377
1378	<li>
1379	Create an experiment:
1380	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1381	<tr>
1382	<th>Name</th>
1383	<th>Raw data type</th>
1384	<th>Raw bioassays</th>
1385	<th>Experimental factors</th>
1386	</tr>
1387	<tr>
1388	<td>Experiment A</td>
1389	<td>GenePix</td>
1390	<td>Raw bioassay A.00h,<br>Raw bioassay A.24h,<br>Raw bioassay A.00h (dye-swap),<br>
1391	Raw bioassay A.24h (dye-swap)</td>
1392	<td>Drug resistance, Time (hours)</td>
1393	</tr>
1394	</table>
1395	<p>
1396	</li>
1397	</ol>
1398
1399	<a name="analysis"></a>
1400	<h2>6. Analysis tests</h2>
1401	<p>
1402	Now it is time to analyse the data. The analysis test should be done
1403	by both a regular user and a guest.
1404	</p>
1405
1406	<ol>
1407	<li>
1408	Activate the <code>Project A</code> project<p>
1409	</li>
1410
1411	<li>
1412	Go to the <code>Experiment A</code> experiment and select
1413	the <code>Bioassay sets</code> tab.
1414	<p>
1415	</li>
1416
1417	<li>
1418	Create a new root bioassay set:
1419	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1420	<tr>
1421	<th>Bioassay set name</th>
1422	<th>Raw bioassays</th>
1423	<th>Formula</th>
1424	</tr>
1425	<tr>
1426	<td>Root bioassay set</td>
1427	<td>all</td>
1428	<td>Mean FG - Mean BG</td>
1429	</tr>
1430	</table>
1431	Wait for the plug-in to finish.
1432	<p>
1433	</li>
1434
1435	<li>
1436	Select the created bioassay set and create a filtered bioassayset:
1437	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1438	<tr>
1439	<th>Child name</th>
1440	<th>Filter preset</th>
1441	<th>Expression</th>
1442	</tr>
1443	<tr>
1444	<td>Filtered bioassay set</td>
1445	<td>All intensities > 0</td>
1446	<td>ch(1) > 0 && ch(2) > 0</td>
1447	</tr>
1448	</table>
1449	Wait for the plug-in to finish. It should report that 136,498 spots remain and
1450	that 8,430 spots has been removed.
1451	<p>
1452	</li>
1453
1454	<li>
1455	Select the filtered bioassay set and run a normalization plug-in:
1456	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1457	<tr>
1458	<th>Plugin</th>
1459	<th>Parameters</th>
1460	</tr>
1461	<tr>
1462	<td>Normalization: Lowess</td>
1463	<td>Accept the most of default parameters, but change the
1464	"Block group size" to 12. Otherwise it will take too long time.</td>
1465	</tr>
1466	</table>
1467	Wait for the plug in to finish. It should report that 136,498 spots has been
1468	normalized and 0 spots has been removed.
1469	<p>
1470	</li>
1471
1472	<li>
1473	Select the normalized bioassay set and check the overview plots and
1474	the correction factor plots. Here are four examples:
1475	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1476	<tr>
1477	<th>Overview plots</th>
1478	<th>Correction factor plots</th>
1479	</tr>
1480	<tr>
1481	<td><img src="overview.png"><br><img src="overview.dyeswap.png"></td>
1482	<td><img src="correction.png"><br><img src="correction.dyeswap.png"></td>
1483	</tr>
1484	</table>
1485	<p>
1486	</li>
1487
1488	<li>
1489	Try the plot tool with the following plots. Use the <code>Save</code> function
1490	to save one them as a file in the BASE file system, and the <code>Download</code>
1491	function to download a plot to your computer.
1492	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1493	<tr>
1494	<th>Plot type</th>
1495	<th>Y-axis preset</th>
1496	<th>X-axis preset</th>
1497	<th>Other options</th>
1498	</tr>
1499	<tr>
1500	<td>Scatter plot</td>
1501	<td>M, log2(ch1 / ch2)</td>
1502	<td>A, log10(ch1 * ch2) / 2</td>
1503	<td>-</td>
1504	</tr>
1505	<tr>
1506	<td>Histogram plot</td>
1507	<td>Count</td>
1508	<td>Ratio, ch1 / ch2</td>
1509	<td>
1510	<table border="0" cellspacing="0" cellpadding="2">
1511	<tr>
1512	<td><i>Log scale</i></td>
1513	<td>checked</td>
1514	</tr>
1515	<tr>
1516	<td><i>Bin size</i></td>
1517	<td>0.1</td>
1518	</tr>
1519	<tr>
1520	<td><i>Annotation</i></td>
1521	<td>Time (hours)</td>
1522	</tr>
1523	</table>
1524	</td>
1525	</tr>
1526	</table>
1527	<p>
1528	Here are two examples:
1529	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1530	<tr>
1531	<th>Scatter plot</th>
1532	</tr>
1533	<tr>
1534	<td><img src="scatter.png"></td>
1535	</tr>
1536	</table>
1537	<p>
1538	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1539	<tr>
1540	<th>Histogram plot</th>
1541	</tr>
1542	<tr>
1543	<td><img src="histogram.png"></td>
1544	</tr>
1545	</table>
1546	<p>
1547	</li>
1548
1549	</ol>
1550
1551
1552	</body>
1553	</html>

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