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Last change on this file since 5796 was 5796, checked in by Nicklas Nordborg, 11 years ago

References #1590: Documentation cleanup

New and updated screenshots for chapter 15 - Array LIMS.

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1	<?xml version="1.0" encoding="UTF-8"?>
2	<!DOCTYPE chapter PUBLIC
3	"-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN"
4	"../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd">
5	<!--
6	$Id: array_lims.xml 5796 2011-10-10 11:38:22Z nicklas $
7
8	Copyright (C) 2007 Nicklas Nordborg, Philippe Rocca-Serra, Martin Svensson
9	Copyright (C) 2007 Jari Häkkinen, Nicklas Nordborg
10
11	This file is part of BASE - BioArray Software Environment.
12	Available at http://base.thep.lu.se/
13
14	BASE is free software; you can redistribute it and/or
15	modify it under the terms of the GNU General Public License
16	as published by the Free Software Foundation; either version 3
17	of the License, or (at your option) any later version.
18
19	BASE is distributed in the hope that it will be useful,
20	but WITHOUT ANY WARRANTY; without even the implied warranty of
21	MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
22	GNU General Public License for more details.
23
24	You should have received a copy of the GNU General Public License
25	along with BASE. If not, see <http://www.gnu.org/licenses/>.
26	-->
27
28	<chapter id="array_lims" chunked="0">
29	<title>Array LIMS</title>
30
31	<para>
32	Arrays are at the core of the BASE business and are essential
33	elements to describe in order to
34	be <ulink url='http://www.mged.org/Workgroups/MIAME/miame.html'>MIAME</ulink>
35	compliant. It is also critical to track and manage information
36	about microarray design as accurately as possible since mistakes
37	could prove extremely costly in downstream analysis.
38	As a good practice, all array related information should be
39	entered into BASE prior to work on describing the sample
40	processing and hybridizations or other events making up an
41	experiment is begun.
42	</para>
43
44	<sect1 id="array_lims.arraydesign">
45	<title>Array designs</title>
46
47	<para>
48	Array designs should be understood as a plan which can be realized during a printing
49	process producing microarray slides. During the course of the printing process, reagents
50	may run out leading to the interruption of this process. All slides created during this
51	printing process belong to the same printing batch. It is the array slide that will
52	eventually be used in a hybridization event. BASE allows user to track those 3 entities
53	with great details. This is an important functionality for users producing their own
54	arrays and for those caring for quality control and tracking of microarray slides in a
55	printing facility. The following sections detail how to use BASE to help in these
56	tasks.
57	</para>
58
59	<note>
60	<title>Non-array platforms also need array designs</title>
61	<para>
62	Array designs are needed also for non-array platforms (eg. sequencing). In this
63	case a "virtual array design" is created which is simply a list of all features
64	that is of interest in the experiment. Since there are no coordinates or positions
65	to identify features a unique id need to be constructed in some other way.
66	For example, in sequencing experiments we may use a GTF file to create a
67	virtual array design using the <emphasis>transcript_id</emphasis> and
68	<emphasis>chromosome</emphasis> as a unique identifier.
69	</para>
70	</note>
71
72	<para>
73	Use
74	<menuchoice>
75	<guimenu>Array LIMS</guimenu>
76	<guimenuitem>Array designs</guimenuitem>
77	</menuchoice>
78	to get to the list page with array designs.
79	</para>
80
81	<sect2 id="array_lims.arraydesign.properties">
82	<title>Properties</title>
83
84	<figure id="array_lims.figures.arraydesign">
85	<title>Array design properties</title>
86	<screenshot>
87	<mediaobject>
88	<imageobject>
89	<imagedata
90	fileref="figures/arraydesign_edit.png" format="PNG" />
91	</imageobject>
92	</mediaobject>
93	</screenshot>
94	</figure>
95
96	<helptext external_id="arraydesign.edit" title="Edit array design">
97	<variablelist>
98	<varlistentry>
99	<term>
100	<guilabel>Name</guilabel>
101	</term>
102	<listitem>
103	<para>Provide an sensible name for the design (required).</para>
104	</listitem>
105	</varlistentry>
106	<varlistentry>
107	<term>
108	<guilabel>Platform</guilabel>
109	</term>
110	<listitem>
111	<para>
112	Select the platform / variant used for the
113	array design. The selected options affects which
114	files that can be selected on the <guilabel>Data files</guilabel>
115	tab.
116	</para>
117	</listitem>
118	</varlistentry>
119	<varlistentry>
120	<term>
121	<guilabel>Arrays/slide</guilabel>
122	</term>
123	<listitem>
124	<para>
125	The number of sub-arrays that can be placed on a
126	single slide. The default value is 1, but some
127	platforms, for example Illumina, has slides
128	with 6 or 8 arrays. In sequencing platforms, this value
129	is the number of lanes on a flow cell.
130	</para>
131	</listitem>
132	</varlistentry>
133	<varlistentry>
134	<term>
135	<guilabel>Description</guilabel>
136	</term>
137	<listitem>
138	<para>
139	Provide other useful information about the array design in this text
140	area.
141	</para>
142	</listitem>
143	</varlistentry>
144	</variablelist>
145	<para>
146	Click on the &gbSave; button to store the information in BASE or on the
147	&gbCancel; button to abort.
148	</para>
149	<seeother>
150	<other external_id="datafiles.edit">Data files</other>
151	<other external_id="annotations.edit">Annotations</other>
152	<other external_id="annotations.edit.inerited">Inherit annotations</other>
153	</seeother>
154	</helptext>
155
156	<para>
157	The <guilabel>Data files</guilabel> tab allows BASE users to
158	attach files to the array design. The possible file types are defined
159	by the array design's platform. See <xref linkend="platforms.selectfiles"/>
160	for more information.
161	</para>
162
163	<para>
164	The <guilabel>Annotations</guilabel> tab allows BASE users to use
165	annotation types to refine array design description. More about annotating items
166	can be read in <xref linkend="annotations.annotating" />.
167	</para>
168
169	<para>
170	This <guilabel>Inherited annotations</guilabel> tab contains a list of those annotations
171	that are inherited from the array design's parents (eg. plates). Information about
172	working with inherited annotations can be found in <xref linkend="annotations.inheriting" />.
173	</para>
174
175	</sect2>
176
177
178	<sect2 id="array_lims.arraydesign.importfeature">
179	<title>Importing features to an array design</title>
180
181	<para>
182	Importing features is an important step in order to fully
183	define an array design. It should be noted that BASE does not
184	enforce the immediate feature import upon creation of array
185	design. However, it is STRONGLY advised to do so when creating
186	an array design. Performing the import enables use of the
187	array design in downstream analysis with no further
188	trouble. It also matters when importing raw bioassay data and
189	matching those to the corresponding array design.
190	</para>
191
192	<para>
193	Depending on which platform and/or data files you selected when you
194	created the array design the process to import features is different.
195	For example, if you selected the Affymetrix platform, which is a file-only
196	platform, the feature information has already been extracted from
197	the CDF file (if you selected one). If the selected platform
198	doesn't extract information from the selected data file automatically
199	this may be done manually by executing an import plug-in.
200	</para>
201
202	<para>
203	From the array design item view, click on the &gbImport; button and use the
204	reporter map importer and an appropriate plug-in configuration when following the
205	instructions in
206	<xref linkend="import_data" />.
207	If the import run is successful, go to the array design list view. The
208	<guilabel>Has features</guilabel>
209	column will show
210	<guilabel>Yes (db: x, file: y)</guilabel>
211	where x is the number of features actually imported into the database.
212	</para>
213
214	<note>
215	<para>
216	The &gbImport; button only shows up if the logged in user has
217	enough permissions.
218	</para>
219	</note>
220
221	<note>
222	<title>Verify that probsets in a CDF file exist as reporters</title>
223	<para>
224	File-only platforms, such as Affymetrix, require that all probesets
225	must exist as reporters before data can be analysed. For other
226	platforms this is usually checked when importing the features to
227	the database. Since no import takes place for file-only platforms,
228	another manual step takes it place. Use the &gbImport; button
229	in the array design item view and select the
230	<guilabel>Affymetrix CDF probeset importer</guilabel> plug-in.
231	If you have enough permissions this function will also let you create
232	missing reporters.
233	</para>
234	</note>
235	</sect2>
236	</sect1>
237
238
239	<sect1 id="array_lims.arraybatch">
240	<title>Array batches</title>
241
242	<para>
243	Beside the common way of creating items in BASE, an array batch can also be created
244	directly from an array design, both in list view and single item view.
245	</para>
246	<variablelist>
247	<varlistentry>
248	<term>In list view of array design</term>
249	<listitem>
250	<para>
251	Click on the
252	<guiicon>
253	<inlinemediaobject>
254	<imageobject>
255	<imagedata fileref="figures/add.png" format="PNG" />
256	</imageobject>
257	</inlinemediaobject>
258	</guiicon>
259	icon available from the
260	<guilabel>Batches</guilabel>
261	column of the array design you want to use.
262	<tip>
263	<para>
264	As default in BASE the
265	<guilabel>Batches</guilabel>
266	column is hidden and need therefore be made visible first, see
267	<xref linkend="webclient.itemlist.columns" />
268	</para>
269	</tip>
270	</para>
271	</listitem>
272	</varlistentry>
273	</variablelist>
274	<para>
275	<guibutton>New batch…</guibutton>
276	is the corresponding button in single item view. The current array design will
277	automatically be filled in the array design property for the new batch.
278	</para>
279
280
281	<figure id="array_lims.figures.arraybatch">
282	<title>Array batch properties</title>
283	<screenshot>
284	<mediaobject>
285	<imageobject>
286	<imagedata
287	fileref="figures/arraybatch_edit.png" format="PNG" />
288	</imageobject>
289	</mediaobject>
290	</screenshot>
291	</figure>
292
293	<helptext external_id="arraybatch.edit"
294	title="Edit array batch">
295
296	<variablelist>
297	<varlistentry>
298	<term>
299	<guilabel>Name</guilabel>
300	</term>
301	<listitem>
302	<para>The name of the array batch (required).</para>
303	</listitem>
304	</varlistentry>
305	<varlistentry>
306	<term>
307	<guilabel>Array design</guilabel>
308	</term>
309	<listitem>
310	<para>Array design that is used for the batch.</para>
311	</listitem>
312	</varlistentry>
313	<varlistentry>
314	<term>
315	<guilabel>Print robot</guilabel>
316	</term>
317	<listitem>
318	<para>The print robot that is used.</para>
319	</listitem>
320	</varlistentry>
321	<varlistentry>
322	<term>
323	<guilabel>Protocol</guilabel>
324	</term>
325	<listitem>
326	<para>
327	The printing protocol that was followed when producing the array batch
328	</para>
329	</listitem>
330	</varlistentry>
331	<varlistentry>
332	<term>
333	<guilabel>Description</guilabel>
334	</term>
335	<listitem>
336	<para>
337	Provide other useful information about the array batch in this text
338	area.
339	</para>
340	</listitem>
341	</varlistentry>
342	</variablelist>
343	<para>
344	Click on the &gbSave; button to store the information in BASE or on the &gbCancel;
345	button to abort.
346	</para>
347
348	<seeother>
349	<other external_id="annotations.edit">Annotations</other>
350	<other external_id="annotations.edit.inerited">Inherit annotations</other>
351	</seeother>
352	</helptext>
353
354	</sect1>
355
356	<sect1 id="array_lims.arrayslide">
357	<title>Array slides</title>
358	<para>
359	Use
360	<menuchoice>
361	<guimenu>Array LIMS</guimenu>
362	<guimenuitem>Array slides</guimenuitem>
363	</menuchoice>
364	to get to the list page of array slides.
365	</para>
366	<sect2 id="array_lims.arrayslide.create">
367	<title>Creating array slides</title>
368	<para>In BASE, array slides can be created, except the common way, by 2 routes:</para>
369	<variablelist>
370	<varlistentry>
371	<term>from the array batch list page</term>
372	<listitem>
373	<para>
374	Clicking on the
375	<guiicon>
376	<inlinemediaobject>
377	<imageobject>
378	<imagedata fileref="figures/add.png" format="PNG" />
379	</imageobject>
380	</inlinemediaobject>
381	</guiicon>
382	icon in the
383	<guilabel>Slides</guilabel>
384	column for the batch you want to add a slide to. Corresponding button in
385	the view page of a batch is
386	<guibutton>New slide…</guibutton>
387	.
388	</para>
389	</listitem>
390	</varlistentry>
391	<varlistentry>
392	<term>using a wizard to create multiple slides simultaneously</term>
393	<listitem>
394	<para>
395	This can be started from three different places:
396	<itemizedlist>
397	<listitem>
398	<para>
399	array batch list view by clicking on
400	<guiicon>
401	<inlinemediaobject>
402	<imageobject>
403	<imagedata fileref="figures/new_wizard.gif"
404	format="GIF" />
405	</imageobject>
406	</inlinemediaobject>
407	</guiicon>
408	in the
409	<guilabel>Slides</guilabel>
410	column of the batch that should be used.
411	</para>
412	</listitem>
413	<listitem>
414	<para>
415	Using the
416	<guibutton>Create slides</guibutton>
417	in a single item view of an array batch.
418	</para>
419	</listitem>
420	<listitem>
421	<para>
422	In the list page of array slides, using the
423	<guibutton>Create multiple…</guibutton>
424	button
425	</para>
426	</listitem>
427	</itemizedlist>
428	The wizard is described further down in
429	<xref linkend="array_lims.arrayslide.wizard" />.
430	</para>
431	</listitem>
432	</varlistentry>
433	</variablelist>
434
435	<figure id="write_docbook_doc.figures.arrayslide-single-create">
436	<title>Create new array slide</title>
437	<screenshot>
438	<mediaobject>
439	<imageobject>
440	<imagedata
441	fileref="figures/arrayslide-single-create.png" format="PNG" />
442	</imageobject>
443	</mediaobject>
444	</screenshot>
445	</figure>
446	<helptext
447	external_id="arrayslide.edit"
448	title="Edit array slide">
449	<variablelist>
450	<varlistentry>
451	<term>
452	<guilabel>Name</guilabel>
453	</term>
454	<listitem>
455	<para>The name of the array slide (required).</para>
456	</listitem>
457	</varlistentry>
458	<varlistentry>
459	<term>
460	<guilabel>Barcode</guilabel>
461	</term>
462	<listitem>
463	<para>Does the array slide have a barcode, it can be put here.</para>
464	</listitem>
465	</varlistentry>
466	<varlistentry>
467	<term>
468	<guilabel>Destroyed</guilabel>
469	</term>
470	<listitem>
471	<para>
472	This check-box can be ticked to mark the slide as destroyed, lost or
473	damaged.
474	</para>
475	</listitem>
476	</varlistentry>
477	<varlistentry>
478	<term>
479	<guilabel>Array batch</guilabel>
480	</term>
481	<listitem>
482	<para>Array batch that the slide belongs to (required).</para>
483	</listitem>
484	</varlistentry>
485	<varlistentry>
486	<term>
487	<guilabel>Index</guilabel>
488	</term>
489	<listitem>
490	<para>The index of the array slide in selected array batch.</para>
491	</listitem>
492	</varlistentry>
493	<varlistentry>
494	<term>
495	<guilabel>Description</guilabel>
496	</term>
497	<listitem>
498	<para>
499	Any information useful information about the slide can be in this field.
500	</para>
501	</listitem>
502	</varlistentry>
503	</variablelist>
504	<para>
505	Click on the &gbSave; button to store the information in BASE or on the &gbCancel;
506	button to abort.
507	</para>
508	<seeother>
509	<other external_id="arrayslide.createwizard.1">Create array slides - step 1</other>
510	<other external_id="arrayslide.createwizard.2">Create array slides - step 2</other>
511	</seeother>
512	</helptext>
513	</sect2>
514
515	<sect2 id="array_lims.arrayslide.wizard">
516	<title>Multiple slides wizard</title>
517	<para>
518	As mentioned above there is an alternative to create one slide at a time if you
519	have many to add. There is a wizard that can help you to create at the most 999
520	slides in one go. The wizard is in two steps:
521	</para>
522
523	<figure id="array_lims.figures.arrayslide-wizard-step1">
524	<title>Create multiple array slides - step 1</title>
525	<screenshot>
526	<mediaobject>
527	<imageobject>
528	<imagedata fileref="figures/arrayslide-wizard-step1.png" format="PNG" />
529	</imageobject>
530	</mediaobject>
531	</screenshot>
532	</figure>
533
534	<helptext external_id="arrayslide.createwizard.1"
535	title="Create array slides - step 1">
536
537	<para>
538	The first step reminds alot of the normal edit window of an array
539	slide:
540	</para>
541
542	<variablelist>
543	<varlistentry>
544	<term>
545	<guilabel>Name</guilabel>
546	</term>
547	<listitem>
548	<para>
549	The name prefix of the array slides. Each array slide will be
550	numbered according to the <emphasis>start at</emphasis> and
551	<emphasis>pad size</emphasis> settings below.
552	</para>
553	</listitem>
554	</varlistentry>
555	<varlistentry>
556	<term>
557	<guilabel>Array batch</guilabel>
558	</term>
559	<listitem>
560	<para>Array batch that the slides belongs to (required).</para>
561	</listitem>
562	</varlistentry>
563	<varlistentry>
564	<term>
565	<guilabel>Quantity</guilabel>
566	</term>
567	<listitem>
568	<para>
569	Number of slides to create with this wizard
570	(required and must be between 1 and 999)
571	</para>
572	</listitem>
573	</varlistentry>
574	<varlistentry>
575	<term>
576	<guilabel>Start at</guilabel>
577	</term>
578	<listitem>
579	<para>
580	The index number to start from when indexing the
581	name of the slides.
582	</para>
583	</listitem>
584	</varlistentry>
585	<varlistentry>
586	<term>
587	<guilabel>Pad size</guilabel>
588	</term>
589	<listitem>
590	<para>
591	The index will be filled out with zeros in front to
592	always have this length.
593	</para>
594	</listitem>
595	</varlistentry>
596	</variablelist>
597
598	<para>
599	Click on &gbNext; to move on to the second step of the wizard.
600	</para>
601
602	<seeother>
603	<other external_id="arrayslide.createwizard.2">Create array slides - step 2</other>
604	<other external_id="arrayslide.edit">Edit array slide</other>
605	</seeother>
606
607	</helptext>
608
609
610	<figure id="array_lims.figures.arrayslide-wizard-step2">
611	<title>Create multiple array slides - step 2</title>
612	<screenshot>
613	<mediaobject>
614	<imageobject>
615	<imagedata fileref="figures/arrayslide-wizard-step2.png" format="PNG" />
616	</imageobject>
617	</mediaobject>
618	</screenshot>
619	</figure>
620
621	<helptext external_id="arrayslide.createwizard.2" title="Create array slides - step 2">
622	<para>
623	This step allows the names of the array slides to be adjusted
624	if needed. It is also possible to enter barcodes for each of the
625	new slides. The information can either be filled in one-by-one
626	or by using the "scratchpad" icon
627	<guiicon>
628	<inlinemediaobject>
629	<imageobject>
630	<imagedata fileref="figures/paste.png"
631	format="PNG" />
632	</imageobject>
633	</inlinemediaobject>
634	</guiicon>. This opens up a larger text window where the names or barcodes
635	can be entered one per line. This can be useful if the information can be
636	pasted from an external source.
637	</para>
638
639	<seeother>
640	<other external_id="arrayslide.createwizard.1">Create array slides - step 1</other>
641	<other external_id="arrayslide.edit">Edit array slide</other>
642	</seeother>
643
644	<para>
645	Click on the &gbSave; button to store the information in BASE or on the
646	&gbCancel; button to abort the wizard.
647	</para>
648
649	</helptext>
650
651	</sect2>
652	</sect1>
653	</chapter>

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