source: trunk/doc/src/docbook/userdoc/array_lims.xml @ 4131

Last change on this file since 4131 was 4131, checked in by Nicklas Nordborg, 15 years ago

Fixes #868: Support for chips with multiple arrays

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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 4131 2008-02-08 08:55:48Z nicklas $
7 
8  Copyright (C) 2007 Nicklas Nordborg, Philippe Rocca-Serra, Martin Svensson
9 
10  This file is part of BASE - BioArray Software Environment.
11  Available at http://base.thep.lu.se/
12 
13  BASE is free software; you can redistribute it and/or
14  modify it under the terms of the GNU General Public License
15  as published by the Free Software Foundation; either version 2
16  of the License, or (at your option) any later version.
17 
18  BASE is distributed in the hope that it will be useful,
19  but WITHOUT ANY WARRANTY; without even the implied warranty of
20  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
21  GNU General Public License for more details.
22 
23  You should have received a copy of the GNU General Public License
24  along with this program; if not, write to the Free Software
25  Foundation, Inc., 59 Temple Place - Suite 330,
26  Boston, MA  02111-1307, USA.
27-->
28
29<chapter id="array_lims">
30  <?dbhtml dir="array_lims"?>
31  <title>Array LIMS</title>
32  <sect1 id="array_lims.introduction">
33    <title>Introduction</title>
34    <para>
35      Arrays are at the core of the BASE2 business and are essential elements to describe in
36      order to be MIAME compliant. It is also critical to track and manage information about
37      microarray design as accurately as possible since mistakes could prove extremely costly
38      in downstream analysis.
39    </para>
40    <para>
41      Finally, as a good practice, all array related information should be entered into BASE2
42      system prior to start describing the sample processing and hybridizations events making
43      up a microarray experiment.
44    </para>
45
46    <para>
47      BASE2 has been engineered to support microarray printing facilities. The system
48      therefore offers objects to describe plates, their geometries and the events (merging,
49      printing) affected them. The first section of the chapter deals with this functionality.
50      as well as plate management.
51    </para>
52
53    <para>
54      For users buying their arrays from commercial sources, the plate management component
55      can be ignored and they can go immediately to
56      <xref linkend="array_lims.arraydesign" />.
57    </para>
58
59  </sect1>
60
61  <sect1 id="array_lims.platemanagement">
62    <title>Plates</title>
63    <para>TODO</para>
64  </sect1>
65
66  <sect1 id="array_lims.arraydesign">
67    <title>Array designs</title>
68   
69    <para>
70      Array designs should be understood as a plan which can be realized during a printing
71      process producing microarray slides. During the course of the printing process, reagents
72      may run out leading to the interruption of this process. All slides created during this
73      printing process belong to the same printing batch. It is the array slide that will
74      eventually be used in a hybridization event. BASE2 allows user to track those 3 entities
75      with great details. This is an important functionality for users producing their own
76      arrays and for those caring for quality control and tracking of microarray slides in a
77      printing facility. The following sections detail how to use BASE2 to help in these
78      tasks.
79    </para>
80    <tip>
81      <para>
82        It's highly recommended to have read
83        <xref linkend="webclient.items" />
84        before continuing with this chapter.
85      </para>
86    </tip>
87    <para>
88      Use
89      <menuchoice>
90        <guimenu>Array LIMS</guimenu>
91        <guimenuitem>Array designs</guimenuitem>
92      </menuchoice>
93      to get to the list page with array designs.
94    </para>
95   
96    <sect2 id="array_lims.arraydesign.properties">
97      <title>Properties</title>
98      <sect3 id="array_lims.arraydesign.properties.arraydesign">
99        <title>Array design</title>
100       
101        <helptext external_id="arraydesign.edit" title="Edit array design">
102        <variablelist>
103          <varlistentry>
104            <term>
105              <guilabel>Name</guilabel>
106            </term>
107            <listitem>
108              <para>Provide an sensible name for the design (required).</para>
109            </listitem>
110          </varlistentry>
111          <varlistentry>
112            <term>
113              <guilabel>Platform</guilabel>
114            </term>
115            <listitem>
116              <para>
117                Select the platform / variant used for the
118                array design. The selected options affects which
119                files that can be selected on the <guilabel>Data files</guilabel>
120                tab.
121              </para>
122            </listitem>
123          </varlistentry>
124          <varlistentry>
125            <term>
126              <guilabel>Arrays/slide</guilabel>
127            </term>
128            <listitem>
129              <para>
130                The number of sub-arrays that can be placed on a
131                single slide. The default value is 1, but some
132                platforms, for example Illumina, has slides
133                with 6 or 8 arrays.
134              </para>
135            </listitem>
136          </varlistentry>
137          <varlistentry>
138            <term>
139              <guilabel>Description</guilabel>
140            </term>
141            <listitem>
142              <para>
143                Provide other useful information about the array design in this text
144                area.
145              </para>
146            </listitem>
147          </varlistentry>
148        </variablelist>
149        <para>
150          Click on the &gbSave; button to store the information in BASE2 or on the
151          &gbCancel; button to abort.
152        </para>
153        <seeother>
154          <other external_id="datafiles.edit">Data files</other>
155          <other external_id="annotations.edit">Annotations</other>
156          <other external_id="annotations.edit.inerited">Inherit annotations</other>
157        </seeother>
158        </helptext>
159       
160      </sect3>
161
162      <sect3 id="array_lims.arraydesign.properties.annotations">
163        <title>Annotations and inherited annotations</title>
164        <para>
165          This allows you to input values associated to annotation types devised to refine
166          array design description. Read more about annotations in
167          <xref linkend="annotations" />.
168        </para>
169      </sect3>
170    </sect2>
171
172
173    <sect2 id="array_lims.arraydesign.importfeature">
174      <title>Importing features to an array design</title>
175
176      <para>
177        Importing features is an important step in
178        order to fully define an array design. It should be noted that BASE2 does not
179        enforce the immediate feature import upon creation of array design. However, it
180        is STRONGLY advised to do so when creating an array design. Doing so enables to
181        use the array design for downstream analysis with no further trouble. It also
182        matters when importing raw bioassay data and matching those to the corresponding
183        array design.
184      </para>
185
186      <para>
187        Depending on which platform and/or data files you selected when you
188        created the array design the process to import features is different.
189        For example, if you selected the Affymetrix platform, which is a file-only
190        platform, the feature information has already been extracted from
191        the CDF file (if you selected one). If the selected platform
192        doesn't extract information from the selected data file automatically
193        this may be done manually by executing an import plug-in.
194      </para>
195
196      <para>
197        From the array design item view, click on the &gbImport; button and use the
198        reporter map importer and an appropriate plug-in configuration when following the
199        instructions in
200        <xref linkend="import_export_data.import" />.
201        If the import run is successful, go to the array design list view. The
202        <guilabel>Has features</guilabel>
203        column will show
204        <guilabel>Yes (db: x, file: y)</guilabel>
205        where x is the number of features actually imported into the database.
206      </para>
207
208      <note>
209        <para>
210          The &gbImport; button only shows up if the logged in user has
211          enough permissions.
212        </para>
213      </note>     
214     
215      <note>
216        <title>Verify that probsets in a CDF file exist as reporters</title>
217        <para>
218          File-only platforms, such as Affymetrix, require that all probesets
219          must exist as reporters before data can be analysed. For other
220          platforms this is usually checked when importing the features to
221          the database. Since no import takes place for file-only platforms,
222          another manual step takes it place. Use the &gbImport; button
223          in the array design item view and select the
224          <guilabel>Affymetrix CDF probeset importer</guilabel> plug-in.
225          If you have enough permissions this function will also let you create
226          missing reporters.
227        </para>
228      </note>
229    </sect2>
230  </sect1>
231
232
233  <sect1 id="array_lims.arraybatch">
234    <title>Array batches</title>
235
236    <sect2 id="array_lims.arraybatch.create">
237      <title>Creating array batches</title>
238      <para>
239        Beside the common way of creating items in BASE, an array batch can also be created
240        directly from an array design, both in list view and single item view.
241      </para>
242      <variablelist>
243        <varlistentry>
244          <term>In list view of array design</term>
245          <listitem>
246            <para>
247              Click on the
248              <guiicon>
249                <inlinemediaobject>
250                  <imageobject>
251                    <imagedata fileref="figures/add.png" format="PNG" />
252                  </imageobject>
253                </inlinemediaobject>
254              </guiicon> 
255              icon available from the
256              <guilabel>Batches</guilabel>
257              column of the array design you want to use.
258              <tip>
259                <para>
260                  As default in BASE the
261                  <guilabel>Batches</guilabel>
262                  column is hidden and need therefore be made visible first, see
263                  <xref linkend="webclient.itemlist.columns" />
264                </para>
265              </tip>
266            </para>
267          </listitem>
268        </varlistentry>
269      </variablelist>
270      <para>
271        <guibutton>New batch&hellip;</guibutton>
272        is the corresponding button in single item view. The current array design will
273        automatically be filled in the array design property for the new batch.
274      </para>
275    </sect2>
276    <sect2 id="array_lims.arraybatch.properties">
277      <title>Properties</title>
278      <variablelist>
279        <varlistentry>
280          <term>
281            <guilabel>Name</guilabel>
282          </term>
283          <listitem>
284            <para>The name of the array batch (required).</para>
285          </listitem>
286        </varlistentry>
287        <varlistentry>
288          <term>
289            <guilabel>Array design</guilabel>
290          </term>
291          <listitem>
292            <para>Array design that is used for the batch.</para>
293          </listitem>
294        </varlistentry>
295        <varlistentry>
296          <term>
297            <guilabel>Print robot</guilabel>
298          </term>
299          <listitem>
300            <para>The print robot that is used.</para>
301          </listitem>
302        </varlistentry>
303        <varlistentry>
304          <term>
305            <guilabel>Protocol</guilabel>
306          </term>
307          <listitem>
308            <para>
309              The printing protocol that was followed when producing the array batch
310            </para>
311          </listitem>
312        </varlistentry>
313      </variablelist>
314      <para>
315        Click on the &gbSave; button to store the information in BASE2 or on the &gbCancel;
316        button to abort.
317      </para>
318      <para>
319        See
320        <xref linkend="annotations" />
321        for information about annotating items and inherit annotations.
322      </para>
323      <para>
324        How many slides each batch has can be found in the
325        <guilabel>Slides</guilabel>
326        column, list view page.
327      </para>
328    </sect2>
329  </sect1>
330
331  <sect1 id="array_lims.arrayslide">
332    <title>Array slides</title>
333    <para>
334      Use
335      <menuchoice>
336        <guimenu>Array LIMS</guimenu>
337        <guimenuitem>Array slides</guimenuitem>
338      </menuchoice>
339      to get to the list page of array slides.
340    </para>
341    <sect2 id="array_lims.arrayslide.create">
342      <title>Creating array slides</title>
343      <para>In BASE2, array slides can be created, except the common way, by 2 routes:</para>
344      <variablelist>
345        <varlistentry>
346          <term>from the array batch list page</term>
347          <listitem>
348            <para>
349              Clicking on the
350              <guiicon>
351                <inlinemediaobject>
352                  <imageobject>
353                    <imagedata fileref="figures/add.png" format="PNG" />
354                  </imageobject>
355                </inlinemediaobject>
356              </guiicon>
357              icon in the
358              <guilabel>Slides</guilabel>
359              column for the batch you want to add a slide to. Corresponding button in
360              the view page of a batch is
361              <guibutton>New slide&hellip;</guibutton>
362              .
363            </para>
364          </listitem>
365        </varlistentry>
366        <varlistentry>
367          <term>using a wizard to create multiple slides simultaneously</term>
368          <listitem>
369            <para>
370              This can be started from three different places:
371              <itemizedlist>
372                <listitem>
373                  <para>
374                    array batch list view by clicking on
375                    <guiicon>
376                      <inlinemediaobject>
377                        <imageobject>
378                          <imagedata fileref="figures/new_wizard.gif"
379                            format="GIF" />
380                        </imageobject>
381                      </inlinemediaobject>
382                    </guiicon>
383                    in the
384                    <guilabel>Slides</guilabel>
385                    column of the batch that should be used.
386                  </para>
387                </listitem>
388                <listitem>
389                  <para>
390                    Using the
391                    <guibutton>Create slides</guibutton>
392                    in a single item view of an array batch.
393                  </para>
394                </listitem>
395                <listitem>
396                  <para>
397                    In the list page of array slides, using the
398                    <guibutton>Create multiple&hellip;</guibutton>
399                    button
400                  </para>
401                </listitem>
402              </itemizedlist>
403              The wizard is described further down in
404              <xref linkend="array_lims.arrayslide.properties.wizard" />
405              .
406            </para>
407          </listitem>
408        </varlistentry>
409      </variablelist>
410    </sect2>
411    <sect2 id="array_lims.arrayslide.properties">
412      <title>Properties</title>
413
414      <figure id="write_docbook_doc.figures.arrayslide-single-create">
415        <title>Create new array slide</title>
416        <screenshot>
417          <mediaobject>
418            <imageobject>
419              <imagedata 
420                fileref="figures/arrayslide-single-create.png" format="PNG" />
421            </imageobject>
422          </mediaobject>
423        </screenshot>
424      </figure>
425      <variablelist>
426        <varlistentry>
427          <term>
428            <guilabel>Name</guilabel>
429          </term>
430          <listitem>
431            <para>The name of the array slide (required).</para>
432          </listitem>
433        </varlistentry>
434        <varlistentry>
435          <term>
436            <guilabel>Barcode</guilabel>
437          </term>
438          <listitem>
439            <para>Does the array slide have a barcode, it can be put here.</para>
440          </listitem>
441        </varlistentry>
442        <varlistentry>
443          <term>
444            <guilabel>Destroyed</guilabel>
445          </term>
446          <listitem>
447            <para>
448              This check-box can be ticked to mark the slide as destroyed, lost or
449              damaged.
450            </para>
451          </listitem>
452        </varlistentry>
453        <varlistentry>
454          <term>
455            <guilabel>Array batch</guilabel>
456          </term>
457          <listitem>
458            <para>Array batch that the slide belongs to (required).</para>
459          </listitem>
460        </varlistentry>
461        <varlistentry>
462          <term>
463            <guilabel>Index</guilabel>
464          </term>
465          <listitem>
466            <para>The index of the array slide in selected array batch.</para>
467          </listitem>
468        </varlistentry>
469        <varlistentry>
470          <term>
471            <guilabel>Description</guilabel>
472          </term>
473          <listitem>
474            <para>
475              Any information useful information about the slide can be in this field.
476            </para>
477          </listitem>
478        </varlistentry>
479      </variablelist>
480      <para>
481        Click on the &gbSave; button to store the information in BASE2 or on the &gbCancel;
482        button to abort.
483      </para>
484      <sect3 id="array_lims.arrayslide.properties.wizard">
485        <title>Multiple slides wizard</title>
486        <para>
487          As mentioned above there is an alternative to create one slide at a time if you
488          have many to add. There is a wizard that can help you to create at the most 999
489          slides in one go. The wizard is in two steps, both showed in the picture
490          <xref linkend="write_docbook_doc.figures.arrayslide-multiple-create" />
491          .
492          <orderedlist>
493            <listitem>
494              <para>
495                The first step reminds alot of the normal edit window of an array
496                slide, but there are some differences:
497                <variablelist>
498                  <varlistentry>
499                    <term>
500                      <guilabel>Quantity</guilabel>
501                    </term>
502                    <listitem>
503                      <para>
504                        Number of slides to create with this wizard
505                        (required and must be between 1 and 999)
506                      </para>
507                    </listitem>
508                  </varlistentry>
509                  <varlistentry>
510                    <term>
511                      <guilabel>Start at</guilabel>
512                    </term>
513                    <listitem>
514                      <para>
515                        The index number to start from when indexing the
516                        name of the slides.
517                      </para>
518                    </listitem>
519                  </varlistentry>
520                  <varlistentry>
521                    <term>
522                      <guilabel>Pad size</guilabel>
523                    </term>
524                    <listitem>
525                      <para>
526                        The index will be filled out with zeros in front to
527                        always have this length.
528                      </para>
529                    </listitem>
530                  </varlistentry>
531                </variablelist>
532                Press
533                <guibutton>Next</guibutton>
534                to continue to next step of the wizard.
535                <important>
536                  <para>
537                    Be sure to get everything right before proceeding, because
538                    it is not possible to go back from step 2.
539                  </para>
540                </important>
541              </para>
542            </listitem>
543            <listitem>
544              <para>
545                In step 2 should the barcodes for the array slides be entered, for
546                those which have one. The autogenerated names of the slides can also
547                be changed if that is wanted, as long as no name-field is left
548                empty.
549              </para>
550            </listitem>
551          </orderedlist>
552
553          <figure id="write_docbook_doc.figures.arrayslide-multiple-create">
554            <title>Create multiple array slide</title>
555            <screenshot>
556              <mediaobject>
557                <imageobject>
558                  <imagedata scalefit="1" width="100%"
559                    fileref="figures/arrayslide-multiple-create.png" format="PNG" />
560                </imageobject>
561              </mediaobject>
562            </screenshot>
563          </figure>
564          Fill in the necessary information as exhaustively as possible.
565        </para>
566        <para>
567          Click on the &gbSave; button to store the information in BASE2 or on the
568          &gbCancel; button to abort.
569        </para>
570        <para>
571          See
572          <xref linkend="annotations" />
573          for information about annotating items and inherit annotations.
574        </para>
575      </sect3>
576    </sect2>
577  </sect1>
578</chapter>
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