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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 3381 2007-05-25 07:45:07Z martin $
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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
35    <para>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.</para>
39    <para>Finally, as a good practice, all Array related information should be entered into
40      BASE2 system prior to start describing the sample processing and hybridizations events
41      making up a microarray experiment.</para>
42
43    <para>BASE2 has been engineered to support microarray printing facilities. The system
44      therefore offers objects to describe plates, their geometries and the events (merging,
45      printing) affected them. The first section of the chapter deals with this functionality.
46      as well as plate management.</para>
47
48    <para>For users buying their arrays from commercial sources, the Plate Management component
49      can be ignored and they can go immediately to the second section <xref
50        linkend="array_lims.arraydesign"/> of the chapter.</para>
51
52  </sect1>
53
54  <sect1 id="array_lims.platemanagement">
55    <title>Managing Plates</title>
56    <para>TO DO</para>
57  </sect1>
58
59  <sect1 id="array_lims.arraydesign">
60    <title>Managing ArrayDesigns</title>
61    <para> ArrayDesign should be understood as a plan which can be realized during a printing
62      process producing microarray slides. During the course of the printing process, reagents
63      may run out leading to the interruption of this process. All slides created during this
64      printing process belong to the same printing 'batch'. It is the array slide that will
65      eventually be used in a Hybridization event. BASE2 allows user to track those 3 entities
66      with great details. This is an important functionality for users producing their own
67      arrays and for those caring for quality control and tracking of microarray slides in a
68      printing facility. The following sections detail how to use BASE2 to help in these
69      tasks. </para>
70    <sect2 id="array_lims.arraydesign.create">
71      <title>Creating ArrayDesigns</title>
72      <para>To create an ArrayDesign, do the following</para>
73      <para>Go To <menuchoice>
74          <guimenu>Array LIMS</guimenu>
75          <guimenuitem>Array designs</guimenuitem>
76        </menuchoice>
77      </para>
78      <para>The ArrayDesign List view now presents all ArrayDesigns available to the user
79        (shared to or owned by).</para>
80      <para>Click on <guibutton>New&hellip;</guibutton> button</para>
81      <para>A 'Create' pop-up window opens. It contains 3 tabs</para>
82
83      <variablelist>
84        <varlistentry>
85          <term>
86            <guilabel>Array design</guilabel>
87          </term>
88          <listitem>
89
90            <para>The tab contains four fields, namely:</para>
91
92            <variablelist>
93
94              <varlistentry>
95                <term>
96                  <guilabel>Name</guilabel>
97                </term>
98                <listitem>
99                  <para> Provide a unique sensible name for the design. Possibly
100                    follow the convention [organisation-species-feature
101                    number-version] as in EMBL-Hsapiens-wholegenome-45k-v1. For
102                    commercial platforms such as Agilent and Affymetrix, it is
103                    probably better to use the commercial names, such as Agilent
104                    Whole Mouse Genome G4122A or HG_U133A respectively</para>
105                </listitem>
106              </varlistentry>
107
108              <varlistentry>
109                <term>
110                  <guilabel>Description</guilabel>
111                </term>
112                <listitem>
113                  <para>Provide a short but meaningful of the ArrayDesign</para>
114                </listitem>
115              </varlistentry>
116
117              <varlistentry>
118                <term>
119                  <guilabel>Affy Chip</guilabel>
120                </term>
121                <listitem>
122                  <para>This is a radio button for providing a boolean entry,
123                    essentially telling the system whether the ArrayDesign being
124                    created is of Affymetrix technology or not.</para>
125                  <warning>
126                    <para>As indicated on the interface, once saved, this
127                      information cannot be modified, so if a mistake is made,
128                      the entry will have to be deleted.</para>
129                  </warning>
130                </listitem>
131              </varlistentry>
132
133              <varlistentry>
134                <term>
135                  <guilabel>CDF file</guilabel>
136                </term>
137                <listitem>
138                  <para>This field allows to upload an Affymetrix CDF file. A CDF
139                    file is a binary file describing Affymetrix chip layout.
140                    This file is necessary for performing analysis using BASE2
141                    plugins (e.g RMAExpress plugin).</para>
142                  <note>
143                    <para>Affymetrix users, you can also upload CLF or BPMAP
144                      files defined for exon and tiling arrays
145                    respectively.</para>
146                  </note>
147                </listitem>
148              </varlistentry>
149
150            </variablelist>
151          </listitem>
152        </varlistentry>
153
154        <varlistentry>
155          <term>
156            <guilabel>Annotations</guilabel>
157          </term>
158          <listitem>
159            <para>This tab allows to input values associated to Annotation Types devised
160              to refine ArrayDesign description.</para>
161            <para>The windows will be empty if no Annotation Types have been declared to
162              annotation ArrayDesign item or if none are shared to the user</para>
163          </listitem>
164        </varlistentry>
165
166        <varlistentry>
167          <term>
168            <guilabel>Inherited Annotations</guilabel>
169          </term>
170          <listitem>
171            <para>TO DO</para>
172          </listitem>
173        </varlistentry>
174
175      </variablelist>
176      <para>Click on the <guibutton>Save</guibutton> button to store the information in BASE2 or on the
177          <guibutton>Cancel</guibutton> button to abort. </para>
178      <para>Upon saving, the Array Design List View page is displayed. Users should pay
179        attention to the column <guilabel>Has features</guilabel>. Unless an Affymetrix
180        ArrayDesign was created, the value will be by default set to
181        <guilabel>no</guilabel>. For all other cases, this value will only be updated
182        following <guilabel>Importing the Features</guilabel>, a process which is detailed
183        in the next section.</para>
184
185    </sect2>
186
187    <sect2 id="array_lims.arraydesign.importfeature">
188      <title>Importing Features associated to an ArrayDesign</title>
189      <important>
190        <para>For non-Affymetrix ArrayDesigns, Importing Features is an important step in
191          order to fully define an ArrayDesign. It should be noted that BASE2 does not
192          enforce the immediate Feature import upon creation of ArrayDesign. However, It
193          is STRONGLY advised to do so when creating an ArrayDesign. Doing so enables to
194          use the Array Design for downstream analysis with no further trouble. It also
195          matters when importing rawBioassay data and matching those to the corresponding
196          ArrayDesign. It is interesting to note that the processes of importing features
197          associated to Array Design and importing Data associated to Raw BioAssay are in
198          essence very similar.</para> Please see section <xref
199          linkend="experiments_analysis.rawbioassay.rawdata"/> for more information. </important>
200      <para>This section applies only to non-affymetrix ArrayDesign since Affymetrix designs
201        are handled differently. For Affymetrix platform, features are considered imported
202        when the Affymetrix CDF file is actually uploaded.</para>
203      <para>From the ArrayDesign Item View, click on the <guibutton>Import</guibutton>
204      button.</para>.<note>
205        <para>The button only shows up if the logged in user has enough permissions.</para>
206      </note>
207      <para>A plugin interface is launched. One can either run the import using the autodetect
208        settings or for more control, select a <guilabel>'Reporter Map Importer'</guilabel>
209        plugin and then choose a <guilabel>plugin configuration</guilabel> available from
210        the drop-down list populated from configurations shared to or owned by the user.</para>
211      <para>BASE2 ships with Reporter Map Importer plugin configurations allowing to import
212        features from Axon gal files and also gpr files (2 configurations_Block/Column/Row
213        and Block/Row/Column for each file formats) and for Agilent FeatureExtraction files
214        (to be confirmed). </para>
215      <para>For more about the plugin configuration, refer to section <xref
216          linkend="plugins.installation"/>.</para>
217      <para>If the import run is successful, go to the ArrayDesign List view. The
218          <guilabel>Has features</guilabel> column will show <guilabel>Yes (n)</guilabel>
219        where n is the number of features actually present on the microarray and now
220        associated to the newly created ArrayDesign.</para>
221      <tip>
222        <para>A list of Reporter Map Importer plugin configurations is maintained at BASE2
223          site and each can be downloaded as xml file from
224          <ulink url="http://base.thep.lu.se/chrome/site/doc/admin/plugin_configuration/coreplugins.html"/>.</para>
225      </tip>
226    </sect2>
227    <para>If both actions have been successfully completed, the ArrayDesign is now fully defined
228      and ArrayBatches and Array slides items can be created. This process is described in the
229      following sections.</para>
230
231
232    <sect2 id="array_lims.arraydesign.detail_view">
233      <title>Viewing/Editing ArrayDesigns</title>
234      <itemizedlist>
235        <listitem>
236          <para> Press and hold one of the <keycap>CTRL</keycap>, <keycap>ALT</keycap> or
237              <keycap>SHIFT</keycap> keys while clicking on the name of an ArrayDesign
238            Item, which is a live link. </para>
239        </listitem>
240        <listitem>
241          <para> Alternately, navigating to the ArrayDesign Item View, one can hit the
242              <guibutton>Edit&hellip;</guibutton> to performed the task.</para>
243          <para>In both cases, an Edit pop-up windows opens. It is essentially identical
244            to a Create window and allows updating information about a particular
245            ArrayDesign item stored in BASE2.</para>
246          <figure id="write_docbook_doc.figures.arraydesign-itemview">
247            <title>ArrayDesign Item View</title>
248            <screenshot>
249              <mediaobject>
250                <imageobject>
251                  <imagedata contentwidth="10cm" width="10cm" fileref="figures/arraydesign-itemview.png" format="PNG"/>
252                </imageobject>
253              </mediaobject>
254            </screenshot>
255          </figure>
256        </listitem>
257        <listitem>
258          <para>From the ArrayDesign item View, all associated
259            <guilabel>ArrayBatches</guilabel> are indicated as navigable links. Also
260            present on the ArrayDesign Item View are the links back to
261            <guilabel>Plates</guilabel> possibly used to define the ArrayDesign (none
262            used in the screenshot).</para>
263        </listitem>
264      </itemizedlist>
265    </sect2>
266    <sect2 id="array_lims.arraydesign.delete">
267      <title>Deleting/Restoring ArrayDesigns</title>
268      <para>As for other items in BASE2, ArrayDesigns can be removed and restored. To do so,
269        do the following:</para>
270      <itemizedlist>
271        <listitem>
272          <para>Select one or more ArrayDesigns and click <guibutton>Delete</guibutton>
273            button in the menu bar. </para>
274          <para>All the selected ArrayDesigns have been marked as deleted and are no
275            longer available from the interface. </para>
276          <para>Only by selecting from the <guilabel>view/preset&hellip;</guilabel>
277            select box the <guilabel>Removed</guilabel> option, one can see those of the
278            ArrayDesigns earmarked for deletion. They will be shown with a symbol <inlinemediaobject>
279              <imageobject>
280                <imagedata fileref="figures/deleted.gif" format="GIF"/>
281              </imageobject>
282            </inlinemediaobject> in front of them. </para>
283        </listitem>
284        <listitem>
285          <para>Alternately, navigating to the ArrayDesign Item View, one can hit the
286              <guibutton>Delete</guibutton> to performed the task. </para>
287        </listitem>
288        <listitem>
289          <para>Deletion errors at this stage can be easily recovered. Select the item to
290            recover from the List View (be sure to check the
291            <guilabel>Removed</guilabel> option in the
292            <guilabel>view/preset&hellip;</guilabel> filter) and hit the
293              <guibutton>Restore</guibutton> button to performed the task. </para>
294        </listitem>
295      </itemizedlist>
296      <important>
297        <para>To really delete an item from the database you must use the trashcan. Items
298          deleted from the Trashcan can not be recovered. To learn more about the trashcan
299          function, please refer to <xref linkend="trashcan"/>
300        </para>
301      </important>
302    </sect2>
303
304  </sect1>
305  <sect1 id="array_lims.arraybatch">
306    <title>Managing Array Batches</title>
307
308    <sect2 id="array_lims.arraybatch.create">
309      <title>Creating Array Batches </title>
310      <para>In BASE2, Array Batches can be created by 2 routes:</para>
311      <orderedlist>
312        <listitem>
313          <para>Creating Array Batch from the ArrayDesign List View page</para>
314          <para>Clicking on the <inlinemediaobject>
315              <imageobject>
316                <imagedata fileref="figures/add.gif" format="GIF"/>
317              </imageobject>
318            </inlinemediaobject> add Array batch button available from the
319              <guilabel>Batches</guilabel> column of the ArrayDesign list view page.
320          </para>
321        </listitem>
322        <listitem>
323          <para>Creating ArrayBatch from the ArrayBatch List View page</para>
324          <para>Go to <menuchoice>
325              <guimenu>Array LIMS</guimenu>
326              <guimenuitem>Array batches</guimenuitem>
327            </menuchoice></para>
328          <para>Click on <guibutton>New&hellip;</guibutton> button </para>
329        </listitem>
330      </orderedlist>
331
332      <para>In both cases, an ArrayBatch Create pop-up window opens. The window contains 2
333        mandatory fields:</para>
334      <figure id="write_docbook_doc.figures.arraybatch-create">
335        <title>Create New Array batch from the ArrayDesign List View</title>
336        <screenshot>
337          <mediaobject>
338            <imageobject>
339              <imagedata contentwidth="10cm" width="10cm" fileref="figures/arraybatch-create.png" format="PNG"/>
340            </imageobject>
341          </mediaobject>
342        </screenshot>
343      </figure>
344      <itemizedlist>
345        <listitem>
346          <para>
347            <guilabel>Name</guilabel> and <guilabel>ArrayDesign</guilabel>.</para>
348          <para>The later is a select-list population from ArrayDesigns owned by or shared
349            to the user.</para>
350        </listitem>
351        <listitem>
352          <para><guilabel>Print robot</guilabel> and <guilabel>Protocol</guilabel>, the
353            other 2 fields, are optional and self explanatory.</para>
354        </listitem>
355      </itemizedlist>
356      <para>Click on the <guibutton>Save</guibutton> button to store the information in BASE2 or on the
357      <guibutton>Cancel</guibutton> button to abort.</para>
358    </sect2>
359
360    <sect2 id="array_lims.arraybatch.detail_view">
361      <title>Viewing/Editing ArrayBatches</title>
362      <itemizedlist>
363        <listitem>
364          <para> Press and hold one of the <keycap>CTRL</keycap>, <keycap>ALT</keycap> or
365              <keycap>SHIFT</keycap> keys while clicking on the name of an ArrayBatch
366            Item, which is a live link. </para>
367        </listitem>
368        <listitem>
369          <para> Alternately, navigating to the ArrayBatch Item View, one can hit the
370              <guibutton>Edit&hellip;</guibutton> to performed the task.</para>
371          <para>In both cases, an Edit pop-up windows opens. It is essentially identical
372            to a Create window and allows updating information about a particular
373            ArrayBatch item stored in BASE2</para>
374          <figure id="write_docbook_doc.figures.arraybatch-itemview">
375            <title>ArrayBatch Item View</title>
376            <screenshot>
377              <mediaobject>
378                <imageobject>
379                  <imagedata contentwidth="10cm" width="10cm" fileref="figures/arraybatch-itemview.png" format="PNG"/>
380                </imageobject>
381              </mediaobject>
382            </screenshot>
383          </figure>
384        </listitem>
385        <listitem>
386          <para>From the ArrayBatch item View, all associated <guilabel/>ArraySlides are
387            indicated as their use in Hybridization events. Both ArraySlides and
388            Hybridizations are clickable items, enabling easy navigation.</para>
389        </listitem>
390      </itemizedlist>
391    </sect2>
392    <sect2 id="array_lims.arraybatch.delete">
393      <title>Deleting/Restoring ArrayBatches</title>
394      <para>As for other items in BASE2, ArrayBatches can be removed and restored. To do so,
395        do the following</para>
396      <itemizedlist>
397        <listitem>
398          <para>Select one or more ArrayBatches and click <guibutton>Delete</guibutton>
399            button in the menu bar. </para>
400          <para>All the selected ArrayBatches have been marked as deleted and are no
401            longer available from the interface. </para>
402          <para>Only by selecting from the <guilabel>view/preset&hellip;</guilabel>
403            select box the <guilabel>Removed</guilabel> option, one can see those of the
404            ArrayBatches earmarked for deletion. They will be shown with a symbol <inlinemediaobject>
405              <imageobject>
406                <imagedata fileref="figures/deleted.gif" format="GIF"/>
407              </imageobject>
408            </inlinemediaobject> in front of them. </para>
409        </listitem>
410        <listitem>
411          <para>Alternately, navigating to the ArrayBatch Item View, one can hit the
412              <guibutton>Delete</guibutton> to performed the task. </para>
413        </listitem>
414        <listitem>
415          <para>Deletion errors at this stage can be easily recovered. Select the item to
416            recover from the List View (be sure to check the
417            <guilabel>Removed</guilabel> option in the
418            <guilabel>view/preset&hellip;</guilabel> filter) and hit the
419              <guibutton>Restore</guibutton> button to performed the task. </para>
420        </listitem>
421      </itemizedlist>
422      <important>
423        <para>To really delete an item from the database you must use the trashcan. Items
424          deleted from the Trashcan can not be recovered. To learn more about the trashcan
425          function, please refer to <xref linkend="trashcan"/>
426        </para>
427      </important>
428    </sect2>
429  </sect1>
430  <sect1 id="array_lims.arrayslide">
431    <title>Managing Array Slides</title>
432    <sect2 id="array_lims.arrayslide.create">
433      <title>Creating Array Slides </title>
434      <para>In BASE2, Array Slides can be created by 2 routes:</para>
435      <orderedlist>
436        <listitem>
437          <para>Creating Array Slides from the ArrayBatch View page</para>
438          <para>Clicking on the <inlinemediaobject>
439              <imageobject>
440                <imagedata fileref="figures/add.gif" format="GIF"/>
441              </imageobject>
442            </inlinemediaobject> add Array slides button. </para>
443          <figure id="write_docbook_doc.figures.arrayslide-single-create">
444            <title>Create New Array Slide from the ArrayBatch List View</title>
445            <screenshot>
446              <mediaobject>
447                <imageobject>
448                  <imagedata contentwidth="10cm" width="10cm" fileref="figures/arrayslide-single-create.png" format="PNG"/>
449                </imageobject>
450              </mediaobject>
451            </screenshot>
452          </figure>
453        </listitem>
454        <listitem>
455          <para>Creating ArraySlides from the ArrayBatch List View page</para>
456          <para>Go to <menuchoice>
457              <guimenu>Array LIMS</guimenu>
458              <guimenuitem>Array slides</guimenuitem>
459            </menuchoice></para>
460          <para>Click on <guibutton>New&hellip;</guibutton> button </para>
461        </listitem>
462      </orderedlist>
463
464      <para>In both cases, an ArraySlide Create pop-up window opens. The window contains 2
465        mandatory fields:</para>
466      <itemizedlist>
467        <listitem>
468          <para>
469            <guilabel>Name</guilabel> and <guilabel>ArrayBatch</guilabel>.</para>
470          <para>The later is a select-list populated with ArrayBatches owned by or shared
471            to the user.</para>
472        </listitem>
473        <listitem>
474          <para><guilabel>Barcode</guilabel>, <guilabel>Index</guilabel> and
475              <guilabel>Destroyed</guilabel>, a tick box enabling to record microarray
476            slides lost by accident.</para>
477        </listitem>
478      </itemizedlist>
479      <para>Click on the <guibutton>Save</guibutton> button to store the information in BASE2 or on the
480          <guibutton>Cancel</guibutton> button to abort. </para>
481
482      <para> In addition to this classic way of creating BASE items, Arrays Slides can be
483        created with a wizard available from both the ArraySlide Item view or from the
484        ArrayBatch List View page. To call the wizard:</para>
485      <para>Click on the <inlinemediaobject>
486          <imageobject>
487            <imagedata fileref="figures/new_wizard.gif" format="GIF"/>
488          </imageobject>
489        </inlinemediaobject> add multiple Array slides button in the
490        <guilabel>Slides</guilabel> column of the ArrayBatch List view page.</para>
491
492      <para> or </para>
493      <para>Click on the <inlinemediaobject>
494          <imageobject>
495            <imagedata fileref="figures/new_wizard.gif" format="GIF"/>
496          </imageobject>
497        </inlinemediaobject>
498        <guibutton>Create multiple&hellip;</guibutton> button from the menu bar of the
499        ArraySlides List View page </para>
500
501      <para>Either way will open the wizard window as shown below</para>
502      <figure id="write_docbook_doc.figures.arrayslide-multiple-create">
503        <title>Create Multiple Array Slide from the ArrayBatch List View wizard</title>
504        <screenshot>
505          <mediaobject>
506            <imageobject>
507              <imagedata contentwidth="10cm" width="10cm" fileref="figures/arrayslide-multiple-create.png" format="PNG"/>
508            </imageobject>
509          </mediaobject>
510        </screenshot>
511      </figure>
512      <para>Fill in the necessary information as exhaustively as possible.</para>
513      <para>Click on the <guibutton>Save</guibutton> button to store the information in BASE2
514      or on the <guibutton>Cancel</guibutton> button to abort. </para>
515    </sect2>
516
517    <sect2 id="array_lims.arrayslide.detail_view">
518      <title>Viewing/Editing ArraySlides</title>
519      <itemizedlist>
520        <listitem>
521          <para> Press and hold one of the <keycap>CTRL</keycap>, <keycap>ALT</keycap> or
522              <keycap>SHIFT</keycap> keys while clicking on the name of an ArraySlide
523            Item, which is a live link. </para>
524        </listitem>
525        <listitem>
526          <para> Alternately, navigating to the ArraySlide Item View, one can hit the
527              <guibutton>Edit&hellip;</guibutton> to performed the task.</para>
528          <para>In both cases, an Edit pop-up windows opens. It is essentially identical
529            to a Create window and allows updating information about a particular
530            ArraySlide item stored in BASE2</para>
531          <figure id="write_docbook_doc.figures.arrayslide-itemview">
532            <title>ArraySlide Item View</title>
533            <screenshot>
534              <mediaobject>
535                <imageobject>
536                  <imagedata contentwidth="10cm" width="10cm" fileref="figures/arrayslide-itemview.png" format="PNG"/>
537                </imageobject>
538              </mediaobject>
539            </screenshot>
540          </figure>
541        </listitem>
542
543        <listitem>
544          <para>From the ArraySlide item View, the associated
545            <guilabel>Hybridization</guilabel> can be indicated as navigable
546          links</para>
547        </listitem>
548      </itemizedlist>
549    </sect2>
550    <sect2 id="array_lims.arrayslide.delete">
551      <title>Deleting/Restoring ArraySlides</title>
552      <para>As for other items in BASE2, ArraySlides can be removed and restored. To do so, do
553        the following</para>
554      <itemizedlist>
555        <listitem>
556          <para>Select one or more ArraySlides and click <guibutton>Delete</guibutton>
557            button in the menu bar. </para>
558          <para>All the selected ArraySlides have been marked as deleted and are no longer
559            available from the interface. </para>
560          <para>Only by selecting from the <guilabel>view/preset&hellip;</guilabel>
561            select box the <guilabel>Removed</guilabel> option, one can see those of the
562            ArraySlides earmarked for deletion. They will be shown with a symbol <inlinemediaobject>
563              <imageobject>
564                <imagedata fileref="figures/deleted.gif" format="GIF"/>
565              </imageobject>
566            </inlinemediaobject> in front of them. </para>
567        </listitem>
568        <listitem>
569          <para>Alternately, navigating to the ArraySlide Item View, one can hit the
570              <guibutton>Delete</guibutton> to performed the task. </para>
571        </listitem>
572        <listitem>
573          <para>Deletion errors at this stage can be easily recovered. Select the item to
574            recover from the List View (be sure to check the
575            <guilabel>Removed</guilabel> option in the
576            <guilabel>view/preset&hellip;</guilabel> filter) and hit the
577              <guibutton>Restore</guibutton> button to performed the task. </para>
578        </listitem>
579      </itemizedlist>
580      <important>
581        <para>To really delete an item from the database you must use the trashcan. Items
582          deleted from the Trashcan can not be recovered. To learn more about the trashcan
583          function, please refer to <xref linkend="trashcan"/>
584        </para>
585      </important>
586    </sect2>
587
588
589  </sect1>
590
591</chapter>
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