source: trunk/doc/user/getting_started.html @ 3053

Last change on this file since 3053 was 2955, checked in by Jari Häkkinen, 16 years ago

Minor clarification for genepix reporter map imports.

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  • Property svn:keywords set to Id Date
File size: 23.2 KB
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2
3<!--
4    $Id: getting_started.html 2955 2006-11-26 21:05:01Z jari $
5
6    Copyright (C) 2006 Jari Hakkinen
7
8    This file is part of BASE - BioArray Software Environment.
9    Available at http://base.thep.lu.se/
10
11    BASE is free software; you can redistribute it and/or modify it
12    under the terms of the GNU General Public License as published by
13    the Free Software Foundation; either version 2 of the License, or
14    (at your option) any later version.
15
16    BASE is distributed in the hope that it will be useful, but
17    WITHOUT ANY WARRANTY; without even the implied warranty of
18    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19    General Public License for more details.
20
21    You should have received a copy of the GNU General Public License
22    along with this program; if not, write to the Free Software
23    Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
24    02111-1307, USA.
25-->
26
27<html>
28  <head>
29    <title>BASE 2.1 - User documentation: Getting started</title>
30    <link rel=stylesheet type="text/css" href="../styles.css">
31  </head>
32  <body>
33
34    <div class="navigation">
35      <a href="../index.html">BASE</a>
36      <img src="../next.gif">
37      <a href="index.html">User documentation</a>
38      <img src="../next.gif">
39      Getting started
40    </div>
41
42    <h1>BASE 2.1 - User documentation: Getting started</h1>
43
44    <div class="abstract">
45
46      <p>
47        This document describes how to get started with your new shiny
48        BASE box.
49      </p>
50
51      <b>Contents</b>
52      <ol>
53        <li><a href="#administative">Administrative tasks</a></li>
54        <li><a href="#user">User tasks</a></li>
55      </ol>
56
57      <p class="authors">
58        <b>Last updated:</b> $Date: 2006-11-26 21:05:01 +0000 (Sun, 26 Nov 2006) $ <br>
59        <b>Copyright &copy;</b> 2006 The respective authors. All
60        rights reserved.
61      </p>
62
63    </div>
64
65    <p> This description will take you from uploading raw data to
66    running the first analysis plug-ins. Both Affymetrix and Genepix
67    data will be used as examples. </p>
68
69    <ol>
70
71      <li>
72        <a name="administrative"></a>
73        <h2>Administrative tasks</h2>
74
75        <p> Most of the task in this section requires more privileges
76        than the normal user credentials. You should log in as an
77        administrator when you perform these tasks. As always, there
78        are many ways to do things and what is presented here is the
79        path to get going with BASE as fast as possible without
80        creating havoc in future use of the BASE server. </p>
81
82        <ol type=a>
83
84          <li>
85            <p> <b>Create an administrator account</b> <br> Log in as
86            'root' using the password you set during BASE
87            initialization. Create an administrator account. Log out,
88            and use the admin account for all administrative
89            tasks. The root account should not be used as the
90            administrator account. </p>
91          </li>
92
93          <li>
94            <p> <b>Create user accounts</b> <br> Create user accounts
95            using the newly created administrator account. You should
96            give your users appropriate roles, most of them should be
97            assigned to the 'User' role. (Link to role docs?) You can
98            create new roles if the default ones does not fit your
99            needs. </p>
100          </li>
101
102          <li>
103            <p> <b>Create essential plug-in configurations</b> <br>
104            Some plug-ins need to be configured before use, whereas
105            other works out of the box. Some external plug-ins as the
106            <a
107            href=http://baseplugins.thep.lu.se/wiki/thep.lu.se.RMAExpress>RMAExpress
108            plug-in for BASE</a> has to be compiled before including
109            them into your BASE server.</p>
110
111            <p> Core plug-ins are a set of plug-ins that are
112            automatically installed during setup. As pointed out
113            above, these may need a configuration to work. The way to
114            find out which plug-ins need a configuration is to choose
115            Administrate -> Plugins -> Definitions. This will display
116            a list all plug-ins available for your BASE
117            server. Nothing is shown? The reason for this is that your
118            newly created administrator does not own the definitions,
119            change the view/preset to show shared items as well. By
120            clicking on the 'Columns' tab you can select what
121            information should be displayed in the list. Please select
122            'Requires config' in the 'Columns' tab, and move it up in
123            the left panel. Finalize by clicking 'Ok'. The list now
124            has an extra column with yes and no's. Mark the 'true'
125            radio button in the 'Requires config' column to only list
126            plug-ins that need a configuration.
127
128            <p> The exercise above had two important aims. i) To show
129            you what plug-ins already exists, and ii) find three
130            essential plug-ins that needs a configuration each. Before
131            any raw data can be stored in BASE some information has to
132            be available in BASE. The slide design (reporter map) and
133            reporter information (probe set information in Affymetrix
134            vocabulary). For these imports to work for Genepix data we
135            need to create configurations for the "Reporter map
136            importer" and "Reporter importer" respectively, and a
137            configuration is needed for the raw data import plug-in,
138            "Raw data importer", as well. Affymetrix data import works
139            differently and only a "Reporter map importer"
140            configuration is needed.</p>
141
142            <p> The pre-installed plug-in definitions are already
143            shared to group 'Everyone' (all users are members of this
144            group) but the configurations created are not shared by
145            default. The configurations should be shared to the users
146            who should have access to them, normally group
147            'Everyone'. As counterexamples, the reporter importers and
148            reporter map importers do not have to be share to everyone
149            since these imports should only be allowed to be done by a
150            small group of users. Every reporter and reporter map
151            should only be imported once and all users should use the
152            same reporter and reporter map information. The raw data
153            importers should normally be shared to everyone since all
154            users import data into BASE. </p>
155
156            <p> <i>Reporter importer</i> <br> Select the "Reporter
157            importer", and click on the 'New configuration ...'
158            tab. Enter a name in the 'Name' field (Affymetrix probe
159            set importer / Genepix reporter import) and click 'Save
160            and configure' button. The next pop-up expects input of
161            regular expression needed to import reporter data. Here we
162            just give the values to add to the panel, but as of
163            version 2.1 it is possible to use a import format
164            wizard. The wizard is started by clicking on the 'Test
165            with file ...'  button. </p>
166
167            <p> Below we tabulate regexps to enter for a few file
168            formats if you prefer to enter the regexp manually. Note
169            1: Here it is assumed that the default
170            <a
171            href="../admin/extended-properties.html">extended-properties.xml</a>
172            is used. Note 2: your browser may break lines in the
173            table cells, treat these line breaks as a ' ' (space)
174            character. Note 3: Depending on your files the values to
175            input may be different.
176            <table cellspacing=3>
177              <tr>
178                <td align=left> <i>Column</i> </td>
179                <td align=left> <i>Affymetrix</i> </td>
180                <td align=left> <i>Genepix .gpr</i> </td>
181                <td align=left> <i>Genepix .txt</i> </td>
182              </tr>
183              <tr>
184                <td> Data Header </td>
185                <td> "Probe Set ID","GeneChip Array",.* </td>
186                <td> "Block"\t"Column"\t"Row"\t"Name"\t"ID"\t.* </td>
187                <td> 384_number\t384_column\t384_row\t384_position\toligo_id.* </td>
188              </tr>
189              <tr>
190                <td> Data splitter </td>
191                <td> (?!"),(?=") </td>
192                <td> \t</td>
193                <td> \t</td>
194              </tr>
195              <tr>
196                <td> Remove quotes </td>
197                <td> true </td>
198                <td> true </td>
199                <td> true </td>
200              </tr>
201              <tr>
202                <td> Name </td>
203                <td> \Probe Set ID\ </td>
204                <td> \Name\</td>
205                <td> \oligo_id\</td>
206              </tr>
207              <tr>
208                <td> Reporter ID </td>
209                <td> \Probe Set ID\ </td>
210                <td> \ID\</td>
211                <td> \oligo_id\ </td>
212              </tr>
213              <tr>
214                <td> Gene symbol </td>
215                <td> \Gene Symbol\ </td>
216                <td> </td>
217                <td> \gene_symbol_Ensembl*\ </td>
218              </tr>
219              <tr>
220                <td> Cluster ID </td>
221                <td> \UniGene ID\ </td>
222                <td> </td>
223                <td> \RefSeq\ </td>
224              </tr>
225            </table>
226            <br> Finalize with clicking 'Next'. You can of course fill
227            the other entries as well. </p>
228
229            <p> <i>Reporter map importer</i> <br> Affymetrix CDF files
230            do not need a configuration since these are not imported
231            to BASE with a plug-in. Genepix data requires a
232            configuration. To configure a plug-in for Genepix reporter
233            map imports select the "Reporter map importer" from the
234            plug-in definition list. Click on the 'New configuration
235            ...'  tab. Enter a name in the 'Name' field (Affymetrix
236            probe set importer / Genepix reporter map importer) and
237            click 'Save and configure' button. The next pop-up expects
238            input of regular expression needed to import reporter map
239            data. Here we just give the values to add to the panel,
240            but as of version 2.1 it is possible to use a import
241            format wizard. The wizard is started by clicking on the
242            'Test with file ...'  button. Below we tabulate regexps to
243            enter if you prefer to enter the regexp manually:
244            <table cellspacing=3>
245              <tr>
246                <td align=left> <i>Column</i> </td>
247                <td align=left> <i>Genepix .gpr</i> </td>
248              </tr>
249              <tr>
250                <td> Data Header </td>
251                <td> "Block"\t"Column"\t"Row"\t"Name"\t"ID"\t.* </td>
252              </tr>
253              <tr>
254                <td> Data splitter </td>
255                <td> \t</td>
256              </tr>
257              <tr>
258                <td> Remove quotes </td>
259                <td> true </td>
260              </tr>
261              <tr>
262                <td> Reporter ID </td>
263                <td> \ID\</td>
264              </tr>
265              <tr>
266                <td> Block </td>
267                <td> \Block\ </td>
268              </tr>
269              <tr>
270                <td> Column </td>
271                <td> \Column\ </td>
272              </tr>
273              <tr>
274                <td> Row </td>
275                <td> \Row\ </td>
276              </tr>
277            </table>
278            <br> Finalize with clicking 'Next'. You can of course fill
279            the other entries as well. </p>
280
281            <p> <i>Raw data importer</i> <br> Affymetrix CEL files do
282            not need a configuration since these are not imported to
283            BASE with a plug-in. Genepix data requires a
284            configuration. Create a configuration for Genepix raw data
285            import by selecting the "Raw data importer" from the
286            plug-in definition list. Click on the 'New configuration
287            ...'  tab. Enter a name in the 'Name' field (Genepix raw
288            data importer) and click 'Save and configure' button. The
289            next pop-up expects input of regular expression needed to
290            import raw data. Here we just give the values to add to
291            the panel, but as of version 2.1 it is possible to use a
292            import format wizard. The wizard is started by clicking on
293            the 'Test with file ...'  button. Below we tabulate
294            regexps to enter if you prefer to enter the regexp
295            manually:
296
297            <table cellspacing=3>
298              <tr>
299                <td align=left> <i>Column</i> </td>
300                <td align=left> <i>Genepix .gpr</i> </td>
301              </tr>
302              <tr>
303                <td>Raw data type</td>
304                <td>Genepix</td>
305              </tr>
306              <tr>
307                <td>Header</td>
308                <td>"(.+)=(.*)"</td>
309              </tr>
310              <tr>
311                <td>Data header</td>
312                <td>"Block"\t"Column"\t"Row"\t"Name"\t"ID"\t.*"Ratio of Medians \(532\/635\)".*</td>
313              </tr>
314              <tr>
315                <td>Data splitter</td>
316                <td>\t</td>
317              </tr>
318              <tr>
319                <td>Min data columns</td>
320                <td>48</td>
321              </tr>
322              <tr>
323                <td>Max data columns</td>
324                <td>48</td>
325              </tr>
326              <tr>
327                <td>Block</td>
328                <td>\Block\</td>
329              </tr>
330              <tr>
331                <td>Column</td>
332                <td>\Column\</td>
333              </tr>
334              <tr>
335                <td>Row</td>
336                <td>\Row\</td>
337              </tr>
338              <tr>
339                <td>X</td>
340                <td>\X\</td>
341              </tr>
342              <tr>
343                <td>Y</td>
344                <td>\Y\</td>
345              </tr>
346              <tr>
347                <td>Reporter ID</td>
348                <td>\ID\</td>
349              </tr>
350              <tr>
351                <td>Spot diameter</td>
352                <td>\Dia.\</td>
353              </tr>
354              <tr>
355                <td>Channel 1 foreground median</td>
356                <td>\F635 Median\</td>
357              </tr>
358              <tr>
359                <td>Channel 1 foreground mean</td>
360                <td>\F635 Mean\</td>
361              </tr>
362              <tr>
363                <td>Channel 1 foreground standard deviation</td>
364                <td>\F635 SD\</td>
365              </tr>
366              <tr>
367                <td>Channel 1 background median</td>
368                <td>\B635 Median\</td>
369              </tr>
370              <tr>
371                <td>Channel 1 background mean</td>
372                <td>\B635 Mean\</td>
373              </tr>
374              <tr>
375                <td>Channel 1 background standard deviation</td>
376                <td>\B635 SD\</td>
377              </tr>
378              <tr>
379                <td>Percent pixels within 1 standard deviation</td>
380                <td>\% > B635+1SD\</td>
381              </tr>
382              <tr>
383                <td>Percent pixels within 2 standard deviations</td>
384                <td>\% > B635+2SD\</td>
385              </tr>
386              <tr>
387                <td>Percent saturated pixels</td>
388                <td>\F635 % Sat.\</td>
389              </tr>
390              <tr>
391                <td>Channel 2 foreground median</td>
392                <td>\F532 Median\</td>
393              </tr>
394              <tr>
395                <td>Channel 2 foreground mean</td>
396                <td>\F532 Mean\</td>
397              </tr>
398              <tr>
399                <td>Channel 2 foreground standard deviation</td>
400                <td>\F532 SD\</td>
401              </tr>
402              <tr>
403                <td>Channel 2 background median</td>
404                <td>\B532 Median\</td>
405              </tr>
406              <tr>
407                <td>Channel 2 background mean</td>
408                <td>\B532 Mean\</td>
409              </tr>
410              <tr>
411                <td>Channel 2 background standard deviation</td>
412                <td>\B532 SD\</td>
413              </tr>
414              <tr>
415                <td>Percent pixels within 1 standard deviation</td>
416                <td>\% > B532+1SD\</td>
417              </tr>
418              <tr>
419                <td>Percent pixels within 2 standard deviations</td>
420                <td>\% > B532+2SD\</td>
421              </tr>
422              <tr>
423                <td>Percent saturated pixels</td>
424                <td>\F532 % Sat.\</td>
425              </tr>
426              <tr>
427                <td>Foreground pixels</td>
428                <td>\F Pixels\</td>
429              </tr>
430              <tr>
431                <td>Background pixels</td>
432                <td>\B Pixels\</td>
433              </tr>
434              <tr>
435                <td>Flags</td>
436                <td>\Flags\</td>
437              </tr>
438            </table>
439            <br> Finalize with clicking 'Next'. You can of course fill
440            the other entries as well. </p>
441          </li>
442
443          <li>
444            <p> (Affymetrix only) <b>Install
445            <a name=RMAExpressInstall
446            href=http://baseplugins.thep.lu.se/wiki/thep.lu.se.RMAExpress>RMAExpress
447            plug-in for BASE</a></b> <br> This plug-in is required for
448            Affymetrix data. The plug-in will create a bioassay set,
449            i.e., to be able to analyse the data in BASE.</p>
450          </li>
451
452          <li>
453            <p> <b>Upload files</b> <br> Before import you can upload
454            files to the server, or if preferred, files to be imported
455            can be uploaded at import time. To upload files, choose
456            'View' -> 'Files' and click in the 'Upload file...'
457            button. At upload time you assign a type to the file (can
458            be changed later if needed), and batch upload of files is
459            possible in a zip-file or tar archive. </p>
460
461            <p> As administrator you need to upload the reporter map
462            (array design) files and corresponding reporter files. For
463            Affymetrix this translates to Affydesign.cdf files and
464            Affydesign_annot.csv files. </p>
465          </li>
466
467          <li>
468            <p> <b> Reporter import </b> <br> Choose 'View' ->
469            'Reporters' and click on the 'Import...' tab. Click 'Next'
470            in the pop-up without changing anything. Select the file
471            with reporter information and click 'Next'. In the panel
472            you can choose to update reporter information for already
473            stored reporters. Click 'Next'. Set the job name and click
474            'Finish' to start the import. A progress report will be
475            displayed. It is safe to close this page, the job
476            will finish anyway. </p>
477          </li>
478
479          <li>
480            <p> <b> Import reporter maps </b> <br> Performing an
481            import of array designs is only needed once for every
482            design added into BASE. Remember to share your designs
483            (normally to group 'Everyone'). </p>
484
485            <p> To create a new design, choose 'Array LIMS' -> 'Array
486            designs' and click on the 'New...' tab. Select a name for
487            the design. If it is an Affymetrix design, mark the 'Affy
488            chip' box and select a 'CDF file' (make sure that also the
489            CDF file is shared). Hint: For Affymetrix design you
490            should choose the name to be the same as the cdf file
491            name. If you are importing something else than Affymetrix
492            designs make sure that you unmark the 'Affy chip'
493            box. Finalize with 'Save'. For Affymetrix the import is
494            done, whereas Genepix have to perform reporter map
495            import. </p>
496
497            <p> <i>Genepix reporter map import</i> <br> Click on the
498            newly created array design, and click on the 'Import...'
499            tab. In the pop up, click 'Next'. Browse for the reporter
500            map file and click 'Next'. In the following dialogue you
501            can specify how to treat errors encountered. The default
502            is 'fail' which may be too restrictive, trial and error is
503            the way to go here for now. If you have trouble importing
504            try 'skip' for 'Default error handling' and 'Reporter not
505            found'. You can safely leave the 'Character set' as it
506            is. </p>
507          </li>
508
509        </ol>
510      </li>
511
512      <li>
513        <a name="user"></a>
514        <h2>User tasks</h2>
515      </li>
516
517      <p> A normal user is not allowed to add array design, reporter
518      information, and a lot of other information to BASE. The reason
519      for this is that a lot of information should only exist as one
520      copy in the database. For example, reporters should only exist in
521      one copy because everyone uses the same reporters. There is no
522      need to store several copies of the same array design. </p>
523
524      <p> A user will normally upload experimental data to BASE for
525      import into the database. To be able to import the data, the
526      array design used must be available in BASE at import time. If
527      the array design is not available, a user with the proper
528      credential must add the array design to BASE. </p>
529
530      <ol type=a>
531
532      <li>
533        <p> <b> Create a new Project </b> <br> Go to 'View' ->
534        'Projects' and click on the 'New...' tab. Name the project and
535        save. In the projects listing page, click 'Set active' for the
536        new project. The selected project should be displayed on top
537        right as 'Active project'. Selecting an active project will
538        influence the behaviour of BASE. Only information related to
539        the active project will be displayed and items created will
540        automatically be shared to the active project. </p>
541
542        <p> The display of items shared to the active project only
543        requires that the 'view/presets' pull-down menu options are
544        properly set. In 'view/preset' you can select what should be
545        displayed, and if only 'In current project' is selected then
546        only information shared to a project will be shown. </p>
547      </li>
548
549      <li>
550        <p> <b>Create raw bioassays</b> <br> Upload your raw data
551        files. Go to 'View' -> 'Raw bioassays' and click on the
552        'New...' tab. Name the raw bioassay. Select 'Raw data
553        type'. Select the 'Array design', if you cannot see see
554        designs in the pop-up the make sure that the 'view/presets'
555        pull-down menu has 'Shared to me' marked and select appropriate
556        design. Select 'CEL file' if you create an Affymetrix raw
557        bioassay. You can leave the rest untouched. Redo for all raw
558        data files. (Yes a batch creator would be nice.) </p>
559      </li>
560
561      <li>
562        <p> <b>Create a new experiment</b> <br> Go to 'View' ->
563        'Experiments' and click on the 'New...' tab. Name the
564        experiment. Click 'Add raw bioassays...' button and mark the
565        raw bioassays to add to the experiment and click
566        'Ok'. Finalize with clicking the 'Save' button. </p>
567      </li>
568
569      <li>
570        <p> <b>Analysing an experiment step I</b> <br> Select the
571        newly created experiment and in the the experiment window
572        select the 'Bioassay sets' tab. There are no bioassay sets and
573        you must create a root bioassay set. This step is different
574        depending on what data is used in the experiment but note that
575        this paragraph ends with information valid for all type of
576        data. </p>
577 
578        <p> <i>Affymetrix</i> <br> Click on the 'New root bioassay set
579        ...' tab and select the RMAExpress plug-in in the pop up. (If
580        the plug-in does not appear as an option, the installation of
581        the plug-in has failed. Please refer
582        to <a href=#RMAExpressInstall>Installing RMAExpress plug-in
583        for BASE</a>.) Click on the 'Next' button and in the new
584        window set the name for the bioassay set and select the
585        bioassays you want to include for this analysis. Click
586        'Next'. In the next pop up you can change information if you
587        like but it is not necessary, when done click on 'Finish' to
588        add the analysis job to the job queue. The job will start
589        automatically when the server as an open slot for it. The last
590        pop up window will report progress on the job. </p>
591
592        <p> <i>All flavours</i> <br> You can safely close the job
593        progress window, the server will run the job anyway. If you
594        want to monitor the progress of the job after closing the job
595        window just go to 'View' -> 'Jobs' and locate your job in the
596        list and select it. When the job is done the new bioassay set
597        will be added to the list of bioassay set for the
598        experiment. Unfortunately the list does not auto update so you
599        need to click on the 'Properties' tab and the on the 'Bioassay
600        sets' tab to refresh the list of bioassay sets. </p>
601      </li>
602
603      <li>
604        <p> <b>Analysing an experiment step II</b> <br> Now you should
605        have the first bioassay set. In the list of bioassay sets you
606        will have a number of icons attached that will start
607        tools. The set of tools available for bioassay sets is context
608        sensitive, <i>i.e.</i>, only tools that can handle the
609        bioassay sets are shown. At the time of writing of this
610        document there are four icons available; A simple plot tool,
611        experiment explorer, a filtering tool, and a plug-in
612        runner. You have to try these on your own. The aim with this
613        paragraph is to highlight the fact that you can export the
614        bioassay set data for use outside BASE. </p>
615
616        <p> To export bioassay set data select a bioassay set. In the
617        bioassay set presentation window you will have an export
618        button just below the tabs on the top. (There is also an
619        export button for the Sub analysis tree which may be confusing
620        at first, but his button will export information about the
621        analysis tree.) So, assuming you select the proper export
622        button you will be given a list of different export
623        formats. The list of supported exports depends on what plug-ins
624        are added to the server, but there should at least be an
625        export to <a href=http://www.tm4.org/mev.html>MultiExperiment
626        Viewer</a> maintained by the Dana Farber Cancer Institute. </p>
627      </li>
628
629      </ol>
630
631    </ol>
632
633    <p> This concludes this short document on how to get going with
634    BASE. We have not covered how to use the LIMS part of BASE, nor
635    annotations, and much more. We are creating documentation, please
636    browse <a href=http://base.thep.lu.se/>BASE web site</a> for the
637    latest available documents. </p>
638
639  </body>
640</html>
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