source: trunk/doc/user/getting_started.html @ 2954

Last change on this file since 2954 was 2954, checked in by Jari Häkkinen, 16 years ago

Improved Genepix information in the getting started doc.

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1<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "">
4    $Id: getting_started.html 2954 2006-11-26 20:38:24Z jari $
6    Copyright (C) 2006 Jari Hakkinen
8    This file is part of BASE - BioArray Software Environment.
9    Available at
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.
16    BASE is distributed in the hope that it will be useful, but
17    WITHOUT ANY WARRANTY; without even the implied warranty of
19    General Public License for more details.
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.
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>
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>
42    <h1>BASE 2.1 - User documentation: Getting started</h1>
44    <div class="abstract">
46      <p>
47        This document describes how to get started with your new shiny
48        BASE box.
49      </p>
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>
57      <p class="authors">
58        <b>Last updated:</b> $Date: 2006-11-26 20:38:24 +0000 (Sun, 26 Nov 2006) $ <br>
59        <b>Copyright &copy;</b> 2006 The respective authors. All
60        rights reserved.
61      </p>
63    </div>
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>
69    <ol>
71      <li>
72        <a name="administrative"></a>
73        <h2>Administrative tasks</h2>
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>
82        <ol type=a>
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>
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>
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=>RMAExpress
108            plug-in for BASE</a> has to be compiled before including
109            them into your BASE server.</p>
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.
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>
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>
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>
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>
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>
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:
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>
443          <li>
444            <p> (Affymetrix only) <b>Install
445            <a name=RMAExpressInstall
446            href=>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>
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>
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>
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>
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>
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>
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. You can safely leave the
504            'Character set' as it is. </p>
505          </li>
507        </ol>
508      </li>
510      <li>
511        <a name="user"></a>
512        <h2>User tasks</h2>
513      </li>
515      <p> A normal user is not allowed to add array design, reporter
516      information, and a lot of other information to BASE. The reason
517      for this is that a lot of information should only exist as one
518      copy in the database. For example, reporters should only exist in
519      one copy because everyone uses the same reporters. There is no
520      need to store several copies of the same array design. </p>
522      <p> A user will normally upload experimental data to BASE for
523      import into the database. To be able to import the data, the
524      array design used must be available in BASE at import time. If
525      the array design is not available, a user with the proper
526      credential must add the array design to BASE. </p>
528      <ol type=a>
530      <li>
531        <p> <b> Create a new Project </b> <br> Go to 'View' ->
532        'Projects' and click on the 'New...' tab. Name the project and
533        save. In the projects listing page, click 'Set active' for the
534        new project. The selected project should be displayed on top
535        right as 'Active project'. Selecting an active project will
536        influence the behaviour of BASE. Only information related to
537        the active project will be displayed and items created will
538        automatically be shared to the active project. </p>
540        <p> The display of items shared to the active project only
541        requires that the 'view/presets' pull-down menu options are
542        properly set. In 'view/preset' you can select what should be
543        displayed, and if only 'In current project' is selected then
544        only information shared to a project will be shown. </p>
545      </li>
547      <li>
548        <p> <b>Create raw bioassays</b> <br> Upload your raw data
549        files. Go to 'View' -> 'Raw bioassays' and click on the
550        'New...' tab. Name the raw bioassay. Select 'Raw data
551        type'. Select the 'Array design', if you cannot see see
552        designs in the pop-up the make sure that the 'view/presets'
553        pull-down menu has 'Shared to me' marked and select appropriate
554        design. Select 'CEL file' if you create an Affymetrix raw
555        bioassay. You can leave the rest untouched. Redo for all raw
556        data files. (Yes a batch creator would be nice.) </p>
557      </li>
559      <li>
560        <p> <b>Create a new experiment</b> <br> Go to 'View' ->
561        'Experiments' and click on the 'New...' tab. Name the
562        experiment. Click 'Add raw bioassays...' button and mark the
563        raw bioassays to add to the experiment and click
564        'Ok'. Finalize with clicking the 'Save' button. </p>
565      </li>
567      <li>
568        <p> <b>Analysing an experiment step I</b> <br> Select the
569        newly created experiment and in the the experiment window
570        select the 'Bioassay sets' tab. There are no bioassay sets and
571        you must create a root bioassay set. This step is different
572        depending on what data is used in the experiment but note that
573        this paragraph ends with information valid for all type of
574        data. </p>
576        <p> <i>Affymetrix</i> <br> Click on the 'New root bioassay set
577        ...' tab and select the RMAExpress plug-in in the pop up. (If
578        the plug-in does not appear as an option, the installation of
579        the plug-in has failed. Please refer
580        to <a href=#RMAExpressInstall>Installing RMAExpress plug-in
581        for BASE</a>.) Click on the 'Next' button and in the new
582        window set the name for the bioassay set and select the
583        bioassays you want to include for this analysis. Click
584        'Next'. In the next pop up you can change information if you
585        like but it is not necessary, when done click on 'Finish' to
586        add the analysis job to the job queue. The job will start
587        automatically when the server as an open slot for it. The last
588        pop up window will report progress on the job. </p>
590        <p> <i>All flavours</i> <br> You can safely close the job
591        progress window, the server will run the job anyway. If you
592        want to monitor the progress of the job after closing the job
593        window just go to 'View' -> 'Jobs' and locate your job in the
594        list and select it. When the job is done the new bioassay set
595        will be added to the list of bioassay set for the
596        experiment. Unfortunately the list does not auto update so you
597        need to click on the 'Properties' tab and the on the 'Bioassay
598        sets' tab to refresh the list of bioassay sets. </p>
599      </li>
601      <li>
602        <p> <b>Analysing an experiment step II</b> <br> Now you should
603        have the first bioassay set. In the list of bioassay sets you
604        will have a number of icons attached that will start
605        tools. The set of tools available for bioassay sets is context
606        sensitive, <i>i.e.</i>, only tools that can handle the
607        bioassay sets are shown. At the time of writing of this
608        document there are four icons available; A simple plot tool,
609        experiment explorer, a filtering tool, and a plug-in
610        runner. You have to try these on your own. The aim with this
611        paragraph is to highlight the fact that you can export the
612        bioassay set data for use outside BASE. </p>
614        <p> To export bioassay set data select a bioassay set. In the
615        bioassay set presentation window you will have an export
616        button just below the tabs on the top. (There is also an
617        export button for the Sub analysis tree which may be confusing
618        at first, but his button will export information about the
619        analysis tree.) So, assuming you select the proper export
620        button you will be given a list of different export
621        formats. The list of supported exports depends on what plug-ins
622        are added to the server, but there should at least be an
623        export to <a href=>MultiExperiment
624        Viewer</a> maintained by the Dana Farber Cancer Institute. </p>
625      </li>
627      </ol>
629    </ol>
631    <p> This concludes this short document on how to get going with
632    BASE. We have not covered how to use the LIMS part of BASE, nor
633    annotations, and much more. We are creating documentation, please
634    browse <a href=>BASE web site</a> for the
635    latest available documents. </p>
637  </body>
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