source: trunk/doc/user/getting_started.html @ 2810

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Improving getting started doc.

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1<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "">
4    $Id: getting_started.html 2810 2006-10-26 10:03:06Z 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 2.0 - 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 2.0 - 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: 2006-10-26 10:03:06 +0000 (Thu, 26 Oct 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 member 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 / ) and click 'Save and configure'
160            button. The next pop-up expects input of regular
161            expression needed to import reporter data. Here we just
162            give the values to add to the panel, but as of version 2.1
163            it is possible to use a import format wizard. The wizard
164            is started by clicking on the 'Test with file ...'
165            button. Here we tabulated the regexp to enter (assuming
166            that the default
167            <a
168            href="../admin/extended-properties.html">extended-properties.xml</a>
169            is used):
170            <table>
171              <tr>
172                <td> <b>Column</b> </td>
173                <td> <b>Regexp</b> (Affymetrix) </td>
174                <td> <b>Regexp</b> (Genepix) </td>
175              </tr>
176              <tr>
177                <td> Data Header </td>
178                <td> "Probe Set ID","GeneChip Array",.* </td>
179                <td> </td>
180              </tr>
181              <tr>
182                <td> Data splitter </td>
183                <td> (?!"),(?=") </td>
184                <td> </td>
185              </tr>
186              <tr>
187                <td> Remove quotes </td>
188                <td> true </td>
189                <td> </td>
190              </tr>
191              <tr>
192                <td> Name </td>
193                <td> \Probe Set ID\ </td>
194                <td> </td>
195              </tr>
196              <tr>
197                <td> Reporter ID </td>
198                <td> \Probe Set ID\ </td>
199                <td> </td>
200              </tr>
201              <tr>
202                <td> Gene symbol </td>
203                <td> \Gene Symbol\ </td>
204                <td> </td>
205              </tr>
206              <tr>
207                <td> Cluster ID </td>
208                <td> \UniGene ID\ </td>
209                <td> </td>
210              </tr>
211            </table>
212            <br> Finalize with clicking 'Next'. You can of course fill
213            the other entries as well. </p>
215            <p> <i>Reporter map importer</i> <br> Affymetrix CDF files
216            do not need a configuration since these are not imported
217            to BASE with a plug-in. Genepix data requires a
218            configuration. Select the "Reporter map importer" from the
219            plug-in definition list. Genepix documentation missing
220            here. </p>
222            <p> <i>Raw data importer</i> <br> Affymetrix CEL files
223            do not need a configuration since these are not imported
224            to BASE with a plug-in. Genepix data requires a
225            configuration. Select the "Raw data importer" from the
226            plug-in definition list. Genepix documentation missing
227            here. </p>
228          </li>
230          <li>
231            <p> (Affymetrix only) <b>Install
232            <a
233            href=>RMAExpress
234            plug-in for BASE</a></b> <br> This plug-in is required for
235            Affymetrix data. The plug-in will create a bioassay set,
236            i.e., to be able to analyse the data in BASE.</p>
237          </li>
239          <li>
240            <p> <b>Upload files</b> <br> Before import you can upload
241            files to the server, or if preferred, files to be imported
242            can be uploaded at import time. To upload files, choose
243            'View' -> 'Files' and click in the 'Upload file...'
244            button. At upload time you assign a type to the file (can
245            be changed later if needed), and batch upload of files is
246            possible in a zip-file or tar archive. </p>
248            <p> As administrator you need to upload the reporter map
249            (array design) files and corresponding reporter files. For
250            Affymetrix this translates to Affydesign.cdf files and
251            Affydesign_annot.csv files. </p>
252          </li>
254          <li>
255            <p> <b> Reporter import </b> <br> Choose 'View' ->
256            'Reporters' and click on the 'Import...' tab. Click 'Next'
257            in the pop-up without changing anything. Select the file
258            with reporter information and click 'Next'. In the panel
259            you can choose to update reporter information for already
260            stored reporters. Click 'Next'. Set the job name and click
261            'Finish' to start the import. A progress report will be
262            displayed. It is safe to close this page since the job
263            will finish anyway. </p>
264          </li>
266          <li>
267            <p> <b> Import reporter maps </b> <br> To create a new
268            design, choose 'Array LIMS' -> 'Array designs' and click
269            on the 'New...' tab. Select a name for the design. If it
270            is an Affymetrix design, mark the 'Affy chip' box and
271            select a 'CDF file'. Hint: For Affymetrix design you
272            should choose the name to be the same as the cdf file
273            name. If you are importing something else than Affymetrix
274            designs make sure that you unmark the 'Affy chip'
275            box. Finalize with 'Save'. For Affymetrix the import is
276            done, whereas Genepix have to perform reporter map
277            import. Remember to share your designs (normally to group
278            'Everyone'). </p>
280            <p> <i>Genepix reporter map import</i> <br> Click on the
281            newly created array design, and click on the 'Import...'
282            tab. More information needed here. </p>
283          </li>
285        </ol>
286      </li>
288      <li>
289        <a name="user"></a>
290        <h2>User tasks</h2>
291      </li>
293      <p> A normal user is not allowed to add array design, reporter
294      information, and a lot of other information to BASE. The reason
295      for this is that a lot of information should only exist as one
296      copy in the database. For example, reporters should only exist in
297      one copy because everyone uses the same reporters. There is no
298      need to store several copies of the same array design. </p>
300      <p> A user will normally upload experimental data to BASE for
301      import into the database. To be able to import the data, the
302      array design used must be available in BASE at import time. If
303      the array design is not available, a user with the proper
304      credential must add the array design to BASE. </p>
306      <ol type=a>
308      <li>
309        <p> <b> Create a new Project </b> <br> Go to 'View' ->
310        'Projects' and click on the 'New...' tab. Name the project and
311        save. In the projects listing page, click 'Set active' for the
312        new project. The selected project should be displayed on top
313        right as 'Active project'. Selecting an active project will
314        influence the behaviour of BASE. Only information related to
315        the active project will be displayed and items created will
316        automatically be shared to the active project. </p>
318        <p> The display of items shared to the active project only
319        requires that the 'view/presets' pull-down menu options are
320        properly set. In 'view/preset' you can select what should be
321        displayed, and if only 'In current project' is selected then
322        only information shared to a project will be shown. </p>
323      </li>
325      <li>
326        <p> <b>Create raw bioassays</b> <br> Upload your raw data
327        files. Go to 'View' -> 'Raw bioassays' and click on the
328        'New...' tab. Name the raw bioassay. Select 'Raw data
329        type'. Select the 'Array design', if you cannot see see
330        designs in the pop-up the make sure that the 'view/presets'
331        pull-down menu has 'Shared to me' marked and select appropriate
332        design. Select 'CEL file' if you create an Affymetrix raw
333        bioassay. You can leave the rest untouched. Redo for all raw
334        data files. (Yes a batch creator would be nice.) </p>
335      <li>
337      <li>
338        <p> <b>Create a new experiment</b> <br> Go to 'View' ->
339        'Experiments' and click on the 'New...' tab. Name the
340        experiment. Click 'Add raw bioassays...' button and mark the
341        raw bioassays to add to the experiment and click
342        'Ok'. Finalize with clicking the 'Save' button. </p>
343      </li>
345      </ol>
347    </ol>
349  </body>
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