Changeset 4487


Ignore:
Timestamp:
Sep 8, 2008, 10:52:34 AM (15 years ago)
Author:
Jari Häkkinen
Message:

Fixes #1107. BASE2 is now BASE. Also checked spelling in many files.

Location:
trunk/doc
Files:
24 edited

Legend:

Unmodified
Added
Removed

  • trunk/doc/src/docbook/admindoc/installation_upgrade.xml

    r4477 r4487  
    3939  <para>
    4040    This chapter is divided into four parts. First, the process of
    41     upgrading a BASE 2 server is described. Followed by set up of job
     41    upgrading a BASE server is described. Followed by set up of job
    4242    agents. (For these two first parts it is assumed that there is a
    4343    running server.) Then, the first time installation instructions
    4444    follows, and the chapter is concluded with information on how to
    45     migrate data from a BASE 1.2.17 server to a BASE 2 server.
     45    migrate data from a BASE 1.2.17 server to a current BASE server.
    4646  </para>
    4747
    … …  
    4949    The first time installation is only to be performed once,
    5050    optionally followed by a migration. The migration can only be done
    51     to a pristine (empty) BASE 2 server with one exception; The
     51    to a pristine (empty) BASE version 2 server with one exception; The
    5252    migration can be restarted if it fails during the RawBioAssaysData
    5353    transfer. For all other failure points the migration has to be
    54     restarted with an empty database. Migration from several BASE 1
    55     installations to one BASE 2 server is not supported.
     54    restarted with an empty database. Migration from several BASE
     55    version 1 installations to one BASE server is not supported.
    5656  </para>
    5757
    … …  
    122122        you must also make sure that you are running Tomcat 6 or higher.
    123123        Earlier BASE versions only required Tomcat 5.5. If you are not
    124         already running Tomcat 6 you need to upgrade. Other serlvet
     124        already running Tomcat 6 you need to upgrade. Other servlet
    125125        engines may work if they implement the Servlet 2.5 and JSP
    126126        2.1 specifications.
    … …  
    192192        <listitem>
    193193          <para>
    194             Rename your current BASE 2 installation <command>mv
     194            Rename your current BASE installation <command>mv
    195195              /path/to/base /path/to/base_old</command>.
    196196          </para>
    … …  
    494494        <variablelist>
    495495          <varlistentry>
    496             <term>Download and unpack a regular BASE 2 distribution</term>
     496            <term>Download and unpack a regular BASE distribution</term>
    497497            <listitem>
    498498              <para>
    … …  
    737737        <listitem>
    738738          <para>
    739             BASE 2
     739            BASE
    740740            utilize <ulink
    741741            url="http://www.hibernate.org/">Hibernate</ulink> for
    … …  
    777777                  edit
    778778                  your <filename>&lt;base-dir&gt;/www/WEB-INF/classes/base.config</filename>
    779                   file. Uncomment the settings for Postgres and
     779                  file. Uncomment the settings for PostgreSQL and
    780780                  comment out the settings for MySQL.
    781781                </para>
    … …  
    783783                <note>
    784784                  <para>
    785                   Postgres versions prior to 8.2 have a non-optimal solution
     785                  PostgreSQL versions prior to 8.2 have a non-optimal solution
    786786                  for locking rows in certain situations. This may cause two
    787787                  seemingly independent transactions to lock if they just
    788788                  reference a common database row. This may happen, for example,
    789789                  when importing raw data that have references to the same
    790                   reporters. The problem has been solved in Postgres 8.2.
     790                  reporters. The problem has been solved in PostgreSQL 8.2.
    791791                  </para>
    792792                </note>
    … …  
    815815          <para>
    816816            If you choose to download the binary package, skip to the
    817             next item. The rest of us, read on and compile BASE 2. If
     817            next item. The rest of us, read on and compile BASE. If
    818818            you downloaded a source distribution, unpack the
    819819            downloaded file <command>tar zxpf
    … …  
    980980            url="http://base.thep.lu.se/chrome/site/doc/admin/extended-properties.html">document
    981981            discussing extended properties</ulink> available. If you
    982             plan to perform a migration of a BASE 1.2 database you
     982            plan to perform a migration of a BASE version 1.2 database you
    983983            should probably not remove any extended properties
    984984            columns (this is not tested so the outcome is currently
    … …  
    11131113        <listitem>
    11141114          <para>
    1115             Happy BASEing. Now you can log on to your BASE 2 server as
     1115            Happy BASEing. Now you can log on to your BASE server as
    11161116            user <emphasis>root</emphasis> (use
    11171117            the <emphasis>base_root_password</emphasis> from the
    … …  
    11231123          <para>
    11241124            If you are planning to perform a migration of data from
    1125             BASE 1.2.x please perform the steps in
     1125            BASE version 1.2.x please perform the steps in
    11261126            <xref linkend="installation_upgrade.migration"/> before
    11271127            doing anything else with your new BASE installation.
    … …  
    11591159                  <para>
    11601160                    This is a limit of how many bytes of data that should be
    1161                     transfered per second when uploading files to BASE. Prefixes
     1161                    transferred per second when uploading files to BASE. Prefixes
    11621162                    like k, M or G can be used for larger values, just like
    11631163                    described in the tab. The limit is per ongoing upload
    … …  
    11711171                  <para>
    11721172                    Check this to not limit the transfer rate. In this case, the
    1173                     internet connection of the server is the limit.
     1173                    Internet connection of the server is the limit.
    11741174                  </para>
    11751175                </listitem>
    … …  
    12131213                    <guilabel>About this server</guilabel> section on the login
    12141214                    page and in the about-dialog window. We recommend changing the
    1215                     default latin text to something meaningful, or remove it
     1215                    default Latin text to something meaningful, or remove it
    12161216                    to hide the section completely.
    12171217                  </para>
    … …  
    12331233              an account on the particular BASE-server. This text is linked
    12341234              to the <guilabel>Get an account!</guilabel> link on the login
    1235               page. We recommend that the latin text is replaced with some useful
     1235              page. We recommend that the Latin text is replaced with some useful
    12361236              information, or that it is removed to hide the link.
    12371237            </para>
    … …  
    12501250              This text is linked
    12511251              to the <guilabel>Forgot your password?</guilabel> link on the login
    1252               page. We recommend that the latin text is replaced with some useful
     1252              page. We recommend that the Latin text is replaced with some useful
    12531253              information, or that it is removed to hide the link.
    12541254            </para>
    … …  
    13251325      <title>The disclaimer section</title>
    13261326      <para>
    1327         We have made extensive testing of the migration from BASE 1.2
    1328         to BASE 2. To our knowledge the migration works but we cannot
     1327        We have made extensive testing of the migration from BASE
     1328        version 1.2 (BASE1.2) to BASE version 2 (BASE2). To our
     1329        knowledge the migration works but we cannot
    13291330        guarantee perfect functionality. The migration tool is
    13301331        supplied as is and usage is done at your risk. We are
    13311332        committed to solve migration problems at the level of
    1332         transferring data from BASE 1.2 to BASE 2, but cannot resolve
    1333         data loss issues in a running BASE 2 server due to imperfect
     1333        transferring data from BASE1.2 to BASE2, but
     1334        cannot resolve data loss issues in a running BASE2
     1335        server due to imperfect
    13341336        migration. When you start the migration tool you are required
    13351337        to pass parameter <emphasis>"disclaimer_understood"</emphasis>
    … …  
    13491351
    13501352    <para>
    1351       Verify that your BASE 2 installation is up and running before
     1353      Verify that your new BASE installation is up and running before
    13521354      attempting migration. Preferably try to log in using the root
    13531355      user through the web interface.
    … …  
    13551357
    13561358    <para>
    1357       Make sure your BASE 1.2 runs with the latest
     1359      Make sure your BASE1.2 runs with the latest
    13581360      (<emphasis>pristine</emphasis>) schema
    13591361      version, <emphasis>i.e.,</emphasis> the migration will only
    1360       support an unmodified BASE 1.2 installation. If you have an out
    1361       of date schema version, please upgrade to the latest schema
    1362       using BASE 1.2 tools before migrating. If you have made local
    1363       changes to the BASE 1.2 schema you need to patch the BASE 2
    1364       schema as well as make proper changes to the migration program.
    1365       If there are added columns to the reporter table in your BASE
    1366       1.2 database you need to transfer the additional information
    1367       after migration (even if you modified the BASE
    1368       2 <filename>extended-properties.xml</filename> file).
     1362      support an unmodified BASE1.2 installation. If you have
     1363      an out of date schema version, please upgrade to the latest
     1364      schema using BASE1.2 tools before migrating. If you
     1365      have made local changes to the BASE1.2 schema you need
     1366      to patch the BASE2 schema as well as make proper
     1367      changes to the migration program.  If there are added columns to
     1368      the reporter table in your BASE1.2 database you need to
     1369      transfer the additional information after migration (even if you
     1370      modified the BASE2 <filename>extended-properties.xml</filename> file).
    13691371    </para>
    13701372
    … …  
    13901392        <listitem>
    13911393          <para>
    1392             To transfer files from BASE 1.2 (default migration
    1393             behaviour), you must have file system access to BASE 1.2
    1394             files, <emphasis>i.e.,</emphasis> the <filename
    1395             class="directory">/BASE 1.2/data</filename>
     1394            To transfer files from BASE1.2 (default migration
     1395            behaviour), you must have file system access to BASE1.2
     1396            files, <emphasis>i.e.,</emphasis>
     1397            the <filename class="directory">/BASE 1.2/data</filename>
    13961398            directory containing directories
    13971399            <filename class="directory">rawdata</filename>,
    … …  
    14101412                <para>
    14111413                  Modify <emphasis>db1.*</emphasis> parameters to
    1412                   match your BASE 1.2 installation.
     1414                  match your BASE1.2 installation.
    14131415                </para>
    14141416              </listitem>
    … …  
    14181420                  not the same parameter as
    14191421                  in <filename>base.config</filename>) to point to the
    1420                   directory containing the BASE 1.2 files (defined in a
     1422                  directory containing the BASE1.2 files (defined in a
    14211423                  previous step above).
    14221424                </para>
    … …  
    14251427                <para>
    14261428                  Set the <emphasis>pluginDir</emphasis> to point to
    1427                   the directory where your BASE 1.2 plug-ins are
     1429                  the directory where your BASE1.2 plug-ins are
    14281430                  installed. The default is
    14291431                  <filename
    … …  
    14401442                  Change the <emphasis>deletefiles</emphasis> setting
    14411443                  wisely. If you
    1442                   set <emphasis>deletefiles=yes</emphasis> all BASE
    1443                   1.2 files will be physically removed when copied to
    1444                   BASE 2. Leave this options
     1444                  set <emphasis>deletefiles=yes</emphasis> all BASE1.2
     1445                  files will be physically removed when copied to the
     1446                  BASE2 server. Leave this options
    14451447                  as <emphasis>deletefiles=no</emphasis> unless you
    14461448                  are absolutely sure of what you are doing.
    … …  
    14691471        <listitem>
    14701472          <para>
    1471             <emphasis>Optional, depends on your BASE 1.2 reporter
     1473            <emphasis>Optional, depends on your BASE1.2 reporter
    14721474            table.</emphasis> Additional columns (as compared with a
    14731475            pristine database schema) in the reporter table in the
    1474             BASE 1.2 schema are not transferred during migration. You
     1476            BASE1.2 schema are not transferred during migration. You
    14751477            have to perform the transfer manually after
    14761478            migration. Simply export the reporter information from
    1477             BASE 1.2, and import the data into BASE 2. In BASE 1.2: i)
     1479            BASE1.2, and import the data into the new BASE installation. In BASE1.2: i)
    14781480            View the reporters, ii) Use `Get as tab-separated text` to
    14791481            create a tab separated file (right click and save). In
    1480             BASE 2, to import the file follow the instructions in
     1482            BASE2, to import the file follow the instructions in
    14811483            <xref linkend="reporters.import"/>.
    14821484          </para>

  • trunk/doc/src/docbook/admindoc/user_administration.xml

    r4477 r4487  
    3434    <title>Read <link linkend="project_permission"><xref linkend="project_permission" /></link></title>
    3535    <para>
    36       This chapter contains importants information about the
     36      This chapter contains important information about the
    3737      permission system BASE uses. It is essential that an
    3838      administrator knows how this works to be able to set up
    … …  
    9494                <para>
    9595                  An id that is used to identify the user outside BASE (optional).
    96                   If a valus is given it must be unique among all users.
     96                  If a value is given it must be unique among all users.
    9797                </para>
    9898              </listitem>
    … …  
    158158                  or from a template, can be created if editing a new user. Select
    159159                  <guilabel>- none -</guilabel>
    160                   if there should not be any home directory asocciated with the
     160                  if there should not be any home directory associated with the
    161161                  account.
    162162                </para>
    … …  
    194194                  password, contact information and other settings. It will
    195195                  also reset all list filters, column configurations, etc.
    196                   when the user logs out. Normally, these settings are rememembered
    197                   between logins.
     196                  when the user logs out. Normally, these settings are remembered
     197                  between log ins.
    198198                </para>
    199199              </listitem>
    … …  
    229229        <helptext external_id="user.edit.contact" title="Edit user's contact information">
    230230          <para>
    231             Information about how to get in contact with the user that is asocciated
     231            Information about how to get in contact with the user that is associated
    232232            with the account. All fields on this tab are optional and do not necessarily
    233233            need to have a value but some can be good to set, like email or phone
    … …  
    344344          <para>
    345345            This tab contains fields that hold various information about the user. There are
    346             by default two fields in BASE2 but this could easily be changed by the
     346            by default two fields in BASE but this could easily be changed by the
    347347            server administrator. How this configuration is done can be read in
    348348            <xref linkend="appendix.extendedproperties" />
    … …  
    357357            </note>
    358358           
    359             These are the fields that are installed with BASE2
     359            These are the fields that are installed with BASE
    360360            <variablelist>
    361361              <varlistentry>
    … …  
    377377                  <para>
    378378                    Skype contact information, if the user has a registered
    379                     skype account. This field could be left empty.
     379                    Skype account. This field could be left empty.
    380380                  </para>
    381381                </listitem>
    … …  
    430430              <listitem>
    431431                <para>
    432                 Opens a popup window that allows you to select
    433                 groups. In the popup window, mark
     432                Opens a pop-up window that allows you to select
     433                groups. In the pop-up window, mark
    434434                one or more groups and click on the &gbOk;
    435                 button. The popup window will not list groups that
     435                button. The pop-up window will not list groups that
    436436                the user already is a member of.
    437437                </para>
    … …  
    443443              <listitem>
    444444                <para>
    445                 Opens a popup window that allows you to select
    446                 roles. In the popup window, mark
     445                Opens a pop-up window that allows you to select
     446                roles. In the pop-up window, mark
    447447                one or more roles and click on the &gbOk;
    448                 button. The popup window will not list roles that
     448                button. The pop-up window will not list roles that
    449449                the user already is a member of.
    450450                </para>
    … …  
    508508            <guimenuitem>Users</guimenuitem>
    509509          </menuchoice>
    510           page and select groups and roles in a popup dialog.
     510          page and select groups and roles in a pop-up dialog.
    511511          The dialog lists all groups and roles that are currently
    512512          assigned as default. Use the <guibutton>Add groups</guibutton>
    … …  
    536536    <para>
    537537      Groups in BASE are meant to represent the organizational structure of
    538       a company or instituion. For example, there can be one group for each
     538      a company or institution. For example, there can be one group for each
    539539      department and subgroups for the teams in the departments.
    540540      The group-membership is normally set when the user is added to BASE and
    … …  
    605605                  <guilabel>-none-</guilabel>
    606606                  from the drop-down list if the group should not have any quota.
    607                   There are some presets of quotas that comes with the BASE2
     607                  There are some presets of quotas that comes with the BASE
    608608                  installation, besides a couple with different size of total disk
    609609                  space there are one called
    … …  
    666666              <listitem>
    667667                <para>
    668                 Opens a popup window that allows you to add
    669                 users to the group. In the popup window, mark
     668                Opens a pop-up window that allows you to add
     669                users to the group. In the pop-up window, mark
    670670                one or more users and click on the &gbOk;
    671                 button. The popup window will not list users that
     671                button. The pop-up window will not list users that
    672672                are already members of the group.
    673673                </para>
    … …  
    679679              <listitem>
    680680                <para>
    681                 Opens a popup window that allows you to add
    682                 other groups to the group. In the popup window, mark
     681                Opens a pop-up window that allows you to add
     682                other groups to the group. In the pop-up window, mark
    683683                one or more groups and click on the &gbOk;
    684                 button. The popup window will not list groups that
     684                button. The pop-up window will not list groups that
    685685                are already members of the group.
    686686                </para>
    … …  
    763763              like reporters, the array lims and plug-ins.
    764764              This role can be proper for those users that are in
    765               some kind of leading position over workgroups or projects.
     765              some kind of leading position over work groups or projects.
    766766            </para>
    767767          </listitem>
    … …  
    901901        <helptext external_id="role.edit.permissions" title="Edit role permissions">
    902902          <para>
    903             A role's permissions are defined for each item type within BASE 2. Set the
     903            A role's permissions are defined for each item type within BASE. Set the
    904904            role's permission on an item type by first selecting the item(s) in the list
    905905            and then tick those permissions that should be applied. Not all permissions

  • trunk/doc/src/docbook/appendix/base.config.xml

    r4477 r4487  
    5959          <listitem>
    6060            <userinput>org.hibernate.dialect.PostgreSQLDialect</userinput>
    61             for Postgres
     61            for PostgreSQL
    6262          </listitem>
    6363          </itemizedlist>
    … …  
    7979          <listitem>
    8080            <userinput>org.postgresql.Driver</userinput>
    81             for Postgres
     81            for PostgreSQL
    8282          </listitem>
    8383          </itemizedlist>
    … …  
    9191      <listitem>
    9292        <para>
    93           The connection URL that locates the BASE 2 database. The exact syntax
     93          The connection URL that locates the BASE database. The exact syntax
    9494          of the string depends on the JDBC driver. Here are two examples which
    9595          leaves all other settings to their defaults:
    … …  
    101101          <listitem>
    102102            <userinput>jdbc:postgresql:base2</userinput>
    103             for Postgres
     103            for PostgreSQL
    104104          </listitem>
    105105          </itemizedlist>
    … …  
    110110            >MySQL</ulink> and
    111111          <ulink url="http://jdbc.postgresql.org/documentation/81/connect.html"
    112             >Postgres</ulink>.
     112            >PostgreSQL</ulink>.
    113113           
    114114           
    … …  
    143143        database is used. The exact meaning of catalog depends on the actual database.
    144144        For MySQL the catalog is the name of the database so this value is simply the
    145         name of the dynamic database. Postgres does not support connecting to multiple
     145        name of the dynamic database. PostgreSQL does not support connecting to multiple
    146146        databases with the same connection so this should have the same value as the
    147147        database in the <property>db.url</property> setting.
    … …  
    156156        The name of the schema where the dynamic database used to store
    157157        analysed data is located. MySQL does not have schemas so this value should
    158         be left empty. Postgres supports schemas and we recommend that the dynamic
     158        be left empty. PostgreSQL supports schemas and we recommend that the dynamic
    159159        part is created in it's own schema to avoid mixing the dynamic tables with
    160160        the regular ones.
    … …  
    204204        <itemizedlist>
    205205          <listitem><userinput>/mysql-queries.xml</userinput> for MySQL</listitem>
    206           <listitem><userinput>/postgres-queries.xml</userinput> for Postgres</listitem>
     206          <listitem><userinput>/postgres-queries.xml</userinput> for PostgreSQL</listitem>
    207207        </itemizedlist>
    208208          See also <xref linkend="appendix.otherconfig.sql" />.
    … …  
    242242        query. This setting exists because MySQL prior to 5.0.2 does not support scrollable
    243243        result sets, but loads all data into memory. This will result in out of memory
    244         exception if exporting too many items at the same time. Postgres does not have
     244        exception if exporting too many items at the same time. PostgreSQL does not have
    245245        this problem. Use:
    246246       
    247247        <itemizedlist>
    248         <listitem><para>0 for Postgres</para></listitem>
     248        <listitem><para>0 for PostgreSQL</para></listitem>
    249249        <listitem>
    250250          <para>
    … …  
    286286        <para>
    287287        The class name of the plug-in that acts as the authentication driver.
    288         BASE ships with a simple plugin that checks if a user has a valid email
     288        BASE ships with a simple plug-in that checks if a user has a valid email
    289289        account on a POP3 server. It is not enabled by default. The class name
    290         of that plugin is <classname docapi="net.sf.basedb.core.authentication">net.sf.basedb.core.authentication.POP3Authenticator</classname>.
     290        of that plug-in is <classname docapi="net.sf.basedb.core.authentication">net.sf.basedb.core.authentication.POP3Authenticator</classname>.
    291291        If no class is specified internal authentication is used.
    292292          </para>
    … …  
    300300        Initialisation parameters sent to the plug-in when calling the
    301301        <methodname>init()</methodname> method. The syntax and meaning of this
    302         string depends on the plugin. For the <classname docapi="net.sf.basedb.core.authentication">POP3Authenticator</classname>
     302        string depends on the plug-in. For the <classname docapi="net.sf.basedb.core.authentication">POP3Authenticator</classname>
    303303        this is simply the name or IP-address of the mail server.
    304304          </para>
    … …  
    404404        Initialisation string sent to <methodname>SignalReceiver.init()</methodname>.
    405405        The syntax and meaning of the string depends on the actual implementation
    406         that is used. Please see the javadoc for more information.
     406        that is used. Please see the Javadoc for more information.
    407407         </para>
    408408      </listitem>
    … …  
    565565        for information about how to configure the secondary storage. Files are not
    566566        stored in the same directory structure or with the same names as in
    567         the BASE filesystem. The internal structure may contain subdirectories.
     567        the BASE file system. The internal structure may contain sub-directories.
    568568          </para>
    569569      </listitem>
    … …  
    624624          and automatically load and use the new code instead of the old code.
    625625          This setting is useful for plug-in developers since they don't have to
    626           restart the webserver each time the plug-in is recompiled.
     626          restart the web server each time the plug-in is recompiled.
    627627          <itemizedlist>
    628628            <listitem>
    … …  
    648648          The path to the directory where jar-files for external plugins should be located
    649649          if they should be used with the auto-installer. All new plugins found in this directory,
    650           or in any of it's subdirectories, can be selected for installation, see
     650          or in any of it's sub-directories, can be selected for installation, see
    651651          <xref linkend="plugins.installation" />.
    652           The plugin auto-installer will not be availble if this property isn't defined.
     652          The plugging auto-installer will not be available if this property isn't defined.
    653653        </para>
    654654

  • trunk/doc/src/docbook/appendix/coreplugins.xml

    r4477 r4487  
    3232
    3333  <para>
    34     A categorized list of all plugins installed with a pristine BASE
    35     installation. Some plugins must be configured before use,
     34    A categorized list of all plug-ins installed with a pristine BASE
     35    installation. Some plug-ins must be configured before use,
    3636    requirements are listed below and configuration samples are given
    37     for for plugins that supports/requires configurations. Use the
     37    for for plug-ins that supports/requires configurations. Use the
    3838    right-click menu of the mouse to download these XML files for
    3939    further import into BASE (see <xref
    … …  
    4444    Contributed plug-ins are available at <ulink
    4545    url="http://baseplugins.thep.lu.se" >http://baseplugins.thep.lu.se
    46     </ulink>. These plugins are either developed outside the core team
     46    </ulink>. These plug-ins are either developed outside the core team
    4747    or require external non-Java compilers and tools. These packages
    4848    are excluded from the BASE package to make the installation
    … …  
    6363            <emphasis>Since BASE 2.2, no configuration needed for the
    6464            Base1PluginExecuter but may be required for the underlying
    65             BASE 1.2 plugins.</emphasis>
     65            BASE version 1.2 plug-ins.</emphasis>
    6666          </para>
    6767        </listitem>
    … …  
    8181
    8282      <varlistentry>
    83         <term>JEP filter plugin</term>
     83        <term>JEP filter plug-in</term>
    8484        <listitem>
    8585          <para>
    … …  
    140140        <listitem>
    141141          <para>
    142             Exports bioassay sets in different formats. See plugin
     142            Exports bioassay sets in different formats. See plug-in
    143143            definition in BASE for listing of supported formats.
    144144          </para>
    … …  
    189189        <listitem>
    190190          <para>
    191             Exports plugin configurations to an XML file.
     191            Exports plug-in configurations to an XML file.
    192192          </para>
    193193          <para>
    … …  
    238238            in import mode from the reporter list view and from the
    239239            array design view and in verification mode from the array
    240             design view. The plugin can only set the name and ID of
     240            design view. The plug-in can only set the name and ID of
    241241            the reporters, since the CDF file doesn't contains any
    242242            annotation information. Probesets already in BASE will not
    … …  
    253253        <listitem>
    254254          <para>
    255             Imports annotation to any annotable item in BASE.
     255            Imports annotation to any annotatable item in BASE.
    256256          </para>
    257257          <para>
    … …  
    277277        <listitem>
    278278          <para>
    279             This plugin is used to import raw data from Illumina data
     279            This plug-in is used to import raw data from Illumina data
    280280            files.
    281281          </para>
    … …  
    318318        <listitem>
    319319          <para>
    320             Imports plugin configurations from an XML file.
     320            Imports plug-in configurations from an XML file.
    321321          </para>
    322322          <para>
    … …  
    591591        <listitem>
    592592          <para>
    593             Unpacks zip and jar file on the BASE2's file system.
     593            Unpacks zip and jar file on the BASE's file system.
    594594          </para>
    595595          <para>

  • trunk/doc/src/docbook/appendix/extended_properties.xml

    r4477 r4487  
    4343  <para>
    4444    The default <filename>extended-properties.xml</filename> that ships
    45     with BASE is biased towards the BASE 1.2 setup for 2-spotted microarray
     45    with BASE is biased towards the BASE version 1.2 setup for 2-spotted microarray
    4646    data. If you want your BASE installation to be configured differently we
    4747    recommend that you do it before the first initialisation of the database.
    … …  
    6969    Run the <filename>updatedb.sh</filename> script. New
    7070    columns will automatically be created, but the script can't delete columns that
    71     have been removed, or modify columns that have changed datatype. You will have to
     71    have been removed, or modify columns that have changed data type. You will have to
    7272    do these kind of changes by manually executing SQL against your database. Check your
    7373    database documentation for information about SQL syntax.
    … …  
    7575   
    7676    <tip>
    77       <title>Create a parallell installation</title>
     77      <title>Create a parallel installation</title>
    7878      <para>
    79       You can always create a new temporary parallell installation to check
     79      You can always create a new temporary parallel installation to check
    8080      what the table generated by installation script looks like. Compare the
    8181      new table to the existing one and make sure they match.
    … …  
    107107    After installing BASE the default <filename>extended-properties.xml</filename>
    108108    is located in the <filename>&lt;basedir&gt;/www/WEB-INF/classes</filename> directory.
    109     This setup is biased towards the BASE 1.2 setup for 2-spotted cDNA arrays.
    110     If you are migrating from BASE 1.2 you need to use the default setup.
     109    This setup is biased towards the BASE version 1.2 setup for
     110    2-spotted cDNA arrays.  If you are migrating from BASE version 1.2
     111    you <emphasis>must</emphasis> to use the default setup.
    111112    </para>
    112113  </listitem>
    … …  
    129130    new columns. To remove or change existing columns you still have
    130131    to modify the original extended properties file. It is rather simple
    131     to use this feature. Create a new subdirectory with the name
     132    to use this feature. Create a new directory with the name
    132133    <filename>extended-properties</filename> in the same directory as
    133134    the <filename>extended-properties.xml</filename>. In this directory
    … …  
    229230          <entry>
    230231            The title of the extra property as it is displayed in client applications.
    231             If not specified the value of the <sgmltag>name</sgmltag> attrbiute is used.
     232            If not specified the value of the <sgmltag>name</sgmltag> attribute is used.
    232233          </entry>
    233234        </row>
    … …  
    385386    <para>
    386387    If the link contains the character <constant>&amp;</constant> it must be
    387     escaped as <constant>&amp;amp;</constant>. For example, to link to a Unigene
     388    escaped as <constant>&amp;amp;</constant>. For example, to link to a UniGene
    388389    entry:
    389390    </para>

  • trunk/doc/src/docbook/appendix/incompatible.xml

    r4477 r4487  
    5151    <bridgehead>Type.BOOLEAN.parseString()</bridgehead>
    5252    <para>
    53       This method now converts the empty string, "no", "0", and "false" (ingoring case)
     53      This method now converts the empty string, "no", "0", and "false" (ignoring case)
    5454      to boolean <constant>false</constant>. A <constant>null</constant>
    5555      value as input still returns <constant>null</constant> as output.
    … …  
    9898    <listitem>
    9999      <para>
    100       The POSITION identification method will require a unqiue position number.
     100      The POSITION identification method will require a unique position number.
    101101      This value used to be an auto-generated sequence starting at 1. The other
    102102      identification methods will still do that, but when using the POSITION identification
    103103      method the only requirement is that the position value is a unique positive integer.
    104       Client or plug-in code that depends on the position beeing a number between
     104      Client or plug-in code that depends on the position being a number between
    105105      1 and the number of features may fail if used with an array design using
    106106      the POSITION identification method.
    … …  
    148148    <para>
    149149      A similar issue arises when inheriting annotations to a raw bioassay
    150       which stems from a specific sub-array on a mutli-array hybridization.
     150      which stems from a specific sub-array on a multi-array hybridization.
    151151      This raw bioassay should only inherit annotations from the labeled
    152152      extracts that are part of the same sub-array. For API compatibility
    … …  
    161161   
    162162    <para>
    163       A related issue ariese when querying labeled extracts and joining
     163      A related issue arise when querying labeled extracts and joining
    164164      the source events collection to use the linked hybridizations in
    165165      the query. Here is an example:
    … …  
    189189
    190190    <para>
    191       The good new is that the modifcations makes it possible to filter
    192       the query on used quantity and sub-array. See the javadoc for
     191      The good new is that the modifications makes it possible to filter
     192      the query on used quantity and sub-array. See the Javadoc for
    193193      <classname docapi="net.sf.basedb.core">Hybridization</classname>
    194194      to get more information.
    … …  
    400400    <para>
    401401      Changed to store information about plug-in parameters as XML in the
    402       database instead of in the orignal BASE 1 plug-in definition file.
    403       Existing BASE 1 plug-ins must be re-configured before they can be
     402      database instead of in the original BASE version 1 plug-in definition file.
     403      Existing BASE version 1 plug-ins must be re-configured before they can be
    404404      used. To do this:
    405405    </para>
    … …  
    418418    <listitem>
    419419      <para>
    420       Step through the configuration wizard for all BASE 1 plug-in
     420      Step through the configuration wizard for all BASE version 1 plug-in
    421421      configurations. You do not need to change any parameters.
    422422      Just click on the <guibutton>Next</guibutton> button
    … …  
    433433   
    434434    <para>
    435       No longer provides a default mapping between BASE 1 and BASE 2
    436       raw data columns. To solve this add a <guilabel>Formula</guilabel>
    437       item with the same name as the BASE 1 column name and an expression
    438       that picks the BASE 2 raw data property. For example:
     435      No longer provides a default mapping between BASE version 1 and
     436      BASE version 2 raw data columns. To solve this add
     437      a <guilabel>Formula</guilabel> item with the same name as the
     438      BASE version 1 column name and an expression that picks the BASE
     439      version 2 raw data property. For example:
    439440    </para>
    440441   

  • trunk/doc/src/docbook/appendix/menuguide.xml

    r4477 r4487  
    3131  <para>
    3232    This appendix covers all menu items in BASE, including submenus. You should use it as a map
    33     to easily find your way through the menus. Some menu items are refering to other section of
     33    to easily find your way through the menus. Some menu items are referring to other section of
    3434    the documentation, that holds more information. The list of menu items is organized after
    3535    three different types,
    … …  
    7272        <tbody>
    7373          <row>
    74             <entry>Appearance of webclient</entry>
     74            <entry>Appearance of web client</entry>
    7575            <entry>
    7676              <menuchoice>
    … …  
    199199              </menuchoice>
    200200            </entry>
    201             <entry>The home page of the BASE2 project</entry>
     201            <entry>The home page of the BASE project</entry>
    202202          </row>
    203203          <row>
    … …  
    221221              </menuchoice>
    222222            </entry>
    223             <entry>You are loged out and redirected to the login page.</entry>
     223            <entry>You are logged out and redirected to the login page.</entry>
    224224          </row>
    225225          <row>
    … …  
    242242            </entry>
    243243            <entry>
    244               This updates the loged in user's permissions. See
     244              This updates the logged in user's permissions. See
    245245              <xref linkend="project_permission.permissions" />
    246246            </entry>
    … …  
    267267            </entry>
    268268            <entry>
    269               Restarts the program. Requires everyone, that were loged in, to identify
    270               themself again with username and password.
     269              Restarts the program. Requires everyone, that were logged in, to identify
     270              themselves again with username and password.
    271271            </entry>
    272272          </row>

  • trunk/doc/src/docbook/developerdoc/base_overview.xml

    r4477 r4487  
    2929<chapter id="base_develop_overview">
    3030  <?dbhtml dir="develop_overview"?>
    31   <title>Developer overview of BASE2</title>
     31  <title>Developer overview of BASE</title>
    3232
    3333  <para>

  • trunk/doc/src/docbook/developerdoc/documentation.xml

    r4477 r4487  
    3535
    3636    <para>
    37       This chapter is for those who intent to contribute to the BASE2 user documentation.
     37      This chapter is for those who intent to contribute to the BASE user documentation.
    3838      The chapter contains explanations of how the documentation is organized, what the
    3939      different parts is about and other things that will make it easier to know
    … …  
    4343      The documentation is written with the docbook standard, which is a bunch of defined XML
    4444      elements and XSLT style sheets that are used to format the text. Later on in this chapter
    45       is a reference, over those docbook elements that are recommended to use when writing BASE2
     45      is a reference, over those docbook elements that are recommended to use when writing BASE
    4646      documentation. Further information about docbook can be found in the on-line version of
    4747      O'Reilly's
    … …  
    6464        <listitem>
    6565          <para>
    66             The overview part contains, like the name says, an overview of BASE2.
    67             For example an explanation about what the purpose with BASE2 is, the terms
     66            The overview part contains, like the name says, an overview of BASE.
     67            For example an explanation about what the purpose with BASE is, the terms
    6868            that are used in the program and other general things that anyone that is
    6969            interested in the program wants/needs to know before exploring it further.
    … …  
    7575        <listitem>
    7676          <para>
    77             This part contains information that are relevant for the common BASE2-user.
     77            This part contains information that are relevant for the common BASE-user.
    7878            More or less should everything that a power user role or an user role needs
    7979            to know be included here.
    … …  
    9595        <listitem>
    9696          <para>
    97             Documentation concerning the participation of BASE2 development should be placed
     97            Documentation concerning the participation of BASE development should be placed
    9898            in this part, e.g. coding standards, the java doc from the source code, how
    99             to develop a plugin etc.
     99            to develop a plug-in etc.
    100100          </para>
    101101        </listitem>
    … …  
    108108    <title>Getting started</title>
    109109    <para>
    110       Before writing any documentation in BASE2 there are a couple of things, some
     110      Before writing any documentation in BASE there are a couple of things, some
    111111      rules and standards, to have in mind.
    112112    </para>
    … …  
    244244      <title>Controlling chunking</title>
    245245      <para>
    246         We have configured docbook to create a new subdirectory for each
     246        We have configured docbook to create a new sub-directory for each
    247247        <sgmltag class="starttag">chapter</sgmltag> and a new output file for each
    248248        <sgmltag class="starttag">sect1</sgmltag> tag. In most cases this
    … …  
    281281        attribute that can be used to identify the
    282282        element with. The value must be unique for the entire documentation.
    283         Most of the elements that are used inside the BASE2 documentation do not
     283        Most of the elements that are used inside the BASE documentation do not
    284284        need to have an id if they do not are used in any cross references from other part of
    285285        the text.
    … …  
    356356        tags. These texts will be exported to a XML-file at the same time as the
    357357        HTML-documentation is generated. The generated XML-file is compatible with the help
    358         text importer in BASE2 and will be imported when running the update script or
     358        text importer in BASE and will be imported when running the update script or
    359359        installation script.
    360360      </para>
    … …  
    382382              <para>
    383383                Is used to identify and to find a help text in the web client.
    384                 BASE2's web client already has several IDs to help texts defined,
     384                The BASE web client already has several IDs to help texts defined,
    385385                it could therefore be a good idea to have a look in the
    386386                program to see if there already is an external id to use for the
    … …  
    396396              <para>
    397397                Is directly connected to the name/title property for a help text
    398                 item in BASE2.
     398                item in BASE.
    399399              </para>
    400400            </listitem>
    … …  
    437437          an image or an example, or a link to another chapter or
    438438          section. Put a <sgmltag class="starttag">nohelp</sgmltag>
    439           tag around the problematic part to avoid it from beeing
     439          tag around the problematic part to avoid it from being
    440440          outputted to the help texts.
    441441        </para>     
    … …  
    485485        <filename class="directory">data</filename>
    486486        directory to the BASE-server's file system and then use the help text importer
    487         plugin to import the help text items from that file.
     487        plug-in to import the help text items from that file.
    488488      </para>
    489489     
    … …  
    519519            XsltProc but the compilation will most likely take much much longer time.
    520520            Therefore it's not recommended to be used when generating/compiling the
    521             documentation in BASE 2.
     521            documentation in BASE.
    522522          </para>
    523523        </note>
    … …  
    533533          <command>ant docbook</command>. This documentation is also generated with
    534534          <command>ant dist</command>, which will put the output files in the right location for distribution with
    535           BASE 2.
     535          BASE.
    536536        </para>
    537537      </sect4>
    … …  
    636636            </row>
    637637            <row>
    638               <entry>Fith level section</entry>
     638              <entry>Fifth level section</entry>
    639639              <entry>
    640640                <sgmltag class="starttag">sect5</sgmltag>
    … …  
    674674                  The name of a (Java) class.
    675675                  <sgmltag class="attribute">docapi</sgmltag>-attribute
    676                   can be used to link the class to it's javadoc(only
    677                   html-version). This is done by setting the attribute to the
     676                  can be used to link the class to it's Javadoc (only
     677                  HTML-version). This is done by setting the attribute to the
    678678                  package name of the class, like
    679679                  <synopsis>net.sf.basedb.core</synopsis>
    … …  
    841841        <title>Gui elements</title>
    842842        <para>
    843           Docbook has some elements that can be used to symbolize gui items in a program.
     843          Docbook has some elements that can be used to symbolize GUI items in a program.
    844844          Following list contains the ones that are most common in this document.
    845845        </para>
    … …  
    10571057        <listitem>
    10581058          <simpara>
    1059             The verbatim text is splitted into several lines if the text contains
     1059            The verbatim text is split into several lines if the text contains
    10601060            more then 80 characters. This could give the text an unwanted look and
    1061             it's therefore recommended to manually insert new lines to have controll
     1061            it's therefore recommended to manually insert new lines to have control
    10621062            over layout of the text
    10631063          </simpara>
    … …  
    10651065        <listitem>
    10661066          <simpara>
    1067             We have added support for syntax highlightning of program
     1067            We have added support for syntax highlighting of program
    10681068            examples in the HTML version. To enable it add a
    10691069            <sgmltag class="attribute">language</sgmltag>
    10701070            attribute with one of the following values: <constant>java</constant>,
    1071             <constant>xml</constant> or <constant>sql</constant>. The highlightning engine
     1071            <constant>xml</constant> or <constant>sql</constant>. The highlighting engine
    10721072            support more languages. To add support for those in docbook, change
    1073             the <filename>customized.chunked.xsl</filename> file. The syntax highlightning
     1073            the <filename>customized.chunked.xsl</filename> file. The syntax highlighting
    10741074            engine doesn't handle markup inside the <sgmltag class="starttag">programlisting</sgmltag>
    10751075            tag very well. You should avoid that. By default, java program examples
    … …  
    12701270                <sgmltag class="starttag">xref linkend=""</sgmltag>
    12711271              </entry>
    1272               <entry>Use this to linke to other parts of the document.</entry>
     1272              <entry>Use this to Link to other parts of the document.</entry>
    12731273            </row>
    12741274            <row>
    … …  
    13211321      classes in the Core API. To create the diagrams we use the community edition (version 12.5)
    13221322      of a program called MagicDraw. This is a Java program and it should be possible
    1323       to run it on any platform which has at least a Java 1.5 runtime.
     1323      to run it on any platform which has at least a Java 1.5 run-time.
    13241324      To get more information about MagicDraw and to download the program
    13251325      go to their website:
    … …  
    13391339        Everything in MagicDraw has been organised into packages and
    13401340        modules. At the top we have the <code>Core layer</code> and
    1341         the <code>Data layer</code>. The <code>Java</code> moduled is
     1341        the <code>Data layer</code>. The <code>Java</code> module is
    13421342        for classes that related to the Java programming language, such
    13431343        as <code>Map</code> and <code>Set</code> that are not pre-defined
    … …  
    13611361      <title>Classes</title>
    13621362        <para>
    1363           New classes should be added to one of the subpackages inside
     1363          New classes should be added to one of the sub-packages inside
    13641364          the <code>Data layer/Classes</code> or <code>Core layer/Classes</code>
    13651365          modules. It is very simple:
    … …  
    13691369        <listitem>
    13701370          <para>
    1371           Select the subpackage in the overview and click with the right mouse button.
     1371          Select the sub-package in the overview and click with the right mouse button.
    13721372          </para>
    13731373        </listitem>
    … …  
    14371437
    14381438          <para>
    1439             To achive this we have slightly altered the meaning of some UML symbols.
     1439            To achieve this we have slightly altered the meaning of some UML symbols.
    14401440            For example we use the access modified symbols (+, ~ and -) to indicate
    14411441            if a property is updatable or not.
    … …  
    16911691         
    16921692          <para>
    1693             New diagrams should be added to one of the subpackages inside
     1693            New diagrams should be added to one of the sub-packages inside
    16941694            the <code>Data layer/Diagrams</code> or <code>Core layer/Diagrams</code>
    16951695            modules. It is very simple:
    … …  
    16991699          <listitem>
    17001700            <para>
    1701             Select the subpackage in the overview and click with the right mouse button.
     1701            Select the sub-package in the overview and click with the right mouse button.
    17021702            </para>
    17031703          </listitem>
    … …  
    17441744            <menuchoice><guimenuitem>Symbol properties</guimenuitem></menuchoice>
    17451745            menu item. In the bottom of the
    1746             popup, use the <guilabel>Apply style</guilabel> selection list to select
     1746            pop-up, use the <guilabel>Apply style</guilabel> selection list to select
    17471747            one of the predefined styles.
    17481748          </para>
    … …  
    17571757          <listitem>
    17581758            <para>
    1759             External class: Use this style for related classes that are actaully part of
     1759            External class: Use this style for related classes that are actually part of
    17601760            another diagram. This style will hide all information except the class name.
    17611761            This style can be used for both data layer and core layer classes.
    … …  
    17891789
    17901790    <para>
    1791       Existing Javadoc documentation is available online at:
     1791      Existing Javadoc documentation is available on-line at:
    17921792      <ulink url="http://base.thep.lu.se/chrome/site/doc/api/index.html"
    17931793        >http://base.thep.lu.se/chrome/site/doc/api/index.html</ulink>.
    … …  
    17951795   
    17961796    <para>
    1797       The BASE API is devided into four different parts on the package level.
     1797      The BASE API is divided into four different parts on the package level.
    17981798    </para>
    17991799   
    … …  
    18251825      <para>
    18261826      Mixed Public and Internal API - Contains a mix of public and internal
    1827       classes. Check the javadoc for each class/method before using it.
     1827      classes. Check the Javadoc for each class/method before using it.
    18281828      </para>
    18291829    </listitem>
    … …  
    18381838
    18391839    <sect2 id="javadoc.writing">
    1840       <title>Writing javadoc</title>
     1840      <title>Writing Javadoc</title>
    18411841      <para>
    18421842        This section only covers Javadoc comments, how to write proper none-Javadoc comments
    … …  
    18601860          <listitem>
    18611861            <para>
    1862               General things that are common for all Javadocs comments in Base.
     1862              General things that are common for all Javadoc comments in Base.
    18631863            </para>
    18641864            <itemizedlist>

  • trunk/doc/src/docbook/faq/faqs.xml

    r4477 r4487  
    148148          <question>
    149149            <para>
    150               What it the best way to create an array design in BASE2 when starting
     150              What it the best way to create an array design in BASE when starting
    151151              from a GAL file?
    152152            </para>
    … …  
    331331            <para>
    332332              I have to create pools of samples in my experiment due to scarcity of
    333               the biological material. Can I represent those pooled samples is BASE2?
     333              the biological material. Can I represent those pooled samples is BASE?
    334334            </para>
    335335          </question>
    … …  
    347347          <question>
    348348            <para>
    349               I would like to add a software type in BASE2 but there is no button for
     349              I would like to add a software type in BASE but there is no button for
    350350              doing so. Is it possible?
    351351            </para>
    … …  
    371371            <para>
    372372              Your privileges are not high enough and you have not been granted
    373               permission to create hardware types. Contact your BASE2 administrator.
     373              permission to create hardware types. Contact your BASE administrator.
    374374              For more information about permissions, please refer to
    375375              <xref linkend="user_administration" />.
    … …  
    389389              The most likely explanation is that this particular annotation
    390390              type has been declared as a protocol parameter. This means that it will
    391               only be displayed in BASE2 if you have used a sample creation protocol
     391              only be displayed in BASE if you have used a sample creation protocol
    392392              which uses that parameter.
    393393            </para>
    … …  
    399399            <para>
    400400              I have carried out an experiment using both Affymetrix and Agilent
    401               arrays but I can not select more than one raw data type in BASE2. What
     401              arrays but I can not select more than one raw data type in BASE. What
    402402              should I do?
    403403            </para>
    … …  
    424424          <question>
    425425            <para>
    426               It seems that BASE2 does not support the data files generated by my brand
    427               new scanner. Is it possible to add it to BASE2?
    428             </para>
    429           </question>
    430           <answer>
    431             <para>
    432               Yes it is possible to extend BASE2 so that it can support your system.
    433               You will need to define a new raw data type for BASE2 by modifying
     426              It seems that BASE does not support the data files generated by my brand
     427              new scanner. Is it possible to add it to BASE?
     428            </para>
     429          </question>
     430          <answer>
     431            <para>
     432              Yes it is possible to extend BASE so that it can support your system.
     433              You will need to define a new raw data type for BASE by modifying
    434434              the <filename>raw-datatypes.xml</filename> configuration file.
    435435            </para>
    … …  
    460460          <answer>
    461461            <para>
    462               This is normal. BASE2 deals with Affymetrix data files differently. BASE2
     462              This is normal. BASE deals with Affymetrix data files differently. BASE
    463463              stores native Affymetrix file and does not load the value in tables as
    464464              it does for other platforms. See <xref linkend="experiments_analysis.rawbioassay.rawdata" />
    … …  
    488488        <qandaentry>
    489489          <question>
    490             <para>Are Affymetrix CDT and CAB files supported by BASE2?</para>
     490            <para>Are Affymetrix CDT and CAB files supported by BASE?</para>
    491491          </question>
    492492          <answer>
    … …  
    526526        <qandaentry>
    527527          <question>
    528             <para>Are Illumina data files supported by BASE2 ?</para>
     528            <para>Are Illumina data files supported by BASE?</para>
    529529          </question>
    530530          <answer>
    … …  
    584584            <para>
    585585              I am asked by reviewers to deposit my microarray data in a public
    586               repository. How can BASE2 help me?
    587             </para>
    588           </question>
    589           <answer>
    590             <para>
    591               The BASE2 development team are working on a plug-in
     586              repository. How can BASE help me?
     587            </para>
     588          </question>
     589          <answer>
     590            <para>
     591              The BASE development team are working on a plug-in
    592592              that produces a Tab2Mage file accepted by ArrayExpress.
    593593              For the plug-in to work properly, a series of rules need to be
    … …  
    662662              compliance depends very much on the kind of annotation you have
    663663              supplied. Please refer to the previous question for more information
    664               about how to check for MIAME compliance in BASE2 using the Experiment
     664              about how to check for MIAME compliance in BASE using the Experiment
    665665              overview function.
    666666            </para>
    … …  
    671671          <question>
    672672            <para>
    673               I have deleted the data files from BASE2 file systems since I have
     673              I have deleted the data files from BASE file system since I have
    674674              imported them in tables. So I do not have data files to send to
    675675              ArrayExpress anymore.
    … …  
    691691          <question>
    692692            <para>
    693               I have created pooled samples in BASE2. Can I export in Tab2Mage format?
     693              I have created pooled samples in BASE. Can I export in Tab2Mage format?
    694694            </para>
    695695          </question>
    … …  
    730730          <question>
    731731            <para>
    732               OK, I have uploaded 40 CEL files in BASE2 but are there any tool to
     732              OK, I have uploaded 40 CEL files in BASE but are there any tool to
    733733              perform normalisation on Affymetrix raw data?
    734734            </para>
    … …  
    736736          <answer>
    737737            <para>
    738               Yes, there is. BASE2 team has created a plug-in based on
     738              Yes, there is. BASE team has created a plug-in based on
    739739              <ulink url="http://rmaexpress.bmbolstad.com/">
    740740              RMAExpress methods from Bolstad and Irizarry</ulink> so you can normalise

  • trunk/doc/src/docbook/index.xml

    r4477 r4487  
    3131    <pubdate/>
    3232  </bookinfo>
    33   <title>BASE2 Documentation</title>
     33  <title>BASE Documentation</title>
    3434  <include file="overviewdoc/index.xml"/>
    3535  <include file="userdoc/index.xml"/>

  • trunk/doc/src/docbook/overviewdoc/base_overview.xml

    r4477 r4487  
    2929<chapter id="base_overview">
    3030  <?dbhtml dir="overview"?>
    31   <title>Overview of BASE2</title>
     31  <title>Overview of BASE</title>
    3232    <sect1 id="nolabelhereyet2">
    3333      <title></title>

  • trunk/doc/src/docbook/overviewdoc/resources.xml

    r4477 r4487  
    3131  <title>Resources</title>
    3232  <para>
    33     There are several resources available for those who are using BASE 2 or have some other
    34     kind of interested in the BASE 2 project. This chapter contains information about those
    35     resources and also some short instructions on how to use each
    36     one of them.
     33    There are several resources available for those who are using BASE
     34    or have some other kind of interested in the BASE project. This
     35    chapter contains information about those resources and also some
     36    short instructions on how to use each one of them.
    3737  </para>
    3838  <sect1 id="resources.home_page">
    … …  
    5252        <guilabel><ulink url='http://base.thep.lu.se/wiki/DownloadPage'
    5353          >Download Page</ulink></guilabel>.
    54         From this page you can download BASE 2 releases as packaged tar.gz
     54        From this page you can download BASE releases as packaged tar.gz
    5555        files or checkout the source code directly from the Subversion repository.
    5656        See the separate parts on the web page to get more information how to
    … …  
    5959        <variablelist>
    6060          <varlistentry>
    61             <term>Packaged BASE 2 releases</term>
     61            <term>Packaged BASE releases</term>
    6262            <listitem>
    6363              <para>
    … …  
    113113        implemented. To show the list of outstanding tickets use the
    114114        <guibutton><ulink url="http://base.thep.lu.se/query"
    115           >View Tickets</ulink></guibutton> button on BASE 2's home-page.
     115          >View Tickets</ulink></guibutton> button on BASE web site.
    116116        It is a good idea to have a look at this list before reporting a bug
    117117        or requesting a new feature. Perhaps someone has registered the issue as a ticket
    118         already. This list can also be used to see how the BASE 2 development is proceeding
     118        already. This list can also be used to see how the BASE development is proceeding
    119119        and when some particular request is planned to be fixed.
    120120      </para>
    … …  
    132132
    133133      <para>
    134         The roadmap of BASE 2 is accessed from the
     134        The roadmap of BASE is accessed from the
    135135        <guibutton><ulink url="http://base.thep.lu.se/roadmap"
    136136          >Roadmap</ulink></guibutton> button on the home page. This page
    … …  
    175175              <para>
    176176                Information for those who are interested to be involved in the
    177                 development of BASE 2.
     177                development of BASE.
    178178              </para>
    179179            </listitem>
    … …  
    203203        a page that lists the core plug-ins</ulink>.
    204204      All plug-ins that are included in the installation of
    205       BASE 2 are listed on this page, some together with one or several examples of suitable
     205      BASE are listed on this page, some together with one or several examples of suitable
    206206      configuration files. These configuration files can be downloaded and imported with the
    207       plug-in configuration importer in BASE 2.
     207      plug-in configuration importer in BASE.
    208208    </para>
    209209  </sect1>
    … …  
    211211    <title>BASE plug-ins site</title>
    212212    <para>
    213       Plug-ins which are not included in the installation of BASE 2, have their own site,
     213      Plug-ins which are not included in the installation of BASE, have their own site,
    214214      called
    215215      <ulink url="http://baseplugins.thep.lu.se/">BASE plug-ins web site</ulink>
    … …  
    224224    <title>Demo server</title>
    225225    <para>
    226       There is a demo server up running for anyone who wants to explore BASE 2 without having
    227       to install it. Follow the link on BASE 2's home page to the demo server or go directly
    228       to
     226      There is a demo server up running for anyone who wants to
     227      explore BASE without having to install it. Follow the link on
     228      BASE web site to the demo server or go directly to
    229229      <ulink url="http://base2.thep.lu.se/demo/">
    230230        http://base2.thep.lu.se/demo/
    … …  
    269269    <title>IRC channel</title>
    270270    <para>
    271       There is an irc channel on the FreeNode network where real-time BASE
     271      There is an IRC channel on the FreeNode network where real-time BASE
    272272      discussion can take place twentyfour-seven. Use
    273273      <userinput>#basedb</userinput>

  • trunk/doc/src/docbook/overviewdoc/why_base.xml

    r4477 r4487  
    2929<chapter id="why_base">
    3030  <?dbhtml dir="why_base"?>
    31   <title>Why use BASE2</title>
     31  <title>Why use BASE</title>
    3232    <sect1 id="nolabelhereyet">
    3333      <title></title>

  • trunk/doc/src/docbook/userdoc/annotations.xml

    r4477 r4487  
    3737      title="Annotation types">
    3838    <para>
    39       BASE2 has been engineered to closely map the
     39      BASE has been engineered to closely map the
    4040      <ulink
    4141        url="http://www.mged.org/Workgroups/MIAME/miame.html">
    … …  
    4343      However, since MIAME is focused on microarray processing
    4444      workflow, information about the description biological
    45       samples themselves was left out. BASE2 users are free to
    46       annotate biomaterials (and most BASE2 items) as they wish,
     45      samples themselves was left out. BASE users are free to
     46      annotate biomaterials (and most BASE items) as they wish,
    4747      from basic free text description to more advanced ontology
    48       based terms. To accomodate the annotation needs of users
     48      based terms. To accommodate the annotation needs of users
    4949      eager with detailed sample annotations and also the needs of
    50       very different communities, BASE2 provides a mechanism that
    51       allows a high level of annotation customization. BASE2
     50      very different communities, BASE provides a mechanism that
     51      allows a high level of annotation customization. BASE
    5252      allows to create descriptive elements for both quantitative
    5353      annotation and qualitative annotation of Biomaterials via
    5454      the <emphasis>Annotation Type mechanism</emphasis>.
    5555      Actually, annotation types can be used to annotate not
    56       only <emphasis>Biomaterials</emphasis> but almost all BASE2 items, from
     56      only <emphasis>Biomaterials</emphasis> but almost all BASE items, from
    5757      <emphasis>Plates</emphasis>
    5858      to
    … …  
    9999        have a maximum length of 255 characters and can have an attached
    100100        list of predefined value. <guilabel>Text</guilabel>
    101         annotation types have no practival limit and are always
     101        annotation types have no practical limit and are always
    102102        free-text.
    103103      </para>
    … …  
    138138    <para>
    139139      The <guilabel>Edit annotation type</guilabel> window is opened in a
    140       popup. It contains four different tabs.
     140      pop-up. It contains four different tabs.
    141141    </para>
    142142 
    … …  
    310310                navigated especially when the
    311311                number of possible values is
    312                 large, and because selectionlist
     312                large, and because selection-list
    313313                and drop-down list allow use of
    314314                arrow and tab for selection.
    … …  
    585585        <listitem>
    586586          <para>
    587           <guilabel>all</guilabel>: Display all annotatation types
     587          <guilabel>all</guilabel>: Display all annotation types
    588588          </para>
    589589        </listitem>
    … …  
    701701        BASE includes a plug-in for importing annotations to multiple items
    702702        in one go. The plug-in read annotation values from a simple column-based
    703         text file. Ususally, a tab is used as the delimiter between columns.
     703        text file. Usually, a tab is used as the delimiter between columns.
    704704        The first row should contain the column headers. One column should contain
    705705        the name or the external ID of the item. The rest of the columns can each be

  • trunk/doc/src/docbook/userdoc/biomaterials.xml

    r4477 r4487  
    3434      The generic term biomaterial refers to any biological material used in an experiment.
    3535      biomaterials are subdivided in 4 components, biosource, sample, extract and labeled
    36       extract. The order use in presenting those entities is not inocuous as it represents the
     36      extract. The order used in presenting those entities is not innocuous as it represents the
    3737      sequence of transformation a source material undergoes until it is in a state compatible
    3838      with the realization of a microarray hybridization. This progression is actually
    39       mimicked in the BASE2
     39      mimicked in the BASE
    4040      <guimenu>View</guimenu>
    4141      menu again to insist on this natural progression.
    … …  
    5050      <listitem>
    5151        <simpara>
    52           Samples are central to BASE2 to describe the sample processing. So samples can
     52          Samples are central to BASE to describe the sample processing. So samples can
    5353          be created from other samples if user want to track sample processing event in a
    5454          finely granular fashion.
    … …  
    7070    </itemizedlist>
    7171    <para>
    72       BASE2 allows users to create any of the these entities fairly freely, however it is
     72      BASE allows users to create any of the these entities fairly freely, however it is
    7373      expected that users will follow the natural path of the laboratory workflow.
    7474    </para>
    … …  
    9797            <listitem>
    9898              <para>
    99                 This is the only mandatory field. BASE2 by default assigns
     99                This is the only mandatory field. BASE by default assigns
    100100                <replaceable>New biosource</replaceable>
    101101                as name but it is advised to provide unique sensible names.
    … …  
    138138        <title>Annotations</title>
    139139        <para>
    140           This allows BASE2 users to use annotation types to refine biosource description.
     140          This allows BASE users to use annotation types to refine biosource description.
    141141          More about annotating items can be read in
    142142          <xref linkend="annotations.annotating" />
    … …  
    156156    <para>
    157157      For every step of transformation from biosource to sample, it is possible to provide
    158       information about the protocol used to perform this task. It is not enforced in BASE2
     158      information about the protocol used to perform this task. It is not enforced in BASE
    159159      but it should serve as guidance when devising the granularity of the sample processing
    160160      task. Also, it is good practice to provide protocol information to ensure MIAME
    … …  
    222222              <listitem>
    223223                <para>
    224                   The sample's name(required). BASE2 by default assigns names to
     224                  The sample's name(required). BASE by default assigns names to
    225225                  samples (by suffixing
    226226                  <replaceable>s#</replaceable>
    … …  
    269269              </term>
    270270              <listitem>
    271                 <para>The date at which the sample was entered in BASE2.</para>
     271                <para>The date at which the sample was entered in BASE.</para>
    272272              </listitem>
    273273            </varlistentry>
    … …  
    309309        <helptext external_id="sample.parents" title="Sample's parents">
    310310          <para>
    311             This is meant to keep track of the sample origin. BASE2 distinguished
    312             between 2 cases which are controled by the
     311            This is meant to keep track of the sample origin. BASE
     312            distinguished between two cases which are controlled by the
    313313            <guilabel>Pooled</guilabel>
    314314            radio-button in the edit pop-up window.
    … …  
    353353        <para>
    354354          This tab contains a list of those annotations that are inherited from the
    355           sample's parents. Information about working with innherited annotations can be
     355          sample's parents. Information about working with inherited annotations can be
    356356          found in
    357357          <xref linkend="annotations.inheriting" />
    … …  
    372372    <para>
    373373      During the transformation from samples to extracts, it is possible to provide
    374       information about the protocol used to perform this task. It is not enforced in BASE2
     374      information about the protocol used to perform this task. It is not enforced in BASE
    375375      but it should serve as guidance when devising the granularity of the sample processing
    376376      task. Also, it is good practice to provide protocol information.
    … …  
    433433              <listitem>
    434434                <para>
    435                   A mandatory field for providing the extract's name. BASE2 by
     435                  A mandatory field for providing the extract name. BASE by
    436436                  default assigns names to extract (by suffixing
    437437                  <replaceable>e#</replaceable>
    … …  
    480480                <para>
    481481                  This is automatically populated with a date at which the sample
    482                   was entered in BASE2 system.
     482                  was entered in BASE system.
    483483                </para>
    484484              </listitem>
    … …  
    524524        <helptext external_id="extract.parents" title="Extract's parents">
    525525          <para>
    526             This important tab allows users to select the extract origin. BASE2
    527             distinguished between 2 cases which are controled by the
     526            This important tab allows users to select the extract
     527            origin. BASE distinguished between two cases which are
     528            controlled by the
    528529            <guilabel>Pooled</guilabel>
    529530            radio-button.
    … …  
    566567        <para>
    567568          This tab contains a list of those annotations that are inherited from the
    568           extract's parents. Information about working with innherited annotations can be
     569          extract parents. Information about working with inherited annotations can be
    569570          found in
    570571          <xref linkend="annotations.inheriting" />
    … …  
    579580    <para>
    580581      Before attempting to create labeled extracts, users should make sure that the
    581       appropriate label object is present in BASE2. To browse the list of labels, go to
     582      appropriate label object is present in BASE. To browse the list of labels, go to
    582583      <menuchoice>
    583584        <guimenu>View</guimenu>
    … …  
    628629    <para>
    629630      During the transformation from extracts to labeled extracts, it is possible to provide
    630       information about the protocol used to perform this task. It is not enforced in BASE2
     631      information about the protocol used to perform this task. It is not enforced in BASE
    631632      but it should serve as guidance when devising the granularity of the extract processing
    632633      task. Also, it is good practice to provide protocol information.
    … …  
    709710            <listitem>
    710711              <para>
    711                 The name of the labeled extract (required). BASE2 by default assigns
     712                The name of the labeled extract (required). BASE by default assigns
    712713                names to labeled extract(by suffixing
    713714                <replaceable>lbe#</replaceable>
    … …  
    759760          <varlistentry>
    760761            <term>
    761               <guilabel>Registred</guilabel>
     762              <guilabel>Registered</guilabel>
    762763            </term>
    763764            <listitem>
    764765              <para>
    765766                This is automatically populated with a date at which the labeled
    766                 extract was actually entered in BASE2 system.
     767                extract was actually entered in BASE system.
    767768              </para>
    768769            </listitem>
    … …  
    805806        <title>Parents</title>
    806807        <para>
    807           This important tab allows users to select the labeled extract origin. BASE2
    808           distinguished between 2 cases which are controled by the
     808          This important tab allows users to select the labeled
     809          extract origin. BASE distinguished between two cases which
     810          are controlled by the
    809811          <guilabel>Pooled</guilabel>
    810812          radio-button.
    … …  
    855857        <para>
    856858          This tab contains a list of those annotations that are inherited from the
    857           parents of the labeled extract. Information about dealing with innherited
     859          parents of the labeled extract. Information about dealing with inherited
    858860          annotations can be found in
    859861          <xref linkend="annotations.inheriting" />
    … …  
    872874      <menuchoice>
    873875        <guimenu>View</guimenu>
    874         <guimenuitem>Hybridizatons</guimenuitem>
     876        <guimenuitem>Hybridizations</guimenuitem>
    875877      </menuchoice>
    876878      to get to the hybridizations.
    … …  
    879881      <title>Creating hybridizations</title>
    880882      <para>
    881         In BASE2, there are 2 possible routes to create an hybridization object except the
     883        In BASE, there are two possible routes to create an hybridization object except the
    882884        common way with the &gbNew; button at hybridization list page.
    883885      </para>
    … …  
    892894            <para>
    893895              Click on the
    894               <guibutton>New hybridzation&hellip;</guibutton>
     896              <guibutton>New hybridization&hellip;</guibutton>
    895897              from the toolbar of labeled extract list view.
    896898            </para>
    … …  
    936938              <para>
    937939                <replaceable>New hybridization</replaceable>
    938                 is BASE2 default name but it is strongly advise to provide a
     940                is the BASE default name but it is strongly advise to provide a
    939941                meaningful and unique name (required).
    940942              </para>
    … …  
    975977              <para>
    976978                This field is automatically populated with a date at which the
    977                 hybridization was entered in BASE2 system.
     979                hybridization was entered in BASE system.
    978980              </para>
    979981            </listitem>
    … …  
    10781080        <para>
    10791081          This tab contains a list of those annotations that are inherited from the
    1080           labeled extracts. Information about dealing with innherited annotations can be
     1082          labeled extracts. Information about dealing with inherited annotations can be
    10811083          found in
    10821084          <xref linkend="annotations.inheriting" />

  • trunk/doc/src/docbook/userdoc/experiments.xml

    r4477 r4487  
    167167              The date the article was published. Use the
    168168              <guibutton>Calendar</guibutton> button to select
    169               a date from a popup window.
     169              a date from a pop-up window.
    170170            </para>
    171171          </listitem>
    … …  
    457457              you have specified values for optional items.
    458458              For example, there is an option that warns you if
    459               you hav not specified a protocol.
     459              you have not specified a protocol.
    460460              </para>
    461461            </listitem>
    … …  
    710710     
    711711    <para>
    712       BASE2 has been engineered to closely map the MIAME
    713       concepts and a number of BASE2 entities can be mapped
     712      BASE has been engineered to closely map the MIAME
     713      concepts and a number of BASE entities can be mapped
    714714      directly to Tab2Mage elements. However, since MIAME is
    715715      focused on microarray processing workflow, information
    716716      about the biological sample is down to the user. To
    717       accomodate the annotation needs of users, BASE2 provides
     717      accommodate the annotation needs of users, BASE provides
    718718      a mechanism that allows annotation customization to meet
    719719      user specific requirements. BASE allows to create
    … …  
    723723
    724724    <para>
    725       BASE2 can export an experiment to Tab2Mage
     725      BASE can export an experiment to Tab2Mage
    726726      format thanks to a dedicated export plug-in.
    727727      For the plug-in to work, it is important to understand that
    … …  
    747747      <warning>
    748748        <para>
    749           All BASE2 Annotation Types used to annotate at
     749          All BASE Annotation Types used to annotate at
    750750          the level of <emphasis>Sample</emphasis> and
    751751          <emphasis>Extract</emphasis> items will
    … …  
    759759          In the context of data exchange between BASE
    760760          instances, the export function can be altered to
    761           allow attachement of annotations to items
     761          allow attachment of annotations to items
    762762          other than biosources, therefore avoiding loss of
    763763          information.
    … …  
    769769      <title>Annotation units</title>
    770770      <para>
    771         To associate units to BASE2 annotation types and
     771        To associate units to BASE annotation types and
    772772        remain compatible with Tab2Mage specifications,
    773773        users need to adhere to the following convention:
    … …  
    806806     
    807807      <para>
    808         In BASE2 terms, Tab2Mage elements such as
     808        In BASE terms, Tab2Mage elements such as
    809809        <emphasis>BioMaterialCharacteristics</emphasis>,
    810810        <emphasis>Parameter</emphasis> or
    … …  
    850850        Variables</emphasis> when submitting data to ArrayExpress
    851851        (provided the study is an intervention study).
    852         Therefore, BASE2 users willing to use the Tab2Mage
     852        Therefore, BASE users willing to use the Tab2Mage
    853853        export function will have to declare <emphasis>Experimental
    854854        Factors</emphasis> using the the <guilabel>Experimental Factor</guilabel>

  • trunk/doc/src/docbook/userdoc/file_system.xml

    r4477 r4487  
    3333    <title>File system</title>
    3434    <para>
    35       Files in BASE 2 are managed from the page at
     35      Files in BASE are managed from the page at
    3636      <menuchoice>
    3737        <guimenu>View</guimenu>
    3838        <guimenuitem>Files</guimenuitem>
    3939      </menuchoice>. The basic layout on the page is the same as for all the other list pages
    40       in BASE 2 but
     40      in BASE but
    4141      there are some differences e.g. there is a navigation tree to the left, used to browse
    4242      the directory structure, and there are some buttons in the toolbar, that are special for
    … …  
    104104        </term>
    105105        <listitem>
    106           <para>Shows the full BASE 2 path to current directory.</para>
     106          <para>Shows the full BASE path to current directory.</para>
    107107        </listitem>
    108108      </varlistentry>
    … …  
    147147            <title>Replace an existing file</title>
    148148            <para>
    149               It is possible to re-upload file that are online, but this
     149              It is possible to re-upload file that are on-line, but this
    150150              has to be done from the single-item view.
    151151            </para>
    … …  
    158158      <title>Browse the file system</title>
    159159      <para>
    160         Browsing thr BASE 2 file system is done from the navigation bar by clicking on a
     160        Browsing the BASE file system is done from the navigation bar by clicking on a
    161161        directory in the tree to view it's contents. Both sub directories and files in the
    162162        selected directory are showed. A directory with sub directories can be expand with a
    … …  
    206206      <title>Disk space quota</title>
    207207      <para>
    208         Normally, a user is assigned limited disk spacefor files.
     208        Normally, a user is assigned limited disk space for files.
    209209        More information about how much quota the current account has and how much of it
    210210        that is occupied can be found at the account's home page, described in
    … …  
    380380                        Mark this checkbox if the compressed file should
    381381                        be unpacked after it had been uploaded. The
    382                         files will be unpacked with the same subdirectory
     382                        files will be unpacked with the same sub-directory
    383383                        structure as in the compressed file.
    384384                      </para>
    … …  
    588588        <para>
    589589          Choose a directory which the selected items should be moved to. It
    590           is possible to create new subdirectories with the
     590          is possible to create new sub-directories with the
    591591          &gbNew; button.
    592592        </para>
    … …  
    816816              <varlistentry>
    817817                <term>
    818                   <guilabel>Share new files and subdirectories automatically</guilabel>
     818                  <guilabel>Share new files and sub-directories automatically</guilabel>
    819819                </term>
    820820                <listitem>
    … …  
    886886    <title>File types</title>
    887887    <para>
    888       A file can be associated with one of the file types that exists in BASE 2. File types
     888      A file can be associated with one of the file types that exists in BASE. File types
    889889      make it possible to filter the files depending of what kind of file it is. Here
    890890      is a list of file types that are defined in BASE.

  • trunk/doc/src/docbook/userdoc/hardware.xml

    r4477 r4487  
    4242      <para>
    4343        <guilabel>Hardware Type</guilabel>
    44         allows classification of hardwares based on their usage
    45         and purpose in the laboratory workflow. By default, BASE2
     44        allows classification of hardware based on their usage
     45        and purpose in the laboratory workflow. By default, BASE
    4646        creates the 3 main hardware types and
    4747        those correspond to the main hardware families
    … …  
    120120   
    121121    <para>
    122       In BASE, hardware can be created by 2 routes. Either
     122      In BASE, hardware can be created by two routes. Either
    123123      from the single-item view of a hardware type or from the
    124124      list view of hardware.

  • trunk/doc/src/docbook/userdoc/overview.xml

    r4484 r4487  
    3030  <?dbhtml dir="overview"?>
    3131  <title>Overview of user documentation</title>
    32   <para> The 'User documentation' part is quite extensive and covers everything from how to login on
    33     a BASE2 server and find your way through the program, to working with experiments and doing some
     32  <para> The 'User documentation' part is quite extensive and covers everything from how to Log in on
     33    a BASE server and find your way through the program, to working with experiments and doing some
    3434    useful analysis. The intention with this chapter is to give an overview of the following chapters
    3535    so it will be easier for you to know where to look for certain information in case you don't want
    … …  
    5151      The second subsection,
    5252      <xref linkend="webclient.configuration" />
    53       , describes how to personlize BASE with contact information, preferences and changing password.
     53      , describes how to personalize BASE with contact information, preferences and changing password.
    5454      The preferences are for instance some appearance like date format, text size or the look of the
    5555      toolbar buttons.
    … …  
    6060      and
    6161      <xref linkend="webclient.itemlist" />
    62       , in the webclient chapter explains how to work with BASE. No matter what you are going to do the
     62      , in the web client chapter explains how to work with BASE. No matter what you are going to do the
    6363      user interface contains a lot of common functions that works the same everywhere. For example,
    6464      how to list and search for items, how to create new items and modify and delete existing items.
    … …  
    8383      The next thing to do is to add some relevant data to work with. Most of the different items can
    8484      be created manually from the web client, but some items and data must be imported from files.
    85       Before importing a file, it has to be uploaded on the BASE-server's filesystem.
     85      Before importing a file, it has to be uploaded on the BASE-server's file system.
    8686      <xref linkend="file_system" />
    8787      gives you information about the server's file system and how to upload the files.
    … …  
    240240        </orderedlist>
    241241        <para>
    242           This concludes the short step-by-step get going text. Far from all functionallity in BASE
    243           has been convered here. E.g. nothing about LIMS or biomaterials have been mentioned. But you
     242          This concludes the short step-by-step get going text. Far from all functionality in BASE
     243          has been covered here. E.g. nothing about LIMS or biomaterials have been mentioned. But you
    244244          should now at least be familiar with getting to that point when it is possible to do some
    245245          analysis.

  • trunk/doc/src/docbook/userdoc/protocols.xml

    r4477 r4487  
    3131  <para>
    3232    Information about laboratory standard operating procedure
    33     and protocols can be tracked in BASE2 using two structures,
     33    and protocols can be tracked in BASE using two structures,
    3434    the use of which is detailed in the following sections.
    3535  </para>
    … …  
    4343        allows classification of protocols based on their
    4444        usage and purpose in the laboratory workflow. By
    45         default, BASE2 creates the 8 main pProtocol types and
     45        default, BASE creates the 8 main Protocol types and
    4646        those correspond to the main protocol families
    4747        identified by MIAME requirements and applied in a
    … …  
    6262        instance DNA binding site identification, imposes
    6363        the creation of new protocol type in addition to
    64         those built-in in BASE2.
     64        those built-in in BASE.
    6565      </para>
    6666      <tip>
    … …  
    124124    <title>Protocols</title>
    125125    <para>
    126       In BASE, protocols can be created by 2 routes. Either
     126      In BASE, protocols can be created by two routes. Either
    127127      from the single-item view of a protocol type or from the
    128128      list view of protocols.
    … …  
    243243          <listitem>
    244244            <para>
    245             Use this button to open a popup where you can select
     245            Use this button to open a pop-up where you can select
    246246            annotation type to use for parameters. The list only
    247247            shows annotations types which has the

  • trunk/doc/src/docbook/userdoc/reporters.xml

    r4477 r4487  
    4343    </para>
    4444    <para>
    45       In BASE2, reporters also refer to Affymetrix Probeset ID but
     45      In BASE, reporters also refer to Affymetrix Probeset ID but
    4646      reporters can be used to describe genes, transcripts, exons
    4747      or any other sequence entity of biological relevance.
    … …  
    135135        Reporters are used to represent genes, transcripts,
    136136        exons and therefore come in their thousands. To solve
    137         this problem, BASE2 relies on
     137        this problem, BASE relies on
    138138        <emphasis>Reporter import plug-ins</emphasis>.
    139139        Those need to be specifically configured to deal with
    … …  
    152152          As for any other plug-in, configuration parameters
    153153          can be saved as an XML file and exchanged with
    154           another BASE2 instance, thereby reducing
    155           configuration burden (provided the 2 instances have
     154          another BASE instance, thereby reducing
     155          configuration burden (provided the two instances have
    156156          identical <filename>extended-properties.xml</filename> files).
    157157          See <xref linkend="resources.coreplugins" /> for information
    … …  
    163163        <title>Dealing with Affymetrix probesets</title>
    164164        <para>
    165         In BASE2, Affymetrix probesets should be treated as reporters.
     165        In BASE, Affymetrix probesets should be treated as reporters.
    166166        The probeset ID could be stored in both the
    167167        <guilabel>Name</guilabel> and the <guilabel>External ID</guilabel>
    … …  
    304304                is linked to the <ulink
    305305                  url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene"
    306                   >Unigene database at NCBI</ulink>.
     306                  >UniGene database at NCBI</ulink>.
    307307              </para>
    308308            </note>
    … …  
    369369    <title>Reporter lists</title>
    370370    <para>
    371       BASE2 allows for defining sets of reporters for a
     371      BASE allows for defining sets of reporters for a
    372372      particular use, for instance to define a list of
    373       reporters to be used on an array. There are 2 ways to do
     373      reporters to be used on an array. There are two ways to do
    374374      so:
    375375    </para>

  • trunk/doc/src/docbook/userdoc/webclient.xml

    r4477 r4487  
    4747       
    4848        <para>
    49           You may, for example, try the BASE 2 demo server. Go to the
     49          You may, for example, try the BASE demo server. Go to the
    5050          URL <ulink url="http://base2.thep.lu.se:8080/demo/">http://base2.thep.lu.se:8080/demo/</ulink>
    5151          and enter <userinput>base2</userinput> for the login and <userinput>base2</userinput>
    … …  
    184184          Most of the menu is in two levels, ie. clicking on a top-level menu
    185185          will open a submenu just below it. Clicking on something in the
    186           submenu will take you to another page or open a popup dialog window.
     186          submenu will take you to another page or open a pop-up dialog window.
    187187          For example, the
    188188          <menuchoice><guimenu>View</guimenu><guimenuitem>Samples</guimenuitem></menuchoice>
    … …  
    285285            <para>
    286286            Displays the name of the currently logged in user and allows
    287             you to quickly logout and switch to another user.
     287            you to quickly log out and switch to another user.
    288288            </para>
    289289          </listitem>
    … …  
    302302          <varlistentry>
    303303            <term>
    304               Online context-sensitive help
     304              On-line context-sensitive help
    305305            </term>
    306306            <listitem>
    … …  
    315315              click it to get help about the part of the page
    316316              you are currently viewing. The icon is located in the title
    317               bar in most popup dialog windows and in the toolbar in most
     317              bar in most pop-up dialog windows and in the toolbar in most
    318318              other pages.
    319319              </para>
    … …  
    328328              <para>
    329329              The <menuchoice><guimenu>Help</guimenu></menuchoice> menu
    330               contains links for getting online help. These links
     330              contains links for getting on-line help. These links
    331331              may be configured by a server administrator, so they may be
    332332              different from server to server. By default links for reporting
    … …  
    495495            The look of the
    496496            <guilabel>Other information</guilabel>
    497             tab can differe abit between different servers, depending on what settings
    498             the server is installed with. There are three inputs in a fresh BASE2
     497            tab can differ a bit between different servers, depending on what settings
     498            the server is installed with. There are three inputs in a fresh BASE
    499499            installation but it is only the
    500500            <guilabel>Description</guilabel>
    501             textarea that is static, the others can be removed or more fields can be
     501            text area that is static, the others can be removed or more fields can be
    502502            added (managed by the server administrator). The three fields, included in a
    503             the BASE2 installation, are
     503            the BASE installation, are
    504504            <variablelist>
    505505              <varlistentry>
    … …  
    516516                </term>
    517517                <listitem>
    518                   <para>Your skype contact information(Optional).</para>
     518                  <para>Your Skype contact information(Optional).</para>
    519519                </listitem>
    520520              </varlistentry>
    … …  
    645645              <listitem>
    646646                <para>
    647                 The scale factor affects the size of popup windows.
     647                The scale factor affects the size of pop-up windows.
    648648                This setting exists because different browsers render
    649                 pages differently. If you often find that popup windows
     649                pages differently. If you often find that pop-up windows
    650650                are too small you can change this setting to make them
    651651                bigger.
    … …  
    682682                experiments. The default setting is blue-black-yellow.
    683683                The list of presets contains other useful color combinations
    684                 (for example, the BASE 1 red-yellow-green) and the most
     684                (for example, the BASE version 1 red-yellow-green) and the most
    685685                recently used color combinations.
    686686                </para>
    … …  
    950950            <para>
    951951            This view is used for editing the information
    952             about a single item. It is always displayed as a popup window.
     952            about a single item. It is always displayed as a pop-up window.
    953953            </para>
    954954          </listitem>
    … …  
    965965          page. Here you will find a &gbNew; button in the
    966966          toolbar. The button is disabled if you do not have permission to create new experiments.
    967           Otherwise, click on it and enter any required information in the popup dialog.
     967          Otherwise, click on it and enter any required information in the pop-up dialog.
    968968          Sometimes there are multiple tabs in this dialog. In the case of experiments
    969969          there are three tabs: <guilabel>Experiment</guilabel>, <guilabel>Publication</guilabel>
    … …  
    10431043        <para>
    10441044          On all single-item views there is an &gbEdit;
    1045           button in the toolbar that opens a popup dialog for editing the properties
     1045          button in the toolbar that opens a pop-up dialog for editing the properties
    10461046          of the item. This button is disabled if the logged in user does not have
    10471047          write permission for the item.
    … …  
    10491049       
    10501050        <para>
    1051           You can also open the edit popup in most other places where
     1051          You can also open the edit pop-up in most other places where
    10521052          the item appears, for example, in lists or the single-item view
    10531053          of a related item. Press and hold one of the <keycap>CTRL</keycap>,
    10541054          <keycap>ALT</keycap> or <keycap>SHIFT</keycap> keys while clicking
    1055           on the link and the edit window will open in a popup.
     1055          on the link and the edit window will open in a pop-up.
    10561056          If you do not have write permission
    1057           on the item there is no meaning to open the edit popup and you will
     1057          on the item there is no meaning to open the edit pop-up and you will
    10581058          be taken to the single-item view page instead.
    10591059        </para>
    … …  
    12411241              <listitem>
    12421242                <para>
    1243                 Opens a popup window that allows you to select
    1244                 users to share the items to. In the popup window, mark
     1243                Opens a pop-up window that allows you to select
     1244                users to share the items to. In the pop-up window, mark
    12451245                one or more users and click on the &gbOk;
    1246                 button. The popup window will only list users that you have
     1246                button. The pop-up window will only list users that you have
    12471247                permission to read. Unless you are an administrator, this
    12481248                usually means that you can only see users that:
    … …  
    12741274              <listitem>
    12751275                <para>
    1276                 Opens a popup window that allows you to select
    1277                 groups to share the items to. In the popup window, mark
     1276                Opens a pop-up window that allows you to select
     1277                groups to share the items to. In the pop-up window, mark
    12781278                one or more groups and click on the &gbOk;
    1279                 button. Unless you are an administrator, the popup window
     1279                button. Unless you are an administrator, the pop-up window
    12801280                will only list groups where you are a member. It will not list
    12811281                groups that already have access to the items.
    … …  
    12881288              <listitem>
    12891289                <para>
    1290                 Opens a popup window that allows you to select
    1291                 projects to share the items to. In the popup window, mark
     1290                Opens a pop-up window that allows you to select
     1291                projects to share the items to. In the pop-up window, mark
    12921292                one or more projects and click on the &gbOk;
    1293                 button. Unless you are an administrator, the popup window
     1293                button. Unless you are an administrator, the pop-up window
    12941294                will only list projects where you are a member. It will not list
    12951295                projects that already have access to the items.
    … …  
    13091309           
    13101310            <varlistentry>
    1311               <term><guilabel>Apply permissions to all subdirectories and their files</guilabel></term>
     1311              <term><guilabel>Apply permissions to all sub-directories and their files</guilabel></term>
    13121312              <listitem>
    13131313                <para>
    … …  
    13151315                is a directory. If this option is selected the permissions given
    13161316                to the directory will recursively be copied to all files and
    1317                 subdirectories. Existing permissions on those items will be
     1317                sub-directories. Existing permissions on those items will be
    13181318                overwritten with the new permissions.
    13191319                </para>
    … …  
    13251325            Use the &gbSave; button to save your
    13261326            changes or the &gbCancel; button to
    1327             close the popup without saving.
     1327            close the pop-up without saving.
    13281328          </para>
    13291329        </helptext>
    … …  
    14401440              single-item view of that item. Holding down <keycap>CTRL</keycap>,
    14411441              <keycap>ALT</keycap> or <keycap>SHIFT</keycap> while clicking,
    1442               will open the edit popup.
     1442              will open the edit pop-up.
    14431443            </para>
    14441444          </listitem>
    … …  
    15641564        <para>
    15651565          The free-text filter is a bit more complex. By default, an exact match is
    1566           required, use % as a wildcard that matches any character.
     1566          required, use % as a wildcard character that matches any character.
    15671567          For example, the filter <informalexample>Experiment A</informalexample>
    15681568          only matches the same exact string, but the filter
    … …  
    17091709            Use the &gbSave; button to apply your
    17101710            changes or the &gbCancel; button to
    1711             close the popup without saving.
     1711            close the pop-up without saving.
    17121712          </para>
    17131713
    … …  
    19041904            Use the &gbOk; button to save the preset
    19051905            or the &gbCancel; button to
    1906             close the popup without saving.
     1906            close the pop-up without saving.
    19071907          </para>
    19081908         
    … …  
    19621962          <para>
    19631963            Use the &gbClose; button to
    1964             close the popup.
     1964            close the pop-up.
    19651965          </para>
    19661966         
    … …  
    19861986        most significant difference is that the trashcan page can
    19871987        contain more then one item type, actually all removable item
    1988         types in BASE can be listed in the trascan. Items that neither
     1988        types in BASE can be listed in the trashcan. Items that neither
    19891989        can be removed or deleted, <emphasis>i.e.,</emphasis> items
    19901990        like sessions, nor clients' help texts since these are deleted

  • trunk/doc/test/performance/index.html

    r4477 r4487  
    44
    55  Copyright (C) 2007 Nicklas Nordborg
     6  Copyright (C) 2008 Jari Hakkinen
    67
    78  This file is part of BASE - BioArray Software Environment.
    … …  
    4344    <p>
    4445      This document defines a procedure for testing the performance
    45       of BASE. The intention is that BASE 2 should be compared to BASE 1
    46       with respect to performance. The tests on a BASE 1 server must be done
    47       by hand. For BASE 2, there is a test program. The current test program
     46      of BASE. The intention is that BASE should be compared to the
     47      earlier BASE version 1 with respect to performance. The tests on
     48      a BASE version 1 server must be done by hand. For later BASE
     49      versions, there is a test program. The current test program
    4850      is a prototype which includes the following tests:
    4951    </p>
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