Ignore:
Timestamp:
Nov 1, 2011, 7:02:40 PM (10 years ago)
Author:
Jari Häkkinen
Message:

Fixes #523.

File:
1 edited

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

    r5845 r5846  
    4141    very large and complex, especially since BASE itself works with
    4242    objects posing additional database tables to keep track of objects
    43     stored in a relational database. Thus, rather than trying to 
    44     describe every feature in detail here, we highlight some of the 
     43    stored in a relational database. Thus, rather than trying to
     44    describe every feature in detail here, we highlight some of the
    4545    more important features.
    4646  </para>
     
    7575      tracked and information on used and remaining quantities,
    7676      physical sample locations, quality control information, and
    77       sample relations is stored in BASE. Racks or boxes holding 
     77      sample relations is stored in BASE. Racks or boxes holding
    7878      biomaterials can be created as BioPlates and plate events are
    79       easily performed for extraction or labelling events. Although 
    80       becoming less commonly used, the array production LIMS of 
    81       previous BASE versions is retained to support researchers
    82       with spotting facilities, e.g., protein array production and
    83       BAC array printing that may not be commercially available.
     79      easily performed for extraction or labelling events. Although
     80      becoming less commonly used, the array production LIMS of
     81      previous BASE versions is retained to support researchers with
     82      spotting facilities, e.g., protein array production and BAC
     83      array printing that may not be commercially available.
    8484    </para>
    8585
     
    8888      protocols and event dates, and most items can be annotated with
    8989      customisable annotation types such as floats, integers, dates,
    90       and Boolean flags. Change history for biomaterial items is available
    91       if configured and can be used to track modifications in the database.
    92       Annotations are either free form or from a preset list of values,
    93       and can be marked as required for MIAME compliance. The annotation
    94       system is searchable and the user can select any annotations to be
    95       an experimental factors in analysis whereby it becomes availabe to
    96       analysis plugins and plot-tools.
     90      and Boolean flags. Change history for biomaterial items is
     91      available if configured and can be used to track modifications
     92      in the database.  Annotations are either free form or from a
     93      preset list of values, and can be marked as required for MIAME
     94      compliance. The annotation system is searchable and the user can
     95      select any annotations to be an experimental factors in analysis
     96      whereby it becomes available to analysis plugins and plot-tools.
    9797    </para>
    9898
     
    108108      project is used to group items (biomaterial, raw data, and
    109109      experiments) into a logical entity, and a BASE experiment is a
    110       collection of bioassays, e.g., array data, grouped logically together
    111       for further analysis. All items can co-exist in several projects
    112       and experiments without any unnecessary copying of information.
     110      collection of bioassays, e.g., array data, grouped logically
     111      together for further analysis. All items can co-exist in several
     112      projects and experiments without any unnecessary copying of
     113      information.
    113114    </para>
    114115
     
    133134
    134135    <para>
    135       BASE has an integrated file system to provide the possibility for
    136       researchers to collect all data files related to a project in
    137       one single storage location. Data files are uploaded using a web
    138       browser or an ftp client. The file storage is an integral part
    139       of a strategy to store all experiment relevant data in BASE,
    140       even data types not already supported in analysis. Collecting
    141       all data allows future reuse of the data as more data are
    142       produced, and new analysis tools becomes available.
     136      BASE has an integrated file system to provide the possibility
     137      for researchers to collect all data files related to a project
     138      in one single storage location. Data files are uploaded using a
     139      web browser or an ftp client. The file storage is an integral
     140      part of a strategy to store all experiment relevant data in
     141      BASE, even data types not already supported in
     142      analysis. Collecting all data allows future reuse of the data as
     143      more data are produced, and new analysis tools becomes
     144      available.
    143145    </para>
    144146
     
    148150    <title>Plugin and extension infrastructure</title>
    149151
    150 <!--
    151 Analysis, extensions, and plug-ins
    152 -->
    153152    <para>
    154153      BASE features a hierarchically organised analysis interface that
     
    177176      additions of new analysis tools. The use of the APIs is well
    178177      documented and there are numerous examples on how to create
    179       extensions. The MEV and ftp-server integrations all utilise the
     178      extensions. The MEV and ftp-server integration all utilise the
    180179      extension mechanism, and the automatically generated overview
    181180      plots available in the experimental analysis view are also
     
    228227      spotted cDNA/oligo arrays, Affymetrix (GeneChip), Illumina (SNP,
    229228      DASL, WGEX, microRNA), aCGH, SNP, tiling arrays, and many
    230       more. Data are produced in different file formats that must be
    231       treated differently depending on type.
     229      more. In addition expression data can be derived from sequencing
     230      data, i.e., RNASeq. Data is produced in different file formats
     231      that must be treated differently depending on type.
    232232    </para>
    233233
     
    247247    <para>
    248248      For two channel array platforms it is straightforward to
    249       customize BASE for a specific array platform, the platform
     249      customise BASE for a specific array platform, the platform
    250250      simply needs to be adapted to the (BASE) Generic platform. The
    251251      adaptation is to create a raw data format definition and to
     
    256256      mapped on to the Generic two channel platform. For Affymetrix,
    257257      BASE comes with a specific Affymetrix platform and Illumina can
    258       be supported by customizing BASE (go to the <ulink
     258      be supported by customising BASE (go to the <ulink
    259259      url="http://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina">
    260260      Illumina package</ulink> web site for more information on adding
     
    266266      or how to create a new platform type in BASE can be read
    267267      elsewhere in this document. Here we list different array
    268       platforms used in BASE and also list raw data types supported
    269       by BASE. However, not all platforms nor raw data types listed
    270       below are available out-of-the box and a BASE administrator must
    271       customize his local BASE installation for their specific
     268      platforms used in BASE and also list raw data types supported by
     269      BASE. However, not all platforms nor raw data types listed below
     270      are available out-of-the box and a BASE administrator must
     271      customise his local BASE installation for their specific
    272272      need. What comes pre-configured when BASE is installed is
    273273      indicated in the lists below.
     
    291291          <listitem>
    292292            <para>
    293               The Affymetrix platform comes pre-configured with a
    294               new BASE installation. Affymetrix platform in this
    295               context are the Affymetrix expression arrays. So far
    296               there has been no reason for expanding the Array
    297               platform to other chip-types. In principle any
    298               Affymetrix chip type can be stored in BASE but current
    299               plug-ins will always assume that expression data is
    300               stored and analyzed. This can be resolved by adding
    301               variants of the Affymetrix platform but the Lund BASE
    302               team currently has no plans to create Affymetrix
    303               variants.
     293              The Affymetrix platform comes pre-configured with a new
     294              BASE installation. Affymetrix platform in this context
     295              are the Affymetrix expression arrays. So far there has
     296              been no reason for expanding the Array platform to other
     297              chip-types. In principle any Affymetrix chip type can be
     298              stored in BASE but current plug-ins will always assume
     299              that expression data is stored and analysed. This can be
     300              resolved by adding variants of the Affymetrix platform
     301              but the Lund BASE team currently has no plans to create
     302              Affymetrix variants.
    304303            </para>
    305304          </listitem>
     
    331330          <listitem>
    332331            <para>
    333               There are several variants of the Illumina platform. Using
    334               several variants allows BASE to adapt its handling of
    335               different Illumina chip types. Illumina platform support
    336               is not included in a standard BASE installation but there
    337               is
    338               a <ulink url="http://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina">
    339                 Illumina package</ulink> available for seamless
     332              There are several variants of the Illumina
     333              platform. Using several variants allows BASE to adapt
     334              its handling of different Illumina chip types. Illumina
     335              platform support is not included in a standard BASE
     336              installation but there is a <ulink
     337              url="http://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina">
     338              Illumina package</ulink> available for seamless
    340339              integration of the Illumina array platform to BASE.
    341340            </para>
     
    354353
    355354        <varlistentry>
     355          <term>Sequencing</term>
     356          <listitem>
     357            <para>
     358              Expression data from sequencing experiments. Cufflinks
     359              raw-data type is available for expression values from
     360              sequencing experiments.
     361            </para>
     362          </listitem>
     363        </varlistentry>
     364
     365        <varlistentry>
    356366          <term>Unlisted</term>
    357367          <listitem>
    358368            <para>
    359               In principle any platform generating a matrix of data can
    360               be imported into BASE. Simply utilize the available raw
    361               data formats and data importers.
     369              In principle any platform generating a matrix of data
     370              can be imported into BASE. Simply utilise the available
     371              raw data formats and data importers.
    362372            </para>
    363373          </listitem>
     
    374384        usually defined by scanner software vendors and BASE must keep
    375385        track of the different formats for analysis and plotting. BASE
    376         supports many formats out the box, but some formats need to
    377         be added manually by the BASE administrator (indicated in the
     386        supports many formats out the box, but some formats need to be
     387        added manually by the BASE administrator (indicated in the
    378388        list below).
    379389      </para>
     
    415425        <varlistentry>
    416426          <term>ChipSkipper</term>
     427          <listitem>
     428            <para>
     429            </para>
     430          </listitem>
     431        </varlistentry>
     432
     433        <varlistentry>
     434          <term>Cufflinks</term>
    417435          <listitem>
    418436            <para>
     
    452470          <listitem>
    453471            <para>
    454               Not available in BASE directly but it is added with
    455               the <ulink url="http://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina">
     472              Not available in BASE directly but it is added with the
     473              <ulink
     474              url="http://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina">
    456475              Illumina plug-in</ulink> that adds Illumina array
    457476              platform support to BASE.
     
    495514
    496515    </sect2>
     516
     517  </sect1>
     518
     519  <sect1 id="features.supportedsequencing">
     520    <title>Supported sequencing applications</title>
     521
     522    <para>
     523      BASE was originally developed for management and analysis of
     524      array based data. Recent version, starting at version 3, have
     525      been adopted to support sequencing based data. Being a newly
     526      developed feature it is not as mature as the array part of BASE.
     527    </para>
     528
     529    <para>
     530      For sequencing data in general, BASE can be used for data
     531      management and sharing. BASE currently has extended support for
     532      sequencing applications such as RNAseq where data is transformed
     533      to gene expression measurements. For such applications array
     534      designs can be created based on gene structure defined in <ulink
     535      url='http://en.wikipedia.org/wiki/Gene_transfer_format'>GTF
     536      formatted files</ulink>. For example, GTF files for all RefSeqs
     537      or known genes.
     538    </para>
    497539
    498540  </sect1>
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