Difference between revisions of "SOBA"
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{{ComponentBox|{{SobaResourcesBoxItem}}|{{ComponentBoxEventsHeader}}|{{GMODAmericas2011BoxItem|2011 GMOD Spring Training|GMOD Spring Training|March 8-12}}| | |}} | {{ComponentBox|{{SobaResourcesBoxItem}}|{{ComponentBoxEventsHeader}}|{{GMODAmericas2011BoxItem|2011 GMOD Spring Training|GMOD Spring Training|March 8-12}}| | |}} | ||
| − | '''[http://www.sequenceontology.org/wiki/index.php/SOBA_-_Sequence_Ontology_Bioinformatics_Analysis SOBA]''' is a command line | + | '''[http://www.sequenceontology.org/wiki/index.php/SOBA_-_Sequence_Ontology_Bioinformatics_Analysis SOBA]''' is a command line tool and web application for analyzing [[GFF3]] annotations. [[GFF3]] is a standard file format for genomic annotation data. SOBA gathers statistics from GFF3 files and renders them as tables and graphs. |
The web version of SOBA will produce the following: | The web version of SOBA will produce the following: | ||
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* Suggestions to improve SO compliance for invalid terms | * Suggestions to improve SO compliance for invalid terms | ||
| − | In addition, the command line | + | In addition, the command line tool (SOBAcl) flexibly produces a much wider variety of tables, figures and graphs based on the data in a [[GFF3] file as well as the the ability to produce complex and extensible custom reports via a robust template system. |
| − | SOBA is intended | + | SOBA is intended is a tool for those dealing with genomic sequence annotation who want to view genome wide summaries their annotation files. For example: SOBA would be a useful tool at an annotation jamboree for a newly sequenced organism and when preparing a the resulting genome paper; SOBA would help those developing annotation tools to quickly evaluate updates to their tool; SOBA assists comparative genomics analyses by providing a high-level overview of the genome of multiple organisms. SOBA complements genome browsers by providing a summary of all the features annotated in the genome. |
SOBA is built with Perl (and JavaScript for the web interface). The web interface uses {{CPAN|CGI::Application}} as a Perl webapp framework and the JQuery JavaScript library for Web 2.0 effects and {{GlossaryLink|AJAX|AJAX}}. Both versions of SOBA use the [http://template-toolkit.org/ Template Tooklit (TT)] to generate html/txt reports, graphviz for the ontology graphs, and GD for charts. Template Toolkit makes extensibility very easy, at least for someone who's willing to learn the fairly simple template language of TT (you don't need to know Perl or any other programming to use TT). | SOBA is built with Perl (and JavaScript for the web interface). The web interface uses {{CPAN|CGI::Application}} as a Perl webapp framework and the JQuery JavaScript library for Web 2.0 effects and {{GlossaryLink|AJAX|AJAX}}. Both versions of SOBA use the [http://template-toolkit.org/ Template Tooklit (TT)] to generate html/txt reports, graphviz for the ontology graphs, and GD for charts. Template Toolkit makes extensibility very easy, at least for someone who's willing to learn the fairly simple template language of TT (you don't need to know Perl or any other programming to use TT). | ||
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</pre> | </pre> | ||
| − | A README and INSTALL document included with SOBAcl | + | A README and INSTALL document are also included with SOBAcl. |
= Requirements = | = Requirements = | ||
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*[http://www.graphviz.org/ The Graphviz library] | *[http://www.graphviz.org/ The Graphviz library] | ||
*[http://www.libgd.org/Main_Page The libgd graphics library] | *[http://www.libgd.org/Main_Page The libgd graphics library] | ||
| − | *[http:// | + | *[http://search.cpan.org/~lbrocard/GraphViz-2.04/lib/GraphViz.pm GraphViz] |
| − | *[http:// | + | *[http://search.cpan.org/~abw/Template-Toolkit-2.22/lib/Template.pm Template] |
| − | *[http:// | + | *[http://search.cpan.org/search?query=getopt%3A%3Along&mode=all Getopt::Long] |
| − | *[http:// | + | *[http://search.cpan.org/~timb/DBI-1.616/DBI.pm DBI] |
| − | *[http:// | + | *[http://search.cpan.org/~shlomif/Statistics-Descriptive-3.0201/lib/Statistics/Descriptive.pm Statistics::Descriptive] |
| − | + | *[http://search.cpan.org/~andya/Set-IntSpan-Fast-XS-0.05/lib/Set/IntSpan/Fast/XS.pm Set::IntSpan::Fast] | |
| − | *[http:// | + | *[http://search.cpan.org/~anno/Text-Table-1.116/lib/Text/Table.pm Text::Table] |
| − | *[http:// | + | *[http://search.cpan.org/~wrw/Number-Format-1.73/Format.pm Number::Format] |
| − | *[http:// | + | *[http://search.cpan.org/~frew/SQL-Abstract-1.72/lib/SQL/Abstract.pm SQL::Abstract] |
| − | *[http:// | + | *[http://search.cpan.org/~cmungall/go-perl-0.13/GO/Parser.pm GO::Parser] |
| − | *[http:// | + | *[http://search.cpan.org/~bwarfield/GDGraph-1.44/Graph.pm GD::Graph] |
| − | *[http:// | + | |
= Download = | = Download = | ||
Revision as of 03:48, 7 March 2011
__NOTITLE__
This page or section is under construction.
SOBA is a GFF3 analysis tool that has been nominated and approved for GMOD Membership. It is in the process of being incorporated into GMOD.
SOBA is a command line tool and web application for analyzing GFF3 annotations. GFF3 is a standard file format for genomic annotation data. SOBA gathers statistics from GFF3 files and renders them as tables and graphs.
The web version of SOBA will produce the following:
- Summary statistics of feature types and attributes used
- Histograms of feature lengths
- Graphs of Sequence Ontology terms used
- Histograms of intron density
- Suggestions to improve SO compliance for invalid terms
In addition, the command line tool (SOBAcl) flexibly produces a much wider variety of tables, figures and graphs based on the data in a [[GFF3] file as well as the the ability to produce complex and extensible custom reports via a robust template system.
SOBA is intended is a tool for those dealing with genomic sequence annotation who want to view genome wide summaries their annotation files. For example: SOBA would be a useful tool at an annotation jamboree for a newly sequenced organism and when preparing a the resulting genome paper; SOBA would help those developing annotation tools to quickly evaluate updates to their tool; SOBA assists comparative genomics analyses by providing a high-level overview of the genome of multiple organisms. SOBA complements genome browsers by providing a summary of all the features annotated in the genome.
SOBA is built with Perl (and JavaScript for the web interface). The web interface uses CGI::Application as a Perl webapp framework and the JQuery JavaScript library for Web 2.0 effects and AJAX. Both versions of SOBA use the Template Tooklit (TT) to generate html/txt reports, graphviz for the ontology graphs, and GD for charts. Template Toolkit makes extensibility very easy, at least for someone who's willing to learn the fairly simple template language of TT (you don't need to know Perl or any other programming to use TT).
Documentation
Documentation for the web interface to SOBA is available on the Sequence Ontology Wiki as well as via tool-tips on the site itself.
Documentation for the command line version - SOBAcl - is available as a usage statement with the script itself:
SOBAcl --help
A README and INSTALL document are also included with SOBAcl.
Requirements
The web interface to SOBA should work on any modern browser that has Javascript enabled.
SOBAcl requires:
- Perl
- The Graphviz library
- The libgd graphics library
- GraphViz
- Template
- Getopt::Long
- DBI
- Statistics::Descriptive
- Set::IntSpan::Fast
- Text::Table
- Number::Format
- SQL::Abstract
- GO::Parser
- GD::Graph
Download
The SOBA web interface is available at:
http://www.sequenceontology.org/cgi-bin/soba.cgi
SOBAcl is available (via svn) from:
svn co svn://malachite.genetics.utah.edu/SOBA/trunk SOBA
Mailing List(s)
SOBA is supported by the Sequence Ontology Developers Mailing list at:
https://lists.sourceforge.net/lists/listinfo/song-devel
