Difference between revisions of "Summary"

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An interactive platform for analysis and publication of bacterial “omics” data.
  
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Consult the [//meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.
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[[File:OverviewBacnet.png|thumb|300px|right|Tools available in BACNET platform]]
  
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== Getting started ==
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= Summary =
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BACNET is a Java based platform, which allows to develop in parallel a highly interactive platform which work both on a local computers and internet servers. To reach this goal we use two highly connected APis , [http://wiki.eclipse.org/index.php/Rich_Client_Platform Eclipse RCP] and [http://eclipse.org/rap/ Eclipse RAP] ([http://fr.slideshare.net/caniszczyk/single-sourcing-rcp-and-rap single sourcing]). Our platform integrates different type of tools, the three most important being: A table tools for Heatmap drawing and manipulation. Genome viewer for displaying gene expression array ([http://en.wikipedia.org/wiki/DNA_microarray DNA microarray]), tiling array, and [http://en.wikipedia.org/wiki/RNA-Seq RNA-Seq] data along with [http://en.wikipedia.org/wiki/Proteomics proteomics] and [http://en.wikipedia.org/wiki/Genomics genomics] data. This genome viewer is able to load quickly every data using streaming techniques, to zoom through the data from a nucleotide scale to a genome-wide scale, and overlay heterogeneous “omics” data.  And an expression atlas, inspired from [http://www.ebi.ac.uk/gxa/ EBI Expression Atlas], for easily design a query based tool which connects every genomics elements (genes, smallRNAs, antisenseRNAs) to the most relevant “omics” data.
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* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]
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* [//www.mediawiki.org/wiki/Special:MyLanguage/Localisation#Translation_resources Localise MediaWiki for your language]
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= Tutorials =
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{| class="wikitable"
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|-
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| [[Install BACNET]]
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| Install and compile BACNET platform
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|}
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{| class="wikitable"
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|-
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| [[First step in BACNET architecture]]
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| Create your own application, add a view, a menu, and you own ''Omics'' data.
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|-
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| [[First step in single sourcing]]
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| Rules on how to manage single sourcing and develop in parallel desktop and web application
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|-
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| [[First step in the desktop version]]
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| Create a desktop version of BACNET
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|-
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| [[First step in the web version]]
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| Deploy a BACNET website
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|}
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{| class="wikitable"
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|-
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| [[Main class of BACNET]]
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| We explain the class architecture, focusing on the main class used
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|-
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| [[How-to - Genomics]]
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| Tutorials for different tools related to genomics
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|-
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| [[How-to - Transcriptomics]]
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| Tutorials for different tools related to transcriptomics (Arrays and RNASeq)
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|-
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| [[How-to]]
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| Every tutorial available
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|}
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= Screenshots =
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<gallery>
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Image:MultiOmicsViewBacnet.png|Multi omics view: Tiling array, Proteomics, TSS data, RNAseq, Genome annotation. Desktop version
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Image:SingleSourcingBacnet.png|Single sourcing allows to develop with same Java code a desktop and a web application
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Image:SplashScreen.png|Splash screen of BACNET platform
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Image:ListeriomicsWebsite.png|View of the Listeriomics website developed thanks to BACNET platform
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Image:Environmentbacnet.png|View of Eclipse environment in which BACNET is developed
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Image:HeatMapBacnet.png|HeatMap view (desktop version)
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Image:VennDiagramBacnet.png|Venn Diagram view (desktop version)
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Image:SmallRnaBacnet.png|Small RNA tool (desktop version)
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Image:ExpressionAtlasWebBacnet.png|Expression Atlas tool (web version)
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</gallery>

Revision as of 12:05, 16 April 2015

An interactive platform for analysis and publication of bacterial “omics” data.

File:OverviewBacnet.png
Tools available in BACNET platform

Summary

BACNET is a Java based platform, which allows to develop in parallel a highly interactive platform which work both on a local computers and internet servers. To reach this goal we use two highly connected APis , Eclipse RCP and Eclipse RAP (single sourcing). Our platform integrates different type of tools, the three most important being: A table tools for Heatmap drawing and manipulation. Genome viewer for displaying gene expression array (DNA microarray), tiling array, and RNA-Seq data along with proteomics and genomics data. This genome viewer is able to load quickly every data using streaming techniques, to zoom through the data from a nucleotide scale to a genome-wide scale, and overlay heterogeneous “omics” data. And an expression atlas, inspired from EBI Expression Atlas, for easily design a query based tool which connects every genomics elements (genes, smallRNAs, antisenseRNAs) to the most relevant “omics” data.

Tutorials

Install BACNET Install and compile BACNET platform
First step in BACNET architecture Create your own application, add a view, a menu, and you own Omics data.
First step in single sourcing Rules on how to manage single sourcing and develop in parallel desktop and web application
First step in the desktop version Create a desktop version of BACNET
First step in the web version Deploy a BACNET website
Main class of BACNET We explain the class architecture, focusing on the main class used
How-to - Genomics Tutorials for different tools related to genomics
How-to - Transcriptomics Tutorials for different tools related to transcriptomics (Arrays and RNASeq)
How-to Every tutorial available

Screenshots

  • MultiOmicsViewBacnet.png

    Multi omics view: Tiling array, Proteomics, TSS data, RNAseq, Genome annotation. Desktop version

  • SingleSourcingBacnet.png

    Single sourcing allows to develop with same Java code a desktop and a web application

  • SplashScreen.png

    Splash screen of BACNET platform

  • ListeriomicsWebsite.png

    View of the Listeriomics website developed thanks to BACNET platform

  • Environmentbacnet.png

    View of Eclipse environment in which BACNET is developed

  • HeatMapBacnet.png

    HeatMap view (desktop version)

  • VennDiagramBacnet.png

    Venn Diagram view (desktop version)

  • SmallRnaBacnet.png

    Small RNA tool (desktop version)

  • ExpressionAtlasWebBacnet.png

    Expression Atlas tool (web version)

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