Difference between revisions of "Summary"

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An interactive platform for analysis and publication of bacterial “omics” data.
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[[File:HomePageListeriomics.png|thumb|300px|right|Home page of the Listeriomics website]]
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Listeriomics integrates all complete genomes, transcriptomes and proteomes published for <i>Listeria</i> species to date. It allows navigating among all these datasets with enriched metadata in a user-friendly format.
  
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[[File:OverviewBacnet.png|thumb|300px|right|Tools available in BACNET platform]]
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The main purpose of the website is to give scientists a quick and easy access to tools created for answering the four questions one has when starting a study on a specific genomic element:
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# What are the known functions of a genomic feature in a given strain and homologies in closely related strains?
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# What are the biological conditions in which a genomic feature is transcribed?
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# What are the biological conditions in which a genomic feature is translated?
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# What is the regulation network involved with a genomic feature of interest?
  
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= Summary =
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The website integrates different type of tools for “omics” data analyses:
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* A highly interactive genome viewer for display of gene expression arrays, tiling arrays, and RNA-Seq datasets along with proteomics and genomics datasets.
 +
* Expression and protein atlas, which are tools to connect every genomic feature (genes, smallRNAs, antisenseRNAs) or proteins to the most relevant “omics” data.
 +
* A tool to explore gene conservation throughout ''Listeria'' strains.
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* A co-expression network tool to discover new potential regulation.
  
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The Listeriomics website is a web-based software design to manage genomic, transcriptomic and proteomic data for 'Listeria' species.
 
  
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It integrates different type of tools for “omics” data analyses: 1) A highly interactive genome viewer for display of gene expression arrays, tiling arrays, and RNA-Seq datasets along with proteomics and genomics datasets, 2) expression and protein atlas, which are tools to connect every genomic feature (genes, smallRNAs, antisenseRNAs) or proteins to the most relevant “omics” data, 3) a tool to explore gene conservation throughout Listeria strains, 4) a co-expression network tool to discover new potential regulation.
 
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The Listeriomics database includes all complete genomes, transcriptomes and proteomes published on 'Listeria' species to date. It allows biologists to analyse dynamically all these datasets in a user-friendly format, and can be used by bio-informaticians as a central database for systems biology analysis.
 
  
 
= Tutorials =
 
= Tutorials =
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{| class="wikitable"
 
{| class="wikitable"
 
|-
 
|-
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| [[Install BACNET]]
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| [[First hands on Listeriomics]]
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| Install and compile BACNET platform
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| General organization of the website and principal features
 
|}
 
|}
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=== Tools ===
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{| class="wikitable"
 
{| class="wikitable"
 
|-
 
|-
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| [[First step in BACNET architecture]]
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| [[Genomic tools]]
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| Create your own application, add a view, a menu, and you own ''Omics'' data.
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| How-to access all the genomes.
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|-
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| [[Gene tools]]
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| How-to access a specific gene and get information about its annotation, its conservation, its transcription or translation.
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|-
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| [[Small RNA tools]]
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| How-to access a specific Small RNA
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|-
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| [[Transcriptomic tools]]
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| How-to access transcriptomic dataset and display it or perform an analysis with the expression atlas
 
|-
 
|-
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| [[First step in single sourcing]]
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| [[Proteomic tools]]
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| Rules on how to manage single sourcing and develop in parallel desktop and web application
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| How-to access proteomic dataset and display it or perform an analysis with the protein atlas
 
|-
 
|-
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| [[First step in the desktop version]]
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| [[Co-Expression_network_tools|Co-expression network tools]]
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| Create a desktop version of BACNET
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| How-to access to the co-expression network and search for potential co-regulation of genomic feature
 
|-
 
|-
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| [[First step in the web version]]
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| [[Submit_Data|Submit your datasets]]
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| Deploy a BACNET website
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| How-to access to the submit section of Listeriomics in which you can inform us of important database update to make
 
|}
 
|}
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=== Viewers ===
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{| class="wikitable"
 
{| class="wikitable"
 
|-
 
|-
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| [[Main class of BACNET]]
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| [[Genome viewer]]
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| We explain the class architecture, focusing on the main class used
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| How-to use the genome viewer for visualizing "omics" datasets
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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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| [[How-to - Transcriptomics]]
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| [[Transcriptomic HeatMap viewer]]
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| Tutorials for different tools related to transcriptomics (Arrays and RNASeq)
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| How-to use the transcriptomic heatmap viewer and decipher differently expressed genomic features
 
|-
 
|-
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| [[How-to]]
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| [[Proteomic HeatMap viewer]]
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| Every tutorial available
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| How-to use the proteomic heatmap viewer and decipher detected protein in every proteomic experiment
 
|}
 
|}
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= Database =
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The Listeriomics database includes all complete genomes, transcriptomes and proteomes published on ''Listeria'' species to date. It allows scientists to analyse dynamically all these datasets in a user-friendly format, and can be used by bio-informaticians as a central database for systems biology analysis.
 +
 +
List of data available:
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* 83 Listeria complete genomes
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* 492 transcriptome datasets
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* 74 proteome datasets
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 +
The whole database can be downloaded [http://listeriomics01.hosting.pasteur.fr/DatabaseListeriomics.zip Here]
  
 
= Screenshots =
 
= Screenshots =
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<gallery>
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<gallery widths=200px>
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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:BHIViewer.png|Genome viewer
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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:GenomeviewerChangeView.png|Example of the zoom capability of the Genome Viewer
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Image:SplashScreen.png|Splash screen of BACNET platform
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Image:genomes.png|Genome webpage
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Image:ListeriomicsWebsite.png|View of the Listeriomics website developed thanks to BACNET platform
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Image:Genepanel.png|Gene webpage
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Image:Environmentbacnet.png|View of Eclipse environment in which BACNET is developed
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Image:Synteny.png|Synteny webpage
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Image:HeatMapBacnet.png|HeatMap view (desktop version)
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Image:smallRNA.png|Small RNA webpage
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Image:VennDiagramBacnet.png|Venn Diagram view (desktop version)
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Image:transcriptome.png|Transcriptome webpage
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Image:SmallRnaBacnet.png|Small RNA tool (desktop version)
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Image:Heatmap.png|Heatmap visualization of transcriptomics datasets
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Image:ExpressionAtlasWebBacnet.png|Expression Atlas tool (web version)
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Image:proteome.png|Proteome webpage
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Image:HeatmapProteomic.png|Heatmap visualization of proteomics datasets
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Image:SeqInfo.png|Sequence information panel
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Image:coexpression.png|Co-expression network webpage
 
</gallery>
 
</gallery>

Latest revision as of 14:01, 29 November 2022

Home page of the Listeriomics website

Listeriomics integrates all complete genomes, transcriptomes and proteomes published for Listeria species to date. It allows navigating among all these datasets with enriched metadata in a user-friendly format.

The main purpose of the website is to give scientists a quick and easy access to tools created for answering the four questions one has when starting a study on a specific genomic element:

  1. What are the known functions of a genomic feature in a given strain and homologies in closely related strains?
  2. What are the biological conditions in which a genomic feature is transcribed?
  3. What are the biological conditions in which a genomic feature is translated?
  4. What is the regulation network involved with a genomic feature of interest?

The website integrates different type of tools for “omics” data analyses:

  • A highly interactive genome viewer for display of gene expression arrays, tiling arrays, and RNA-Seq datasets along with proteomics and genomics datasets.
  • Expression and protein atlas, which are tools to connect every genomic feature (genes, smallRNAs, antisenseRNAs) or proteins to the most relevant “omics” data.
  • A tool to explore gene conservation throughout Listeria strains.
  • A co-expression network tool to discover new potential regulation.


Tutorials[edit]

First hands on Listeriomics General organization of the website and principal features

Tools[edit]

Genomic tools How-to access all the genomes.
Gene tools How-to access a specific gene and get information about its annotation, its conservation, its transcription or translation.
Small RNA tools How-to access a specific Small RNA
Transcriptomic tools How-to access transcriptomic dataset and display it or perform an analysis with the expression atlas
Proteomic tools How-to access proteomic dataset and display it or perform an analysis with the protein atlas
Co-expression network tools How-to access to the co-expression network and search for potential co-regulation of genomic feature
Submit your datasets How-to access to the submit section of Listeriomics in which you can inform us of important database update to make

Viewers[edit]

Genome viewer How-to use the genome viewer for visualizing "omics" datasets
Transcriptomic HeatMap viewer How-to use the transcriptomic heatmap viewer and decipher differently expressed genomic features
Proteomic HeatMap viewer How-to use the proteomic heatmap viewer and decipher detected protein in every proteomic experiment

Database[edit]

The Listeriomics database includes all complete genomes, transcriptomes and proteomes published on Listeria species to date. It allows scientists to analyse dynamically all these datasets in a user-friendly format, and can be used by bio-informaticians as a central database for systems biology analysis.

List of data available:

  • 83 Listeria complete genomes
  • 492 transcriptome datasets
  • 74 proteome datasets

The whole database can be downloaded Here

Screenshots[edit]

  • Genome viewer

  • Example of the zoom capability of the Genome Viewer

  • Genome webpage

  • Gene webpage

  • Synteny webpage

  • Small RNA webpage

  • Transcriptome webpage

  • Heatmap visualization of transcriptomics datasets

  • Proteome webpage

  • Heatmap visualization of proteomics datasets

  • Sequence information panel

  • Co-expression network webpage

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