Difference between revisions of "Summary"
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The Listeriomics website is a web-based software design to manage genomic, transcriptomic and proteomic data for 'Listeria' species. | 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: | It 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. | # A highly interactive genome viewer for display of gene expression arrays, tiling arrays, and RNA-Seq datasets along with proteomics and genomics datasets. | ||
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# A tool to explore gene conservation throughout Listeria strains. | # A tool to explore gene conservation throughout Listeria strains. | ||
# A co-expression network tool to discover new potential regulation. | # 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. | 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. | ||
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| + | List of data available: | ||
| + | * 50 Listeria complete genomes | ||
| + | * 492 transcriptome datasets | ||
| + | * 74 proteome datasets | ||
= Tutorials = | = Tutorials = | ||
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{| class="wikitable" | {| class="wikitable" | ||
|- | |- | ||
| − | | [[ | + | | [[First hand on Listeriomics]] |
| − | | | + | | Here we show the general organization of the website |
|} | |} | ||
{| class="wikitable" | {| class="wikitable" | ||
|- | |- | ||
| − | | [[ | + | | [[Genomic tools]] |
| − | | | + | | How-to scroll 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]] |
| Create a desktop version of BACNET | | Create a desktop version of BACNET | ||
|- | |- | ||
Revision as of 12:34, 16 April 2015
A web-based software for manipulating Listeria "omics" data.
Summary
The Listeriomics website is a web-based software design to manage genomic, transcriptomic and proteomic data for 'Listeria' species. It 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.
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.
List of data available:
- 50 Listeria complete genomes
- 492 transcriptome datasets
- 74 proteome datasets
Tutorials
| First hand on Listeriomics | Here we show the general organization of the website |
| Genomic tools | How-to scroll 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 | 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)
