About the Project

×

Status message

New Feature: Guest Login function added to facilitate site exploration without registering. Try it out!

Araport is a rich resource...

The Arabidopsis Information Portal is an open-access online community resource for Arabidopsis research. Araport enables biologists to navigate from the Arabidopsis thaliana Col-0 reference genome sequence to its associated annotation including gene structure, gene expression, protein function, and interaction networks. Araport was funded in 2013 and came on line in 2014. Araport already offers a single interface through which to access a wide range of Arabidopsis information. Araport will grow through contributions of other labs in the form of modules: data, computation, and visualization tools.

Araport houses the gene structures...

Araport hosts the community standard ("TAIR10") gene structure of the Arabidopsis thaliana Col-0 reference genome sequence. Araport integrates gene structure with public data from TAIR, UniProt, PubMed, BAR, EPIC-CoGe, and other sources. Araport will release updates, named Araport11 etc., containing splice variants computed with tissue-specific transcript assemblies of RNA seq data. Araport annotation will incorporate community curation facilitated through the Araport web site. Araport users can query and view gene structure data with powerful GMOD software including InterMine, JBrowse and GBrowse. Users can not only save results but manipulate them, visualize them, and expose them as web services.

Araport offers community resources...

Araport currently provides a space where the community can post announcements about jobs, meetings, etc. Soon, users will be able to keep up with news from many sources, link out to stock centers, leverage iPlant resources, and interact with other users. Araport is recruiting labs that will contribute modules that offer data and visualization services. The modular architecture will enable the community to use Araport as its data distribution and integration platform.

Araport is designed to grow with the community...

Araport is designed to grow with the Arabidopsis community by providing an extensible framework for incorporation of new data sources and creation of user interfaces to consume them. Araport relies on a data mart (InterMine) to provide a searchable index of sequence-associated data. Araport relies on data federation to deliver in-depth information at run time. Araport relies on the community to contribute modules that extend its functionality. Modules can present federated data (obtained via RESTful web services) with in-browser visualization software (JavaScript, jQuery, etc.). To support data federation, Araport uses innovative middleware based on the iPlant Agave platform to support enrollment, discovery, and access to community-developed web services within a unified framework. Araport incorporates and integrates GMOD genomics applications including InterMine, JBrowse, GBrowse, WebApollo, Tripal, and Chado. The Araport project is fully open source, maintaining an active GitHub repository and virtual organization. Araport hosts tutorials, workshops, and hackathons to help the community enrich and exploit this resource. Designed for sustainability, the Araport strategy exploits existing scientific computing infrastructure, adopts a practical mix of data integration technologies, and encourages its user community to contribute suggestions, data sets, web services, and software.