Technology

Legume Federation projects are using a variety of open-source technologies. Not every partner site uses all of the technologies below.

   Data Stores  |  GBrowse  |  JBrowse  |  InterMine  |  Github  |  Genome Context Viewer (GCV)  |  Tripal  |  Chado  |  CMap

Data Stores
The Legume Federation maintains data at a central repository for public and private data: genomes, annotations, transcriptomes, etc. This repository is currently (2017) mirrored at two locations: at LegumeInfo and at CyVerse. Data deposited in the public Legume Federation directory are available for the legume research community. Data can also be held in a private directory while under embargo, or for research data that is not yet published but shared with specified collaborators.
GBrowsedocumentation
Legume genomes:


JBrowsedocumentation
Legume genomes:


InterMinedocumentation and project
The Legume Federation has developed a federation of legume InterMine instances.

GithubGithub website and Github Blog
Legume Federation and the teams have multiple github code repositories available:

Genome Context Viewer (GCV)documentation
The Genomic Context Viewer (GCV) is a web-app that visualizes genomic context data provided by third party services. It allows users to view regions of genomes considered primarily with respect to the ordering and orientation of their annotated gene content. By handling sequences of gene family memberships as a unit of search and comparison, the user interface is made sufficiently responsive to enable quick assessment of the levels of conservation, novelty, and various types of structural events that can serve to direct the user to more detailed explorations at finer levels of granularity in other tools. For a detailed tour of the GCV tool click the "Help" button on the top left of the page.
Federation GDPs that use Context Viewer:

Tripaldocumentation
The Legume Federation is working with the Tripal developers to create and improve modules that are applicable across a wide range of plant GDPs.
Federation GDPs that use Tripal:

Multiple Tripal extension modules are under active development by Legume Federation partners including but not limited to the BlastUI. See the list of Tripal extension modules for more information.
Federation GDPs that use Tripal BlastUI:

Chado
Members of the Legume Federation are working with the Chado team to improve support for various data types, especially phenotype data.
Note that not all Tripal sites use Chado.

CMapdocumentation.
One objective of the Legume Federation project is to replace/rewrite CMap, using more interactive web technologies. The alpha version of this new genetic map viewer, CMap-js is available. We intend this as a replacement for CMap, which has served researchers well for a long time, but which lacks the kind of interactivity that modern client-side web technologies allow – and which won’t scale well with larger datasets. Try clicking and dragging over the blue map background and on the marker lists or the QTL features on the right. Get the code here: https://github.com/LegumeFederation/cmap-js. We welcome developers to join in - or users to send feature requests.

Some of our design objectives are:
  • Flexible configuration.
  • Simple data formats (accepting CMap tabular data for backward compatibility).
  • Ability to pass in data via API (no database requirement and including cross-site or user generated maps).
  • Minimal use of external libraries.
  • Ease of installation.
  • High interactivity (panning, zooming, clicking, adding or removing maps, etc.).
  • and scalability to a very large number of markers.

Theses structural goals are in addition to the ability to compare maps, ability to display region data (QTLs, GWAS, etc.), the ability to represent genetic-genomic comparisons (both within and cross-species), and the ability to represent relations between features for any given map. We still have quite a large set of features to add, but please let us know if there are things that you would particularly like to see.

Federation GDPs using the current CMap: