Difference between revisions of "GMOD Components"

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==Architecture Diagram==
 
==Architecture Diagram==
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GMOD components fulfilling the requirements of an interface are linked to the interface, as well as to the Chado schema modules if they are known to interact with Chado. The requirements of an interface, as well as the components that implement a given interface are described in the documents linked at the end of this document.
 
GMOD components fulfilling the requirements of an interface are linked to the interface, as well as to the Chado schema modules if they are known to interact with Chado. The requirements of an interface, as well as the components that implement a given interface are described in the documents linked at the end of this document.
 
[[Category:Biologist]]
 
[[Category:GMOD Components]]
 

Revision as of 19:50, 27 August 2009

By Category

GMOD is a federation of software applications (components) aimed at providing the functionality that is needed by all organism databases. The table below classifies GMOD components according to their functional categories.


Community Annotation

Apollo

BioDIG

Canto

WebApollo

Wiki TableEdit


Comparative Genome Visualization

CMap

GBrowse_syn

Pathway Tools

SynView

Sybil


Database schema

Chado


Database tools

Argos

BioMart

Genome grid

GMODTools

InterMine

LuceGene

XORT


Gene Expression Visualization

Caryoscope

GeneXplorer

Pathway Tools


Genome Annotation

Apollo

DIYA

MAKER

SOBA

WebApollo


Genome Visualization & Editing

Apollo

Flash GViewer

GBrowse

JBrowse

Pathway Tools

WebGBrowse

WebApollo


Literature and Curation Tools

BioDIG

Canto

Textpresso

Molecular Pathway Visualization

Pathway Tools


Ontology Visualization

Go Graphic Viewer


Workflow Management

Galaxy

Ergatis

DIYA

ISGA


Middleware

Modware

Chado::AutoDBI

Bio::Chado::Schema


Tool Integration

Galaxy


Sequence Alignment

Blast Graphic


Website front end for Chado DB

Tripal


Architecture Diagram

The diagram below represents a model organism database (MOD) and its typical components. The top ten types of functionality are represented in the top row of the diagram as a set of interfaces. The Vis prefix on the end of each interface is an abbreviation of Visualization, and should be interpreted literally -- an alignment visualization interface should not merely allow users to passively view pre-existing alignments, but should also to user interaction to create and visualize alignments of their own.



Symbols used in this UML diagram

  • boxes
    • tabbed white boxes are packages -- logical groups of related components
    • boxes marked with <<interface>> are abstract interfaces required by GMOD-Web. All other labeled boxes are concrete components of the GMOD system.
  • connectors
    • solid arrows indicate a relationship between components that currently exists.
    • dashed arrows indicate a relationship between components that does NOT currently exist.
    • dashed arrows with a solid white head indicate an interface/realization relationship between a GMOD-Web required interface and a component that provides that interface. e.g. gbrowse implements the genomeVis interface.
  • coloration
    • white: components or interfaces that currently exist and integrated into the GMOD system.
    • green: components or interfaces that currently exist and are integrated into the GMOD system.
    • pink: components or interfaces that currently exist, but the feasibility of integrating their functionality into the GMOD system is unknown.
    • red: components that do not currently exist, but may need to be implemented.
    • orange: a common set of templates to provide a consistent look and feel for all GMOD systems. The "common gene page" concept is in this group.
    • cyan: components that are specific to each MOD, and are not deployable as part of a GMOD system.

GMOD components fulfilling the requirements of an interface are linked to the interface, as well as to the Chado schema modules if they are known to interact with Chado. The requirements of an interface, as well as the components that implement a given interface are described in the documents linked at the end of this document.