Package Bio :: Package Pathway
[hide private]
[frames] | no frames]

Package Pathway

source code

BioPython Pathway module.

Bio.Pathway is a lightweight class library designed to support the following tasks:

 - Data interchange and preprocessing between pathway databases and analysis software.
 - Quick prototyping of pathway analysis algorithms

The basic object in the Bio.Pathway model is Interaction, which represents an arbitrary
interaction between any number of biochemical species.

Network objects are used to represent the connectivity between species in pathways
and reaction networks.

For applications where it is not necessary to explicitly represent network connectivity,
the specialized classes Reaction and System should be used in place of Interacton and

The Bio.Pathway classes, especially Interaction, are intentionally
designed to be very flexible. Their intended use are as wrappers around database
specific records, such as BIND objects. The value-added in this module is a
framework for representing collections of reactions in a way that supports
graph theoretic and numeric analysis.

Note: This module should be regarded as a prototype only. API changes are likely.
      Comments and feature requests are most welcome.

Submodules [hide private]

Classes [hide private]
Abstraction for a biochemical transformation.
Abstraction for a collection of reactions.
An arbitrary interaction between any number of species.
A set of species that are explicitly linked by interactions.
Variables [hide private]
  __package__ = 'Bio.Pathway'