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org.biomage.Protocol: Javadoc index of package org.biomage.Protocol.

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Protocol_package: Provides a relatively immutable class, Protocol, that can describe a generic laboratory procedure or analysis algorithm, for example, and an instance class, ProtocolApplication, which can describe the actual application of a protocol. The ProtocolApplication provides values for the replaceable parameters of the Protocol and, through the Description association of Describable, any variation from the Protocol.
Parameter: A Parameter is a replaceable value in a Parameterizable class. Examples of Parameters include: scanning wavelength, laser power, centrifuge speed, multiplicative errors, the number of input nodes to a SOM, and PCR temperatures.
Protocol: A Protocol is a parameterizable description of a method. ProtocolApplication is used to specify the ParameterValues of it's Protocol's Parameters.
Software: Software represents the software used. Examples of Software include: feature extraction software, clustering software, etc...
Hardware: Hardware represents the hardware used. Examples of Hardware include: computers, scanners, wash stations etc...
Parameterizable: The Parameterizable interface encapsulates the association of Parameters with ParameterValues.
SoftwareApplication: The use of a piece of software with the requisite Parameters and ParameterValues.
HardwareApplication: The use of a piece of hardware with the requisite Parameters and ParameterValues.
ProtocolApplication: The use of a protocol with the requisite Parameters and ParameterValues.
ParameterizableApplication: The interface that is the use of a Parameterizable class.
ParameterValue: The value of a Parameter.

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