PAPAyA: a platform for breast cancer biomarker signature discovery, evaluation and assessment

BMC Bioinformatics

Table 1 Flow Definition.

*Field*	*Description*
StateFrom	Current state
Type	Tool execution; internal transition; ...
Description	Free-text description
Action	Tool name; initialization; internal actions
ConstraintExist	User-defined variables that can be set to define constraints. For example methylation modality active vs. expression modality active; analysis mode vs. decision support mode; etc.
ConstraintSet	Constraints to set with this transition
Constraint-Unset	Constraints to unset with this transition
StateTo	New state

The flow is defined with transitions between states (from StateFrom to StateTo) based on use Action. Example state may be pre-processing, analysis, post-processing, and single-patient evaluation. Each state uses internal constraints that can be set or unset during transitions (based on ConstraintSet and ConstraintUnset). The current state and the constraints currently set (ConstraintExist) define a context. Example constraints can be based on the molecular modality used. For example, constraint EXP (for expression) and AFFY (for an Affymetrix platform) when set in the pre-processing state will make available only the tools suitable for the platform and modality.

ISSN: 1471-2105