  This work presents MeKDDaM-SAGA, computer-aided automation software for
implementing a novel knowledge discovery and data mining process model that was
designed for performing justifiable, traceable and reproducible metabolomics
data analysis. The process model focuses on achieving metabolomics analytical
objectives and on considering the nature of its involved data. MeKDDaM-SAGA was
successfully used for guiding the process model execution in a number of
metabolomics applications. It satisfies the requirements of the proposed
process model design and execution. The software realises the process model
layout, structure and flow and it enables its execution externally using
various data mining and machine learning tools or internally using a number of
embedded facilities that were built for performing a number of automated
activities such as data preprocessing, data exploration, data acclimatization,
modelling, evaluation and visualization. MeKDDaM-SAGA was developed using
object-oriented software engineering methodology and was constructed in Java.
It consists of 241 design classes that were designed to implement 27 use-cases.
The software uses an XML database to guarantee portability and uses a GUI
interface to ensure its user-friendliness. It implements an internal embedded
version control system that is used to realise and manage the process flow,
feedback and iterations and to enable undoing and redoing the execution of the
process phases, activities, and the internal tasks within its phases.
