Computational Feature Performance and Domain Specific Architecture Evaluation of Software Applications Towards Metabolic Flux Analysis

Zeeshan      Ahmed; Saman      Majeed; Thomas      Dandekar

doi:10.2174/2213275911205030165

Abstract

New experimental data on metabolites and enzymes induce high interest in metabolic modelling including metabolic flux calculations. Data analysis of metabolites, calculation of metabolic fluxes, pathways and their conditionspecific strengths is now possible by an advantageous combination of specific software. How can available software for metabolic modelling be improved from a computational point of view? A number of available and well established software solutions are first discussed individually. This includes information on software origin, capabilities, development and used methodology. Performance information is obtained for the compared software using provided example data sets. A feature based comparison shows limitations and advantages of the compared software for specific tasks in metabolic modelling. Often found limitations include third party software dependence, no comprehensive database management and no standard format for data input and output. Graphical visualization can be improved for complex data visualization and at the web based graphical interface. Other areas for development are platform independency, product line architecture, data standardization, open source movement and new methodologies along with the discussion of few of the patents related to Computational features.

Keywords: Applications, computational logic, domain-specific architectures, performance evaluation, feature extraction, feature construction, bioinformatics, MODELLING SOFTWARE, Flux balance analysis, Metatool