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Science Gateways have been widely accepted as an important tool in academic research, due to their flexibility, simple use and extension. However, such systems may yield performance traps that delay work progress and cause waste of resources or generation of poor scientific results. This paper addresses an investigation on some of the failures in a Galaxy system and analyses of their impacts. The use case is based on protein structure prediction experiments performed. A novel science gateway component is proposed towards the definition of the relation between general parameters and capacity of machines. The machine-learning strategies used appoint the best machine setup in a heterogeneous environment and the results show a complete overview of Galaxy, a diverse platform organization, and the workload behavior. A Support Vector Regression (SVR) model generated and based on a historic data-set provided an excellent learning module and proved a varied platform configuration is valuable as infrastructure in a science gateway. The results revealed the advantages of investing in local cluster infrastructures as a base for scientific experiments.