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This document is a compilation of Standard Operating Procedures (SOPs) deployed by the EnAlgae microalgal pilot facilities. EnAlgae was a four year Strategic Initiative of INTERREG IVB North West Europe programme. One of the outputs of the EnAlgae project was the development of an integrated network of pilot plants for growing microalgae. An important part of this activity was an exchange of views on operating procedures both with respect to best practices (documented elsewhere) and SOPs. The use of such SOPs provides a unified mechanism for the acquisition and management of data collection. Methods of analysis are described together with data collection (continuous and discrete) on the following types of parameters: environmental parameters, nutrients, algal growth during cultivation, and composition of harvested biomass. Considerations of accuracy and precision are included, with the aim of standardising methods between different analysts and institutions. The document brings together SOPs used by the microalgal partners to serve as a useful starting point for those new to pilot and commercial scale algal cultivation. In addition the generation of such data series is an essential prerequisite for the parameterisation and validation of mathematical models of algal biomass production for commercial exploitation.