The discussion with partners involved in the testing of the BioWes system identified the bottle necks of the developing solution. The definition of the electronic template of the protocol was the main issue. The XML language was originally used for the definition of the protocol template. This way of definition is very beneficial from standardization point of view but it is not very user friendly. Therefore the WYSIWYG (graphical user interface) editor Protocol designer has been developed to solve this issue. Using the Protocol designer, every technician can prepare the protocol template and use it for description of experiments.