It is an independent application that should ensure the repeatability and correctness of the biological experiments. The tool is designed to lead the experimenter through the particular type of experiment as a supervisor and help. Protocol generator has two purposes: the first one is to check that the procedure of the experiment has been done precisely and the second one is to produce all important settings that are part of the experiment in the form of report on the experiment. The method to ensure precise realization of experiment is to check if all necessary parameters and steps of the experiment have been set and done. The list of necessary parameters and steps for the particular type of experiment comes up from the analysis of biological experiment for different research institutes.

The description of the experiment can be created by the user for specific experiment. Graphical user interface Protocol designer has been implemented for this purpose. The protocol template is created by the person who fully understands the experiment and who can define all the important conditions of the experiment. The user can use 10 basic components for definition of the protocol. The protocol of experiment can be shared among the people who realize the experiment (students) to ensure the repeatability of the experiment.

The protocol is internally defined by XML language and has to follow the XSD scheme prescribed for experiment description. Templates of protocols can be stored in the local database for future usage. The template can be later modified for new experiment to speed up the process.

Main advantage of the electronic protocol is that there is a direct link between the protocol and experimental data. Both are stored in the central database and can be used for obtaining future data.

Protocol generator supports external plugins for mining information about setting of devices from external files. The plugins can read the information about some parameters of experiment form files produced by measurement device (magnification of microscope) and fill it into the protocol. Plugins are using open interface and therefore it can be created by the users for specific devices.