1. Institute of Physical Biology Concept of protocol generator 2010-08

2. Institute of Physical Biology Protocol generator Motivation Repeatability of experiment Chaotic and incomplete description of experiments Lack of usage of measuring device outputs Settings Conditions Subjective knowledge of experiment Description just in written form

3. Institute of Physical Biology Protocol generator Goal Develop software tool for precise experiment description (standard) Usage of measuring device outputs Usage of subjective knowledge of experimenter Unify experiment description

4. Institute of Physical Biology Protocol generator Concept One software tool for one experimental area The software read the accessible information from measuring device The software force the experimenter to provide minimal set of experiment description The set is defined by experts Generation of protocol about the experiment Storage of experiments

5. Institute of Physical Biology Protocol generator Minimal set of experiment description The experimenter has to be able to reproduce the results by the protocol about experiment All main factors of the experiment have to be contained in the set The set has to be extendible Global storage of the minimal sets Minimal set update via internet Predefined possibilities of individual set items Simple possibilities extension - xml

6. Institute of Physical Biology Protocol generator Example Time lapse microscopy experiments Study of cell cycle Protocol generator: Cells preparation Photography process description Microscope description Global storage of experiments on the server

7. Institute of Physical Biology Protocol generator Cells preparation Cell type Cultivation medium Cultivation conditions Cell concentration Type of specimen – between glasses, plastic chamber

8. Institute of Physical Biology Protocol generator Photography process description Camera setting (EXIF) Delay between photographs Focusing Size of pixel Duration of experiment Start of experiment Non-standard operations

9. Institute of Physical Biology Protocol generator Microscope description Type of microscope Magnification Microscopy method Type of lighting

10. Institute of Physical Biology www.ufb.jcu.cz