Institute of Physical Biology

Concept of protocol generator

2010-08

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

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

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

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

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

Institute of Physical Biology

Protocol generator

• Cells preparation• Cell type• Cultivation medium• Cultivation conditions• Cell concentration• Type of specimen – between glasses, plastic

chamber

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

Institute of Physical Biology

Protocol generator

• Microscope description• Type of microscope• Magnification• Microscopy method• Type of lighting

Institute of Physical Biology

Institute of Physical Biology

www.ufb.jcu.cz