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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
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