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Concept of protocol generator

Concept of protocol generator. 2010-08. 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.

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Concept of protocol generator

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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

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

  8. 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

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

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

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