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Continuous processing and evaluation of experimental data is highly needed

B130P16E: Practical basics of scientific work http:/lhr.ueb.cas.cz/petrasek Department of Plant Physiology FS CU RNDr. Jan Petrášek, Ph.D. 2. Helpful hints in the processing of experimental data. 2.1. Organization of work, type o f data.

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Continuous processing and evaluation of experimental data is highly needed

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  1. B130P16E: Practical basics of scientific work http:/lhr.ueb.cas.cz/petrasekDepartment of Plant Physiology FS CU RNDr. Jan Petrášek, Ph.D. 2. Helpful hints in the processing of experimental data 2.1. Organization of work, type of data Continuous processing and evaluation of experimental data is highly needed - Avoid the approach „I am experimenting this year and next year is for the evaluation“ - Spectrum of software must be managed Type od data: - Numerical data - raw data or data converted to the numerical form, may be obtained with certain tool (ruler) or equipment (spectrophotometer) - Graphical data - very important set of results, their quantification is highly needed - Structural data - analytical data, outcomes from sequencing machines, etc..

  2. B130P16E: Practical basics of scientific work http:/lhr.ueb.cas.cz/petrasekDepartment of Plant Physiology FS CU RNDr. Jan Petrášek, Ph.D. 2. Helpful hints in the processing of experimental data 2.1. Organization of work, type of data Software used in modern laboratory: - Software controlling machines - sometimes very complex (PCR cycler), the most important is the form of the output (table, text) - Specialized software - very important in the field of image analysis and processing of sequence data - General software - text and spreadsheet editors, graphical software, presentation software, mainly products of Microsoft - Open source software - very good tools, often problems with the compatibility - online software – mainly in bioinformatics

  3. B130P16E: Practical basics of scientific work http:/lhr.ueb.cas.cz/petrasekDepartment of Plant Physiology FS CU RNDr. Jan Petrášek, Ph.D. 2. Helpful hints in the processing of experimental data 2.1. Organization of work, type of data Windows Explorer or similar software (Windows Commander) Protocols named according to date - the folder in format YYMMDD (081030). Must correspond to date in the laboratory book. Never modify folder with raw data - copying to the folder with other files accompanying the experiment. Back up data - external HDD or DVD or CD, online hard drives Do not delay backuping!!! Experiment must be always finished with complete documentation, do not start others without finishing the previous.

  4. B130P16E: Practical basics of scientific work http:/lhr.ueb.cas.cz/petrasekDepartment of Plant Physiology FS CU RNDr. Jan Petrášek, Ph.D. 2. Helpful hints in the processing of experimental data 2.2. Data explorers, correct data handling and saving Windows Explorer

  5. B130P16E: Practical basics of scientific work http:/lhr.ueb.cas.cz/petrasekDepartment of Plant Physiology FS CU RNDr. Jan Petrášek, Ph.D. 2. Helpful hints in the processing of experimental data 2.2. Data explorers, correct data handling and saving

  6. B130P16E: Practical basics of scientific work http:/lhr.ueb.cas.cz/petrasekDepartment of Plant Physiology FS CU RNDr. Jan Petrášek, Ph.D. 2. Helpful hints in the processing of experimental data 2.2. Data explorers, correct data handling and saving Windows Commander

  7. B130P16E: Practical basics of scientific work http:/lhr.ueb.cas.cz/petrasekDepartment of Plant Physiology FS CU RNDr. Jan Petrášek, Ph.D. 2. Helpful hints in the processing of experimental data 2.3. Spreadsheets, statistical software, graph editors Bulk data processing, their editing and graphical output Microsoft Excel – suitable for all basic jobs including statistics Specialized statistical software - in case of need of more parameters, software Statgraphics, NCSS

  8. B130P16E: Practical basics of scientific work http:/lhr.ueb.cas.cz/petrasekDepartment of Plant Physiology FS CU RNDr. Jan Petrášek, Ph.D. 2. Praktické postupy zpracování experimentálních dat 2.3. Spreadsheets, statistical software, graph editors Microsoft Excel – whole protocol management, automation of numerical operations

  9. B130P16E: Practical basics of scientific work http:/lhr.ueb.cas.cz/petrasekDepartment of Plant Physiology FS CU RNDr. Jan Petrášek, Ph.D. 2. Helpful hints in the processing of experimental data 2.3. Spreadsheets, statistical software, graph editors Sigma Plot – line/scatter plots, bar charts, histograms

  10. B130P16E: Practical basics of scientific work http:/lhr.ueb.cas.cz/petrasekDepartment of Plant Physiology FS CU RNDr. Jan Petrášek, Ph.D. 2. Helpful hints in the processing of experimental data 2.3. Processing of structural and sequence data • Notepad • Avoiding excessive formatting • Plenty of online and stand alone applications for the processing of sequences

  11. B130P16E: Practical basics of scientific work http:/lhr.ueb.cas.cz/petrasekDepartment of Plant Physiology FS CU RNDr. Jan Petrášek, Ph.D. 2. Helpful hints in the processing of experimental data 2.3. Processing of structural and sequence data Vector NTI(Invitrogen)

  12. B130P16E: Practical basics of scientific work http:/lhr.ueb.cas.cz/petrasekDepartment of Plant Physiology FS CU RNDr. Jan Petrášek, Ph.D. 2. Helpful hints in the processing of experimental data 2.3. Image analysis, graphical software, presentation software ImageJ (NIH)

  13. B130P16E: Practical basics of scientific work http:/lhr.ueb.cas.cz/petrasekDepartment of Plant Physiology FS CU RNDr. Jan Petrášek, Ph.D. 2. Helpful hints in the processing of experimental data 2.3. Image analysis, graphical software, presentation software NIS elements(Lucia)

  14. B130P16E: Practical basics of scientific work http:/lhr.ueb.cas.cz/petrasekDepartment of Plant Physiology FS CU RNDr. Jan Petrášek, Ph.D. 2. Helpful hints in the processing of experimental data 2.3. Image analysis, graphical software, presentation software NIS elements (Lucia)

  15. B130P16E: Practical basics of scientific work http:/lhr.ueb.cas.cz/petrasekDepartment of Plant Physiology FS CU RNDr. Jan Petrášek, Ph.D. 2. Helpful hints in the processing of experimental data 2.3. Image analysis, graphical software, presentation software Leica LSM

  16. B130P16E: Practical basics of scientific work http:/lhr.ueb.cas.cz/petrasekDepartment of Plant Physiology FS CU RNDr. Jan Petrášek, Ph.D. 2. Helpful hints in the processing of experimental data 2.3. Image analysis, graphical software, presentation software Zeiss LSMbrowser

  17. 2. Helpful hints in the processing of experimental data From the gallery of optical slices to the maximal projection PIN3::PIN3:YFPMaximální projekce MD 2009, Malenovice, Beskydy

  18. 2. Helpful hints in the processing of experimental data 8 bit - 256 grey scale 12 bit - 4096 grey scale 16 bit - grey scale Kleine-Vehn, unpublished

  19. B130P16E: Practical basics of scientific work http:/lhr.ueb.cas.cz/petrasekDepartment of Plant Physiology FS CU RNDr. Jan Petrášek, Ph.D. 2. Helpful hints in the processing of experimental data 2.3. Image analysis, graphical software, presentation software Dynamic distribution of PIN1 auxin carrier in the plasma membrane of tobacco cells. Prebleach Postbleach FRAP 30 min FRAP in cells of BY-2 expressing AtPIN1-GFP

  20. 2. Helpful hints in the processing of experimental data Vandenbussche et al., 2009, Development, accepted

  21. Vandenbussche et al., 2009, Development, accepted MD 2009, Malenovice, Beskydy

  22. 2. Helpful hints in the processing of experimental data Colocalization analysis Jelínková et al., prov. accepted, Plant Journal, 2009

  23. 2. Helpful hints in the processing of experimental data Colocalization analysis Jelínková et al., prov. accepted, Plant Journal, 2009

  24. Interaction between two proteins - FRET analysis in vivo (PIN1-ADL1) GFP peak RFP peak Spectral detection using ZEISS META 510 detector, laser 477 nm

  25. Interaction between two proteins - FRET analysis in vivo (PIN1-ADL1) 5 Average fluorescence intensity measured over the emission spectrum in the following region of interests: ROI1 - middle cell plate ROI2, ROI3 - growing ends of the cell plate ROI4, ROI5 - transversal and longitudinal plasma membranes 4 2 1 3 500-520 nm unmixed ROI1- low FRET ROI2, ROI3- high FRET ROI4, ROI5 - no FRET 600-620 nm unmixed

  26. B130P16E: Practical basics of scientific work http:/lhr.ueb.cas.cz/petrasekDepartment of Plant Physiology FS CU RNDr. Jan Petrášek, Ph.D. 2. Helpful hints in the processing of experimental data 2.3. Image analysis, graphical software, presentation software Irfan View – ideal for every day browsing through image documentation

  27. B130P16E: Practical basics of scientific work http:/lhr.ueb.cas.cz/petrasekDepartment of Plant Physiology FS CU RNDr. Jan Petrášek, Ph.D. 2. Helpful hints in the processing of experimental data 2.3. Image analysis, graphical software, presentation software Corel Photo Paint Adobe Photoshop

  28. B130P16E: Practical basics of scientific work http:/lhr.ueb.cas.cz/petrasekDepartment of Plant Physiology FS CU RNDr. Jan Petrášek, Ph.D. 2. Helpful hints in the processing of experimental data 2.3. Image analysis, graphical software, presentation software Corel Photo Paint or Corel Photoshop – avoid excessive image adjustment!

  29. B130P16E: Practical basics of scientific work http:/lhr.ueb.cas.cz/petrasekDepartment of Plant Physiology FS CU RNDr. Jan Petrášek, Ph.D. 2. Helpful hints in the processing of experimental data 2.3. Image analysis, graphical software, presentation software Corel Draw Adobe Illustrator

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