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Continuous processing and evaluation of experimental data is highly needed

2. Helpful hints in the processing of experimental data. 2.1. Organization of work, type o f data. Continuous processing and evaluation of experimental data is highly needed. - Avoid the approach „This year I am experimenting and next year is for the evaluation of what I w ould obtain“.

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Continuous processing and evaluation of experimental data is highly needed

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  1. 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 „This year I am experimenting and next year is for the evaluation of what I would obtain“ - 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.. B130P16E: Practical basics of scientific work Department Experimental Plant Biology FSCU http:/lhr.ueb.cas.cz/petrasek

  2. 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 B130P16E: Practical basics of scientific work Department Experimental Plant Biology FSCU http:/lhr.ueb.cas.cz/petrasek

  3. 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. B130P16E: Practical basics of scientific work Department Experimental Plant Biology FSCU http:/lhr.ueb.cas.cz/petrasek

  4. 2. Helpful hints in the processing of experimental data 2.2. Data explorers, correct data handling and saving Windows Explorer B130P16E: Practical basics of scientific work Department Experimental Plant Biology FSCU http:/lhr.ueb.cas.cz/petrasek

  5. 2. Helpful hints in the processing of experimental data 2.2. Data explorers, correct data handling and saving B130P16E: Practical basics of scientific work Department Experimental Plant Biology FSCU http:/lhr.ueb.cas.cz/petrasek

  6. 2. Helpful hints in the processing of experimental data 2.2. Data explorers, correct data handling and saving Windows Commander B130P16E: Practical basics of scientific work Department Experimental Plant Biology FSCU http:/lhr.ueb.cas.cz/petrasek

  7. 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 B130P16E: Practical basics of scientific work Department Experimental Plant Biology FSCU http:/lhr.ueb.cas.cz/petrasek

  8. 2. Praktické postupy zpracování experimentálních dat 2.3. Spreadsheets, statistical software, graph editors Microsoft Excel – whole protocol management, automation of numerical operations B130P16E: Practical basics of scientific work Department Experimental Plant Biology FSCU http:/lhr.ueb.cas.cz/petrasek

  9. 2. Helpful hints in the processing of experimental data 2.3. Spreadsheets, statistical software, graph editors Sigma Plot – line/scatter plots, bar charts, histograms B130P16E: Practical basics of scientific work Department Experimental Plant Biology FSCU http:/lhr.ueb.cas.cz/petrasek

  10. 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 B130P16E: Practical basics of scientific work Department Experimental Plant Biology FSCU http:/lhr.ueb.cas.cz/petrasek

  11. 2. Helpful hints in the processing of experimental data 2.3. Processing of structural and sequence data Vector NTI(Invitrogen) B130P16E: Practical basics of scientific work Department Experimental Plant Biology FSCU http:/lhr.ueb.cas.cz/petrasek

  12. 2. Helpful hints in the processing of experimental data 2.3. Image analysis, graphical software, presentation software ImageJ (NIH) B130P16E: Practical basics of scientific work Department Experimental Plant Biology FSCU http:/lhr.ueb.cas.cz/petrasek

  13. 2. Helpful hints in the processing of experimental data 2.3. Image analysis, graphical software, presentation software NIS elements(Lucia) B130P16E: Practical basics of scientific work Department Experimental Plant Biology FSCU http:/lhr.ueb.cas.cz/petrasek

  14. 2. Helpful hints in the processing of experimental data 2.3. Image analysis, graphical software, presentation software NIS elements (Lucia) B130P16E: Practical basics of scientific work Department Experimental Plant Biology FSCU http:/lhr.ueb.cas.cz/petrasek

  15. 2. Helpful hints in the processing of experimental data 2.3. Image analysis, graphical software, presentation software Leica LSM B130P16E: Practical basics of scientific work Department Experimental Plant Biology FSCU http:/lhr.ueb.cas.cz/petrasek

  16. 2. Helpful hints in the processing of experimental data 2.3. Image analysis, graphical software, presentation software Zeiss LSMbrowser B130P16E: Practical basics of scientific work Department Experimental Plant Biology FSCU http:/lhr.ueb.cas.cz/petrasek

  17. 2. Helpful hints in the processing of experimental data From the gallery of optical slices to the maximal projection PIN3::PIN3:YFPMaximální projekce Žádníková et al., Development 137, 607-617, 2009 B130P16E: Practical basics of scientific work Department Experimental Plant Biology FSCU http:/lhr.ueb.cas.cz/petrasek

  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 B130P16E: Practical basics of scientific work Department Experimental Plant Biology FSCU http:/lhr.ueb.cas.cz/petrasek

  19. 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 B130P16E: Practical basics of scientific work Department Experimental Plant Biology FSCU http:/lhr.ueb.cas.cz/petrasek

  20. 2. Helpful hints in the processing of experimental data Vandenbussche et al., 2009, Development 137, 597-606 B130P16E: Practical basics of scientific work Department Experimental Plant Biology FSCU http:/lhr.ueb.cas.cz/petrasek

  21. Vandenbussche et al., 2009, Development 137, 597-606 B130P16E: Practical basics of scientific work Department Experimental Plant Biology FSCU http:/lhr.ueb.cas.cz/petrasek

  22. 2. Helpful hints in the processing of experimental data Colocalization analysis Jelínková et al., Plant Journal 61, 883-891, 2009 B130P16E: Practical basics of scientific work Department Experimental Plant Biology FSCU http:/lhr.ueb.cas.cz/petrasek

  23. 2. Helpful hints in the processing of experimental data Colocalization analysis Jelínková et al., Plant Journal 61, 883-891, 2009 B130P16E: Practical basics of scientific work Department Experimental Plant Biology FSCU http:/lhr.ueb.cas.cz/petrasek

  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 B130P16E: Practical basics of scientific work Department Experimental Plant Biology FSCU http:/lhr.ueb.cas.cz/petrasek

  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 B130P16E: Practical basics of scientific work Department Experimental Plant Biology FSCU http:/lhr.ueb.cas.cz/petrasek

  26. 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 B130P16E: Practical basics of scientific work Department Experimental Plant Biology FSCU http:/lhr.ueb.cas.cz/petrasek

  27. 2. Helpful hints in the processing of experimental data 2.3. Image analysis, graphical software, presentation software Corel Photo Paint Adobe Photoshop B130P16E: Practical basics of scientific work Department Experimental Plant Biology FSCU http:/lhr.ueb.cas.cz/petrasek

  28. 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! B130P16E: Practical basics of scientific work Department Experimental Plant Biology FSCU http:/lhr.ueb.cas.cz/petrasek

  29. 2. Helpful hints in the processing of experimental data 2.3. Image analysis, graphical software, presentation software Corel Draw Adobe Illustrator B130P16E: Practical basics of scientific work Department Experimental Plant Biology FSCU http:/lhr.ueb.cas.cz/petrasek

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