1. Continuous processing and evaluation of experimental data is highly needed 2.1. Organization of work, type of data 2. Helpful hints in the processing of experimental data - 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.. B130P16E: Practical basics of scientific work http:/lhr.ueb.cas.cz/petrasek Department of Plant Physiology FS CU RNDr. Jan Petrášek, Ph.D.

2. 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 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 of data

3. 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 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 of data

4. Windows Explorer 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 2.2. Data explorers, correct data handling and saving

5. 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 2.2. Data explorers, correct data handling and saving

6. Windows Commander 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 2.2. Data explorers, correct data handling and saving

7. 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 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 2.3. Spreadsheets, statistical software, graph editors

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

9. Sigma Plot – line/scatter plots, bar charts, histograms 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

10. Notepad 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 2.3. Processing of structural and sequence data

11. Vector NTI (Invitrogen) 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

12. ImageJ (NIH) 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 2.3. Image analysis, graphical software, presentation software

13. NIS elements (Lucia) 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 2.3. Image analysis, graphical software, presentation software

14. NIS elements (Lucia) 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 2.3. Image analysis, graphical software, presentation software

15. Leica LSM 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 2.3. Image analysis, graphical software, presentation software

16. Zeiss LSM browser 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 2.3. Image analysis, graphical software, presentation software

17. FRAP in cells of BY-2 expressing AtPIN1-GFP PrebleachPostbleachFRAP 30 min Dynamic distribution of PIn1 auxin carrier in the plasma membrane of tobacco cells. 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 2.3. Image analysis, graphical software, presentation software

18. Irfan View – ideal for every day browsing through image documentation 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 2.3. Image analysis, graphical software, presentation software

19. Corel Photo Paint Adobe Photoshop 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 2.3. Image analysis, graphical software, presentation software

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

21. 2.3. Image analysis, graphical software, presentation software Corel Draw Adobe Illustrator 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