Using Fluorit

Fluorit is still at a very early version. Before proceeding, please read about the Known Issues on the Fluorit home page. These issues discuss exceptions and caveats applicable to the following instructions.

Basic Instructions

Exporting Data

Fluorit's ability to use data is contingent on its proper export from the Varioskan Skanit software. Version 2.4.3 of the Skanit software (Varioskan Flash) is exported correctly by default (all information about the data collection is exported). In version 2.2 of the Skanit Software (Varioskan), you must ensure to export at least "Sample", "Measurement time" and "Value" for Fluorit to have enough information to process and organize the data.

Loading Data

Fluorit can read and automatically detect the file type and data organization of files exported from the Varioskan (version 2.2 of Skanit) and Varioskan Flash (version 2.4.3 of Skanit). Parsers for other versions of Skanit can be easily added to Fluorit if sample data files are provided.

1. Export the data properly from Skanit.
   
2. Open the Fluorit application.
3. Click the "Add Files" button.
4. Select some files in the dialog. Linux currently has a problem with selecting multiple files from the file dialog. Please read the Known Issues.
5. Arrange the files with the ^ and v buttons.
6. Enter the time between the files in the "Gap Time (sec)" entries next to the file names. For example, if 180 seconds elapsed between the end of collecting the first file and starting collection of the second, enter "180" next to the second file.
7. Files can be removed or added arbitrarily.
8. Press the "Process Files" button. Currently, Fluorit freezes if you select a file that isn't a Skanit file or a file that wasn't exported correctly. This bug will be corrected soon. If you realize you are processing a malformed file, just close the progress bar window and start over. See the Known Issues.
9. A progress window will give you something to watch. When its done, all of your data series in the experiment will be listed in the "Measurements" panel.

Plotting

Plotting, like lag time analysis, can be done with either grouped or ungrouped data.

• To plot an ungrouped series, simply press the Inspect Button  next to the series you want to plot.
• To plot a group of series, select the series to group with the checkboxes next to the desired series and press the "Plot" button in the toolbar at the top of the main window.
• To save:
1. Click the Save Button
2. On Windows and Linux, the file dialog opens in the application directory by default when saving plots. You will need to navigate to a good location to save the file. Please read the Known Issues.
3. If on Windows or Linux, save either a png file (e.g. "myplot.png") for a bitmap image or a pdf file for a publication quality image (e.g. "myplot.pdf"). Bitmap images work well in Powerpoint while pdf images work well in drawing programs like Illustrator, or desktop publishing programs like InDesign. The OS X version of Fluorit can not yet save in pdf format directly. In OS X, save as an eps file (e.g. "myplot.eps") and open the eps file with Preview. Preview can then save as a pdf file with a perfect preservation of quality.

Lag Time Analysis

Lag time analysis can be done with either grouped series or single series. The user also has the choice of using Fluorit to calculate the lag time and standard error of the lag time or having Lukasz Salwinski's Lag Time Server perform a stochastic analysis of the data.

• To do lag time analysis on a single series:
1. Click the Lag Button next to the series for which you want to calculate a lag time.
2. Select whether you would like to use Fluorit ("Local-Deterministic") or the Lag Time Server ("Server").
3. Enter a value for the Cutoff that you determined when inspecting the data using the plotting functionality.
4. Click OK. There is no reason to do the plot here. See the Known Issues for details.
5. If you selected "Local-Deterministic" a window will open showing the results of the calculation. If you chose to use the Lag Time Server ("Server"), your browser will open a window with the results.
• To do lag time analysis on a group of series:
1. If you will want a Lag Plot, enter values for the Independent Variable in the "Ind. Var." entries next to the series in which you are interested.
   
2. Select the series to group with the checkboxes next to the desired series.
3. Press the "Lag Times" button in the toolbar at the top of the main window.
4. Select whether you would like to use Fluorit ("Local-Deterministic") or the Lag Time Server ("Server") to perform the lag time analysis.
5. Enter a value for the Cutoff that you determined when inspecting the data using the plotting functionality.
6. If you selected "Server", a plot will not be performed, even if you select the "Do Plot" checkbox. See the Known Issues for details.
7. If you selected "Local-Deterministic", you may select "Do Plot":
• Optionally enter text for the various labels.
• You can also perform a semi-log X plot by checking the "Do Log X" button and entering a value for the base of the logarithm. The default value is 10.
• If you choose "Do Log X" and one of your independent variable values is zero, the plot will not be created.
• If one of your series did not have any replicates that exceed the cutoff, the plot will not be created.
• If clipping occurs, click the Plot Adjust Button  and adjust the sliders to unclip text. See the Known Issues for details.
• The resulting plot can be saved. See the Plotting subsection above for details.
8. Click "OK" in the "Lag Time Preferences" window. You may find yourself waiting a while if you chose "Local-Deterministic" lag time analysis. I haven't yet added a progress bar for this function. See the Known Issues for details.
9. If you are on Linux and using Mozilla/Firefox and selected "Server", your second and later series will not open due to a bug in Firefox. I hope to find a workaround for this bug. Firefox works fine in OS X and Windows. See the Known Issues for details.
10. If you selected "Local-Deterministic" a window will open showing the results of the calculation.