Skip to content. | Skip to navigation

Personal tools
Log in
Sections
You are here: Home Software Fluorit

Fluorit

Fluorit is a program for managing fluorometric fibrillogenesis data.

 


 

Fluorit Logo Getting Started

 

Fluorit Logo Introduction to Fluorit

Fluorit is a fully open source graphical program to manage and view fluorimeter data originating from Varioskan automated fluorimeters. I wrote Fluorit in parts over the course of a few months in an effort to facilitate painfully tedious data processing and visualization tasks. By designing a system where the program relieves the experimenter of tedium, I hope to free the experimenter's mind up to think about what the data actually means. It was a small leap to bundle Fluorit into a more-or-less seamless application. Hopefully others will use Fluorit and benefit from my efforts to simplify my own science.

Since I focus on amyloid fibrillogenesis studies, Fluorit is designed to handle fluorometric fibrillogenesis data. Currently, Fluorit is able to

  1. identify and read exported data files from different versions of the Varioskan software,
  2. organize the time series automatically,
  3. plot the raw data and/or specific subsets of the raw data,
  4. interact with Lukasz Salwinski's Lag Time Server for stochastic analysis,
  5. create lag plots of multiple series as a function of an independent variable,
  6. create publication quality output in a variety of formats,
  7. save an experimenter much time and effort analyzing and organizing data.

Executables are available for Linux, Windows, and OS X (both PPC and Intel).

 

Fluorit Logo News

  • 20080916 - Fluorit is released to the public! Version 0.9 is now available for testing on all major platforms and the web pages are live.

 

Fluorit Logo Feature Requests

I love feature requests almost as much as I love bug reports. My gratitude to the users who have suggested these:

  1. [Done 20081102] Bar chart for plotting lag times as a function of parameters that can't be described with an independent variable. For example, when comparing three different lengths of the same fiber forming peptide.
    Note: Labels for bars can be set Using the "Nick" attribute of series.
  2. Grouping various series into a single series for plots and lag times.
  3. [Done 20081107] On lag plots and reports, provide some indication that some values did not cross the threshold.
    Note: This is now part of the lag time report that is now in the "Info" tab and is formatted as a scrolled table.

 

Fluorit Logo Known Issues

Version 0.9 is a first release. It has not been tested by anyone but the author for the most part, so it has some kinks. Following are some issues with this software that I know about it. I am working on these. I would appreciate knowing about other problems, so bug reports are very helpful. Email me at jstroud@mbi.ucla.edu.

Issues labeled as "Fixed" will be incorporated in the next release.

  1. If the last directory accessed by Fluorit is deleted or removed, Fluorit will hang when attempting to add files. The work-around until this bug is fixed is to remove the hidden ".Fluorit" directory in your home directory and then restart Fluorit.
  2. [Fixed 20080918] There is no error checking when choosing the wrong file type to process. The program will hang. To quit, just close the progress bar and try again.

  3. [Fixed 20080918]  On Linux with Firefox, Firefox has trouble opening a page that an external program tells it to open, so doing multiple series from Lukasz's lag time server will result in an error. Right now, the workaround is to do one at a time.
    Note: This appeared to be an isolated instance with my Linux. I don't think this is a general problem because it seems to have been fixed by rebooting. I'm running Firefox 3.0b5 on Ubuntu 8.04. Your best bet is to run this version of Firefox or later.
  4. [Fixed 20080918] The "Do Plot" checkbutton is enabled in the "Lag Time Preferences" window if only doing one series or if using the server to check for stochasticity. You'll get a plot with one data point in the former case.
  5. [Fixed 20080918] The formatting of the graph is clipped on certain platforms if doing a log x for the lag plot. The workaround is to adjust the margins with the Adjust Plot Button Adjust Plot Button Icon. This is discussed in the Usage Instructions.
    Note: I simply added some more padding around the plot. I might get more sophisticated by trying to standardize fonts and sizes across platforms in the future, but this will do for now.
  6. [Fixed 20080924] The built-in lag time analysis needs a progress bar. It can appear that the program is hanging on large data sets.
  7. [Fixed 20080930] Baseline pairs in the measurements tab do not handle bad values gracefully.
  8. [Fixed 20081003] The scroll wheel does not work in general.
    Note: Because of varying behaviors between different platforms, the fix has entailed that focus will be lost for entries in scrolled frames when the mouse exits the frame and then reenters. I will probably fix this behavior in future versions if I find it to be distracting.
  9. [Fixed 20081001] When saving plots as image files, the file dialog opens in the application directory on windows and linux.
  10. [Fixed 20080925] Tab order within the data series should be more intuitive.
    Note: I think it makes more sense for the tab order to go in columns (all baseline pairs in sequence then all independent variable entries).
  11. [Fixed 20080924] The top panel in the main window needs a resize handle.
    Note: This is fixed by virtue of a major change in the structure of the gui. The "Files" panel is now a tab in the project notebook.
  12. [Fixed 20081003] The "Process Files" button is active before any files are added.
  13. [Fixed 20081003] The "Process Files", "Plot", and "Lag Times" buttons stay active when all files are removed if files have already been processed.
    Note: The program no longer resets the measurement data after all files are removed, so "Plot" and "Lag Times" remain functional and activated. "Process Files" is now disabled when all files become removed.
  14. The OS X version needs a version number in the plist file so that the Finder reports the version correctly.
  15. Selection of multiple files does not work under Linux. The unfortunate workaround is to add one file at a time.
  16. Saving as a pdf file does not work under OS X. The latest updates of OS X 10.4 and 10.5 have a "Preview" program that knows how to interpret eps files. From "Preview" it is possible to save as a pdf. So the work around is to save as an eps file (e.g. "something.eps"), open the eps file with Preview, and save as a pdf file.
  17. [Fixed 20080923] The main window needs to be retitled to "Fluorit".
    Note: With major restructuring of the gui, the main window is now called "Fluorit - Main Window".

Fluorit Logo Wish List

These are some features that the author would like to see:
  1. [Done 20080920] Move the progress bar to the project window.
  2. The icon needs transparency and shadows to make it look good on all backgrounds.
  3. [Done 20081030] Needs the ability to rename the series.
    Note: The "Name" field provides a way to rename the series. Among other uses, these names will title plots. I will likely put in a "Nick"-name field for bar charts.
  4. [Done 20081105] It needs some way to remember preferences and settings for a given experiment, so the user doesn't need to set everything up (e.g. Independent Variables, Gap Times, Series Names, etc.) more than once for any given experiment.
    Note: Major overhaul of the code-base yielded a multi-document architecture with file saving/loading capabilities that can store all data, forms, and preferences for documents independently. This has been a chore.
  5. [Done 20080924] Should be able to have more than one project open at once.
    Note: Controls for opening, saving, and starting new projects have been added to the "File" menu.
  6. [Non-Issue] Currently no way to increase the limits of the axes on any plot. A preference window is planned or maybe a couple of buttons in the tool bar will work.
    Note: Careful use of "reverse-zoom" (2nd mouse button in Zoom Mode) combined with the Adjust Plot Button Adjust Plot Button Icon can achieve any arrangement possible of whitespace and axes limits. However, I may add some configurability for axes and whitespace in a plotting preference window.
  7. Needs to ping the website for updates and alert user with link.
  8. Needs a bug report mechanism on uncaught errors.
  9. Arrows that order files should be icons.
  10. Needs the ability to have multiple experiments (runs) within a project.
  11. [In Progress 20090114] Needs the ability to reorder measurement series in the Measurements tab.
  12. Need to perform auto analysis when files are processed and cache lag times and filter levels.
  13. Needs caching of manual lag time determination.
  14. [Done 20081016] The Info Window should be a tab.
  15. [Done 20081016] Should be a "Project" panel.