‹‹ Back to SVS Home

1.2 Release Notes

[prev] [prev-tail] [tail] [up]

1.2 Release Notes

ChemTreeTM is a software system for analyzing compound screening results. ChemTree is an especially powerful tool for disentangling complex interactions, such as occurrences of multiple binding modes. It provides an efficient means for cherry-picking new compounds with much higher chances of activity. It finds and portrays the relationship between the structural features of compounds and their biological activity. Used in an in vitro/in silico sequential screening process, it is possible to perform accelerated drug discovery. This is a particularly powerful approach when coupled with combinatorial chemistry approaches.

ChemTree employs novel recursive partitioning algorithms to understand relationships among variables using statistical hypothesis testing.

1.2.1 Improvements in version 5.1

  • A new regression feature has been added. Both linear and logistic regressions from one or more binary, continuous, or categorical variables and/or first-order interactions between these variables may be done against one dependent variable. The regression itself may be either normal (all variables at once) or stepwise.
  • The spreadsheet edit menu has been reorganized for better clarity. Features for activating all rows and inverting the column selection have been added.
  • The default maximum number of segments (for new installations of ChemTree) has been changed to 3 for more optimum performance.
  • The manual split window has been optimized.
  • An “X” in the lower-right corner of every tabbed viewer (spreadsheets, trees,and distance matrix plots) is available for deleting the currently-shown tab, not only from view, but also from the project. Such a deletion is only made permanent if the project is saved. This change is mainly designed to aid in quickly removing a zoom view that didn’t come out right from a distance matrix plot, so as to reduce clutter.
  • A project version is now kept track of. If this version (or a future version) of ChemTree is used on a project of a later version (than that version of ChemTree uses), a warning message will be given.
  • Support for one or more categorical dependents has been added to the recursive partitioning.
  • A "false discovery rate" calculation and Simes’ method for p-value adjustment have been added to the manual split p-value display.
  • Many enhancements have been made related to Python scripting:
    • New Python capabilities include temporary projects and importing legacy trees.
    • The dynamic scripting menu system has been reworked, and the directory structure reorganized so that most widgets support adding Python scripts to any of the tool bar menus.
    • The “Run Script” command in the Tools menu of the main window now uses a straightforward file chooser which runs a Python script rather than a legacy script.
    • Other new Python capabilities include a file selector, a directory selector, progress bars, and obtaining the status of a spreadsheet row.
    • New datasets created in scripting may now be added as a child of any project node.
    • A completion message prints after a (Python) script finishes if it was invoked from the command line.
  • Because Python scripting from the command line can now do everything that legacy scripting from the command line could do, legacy scripting has been de-activated.

1.2.2 Bug Fixes

  • If no descriptors at all have either been imported or generated from the imported compounds, ChemTree will show a nice message saying so, rather than crashing.
  • If the only field in the “footer” of a compound is one that is needed for the compound name, ChemTree will properly allow you to import both your compound and your descriptor/potency file, rather than giving you a strange error message.
  • The error message that occurs for an SD file error will continue to work properly, even if it must be shown many times.
  • Resolved performance issue with Mac OS X progress dialogs by switching to a more plain GUI style.
  • Long row names no longer overwrite other text in plots.
  • Quickly deleting multiple navigator nodes caused a crash.
  • Saving a large tree image to bitmap crashed the program by exceeding system resources.
  • Focusing upon certain viewers did not always cause the correct navigator node to highlight.

1.2.3 Known Bugs

  • When using the toolbar Feedback feature from behind a firewall the email is sometimes prevented from going out. The current workaround is to copy the TO and Subject fields generated by ChemTree and put them along with your feedback in your normal email program.
  • Multiple threading is disabled, for now, because there have been problems with multiple threading, perhaps related to the third-party library we use to handle threading and strings.
  • Exceeding 4GB of memory use will crash the program as it is a 32-bit application.
  • To improve performance for manual splitting, once the variables have been scanned, a question box will pop up if there are too many splits for the manual split window to appear quickly. You may choose to list only the most important splits. P-Value plots will still show data for all potential splitters.
  • Under some circumstances, the iteration procedure for the logistic regression will be unstable and the regression may fail, even when the matrix has sufficient rank and significant regressors are included. (See 17.14.) At this time, the best workaround is to filter out the data that causes such instabilities.

[prev] [prev-tail] [front] [up]