Development Update December 2020

[charlesdavid]

• JEDi Paper submitted to BMC Bioinformatics December 24, 2020: Now in peer review!
• BUGS SQUASHED:
  • All parameters now behaving well
  • PDB file issues solved by re-formatting files that are not in STD format
  • The FORTRAN Format: current format string implements the STD PDB format, but NOT tool specific variations.
• CODE REFACTORING:
  • New drivers for POOL, VIZ, ALIGN, KPCA, and SSA
  • Messages to STD OUT and STD ERR provide more details
  • Log file structure and clarity improved
  • The aligned coordinates (transformed) for each subset processed can be written out to file
  • The output from the Free Energy Surface method now included a 3-D Scatter-plot
  • All JEDi flat-file output (except coordinate matrices) are automatically plotted
• Development:
  • Multi Threading fully implemented: Thread Pool
  • All output is high quality PNG format for immediate inspection of results
  • Outlier processing fully implemented with comparative analysis
  • Sparsification fully implemented with identification of activator and suppressor variables
  • Verbose option to output all text files with most in BZ2 format
  • ML modules planned including SPLOC

[charlesdavid]

This work is now done...