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NOTES.md

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  • [151120F] ** implemented add_ngri_column_0.py *** column names are provisional ** to do *** finalize column names
  • [151124T] ** fixed column names ** changed log10c column to concentration *** changed numeric format to 3 significant figures
  • [151125W] ** changed abbreviation ngri to gr throughout ** changed numeric format of gr column to 3 significant figures ** updated PROTOCOL
  • [151127F] ** fixed numeric format of gr column Previous version only approximated a 3-significant figure format using a string formatting template; it worked fine for numbers like 0.123 but rendered as, e.g., 0.7 what should have been 0.700; the current version gets that right. ** eliminated some abbreviations in the code ...for the sake of clarity
  • [151130M] ** restored line accidentally deleted from add_gr_column_0.py ** reordered columns of input/toy.tsv primarily so that the agent and concentration columns are adjacent
  • [160111M] ** done
    • fix .gitnit -> .gitignore
    • 17AAG -> 17-AAG in ./**/toy*
    • input/ -> INPUT/, &c
    • root_pipeline -> STANDARDIZATION
    • fix add_gr_column_0.py
      • rename to add_gr_column.py
      • run main conditionally
    • update warmup/PROTOCOL.org ** state *** tree % tree -I .git $HOME//projects/gr50_browser /home/berriz//projects/gr50_browser . |-- .gitignore |-- STANDARDIZATION/ | |-- INPUT/ | |-- OUTPUT/ | | -- LOG/ | |-- PROTOCOL.org | -- SRC/ | -- TEST/ -- warmup/ |-- INPUT/ | |-- toy.tsv | -- toy.txt |-- NOTES.org |-- OUTPUT/ | |-- LOG/ | -- toy1.tsv |-- PROTOCOL.org -- SRC/ |-- add_gr_column.py* |-- makefake.py -- TEST/ `-- test_format_sig_figs.py *** git ls-files .gitignore warmup/INPUT/toy.tsv warmup/NOTES.org warmup/OUTPUT/toy1.tsv warmup/PROTOCOL.org warmup/SRC/TEST/test_format_sig_figs.py warmup/SRC/add_gr_column.py

** todo

  • update and commit warmup/SRC/TEST
  • [180118M] and prior days ** done
    • MATLAB implementation
    • Python scripts to generate examples
    • tests and examples for the MATLAB scripts
    • documentation (Word tutorial)

** state major changes on the structure of the repo for publication

** to do - convert the tutorial in .md (such that it is self-contained in GitHub) - additional functionality as described in the MATLAB file GRmetrics.m -- priority: testing of the input! - implementation of the sigmoidal fit in Python - long term: plotting functions