Biologics Formulation Series Generator

The occupancy analysis (occupancy_xls.py) in the final steps of the SILCS-Biologics workflow require an input file (expt_data.csv) defining the combination and concentrations of excipients in a given set of formulations to be analyzed. If the user wishes to analyze a range of formulations with varying excipients and concentrations, SilcsBio provides the utility to generate an input file that systematically varyies the excipients and concentration of each formulation.

The following command will generate the input file for occupancy_xls.py:

python $SILCSBIODIR/utils/python/excipients/create_expt_data.py \
     --in_file <IN_FILE> --n_excip <N_EXCIP> --out_file <OUT_FILE> --advanced_help

Optional parameters:

  • Name of input file specifying excipients

    --in_file <IN_FILE>

    If --in_file is not specified, then the default, specs.csv, will be used. Below is an example of the contents of specs.csv:

    Molecule,Type
arginine,excipient
sucrose,excipient
alanine,excipient
succinate,buffer
histidine,buffer

  • Maximum number of excipients in a single formulation

    --n_excip <N_EXCIP>

    If --n_excip is not specified, then the maximum number of excipients in a given formulation will be set to 1. Values greater than 4 are not currently supported.

  • Output file to be used in occupancy calculations

    --out_file <OUT_FILE>

    If --out_file is not specified, then the output file will be named expt_data.csv. This file can be directly used as input in occupancy_xls.py for formulation analysis.

Advanced parameters:

  • Show all advanced options.

    --advanced_help

  • Concentration of excipients to be analyzed in mM:

    ----excipient_conc <EXCIPIENT_CONC>

    By default, the array of excipient concentrations is [0, 10, 25, 50, 100, 150, 200, 250, 500].

  • Concentration of buffers to be analyzed in mM:

    ----buffer_conc <BUFFER_CONC>

    By default, the array of buffer concentrations is [20]. Note that by default, the buffer concentration will only be evaluated at 20 mM.

  • Concentration of other molecules to be analyzed in mM:

    ----other_conc <OTHER_CONC>

    By default, the array of buffer concentrations is [0.01]. Note that by default, the buffer concentration will only be evaluated at 0.01 mM.