Vanderbilt HTS file format

The Vanderbilt HTS format is the plain-text interchange format for Thunor. Each row represents a single measurement: one well at one timepoint. Files are tab-separated by default; use a .csv extension for comma-separated files.

Load a file with thunor.io.read_vanderbilt_hts() and save one with thunor.io.write_vanderbilt_hts().

Columns

Required

Column	Type	Description
`upid`	string	Unique plate identifier
`well`	string	Well name composed of a row letter and column number, e.g. `A1`, `H12`, `P24`
`time`	float	Elapsed time in hours from the start of the experiment
`cell.count`	float	Cell count; must be ≥ 0

Drug annotation

Drug annotation columns must either all be present or all be absent. When present, rows where all drug concentrations are zero are treated as control wells; all other rows are experiment wells.

Column	Type	Description
`cell.line`	string	Cell line name
`drug1`	string	Drug name; leave blank for control wells
`drug1.conc`	float	Drug concentration in molar; set to `0` for control wells
`drug1.units`	string	Concentration units; must be `M`

For combination screens, include a second set: drug2, drug2.conc, drug2.units.

Optional metadata

Column	Type	Description
`expt.id`	string	Experiment identifier
`expt.date`	string	Experiment date in `YYYY-MM-DD` format

Example

A minimal single-drug file with two experiment wells at two concentrations and one control well, each measured at two timepoints (columns are tab-separated):

upid    well  cell.line  drug1          drug1.conc  drug1.units  time  cell.count
Plate1  A1    MCF7       Staurosporine  1e-9        M            0     1000
Plate1  A1    MCF7       Staurosporine  1e-9        M            24    1250
Plate1  B1    MCF7       Staurosporine  1e-8        M            0     990
Plate1  B1    MCF7       Staurosporine  1e-8        M            24    450
Plate1  C1    MCF7                      0           M            0     1010
Plate1  C1    MCF7                      0           M            24    2020

Reading this file:

from thunor.io import read_vanderbilt_hts
dataset = read_vanderbilt_hts('data.txt')

Plate size

By default, thunor.io.read_vanderbilt_hts() assumes a 384-well plate (24 columns × 16 rows, so wells run from A1 to P24). Pass plate_width and plate_height explicitly for other sizes:

# 96-well plate
dataset = read_vanderbilt_hts('data.txt', plate_width=12, plate_height=8)