Analyzer Menu
Authentication
Help > Upload Help

Well Info Help

The Well Info input allows properties to be assigned to wells for analaysis. For example, wells can be assigned names and later sorted by that name.

The Well Info text area accepts input in the tab-delimited format described below. The first line is used as a header to determine which properties will be assigned to each well. Ordinal and Group columns are required and must be the first two columns in the text. Ordinal describes the position of the well in the run and Group allows wells with the same content to be associated with each other (averages can be done only across groups). All other columns are optional.

Groups can be assigned explicitly using group numbers, or by letter replicates (where replicate 'A' defines the start of a new group). It is only necessay to assign values to the first well ordinal in a group.

Well Info Group-Based Format:
Well Info Replicate-Based Format:
The follwing columns are optional:
Name
identifier for well or group of wells
Media
description of media used in well
Comment
any additional information about the well
Strain
identifier for strain added to well

Upload Runs Help

Upload your Bioscreen run files here. Your files should match the Bioscreen format:

Download a sample files

The first row contains headers for data. The first column contains times in HH:MM:SS format (H = hours, M = minutes, S = seconds). All subsequent columns should contain OD readings for that well at the corresponding time. This follows the format output by the Bioscreen, but as long as you format your input files like this, you can use this program to compute doubling times and survivals for growth curves obtained from other devices (96-well plate readers, using counts instead of ODs from colony forming units, etc...)

Days:

Setting the days for your runs allows computations across runs to be computed (i.e. survival curves).

If experiment date is set, the program will try to guess the relative day of the run using the filename. The run filename must contain "_MMDDYY", where MMDDYY represents the month, day, and year of the run. The relative day is computed by subtracting the experiment date from the run date.

For example, if your experiment date is 2007-07-12 and the run filename is cls22_071407.xls, the program will fill in day 2 for that run.

Backgrounds:

In a typical experiment, a few wells containing only media (no cells) should be used to determine background absorbance. If background name is set to BLANK using the well info input, the program will calculate background from the corresponding wells. Background is calculated as the median of the first 10 OD values in wells matching the given name (BLANK by default). If multiple wells are found, the background is calculated as the median of the individual well medians. You can set your own background value by selecting "value" from the drop down list and typing your number (or 0, for no background) in the input field.

Figure 1. Select either well name or value input for background.

Setting the background corrects for the absorbance due to the media alone (for all calculations, the background is first subtracted from the Bioscreen OD reading):

OD(t) = OD_media + OD(0) * e^alpha*t
OD_media = background