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Obtaining Bioscreen Runs:

Prepare overnight cultures of test strains by inoculating 1 µl of the test strain (from deletion set) into 150 µl fresh YPD media.
Prepare the aging culture by inoculating 50 µl of overnight culture into 5 ml of aging media. Maintain at 30 °C in a roller drum for the course of the experiment.
To obtain Bioscreen outgrowth curves, inoculate 5 µl of the aging culture into 145 µl of rich YPD media (2% glucose, 2% bactopeptone, 1% yeast extract) in each well of the Bioscreen plate. Set incubation parameters to continuous shaking (high) at 30 °C, and take 600 nm (wideband range) readings every 30 minutes for 24 hours. (Murakami CJ et al., 2008)

Save the Bioscreen run as 'name_date.csv'(date in MMDDYY format) and repeat step 3 for as many days as needed. For a typical 2 week experiment, collect Bioscreen outgrowth curves on day 2, 4, 6, 9, 11, and 13. Each run should have the same strains in each well number so that correct survivals can be calculated across each lineage (see Figure 2).

Figure 1.Bioscreen files for multiple days

Figure 2. A run contains all the wells in a single Bioscreen plate. A lineage contains the wells from all runs in a single well position.

Uploading your Data:

To upload an experiment, click the "Upload" link in the Analyzer Menu. This will display the Upload Experiment form (see Figure 3). Fill in the experiment name, start date, and description of your experiment. If you want to use named wells for grouping, fill in the well info input (click the question mark for information about format).

Upload each of your Bioscreen files (the program accepts either .xls or .csv formats). Assign each run a day so the program knows which point in the survival curve belongs to which run (survival curve integrals take into consideration days between runs).

If you have named your wells using the well info input, type the name of the media only well in the background field to compute a background reading for the run. Otherwise, select "value" from the background type drop-down and type in a custom background (the default is 0.15).

When all runs are input, click the "Upload" button. The program will tell you what the computed backgrounds are and if any errors have occurred in the results window (see Figure 4).

Figure 3. Upload experiment form

Figure 4. Experiment upload results window

Exporting your Data:

To export your experiment, click the "Export link in the Analyzer Menu. This will display the Export form (see Figure 5). Select the experiment, runs, and wells you are interested in.

Under the Export window, set the "output" drop-down to either runs or lineages (see Figure 2). By default, selecting "runs" will output well name, run name, run day, doubling times, and OD readings - background (click the "show options" link to adjust what parameters are exported). Selecting "lineages" will output doubling time, survivals, and survival integrals.

To export the growth curves for a single well position across all your runs, select just the desired well in the select box and set the output drop-down to "runs".

The lineage output always uses the selected run that has the lowest day as a reference (survival = 1.0) to compute the survival curve.

Figure 5. Export form

Deleting an Experiment or Run:

To delete an experiment or run, click the "Manage" link in the Analyzer Menu. Select your experiment or run and click the corresponding "Delete" button (see Figure 6).

Figure 6. Manage form