The GUI¶
Importing Data¶
Allowed Formats¶
Currently the accepted input formats are:
Algem Pro text files
Algem HT-24 CSV (comma separated variable) files
Algem HT-24 intermediate text files
Industrial Plankton (IP) T-Iso CSV files
Photon Systems Instruments (PSI) photobioreactor ODS files
ADA export format/user input format CSV files
It should be possible to export files of this format from the software that is supplied with each of these bioreactors.
If you have a different bioreactor that is not currently supported please feel free to contact me and I’ll try my best to add it.
Growth Data¶
Growth data can be imported with the Add Data
button.
This will open up a window that will allow you to select the type of file to upload and include any additional files (such as condition files).
Select data file(s)
will open up a file browser where you can select one or more files of the same type.
Warning
It is not possible to upload different types of files at the same time, you must Add Data
for each file type you want to upload.
After selecting the files, more options will appear depending on the file type:
- Algem Pro
Growth condition files are stored separately and can be added.
There is also an option to downsample the condition data, this will read in every X measurements. If the frequency of the condition measurements is much greater than the frequency of growth measurements it can take a long time to load the file without downsampling.
- Algem HT-24
A growth conditions file can be added.
Condition downsampling can be specified.
A details file can be added, this contains replicate and other information.
The
Merge details
button will use the replicate information from the details file to average replicate measurements together.- Industrial Plankton (IP T-Iso)
The condition data is contained in the file and will be automatically loaded
- Photon Systems Instruments (PSI)
The condition data is contained in the file and will be automatically loaded
- ADA
Other file types can be exported to this type which contains both growth and conditions data.
It is also possible to download a template file from the
Data
tab to upload custom data. Just open up the template file in your favourite spreadsheet software and add the information to the indicated locations and then load in the data with theADA
option.
Hit the Load
button to upload the files, they should appear in the box below the Add Data
button and the condition data will appear in the box below that.
The x
button next to it will remove the data (just from the software, it won’t delete the original file!).
The +
button allows you to add replicate data, any files added this way will be averaged with the top level files.
To plot more data just keep hitting the Add Data
button.
Plotting¶
To plot the data with the default configuration just hit the Plot!
button.
If you want to change how the plot looks or how the data is processed, head over to the Options tabs.
Note
You can change the individual line colours and styles by clicking on the curves.
Saving¶
To save the plot just hit the Save
button, this will open up a file browser to let you choose a file name and location.
Warning
You cannot create new folders with the file browser, this will cause an error.
Exporting Data¶
You can export the loaded growth data to csv format for easy viewing in your favourite spreadsheet software by hitting the Export
button.
Warning
Replicate data is not yet supported, the top level data file will be exported and any replicates will be ignored.
Making Measurements¶
On the Plot¶
You can measure the linear growth rates (gradients) on the plot by pressing the Measure
button.
This will let you click between any two points on any of the plotted curves and display the gradient on the plot.
Fitting¶
You can fit various growth models to the growth data with the Fit
button.
The available fits are (\(y\) = growth data, \(x\) = time data):
Flat line \(y = p_{0}\)
Linear \(y = p_{1}x + p_{0}\)
Quadratic \(y = p_{2}x^2 + p_{1}x + p_{0}\)
Exponential \(y = p_{0}e^{p_{1}x}\)
Zweitering \(y = y_0 + (A - y_0)/(1 + \exp((4\mu/A)\cdot(\lambda - x) + 2))\)
You can specify the time range over which to do the fit, or leave blank to fit the whole range. The starting guess and upper and lower bounds of the fit parameters can be set by checking the Set parameter bounds
box.
Creating a Table of Measurements¶
If you’ve got a lot of growth curves and you don’t want to measure everything manually you can configure standard measurements to be applied to all curves automatically with the To Table
button.
This will open up a new window that contains a dropdown menu with the available measurements/info, add a row to the table by selecting it in the dropdown menu and hit Add Row
.
This will show the row in the list below and allow you to configure it.
The available measurements/info are:
profile
: The profile name from the header information.reactor
: The name of the reactor the sample was grown in.gradient
: The gradient of Y data (selected with dropdown) between two times (entered in the text boxes).time to
: The time taken for the the Y data (selected with dropdown) to reach a certain point (entered in text box).average of condition
: The average of the condition data (associated with the growth data by comparing the reactor ID and start date/time) between two times (entered in the text boxes).condition at time
: The value of the condition data (selected with dropdown) at a certain time (entered in text box).fit parameter
: The value of a fitted parameter from any of the available growth models, the time range can be specified but it is not currently possible to set the parameter limits.
Measurements can be added as many times as you want if you want to measure multiple conditions.
The Create Table
button will show the table in the Table
tab.
The Save Table
button will open up a file browser to let you chose a file name and location, the table will be saved in csv format.
Creating a Correlation Plot¶
The Correlations
button can be used to plot the dependence of fitted growth curve model parameters on different conditions.
Growth data must have associated condition data loaded with it for this to work, and multiple growth measurements should be present for the correlations to make any sense.
The fit range must be specified and the chosen condition data will be averaged in this range.
The titles will be set automatically but they can be overrriden in the Configuration
tab. Other configurations such as the font sizes are inherited from the main options.
Checking Label
will show information about each data point when you hover over it.
Checking Calculate correlation
will calculate the correlation coefficient between the fit parameter and growth condition and display it on the plot.