To begin, download the CLOCCS alignment repo by entering the command into the terminal. Create a conda environment using the conda.rec. yml file by entering the command into the terminal in the folder where the CLOCCS alignment repo was cloned.
Double-click the cloccs_v2023. jar file located in the CLOCCS folder in the CLOCCS alignment repo and wait for a graphical user interface to open. The screen allows input options for the CLOCCS run and displays the results once run.
Input the experimental conditions by specifying the temperature in Celsius using the text box labeled Temperature and specify the synchronization method using the dropdown menu Synchro.method. To input the settings for the budding data, choose the option Bud for budding yeast from the model type dropdown menu. Import the data by uploading a file using the Select File button, or by typing it into the text input boxes of the Data Import panel.
The first column specifies the time points, and the other two columns specify the budding data. To input the settings for flow cytometric data, select the Flow section from the Model type dropdown menu. Import the data using the Data Import panel and click Select File.
Then select the time points in the Times for fitting box for which a flow cytometric CLOCCS fit should be plotted. Once all the inputs have been selected for either budding or flow cytometry, click the Apply button and then the Sample button at the top of the screen. View the budding curve or flow cytometry plots in the Predicted Fits tab.
Obtain the CLOCCS parameters from the fit by selecting the Posterior Parameters tab. The resulting table has each row consisting of the parameter, with the final row being the posterior. The columns consist of the predicted parameter for the mean, 2.5%lower confidence interval, 97.5%upper confidence interval, and acceptance rate.
The CLOCCS budding curves were properly fit as demonstrated by the data points overlaying the corresponding fit curve with a small 95%confidence band. With flow cytometry cell cycle phase data, CLOCCS produces a CLOCCS fit for each selected time point.
