SimulCell is a web tool designed to interactively setup and run cell simulation experiments aimed to reproduce the behaviour of experimental cultures growing on a petri dish or similar surface and to quickly analyse the results. It is available for free access, with no registration or login required, although, as an anonymous user, your results will only be available for a short time while the browser window remains open; the same data will remain accessible for up to 48 hours if an identification cookie is accepted. Alternatively, clicking on the “Sign in” button and going through a brief registration phase where you provide an e-mail address, a username and a password, you can store the results for longer and access an “Exp list” page where you can view all your past simulations or even clone and run them again.
A setup page is used to input data, organised in boxes containing cell, plate and event parameters. In the “Experiments planning” area, for each experiment there is a row where you can set the experiment title, start and end time, simulation time interval, growth mode (asynchronous or synchronous), the plate to be used and the number of cells for each defined cell type and, if defined, the occurring events. The storage column is only available to registered users and is used to select long-term or temporary storage.
In the “Cells” section, starting from a menu of predefined cell types, you can define as many new cell types as you want and modify the various parameters according to need. Within a cell card, you can set the parameters which define cell behaviour in terms of growth, proliferation, attachment and movement features. Registered users can click the “Save” button at the top-right of the cell panel to add the current configuration to the cell type menu as a new custom entry. Clicking on the “Expand” button, you access and modify additional, less frequently used, cell parameters, such as the duration of each of the cycle phases and their relative “reference” end-volumes. Finally, by clicking on the “Clone” or “Trash” buttons, you can duplicate or delete the current cell type.
In the “Plates” section, you can define the features of each of the plates used during experiments, using a card which includes geometry, ROI position and size, cell seeding area, medium composition and the optional presence and position of physical borders.
Finally, you can optionally define specific events, selecting their type from the popup menu and by clicking on the “Add event” button. Currently available events include “Medium change”, “Molecule addition”, “Gradient addition”, “Constraint removal”, “Scratch on plate”, “Transfection”, “Viral infection”. For each of them, you can define the time and location at which they occur in the experiment as well as more features specific of the event type.
As for cells, the “Clone” and “Trash” buttons are also available for plates and events at the top right of each card.
During all the set up procedure, you can click on the “Apply” button to temporarily store a partially changed configuration set up, and later go back to it by pressing the “Reset” button. A full reset of the dialog to the default configuration requires clicking on “SimulCell”.
While running a simulation, you can monitor the process by viewing the line plot reporting cell numbers or other data, the pie chart containing the population composition of cycle phase, or an image of the simulated culture. The bottom right section allows to abort execution and display messages provided by the program. The “Break” and “Exit” buttons will both stop the execution, although only the first will wait until the end of the current simulation interval and store the results which will remain viewable in the same way as for a finished simulation.
After the calculation is finished, you are taken to the result page where you can access the simulation results organized in different tables. The table at the top contains general information about all the experiments simulated within a run, including id, title, duration, plate name and number of cells. You can click on “Clone” or “Save” button, at the right end of the table header, to reload the dialog page with the same setup or to save the run as a .url file. The results of each experiment are shown one at a time, by using the relative link in the experiment row and visualised below by using the different tabs.
The “History” table contains a summary of the state of the culture at each time point; “Path” and “Frame” tables respectively organise data by cell and time point; “Setup” and “Performance” tables report the simulation parameters used to setup the experiment and performance indicators such as run duration and others. At the top right end of each result table, you can click on the “Download” button to download the results in CSV format, or on the +/- buttons to expand/compress tables.
Within SimulCell, you can visualise data as custom graphs produced on the spot: while viewing every table, any data column may be plotted by clicking on its heading to see the column data plotted against the first column. You can further customise the graph by using menus to choose a different plot type or to use another column as the x axis.
In the “Video” tab, you can produce a video of the simulated experiment where cells are represented as round or elliptical shapes coloured according to a colour scheme similar to that of a phase contrast image. In the “Mark cells” section, you can colour in red, green or blue any of a number of cell features and rebuild the video by clicking on the “Rebuild” button.
Use examples
The following use examples are provided to explain how to set up a few simple experiments representing typical examples of experimental procedures carried out on cultured cells.
Wound healing experiment
To simulate a wound healing experiment, you can go to the SimulCell experiment set up page, and set up your experiment by using default parameters with the following changes.
In the cell panel, choose one of the available cell types, for example “NIH3T3”, and click on the “Respond to attractants” and “Depend on cell density” check boxes to make cells responsive to attractant and able to modify movement on the base of cell density.
In the plate panel, define a seeding area larger than the ROI by changing “X zoom” to 2 and “Y zoom” to 1.5, similarly set the constraint “X” to 2 and and “Y” to 1.5 and click on “Use Constraint” check box to prevent cells from moving out of the seeding area.
Choose an event of type “Scratch on plate” and click on “Add event” button; finish setting up your event by choosing the time at which the scratch is supposed to occur (“Time start”) and the location and dimensions of the scratch area, for example, set “Xc” and “Yc” to 422 and 300 and “Width” and “Height” to 550 and 1000, respectively.
Now go to the “Experiment planning” section and choose a “Max time” of 1440/2880 minutes, which is long enough to follow wound closure for most cell types; input 1600 for “Cell pop. 1”, a number of starting cells sufficient to continuously cover the defined working area with “NIH3T3” cells.
Transformation foci produced by transfecting a mutated Ras gene
To simulate a transfection experiment, go to the SimulCell experiment set up page, and set up your experiment by using default parameters with the following changes.
In the cell panel, choose the cell type you want to work with; you can optionally change the value of some cell parameters according to needs, for example, click on the “Depend on cell density” check box to make cells able to modify movement on the base of cell density.
In the plate panel, change ROI dimensions by changing “X Size” to 1600 and “Y Size” to 1200 and click on “Use Constraint” check box to prevent cells from moving out of the seeding area.
Choose an event of type “Transfection” and click on “Add event” button; set up your event by choosing the time at which the transfection is supposed to occur (“Time start”), the transfection efficiency and choose “RasV12 gene” as payload of the added agent.
In the same way, add an event of type “Medium change” to step down serum concentration after a suitable delay, for example one hour after transfection.
Now go to the “Experiment planning” section and define the experiment times and seed the desired number of cells, input, for example, 200 for “Cell pop. 1” and choose a “Max time” of 14400 minutes (10 days).
In the same way, you can see the effect of making cells resistant to antibiotics or a poison: just choose “Antibiotic resistance gene” or “Poison resistance gene” when setting up the transfection event and add a defined concentration of antibiotic or poison while defining the “Medium change” event.
A setup page is used to input data, organised in boxes containing cell, plate and event parameters. In the “Experiments planning” area, for each experiment there is a row where you can set the experiment title, start and end time, simulation time interval, growth mode (asynchronous or synchronous), the plate to be used and the number of cells for each defined cell type and, if defined, the occurring events. The storage column is only available to registered users and is used to select long-term or temporary storage.
While running a simulation, you can monitor the process by viewing the line plot reporting cell numbers or other data, the pie chart containing the population composition of cycle phase, or an image of the simulated culture. The bottom right section allows to abort execution and display messages provided by the program. The “Break” and “Exit” buttons will both stop the execution, although only the first will wait until the end of the current simulation interval and store the results which will remain viewable in the same way as for a finished simulation.
The “History” table contains a summary of the state of the culture at each time point; “Path” and “Frame” tables respectively organise data by cell and time point; “Setup” and “Performance” tables report the simulation parameters used to setup the experiment and performance indicators such as run duration and others. At the top right end of each result table, you can click on the “Download” button to download the results in CSV format, or on the +/- buttons to expand/compress tables.
