Objective

The objective of this tool is to define behavioural experiment to be tested with the virtual worm's neural configuration, achieved through the worm configuration tools (Neuron and Synapse Model development, Network Model development)

Where is the tool

This tool is available in the top navigation bar under Experiment Configuration => Behavioural Experiment

Demo video of the tool usage

The following short video shows a demo usage of the tool:

IMAGE ALT TEXT

Description

The Behavioural Experiment Definition Tool is composed of the behavioural experiment selection / creation and the specific graphical user interface to edit the behavioural experiment.

Behavioural experiment selection / creation

This GUI is available at /behaviouralExperimentDefinition/experimentDefinition_Selection. Following a screenshot of the GUI is included.

behavExpSelection.PNG
Behavioural Experiment Selection Window

On the top right of this GUI the Create a new behavioural experiment button creates a new behavioural experiment definition and launches the GUI to edit the behavioural experiment definition from 0.

Next, in the first table named as MY BEHAVIOURAL EXPERIMENTS, experiments created by the logged users are shown. Information on its id, description, creation date and with whom is shared is provided. The user is able to visualise for editing or getting an export XML for the specific behavioural experiment.

Following, in the second table named as SHARED WITH ME, experiments shared with the logged users are shown (shared with specific users). Information on its id, description and if it is publicly shared is provided. The user is able to visualise for editing or getting an export XML for the specific behavioural experiment.

Finally, in the third table named as PUBLICLY SHARED, experiments shared publicly are shown. Information on its id and description is provided. The user is able to visualise for editing or getting an export XML for the specific behavioural experiment.

Note: Experiments that are shared with specific users, publicly or that have been selected as part of a emulation reservation, are not editable, users will only be able to view them. If it is not editable, the GUI to edit behavioural experiment will show the options to clone or to view the experiment.

Behaviour experiment definition edition tool

Non-editable experiments

Experiments that are shared with specific users, publicly or that have been selected as part of a emulation reservation, are not editable, users will only be able to view them. If it is not editable, the GUI to edit behavioural experiment will show the options to clone or to view the experiment. This option is shown in the figure on the left. If clone is selected a new editable instance of the behavioural experiment is created.

clone.PNG
Figure showing non-editable behavioural experiment configuration. Options to clone or to visualize are provided.

Editable experiments

If a behavioural experiment definition is editable, the GUI to edit it loads with the modify option as it is depicted in the figure on the left.

modify.PNG
Figure showing editable behavioural experiment configuration. Option to modify is provided.

Available behavioural experiments

The behavioural stimuli classification and selection has been structured by duration-based behavioral experiment types at the top level (exact, interval, and permanent). For each duration-based experiment type, each of the behavioral input types (i.e. mechanotaxis, chemotaxis, thermotaxis, galvanotaxis, and phototaxis) is allowed. The modelling of the specific behavioural stimuli has been based on the Wormbook behaviour section and more recent publications.

Up to date the stimuli available for setting up a behavioural experiment are depicted in the following figure.

experiments_available.png
Figure depicts available behavioural stimuli classified according to the described classification.

Note: Experiments that define interactions of the same behavioural input type (i.e. mechanotaxis, chemotaxis, thermotaxis, galvanotaxis or phototaxis) for the same point in time may lead to unreliable results. The exception to this note is the possibility to define multiple chemotaxis type interactions at the same point in time, but only using different chemicals for each interaction.

Available chemicals and their common usage

  • "None", (e.g. No chemical applied to a quadrant)
  • "NaCl (attractant, water soluble)",
  • "biotin (attractant, water soluble)",
  • "ethanol (attractant, odorant/volatile)",
  • "butanone (attractant, odorant/volatile)",
  • "CuSO4 (barrier, repellent, water soluble)",
  • "SDS - Sodium dodecyl sulfate (barrier, repellent, water soluble)",
  • "quinine (repellent, water soluble)",
  • "benzaldehyde (repellent, odorant/volatile)",
  • "diacetyl (repellent, odorant/volatile)",
  • "NaN3 (immobilization agent)");

GUI and interaction description

The edit GUI is depicted in the following figure.

behavExp.PNG
Screenshot of the behavioural experiment edit GUI

The edit GUI is divided in 3 windows. The biggest window on the top left is a 3D window where the worm and the environment is represented. The bottom left window represents a timeline with the different behavioural stimuli defined for the experiment. Last but not least, the window on the right is dynamic panel that updates its content based on the selected content to edit. This panel contents updated from environmental configuration, to a behavioural stimulus definition option, or to the specific behavioural stimulus parameters definition.

Global behavioural experiment description can be change in the right window either in experiment stimuli or environment definition mode. Buttons to switch from / to experiment stimulus / environment configuration mode is provided with buttons labeled in each mode as Go to Experiment / Go to Environment.

Either if we click on the Go to Environment button or a specific behavioural stimuli is selected in the timeline, on the right window, the options to create a New Event, Save Experiment and Go to Environment are provided.

If we click on the 3D window (top left), the panel on the right will be updated to configure the environment definition. This includes worm's status configuration (initial position), plate configuration or obstacles. Environment configuration items not implemented are clearly identified as such. 3D window can be interacted by: mouse scroll to zoom in / out, mouse right button click to move the plate around, mouse left button to change camera's view.

If we click on a behavioural stimuli on the timeline, its configuration is loaded in the right windows' panel and we can interactively change the parameters of a specific behavioural stimulus or change the specific behavioural stimulus type by selecting it from the combo box within the Experiment Type section. After different changes done in the GUI, Save Experiment button needs to be clicked to push the changes done to the server. In this mode we also allow to Delete This Event.