About OpenWorm

OpenWorm aims to build the first comprehensive computational model of Caenorhabditis elegans (C. elegans), a microscopic roundworm. With only a thousand cells, it solves basic problems such as feeding, mate-finding and predator avoidance. Despite being extremely well-studied in biology, a deep, principled understanding of the biology of this organism remains elusive.

We are using a bottom-up approach, aimed at observing the worm behaviour emerge from a simulation of data derived from scientific experiments carried out over the past decade. To do so, we are incorporating the data available from the scientific community into software models. We are also forging new collaborations with universities and research institutes to collect data that fill in the gaps.

You can earn a badge with us simply by trying out this package! Click on the image below to get started.

Quickstart

We have put together a Docker container that pulls together the major components of our simulation and runs it on your machine. When you get it all running it does the following:

1. Run our nervous system model, known as c302, on your computer.
2. In parallel, run our 3D worm body model, known as Sibernetic, on your computer, using the output of the nervous system model.
3. Produce graphs from the nervous system and body model that demonstrate its behavior on your computer for you to inspect.
4. Produce a movie showing the output of the body model.

Example Output

NOTE: Running the simulation for the full amount of time would produce content like the above. However, in order to run in a reasonable amount of time, the default run time for the simulation is limited. As such, you will see only a partial output, equivalent to about 5% of run time, compared to the examples above. To extend the run time, use the -d argument as described below.

Installation

Pre-requisites:

1. You should have at least 60 GB of free space on your machine and at least 2GB of RAM
2. You should be able to clone git repositories on your machine. Install git, or this GUI may be useful.

To Install:

1. Install Docker on your system.
2. If your system does not have enough free space, you can use
   an external hard disk. On MacOS X, the location for image storage
   can be specified in the Advanced Tab in Preferences. See this thread
   in addition for Linux instructions.

Running

1. Ensure the Docker daemon is running in the background (on MacOS/Windows there should be an icon with the Docker whale logo showing in the menu bar/system tray).
2. Open a terminal and run: git clone http://github.com/openworm/openworm; cd openworm
3. Optional: Run ./build.sh (or build.cmd on Windows). If you skip this step, it will download the latest released Docker image from the OpenWorm Docker hub.
4. Run ./run.sh (or run.cmd on Windows).
5. About 5-10 minutes of output will display on the screen as the steps run.
6. The simulation will end. Run stop.sh (stop.cmd on Windows) on your system to clean up the running container.
7. Inspect the output in the output directory on your local machine.

Advanced

Arguments

• -d [num] : Use to modify the duration of the simulation in milliseconds. Default is 15. Use 5000 to run for time to make the full movie above (i.e. 5 seconds).

Other things to try

• Open a terminal and run ./run-shell-only.sh (or run-shell-only.cmd on Windows). This will let you log into the container before it has run master_openworm.py. From here you can inspect the internals of the various checked out code bases and installed systems and modify things. Afterwards you’ll still need to run ./stop.sh to clean up.
• If you wish to modify what gets installed, you should modify Dockerfile. If you want to modify what runs, you should modify master_openworm.py. Either way you will need to run build.sh in order to rebuild the image locally. Afterwards you can run normally.

FAQ

What is the Docker container?

The Docker container is a self-contained environment in which you can run OpenWorm simulations. It’s fully set up to get you started by following the steps above. At the moment,
it runs simulations and produces visualizations for you, but these visualizations must be viewed outside of the Docker container. While you do not need to know
much about Docker to use OpenWorm, if you are planning on working extensively with the platform, you may benefit
from understanding some basics. Docker Curriculum
is an excellent tutorial for beginners that is straightforward to work through (Sections 1 – 2.5 are plenty sufficient).

Is it possible to modify the simulation without having to run build.sh?

Yes, but it is marginally more complex. The easiest way is to modify anything in the Docker container once you are inside of it – it will work just like a bash shell. If you want to modify any code in the container, you’ll need to use an editor that runs in the terminal, like nano. Once you’ve modified somethi