MetaboCraft is a Minecraft plugin designed for visualisation of metabolomic data. It can plot metabolic network maps, as well as 3D graphs of individual metabolic pathways, from data provided by MetExplore. It can also display the effects of experimental conditions on the metabolome, using data obtained from PiMP.
A short demonstration video for MetaboCraft is available here.
- A computer meeting the Minecraft system requirements - mobile and console editions are not currently supported
- Minecraft version 1.11.2 (see here for help) and a valid Minecraft account
- Any modern web browser
The MetaboCraft landing page, which can be accessed using a web browser on port 32909 if the server is running on the local computer, provides an interface for uploading user data, as well as handy access to the MetaboCraft documentation.
To access the MetaboCraft world from Minecraft, after logging in, select Multiplayer, then Add server, select a name for the server and enter its address (which will be simply localhost if running on your local computer). Then select the server you just added and click Join server.
On joining the MetaboCraft server, you will be shown a welcome message informing you of the MetExplore BioSource you are currently viewing, as well as any files uploaded under your name. You will then given access to a map of the metabolic network, including switches to view the subset of the network corresponding to a particular cellular compartment. Selecting a node on this network, representing a specific pathway, will transport you to a view of this pathway. If you have previously uploaded a file of your own metabolomic data, this view will highlight the metabolites identified as changing.
By default, MetaboCraft displays data from MetExplore's BioSource 4324, based on the Recon 2 reconstruction of human metabolism.
Depending on your computer and network speed, building structures can take a few seconds, especially on the first time they are accessed.
A command line interface is provided via the Minecraft console (accessible by pressing / on the keyboard), which provides direct access to the above, as well as exposing some additional functionality.
Available commands are:
/jsp reset
Reinitialises the user's view of the MetaboCraft world from scratch.
/jsp buildNetwork <compartment name (optional)>
Redraws the network map. If no compartment name is specified, it draws the entire network.
/jsp toggleMapMode
Toggles the map view between a force-directed layout (default) and an alphabetical grid.
/jsp buildPath <pathway name>
Draws a view of the specified pathway
/jsp chooseFile <filename>
Allows choosing between different user-uploaded files for displaying changes in pathways. Leaving the filename blank will revert to a vanilla view of the network.
/jsp teleportMe <playername>
Teleports player to the location of another player
/jsp changeBioSource <id>
Allows changing the BioSource to explore the metabolome of different organisms. This option is currently experimental. Applying user-provided data, in particular, is not expected to work properly beyond the default BioSource.
Building and breaking blocks is disabled by default. Server administrators can give full op privileges to particular players wishing to get creative, using the command op <playername> on the server console, or customise the WorldGuard configuration for more advanced setups. Note that ops get full access to the ScriptCraft API, allowing the execution of arbitrary JavaScript code - be selective.
| Entity type | Colour |
|---|---|
| Unchanging metabolite | Black |
| Upregulated metabolite | Blue |
| Downregulated metabolite | Red |
| Side compound | White |
| Edge - substrate to enzyme | Pink |
| Edge - enzyme to product | Green |
This section will be of interest to users intending to run their own instance of the MetaboCraft server.
- A recent computer with at least 2 GB of RAM
- A *nix OS (tested on macOS and Linux) 1
- Outbound HTTP access on port 8080 2
- GNU Screen
- curl
- Git
- Java (SE 8)
- R
There are no concrete CPU or storage space requirements, although a fast CPU can have a significant effect on performance. The base installation takes up around 50 MB of disk space, however the Minecraft world files can increase in size rapidly with usage - do plan accordingly.
Four shell scripts are provided with the server:
- An installer script (install.sh)
- A launcher and stopper for the full MetaboCraft stack (start.sh and stop.sh, respectively)
- A maintenance script to clear the Minecraft world (clearworld.sh). It is recommended to run this script regularly.
Certain R packages need to be installed before using the MetaboCraft server. The installer script will attempt to detect and install them, however depending on the R configuration they might have to be installed manually - all are available on CRAN and can be installed using install.packages(). Those are:
Apart from needing to agree to the Minecraft EULA before beginning the installation, all scripts are non-interactive and self-documenting.
It is recommended to regularly clean the server cache, conveniently located under the cache directory. At a minimum, if the server is externally accessible, user-uploaded data (identified by the "userData" prefix) should be regularly scrubbed.
The MetaboCraft stack is comprised of three distinct components: the Spigot Minecraft server, with the ScriptCraft, WorldEdit and WorldGuard plugins installed, a plumber server and a Shiny server. Access to the Spigot console, as well as the logging output of the other two components, is provided via separate GNU Screen sessions.
[1]: Individual components are cross-platform and have been tested on Windows, however no installation or launch infrastructure is currently provided for that platform.
[2]: Eduroam is known to block this port in some locations.
NOTE: You will still need to separately install the Minecraft client to access MetaboCraft.
MetaboCraft can be run as a Docker container. This contains everything needed
to run the server. The image is at
https://hub.docker.com/r/ronandaly/metabocraft/ and can be downloaded with docker pull ronandaly/metabocraft once Docker is installed correctly. Note that you need to agree to the Minecraft EULA, which you can read at https://account.mojang.com/documents/minecraft_eula, in order to run a container.
To run the container from Kitematic (included with Docker installs), simply search for metabocraft and CREATE a
container. Take note of the port mapped to 25565 - this is the host and port
that needs to be put into the minecraft client. Also take note of the port mapped to 32909 - this is the url that needs to be entered to upload data.
To run the container from the command line, run
docker run -p 25565:25565 -p 80:32909 ronandaly/metabocraft
This will set up a container, with default minecraft and webserver ports.
If you wish to allow block editing, a configuration file needs to be changed. The
file spigot/plugins/WorldGuard/config.yml needs to be changed, and the key
enable, under build-permission-nodes must be set to false.
If running under docker, this can be achieved by passing the environment variable DISALLOW_PLACING_BLOCKS set to false. This can be done by
docker run -e DISALLOW_PLACING_BLOCKS=false -p 25565:25565 -p 80:32909 ronandaly/metabocraft
- Pathway selection from the network map may occasionally malfunction and produce an error message. Resetting the session, either by using the
/jsp resetcommand or by quitting and rejoining the server, fixes the issue.
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.
Incorporates code from bresenham-js, available under the MIT license.