PMN has been serving the plant science community for more than fifteen years, but until now the resource has been limited to the species databses created by the PMN team using our in-house database createion pipeline. Now, however, for the first time, we have released our database pipeline to the public. This pipeline is a packaged series of software tools that allow you to create a database like those found in PMN, for any species within Viridiplantae (land plants + green algae) for which you have a full protein annotation, giving you access to PMN's full-metabolism prediction and metabolic analysis tools for species not yet represented in PMN. You can use the resultant databases privately or publish them to the web on your own. The pipeline works off of control files for reproducability, and we are therefore also working on a process for users to submit their databases for inclusion in future PMN releases by sending us their control files.
You can find the build scripts for the Singularity container at https://github.com/CharlesHawkinsMSU/pmn-container. The pipeline requires an x86 Linux environment (we recommend WSL on Windows and a Linux VM on Mac), a copy of Pathway Tools from SRI International (they offer free licenses for academic, government, and nonprofit-affiliated users), and basic familiarity with the Linux command line. We recommend the Quickstart guide linked in the readme to get up to speed with how to use the pipeline, and there is also a full manual linked from there that describes all the options and has a troubleshooting guide.
If you have any issues or find any bugs, you can contact us at curator@plantcyc.org or submit an issue to the tracker on github.
