This tutorial aims to provide an introduction to the annotation of CellML models. The initial target is the addition of biological annotations to models from the repository during the 2014/2015 summer, but the tutorial itself will evolve to cover other types of annotation and best practices.
This tutorial would not be possible without the documentation efforts of the Auckland Bioengineering Institute and colleagues. Particularly, we make extensive use of the ABI Tutorials available on GitHub.com. The source for this tutorial is also hosted under that organisation.
Contents
A prelimary introduction to CellML can be obtained from the article An overview of CellML 1.1, available in the Zotero database. The modularity and reuse aspects are covered in more detail in Practical application of CellML 1.1 and Standard virtual biological parts, also in the Zotero database.
The main features available in the Physiome Repository (PMR) are described in the PMR documentation, included here for convenience. It is worth having a quick read through that documentation to help with an initial understanding of the repository and how it can be used. Similarly, the documentation for OpenCOR is also available and worth a quick read.
Mercurial is the version control system used in the Physiome Repository. When interacting directly with Mercurial, this tutorial demonstrates how to work with the repository using TortoiseHg, which provides a Windows explorer integrated system for working with Mercurial repositories.
Note
Brief mention of the equivalent command line versions of the TortoiseHg actions will also be mentioned, so that these ideas can also be used without a graphical client, and on Linux or OS X and similar systems. These will be denoted by boxes like this.
In addition to the main PMR instance, there is a teaching instance available for playing with. It is available at http://teaching.physiomeproject.org. Usually user accounts are copied across whenever the teaching instance is re-initialised, but if you have just created a PMR account, you might need to also create yourself an account on the teaching instance. You may also want to simply create yourself extra accounts on the teaching instance to test out various ideas.
Note
The teaching instance of the repository is a mirror of the main repository site found at http://models.physiomeproject.org/, running the latest development version of PMR2.
Any changes you make to the contents of the teaching instance are not permanent, and will be overwritten with the contents of the main repository whenever the teaching instance is upgraded to a new release of PMR2. For this reason, you can feel free to experiment and make mistakes when pushing to the teaching instance. Please subscribe to the cellml-discussion mailing list to receive notifications of when the teaching instance will be refreshed.
See the section Migrating content to the main repository for instructions on how to migrate any content from the teaching instance to the main (permanent) Auckland Physiome Repository.
This tutorial requires you to have:
The following tutorials provide an introduction to some of the features of both OpenCOR and PMR and should be completed to gain some familiarity with these tools.
Now that you have some familiarity with CellML, PMR, and OpenCOR we can dive into some actual model annotation. The previous annotation tutorial pretty much describes the process, but there is some more help available describing the process in a bit more detail.