Model of acclimation publicly available

Institute for Quantitative and Theoretical Biology made available on-line the old photosynthesis model for model organism alga Chlamydomonas reinhardtii and you can now easy download it and play with it! All you need is a working python and scientific packages. I suggest to download Anaconda distribution that comes with all packages needed to smoothly run the model.

We share Python files reproducing the mathematical model described in the paper published by Ebenhoeh et al. 2014, originally developed in MATLAB. The model comprises a set of seven coupled ordinary differential equations and captures the temporal evolution of: PQ, PC, Fd, lumenal H, ATP concentration, NADPH concentration and cross section of PSII.

You can access the model from git repository.

You now have two options: either you download the model as a zip file and use it directly on your computer, or you setup git. Second option is preferred if you would like to be anyhow involved in the development. In this case, I would suggest signing in (free of charge) and cloning the model. So for those who would like to know how to use git, a few simple steps:

*INSTALL GIT INSTRUCTIONS*

If you’re on a Debian-based distribution like myself, try apt-get:

[code language=”bash”]
$ apt-get install git
[/code]

If you are using Windows, an easy way to get Git installed is by installing GitHub for Windows. The installer includes a command line version of Git as well as the GUI and can be downloaded from http://windows.github.com.

If you are using Mac, there are several ways, like simply try to run git from the Terminal the very first time. If you don’t have it installed already, it will prompt you to install it.

*GET THE MODEL COPY ON YOUR COMPUTER*

If you wish to start tracking an existing project in Git, create a new directory of choice, then go to this project directory on your computer and type:

[code language=”bash”]
$ git init
[/code]

You clone a repository with git clone [url]. In our case we copy the url from the right hand side of the website:

[code language=”bash”]
$ git clone https://github.com/QTB-HHU/petcmodel.git
[/code]

You should notice that in the selected directory on your computer you have now all files from the on-line repository. Now, you can construct a branch of the project, for instance named with your name:

[code language=”bash”]
$ git checkout -b Giulio
[/code]

and edit files within this branch. Whatever you will change in the file you need to /add and further /commit. Without going to too many details, we have three stage path from the changing the file to uploading to the github, which helps avoiding publishing mistakes.

You can change a parameter in a file, you can add some simple plotting function. You can do whatever. But whatever you wish to change, you need to type:

[code language=”bash”]
$ git add [name-of-the-changed-file]
$ git commit [name-of-the-changed-file] -m "here-you-can-put-message-with-information-what-you-changed"
[/code]

And what is the coolest part, later you can share it with the others, by sending your project back to the github:

[code language=”bash”]
$ git push origin Giulio
[/code]

*HOW TO USE THE MODEL*

Actually, all you need to know is described in the README file in the repository. The equations are implemented in petcModel.py and their origin is explained in detail in the electronic supplementary material of the publication. If you wish to reproduce for instance the PAM experiment in the darkness, you can easily type:

[code language=”bash”]
python dld.py >/dev/null 2>/dev/null
[/code]

You can also investigate the steady state change in the redox state of the reductant pool under different light conditions, like on the figure below or write your own protocol for an experiment in silco!

I hope that some of you will be interested in playing with the model. Have fun!