Code Policy

Please state “Cell Flux Model” and “Keisuke Inomura” in the acknowledgement when your publication includes the results based on the original/revised code. Or you may consider including Keisuke Inomura as a co-author depending on the contribution. In either case, the publication must cite the following paper: Inomura K, Bragg J, Riemann L Follows MJ. (2018). A quantitative model of nitrogen fixation in the presence of ammonium. PLOS ONE: e0208282 (Paper downloaded from https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0208282&type=printable)

Keisuke Inomura (University of Washington) ki24@uw.edu

Azoto2

For plotting, download all the files and put them in the same folder. The codes are in python 3 and they require Latex and pylab.

1. Plotting Fig 1: Run Fig1.py

2. Plotting Fig 3: Run Fig3.py

3. Plotting Fig 4: Run Fig4.py

4. Plotting Fig 6: Run Fig6_calculation.py and then run Fig6_plot.py. To change oxygen concentration, change values of O2satratio in Fig6_calculation.py and O2p in Fig6_plot.py. O2p must be 100 x O2satratio. To change resolution, alter values in tune CNstep and Ninstep in Fig6_calculation.py.

5. Plotting Fig 7: Run Fig7.py

6. Plotting S2 Fig: Run S2_Fig.py

7. Plotting S3 Fig: Run S3_Fig.py To change oxygen concentration, change a value of O2satratio. Resolution can be changed in the same way as Fig 6.