ags-paper

Supplementary material and extra analyses for the paper:

Flobak, Å., Zobolas, J., Vazquez, M., Steigedal, T. S., Thommesen, L., Grislingås, A.,
Niederdorfer, B., Folkesson, E., Kuiper, M. (2021). Logical modeling: Combining manual 
curation and automated parameterization to predict drug synergies. BioRxiv.
https://doi.org/10.1101/2021.06.28.450165

See the full report here.

Instructions for reproducing the simulation results are available at the last section of the report.

Paper Figures

Since the report includes a lot of analyses that didn't make it to the paper, here we shortlist the figures that are present in the publication and their specific position in the online report (or the section which reproduces them if they are more than one, grouped together in the paper). Note that to be fully able to reproduce these figures you may have to run previous code blocks, usually from the start of each respective section where the input files (simulation results) are parsed. This also means that the report has all the necessary context in relation to each of these figures.

In addition, we also provide separate standalone scripts that can be used to generate each of the figures in the publication from the simulation data results.

Main Figures

• Figure 2B, see script
• Figure 2C, see script
• Figure 3, see script
• Figure 4, see script
• Figure 5, see script
• Figure 6, see script
• Figure 7, see script
• Figure 8, see script
• Figure 9, see script
• Figure 10, see script
• Figure 12B & 12C, see script

Supplementary Figures

• Figure S1, see script
• Figure S2, see script
• Figure S3, see script
• Figure S4, see script
• Figure S5 & S6, see script
• Figure S7, see script