This repository contains code to reproduce the results in the paper Extending BioMASS to construct mathematical models from external knowledge (Arakane et al., 2024).
Information about the dependencies can be found under environment/.
This directory contains the data and code to generate Figure 2 in the paper (generating executable models from KEGG PATHWAYS).
This directory contains the data and code to generate Figure 3 in the paper (generating executable models from PubTator data).
This directory contains the supplementary material for the paper, which applies the methods in the paper to a JAK-STAT pathway model.