I am currently trying to recreate a gene network using BioPAX in R. I am very new to BioPAX and I would like to know if anyone here could please help me understand a few things:
-What is the best way to automatically import BioPAX data for specific pathways from databases (ie. Reactome, KEGG... etc)? I have paxtoolsr and RBiopaxParser.
-Would you recommend using Paxtools in Java or in R? Or is this irrelevant?
-I would like to use BioASF (to generate executable pathway models).... has anyone here used it by any chance and could help me wrap my head around it?
Thank you in advance for your help!