CPT_QSPtutorial

Supplementary material for the CPT tutorial paper:

Title: Logic modeling in quantitative systems pharmacology

Authors: Pauline Traynard^*1, Luis Tobalina^*2, Federica Eduati^*3, Laurence Calzone¹, Julio Saez-Rodriguez^2,3

^* Co-first authors

Affiliations: ¹ Institut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, F-75005, Paris, France. ² RWTH Aachen University, Faculty of Medicine, Joint Research Centre for Computational Biomedicine, MTI2 Wendlingweg 2 D-52074 Aachen ³ European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus CB10 1SD Hinxton

##Included files

#####Construction of Prior Knowledge Network: pypath_code.py Python code for pypath

network_extension.docx Description of step-by-step model extension using pypath

PriorKnowledgeNetwork.sif Final Prior Knowledge Network (PKN)

#####Model training perturbationData_LNCaP_MIDAS.csv Perturbation data from (Lescarbeau et al., 2014) normalised and in MIDAS format

CellNOptR_optimisation.R R code for optimisation with CellNOptR logic ODE

#####Trained model: trainedmodel.bnd

trainedmodel.cfg

logicODEparameters_edges.txt

logicODEparameters_nodes.txt

#####MaBoSS simulations and genetic interactions: table_survivalprobas.xlsx table_epistasis.xlsx

##License This project is licensed under the terms of GPLv3.