https://github.com/saezlab/cpt_qsptutorial
Supplementary material for CPT tutorial on logic modeling for quantitative systems pharmacology
https://github.com/saezlab/cpt_qsptutorial
Last synced: over 1 year ago
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Supplementary material for CPT tutorial on logic modeling for quantitative systems pharmacology
- Host: GitHub
- URL: https://github.com/saezlab/cpt_qsptutorial
- Owner: saezlab
- License: gpl-3.0
- Created: 2017-02-28T13:52:24.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2017-05-29T14:15:07.000Z (about 9 years ago)
- Last Synced: 2025-03-28T05:51:02.278Z (over 1 year ago)
- Language: Python
- Size: 106 KB
- Stars: 4
- Watchers: 5
- Forks: 3
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# 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-Rodriguez2,3
* 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.