Merge branch 'master' of https://github.com/sysbio-curie/Instantiatio…

…n_logical_models

README.md

@@ -1,6 +1,6 @@
-# Instantiation of patient-specific logical models
+# Personalization of patient-specific logical models (PROFILE)
 
-This is a repository of data, code and analyses related to the paper "Instantiation of Patient-Specific Logical Models With Multi-Omics Data Allows Clinical Stratification of Patients". 
+This is a repository of data, code and analyses related to the paper "Personalization of Logical Models With Multi-Omics Data Allows Clinical Stratification of Patients". 
 The paper can accessed here: TBA.
 
 This repository can be cited with its own DOI: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1186270.svg)](https://doi.org/10.5281/zenodo.1186270)
@@ -16,7 +16,7 @@ This set of files and scripts is supposed to be self-sufficient. Please download
 - R
 - MaBoSS requires: flex, bison, gcc and g++
 
-## Patient-specific instantiation pipeline
+## Patient-specific personalization pipeline
 
 In the present pipeline, two different datasets may be used (METABRIC or TCGA) and processed for further simulations with two different logical models, either a generic one (*Fumia* model, see [paper](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0069008)) or a breast-specific one (*Zanudo* model, see [paper](https://cancerconvergence.springeropen.com/articles/10.1186/s41236-017-0007-6)).
 
@@ -33,9 +33,9 @@ rmarkdown::render("Fumia_META_profiles.Rmd", "html_document")
 
 ### Simulation of patient-specific models with MaBoSS
 
-Patient-specific profiles are used to instantiate patient-specific models through different methods based on node activity status, initial conditions or transition rates. Simulations are performed by *MaBoSS* software.
+Patient-specific profiles are used to personalise patient-specific models through different methods based on node activity status, initial conditions or transition rates. Simulations are performed by *MaBoSS* software.
 
-However, model instantiation requires to modify *MaBoSS* model files. The whole simulation process is packed in *python* script. Please note that depending on your operating system, you should choose different versions of that script (either **MaBoSS_specific_Mac** or **MaBoSS_specific_Linux**)
+However, model personalisation requires to modify *MaBoSS* model files. The whole simulation process is packed in *python* script. Please note that depending on your operating system, you should choose different versions of that script (either **MaBoSS_specific_Mac** or **MaBoSS_specific_Linux**)
 
 A minimal example of simulations can be found in the following *shell* script. This is an example of simulations using mutations and CNA information of METABRIC cohort as node activity status. Only values for model output nodes (dead-end nodes regulated by inhibitors/activators but not regulating any other node) are saved.
 
@@ -53,7 +53,4 @@ Another example, computing the scores for all nodes of the model, is available i
 ## Authors
 
 Scripts were mostly designed by Jonas Béal (jonas dot beal at curie dot fr).
-See a complete list of authors in the corresponding paper
-
-
-
+See a complete list of authors in the corresponding paper.