https://github.com/saezlab/combims
combiMS code for Prediction of combination therapy based on perturbation modeling of the multiple sclerosis signaling network. Code started by Marti at EBI on Feb 2013
https://github.com/saezlab/combims
Last synced: over 1 year ago
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combiMS code for Prediction of combination therapy based on perturbation modeling of the multiple sclerosis signaling network. Code started by Marti at EBI on Feb 2013
- Host: GitHub
- URL: https://github.com/saezlab/combims
- Owner: saezlab
- License: gpl-3.0
- Created: 2016-10-26T12:11:09.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2020-05-04T11:31:06.000Z (about 6 years ago)
- Last Synced: 2025-01-22T07:37:38.613Z (over 1 year ago)
- Language: R
- Homepage:
- Size: 61.9 MB
- Stars: 1
- Watchers: 6
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE.txt
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README
# combiMS
Data, code and analysis results of the CombiMS project.
For more information, please visit the [website](https://cordis.europa.eu/project/rcn/106479/factsheet/en) of the project. This project was supported by the European Union Seventh Framework Programme (FP7/2007-2) under grant agreement No. 305397 and the European Sys4MS project (Horizon2020: Eracosysmed: ID-43).
The analysis results compiled here are presented in the following publication:
Bernardo-Faura, M. et al, Prediction of combination therapies based on topological modeling of the immune signaling network in Multiple Sclerosis, [bioRxiv 541458](https://www.biorxiv.org/content/10.1101/541458v1) and under submission, 2019
## Workflow of the Project
1. Normalization of the raw data with [normalization_pipeline.R](https://github.com/saezlab/combiMS/blob/master/code/data_processing_and_normalization/normalization_pipeline.R)
2. Patient-specific modeling with CellNOptR, see [single_model_optimization](https://github.com/saezlab/combiMS/tree/master/code/single_model_optimization)
3. Model merging by subgroups, see [model_merging](https://github.com/saezlab/combiMS/tree/master/code/model_merging)
4. Analysis of model similarities after merging, see [similarity](https://github.com/saezlab/combiMS/tree/master/code/similarity)
5. Prediction of combination therapies, see [prediction_of_combination_therapies](https://github.com/saezlab/combiMS/tree/master/code/prediction_of_combination_therapies)
## License
Distributed under the GNU GPLv3 License. See accompanying file [LICENSE.txt](https://github.com/saezlab/combiMS/blob/master/LICENSE.txt) or copy at [http://www.gnu.org/licenses/gpl-3.0.html](http://www.gnu.org/licenses/gpl-3.0.html).
## Requirements
The scripts collected in this repository are written in [R 3.4.0 (2017-04-21)](https://cran.r-project.org/) and were run in [RStudio Version 0.99.893](https://www.rstudio.com) and on the Cluster of the [Rheinisch-Westfälische Technische Hochschule Aachen](https://www.rwth-aachen.de/), which uses Centos 7.3 and the LSF job scheduling system version 9.1.3.0.
The [CellNOptR](https://saezlab.github.io/cellnopt/) packages to fit the signaling models for each individual patient was used in version 1.22.0.