{"id":24529015,"url":"https://github.com/saezlab/combims","last_synced_at":"2025-03-15T17:44:50.037Z","repository":{"id":77872523,"uuid":"71999483","full_name":"saezlab/combiMS","owner":"saezlab","description":"combiMS code for Prediction of combination therapy based on perturbation modeling of the multiple sclerosis signaling network. 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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).\n\nThe analysis results compiled here are presented in the following publication:\nBernardo-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\n\n\n## Workflow of the Project\n\n1. Normalization of the raw data with [normalization_pipeline.R](https://github.com/saezlab/combiMS/blob/master/code/data_processing_and_normalization/normalization_pipeline.R)\n2. Patient-specific modeling with CellNOptR, see [single_model_optimization](https://github.com/saezlab/combiMS/tree/master/code/single_model_optimization)\n3. Model merging by subgroups, see [model_merging](https://github.com/saezlab/combiMS/tree/master/code/model_merging)\n4. Analysis of model similarities after merging, see [similarity](https://github.com/saezlab/combiMS/tree/master/code/similarity)\n5. Prediction of combination therapies, see [prediction_of_combination_therapies](https://github.com/saezlab/combiMS/tree/master/code/prediction_of_combination_therapies)\n\n\n## License\n\nDistributed 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).\n\n## Requirements\n\nThe 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.\n\nThe [CellNOptR](https://saezlab.github.io/cellnopt/) packages to fit the signaling models for each individual patient was used in version 1.22.0.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2Fcombims","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsaezlab%2Fcombims","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2Fcombims/lists"}