Software used during the course
| Software | Version (if not latest) | Module | Notes |
|---|---|---|---|
| MetaLo | Latest | Model building and analysis sessions | Logic based modelling workflows |
| MaBoSS | Latest | MaBoSS + PhysiBoSS Introduction AM | Stochastic Boolean modelling |
| CellDesigner | Latest | Systems Biology Graphical Notation | SBML and network diagramming |
| CoLoMoTo Notebook | Latest | Introduction to BN analysis and CoLoMoTo Notebook | Docker based notebook environment |
| Google Chrome | Latest | All modules | Browser needed for online tools |
| Cytoscape + GeneMANIA | Latest | Pathways & Networks, Pathway and Network Analysis | Network visualisation and gene interaction analysis |
| JupyterLab | Latest | CoLoMoTo Notebook Practicals | Web based coding environment |
| Reactome | Website | REACTOME demo + hands on | Pathway exploration |
| CellCollective | Website | CaSQ + CellCollective, Cell Collective Intro | Interactive logical model building |
| BioModelAnalyzer | Website | Introduction to BMA , BMA Practical | Quantitative Boolean model analysis |
| GinSim | Latest | Introduction to Boolean Modelling | Logical modelling of regulatory networks |
| PhysiBoSS | Latest | MaBoSS + PhysiBoSS Introduction | Multiscale modelling |
| BioModels | Website | BioModels + Reactome session | Public model repository |
For installation and setup, please refer to the following guides:
- Oracle VM VirtualBox Installation Guide – Detailed instructions for installing and configuring VirtualBox on different operating systems. (Note: Separate installations are needed for Intel-based and ARM-based Macs, and the VDI files will differ.)
The Host Operating System Requirements are:
- RAM requirement: 8GB (preferably 12GB)
- Processor requirement: 4 processors (preferably 8)
- Hard disk space: 200GB
- Admin rights to the computer
The course data are free to reuse and adapt with appropriate attribution. All course data in these repositories are licensed under the Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0).
Each course landing page is assigned a DOI via Zenodo, providing a stable and citable reference. These DOIs can be found on the respective course landing pages and can be included in CVs or research publications, offering a professional record of the course contributions.
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