At the lowest scale, PhysiCell uses BioFVM solver to simulate the chemical microenvironment using partial differential equations which model the diffusion, uptake and secretion of substrates and signalling molecules. At the cell scale, PhysiCell uses mechanical equations to model individual cell...
This is a tutorial to guide the analysis of RNAseq dataset using footprint based tools such as DOROTHEA, PROGENY and CARNIVAL
COBREXA.jl provides tutorials and notebooks with the purpose of explaining the most important concepts and functions for metabolic modelling and model handling to users, and then practicing them.
The documentation contains basic tutorials (explaining the core package concepts and basic design...
This tutorial aims to be an introduction to
i) the preparation of the Prior knowledge network (PKN) of signaling pathways and
ii) the training of the PKN against biochemical data to create cell-specific models.
Boolean modelling uses a simple representation of biological entities as either active or inactive, and describes their relations with logical formulas. MaBoSS extends Boolean modelling by adding a notion of continuous time, with the introduction of rates of (in)activation. This enable the...
COBREXA.jl is a new software package to enable the analysis and simulation of large metabolic models by taking advantages of modern HPC infrastructure. Mainly, it advanced the scalability of constraint-based method, using the Julia programing language and its mathematic ecosystem as a base...
PerMedCoE is the HPC/Exascale Centre of Excellence for Personalised Medicine in Europe. The goal of PerMedCoE is to provide an efficient and sustainable entry point to the HPC/Exascale-upgraded methodology to translate omics analyses into actionable models of cellular functions of medical relevance.
Working Remotely from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/07-ssh.md.
Shell Variables from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/06-shellvar.md.
Forking a Repository from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/02-forking.md.
Branching in Git from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/01-branching.md.
Manual Pages from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/04-man.md.
Why I Teach from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/10-why.md.