Complex Systems Behave Fundamentally in a Similar Way
Thomas Dandekar, Meik Kunz · Bioinformatics · 2023
Biological systems are self-regulating and maintain their own system state (attractorAttractors). Negative feedback loopsFeedback loops help to prevent overshooting, while positive activation loops (feedforward loopsFeedforward loops) activate the system when it is too weak (e.g. heartbeat). BioinformaticsBioinformatics is able to selectively tap central key elements (e.g. central signallingSignalling cascades; highly linked proteins in the centre, so-called “hubs”Hubs; sequence and system structure analyses, e.g. with interactomics and gene ontologyGene Ontology), through whose concurrence the system behaviourSystem behaviour essentially comes about (“emergence”Emergence). The starting point is the machine-readable description of the system structure (software CytoscapeCytoscape, CellDesigner, etc.), which is then used to simulate the dynamics (e.g. SQUADSQUAD, Jimena, CellNetAnalyzer), whereby the comparison with experiments requires many (“iterative”) model improvements. Systems biology is the most important future field of bioinformaticsBioinformatics, especially in combination with molecular medicine, neurobiology and systems ecology, modern omicsOmics techniques and bioinformaticBioinformatics analysis (R/statistics; read mapping and assembly; metagenome).