Cytoscape

Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization. Cytoscape core distribution provides a basic set of features for data integration, analysis, and visualization.



Formalism in the Philosophy of Mathematics

The guiding idea behind formalism is that mathematics is not a body of propositions representing an abstract sector of reality but is much more akin to a game, bringing with it no more commitment to an ontology of objects or properties than ludo or chess.


Computing a Universe Simulation

Imagine a universe in which the most elementary components are stripped of all properties besides some binary notion of existence or non-existence. Like, if the tiniest chunks of spacetime, or chunks of quantum fields, or elements in the abstract space of quantum-mechanical states can either be full or empty. These elements interact with their neighbors by a simple set of rules, leading to oscillations, elementary particles, atoms, and ultimately to all of the emergent laws of physics, physical structure, and ultimately the universe.


How Much Information is in the Universe?

But… is the universe actually made of stuff? An increasing number of physicists view the universe – view reality as informational at its most fundamental level. But how big a memory bank would you even need to compute a universe? Seriously, let’s figure it out.


Gephi

Gephi is an open-source software for network visualization and analysis. It helps data analysts to intuitively reveal patterns and trends, highlight outliers and tells stories with their data. It uses a 3D render engine to display large graphs in real-time and to speed up the exploration. Gephi combines built-in functionalities and flexible architecture to: explore, analyze, spatialize, filter, cluster, manipulate, export. Gephi is based on a visualize-and-manipulate paradigm which allow any user to discover networks and data properties. Moreover, it is designed to follow the chain of a case study, from data file to nice printable maps.






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