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.


Constructs Are Inside and Outside Your Head

“Psychic” objects are phenomenal objects. Phenomenal objects are ones that fit our intuitions of what we think about when we think of “mental” things. Broadly, they are things like concepts, intentionality, intuition, attention, awareness, perception, experience, consciousness, etc. A construct is anything that is an intentional arrangement of elements. This means that any thought that you intentionally think about is a construct because it is an intentional arrangement of experiences, intuitions, concepts, and other things of that nature. This implies that whenever you imagine something, you are technically creating a construct. Metaphysically, there is a question of how this construct Read More



Talisman of Focusing Rings Conceptual Fields, Atomic Concepts, and Energy Flow

So, this is a complex sorcerous talisman of mine. With talismans, the symbols act as conduits. The power comes from the entities (in this case psychic objects) associated with the representation. It’s a talisman of rings that defines a domain that acts as a loci for Experience, Perception, Awareness, Formation, Desire, and Fantasy so that psychic power resonates and is amplified. Those concepts comprise the nodes of the outer ring and the lines throughout the talisman are a mapping of the psychic forces from those concepts – it acts as a vector of psychic forces. Since this is also a Read More


The Power of Your Words: “Non-Magical” Languages Can be More Powerful than Magical Ones

I am a fan of the Dresden Files series. In the Dresden files, there is a branch of elemental battle (or Boom!) magic in the series called evocation magic. It is the creating magical bullet deflecting elemental shields of air, conjuring magical streams of fire, and telekinetic concussive blasts type. It is like the Destruction school of magic in Skyrim. Harry Dresden, the main character of the series, is particularly fond of Fire and Wind evocation spells. Evocation magic in the Dresden universe caught my attention in particular because I specialize in conjuration and evocation of forces albeit I am Read More


Making Probability Mathematical

Throughout much of human history, people consciously and intentionally produced randomness. They frequently used dice – or dice-shaped animal bones and other random objects – to gamble, for entertainment, predict the future and communicate with deities. Despite all this engagement with controlled random processes, people didn’t really think of probability in mathematical terms prior to 1600.


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.



Simplicial Complexes: Part 2

Last episode we saw that your neural network can be modeled as a graph, which — we’ll show in this episode — can be viewed as a higher-dimensional simplicial complex. So… what is a simplicial complex??


Your Mind Is Eight-Dimensional: Part 3

Last episode, we learned that your brain can be modeled as a simplicial complex. And algebraic topology can tell us the Betti numbers of that simplicial complex. Why is that helpful? Let’s find out.


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