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.

## Tag: Mathematics

## Abstract Algebra: Theory and Applications

## 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

## Evolution, Dynamical Systems and Markov Chains

In this post we present a high level introduction to evolution and to how we can use mathematical tools such as dynamical systems and Markov chains to model it. Questions about evolution then translate to questions about dynamical systems and Markov chains – some are easy to answer while others point to gaping holes in current techniques in algorithms and optimization.

## Higher dimensions get really weird…

This video covers a range of what shapes and properties you’d encounter in higher dimensions.

## Make Your Own Magical Rules

When people go about making their own magical “systems”, there tend to be two popular routes they take: making their own magical language without formalizing their ontology or they create random sigils. The problem, though, is that those two popular methods alone technically don’t create a magical system. A magical system is an abstraction comprised of a body of axioms, rules, and operations. If you were to look at classical and historical “magical systems”, you will see a formally articulated set of axioms and rules; an example of this is Western occultism. The problem with informally creating your own magical Read More

## 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.

## Dissecting Hypercubes with Pascal’s Triangle

What does the inside of a tesseract look like? Pascal’s Triangle can tell us.

## Splitting Rent with Triangles

You can find out how to fairly divide rent between three different people even when you don’t know the third person’s preferences! Find out how with Sperner’s Lemma.

## How to Generate Pseudorandom Numbers

What is a the difference between a random and a pseudorandom number? And what can pseudo random numbers allow us to do that random numbers can’t?