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: Science

## 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.

## Bell’s Theorem: The Quantum Venn Diagram Paradox

This video is about Bell’s Theorem, one of the most fascinating results in 20th century physics. Even though Albert Einstein (together with collaborators in the EPR Paradox paper) wanted to show that quantum mechanics must be incomplete because it was nonlocal (he didn’t like “spooky action at a distance”), John Bell managed to prove that any local real hidden variable theory would have to satisfy certain simple statistical properties that quantum mechanical experiments (and the theory that describes them) violate.

## Killing Science Fiction: Why Conscious States Cannot Be Copied or Repeated

Several philosophical problems arising from the physics of consciousness, including identity, duplication, teleportation, simulation, self-location, and the Boltzmann Brain problem, hinge on one of the most deeply held but unnecessary convictions of physicalism: the assumption that brain states and their corresponding conscious states can in principle be copied. In this paper I will argue against this assumption by attempting to prove the Unique History Theorem, which states, essentially, that conscious correlations to underlying quantum mechanical measurement events must increase with time and that every conscious state uniquely determines its history from an earlier conscious state.

## The Holographic Universe Explained

One of the most startling possibilities is that our 3+1 dimensional universe may better described as resulting from a spacetime one dimension lower – like a hologram projected from a surface infinitely far away.

## Precision

Accuracy, precision and reproducibility. These are the foundations of science that make our progress possible. How do these play into a scientist’s daily activities? And just how precise can we get with our measurements?

## How to Detect Extra Dimensions

On this Space Time Journal Club we look at how gravitational waves can be used to search for extra dimensions of space!

## Why String Theory is Wrong

There’s this idea that beauty is a powerful guide to truth in the mathematics of physical theory. String theory is certainly beautiful in the eyes of many physicists. Beautiful enough to pursue even if it’s wrong?

## Why String Theory is Right

Some see string theory as the one great hope for a theory of everything – that it will unite quantum mechanics and gravity and so unify all of physics into one glorious theory.

## What are the Strings in String Theory?

So surely there exists a deeper set of cogs and wheels – a theory that brings all observable phenomena into the same mechanical framework. That would be a theory of everything, and this is the great hope of string theory.