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.
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.
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.
Accuracy and Precision Imagine that you walk into your pitch black home one night. You can’t find your way around because it is dark, so you reach for the light switch and flip it up and…nothing happens. The room is still pitch black. Somehow, you make your way to the kitchen faucet because you need to wash your hands. You turn the handle of the spigot and…no water comes pouring out. You then decide to use your phone to try and call someone or look up what is going on and…no signal. If this was the first time that the Read More
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.
SageMath is a computer algebra system with features covering many aspects of mathematics, including algebra, combinatorics, graph theory, numerical analysis, number theory, calculus and statistics. SageMath is a free open-source mathematics software system licensed under the GPL. It builds on top of many existing open-source packages: NumPy, SciPy, matplotlib, Sympy, Maxima, GAP, FLINT, R and many more. Access their combined power through a common, Python-based language or directly via interfaces or wrappers. Mission: Creating a viable free open source alternative to Magma, Maple, Mathematica and Matlab.