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 Software

## Sorcerous Alchemy: Creating Enchanted Crystals with Magic

When people refer to subtle energies, they tend to be referring to ethereal, ephemeral, and intangible things – things that have no concrete substance that you effectively hold in your hand. A lot of ideas about magic propose that it is facilitated by this ethereal and intangible thing. An intuitive concept of augmenting the attributes of something (enchanting it) is to take that ethereal substance, manipulate its properties, and anchor it in some way to something such that the physical object mediates ethereal properties so that it is augmented. This is effectively like painting or gilding an object. It does Read More

## 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

## 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.

## SageMath

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.

## GeoGebra

GeoGebra is dynamic mathematics software for all levels of education that brings together geometry, algebra, spreadsheets, graphing, statistics and calculus in one easy-to-use package. GeoGebra is a rapidly expanding community of millions of users located in just about every country. GeoGebra has become the leading provider of dynamic mathematics software, supporting science, technology, engineering and mathematics (STEM) education and innovations in teaching and learning worldwide.