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.


Python for Everybody: Exploring Data in Python 3

Python for Everybody is designed to introduce students to programming and software development through the lens of exploring data. You can think of the Python programming language as your tool to solve data problems that are beyond the capability of a spreadsheet.


Automate the Boring Stuff with Python

In Automate the Boring Stuff with Python, you’ll learn how to use Python to write programs that do in minutes what would take you hours to do by hand-no prior programming experience required. Once you’ve mastered the basics of programming, you’ll create Python programs that effortlessly perform useful and impressive feats of automation to: Search for text in a file or across multiple files; Create, update, move, and rename files and folders; Search the Web and download online content; Update and format data in Excel spreadsheets of any size; Split, merge, watermark, and encrypt PDFs; Fill out online forms.


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.


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