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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
A Python-based environment of open-source software for mathematics, science, and engineering. The core packages of SciPy include: NumPy, a base N-dimensional array package; SciPy Library, a fundamental library for scientific computing; and IPython, an enhanced interactive console.
Proper citation: SciPy (RRID:SCR_008058) Copy
http://ipython.org/notebook.html
A web application and interactive computational environment where users can combine code execution, rich text, mathematics, plots, and rich media. IPython Notebook consists of two parts, the web application and plain texts. The Ipython Notebook web application is used for interactive authoring of literate computations, in which explanatory text, mathematics, computations, and rich media output may be combined. Input and output are stored in persistent cells that may be edited in-place. The plain text documents, called notebooks, record and distribute the results of the rich computations. Saved files in the notebook can be put under version control and shared with colleagues.
Proper citation: IPython Notebook (RRID:SCR_013984) Copy
https://github.com/neurodroid/stimfit
Software for viewing and analyzing electrophysiological data. It features an embedded Python shell that allows you to extend the program functionality by using numerical libraries such as NumPy and SciPy.
Proper citation: Stimfit (RRID:SCR_016050) Copy
A web-based interactive computational environment where you can combine code execution, text, mathematics, plots and rich media into a single document. It offers a comprehensive library on top of which more sophisticated systems can be built. The project provides an enhanced interactive environment that includes support for data visualization and facilities for distributed and parallel computation.
Proper citation: IPython (RRID:SCR_001658) Copy
http://www.ni.gsu.edu/~rclewley/PyDSTool/FrontPage.html
Integrated simulation and analysis environment for dynamic systems models of physical systems. It supports symbolic math, optimization, phase plane analysis, continuation and bifurcation analysis, data analysis, and other tools for modeling. It is written in Python with some underlying C and Fortran legacy code.
Proper citation: PyDSTool (RRID:SCR_014771) Copy
The Electrophysiology Analysis Toolkit (Elephant) is a Python library that provides a modular framework for the analysis of experimental and simulated neuronal activity data, such as spike trains, local field potentials, and intracellular data. Elephant builds on the Neo data model to facilitate usability, to enable interoperability, and to support data from dozens of file formats and network simulation tools. Its analysis functions are continuously validated against reference implementations and reports in the literature. Visualizations of analysis results are made available via the Viziphant companion library. Elephant aims to act as a platform for sharing analysis methods across the field.
Proper citation: Elephant (RRID:SCR_003833) Copy
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