Tools   Select Another Resource Report Type

http://www.python.org/

Programming language for all operating systems that lets users work more quickly and integrate their systems more effectively. Often compared to Tcl, Perl, Ruby, Scheme or Java. Some of its key distinguishing features include very clear and readable syntax, strong introspection capabilities, intuitive object orientation, natural expression of procedural code, full modularity, exception-based error handling, high level dynamic data types, extensive standard libraries and third party modules for virtually every task, extensions and modules easily written in C, C (or Java for Python, or .NET languages for IronPython), and embeddable within applications as a scripting interface.

Proper citation: Python Programming Language (RRID:SCR_008394) Copy   

•   Source: SciCrunch Registry

http://ipython.org

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   

•   Source: SciCrunch Registry

http://netpyne.org/

Software Python package for simulation and analysis of neuronal networks using the NEURON simulator.Used to facilitate development, parallel simulation, analysis, and optimization of biological neuronal networks.

Proper citation: NetPyNE (RRID:SCR_014758) Copy   

•   Source: SciCrunch Registry

http://cqb.pku.edu.cn/ZhuLab/PPR_Meta

Software tool to identify metagenomic sequences of phages, chromosomes or plasmids. Used for identifying phages and plasmids from metagenomic fragments using deep learning., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PPR-Meta (RRID:SCR_016915) Copy   

•   Source: SciCrunch Registry

https://github.com/BlaisProteomics/mzStudio

Software tool for proteomics data analysis, visualization, and notebook application. Dynamic digital canvas for user driven interrogation of mass spectrometry data. Operating system Unix/Linux, Windows.

Proper citation: mzStudio (RRID:SCR_017088) Copy   

•   Source: SciCrunch Registry

http://emg.nysbc.org/redmine/projects/leginon/wiki/Leginon_Homepage

System designed for automated collection of images from a transmission electron microscope.

Proper citation: Leginon (RRID:SCR_016731) Copy   

•   Source: SciCrunch Registry

https://github.com/legrandp/xdsme

Software package of python scripts made to simplify the processing of crystal diffraction images.

Proper citation: XDSME (RRID:SCR_016943) Copy   

•   Source: SciCrunch Registry

https://github.com/PGB-LIV/VAPPER

Software tool for analysis of variant antigens in African trypanosomes. Used for quantitative analysis of antigenic diversity in systems data of genomes, transcriptomes, and proteomes, called Variant Antigen Profiling to understand how antigenic diversity relates to clinical outcome, how antigen genes may be used as epidemiological markers of virulence, and in measuring gene expression during experimental infections.

Proper citation: VAPPER (RRID:SCR_016993) Copy   

•   Source: SciCrunch Registry

http://cab.spbu.ru/software/rnaquast/

Software tool for evaluating RNA-Seq assembly quality and benchmarking transcriptome assemblers using reference genome and gene database. Capable to estimate gene database coverage by raw reads and de novo quality assessment using third party software.

Proper citation: rnaQUAST (RRID:SCR_016994) Copy   

•   Source: SciCrunch Registry

http://younglab.wi.mit.edu/super_enhancer_code.html

To create stitched enhancers, and to separate super enhancers from typical enhancers using sequencing data given file of previously identified constituent enhancers .

Proper citation: ROSE (RRID:SCR_017390) Copy   

•   Source: SciCrunch Registry

http://sak042.github.io/Wessim/

Software simulator for a targeted resequencing generally known as exome sequencing. Wessim generates a set of artificial DNA fragments for next generation sequencing (NGS) read simulation.

Proper citation: Wessim (RRID:SCR_002567) Copy   

•   Source: SciCrunch Registry

http://www.pyrosetta.org/

Interactive Python based interface to Rosetta molecular modeling suite. Stand alone Python based implementation of Rosetta molecular modeling package that allows users to write custom structure prediction and design algorithms using major Rosetta sampling and scoring functions.

Proper citation: PyRosetta (RRID:SCR_018541) Copy   

•   Source: SciCrunch Registry

http://www.scipy.org/

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   

•   Source: SciCrunch Registry

http://cython.org/

Cython is a language that makes writing C extensions for the Python language as easy as Python itself. Cython is based on the well-known Pyrex, but supports more cutting edge functionality and optimizations. The Cython language is very close to the Python language, but Cython additionally supports calling C functions and declaring C types on variables and class attributes. This allows the compiler to generate very efficient C code from Cython code. This makes Cython the ideal language for wrapping external C libraries, and for fast C modules that speed up the execution of Python code. Sponsor. Google and Enthought funded Dag Seljebotn to greatly improve Cython integration with NumPy. Kurt Smith and Danilo Freitas were funded through the Google Summer of Code program to work on improved Fortran and C support respectively.

Proper citation: Cython C-Extensions for Python (RRID:SCR_008466) Copy   

•   Source: SciCrunch Registry

https://github.com/QTIM-Lab/DeepNeuro

Software Python package for neuroimaging data. Framework to design and train neural network architectures. Used in medical imaging community to ensure consistent performance of networks across variable users, institutions, and scanners.

Proper citation: DeepNeuro (RRID:SCR_016911) Copy   

•   Source: SciCrunch Registry

https://docs.pymc.io/

Software Python package for Bayesian statistical modeling and probabilistic machine learning which focuses on advanced Markov chain Monte Carlo and variational fitting algorithms. Allows model specification directly in Python code.

Proper citation: PyMC3 (RRID:SCR_018547) Copy   

•   Source: SciCrunch Registry

http://lfpy.github.io

Python package for calculation of extracellular potentials from multicompartment neuron models. LFPy can be used to set up a model, run simulations, and calculate the extracellular potentials arising from activity in the given model neuron. It relies on the Python interface provided by the NEURON simulator.

Proper citation: LFPy (RRID:SCR_014805) Copy   

•   Source: SciCrunch Registry

http://web.cmb.usc.edu/people/alber/Software/tomominer/

Software platform for large-scale cryo electron subtomogram classification, alignment, and averaging.

Proper citation: TomoMiner (RRID:SCR_015045) Copy   

•   Source: SciCrunch Registry

https://github.com/Neuroinflab/kCSD-python

Source code for the Python implementation of the kernel Current Source Density method. The method operates in one-, two-, and three-dimensional space to perform nonparametric estimation of transmembrane current sources from local field potentials recorded from arbitrarily distributed electrodes.

Proper citation: kCSD-python (RRID:SCR_015777) Copy   

•   Source: SciCrunch Registry

https://github.com/common-workflow-language/cwltool

Reference implementation of the Common Workflow Language standards. It provides complete features and tools and comprehensive validation of CWL. The reference implementation consists of two packages. The cwltool package is the primary Python module containing the reference implementation in the cwltool module and console executable by the same name. The cwlref-runner package is optional and provides an additional entry point under the alias cwl-runner, which is the implementation-agnostic name for the default CWL interpreter installed on a host.

Proper citation: cwltool (RRID:SCR_015528) Copy   

•   Source: SciCrunch Registry