Utilities

The following general purpose utilties are also part of NeuroFedora.

Bokeh

sudo dnf install python3-bokeh

The Bokeh Visualization Library

BluePyOpt

sudo dnf install python3-bluepyopt python3-bluepyopt-doc

Blue Brain Python Optimisation Library

chaospy

sudo dnf install python3-chaospy

Numerical tool for performing uncertainty quantification using polynomial.

connection_pool

sudo dnf install python3-connection_pool

Thread-safe connection pool for python.

datalad

sudo dnf install datalad python3-datalad

Keep code, data, containers under control with git and git-annex.

datrie

sudo dnf install python3-datrie

Super-fast, efficiently stored Trie for Python.

exdir

sudo dnf install python3-exdir

Directory structure standard for experimental pipelines.

GNU Octave

sudo dnf install octave

GNU Octave: Scientific programming language. FOSS, compatible with Matlab scripts.

Graph Tool

sudo dnf install python3-graph-tool

An efficient Python module for manipulation and statistical analysis of graphs (a.k.a. networks).

gsl-lite

sudo dnf install gsl-lite-devel

A single-file header-only version of ISO C++ Guidelines Support Library (GSL) for C++98, C++11, and later.

HighFive

sudo dnf install highfive-devel

A modern header-only C++11 friendly interface for libhdf5

JSONLab

sudo dnf install octave-jsonlab

A JSON/UBJSON/MessagePack encoder/decoder for GNU Octave.

llvmlite

sudo dnf install python3-llvmlite

A lightweight LLVM-Python binding for writing JIT compilers.

missingno

sudo dnf install python3-missingno

Missing data visualization module for Python.

MorphIO

sudo dnf install python3-morphio morphio-devel

A python and C++ library for reading and writing neuronal morphologies.

NeuroM

sudo dnf install python3-neurom

Python toolkit for the analysis and processing of neuron morphologies.

OWL_RL

sudo dnf install python3-owl_rl

OWL-RL and RDFS based RDF Closure inferencing for Python.

Pew

sudo dnf install python3-pew

Virtual environment manager written in pure Python.

Plotly

sudo dnf install python3-plotly

An open-source, interactive data visualization library for Python.

pre-commit

sudo dnf install pre-commit

Framework for managing and maintaining multi-language pre-commit hooks.

progressbar2

sudo dnf install python3-progressbar2

A Progressbar library to provide visual progress to long running operations.

PuLP

sudo dnf install python3-pulp

A python Linear Programming API.

pypet

sudo dnf install python3-pypet

Parameter exploration toolbox.

ratelimiter

sudo dnf install python3-ratelimiter

Python module providing rate limiting.

RDFlib-JSON-LD

sudo dnf install python3-rdflib-jsonld

Python rdflib extension adding JSON-LD parser and serializer.

Sklearn-nature-inspired-algorithms

sudo dnf install python3-sklearn-nature-inspired-algorithms

Nature-inspired algorithms for hyper-parameter tuning of Scikit-Learn models.

snakemake

sudo dnf install snakemake

Workflow management system to create reproducible and scalable data analyses.

spyder

sudo dnf install spyder

A powerful scientific environment written in Python, for Python, and designed by and for scientists, engineers and data analysts.

stopit

sudo dnf install python3-stopit

Timeout control decorator and context managers.

toposort

sudo dnf install python3-toposort

Implements a topological sort algorithm.

wxnatpy

sudo dnf install python3-wxnatpy

wxnatpy is a wxPython widget which allows users to browse the contents of a XNAT repository.

xnat

sudo dnf install python3-xnat

A new XNAT client that exposes XNAT objects/functions as python objects/functions.

ZMat

sudo dnf install octave-zmat

A portable data compression/decompression toolbox for GNU Octave.

ZMat Library

sudo dnf install zmat

A portable library with easy-to-use data compression/decompression interfaces.

Python Science Stack

The python-science package group includes commonly used scientific Python libraries. This can be installed using dnf:

sudo dnf install @python-science

The individual packages may also be installed independently:

matplotlib

sudo dnf install python3-matlplotlib

The Python plotting package.

Jupyter Notebook

sudo dnf install python3-notebook

Jupyter notebook.

numpy

sudo dnf install python3-numpy

Fundamental package for array computing with Python.

pandas

sudo dnf install python3-pandas

Python Data Analysis library.

pillow

sudo dnf install python3-pillow

The Python Imaging Library.

scikit-image

sudo dnf install python3-scikit-image

Collection of algorithms for image processing.

scikit-learn

sudo dnf install python3-scikit-learn

Machine learning in Python.

scipy

sudo dnf install python3-scipy

Python library for scientific computing.

statsmodels

sudo dnf install python3-statsmodels

Statistics in Python.

sympy

sudo dnf install python3-sympy

Library for symbolic mathematics.

Reference/bibliography managers

Fedora does not currently include any of these tools. However, the developers provide pre-built binaries that are ready to use.

JabRef

Full featured bibliography manager written in Java.

Zotero

Zotero client. You can also create an account on the Zotero web-service and use it to sync your bibliography between different machines.