Utilità

The following tools are among the software currently tested in NeuroFedora:

The following general purpose utilties are included in the repositories:

Autograd

sudo dnf install python3-autograd

Efficiently computes derivatives of numpy code

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.

devicely

sudo dnf install python3-devicely

Python package for reading, timeshifting and writing sensor data.

earcut.hpp

sudo dnf install earcut-hpp-devel

C++ port of earcut.js, a fast, header-only polygon triangulation library.

edflib

sudo dnf install edflib

C/C++ library to read/write EDF+ and BDF+ files.

exdir

sudo dnf install python3-exdir

Directory structure standard for experimental pipelines.

Git-changelog

sudo dnf install python3-git-changelog

An automatic Changelog generator using Jinja2 templates. From git logs to change logs.

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

inspyred

sudo dnf install python3-inspyred

Library for bio-inspired computational intelligence.

interrogate

sudo dnf install python3-interrogate

Interrogate a codebase for docstring coverage.

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.

mapbox-earcut

sudo dnf install python3-mapbox-earcut

Very fast and quite robust triangulation of 2D polygons.

matplotlib-venn

sudo dnf install python3-matplotlib-venn

Venn diagram plotting routines for Python/Matplotlib.

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.

Pooch

sudo dnf install python3-pooch

A friend to fetch your data files.

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.

pyABF

sudo dnf install python3-pyABF

Python package for reading electrophysiology data from Axon Binary Format (ABF) files.

pyedflib

sudo dnf install python3-pyedflib

Python library to read/write EDF+/BDF+ files, based on EDFlib.

pypet

sudo dnf install python3-pypet

Parameter exploration toolbox.

pyplane

sudo dnf install pyplane

Phase plane analysis of nonlinear systems

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.

vcd

sudo dnf install R-vcd

Visualizing categorical data.

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.

Pila scientifica di Python

Il gruppo di pacchetti python-science include le librerie Python scientifiche di uso comune. Può essere installato usando dnf:

sudo dnf install @python-science

I singoli pacchetti possono anche essere installati in modo indipendente:

matplotlib

sudo dnf install python3-matplotlib

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.

read-roi

sudo dnf install python3-read-roi

Read ROI files .zip or .roi generated with ImageJ.

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.

visidata

sudo dnf install visidata

An interactive multitool for tabular data.

Responsabili di riferimento/bibliografia

Attualmente Fedora non include nessuno di questi strumenti. Tuttavia, gli sviluppatori forniscono file binari precompilati pronti all’uso.

JabRef

Gestore bibliografico completo scritto in Java.

Zotero

Client Zotero. Puoi anche creare un account sul servizio web di Zotero e utilizzarlo per sincronizzare la tua bibliografia tra diverse macchine.