SIGs/NeuroFedora/PackageSet

Suggest more software!
Please use this form to suggest more software for inclusion in NeuroFedora.

Moving to Pagure
We're slowly moving the list of software to be packaged to the Pagure instance. This wiki page is a sort of whiteboard/note taking location only.

Complete list of available software
All software that is already packaged can be seen here on src.fedoraproject.org.

There is a good amount of overlap with other SIGs and Spins and some categories of NeuroFedora can be seen as BigData, Fedora-Medical, ML, Octave and SciTech in general.

Please add software that needs to be packaged to the appropriate table with the status "needs packaging". If a package is in a COPR repository, a status of "COPR" can be used. Once a package is in review, the status should be "In review", and of course, once a package is in the repositories, the final status would be "Packaged".

Please feel free to reorganise the tables as required.

If you use a package that is not available in Fedora yet, please feel free to e-mail us and we'll look into providing it. You can either contact us on the mailing list, the IRC channel, or e-mail us privately too!

Packages for Distributed Computing

Package	Summary	Status	Comment
example		Packaged
h5py	A python interface to the HDF5 library	Packaged
mpi4py	Python bindings for MPI---MPICH and OpenMPI	Packaged

Packages for Image analysis

Package	Summary	Status	Comment
ctk	The CTK core library for Image analysis	Packaged
dcm2niix	Conver neuroimaging data from NIFTI format to DICOM	Packaged
isis	Framework to access a large variety of image libraries	Needs import
libminc	Library to work with the MINC file format	Packaged
python-nibabel	Python package to access a cacophony of neuro-imaging file formats	Packaged
python-pydicom	Read, modify, and write DICOM files with Python	Packaged
rubygem-nifti	Pure-ruby library for handling NIfTI data in Ruby	Packaged
python-nilearn	Python module for fast and easy statistical learning on NeuroImaging data	Needs packaging. Dead review here: 1291877
isis	Framework to access a large variety of image processing libraries	Reviewed: needs import 1279176
itktools	Practical command line tools based on the ITK	Reviewed: needs import 1279579
DiffusionKurtosisFit	Code to reconstruct the Diffusion Kurtosis Tensor from Diffusion Weighted MRI	Packaged
petpvc	Tools for partial volume correction (PVC) in positron emission tomography (PET)	Packaged
python-commit	Convex Optimization Modeling for Microstructure Informed Tractography	Needs review. Dead review here: 1288759
python-petlink	Decode and encode PETlink streams	Needs packaging. Dead review here 1288836
python-neurosynth	Large-scale synthesis of functional neuroimaging data	Needs packaging
python-dipy	Diffusion MRI utilities in python	Needs packaging
python-nipype	Neuroimaging in Python: Pipelines and interfaces	Needs packaging
fsleyes	FSLeyes is the FSL image viewer	Needs packaging
sute2p	Cell detection in calcium imaging recordings	Needs packaging

Packages for Data Analysis

Package	Summary	Status	Comment
openmeeg	Low-frequency bio-electromagnetism solving forward problems in the field of EEG and MEG	Packaged
python-mne	Magnetoencephalography (MEG) and Electroencephalography (EEG) data analysis	Packaged
python-pyactivetwo	Python library for reading signal from BioSemi ActiveTwo EEG device	Packaged
python-PyMVPA	Multivariate pattern analysis	Needs packaging. Dead review here: 1280485
python-pymc3	Bayesian statistical modeling and model fitting	Needs packaging. Dead review here 1288870
python-pyspike	Python library for the numerical analysis of spiketrain similarity	Needs packaging. Dead review here: 1291061
python-epac	Machine learning workflow builder	In review 1293043
python-nitime	Nitime is a library for time-series analysis of data from neuroscience experiments	Needs packaging
PyMICE	PyMICE is a Python library for mice behavioural data analysis.	Needs packaging
pyelectro	Analysis of electrophysiology in Python	Needs packaging
eFEL	Electrophys Feature Extraction Library	Needs packaging

Packages for Modeling of neural systems

Package	Summary	Status	Comment
moose	Multiscale Neuroscience and Systems Biology Simulator	Packaged
nest	NEST-The neural simulation tool	Packaged
Brian	The Brian spiking neural simulator	Needs packaging, dead review 1098754
PyNN	A Python package for simulator independent specification of neuronal network models	Review ready, needs deps 1150105
The NEURON simulator	Empirically based simulations of neurons and networks of neurons	Needs packaging, dead review 1249094
MUSIC	MUSIC, the MUltiSimulation Coordinator	Needs packaging
NetPyNE	A python package to facilitate the development of biological neuronal networks in NEURON	Needs packaging, depends on NEURON
libneurosim	Common interfaces for neuronal simulators	Packaged
GENESIS	GENESIS (the GEneral NEural SImulation System) is a general purpose simululation platform that was developed to support the simulation of neural systems ranging from subcellular components and biochemical reactions to complex models of single neurons, simulations of large networks, and system-level models.	COPR exists
pyNeuroML	A single package in Python unifying scripts and modules for reading, writing, simulating and analysing NeuroML2/LEMS models.	Needs packaging
python-libNeuroML	This package provides Python libNeuroML, for working with neuronal models specified in NeuroML http://neuroml.org	Packaged
NeuroMLlite	Work towards creating a common JSON based format for compact network specification	Needs packaging
PyLEMS	LEMS interpreter implemented in Python	Needs review 1643705
csa	The Python implementation of the Connection-Set Algebra	Needs packaging
example		Packaged

Misc Libraries/Utilities

Package	Summary	Status	Comment
python-neo	Represent electrophysiology data in Python	Packaged
DiffusionKurtosisFit	Reconstruct Diffusion Kurtosis tensor from Diffusion Weighted MRI	Packaged
getdp	Finite element solver	Packaged
gifticlib	Refernce IO implementation and tools of the GIFTI XML based file format for cortical surface data	Packaged
nipy-data	Test data and brain templates for nipy	Packaged
openigtlink	Reference implementation of OpenIGTLink: a set of message formats and protocols used for data exchange over a local area network	Packaged
petpvc	Tools for partial volume correction (PVC) in positron emission tomography (PET)	Packaged
python-amico	Relationships backed by Redis	Packaged
python-baker	Easy, powerful access to Python functions from the command line	Packaged
python-citeproc-py	Citations and bibliography formatter	Packaged
python-gradunwarp	Gradient Unwarping	Packaged
python-h5io	Read and write simple Python objects using HDF5	Packaged
python-interfile	Python module for read/write/parse interfile	Packaged
python-klusta	Spike detection and automatic clustering for spike sorting	Packaged
python-lazyarray	A lazily-evaluated numerical array class	Packaged
python-moss	Assorted utilities for neuroimaging and cognitive science	Packaged
python-nixio	Python bindings for NIX, the Neuroscience Exchange Format	Packaged
python-pydotplus	Python interface to Graphviz's Dot language	Packaged
python-PyLink	Universal communication interface using File-Like API	Packaged
python-pyoptical	Pure Python interface to OptiCAL	Packaged
python-pyriemann	Covariance matrices manipulaton and Biosignal classification	Packaged
python-pyxid	Python library for interfacing with Cedrus XID and StimTracker devices	Packaged
python-quantities	Support for physical quantities with units, based on numpy	Packaged
python-simplewrap	Easy to use wrappers generator for C libraries based on ctypes	Packaged
python-tabulate	Pretty-print tabular data in Python, a library and a command-line utility	Packaged
python-transforms3d	3 dimensional spatial transformations	Packaged
texlive	The LaTeX typesetting system for academic writing	Packaged
python-grabbit	Get grabby with file trees!	Packaged
python-cma	Covariance Matrix Adaptation Evolution Strategy numerical optimizer	Packaged
MorphoPy	a Python 3 package for handling morphological reconstructions of neurons and computing summary statistics	Needs packaging
Btmorph	Small Python library containing a data structure and tools to represent and analyze neuronal morphologies stored in the de facto standard SWC format	Needs packaging
python-psychopy	Psychophysics toolkit for Python	Needs packaging. A dead review is here: 1280141
python-cregg	Utilities for running psychology experiments	In review 1280155
python-duecredit	Automated collection and reporting of citations for used software/methods/datasets	Needs packaging. Dead review here: 1280480
python-visionegg-quest	QUEST algorithm for finding threshold	Reviewed: needs import 1290995
debruijn	Software for the generation de Bruijn sequences for neuroscience experiments	Needs packaging. Dead review here: 1291021
neuroshare	Python bindings for Neuroshare	Needs packaging
expyriment	A Python library for cognitive and neuroscientific experiments	Needs packaging
pyphi	A Python package for computing integrated information	Needs review: 1619458
pyemd	Fast EMD for Python: a wrapper for Pele and Werman's C++ implementation of Earth Mover's Distance metric	Needs packaging
uncertainpy	A Python toolbox for uncertainty quantification and sensitivity analysis	Needs packaging
nuitka	A fully compatible Python compiler	Needs packaging. Dead review here: 1288750
tridesclous	offline/online spike sorting with french touch that light the barbecue	Needs packaging
L2L	Learning to learn: gradient-free optimization framework	Needs packaging
inspyred	Python library for bio-inspired computational intelligence.	Needs packaging
hbp_archive	A high-level API for interacting with the Human Brain Project archival storage at CSCS	Needs packaging