From Fedora Project Wiki
< SIGs | NeuroFedora
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 | In review 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 1288759 | |
| python-petlink | Decode and encode PETlink streams | In review 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 |
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 | In review 1280485 | |
| python-pymc3 | Bayesian statistical modeling and model fitting | In review 1288870 | |
| python-pyspike | Python library for the numerical analysis of spiketrain similarity | In review 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 |
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 | |
| 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 | 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 | In review 1280141 | |
| python-cregg | Utilities for running psychology experiments | In review 1280155 | |
| python-duecredit | Automated collection and reporting of citations for used software/methods/datasets | In review 1280480 | |
| python-visionegg-quest | QUEST algorithm for finding threshold | Reviewed: needs import 1290995 | |
| debruijn | Software for the generation de Bruijn sequences for neuroscience experiments | Reviewed: needs import 1291021 | |
| neuroshare | Python bindings for Neuroshare | Needs packaging | |
| expyriment | A Python library for cognitive and neuroscientific experiments | Needs packaging |