|
|
| Line 1: |
Line 1: |
| {{admon/tip|Suggest more software!|Please use [https://goo.gl/forms/j6AJ82yOh78MPxby1 this form] to suggest more software for inclusion in NeuroFedora.}} | | {{admon/tip|Suggest more software!|Please use [https://goo.gl/forms/j6AJ82yOh78MPxby1 this form] to suggest more software for inclusion in NeuroFedora.}} |
|
| |
|
| {{admon/tip|Moving to Pagure|We're slowly moving the list of software to be packaged to [https://pagure.io/neuro-sig/NeuroFedora/issues the Pagure instance]. This wiki page is a sort of whiteboard/note taking location only.}} | | {{admon/tip|Moved to Pagure|The list of software to be packaged is now at [https://pagure.io/neuro-sig/NeuroFedora/issues the Pagure instance].}} |
|
| |
|
| {{admon/tip|Complete list of available software| All software that is already packaged can be seen [https://src.fedoraproject.org/group/neuro-sig here on src.fedoraproject.org].}} | | {{admon/tip|Complete list of available software| All software that is already packaged can be seen [https://src.fedoraproject.org/group/neuro-sig 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 ==
| |
| {| class="wikitable"
| |
| |-
| |
| ! Package !! Summary !! Status !! Comment
| |
| |-
| |
| | {{FpPackage|example}} || || Packaged ||
| |
| |-
| |
| | {{FpPackage|h5py }} || A python interface to the HDF5 library|| Packaged ||
| |
| |-
| |
| | {{FpPackage|mpi4py }} || Python bindings for MPI---MPICH and OpenMPI|| Packaged ||
| |
| |-
| |
| |}
| |
|
| |
| == Packages for Image analysis ==
| |
|
| |
| {| class="wikitable"
| |
| |-
| |
| ! Package !! Summary !! Status !! Comment
| |
| |-
| |
| | {{FpPackage|ctk }} || The CTK core library for Image analysis || Packaged ||
| |
| |-
| |
| | {{FpPackage|dcm2niix }} || Conver neuroimaging data from NIFTI format to DICOM || Packaged ||
| |
| |-
| |
| | {{FpPackage|isis }} || Framework to access a large variety of image libraries|| Needs import ||
| |
| |-
| |
| | {{FpPackage|libminc }} || Library to work with the MINC file format || Packaged ||
| |
| |-
| |
| | {{FpPackage|python-nibabel }} || Python package to access a cacophony of neuro-imaging file formats|| Packaged ||
| |
| |-
| |
| | {{FpPackage|python-pydicom }} || Read, modify, and write DICOM files with Python|| Packaged ||
| |
| |-
| |
| | {{FpPackage|rubygem-nifti }} || Pure-ruby library for handling NIfTI data in Ruby|| Packaged ||
| |
| |-
| |
| | {{FpPackage|python-nilearn}} ||Python module for fast and easy statistical learning on NeuroImaging data || Needs packaging. Dead review here: [[rhbug:1291877|1291877]] ||
| |
| |-
| |
| | {{FpPackage|isis}} ||Framework to access a large variety of image processing libraries|| Reviewed: needs import [[rhbug:1279176|1279176]]||
| |
| |-
| |
| | {{FpPackage|itktools}} ||Practical command line tools based on the ITK|| Reviewed: needs import [[rhbug:1279579|1279579 ]]||
| |
| |-
| |
| | {{FpPackage|DiffusionKurtosisFit}} || Code to reconstruct the Diffusion Kurtosis Tensor from Diffusion Weighted MRI|| Packaged ||
| |
| |-
| |
| | {{FpPackage|petpvc}} ||Tools for partial volume correction (PVC) in positron emission tomography (PET) || Packaged ||
| |
| |-
| |
| | {{FpPackage|python-commit}} || Convex Optimization Modeling for Microstructure Informed Tractography|| Needs review. Dead review here: [[rhbug:1288759 |1288759 ]] ||
| |
| |-
| |
| | {{FpPackage|python-petlink}} || Decode and encode PETlink streams|| Needs packaging. Dead review here [[rhbug:1288836 |1288836 ]] ||
| |
| |-
| |
| | [https://pypi.org/project/neurosynth/ python-neurosynth] || Large-scale synthesis of functional neuroimaging data|| Needs packaging ||
| |
| |-
| |
| | [https://pypi.org/project/dipy/ python-dipy] || Diffusion MRI utilities in python|| Needs packaging ||
| |
| |-
| |
| | [https://pypi.org/project/nipype/ python-nipype] || Neuroimaging in Python: Pipelines and interfaces|| Needs packaging ||
| |
| |-
| |
| | [https://pypi.org/project/fsleyes/ fsleyes] ||FSLeyes is the FSL image viewer || Needs packaging ||
| |
| |-
| |
| | [https://github.com/MouseLand/suite2p sute2p] || Cell detection in calcium imaging recordings|| Needs packaging ||
| |
| |-
| |
| |}
| |
|
| |
| == Packages for Data Analysis ==
| |
| {| class="wikitable"
| |
| |-
| |
| ! Package !! Summary !! Status !! Comment
| |
| |-
| |
| | {{FpPackage|openmeeg}} || Low-frequency bio-electromagnetism solving forward problems in the field of EEG and MEG|| Packaged ||
| |
| |-
| |
| | {{FpPackage|python-mne }} || Magnetoencephalography (MEG) and Electroencephalography (EEG) data analysis || Packaged ||
| |
| |-
| |
| | {{FpPackage|python-pyactivetwo }} ||Python library for reading signal from BioSemi ActiveTwo EEG device || Packaged ||
| |
| |-
| |
| | {{FpPackage|python-PyMVPA }} ||Multivariate pattern analysis|| Needs packaging. Dead review here: [[rhbug:1280485|1280485]] ||
| |
| |-
| |
| | {{FpPackage|python-pymc3}} || Bayesian statistical modeling and model fitting || Needs packaging. Dead review here [[rhbug: 1288870 | 1288870 ]] ||
| |
| |-
| |
| | {{FpPackage|python-pyspike}} || Python library for the numerical analysis of spiketrain similarity || Needs packaging. Dead review here: [[rhbug: 1291061 | 1291061 ]]||
| |
| |-
| |
| | {{FpPackage|python-epac}} || Machine learning workflow builder|| In review [[rhbug: 1293043 | 1293043 ]]||
| |
| |-
| |
| | [http://nipy.org/nitime/ python-nitime] || Nitime is a library for time-series analysis of data from neuroscience experiments|| Needs packaging ||
| |
| |-
| |
| | [https://github.com/Neuroinflab/PyMICE PyMICE] ||PyMICE is a Python library for mice behavioural data analysis. || Needs packaging ||
| |
| |-
| |
| | [https://github.com/NeuralEnsemble/pyelectro pyelectro] ||Analysis of electrophysiology in Python|| Needs packaging ||
| |
| |-
| |
| | [https://github.com/BlueBrain/eFEL eFEL] ||Electrophys Feature Extraction Library|| Needs packaging ||
| |
| |-
| |
| |}
| |
|
| |
| == Packages for Modeling of neural systems ==
| |
| {| class="wikitable"
| |
| |-
| |
| ! Package !! Summary !! Status !! Comment
| |
| |-
| |
| | {{FpPackage|moose}} || Multiscale Neuroscience and Systems Biology Simulator || Packaged ||
| |
| |-
| |
| | {{FpPackage|nest}} || NEST-The neural simulation tool|| Packaged||
| |
| |-
| |
| | [http://briansimulator.org/ Brian] || The Brian spiking neural simulator || Needs packaging, dead review [[rhbug:1098754|1098754]] ||
| |
| |-
| |
| | [https://github.com/NeuralEnsemble/PyNN PyNN] || A Python package for simulator independent specification of neuronal network models|| Review ready, needs deps [[rhbug:1150105| 1150105]]||
| |
| |-
| |
| | [https://www.neuron.yale.edu/neuron/ The NEURON simulator] || Empirically based simulations of neurons and networks of neurons|| Needs packaging, dead review [[rhbug:1249094|1249094]]||
| |
| |-
| |
| | [https://github.com/INCF/MUSIC MUSIC] || MUSIC, the MUltiSimulation Coordinator || Needs packaging||
| |
|
| |
| |-
| |
| | [https://github.com/Neurosim-lab/netpyne NetPyNE] || A python package to facilitate the development of biological neuronal networks in NEURON || Needs packaging, depends on NEURON ||
| |
| |-
| |
| | {{FpPackage|libneurosim}} || Common interfaces for neuronal simulators || Packaged ||
| |
| |-
| |
| | [http://genesis-sim.org/ 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. || [https://copr.fedorainfracloud.org/coprs/zbyszek/neurord/ COPR] exists ||
| |
| |-
| |
| | [https://github.com/NeuroML/pyNeuroML pyNeuroML] ||A single package in Python unifying scripts and modules for reading, writing, simulating and analysing NeuroML2/LEMS models. || Needs packaging ||
| |
| |-
| |
| | {{FpPackage|python-libNeuroML}} ||This package provides Python libNeuroML, for working with neuronal models specified in NeuroML http://neuroml.org|| Packaged||
| |
| |-
| |
| | [https://github.com/NeuroML/NeuroMLlite NeuroMLlite] ||Work towards creating a common JSON based format for compact network specification|| Needs packaging ||
| |
| |-
| |
| | [https://github.com/LEMS/pylems PyLEMS] ||LEMS interpreter implemented in Python|| Needs review [[rhbug:1643705|1643705]] ||
| |
| |-
| |
| | [https://github.com/INCF/csa csa] ||The Python implementation of the Connection-Set Algebra|| Needs packaging ||
| |
| |-
| |
| | {{FpPackage|example}} || || Packaged ||
| |
| |-
| |
| |}
| |
|
| |
| == Misc Libraries/Utilities ==
| |
|
| |
| {| class="wikitable"
| |
| |-
| |
| ! Package !! Summary !! Status !! Comment
| |
| |-
| |
| | {{FpPackage|python-neo}} || Represent electrophysiology data in Python || Packaged ||
| |
| |-
| |
| | {{FpPackage|DiffusionKurtosisFit }} || Reconstruct Diffusion Kurtosis tensor from Diffusion Weighted MRI || Packaged ||
| |
| |-
| |
| | {{FpPackage|getdp }} || Finite element solver || Packaged ||
| |
| |-
| |
| | {{FpPackage|gifticlib }} || Refernce IO implementation and tools of the GIFTI XML based file format for cortical surface data || Packaged ||
| |
| |-
| |
| | {{FpPackage|nipy-data }} || Test data and brain templates for nipy|| Packaged ||
| |
| |-
| |
| | {{FpPackage|openigtlink }} || Reference implementation of OpenIGTLink: a set of message formats and protocols used for data exchange over a local area network|| Packaged ||
| |
| |-
| |
| | {{FpPackage|petpvc }} || Tools for partial volume correction (PVC) in positron emission tomography (PET)|| Packaged ||
| |
| |-
| |
| | {{FpPackage|python-amico }} || Relationships backed by Redis|| Packaged ||
| |
| |-
| |
| | {{FpPackage|python-baker }} || Easy, powerful access to Python functions from the command line|| Packaged ||
| |
| |-
| |
| | {{FpPackage|python-citeproc-py }} || Citations and bibliography formatter|| Packaged ||
| |
| |-
| |
| | {{FpPackage|python-gradunwarp }} || Gradient Unwarping|| Packaged ||
| |
| |-
| |
| | {{FpPackage|python-h5io }} || Read and write simple Python objects using HDF5|| Packaged ||
| |
| |-
| |
| | {{FpPackage|python-interfile }} || Python module for read/write/parse interfile|| Packaged ||
| |
| |-
| |
| | {{FpPackage|python-klusta }} || Spike detection and automatic clustering for spike sorting|| Packaged ||
| |
| |-
| |
|
| |
| | {{FpPackage|python-lazyarray }} || A lazily-evaluated numerical array class|| Packaged ||
| |
| |-
| |
| | {{FpPackage|python-moss }} || Assorted utilities for neuroimaging and cognitive science|| Packaged ||
| |
| |-
| |
| | {{FpPackage|python-nixio }} || Python bindings for NIX, the Neuroscience Exchange Format|| Packaged ||
| |
| |-
| |
| | {{FpPackage|python-pydotplus }} || Python interface to Graphviz's Dot language|| Packaged ||
| |
| |-
| |
| | {{FpPackage|python-PyLink }} || Universal communication interface using File-Like API|| Packaged ||
| |
| |-
| |
| | {{FpPackage|python-pyoptical }} || Pure Python interface to OptiCAL|| Packaged ||
| |
| |-
| |
| | {{FpPackage|python-pyriemann }} || Covariance matrices manipulaton and Biosignal classification|| Packaged ||
| |
| |-
| |
| | {{FpPackage|python-pyxid }} || Python library for interfacing with Cedrus XID and StimTracker devices|| Packaged ||
| |
| |-
| |
| | {{FpPackage|python-quantities }} || Support for physical quantities with units, based on numpy|| Packaged ||
| |
| |-
| |
| | {{FpPackage|python-simplewrap }} || Easy to use wrappers generator for C libraries based on ctypes|| Packaged ||
| |
| |-
| |
| | {{FpPackage|python-tabulate }} || Pretty-print tabular data in Python, a library and a command-line utility|| Packaged ||
| |
| |-
| |
| | {{FpPackage|python-transforms3d}} || 3 dimensional spatial transformations|| Packaged ||
| |
| |-
| |
| | {{FpPackage|texlive}} || The LaTeX typesetting system for academic writing|| Packaged ||
| |
| |-
| |
| | {{FpPackage|python-grabbit}} || Get grabby with file trees! || Packaged ||
| |
| |-
| |
| | {{FpPackage|python-cma}} || Covariance Matrix Adaptation Evolution Strategy numerical optimizer || Packaged ||
| |
| |-
| |
| | [https://github.com/berenslab/MorphoPy MorphoPy] ||a Python 3 package for handling morphological reconstructions of neurons and computing summary statistics || Needs packaging ||
| |
| |-
| |
| | [https://github.com/btorb/btmorph_v2 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 ||
| |
| |-
| |
| | {{FpPackage|python-psychopy}} || Psychophysics toolkit for Python|| Needs packaging. A dead review is here: [[rhbug:1280141|1280141]] ||
| |
| |-
| |
| | {{FpPackage|python-cregg}} || Utilities for running psychology experiments || In review [[rhbug:1280155|1280155]] ||
| |
| |-
| |
| | {{FpPackage|python-duecredit}} || Automated collection and reporting of citations for used software/methods/datasets || Needs packaging. Dead review here: [[rhbug:1280480 |1280480 ]] ||
| |
| |-
| |
| | {{FpPackage|python-visionegg-quest}} || QUEST algorithm for finding threshold|| Reviewed: needs import [[rhbug:1290995 |1290995 ]]||
| |
| |-
| |
| | {{FpPackage|debruijn}} || Software for the generation de Bruijn sequences for neuroscience experiments|| Needs packaging. Dead review here: [[rhbug: 1291021 | 1291021 ]]||
| |
| |-
| |
| | [https://pypi.org/project/neuroshare neuroshare] || Python bindings for Neuroshare|| Needs packaging ||
| |
| |-
| |
| | [http://www.expyriment.org/ expyriment]|| A Python library for cognitive and neuroscientific experiments|| Needs packaging ||
| |
| |-
| |
| | [https://github.com/wmayner/pyphi pyphi]|| A Python package for computing integrated information || Needs review: [[rhbug:1619458 | 1619458]] ||
| |
| |-
| |
| | [https://github.com/wmayner/pyemd pyemd]||Fast EMD for Python: a wrapper for Pele and Werman's C++ implementation of Earth Mover's Distance metric|| Needs packaging ||
| |
| |-
| |
| | [https://github.com/simetenn/uncertainpy uncertainpy]|| A Python toolbox for uncertainty quantification and sensitivity analysis || Needs packaging ||
| |
| |-
| |
| | [http://www.nuitka.net/pages/overview.html nuitka]|| A fully compatible Python compiler|| Needs packaging. Dead review here: [[rhbug:1288750 | 1288750]] ||
| |
| |-
| |
| | [https://github.com/tridesclous/tridesclous tridesclous]||offline/online spike sorting with french touch that light the barbecue || Needs packaging ||
| |
| |-
| |
| | [https://github.com/IGITUGraz/L2L L2L] ||Learning to learn: gradient-free optimization framework || Needs packaging ||
| |
| |-
| |
| | [https://github.com/aarongarrett/inspyred inspyred] ||Python library for bio-inspired computational intelligence.|| Needs packaging ||
| |
| |-
| |
| | [https://github.com/HumanBrainProject/hbp_archive hbp_archive] ||A high-level API for interacting with the Human Brain Project archival storage at CSCS|| Needs packaging ||
| |
| |-
| |
| |}
| |
