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= NeuroFedora SIG =
= NeuroFedora SIG =
The NeuroFedora SIG's goal is to make Fedora the best platform for neuroscience and neuroimaging research.  
[[File:NeuroFedoraLogo01.png|200px|frameless|right]]


== Members ==
The NeuroFedora SIG's goal is to provide neuroscience researchers (and enthusiasts!) a strong, easy to use, ready-made FOSS platform for their work.


[[User:mhough|Morgan Hough (mhough)]] <[mailto:morgan.hough@gmail.com morgan.hough@gmail.com]>
The first step towards this objective is to package as many of the tools that neuroscientists use to make them available in Fedora.


[[User:Ignatenkobrain|Igor Gnatenko (Ignatenkobrain)]] <[mailto:i.gnatenko.brain@gmail.com i.gnatenko.brain@gmail.com]>
* Providing the package set that the [http://neuro.debian.net/ neuro-debian] project provides is a preliminary goal.
* Add additional packages, in [http://copr.fedoracloud.org/groups/g/neurofedora/coprs/ the neurofedora COPR repositories] or [https://flathub.org/home Flatpaks] if required
* Release a [https://spins.fedoraproject.org/ Fedora spin]
* Publicise the spin (publish a paper outlining the work here again following the [https://www.frontiersin.org/articles/10.3389/fninf.2012.00022/full neurodebian project paper]?)
* Continue to enable neuroscience research, provide [[Communicating_and_getting_help | community support]].


= NeuroFedora Packages =
(A self-contained change request proposed by this SIG in the past is detailed [[Changes/NeuroFedora | here]])


== Interesting software waiting for being packaged ==
== Communication and getting help ==


* [https://pypi.python.org/pypi/dipy dipy]
* We maintain a repository for housekeeping on Pagure.io [https://pagure.io/neuro-sig/NeuroFedora here].
* [http://www.expyriment.org expyriment]
* We have our maling list here: {{fplist|neuro-sig}}. Feel free to ask any questions there.
* [https://pypi.python.org/pypi/nipy nipy - A python package for analysis of neuroimaging data]
* We also hang out on irc.freenode.net at '''{{fpchat|#fedora-neuro}}'''.
* [https://www.fenicsproject.org/ fenics - A finite element package]
* One can also get help on [https://ask.fedoraproject.org Ask Fedora] and use the "Troubleshooting > Software > NeuroFedora" category to mark questions ([https://ask.fedoraproject.org/en/questions/scope:all/sort:activity-desc/tags:neurofedora/page:1/ Current list of questions]).
* [http://sourceforge.net/projects/meshfix/ meshfix - algorithms operating on meshes]


== Work in progress ==
= Artwork =
[https://pagure.io/design/issue/602 Terezahl made us some awesome artwork] for use in various locations, such as the website, and other posts (and T-shirts?!). These live on their own page here: [[SIGs/NeuroFedora/Artwork]].


{|
= Who we are =
! Package !! Status !! Notes
|-
| [http://martinos.org/mne/ python-mne] || {{result|inprogress|ignatenkobrain}} || {{bz|1276880}}
|-
| [http://www.pydicom.org/ python-pydicom] || {{result|inprogress|ignatenkobrain}} || {{bz|1276837}}
|-
| [http://matthew-brett.github.io/transforms3d/ python-transforms3d] || {{result|inprogress|ignatenkobrain}} || {{bz|1276910}}
|-
| [http://nipy.org/nipy/ nipy-data] || {{result|inprogress|ignatenkobrain}} || {{bz|1276926}}
|-
| [http://dipy.org python-dipy] || {{result|inprogress|ignatenkobrain}} || [https://github.com/neurofedora/python-dipy GitHub]
|-
| [http://nipy.org/nitime python-nitime] || {{result|inprogress|ignatenkobrain}} || [https://github.com/neurofedora/python-nitime GitHub] i686 fails: [https://github.com/nipy/nitime/issues/137 Issue1], [https://github.com/nipy/nitime/issues/136 Issue2]
|-
| [http://nipy.org/nipy/ python-nipy] || {{result|inprogress|ignatenkobrain}} || {{bz|1276938}}
|-
| [https://github.com/nipy/nibabel python-nibabel] || {{result|inprogress|ignatenkobrain}} || {{bz|1276871}}
|-
| [http://afni.nimh.nih.gov/afni/ AFNI] || {{result|inprogress|caesarae}} || depends on an old UI lib
|-
| [http://www.fieldtriptoolbox.org/ FieldTrip] || {{result|inprogress|mhough}} ||
|-
| [https://pypi.python.org/pypi/MNE MNE] || {{result|inprogress|ignatenkobrain}} ||
|-
| [http://www.mrtrix.org MRTrix3 - MRTrix3 is a analysis package for diffusion data] || {{result|inprogress|caesarae}} ||
|-
| [http://www.nest-simulator.org nest - nest is a simulator for spiking neural networks] || [[User:ankursinha|ankursinha]] || WIP || depends on [[rhbug:1273579 | review request]]
|-
| [https://www.neuron.yale.edu/neuron/ nrn - nrn is a neural simulator package] || [[User:ankursinha|ankursinha]] || WIP || depends on [[rhbug:1249094 | review request]]
|-
| [http://briansimulator.org python-brian2 - Brian is a simulator for spiking neural networks] || [[User:ankursinha|ankursinha]] || WIP || depends on [[rhbug:1098754 | review request]]
|-
| [https://pythonhosted.org/neo/ python-neo - neo is a package for electrophysiology] || [[User:ankursinha|ankursinha]] || WIP || depends on [[rhbug:1150099 | review request]]
|-
| [http://neuralensemble.org/PyNN/ python-pynn - pynn is a simulator for spiking neural networks] || [[User:ankursinha|ankursinha]] || WIP || depends on [[rhbug:1150105 | review request]]
|-
| [http://www.fil.ion.ucl.ac.uk/spm/ SPM] || [[User:mhough | mhough]] || WIP ||
|}


== New packages ==
* [[User:mhough|Morgan Hough (mhough)]] <[mailto:morgan.hough@gmail.com morgan.hough@gmail.com]>
* [[User:Ignatenkobrain|Igor Gnatenko (ignatenkobrain)]] <[mailto:i.gnatenko.brain@gmail.com i.gnatenko.brain@gmail.com]>
* [[User:alvesadrian|Adrian Alves (alvesadrian)]] <[mailto:alvesadrian@fedoraproject.org alvesadrian@fedoraporject.org]>
* [[User:ankursinha| Ankur Sinha "FranciscoD" (ankursinha)]]
* [[User:Gicmo|Christian Kellner (gicmo)]]


When submitting a new neuro-related package for review, please add "Blocks: [[rhbug:NeuroFedora-SIG|NeuroFedora-SIG]]" to your review-request.  After the review has been granted don't forget to remove it, when filing the SCM-request, please.
== Join us! ==


When you are filing your SCM-admin-request, you should make sure to request InitialCC for "neurofedora-sig".
We encourage everyone to join the group. We're more than happy to help new members learn the skills required to participate in the project. Please contact us using the methods outlined below.  


Example:
Since we use infrastructure provided by the Fedora community, one must have a Fedora account to access it. It can be created [https://admin.fedoraproject.org/accounts here].
<pre>
New Package SCM Request
=======================
Package Name: pkgname
Short Description: summary of package
Owners: foo bar
Branches: f21 f22 f23 el6 el7
InitialCC: nf-sig
</pre>


== Packages waiting for your review ==
There is no formal process for participating. Simply add yourself to [[SIGs/NeuroFedora#Who_we_are | our members-section above]] and apply to the [https://admin.fedoraproject.org/accounts/group/view/neuro-sig Neuro-sig FAS group] to gain access to the package set. While one is required to already be a package maintainer to join the group, we're happy to help you learn packaging and [[PackageMaintainers/HowToGetSponsored#Become_a_co-maintainer | join the package maintainers group by co-maintain packages with us]].


You can find them on the [[rhbug:NeuroFedora-SIG|NeuroFedora-SIG review-tracker]].
== Meetings ==


We would be glad, if you would take one or a few.  :)
We shall have them, and see how it goes.  
 
== Existing packages ==
 
You can't find the existing [https://admin.fedoraproject.org/pkgdb/users/packages/neurofedora-sig neurofedora-related packages on the PkgDB] yet but we are working on it.
 
== Categories ==
 
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. The classification that NeuroDebian uses is as follows:
 
<pre>
*Packages for Distributed Computing
*Packages for Electrophysiology
*Packages for Magnetic Reasonance Imaging
*Packages for Modeling of neural systems
*Packages for Neuroscience Datasets
*Packages for Neuroscience Education
*Packages for Psychophysics
</pre>
 
= What are we going to do? =
 
We are first planning to match packages from the debian-based neurodebian project excluding the debian packaging related tools. The second phase would be to publish a paper outlining the work here again following the neurodebian project paper. The third phase would be to publish a research paper describing new tools available in NeuroFedora
 
= Participation =
 
There is no formal process for participating; joining the mailing list, hanging out on IRC, or participating in meetings are all great ways to get involved.
 
A little self-introduction on the mailing list would be nice, too. And, if you want to, add yourself to [[SIGs/NeuroFedora#Members | our members-section above]].
 
== Mailing list ==
 
* Join: {{fplist|neurofedora}}
* Archives: [http://lists.fedoraproject.org/pipermail/neurofedora/ read]


== IRC ==
= Software =


We will likely hang out on irc.freenode.net at [irc://irc.freenode.net/neurofedora #neurofedora].
* A complete list of packages with their current status can be seen on the [[SIGs/NeuroFedora/PackageSet| packages page]]
* [https://src.fedoraproject.org/group/neuro-sig The Neuro-SIG group's page on src.fp.o] also lists the already packaged software
* Packages under review can be seen using the tracker bug: {{bz|1276941}}. Please feel free to pick them up for review.
* An older progress kanban board is [http://taiga.fedorainfracloud.org/project/ignatenkobrain-neurofedora/kanban here]


Haven't used IRC for communication before? More information on how to use IRC is available [[IRC|here.]]
== Adding new software ==


== Meetings ==
When [[New package process for existing contributors|submitting a new neuro-related package for review]], please add "Blocks: [[rhbug:fedora-neuro|fedora-neuro]]" to your review-request.


We shall have them, and see how it goes.  
When the package is approved. please modify the settings of the package on src.fedoraproject.org and give the [https://src.fedoraproject.org/group/neuro-sig neuro-sig group] commit rights so that we can help maintain the whole package set.


more to come soon.
[[Category:SIGs]]
[[Category:SIGs]]
[[Category:Fedora special-interest groups]]
[[Category:Fedora special-interest groups]]

Revision as of 16:02, 5 October 2018

NeuroFedora SIG

NeuroFedoraLogo01.png

The NeuroFedora SIG's goal is to provide neuroscience researchers (and enthusiasts!) a strong, easy to use, ready-made FOSS platform for their work.

The first step towards this objective is to package as many of the tools that neuroscientists use to make them available in Fedora.

(A self-contained change request proposed by this SIG in the past is detailed here)

Communication and getting help

  • We maintain a repository for housekeeping on Pagure.io here.
  • We have our maling list here: neuro-sig. Feel free to ask any questions there.
  • We also hang out on irc.freenode.net at #fedora-neuro[?].
  • One can also get help on Ask Fedora and use the "Troubleshooting > Software > NeuroFedora" category to mark questions (Current list of questions).

Artwork

Terezahl made us some awesome artwork for use in various locations, such as the website, and other posts (and T-shirts?!). These live on their own page here: SIGs/NeuroFedora/Artwork.

Who we are

Join us!

We encourage everyone to join the group. We're more than happy to help new members learn the skills required to participate in the project. Please contact us using the methods outlined below.

Since we use infrastructure provided by the Fedora community, one must have a Fedora account to access it. It can be created here.

There is no formal process for participating. Simply add yourself to our members-section above and apply to the Neuro-sig FAS group to gain access to the package set. While one is required to already be a package maintainer to join the group, we're happy to help you learn packaging and join the package maintainers group by co-maintain packages with us.

Meetings

We shall have them, and see how it goes.

Software

  • A complete list of packages with their current status can be seen on the packages page
  • The Neuro-SIG group's page on src.fp.o also lists the already packaged software
  • Packages under review can be seen using the tracker bug: RHBZ #1276941. Please feel free to pick them up for review.
  • An older progress kanban board is here

Adding new software

When submitting a new neuro-related package for review, please add "Blocks: fedora-neuro" to your review-request.

When the package is approved. please modify the settings of the package on src.fedoraproject.org and give the neuro-sig group commit rights so that we can help maintain the whole package set.

Retrieved from "https://fedoraproject.org/w/index.php?title=SIGs/NeuroFedora&oldid=526464"