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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]].


[[User:alvesadrian|Adrian Alves (alvesadrian)]] <[mailto:alvesadrian@fedoraproject.org alvesadrian@fedoraporject.org]>
(A self-contained change request proposed by this SIG in the past is detailed [[Changes/NeuroFedora | here]])


[[User:ankursinha| Ankur Sinha "FranciscoD" (ankursinha)]]
== Communication and getting help ==


= NeuroFedora Packages =
* Documentation on using the packages available is at [https://docs.fedoraproject.org/ docs.fedoraproject.org]. Its sources reside in a [https://pagure.io/neuro-sig/documentation/ pagure repository].
* We maintain a repository for housekeeping on Pagure.io [https://pagure.io/neuro-sig/NeuroFedora here].
* We have our maling list here: {{fplist|neuro-sig}}. Feel free to ask any questions there.
* We also hang out on irc.freenode.net at '''{{fpchat|#fedora-neuro}}'''.
* We also have a Telegram supergroup here: https://t.me/NeuroFedora
* 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]).
* Updates on NeuroFedora are currently announced [https://ankursinha.in/tag/neurofedora/ here].
* We have our [https://github.com/neurofedora organisation on Github], although we mainly use our [https://pagure.io/group/neuro-sig Pagure organisation].


== Interesting software waiting for being packaged ==
= 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]].


* [https://pypi.python.org/pypi/dipy dipy]
= Who we are =
* [http://www.expyriment.org expyriment]
* [https://pypi.python.org/pypi/nipy nipy - A python package for analysis of neuroimaging data]
* [https://www.fenicsproject.org/ fenics - A finite element package]
* [http://sourceforge.net/projects/meshfix/ meshfix - algorithms operating on meshes]


== Work in progress ==
NeuroFedora was founded by [[User:mhough|Morgan Hough (mhough)]] <[mailto:morgan.hough@gmail.com morgan.hough@gmail.com]> and [[User:Ignatenkobrain|Igor Gnatenko (ignatenkobrain)]] <[mailto:i.gnatenko.brain@gmail.com i.gnatenko.brain@gmail.com]>.


{|
It is currently maintained by members of the [https://src.fedoraproject.org/group/neuro-sig neuro-sig].
! 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 ==
== Join us! ==


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.
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 above.  


When you are filing your SCM-admin-request, you should make sure to request InitialCC for "neurofedora-sig".
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].


Example:
There is no formal process for participating. Simply 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]].
<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 ==
== Meetings ==
 
You can find them on the {{bz|fedora-neuro}}.
 
We would be glad, if you would take one or a few.  :)


== Existing packages ==
We shall have them, and see how it goes.


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.
= Software =


== Categories ==
{{admon/tip|Suggest more software!|Please use [https://goo.gl/forms/j6AJ82yOh78MPxby1 this form] to suggest more software for inclusion in 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. The classification that NeuroDebian uses is as follows:  
* Already available software can be found on [https://src.fedoraproject.org/group/neuro-sig the Neuro-SIG group's page on src.fp.o].
* The [https://pagure.io/neuro-sig/NeuroFedora/issues pagure issue tracker] shows a list of software that is being packaged.
* 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]


<pre>
== Adding new software ==
*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? =
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 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 ==
 
We hang out on irc.freenode.net at '''{{fpchat|#fedora-neuro}}'''.
 
== Meetings ==


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 15:00, 24 November 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

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

NeuroFedora was founded by Morgan Hough (mhough) <morgan.hough@gmail.com> and Igor Gnatenko (ignatenkobrain) <i.gnatenko.brain@gmail.com>.

It is currently maintained by members of the neuro-sig.

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 above.

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 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

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

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.