February 2021 - Neurofedora - Fedora mailing-lists

[Fwd] [Neuroml-technology] Announcing 3 NeuroML hackathon sessions at HARMONY 2021
by Ankur Sinha 26 Feb '21

26 Feb '21

Hi folks, This may be interesting for folks interested in learning modelling using NeuroML: ----- Forwarded message from Padraig Gleeson ----- Date: Fri, 26 Feb 2021 16:00:07 +0000 From: Padraig Gleeson <p.gleeson(a)ucl.ac.uk> To: neuroml-technology(a)lists.sourceforge.net Subject: [Neuroml-technology] Announcing 3 NeuroML hackathon sessions at HARMONY 2021 List-Id: NeuroML main mailing list <neuroml-technology.lists.sourceforge.net> We will be running 3 online hackathon sessions during the upcoming HARMONY 2021 meeting on 23-25th March. The general theme of the sessions will be: Learn to build, visualise, analyse and simulate your models using NeuroML. Why take part? These hackathons will give members of the modelling community the chance to: • Get high level introductions to the NeuroML language and tool chain • Meet the NeuroML core development team and editors • Find out the latest information on which simulators/applications support NeuroML • Open, discuss and work on issues related to converting your model to NeuroML, or supporting NeuroML in your simulator • Learn how to share your models with the community Times and dates All sessions will be online and take place over 3 hours (9am-noon Pacific; 12-3pm EST time; 4-7pm UK/UTC; 5-8pm CET, 9:30pm-12:30am IST; note non-standard US/EU time differences that week). The broad focus of each of the sessions (dependent on interests of attendees) is: Tues 23rd March: Introduction to NeuroML, general questions about usage Wed 24th March: Detailed cell/conductance based models (e.g. converting channels to NeuroML) Thus 25th March: Abstract/point neuron networks including PyNN interactions Registration To take part in the hackathon, please register at http://co.mbine.org/events/ HARMONY_2021 for the HARMONY meeting (registration is free). You will get sent details to access the agenda on https://harmony2021.sched.com, which will have links to the Zoom sessions for each of the days. Open an issue beforehand! While it will be possible to raise and discuss new issues at the hackathons, it will be easier to manage and plan work/discussions if you open an issue with a description of the problem you are trying to address at: https://github.com/ NeuroML/NeuroML2/issues. Slack To aid communication with the community during (and after) the meeting, we have a Slack channel for NeuroML related discussions. Please reply to this mail for an invite. We look forward to working with the community to drive further uptake of NeuroML compliant models and tools! ----------------------------------------------------- Padraig Gleeson Room 321, Anatomy Building Department of Neuroscience, Physiology& Pharmacology University College London Gower Street London WC1E 6BT United Kingdom +44 207 679 3214 p.gleeson(a)ucl.ac.uk ----------------------------------------------------- Neuroml-technology mailing list Neuroml-technology(a)lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/neuroml-technology ----- End forwarded message ----- -- Thanks, Regards, Ankur Sinha "FranciscoD" (He / Him / His) | https://fedoraproject.org/wiki/User:Ankursinha Time zone: Europe/London

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INCF/OCNS Software WG: Dev sessions on Brian (11th Feb) and NeuroFedora (16th Feb)
by Ankur Sinha 22 Feb '21

22 Feb '21

Hello everyone, Apologies for the cross-posts. The INCF/OCNS Software Working Group (WG)[1] is happy to announce its first set of "Dev sessions" where members of the developer teams of commonly used neuroscience software will introduce their software and then discuss their *development* pipelines. The aim of these sessions is to stimulate discussion of the development practices and tools used by different teams to improve the software we use while also improving our knowledge of these practices and tools. We also hope to encourage more users of these tools to contribute to their development to ensure their longevity. Two sessions are currently scheduled: - Marcel Stimberg will speak about the development of the Brian simulator on Feb 11, 2021 1700 UTC[2]. Zoom link: https://ucl.zoom.us/j/91389216854?pwd=cFVWaXRYVFRUdll2c09Xb3dBS2FWQT09 - Ankur Sinha will speak about the development of the NeuroFedora Linux distribution on Feb 16, 2021 1700 UTC[3]. Zoom link: https://ucl.zoom.us/j/94964460359?pwd=MTJmWEY1NHRxd3l4ZGdtTS9NQ1FaZz09 (To prevent spamming/trolling during these sessions, you will need to login to your Zoom account to join them. These sessions will be recorded and made available for later viewing also.) Sessions on GeNN and Neurolib will also follow shortly. If you develop software for neuroscience, we would love to hear about your development pipeline. Please get in touch with the Software WG either on INCF's Neurostars platform[4] or on our GitHub repository[5]. The WG is a community based group that is open to everyone at all levels of their careers (academic or otherwise). Please introduce yourself to the community on our channels to get involved. [1] https://ocns.github.io/SoftwareWG/pages/about.html [2] https://ocns.github.io/SoftwareWG/2021/02/07/dev-session-marcel-stimberg-br… [3] https://ocns.github.io/SoftwareWG/2021/02/07/dev-session-ankur-sinha-neurof… [4] https://neurostars.org/t/ocns-infrastructure-software-tools-sig-meet-and-gr… [5] https://github.com/OCNS/SoftwareWG/issues On behalf of the WG, -- Thanks, Regards, Ankur Sinha (He / Him / His) Research Fellow at the Silver Lab | http://silverlab.org/ Department of Neuroscience, Physiology, & Pharmacology University College London, London, UK Time zone: Europe/London

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INCF/OCNS Software WG: Dev session on Neurolib (23rd Feb)
by Ankur Sinha 18 Feb '21

18 Feb '21

Hello everyone, Apologies for the cross-posts. The INCF/OCNS Software Working Group (WG)[1] is happy to announce the next "Dev session" on Neurolib[2] where Caglar Cakan will introduce the software and then discuss its *development* pipeline. The session will be held on Feb 23, 2021 at 1700 UTC[3]. Zoom link: https://tu-berlin.zoom.us/j/68960683644?pwd=a2JTTS8xZXhwY0ZtQ0J0aktRVW52Zz09 The aim of these sessions is to stimulate discussion of the development practices and tools used by different teams to improve the software we use while also improving our knowledge of these practices and tools. We also hope to encourage more users of these tools to contribute to their development to ensure their longevity. The abstract of the talk is below: neurolib is a computational framework for whole-brain modelling written in Python. It provides a set of neural mass models that represent the average activity of a brain region on a mesoscopic scale. In a whole-brain network model, brain regions are connected with each other based on structural connectivity data, i.e. the connectome of the brain. neurolib can load structural and functional data sets, set up a whole-brain model, manage its parameters, simulate it, and organize its outputs for later analysis. The activity of each brain region can be converted into a simulated BOLD signal in order to calibrate the model to empirical data from functional magnetic resonance imaging (fMRI). Extensive model analysis is possible using a parameter exploration module, which allows to characterize the model’s behaviour given a set of changing parameters. An optimization module allows for fitting a model to multimodal empirical data using an evolutionary algorithm. Besides its included functionality, neurolib is designed to be extendable such that custom neural mass models can be implemented easily. neurolib offers a versatile platform for computational neuroscientists for prototyping models, managing large numerical experiments, studying the structure-function relationship of brain networks, and for in-silico optimization of whole-brain models. ----- If you develop software for neuroscience, we would love to hear about your development pipeline. Please get in touch with the Software WG either on INCF's Neurostars platform[4] or on our GitHub repository[5]. The WG is a community based group that is open to everyone at all levels of their careers (academic or otherwise). Please introduce yourself to the community on our channels to get involved. [1] https://ocns.github.io/SoftwareWG/pages/about.html [2] https://neurolib-dev.github.io/ [3] https://ocns.github.io/SoftwareWG/2021/02/12/dev-session-caglar-cakan-neuro… [4] https://neurostars.org/t/ocns-infrastructure-software-tools-sig-meet-and-gr… [5] https://github.com/OCNS/SoftwareWG/issues On behalf of the WG, -- Thanks, Regards, Ankur Sinha (He / Him / His) Research Fellow at the Silver Lab | http://silverlab.org/ Department of Neuroscience, Physiology, & Pharmacology University College London, London, UK Time zone: Europe/London

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Introduction - Josh
by Joshua Santos 16 Feb '21

16 Feb '21

Hello Neuro SIG, My name is Josh, and I have been a member of the Fedora community since 2014 (although haven’t been very active). I am excited to start helping out in packaging for compneuro. Brief background in case you find yourself needing assistance in an area that involves something I am experienced in (love to help, and try for transparency when I don’t know something): * 2-3 years python * 4-5 years golang * Hobby/minimal experience in Node/Ruby/C#/Haskell/Scala * NGINX experience Looking forward to helping in any way I can. Cheers!

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Next Open NeuroFedora Meeting: 1300 UTC on Monday, 15 February (Today)
by Ankur Sinha 15 Feb '21

15 Feb '21

Hello everyone, Please join us at the next Open NeuroFedora team meeting on Monday 15 February at 1300UTC in #fedora-neuro on IRC (Freenode). The meeting is a public meeting, and open for everyone to attend. You can join us over: IRC: https://webchat.freenode.net/?channels=#fedora-neuro or Matrix/Element: https://matrix.to/#/!xgwUsLNGIoOAXMxGMQ:matrix.org?via=matrix.org&via=t2bot… The channel is also bridged to Telegram, so you can also join us there on the @NeuroFedora group: https://t.me/NeuroFedora You can convert the meeting time to your local time using this command in a terminal: $ date --date='TZ="UTC" 1300 today' or you can use this link: https://www.timeanddate.com/worldclock/fixedtime.html?msg=NeuroFedora+Meeti… The meeting will be chaired by @ankursinha (me). The agenda for the meeting is: - New introductions and roll call. - Tasks from last week's meeting: https://meetbot.fedoraproject.org/teams/neurofedora/neurofedora.2021-02-01-… - Open Pagure tickets: https://pagure.io/neuro-sig/NeuroFedora/issues?status=Open&tags=S%3A+Next+m… - Open bugs check: https://tinyurl.com/neurofedora-bugs - Open package reviews check: https://bugzilla.redhat.com/show_bug.cgi?id=fedora-neuro - Koschei packages check: https://koschei.fedoraproject.org/groups/neuro-sig - CompNeuro lab compose status check for F33/F34: https://koji.fedoraproject.org/koji/packageinfo?packageID=30691 - Neuroscience query of the week - Next meeting day, and chair. - Open floor. We hope to see you there! You can learn more about NeuroFedora here: https://neuro.fedoraproject.org -- Thanks, Regards, Ankur Sinha "FranciscoD" (He / Him / His) | https://fedoraproject.org/wiki/User:Ankursinha Time zone: Europe/London

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Python contribution opportunity: migrate PyNN from Nose to py.test
by Ankur Sinha 09 Feb '21

09 Feb '21

Hi folks, PyNN still uses Nose for testing, which is now deprecated. So they're looking to move to py.test (this came up in the Fedora package review). Are there any Python folks here who'd like to work on this? https://github.com/NeuralEnsemble/PyNN/issues/705 -- Thanks, Regards, Ankur Sinha "FranciscoD" (He / Him / His) | https://fedoraproject.org/wiki/User:Ankursinha Time zone: Europe/London

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Next Open NeuroFedora Meeting: 1300 UTC on Monday, 01 February (Today)
by Ankur Sinha 01 Feb '21

01 Feb '21

Hello everyone, Please join us at the next Open NeuroFedora team meeting on Monday 1 February at 1300UTC in #fedora-neuro on IRC (Freenode). The meeting is a public meeting, and open for everyone to attend. You can join us over: IRC: https://webchat.freenode.net/?channels=#fedora-neuro or Matrix/Element: https://matrix.to/#/!xgwUsLNGIoOAXMxGMQ:matrix.org?via=matrix.org&via=t2bot… The channel is also bridged to Telegram, so you can also join us there on the @NeuroFedora group: https://t.me/NeuroFedora You can convert the meeting time to your local time using this command in a terminal: $ date --date='TZ="UTC" 1300 today' or you can use this link: https://www.timeanddate.com/worldclock/fixedtime.html?msg=NeuroFedora+Meeti… The meeting will be chaired by @ankursinha (me). The agenda for the meeting is: - New introductions and roll call. - Tasks from last week's meeting: https://meetbot.fedoraproject.org/teams/neurofedora/neurofedora.2021-01-18-… - Open Pagure tickets: https://pagure.io/neuro-sig/NeuroFedora/issues?status=Open&tags=S%3A+Next+m… - Open bugs check: https://tinyurl.com/neurofedora-bugs - Open package reviews check: https://bugzilla.redhat.com/show_bug.cgi?id=fedora-neuro - Koschei packages check: https://koschei.fedoraproject.org/groups/neuro-sig - CompNeuro lab compose status check for F33/F34: https://koji.fedoraproject.org/koji/packageinfo?packageID=30691 - Neuroscience query of the week - Next meeting day, and chair. - Open floor. We hope to see you there! You can learn more about NeuroFedora here: https://neuro.fedoraproject.org -- Thanks, Regards, Ankur Sinha "FranciscoD" (He / Him / His) | https://fedoraproject.org/wiki/User:Ankursinha Time zone: Europe/London

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Neurofedora February 2021