15:06:58 <bt0> #startmeeting "NeuroFedora - 2019-10-03"
15:06:58 <zodbot> Meeting started Thu Oct  3 15:06:58 2019 UTC.
15:06:58 <zodbot> This meeting is logged and archived in a public location.
15:06:58 <zodbot> The chair is bt0. Information about MeetBot at http://wiki.debian.org/MeetBot.
15:06:58 <zodbot> Useful Commands: #action #agreed #halp #info #idea #link #topic.
15:06:58 <zodbot> The meeting name has been set to '"neurofedora_-_2019-10-03"'
15:07:11 <bt0> #meetingname neurofedora
15:07:11 <zodbot> The meeting name has been set to 'neurofedora'
15:07:32 <bt0> #chair MeWjOr mhough FranciscoD alciregi blackfile bt0 zbyszek
15:07:32 <zodbot> Current chairs: FranciscoD MeWjOr alciregi blackfile bt0 mhough zbyszek
15:07:45 <bt0> #topic Introductions and Roll call
15:07:50 <FranciscoD> @keszybz: no worries, we'll send the logs out as usual :)
15:08:13 <bt0> #info Alberto Rodriguez (bt0dotninja), UTC-5 (America/Mexico-City), CommOps, Marketing, packaging, neurofedora, Fedora-Join and more...
15:08:33 <bt0> .fasinfo bt0dotninja
15:08:34 <zodbot> bt0: User: bt0dotninja, Name: Alberto Rodriguez Sanchez, email: hotgalan@gmail.com, Creation: 2016-07-25, IRC Nick: bt0, Timezone: America/Mexico_City, Locale: en, GPG key ID: E74B5808, Status: active
15:08:37 <zodbot> bt0: Approved Groups: neuro-sig fedorabugs packager +advocates @commops +summer-coding +ask-fedora mindshare +fedora-join @fedora-mx ambassadors dotnet-team marketing cla_done cla_fpca
15:08:54 <FranciscoD> #info Ankur Sinha (ankursinha/FranciscoD): UTC+1 (Europe/London), NeuroFedora, Join, Packaging, and a few others :)
15:08:58 <FranciscoD> .fasinfo ankursinha
15:08:59 <zodbot> FranciscoD: User: ankursinha, Name: Ankur Sinha, email: sanjay.ankur@gmail.com, Creation: 2008-05-28, IRC Nick: FranciscoD, Timezone: Europe/London, Locale: en_GB, GPG key ID: E629112D, Status: active
15:09:01 <zodbot> FranciscoD: Approved Groups: provenpackager +packager robotics-sig @ask-fedora scitech @neuro-sig @fedora-join cla_fedora cla_done fedorabugs @freemedia @gitfedora-tour cla_fpca @gitfpaste +qa
15:09:07 <FranciscoD> .fasinfo major
15:09:07 <zodbot> FranciscoD: User: major, Name: Aniket Pradhan, email: aniketpradhan1999@gmail.com, Creation: 2019-02-09, IRC Nick: MeWjOr, major_, Timezone: Asia/Kolkata, Locale: en, GPG key ID: None, Status: active
15:09:10 <zodbot> FranciscoD: Error getting group memberships.
15:09:17 <FranciscoD> uh
15:10:08 <bt0> :(
15:10:56 <bt0> give me 2 minutes for more quorum or the agenda?
15:10:58 <fm-neuro> pagure.commit.flag.added -- Build completed added a flag on the commit ae639506 of the project rpms/python-PyLEMS https://src.fedoraproject.org/rpms/python-PyLEMS/c/ae6395065d38e1ccced6779e028a98b7825f3c01
15:11:23 <fm-neuro> pagure.commit.flag.added -- Build completed added a flag on the commit d6728ddc of the project rpms/neuron https://src.fedoraproject.org/rpms/neuron/c/d6728ddc0908314dfc600f2363b45ee83d79fb5a
15:11:32 <fm-neuro> pagure.commit.flag.added -- Build completed added a flag on the commit c95bf027 of the project rpms/python-PyLink https://src.fedoraproject.org/rpms/python-PyLink/c/c95bf0270fadc3092a45712e2bd80dac5f2109c5
15:11:41 <FranciscoD> bt0: sure
15:12:00 <FranciscoD> ah, another python 3.8 rebuild..
15:12:43 <FranciscoD> Let's hope we don't have too many breakages---I had a hard time fixing things for 3.8---we still have some bugs too
15:13:37 <bt0> #topic Today's agenda
15:13:56 <bt0> #info Pagure tickets at: https://pagure.io/neuro-sig/NeuroFedora/issues?status=Open&tags=S%3A+Next+meeting
15:13:56 <bt0> #info Open bugs at: https://bugzilla.redhat.com/buglist.cgi?bug_status=NEW&bug_status=ASSIGNED&email1=neuro-sig%40lists.fedoraproject.org&emailassigned_to1=1&emailcc1=1&emaildocs_contact1=1&emaillongdesc1=1&emailqa_contact1=1&emailreporter1=1&emailtype1=substring&list_id=10455921&query_format=advanced
15:14:15 <bt0> #info Review of current progress
15:14:16 <bt0> #info Action items from previous meeting
15:14:16 <bt0> #info Planning what we want to do next
15:14:16 <bt0> #info Neuroscience query of the week
15:14:16 <bt0> #info Next meeting chair selection
15:14:16 <bt0> #info Open floor
15:15:29 <bt0> #topic Review of pagure tickets
15:16:00 <bt0> #info  https://pagure.io/neuro-sig/NeuroFedora/issues?status=Open&tags=S%3A+Next+meeting
15:16:56 <FranciscoD> I guess we can discuss the paper in the open floor later
15:17:04 <FranciscoD> I just commented on the badge ticket: https://pagure.io/fedora-badges/issue/678
15:17:09 <FranciscoD> We need to wait for that to proceed
15:17:12 <MeWjOr> +1
15:17:17 <bt0> +1
15:17:52 <FranciscoD> We have one or two tickets on the lab image pagure: https://pagure.io/neuro-sig/neuro-scripts/issues
15:17:58 <bt0> #topic Ticket #293
15:18:06 <bt0> #info https://pagure.io/neuro-sig/NeuroFedora/issue/293
15:19:25 <fm-neuro> pagure.commit.flag.added -- Build completed added a flag on the commit c8ef6f1e of the project rpms/python-SALib https://src.fedoraproject.org/rpms/python-SALib/c/c8ef6f1e7542078f98249379c7d291cd01152a51
15:20:36 <FranciscoD> that's the ticket about the paper---let's delay that to open floor?
15:21:23 <bt0> ok
15:22:49 <fm-neuro> pagure.issue.comment.added -- ankursinha commented on ticket neuro-sig/neuro-scripts#5: "Add jupyter, and ipython" https://pagure.io/neuro-sig/neuro-scripts/issue/5#comment-602115
15:23:06 <bt0> #topic Ticket #250
15:23:11 <bt0> #info https://pagure.io/neuro-sig/NeuroFedora/issue/250
15:23:46 <fm-neuro> pagure.commit.flag.added -- Build completed added a flag on the commit f6ebde13 of the project rpms/python-airspeed https://src.fedoraproject.org/rpms/python-airspeed/c/f6ebde139813fd1989232b9eafe5dc47235d5934
15:24:13 <bt0> looks like its mostly complete
15:24:39 <FranciscoD> Yes, but I guess we can't test it out until the badge has been added
15:25:09 <bt0> umm, it's true
15:25:14 <fm-neuro> pagure.commit.flag.added -- Build completed added a flag on the commit bdd20344 of the project rpms/python-amico https://src.fedoraproject.org/rpms/python-amico/c/bdd20344c910b188ce3b450a63b4efc1ed461428
15:25:39 <fm-neuro> pagure.issue.edit -- major edited the content fields of ticket neuro-sig/neuro-scripts#8 https://pagure.io/neuro-sig/neuro-scripts/issue/8
15:26:40 <FranciscoD> bt0: could we quickly look at these too? https://pagure.io/neuro-sig/neuro-scripts/issues
15:27:34 <bt0> ohh yeah, some ks change name (i don't know why)
15:29:18 <bt0> let me take both
15:29:27 <fm-neuro> pagure.issue.assigned.added -- bt0dotninja assigned ticket neuro-sig/neuro-scripts#8 to bt0dotninja https://pagure.io/neuro-sig/neuro-scripts/issue/8
15:29:36 <fm-neuro> pagure.issue.assigned.added -- bt0dotninja assigned ticket neuro-sig/neuro-scripts#5 to bt0dotninja https://pagure.io/neuro-sig/neuro-scripts/issue/5
15:30:11 <FranciscoD> the warnings in #8 don't seem to affect the ISO---it works fine
15:30:40 <FranciscoD> bt0: alciregi  noticed that the anaconda in the image looks like the netinstall instead of the workstation one
15:30:49 <bt0> yes
15:31:06 <FranciscoD> should that be the case?
15:31:27 <bt0> not, we use the WS kickstart
15:31:30 <bt0> as base
15:31:54 <bt0> so let me take a look
15:32:13 <bt0> i will generate the F30 image first
15:32:25 <MeWjOr> I was thinking maybe I can pursue why anaconda looks like the netinstall image... :/
15:32:46 <fm-neuro> pagure.commit.flag.added -- Build completed added a flag on the commit ee29661e of the project rpms/python-bids-validator https://src.fedoraproject.org/rpms/python-bids-validator/c/ee29661ea591294eb2dc9e377c5b948b8bca7b7a
15:32:58 <FranciscoD> bt0: I generated an F31 image
15:33:05 <FranciscoD> https://fedorapeople.org/groups/neuro-sig/
15:33:07 <bt0> works fine?
15:33:11 <FranciscoD> https://fedorapeople.org/groups/neuro-sig/Fedora-31-Comp-Neuro-20191003-1.iso
15:33:16 <FranciscoD> Yes, very well, no issues at all.
15:33:22 <FranciscoD> alciregi even installed it etc to test :)
15:33:45 <FranciscoD> MeWjOr: sure---I suspect it's because we're possibly using older ks sources maybe? I don't know
15:33:58 <FranciscoD> MeWjOr: do you want to file an issue and assign it to yourself? :)
15:34:04 <MeWjOr> On it, sire
15:34:15 <FranciscoD> XD
15:35:25 <bt0> im using the kickstart from the updated repo
15:35:43 <FranciscoD> hrm, weird then
15:35:47 <mhough> .fas mhough
15:35:49 <zodbot> mhough: adamhough '' <adam@gradientzero.com> - mhough 'Morgan Hough' <morgan.hough@gmail.com>
15:36:05 <FranciscoD> bt0: let's let MeWjOr inspect it and see what they find
15:36:07 <FranciscoD> It isn't urget
15:36:11 <FranciscoD> s/urget/urgent/
15:36:12 <bt0> ok
15:36:16 <FranciscoD> #chair mhough
15:36:16 <zodbot> Current chairs: FranciscoD MeWjOr alciregi blackfile bt0 mhough zbyszek
15:36:23 <MeWjOr> :D
15:36:34 <FranciscoD> mhough: https://fedorapeople.org/groups/neuro-sig/Fedora-31-Comp-Neuro-20191003-1.iso -> comp neuro ISO ready for use (for testing)
15:36:48 <mhough> Cool!
15:36:58 <FranciscoD> MeWjOr: do you think it's worth adding tags on the labs repo like I did on the main housekeeping pagure repo too?
15:37:15 <bt0> +1
15:38:04 <MeWjOr> I guess it would improve the efficiency of looking up issues for the next meeting
15:38:08 <FranciscoD> @Alessio: i invited you to the NeuroFedora github organisation FYI :)
15:38:28 <FranciscoD> MeWjOr: think about it, if you think it's worth it, go ahead and add what tags you like :)
15:38:44 <FranciscoD> #action MeWjOr think about whether tags would help on the neuro-scripts repo and add them if required
15:38:44 <MeWjOr> but the volume is not much for the labs repo... BUT I guess we need to start somewhere
15:38:51 <MeWjOr> Great...will do
15:38:53 <MeWjOr> ;)
15:39:08 <FranciscoD> #action MeWjOr file an issue and investigate why the comp-neuro installer looks like the netinstaller and not the live workstation one
15:39:11 <FranciscoD> there we go :P
15:40:10 <FranciscoD> bt0: sorry, please proceed :)
15:40:24 * FranciscoD randomly remembers stuff and jumps in
15:40:36 <bt0> #Topic Planning what we want to do next
15:40:49 <bt0> so what we need to do
15:41:00 <fm-neuro> pagure.issue.new -- major opened a new ticket neuro-sig/neuro-scripts#11: "The Anaconda installer looks like the Netinstall image installer and not the Workstation image installer." https://pagure.io/neuro-sig/neuro-scripts/issue/11
15:41:13 <fm-neuro> pagure.issue.assigned.added -- major assigned ticket neuro-sig/neuro-scripts#11 to major https://pagure.io/neuro-sig/neuro-scripts/issue/11
15:41:24 <FranciscoD> bt0: I think the comp-neuro bits are going well
15:41:30 <bt0> yes
15:41:35 <FranciscoD> #info Change proposal https://fedoraproject.org/wiki/Changes/Comp_Neuro_Lab
15:41:41 <mhough> definitely
15:41:42 <FranciscoD> #info Tracker bug https://bugzilla.redhat.com/show_bug.cgi?id=1758209
15:41:54 <FranciscoD> #info FESCo approval: https://pagure.io/fesco/issue/2237
15:42:07 <fm-neuro> pagure.commit.flag.added -- Build completed added a flag on the commit f973d246 of the project rpms/python-citeproc-py https://src.fedoraproject.org/rpms/python-citeproc-py/c/f973d2462f796a669a828926d84a9ac665771f0b
15:42:14 <FranciscoD> There are some rough edges, but we'll keep improving things there
15:42:27 <FranciscoD> Still lots of packages in the queue even for comp-neuro
15:42:56 <FranciscoD> But, we've started to see some traction on the neuro-imaging etc sides too, so I think it's the right time to make more noise about it and get more people involved?
15:43:28 <FranciscoD> Ie. more evangelism---use the comp-neuro bits to show people that it can be done well and encourage them to help us with neuro-imaging
15:43:42 <mhough> Sounds great
15:44:04 <FranciscoD> #info At the moment we have 47 neuro-imaging related tools in the packaging queue: https://pagure.io/neuro-sig/NeuroFedora/issues?status=Open&tags=F%3A+Neuroimaging
15:44:19 <FranciscoD> and they're slightly complex from time to time
15:44:29 <FranciscoD> because they depend on complex image processing libraries like gdcm
15:44:39 * FranciscoD gets nightmares when a gdcm build fails
15:45:12 <FranciscoD> bt0: MeWjOr mhough: what actions do you think we can take
15:45:14 <FranciscoD> ?
15:45:21 <mhough> I was going to say that some important tools are all dependent on ITK
15:45:30 <FranciscoD> yeh, that's another complex tool
15:45:41 <FranciscoD> even updating that is such a nightmare---on my list of things
15:45:53 <FranciscoD> igor said it may take a few weeks to update all the patches etc
15:45:55 * FranciscoD cries
15:45:58 <mhough> Yes and we need 5.x at this point
15:46:13 <fm-neuro> pagure.commit.flag.added -- Build completed added a flag on the commit 97694f5a of the project rpms/openmeeg https://src.fedoraproject.org/rpms/openmeeg/c/97694f5a8810a2248cb1ca524bdac5fe16daaf2f
15:46:35 <FranciscoD> I can focus on ITK then
15:46:46 <mhough> To getITK-SNAP,  ANTs, Elastix, MNI-Tools, SCIRun all depend  on ITK
15:46:56 <mhough> sorry ITK-SNAP
15:46:59 <FranciscoD> but then, I won't be able to do other packages---wont have the cycles
15:47:18 <MeWjOr> How difficult does one feel is ITK to package?
15:47:25 <FranciscoD> it's already packaged, but needs updating
15:47:32 <MeWjOr> Ooh
15:47:36 <FranciscoD> https://apps.fedoraproject.org/packages/InsightToolkit/
15:47:47 <MeWjOr> Is ITK on bugzilla?
15:48:08 <FranciscoD> package name is "insighttoolkit"
15:48:17 <MeWjOr> found it
15:48:26 <bt0> share the link
15:48:42 <FranciscoD> looks like zbyszek already updated it to 4.x though, and cleaned up the spec
15:48:51 <MeWjOr> #info InsightToolkit updating bug https://bugzilla.redhat.com/show_bug.cgi?id=1340300
15:48:56 <FranciscoD> try: bugz.fedoraproject.org/InsightToolKit
15:48:57 <mhough> It has many options
15:49:08 <bt0> thanks
15:49:10 <FranciscoD> In general, bugz.fedoraproject.org/<package name> takes you to the bug list
15:49:24 <FranciscoD> mhough: yeh, look at this: https://src.fedoraproject.org/rpms/InsightToolkit/blob/master/f/InsightToolkit.spec#_161
15:49:26 <FranciscoD> XD
15:49:37 <mhough> I started a list of the tools that depend on it and the options they need building it
15:50:04 <FranciscoD> mhough: can you maybe file a ticket on pagure and comment there---and then make this ticket block the other ones
15:50:11 <FranciscoD> that way we have a clear dependency chain
15:50:16 <mhough> Gotcha will do
15:50:33 <FranciscoD> #action mhough create a new ticket to document what ITK features we need enabled
15:50:42 <mhough> I am technically in a lecture right now but I will follow up on this soon:)
15:50:55 <MeWjOr> "technically"
15:50:56 <FranciscoD> #action mhough block other packages that need these features
15:50:58 <FranciscoD> haha, no hurry
15:51:07 <FranciscoD> #action FranciscoD look at updating ITK to new version
15:51:43 <FranciscoD> by the way, FESCo was kind enough to grant me provenpackager powers, so if you are updating a package that needs to rebuild other packages outside the neuro-sig, please ping me and I can help
15:52:11 <mhough> Something like SimpleITK could be an early goal
15:52:37 <FranciscoD> mhough: who can we speak to to help us package and maintain these imaging libraries?
15:52:50 <FranciscoD> as in, it's super awesome that fangq is upstream and is maintaining the package
15:53:00 <mhough> I am going to ask the ANTs/ITK-SNAP poeple about producing their own RPMs
15:53:01 <FranciscoD> that makes it easier for us---also implies that they know what they are doing
15:53:18 <mhough> Totally right
15:53:20 <FranciscoD> mhough: that would be *brilliant*
15:53:27 <FranciscoD> we can always help them learn the workflows
15:53:41 * FranciscoD is very worried about providing packages that we don't use
15:53:53 <FranciscoD> correctness is very important when these packages are being used in science
15:53:59 <mhough> I use ITK-SNAP
15:54:17 <mhough> and ANTs is a competitor to FSL's FNIRT
15:54:18 <FranciscoD> mhough: we need to get you on the packaging ladder XD
15:54:30 <FranciscoD> I can sponsor you now as a co-maintainer---what do you think?
15:54:41 <mhough> I have a package for a real package for review
15:54:43 <mhough> Sure
15:54:56 <FranciscoD> ok, doing so now
15:55:04 <mhough> I did a package of MRIcron the  #1 download of neurodebian
15:55:08 <FranciscoD> will also e-mail the devel list to let the community know
15:55:15 <mhough> its pascal which is hysterical
15:55:18 <FranciscoD> mhough: ah! Nice! XD
15:55:32 <FranciscoD> #action FranciscoD sponsor mhough to packagers and e-mail -devel letting community know
15:55:43 <FranciscoD> #actio FranciscoD write blog post on neurofedora updates
15:55:48 <FranciscoD> #action FranciscoD write blog post on neurofedora updates
15:55:57 <mhough> I don't know if I am making the desktoop icon stuff correctly for it though
15:56:11 <FranciscoD> mhough: do you have a link to the ticket? have you submitted the review already?
15:56:17 <mhough> Not yet
15:56:22 <MeWjOr> You can share the .desktop file with me?
15:56:24 <mhough> Just did it this week
15:56:28 <FranciscoD> OK, nice
15:56:40 <mhough> Will  do
15:56:42 <FranciscoD> bt0: i think we have enough actions for this topic now XD
15:56:48 <MeWjOr> :P
15:56:48 <FranciscoD> let's proceed to the next topic?
15:57:14 <FranciscoD> #action mhough share desktop file with MeWjOr to figure out tweaks
15:57:30 <FranciscoD> (we started 10 min late, so we'll end 10 minutes late too)
15:57:34 <MeWjOr> .ping bt0
15:57:34 <zodbot> pong
15:57:51 <MeWjOr> zodbot: what is that!!
15:57:53 <zodbot> MeWjOr: No such package exists.
15:58:39 <tg-fedneuro1> <l​bazan> Here
15:58:47 <tg-fedneuro1> <l​bazan> Let me turn on my laptop
15:58:52 <FranciscoD> hello @lbazan!
15:58:57 <FranciscoD> .localtime lbazan
15:58:58 <zodbot> FranciscoD: The current local time of "lbazan" is: "10:58" (timezone: America/Panama)
15:59:06 <FranciscoD> oo, early morningish
15:59:21 <mhough> morning
15:59:43 <tg-fedneuro1> <L​oKoMurdoK> 😂
15:59:50 <MeWjOr> Hola!
15:59:59 * lbazan here
16:00:06 <lbazan> saludos! MeWjOr
16:00:11 <lbazan> saludos team!
16:00:14 <lbazan> :-)
16:00:17 <FranciscoD> #chair lbazan
16:00:17 <zodbot> Current chairs: FranciscoD MeWjOr alciregi blackfile bt0 lbazan mhough zbyszek
16:00:21 <lbazan> .fas lbazan
16:00:22 <zodbot> lbazan: lbazan 'Luis Enrique Bazán De León' <bazanluis20@gmail.com>
16:00:52 <FranciscoD> bt0 may be having connection issues
16:00:54 <lbazan> a lot of meetings in the office sorry! my apologize!
16:01:00 <tg-fedneuro1> <M​eWjOr> @bt0dotninja ping
16:01:02 <FranciscoD> lbazan: no worries :)
16:01:09 <MeWjOr> just pinged on TG..
16:01:12 <FranciscoD> #topic Chair for next week
16:01:19 <FranciscoD> Any takers? :)
16:01:47 <tg-fedneuro1> <b​t0dotninja> Sorry, i'm partially here
16:01:50 <MeWjOr> I can do next-to-next week... Have some work piled up for the next week
16:02:06 <FranciscoD> OK, let me do next week then, you can do the week after
16:02:06 <fm-neuro> pagure.commit.flag.added -- Build completed added a flag on the commit 04b106ba of the project rpms/python-biopython https://src.fedoraproject.org/rpms/python-biopython/c/04b106ba9f7c6d815185db3fcfb537b1a6669ecc
16:02:15 <FranciscoD> #info FranciscoD will chair next week's meeting
16:02:24 <MeWjOr> @bt0dotninja no worries... :D
16:02:37 <FranciscoD> #topic Open Floor
16:02:43 <FranciscoD> So, who read the paper? :P
16:02:47 * FranciscoD did
16:02:50 <tg-fedneuro1> <b​t0dotninja> Thanks
16:02:56 <FranciscoD> bt0++
16:03:10 <MeWjOr> I did a bit...was unable to comprehend it after the second page... :'(
16:03:29 <FranciscoD> that's OK, it does get technical in places
16:03:40 <FranciscoD> Where did you get stuck?
16:04:23 <MeWjOr> When the author talks about the different models... by Dayan and Abott
16:04:38 <MeWjOr> And the Hodgkin model
16:04:48 <FranciscoD> OK
16:04:58 <FranciscoD> I can give a short blurb about the Hodkin-Huxley model
16:05:05 <MeWjOr> Sure
16:05:23 <FranciscoD> Stop me when you dont' understand something. So, the brain has specialised cells, called neurons
16:05:38 <MeWjOr> I googled it...and I saw some capacitors... that's when I turned off
16:05:45 <FranciscoD> they're specialised because they "spike" and by  doing that, they conduct electricity
16:06:17 <FranciscoD> Now, until Hodgkin-Huxley began working on it, we knew they did this but we didnt know how or why
16:07:13 <FranciscoD> So, they found a massive neuron---from a squid I think---and studied it
16:07:28 <FranciscoD> since the neuron conducts electricity, we can think of it as a circuit
16:07:46 <FranciscoD> only, instead of electrons moving around a wire all the time, you have ions that move to produce this current
16:07:55 <FranciscoD> Clear so far?
16:07:58 <MeWjOr> Yep
16:08:11 <FranciscoD> Now, all cells have a cell body---with a nucleus etc
16:08:30 <FranciscoD> neurons also have "axons"---these are projections that go out from the cell body (soma)
16:08:55 <FranciscoD> Generally, but not always, the axon of a neuron touches another neuron---and that's how current passes from one neuron to another
16:09:08 <MeWjOr> Different neurons connect to each other through Axons, right?
16:09:18 <FranciscoD> Generally, but not always
16:09:22 <MeWjOr> Ohh...
16:09:39 <FranciscoD> In general, axons are "output" units, and these tiny things on the soma side called "dendrites" are inputs
16:09:57 <FranciscoD> and generall, axons touch dendrites and current passes from an axon to a dendrite
16:10:13 <FranciscoD> *but*, axon-axon connections also exist, and so do dendrite-dendrite
16:10:18 <FranciscoD> and so do axon-soma
16:10:26 <FranciscoD> lots of heterogenity XD
16:10:36 <MeWjOr> :P
16:10:37 <FranciscoD> for simplicity, we generally assume axon-dendrite
16:10:57 <FranciscoD> So, if you think of the axon as a long wire, you can use things like Ohms law, right?
16:11:00 <FranciscoD> V = IR
16:11:12 <MeWjOr> Yes
16:11:32 <FranciscoD> but, because it's ions, not electrons, the potential difference (voltage) is because of the difference in concentration of ions in different places
16:12:32 <FranciscoD> then, these aren't metallic wires so they arent exactly ideal conductors. They have capacitance
16:12:43 <FranciscoD> so current is also I = C (dV/dt)
16:12:49 <FranciscoD> lots of school physics here ;)
16:13:04 <MeWjOr> Lol
16:13:52 <fm-neuro> pagure.commit.flag.added -- Build completed added a flag on the commit 569eeb28 of the project rpms/python-duecredit https://src.fedoraproject.org/rpms/python-duecredit/c/569eeb2824ac3525f652bc2b5ff769977ecd980e
16:14:00 <fm-neuro> pagure.commit.flag.added -- Build completed added a flag on the commit ce58af0f of the project rpms/python-brian2 https://src.fedoraproject.org/rpms/python-brian2/c/ce58af0fa67a62c4dfccc5e2d8573108f66d8029
16:14:18 <mhough> lots:)
16:14:19 <FranciscoD> So, to model a neuron, you simplify it to an electrical circuit
16:14:29 <FranciscoD> next, you decide how detailed you want your model to be
16:14:39 <MeWjOr> So... The electrical circuit is the hodgkin-huxley model?
16:15:19 <FranciscoD> pretty much---they took the three main ions: K, Na, Ca, and created an electrical circuit representation of the neuron
16:15:25 <FranciscoD> hence "biophysical"
16:15:43 <FranciscoD> now it's just a bunch of maths---differential equations etc
16:15:47 <FranciscoD> that can be solved analytically
16:15:56 <FranciscoD> all you need is computers, sometimes lots of them
16:16:01 <FranciscoD> but you have the model of a neuron
16:16:15 <FranciscoD> instead of poking a rat, you can now model a neuron and investigate it
16:16:23 <MeWjOr> ooh... :P
16:16:27 <FranciscoD> also, when you poke a rat, you can't look at everything
16:16:38 <FranciscoD> but in a model, you can record whatever you want, and change whatever you want
16:16:57 <FranciscoD> that's what the paper tries to say in a nutshell
16:17:08 <FranciscoD> https://medium.com/the-spike/why-model-the-brain-c7a8e160e566 -> is an easier post to read
16:17:11 <FranciscoD> less technical
16:17:16 <FranciscoD> try that and see what you think
16:17:22 <MeWjOr> Sure will..
16:17:46 <MeWjOr> One quick question... Assuming there's some current flowing through the neurons
16:17:52 <FranciscoD> yeh
16:17:54 <mhough> So the lecture I am in he just said "more electricity into the brain is not better, it's just different"
16:18:00 <MeWjOr> Do we also have a magnetic field associated with it?
16:18:11 <FranciscoD> MeWjOr: yes---that's how you get MRI scans :)
16:18:26 <FranciscoD> "Magnetic resonance imaging"
16:18:28 <mhough> That's how you get readout from MRI
16:18:35 <MeWjOr> OOOHH!
16:18:52 <FranciscoD> you also have electric fields that can be recorded
16:19:04 <FranciscoD> lots of ways to see what's happening
16:19:21 <FranciscoD> the current is usually quite low though---in the order of 100pA
16:19:31 <FranciscoD> depending on the activity of the region, though
16:20:04 <FranciscoD> capacitances are generally in nS (nano siemens)
16:20:18 <FranciscoD> so, the resistance, which is 1/conductance is very high :)
16:20:55 <MeWjOr> How do you get capacitances in nS?
16:21:03 <MeWjOr> It's in farad, right?
16:21:09 <MeWjOr> Unless we have an AC source?
16:21:15 <mhough> Biksom is speaking here now: https://www.ncbi.nlm.nih.gov/pubmed/?term=Biksom+M
16:21:31 <FranciscoD> MeWjOr: conductance, not capacitance, sorry
16:21:46 <MeWjOr> ohh.. :P
16:21:56 <FranciscoD> capacitances are in the order of ..
16:21:59 * FranciscoD checks his code
16:23:23 <FranciscoD> 200pF I'd think---I've got to double check what units NEST usees
16:23:28 <mhough> haha
16:23:37 <MeWjOr> ahh
16:24:03 <MeWjOr> well... I would have to leave now... I need to get some dinner... :P
16:24:29 <FranciscoD> https://www.nest-simulator.org/helpindex/cc/aeif_cond_alpha.html -> all units listed there
16:24:31 <FranciscoD> pF it is
16:24:36 <FranciscoD> yeh, we're over time too. Let's close
16:24:54 <FranciscoD> We discussed some science---makes me happy :)
16:24:58 <FranciscoD> Closing in 5
16:25:04 <FranciscoD> 4
16:25:20 <FranciscoD> 3
16:25:26 <FranciscoD> 2
16:25:29 <FranciscoD> #endmeeting