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    Brent Huisman
    @brenthuisman
    There have been no recent changes AFAIK to the ebrains lab, did it work before?
    Lennart Landsmeer
    @llandsmeer
    Nope can't see it, but that doesnt matter
    I used find / -name arbor-build-catalogue and some patience
    Still the invalid JUNCTION_PROCESS thing is a problem
    Is that a new arbor breaking change?
    Or is the image misconfigured
    Brent Huisman
    @brenthuisman
    The lab has Arbor v0.6. I'm not sure if this was changed post v0.6, but there have been changes to arbor-build-catalog.
    Sebastian Schmitt
    @schmitts
    Could gap junctions transport ions/particles as well?
    Brent Huisman
    @brenthuisman
    Actual gap junctions, or Arbor gap junctions?
    Sebastian Schmitt
    @schmitts
    Arbor gap junctions :)
    Brent Huisman
    @brenthuisman
    Currently they only transport events. What sort of transmission are you thinking of? Complete connection, as in the cytoplasm, so a continuous exchange of ions as per gradients, or particular ions over a threshold or sth?
    Thorsten Hater
    @thorstenhater
    Errr, Arbor GJ are direct electrical connections according to I=g(VhereVthere)I = g(V_{here} - V_{there})
    7 replies
    So, they are transporting a non-specific current.
    @schmitts You can try to model this using a Junction mechanism.
    Sebastian Schmitt
    @schmitts
    @brent I was thinking about exchanging some proteins depending on some condition.
    Brent Huisman
    @brenthuisman
    There is a ModelDB questionnaire: time to ask for more Arbor/simulator-independent
    models :) https://yalesurvey.ca1.qualtrics.com/jfe/form/SV_3EkPlMkOUDV5xgW
    Thorsten Hater
    @thorstenhater
    Ionic Diffusion is now part of Arbor :tada:
    arbor-sim/arbor#1729
    Brent Huisman
    @brenthuisman
    hurray!
    Jannik Luboeinski
    @jlubo
    Nice! =D
    Thorsten Hater
    @thorstenhater

    Github CoPilot for all. :tada: The function was auto-generated from the comment

    // Get average runtime of successful runs in seconds
    func averageRuntimeInSeconds(runs []Run) float64 {
        var totalTime int
        var failedRuns int
        for _, run := range runs {
            if run.Failed {
                failedRuns++
            } else {
                totalTime += run.Time
            }
        }
        averageRuntime := float64(totalTime) / float64(len(runs) - failedRuns) / 1000
        return averageRuntime
    }

    Oh ... wait ... this is broken and will return NAN or even throw div-by-zero.* :laughing:

    Yes, this is the example they advertise

    * if no runs or all fail

    Sam Yates
    @halfflat
    Bit surprised that run.Time is integral too.
    Also DIFFUSION!!!!! Awesomesauce.
    Sebastian Schmitt
    @schmitts
    :fireworks:
    Brent Huisman
    @brenthuisman
    Why does a meter_manager require a context? And why does the meter_report require it again? Does it only measure time executed in the Arbor .so?
    1 reply
    Sam Yates
    @halfflat
    With the caveat that I haven't looked at this code in probably four or five years, I believe the meter manager uses the context to grab the MPI communicator in order to collate time reports from across ranks.
    Brent Huisman
    @brenthuisman
    OK, I assumed the report was only getting results for the current rank, I'll run it with MPI and see what I get.
    Sebastian Schmitt
    @schmitts
    @halfflat hi! have you found some time to have a look at the proposal to have access to the discretized state?
    Sam Yates
    @halfflat
    Hi! Alas, no. It's been a bit mad. Next week at the earliest I'm afraid.
    Sebastian Schmitt
    @schmitts
    :cry:
    Brent Huisman
    @brenthuisman
    FYI: with the merge of arbor-sim/arbor#1916, which enabled universal (AMD64+ARM64) macos builds, Python <3.8 support was dropped. I hadn't checked that universal wheels require 3.8 and up. If this is a problem for anyone, let me know.
    Ben Cumming
    @bcumming
    About time we moved on from 3.6
    Brent Huisman
    @brenthuisman
    Arbor v0.7 is released! It's up on PyPI: https://pypi.org/project/arbor/0.7/ If you've a minute, let me know if you run into any problems.
    Sebastian Schmitt
    @schmitts
    :thumbsup:
    Sebastian Schmitt
    @schmitts
    Which format for morphology and synapse/neuron dynamics is understood best by NEURON and Arbor?
    35 replies
    Thorsten Hater
    @thorstenhater
    nmlcc-vs-jnml.png
    This nmlcc ./. jnml, both on Arbor. Minor deviations, but the nmlcc simulation is roughly 2x faster
    Sebastian Schmitt
    @schmitts
    nmlcc erstellt bessere mods?
    Thorsten Hater
    @thorstenhater
    Faster ;)
    Sebastian Schmitt
    @schmitts
    harder, better, faster, stronger?
    Brent Huisman
    @brenthuisman
    Hello Arbor users! The next Arbor Developer Meeting will be held 30 August at 10am CEST. Please join and give your opinion on which features must be prioritized for the next release! Add to your calender and more details here.
    3 replies
    Brent Huisman
    @brenthuisman
    Hi everyone, it's spam-thursday :) Ebrains are sending around the news of our v0.7 release: https://ebrains.eu/news/new-update-for-arbor-simulation-library/
    Sebastian Schmitt
    @schmitts
    Thanks, @brenthuisman.
    Thorsten Hater
    @thorstenhater

    Hi all,

    I went through our issue tracker and did some clean-up. If you have an open issue or one assigned to you, please check whether it has been resolved, become obsolete, or you have pending questions. On the inverse, please re-open anything that's still relevant but was closed.

    Sebastian Schmitt
    @schmitts
    @thorstenhater Thanks!
    Sebastian Schmitt
    @schmitts
    Are there plans for implementing a variable time step integrator?
    13 replies
    Sebastian Schmitt
    @schmitts
    grafik.png
    Can we have an explicit euler as well? I might need it (as usual) for comparison with existing simulations.
    Sebastian Schmitt
    @schmitts
    What is the resolution of the spike times? dt? dt/2?