Call for participation: task force to work on resource to allow users to quickly decide on what simulator/tool they want to use

[sanjayankur31]

Please see this ticket for more information on the task:

https://github.com/OCNS/SoftwareWG/issues/61

We would like to set up a task force to deliver the first version of a resources that allows users to quickly decide on what simulator/toll they should/want to use. Please comment on this ticket if you would like to join the task force.

[ree-gupta]

I am available for a meeting :)

[brenthuisman]

I'm here too.

[sanjayankur31]

let's meet for a quick one then? We can use the jitsi thing in the gitter/matrix channel for today?

https://matrix.to/#/#OCNS_SoftwareWG:gitter.im

[mstimberg]

I will join you in a few minutes, sorry!

[brenthuisman]

let's meet for a quick one then? We can use the jitsi thing in the gitter/matrix channel for today?

https://matrix.to/#/#OCNS_SoftwareWG:gitter.im

Strangely enough, the jitsi thing doesn't show up in my non-Element client :/ Can you share a link?

[sanjayankur31]

I can't seem to find a link specifically to the jitsi thing here---it's embedded in element?

[brenthuisman]

Yeah, we switched away from it too for this reason: there's just no trace of it when you use other clients.

Can also go back to the zoom room?

[sanjayankur31]

Sure, if @mstimberg can start the meeting on zoom, happy to use that

[mstimberg]

Started!

[mstimberg]

https://cnrs.zoom.us/j/94102303309?pwd=SkIzOUJSVG1aWURROE5rR3d6Yi9iQT09

[mstimberg]

Thanks to everyone who joined for this "short" meeting, next meeting on September 6th. Have a good summer (if you are in the Northern Hemisphere, that is) :sunglasses:

[mstimberg]

Hi everyone, for all of you that took vacation, hope you had a good one! I am back, but it turns out that I won't be available for a meeting tomorrow afternoon. Since there is no very pressing need for the meeting, I suggest that we postpone our first after-the-break meeting to September 13th, giving everybody a bit of time to remember what the project was about :wink: Or would this interfere with other every-two-week meeting schedules for anyone (@sanjayankur31 I vaguely remember that was an issue for you).

[sanjayankur31]

Hello! Every two weeks from September 13 sounds good. My fortnightly sprint meetings also moved by a week, so the stars have re-aligned :)

[mstimberg]

:wave: Hi everyone, please be reminded that we are back for a new round of meetings, starting today at 13 UTC (time in your timezone).

Here's a new calendar file with the updated schedule for you to download: :calendar: https://cnrs.zoom.us/meeting/tJcpdu2grz8uEtD2zI6ypMt3fvSOoXy4IYe9/ics?icsToken=98tyKuCrqjouEtWRtBGDRowqBoj4LPzzmClbj7d5zgXMVTlDTxelMPRxHb1HCYz5 The meeting link changed as well, but will stay the same from now on: :tv: https://cnrs.zoom.us/j/93414814484?pwd=UzNlQnREMWVrMWVXSTdRMkdhQ1hidz09 Meeting notes: :notebook: https://hackmd.io/@mstimberg/BJA1wl1kp

Hope to see many of you there!

[mstimberg]

I've started the meeting, hope to see you there! 📺 https://cnrs.zoom.us/j/93414814484?pwd=UzNlQnREMWVrMWVXSTdRMkdhQ1hidz09

[mstimberg]

:wave: Hi everyone, please be reminded that we'll have another meeting today at 13 UTC (time in your timezone).

The meeting link (same as last time): :tv: https://cnrs.zoom.us/j/93414814484?pwd=UzNlQnREMWVrMWVXSTdRMkdhQ1hidz09 Meeting notes: :notebook: https://hackmd.io/@mstimberg/Bk8Q_Ybgp

Hope to see many of you there!

[mstimberg]

We've started the meeting, please join if you can! https://cnrs.zoom.us/j/93414814484?pwd=UzNlQnREMWVrMWVXSTdRMkdhQ1hidz09

[mstimberg]

:wave: Hey folks, another reminder that we'll have a meeting in about 40 minutes from now, i.e. today at 13 UTC (time in your timezone).

The meeting link (same as last time): 📺 https://cnrs.zoom.us/j/93414814484?pwd=UzNlQnREMWVrMWVXSTdRMkdhQ1hidz09 Meeting notes: :notebook: https://hackmd.io/@mstimberg/HkgnzGVW6

Hope to see you there!

[ree-gupta]

Hey all! I am in a conflicting meeting right now and will not be able to make it, unfortunately. I will go through the notes later. Thank you!

[mstimberg]

:wave: Hey everyone, the usual reminder that we'll have a meeting in about 30 minutes from now, i.e. today at 13 UTC (time in your timezone).

The meeting link (same as last time): 📺 https://cnrs.zoom.us/j/93414814484?pwd=UzNlQnREMWVrMWVXSTdRMkdhQ1hidz09 Meeting notes: :notebook: https://hackmd.io/@mstimberg/ByTnoHIzp

Hope to see many of you there!

[sanjayankur31]

I'll be there, but I haven't done my homework :face_with_spiral_eyes:

[mstimberg]

Hi everyone, I'll be a few minutes late unfortunately, I will start the zoom session at 13:10 UTC (i.e. ten minutes late).

[edd26]

I’m sorry, but I am not able to attend today's meeting- have some work to catch up on.

From: Marcel Stimberg @.> Date: Wednesday, 25 October 2023 at 13:57 To: OCNS/SoftwareWG @.> Cc: Subscribed @.***> Subject: Re: [OCNS/SoftwareWG] Call for participation: task force to work on resource to allow users to quickly decide on what simulator/tool they want to use (Issue #117)

Hi everyone, I'll be a few minutes late unfortunately, I will start the zoom session at 13:10 UTC (i.e. ten minutes late).

— Reply to this email directly, view it on GitHubhttps://github.com/OCNS/SoftwareWG/issues/117#issuecomment-1779219518, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AEF6CHU44IJKN2SNEMCWCOLYBEEFDAVCNFSM6AAAAAAQ6L5M7SVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONZZGIYTSNJRHA. You are receiving this because you are subscribed to this thread.Message ID: @.***>

[mstimberg]

Hi everyone, I am very sorry for the late notice, but I forgot that our meeting planned for today clashes with a workshop I am attending… I could make this Friday instead, but maybe the easiest is to again skip this meeting and have our next one in two weeks from no? IIRC, shifting it by just one week would lead to a scheduling conflict for @sanjayankur31.

[sanjayankur31]

+1, let's do it in two weeks. I've been away for a bit, and then working on a few deadlines, so haven't done much work on simselect unfortunately :crying_cat_face:

[mstimberg]

In two weeks, it is! Unfortunately, I have a presentation scheduled that partly overlaps, so if is ok for everyone, let's do it one hour later than usual, i.e. at 14 UTC. So to summarize: next meeting, Wednesday 6 December, 14:0015:00 UTC (time in your timezone)

[mstimberg]

Sorry about that, didn't account for the end of daylight-saving time since our last meeting, I meant 15:00 UTC (time in your timezone)

[mstimberg]

Hi everyone, this is a reminder that after a long hiatus, we'll be having a meeting later today, i.e.Wednesday 6 December, 15:00 UTC (time in your timezone)

The meeting link (same as last time): 📺 https://cnrs.zoom.us/j/93414814484?pwd=UzNlQnREMWVrMWVXSTdRMkdhQ1hidz09 Meeting notes: :notebook: https://hackmd.io/@mstimberg/SJz9WJCST

[mstimberg]

👆 And just to make this clear again: this meeting time is an hour later than usual (I'm unavailable earlier). Hope to see many of you there 👋

[mstimberg]

:alarm_clock: A reminder that we are having our last meeting in 2023 later today: Wednesday, December 20th, 14:00 UTC (time in your timezone)

The meeting link (same as last time): 📺 https://cnrs.zoom.us/j/93414814484?pwd=UzNlQnREMWVrMWVXSTdRMkdhQ1hidz09 Meeting notes: 📓 https://hackmd.io/@mstimberg/S1gXwSevT

[sanjayankur31]

I'm afraid I haven't done the action items yet, so I'll have nothing to show :(

[ree-gupta]

I will be there, but I have unfortunately also not made progress on any of the action items 😞

[mstimberg]

Same, same :) In other words, if I will be able to present something, it will be something that I've done in the upcoming 20 minutes :grimacing:

[mstimberg]

Happy end-of-year holidays everyone, our next meek will be in 4 weeks from now, i.e. on January 17th – hope to see many of you there :wave:

PS: After our meeting I did a (not so) quick & (very) dirty implementation of a table-based prototype, it should convey the general idea and be useful as a base for discussion: http://marcel.stimberg.info/simselect-playground/table.html (the workflow would be that after sorting you could select a few rows for the second page/graph display).

[ree-gupta]

Happy end-of-year holidays everyone, our next meek will be in 4 weeks from now, i.e. on January 17th – hope to see many of you there 👋

PS: After our meeting I did a (not so) quick & (very) dirty implementation of a table-based prototype, it should convey the general idea and be useful as a base for discussion: http://marcel.stimberg.info/simselect-playground/table.html (the workflow would be that after sorting you could select a few rows for the second page/graph display).

The prototype already looks great and intuitive! Thank you. This would also help us think about how would we like to structure our data.

Happy end-of-year holidays, everyone!

[mstimberg]

Hello, hello, and a happy 2024 :sparkles:

A reminder that we are having our first meeting in 2024 tomorrow: Wednesday, January 17th, 14:00 UTC (time in your timezone)

The meeting link (same as last time): 📺 https://cnrs.zoom.us/j/93414814484?pwd=UzNlQnREMWVrMWVXSTdRMkdhQ1hidz09 Meeting notes: 📓 https://hackmd.io/@mstimberg/ByYsCf4ta

[mstimberg]

:alarm_clock: Yet another reminder: our meeting starts in about 30 minutes – hope to see many of you there!

[sanjayankur31]

I'll be a few minutes late, we have a grant interview next week so we're running around doing lots of meetings etc. trying to get the presentation sorted XD

I did make progress on the data task (you probably got all the notifications :P)

[mstimberg]

:alarm_clock: Hi everyone, please be reminded that we are having another meeting tomorrow: Wednesday, January 31st, 14:00 UTC (time in your timezone)

The meeting link (same as last time): 📺 https://cnrs.zoom.us/j/93414814484?pwd=UzNlQnREMWVrMWVXSTdRMkdhQ1hidz09 Meeting notes: 📓 https://hackmd.io/@mstimberg/SyV-WsLqa

Hope to see y'all :blush:

[mstimberg]

Hi again everyone. We did not actually have a meeting at the date (which was entirely my fault, but in the end we wouldn't have been a big crowd…). Our next meeting will take place on February 14th, but I will send a reminder closer to the date.

I did, however, play around with cytoscape, so that we have a little graph view to play around with – and to figure out how to make it useful/intuitive, because that isn't quite the case… You can play around with it here: http://marcel.stimberg.info/simselect-playground/graph.html The source code is here: https://github.com/mstimberg/simselect-playground

A few words about how the code works and how it is organized:

• In the main simselect repository, I added a GitHub action that creates a big JSON file (simtools.json) with all the data from the individual yaml files – this is the file that is used for the graph representation.
• The graph.html HTML file does not contain much: there are placeholders for the graph (id=cy), the filter buttons (id=simulators), and the information about the selected simulator (id='details'). The filter buttons are meant to be a proxy for what a first filtering stage would be.
• The graph.js is the main javascript that creates the graph, and handles interactivity, etc. It's neither well documented nor structured, but is hopefully readable/understandable.
• The cy-style.json file defines the styling of the graph in the cytoscape syntax. It uses "selectors" which are similar to CSS selectors, but a bit more powerful.
• One of the main decisions (apart from all the interactivity/hiding/selecting etc.) is how to layout the graph. It currently uses a spring-based layout which does an okayish job, but maybe something more structured would be a better fit.

If you want to change things and run it on your own machine, there's no installation necessary (except for cloning my repo). You need to run it with a local webserver, though, e.g. with either something like Visual Studio's Live Server, or simply by running python -m http.server in the main directory. Note that you need to ask for graph.html, since index.html still refers to another (currently broken) view…

No rush to look into any of this, of course, we'll talk about it on Valentine's day :blush: Let me know if you run into any problems or if you would like more explanations for something :wave:

[mstimberg]

Hello everybody. Valentine's Day is coming up, and with it another meeting of our dear task force :heart: The meeting will take place tomorrow, Wednesday, February 14th, 14:00 UTC (time in your timezone) The meeting link: 📺 https://cnrs.zoom.us/j/93414814484?pwd=UzNlQnREMWVrMWVXSTdRMkdhQ1hidz09 Meeting notes: 📓 https://hackmd.io/@mstimberg/SyV-WsLqa

Hope to see many of you there (and please have a look at the graph example in the comment above :point_up: before our meeting!

[ree-gupta]

Hi again everyone. We did not actually have a meeting at the date (which was entirely my fault, but in the end we wouldn't have been a big crowd…). Our next meeting will take place on February 14th, but I will send a reminder closer to the date.

I did, however, play around with cytoscape, so that we have a little graph view to play around with – and to figure out how to make it useful/intuitive, because that isn't quite the case… You can play around with it here: http://marcel.stimberg.info/simselect-playground/graph.html The source code is here: https://github.com/mstimberg/simselect-playground

A few words about how the code works and how it is organized:

* In the main [simselect repository](https://github.com/OCNS/simselect), I added a GitHub action that creates a big JSON file (`simtools.json`) with all the data from the individual yaml files – this is the file that is used for the graph representation.

* The [`graph.html`](https://github.com/mstimberg/simselect-playground/blob/main/graph.html) HTML file does not contain much: there are placeholders for the graph (`id=cy`), the filter buttons (`id=simulators`), and the information about the selected simulator (`id='details'`). The filter buttons are meant to be a proxy for what a first filtering stage would be.

* The [`graph.js`](https://github.com/mstimberg/simselect-playground/blob/main/graph.js) is the main javascript that creates the graph, and handles interactivity, etc. It's neither well documented nor structured, but is hopefully readable/understandable.

* The [`cy-style.json`](https://github.com/mstimberg/simselect-playground/blob/main/graph.js) file defines the styling of the graph in the cytoscape syntax. It uses "selectors" which are similar to CSS selectors, but a bit more powerful.

* One of the main decisions (apart from all the interactivity/hiding/selecting etc.) is how to layout the graph. It currently uses a spring-based layout which does an okayish job, but maybe something more structured would be a better fit.

If you want to change things and run it on your own machine, there's no installation necessary (except for cloning my repo). You need to run it with a local webserver, though, e.g. with either something like Visual Studio's Live Server, or simply by running python -m http.server in the main directory. Note that you need to ask for graph.html, since index.html still refers to another (currently broken) view…

No rush to look into any of this, of course, we'll talk about it on Valentine's day 😊 Let me know if you run into any problems or if you would like more explanations for something 👋

Hi Marcel! Thank you for working on this.

I tried playing around with it. The representation of nodes, edges, and the UI overall looks very cool. About the graph layout, as you mentioned, do you think it would be a good idea to emphasize the core engines more in the graph and have their positions fixed and aligned?

I did try to implement this by modifying your code but failed 😶‍🌫️ All the video tutorials online about cytoscape seem to be using the GUI and not writing JS.

See you in a few hours!

PS: I might have to leave a little early today, as I have another meeting just following this one.

[mstimberg]

I tried playing around with it. The representation of nodes, edges, and the UI overall looks very cool. About the graph layout, as you mentioned, do you think it would be a good idea to emphasize the core engines more in the graph and have their positions fixed and aligned?

I did try to implement this by modifying your code but failed 😶‍🌫️ All the video tutorials online about cytoscape seem to be using the GUI and not writing JS.

I struggled with finding things in the documentation as well, what worked best in the end was looking at the code of the examples... In the force-based layouts (such as cola that the prototype uses) you can lock the position of certain nodes. In principle, you should also be able to just ask for the horizontal or vertical alignment of certain nodes (without fixing specific positions for them), but for some reason I did not get this to work… Here's code you can put in the layoutNodes function to align the nodes horizontally:

    const simulator_nodes = cy.filter(function(element, i){
        return element.isNode() && element.data("features").includes("simulator");
    });
    let counter = 0;    
    for (let node of simulator_nodes) {
        if (removed.indexOf(node) === -1) {
            node.position({x: 100*counter, y: 300}).lock();
            counter++;
        }
    }

I wouldn't say it's perfect, but I think it is going in the right direction!

PS: I might have to leave a little early today, as I have another meeting just following this one.

Same for me, actually!

[mstimberg]

Final reminder :bell:, we'll have our meeting in ~15 minutes! The meeting link: 📺 https://cnrs.zoom.us/j/93414814484?pwd=UzNlQnREMWVrMWVXSTdRMkdhQ1hidz09 Meeting notes: 📓 https://hackmd.io/@mstimberg/SyV-WsLqa

[sanjayankur31]

I'm joining in too, but I may have to drop off for 5 minutes during the meeting---we have students visiting the lab to see what we all get up to

[mstimberg]

:wave: This is your usual reminder that we are having another taskforce meeting today, February 28th, 14:00 UTC (time in your timezone), i.e. in roughly 1h from now.

The meeting link: 📺 https://cnrs.zoom.us/j/93414814484?pwd=UzNlQnREMWVrMWVXSTdRMkdhQ1hidz09 Meeting notes: 📓 https://hackmd.io/@mstimberg/Bys-5ih3p

As discussed during our last meeting, I have merged the contents of my "simselect-playground" repository into the main https://github.com/OCNS/simselect repository. You can find it in the graph branch. For future development, you can fork the repo, and propose PRs into that branch. The branch gets turned into a GitHub page, so you can find the rendered result at https://ocns.github.io/simselect/

Hope to see many of you at the meeting!

[mstimberg]

I've started the meeting, there's room for some more :sweat_smile:

[ree-gupta]

Hey all! I apologize for not joining the meeting yesterday. I was down with a cold and fever. I see that there was not much attendance yesterday 😅 Sorry for not notifying earlier @mstimberg, and thank you for making progress! Look forward to the next meeting 😄

[sanjayankur31]

Sorry, I was away to present a NeuroML talk too. Am tinkering with things and will have some ideas/branches to show soon :)

[mstimberg]

👋 This is your usual reminder that we are having another taskforce meeting today, March 13th, 14:00 UTC (time in your timezone), i.e. in roughly 2h from now.

The meeting link: 📺 https://cnrs.zoom.us/j/93414814484?pwd=UzNlQnREMWVrMWVXSTdRMkdhQ1hidz09 Meeting notes: 📓 https://hackmd.io/@mstimberg/HJBcPzk0p

Hope to see many of you at the meeting!