# Cannot run an IT tool: PhysiCell Studio **URL:** \ **Category:** usegalaxy.org support\ **Tags:** server-status\ **Created:** [December 31, 2025, 9:29pm UTC](https://help.galaxyproject.org/t/cannot-run-an-it-tool-physicell-studio/16899 "2025-12-31T21:29:50Z")\ **Posts on this page:** 18\ **Page:** 1
**Author:** ![rheiland](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/rheiland/32/6369_2.png) [@rheiland](https://help.galaxyproject.org/u/rheiland)\ **Post date:** [December 31, 2025, 9:29pm UTC](https://help.galaxyproject.org/t/cannot-run-an-it-tool-physicell-studio/16899/1 "2025-12-31T21:29:50Z")
Are there any known issues with [usegalaxy.org](http://usegalaxy.org) running Interactive Tools today? I’ve been unable to run PhysiCell Studio, as well as the JupyterLab Notebook. I didn’t see any notices of downtime on the main page. I can, however, run PhysiCell Studio using [test.galaxyproject.org](https://test.galaxyproject.org) . ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [January 2, 2026, 7:29pm UTC](https://help.galaxyproject.org/t/cannot-run-an-it-tool-physicell-studio/16899/2 "2026-01-02T19:29:16Z")
Hi @rheiland There is a notice on the [UseGalaxy.org](http://UseGalaxy.org) server about maintenance during this time frame. The interactive environments may be impacted sporadically throughout. ![202601-usegalaxy-org-notification](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/4/41d413f3d4ffc3bec26a25f698b7d64ac4a90e17.png) Let’s follow up next week to make sure everything is back up and functioning again as expected! 🙂 ---
**Author:** ![rheiland](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/rheiland/32/6369_2.png) [@rheiland](https://help.galaxyproject.org/u/rheiland)\ **Post date:** [January 5, 2026, 5:42pm UTC](https://help.galaxyproject.org/t/cannot-run-an-it-tool-physicell-studio/16899/3 "2026-01-05T17:42:57Z")
Currently, our IT does work as expected. Thanks. ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [January 5, 2026, 7:20pm UTC](https://help.galaxyproject.org/t/cannot-run-an-it-tool-physicell-studio/16899/4 "2026-01-05T19:20:53Z")
Hi @rheiland Do you mean that your local version is now working? If so, I’m glad to learn that the configuration is now set up! And, I just checked at [UseGalaxy.org](http://UseGalaxy.org) and the **PhysiCell Studio** tool launched correctly for me. Maybe this is what you noticed instead? The work at TACC from the break is now complete. All functions should be back to normal now but please let us know if you notice anything odd we may have missed. Wishing you and everyone else reading a happy new year! 🚀 ---
**Author:** ![rheiland](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/rheiland/32/6369_2.png) [@rheiland](https://help.galaxyproject.org/u/rheiland)\ **Post date:** [January 6, 2026, 4:27pm UTC](https://help.galaxyproject.org/t/cannot-run-an-it-tool-physicell-studio/16899/5 "2026-01-06T16:27:06Z")
Yes, I meant on [usegalaxy.org](http://usegalaxy.org). Happy New Year to you too! ---
**Author:** ![rheiland](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/rheiland/32/6369_2.png) [@rheiland](https://help.galaxyproject.org/u/rheiland)\ **Post date:** [March 14, 2026, 9:41pm UTC](https://help.galaxyproject.org/t/cannot-run-an-it-tool-physicell-studio/16899/7 "2026-03-14T21:41:59Z")
Once again. Unable to run this IT on either test.galaxyproject or [usegalaxy.org](http://usegalaxy.org). It just hangs forever, sometimes the output data stores on the History immediately turn red. I’ve logged out/in each server to make sure I didn’t have an instance running; it didn’t help. I did not see any maintenance notices. I am able to successfully run the same 0.7 version of the IT from its Docker image, using my local Ubuntu galaxy server (25.1). ![Screenshot 2026-03-14 at 5.53.16 PM](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/4/44b4c548932118856e9fb787eac9827897b573ef.jpeg) ---
**Author:** ![rheiland](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/rheiland/32/6369_2.png) [@rheiland](https://help.galaxyproject.org/u/rheiland)\ **Post date:** [March 16, 2026, 2:41pm UTC](https://help.galaxyproject.org/t/cannot-run-an-it-tool-physicell-studio/16899/8 "2026-03-16T14:41:28Z")
another update - tried again just now and it remains in this state. In spite of saying the info was updated “1 minute ago”, it’s been about 15 mins. Any help is much appreciated. We need to decide whether or not to advertise this IT for upcoming workshops. At this point, I don’t feel that we can. Related, how can I update the [usegalaxy.eu](http://usegalaxy.eu) to use this latest version of the IT? well… only if it’s working there. ![Screenshot 2026-03-16 at 10.35.38 AM](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/6/6f3534eb06da49b378593b561b90964cf869dd40.png) ---
**Author:** ![rheiland](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/rheiland/32/6369_2.png) [@rheiland](https://help.galaxyproject.org/u/rheiland)\ **Post date:** [March 16, 2026, 4:55pm UTC](https://help.galaxyproject.org/t/cannot-run-an-it-tool-physicell-studio/16899/9 "2026-03-16T16:55:03Z")
Related to this post: [Cannot run an IT tool: PhysiCell Studio](https://help.galaxyproject.org/t/cannot-run-an-it-tool-physicell-studio/16899) , I am now seeing my IT as “runnable”, but trying to open it results in: [https://2jz5basuq6hkq-2cdpub600qcc8.ep.interactivetool.usegalaxy.org/](https://2jz5basuq6hkq-2cdpub600qcc8.ep.interactivetool.usegalaxy.org/) 502 Bad Gateway nginx/1.20.1 ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [March 16, 2026, 6:28pm UTC](https://help.galaxyproject.org/t/cannot-run-an-it-tool-physicell-studio/16899/10 "2026-03-16T18:28:36Z")
Hi @rheiland The [UseGalaxy.org](http://UseGalaxy.org) server is finalizing the next release. We apologise for the instability! ITs are sensitive to these updates due to the extra containers.. but this should all resolve by the end of the week. I just tested v **0.7** at [UseGalaxy.org](http://UseGalaxy.org) and it launched for me! I didn’t do more but this seems to be different from your error from Saturday. We needed to restart some proxies. [RStudio was also impacted.](https://help.galaxyproject.org/t/rstudio-troubleshooting/17578/3) - [https://usegalaxy.org/u/jen-galaxyproject/h/test-physicell](https://usegalaxy.org/u/jen-galaxyproject/h/test-physicell) Then, to request that a tool be added to the common tools set used at UseGalaxy servers, or the EU server specifically, please see: > [@Tool Installation Request: icescreen](https://help.galaxyproject.org/t/tool-installation-request-icescreen/15421/3): > > Tools on the usegalaxy servers are managed via the following repos: > > [GitHub - usegalaxy-eu/usegalaxy-eu-tools: List of tools included in https://usegalaxy.eu · GitHub](https://github.com/usegalaxy-eu/usegalaxy-eu-tools) [GitHub - galaxyproject/usegalaxy-tools: usegalaxy.\* common tools · GitHub](https://github.com/galaxyproject/usegalaxy-tools) > > You can open a PR if you want them to be added. Common tools would request the updated IT is pushed to [UseGalaxy.org.au](http://UseGalaxy.org.au) too, and likely the others (timing can vary and depends on their resources). I really want to help to make sure these are deployed correctly for your workshops, so let’s please keep following up. Our apologies for the impact some of our infrastructure updates are causing. These will help with stability, speed, and scalability longer term (we hope!) but can be bumpy in unexpected ways! ---
**Author:** ![rheiland](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/rheiland/32/6369_2.png) [@rheiland](https://help.galaxyproject.org/u/rheiland)\ **Post date:** [March 17, 2026, 7:56pm UTC](https://help.galaxyproject.org/t/cannot-run-an-it-tool-physicell-studio/16899/11 "2026-03-17T19:56:17Z")
Thanks once again @jennaj ! Yes, it seems to currently work for me too. I just wish a warning of sorts had been posted on the main page about possible instability due to a new release being finalized, but I’m sure the Admins have their reasons. I’ll try to be more patient and continue to test. And I’ll eventually take a look at the link you shared about getting our IT updated on other servers. Thanks. ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [March 17, 2026, 10:06pm UTC](https://help.galaxyproject.org/t/cannot-run-an-it-tool-physicell-studio/16899/12 "2026-03-17T22:06:37Z")
Thanks and I agree – while a new release moves through the system, we could communicate this better to the dev community. Right now this happens informally at the different Matrix chats. And even knowing when/what may not predicts all the incidentals. I’m going to think about this more but I like the idea. And, glad things are (mostly!) working now! ---
**Author:** ![rheiland](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/rheiland/32/6369_2.png) [@rheiland](https://help.galaxyproject.org/u/rheiland)\ **Post date:** [March 24, 2026, 4:43pm UTC](https://help.galaxyproject.org/t/cannot-run-an-it-tool-physicell-studio/16899/13 "2026-03-24T16:43:27Z")
Is the new release situation still moving through the system? I tried to run my IT just now and seeing the same problem - doesn’t start and never updates the “Last update” time (it’s been “Starting” for \>15 mins and has a last update of “4 mins ago”). I’m really at a loss and cannot recommend this tool for our workshops, which is very unfortunate - for both attendees and for me. ![Screenshot 2026-03-24 at 12.27.21 PM](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/d/d7839197b4d1c8f3db8de24b14c5751d99fed29d.png) ---
**Author:** ![rheiland](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/rheiland/32/6369_2.png) [@rheiland](https://help.galaxyproject.org/u/rheiland)\ **Post date:** [March 27, 2026, 1:02pm UTC](https://help.galaxyproject.org/t/cannot-run-an-it-tool-physicell-studio/16899/14 "2026-03-27T13:02:37Z")
I’m still hoping that someone can help me resolve this. If there are suggestions for things that I can do, please let me know. It still doesn’t seem to start, on either [usegalaxy.org](http://usegalaxy.org) or the test server. ---
**Author:** ![Paul\_Macklin](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/paul_macklin/32/7251_2.png) [@Paul\_Macklin](https://help.galaxyproject.org/u/Paul_Macklin)\ **Post date:** [March 29, 2026, 12:40pm UTC](https://help.galaxyproject.org/t/cannot-run-an-it-tool-physicell-studio/16899/15 "2026-03-29T12:40:36Z")
Hello! We plan to run some substantial K12 outreach with this tool on April 11, and graduate/professional training on April 13th. (And of course we are trying to use this as a daily research tool within our broader user community.) The issue is not resolved. Startup still takes \> 5 minutes (and running), and it does not appear to be starting at all. We are relying upon this tool for substantial NIH work, but we need stability and reliability to increase its use and profile among the NIH and NSF communities. Thank you! ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [March 31, 2026, 5:33pm UTC](https://help.galaxyproject.org/t/cannot-run-an-it-tool-physicell-studio/16899/16 "2026-03-31T17:33:18Z")
Hi @Paul_Macklin and @rheiland I was away but back now! I just launched the v 0.7 at [UseGalaxy.org](http://UseGalaxy.org) and all looks Ok? What happens today for both of you? All of my tests are in here tagged with the version and the date! - [https://usegalaxy.org/u/jen-galaxyproject/h/test-physicell](https://usegalaxy.org/u/jen-galaxyproject/h/test-physicell) I’m testing at the [test.GalaxyProject.org](http://test.GalaxyProject.org) server ~~next and will update here with the results.~~ This works for me too! Please see Nate’s message below! - [https://test.galaxyproject.org/u/jenjackson/h/test-physicell-studio-2026](https://test.galaxyproject.org/u/jenjackson/h/test-physicell-studio-2026) I did notice that loading was fairly quick but it did require that pop-ups are enabled and there was a (required?) click-through before the screen fully resolved. This seems to be example data initializing into the clipboard (the “cells.csv” file). I am using all defaults. Is this expected? Is it actually required? Is this what others are running into as a potential bottleneck? I’ll try to capture a screenshot when starting up on the test server. I’m mentioning since different browsers/privacy settings might interact with this “share step”. Since it is an external share step (distinct from a Galaxy account cookie) I’m wondering if this can or should be smoothed out, or if the launch form could use a Help warning – or if there is another way to get this data pre-loaded into the Docker container? Or, maybe this is nothing! Seemed worth mentioning! More soon! 🙂 ---
**Author:** ![nate](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/nate/32/1752_2.png) [@nate](https://help.galaxyproject.org/u/nate)\ **Post date:** [March 31, 2026, 5:43pm UTC](https://help.galaxyproject.org/t/cannot-run-an-it-tool-physicell-studio/16899/17 "2026-03-31T17:43:25Z")
There was an infrastructure issue that was causing interactive tools to fail to start properly, that was resolved 2 days ago, apologies for not following up then. Can you check again and let us know if it still fails to launch for you? ---
**Author:** ![rheiland](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/rheiland/32/6369_2.png) [@rheiland](https://help.galaxyproject.org/u/rheiland)\ **Post date:** [March 31, 2026, 6:07pm UTC](https://help.galaxyproject.org/t/cannot-run-an-it-tool-physicell-studio/16899/18 "2026-03-31T18:07:58Z")
Thanks both. Yes, I noticed our IT started working again yesterday. As to the pop-ups and click through, @jennaj , yes, this seems to be a somewhat new thing - within the last year or so. I have no idea why, but hope we can resolve it eventually. It’s annoying. ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [March 31, 2026, 6:18pm UTC](https://help.galaxyproject.org/t/cannot-run-an-it-tool-physicell-studio/16899/19 "2026-03-31T18:18:55Z")
Great, glad it is working! The pop-up seems to be browser-specific. Nate wasn’t getting this, but I was with both Safari and Chrome on MacOS. Maybe helps to narrow it down. Likely a privacy/tracking setting somewhere!